diff --git a/.gitignore b/.gitignore index fe260563c..2865edb07 100644 --- a/.gitignore +++ b/.gitignore @@ -29,3 +29,5 @@ log src/main/bin/NCIT_HISTORY/ report.html gradle.lockfile +/.apt_generated/ +/.apt_generated_tests/ diff --git a/CHANGELOG.md b/CHANGELOG.md index 1acc16067..d708d3d52 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,13 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). +## [2.2.0.RELEASE] - 2025-06-10 +### Changed +- FHIR improvements (improved param support, improved swagger, improved metadata, more tests) +- Improvements to computed childhood neoplasm subsets +- Improved handling of complex defintions +- Improved handling of NCI Thesaurus cumulative history + ## [2.1.1.RELEASE] - 2025-04-30 ### Changed - Load childhood neoplasm data from a renamed file and include subsetLink data diff --git a/ELASTICSEARCH.md b/ELASTICSEARCH.md deleted file mode 100644 index f2eba6d48..000000000 --- a/ELASTICSEARCH.md +++ /dev/null @@ -1,16 +0,0 @@ -# EVSRESTAPI - ELASTICSEARCH SETUP - -Information on downloading and using ELASTICSEARCH with EVSRESTAPI. - -Verify the $ES_DIR variable points to the correct path set up in previous steps. If not, set it now:
`export set -ES_DIR=c:$dir/elasticsearch/data` - -## Running Elasticsearch Locally - -In a terminal, run the following to have an elasticsearch instance running. Keep this window open to keep the server running. - - docker run -d --name=es_evs --rm -p $ES_PORT:9200 \ - -v "$ES_DIR":/usr/share/elasticsearch/data -e "xpack.security.enabled=false" \ - -e "discovery.type=single-node" -e ES_JAVA_OPTS="-Xms1g -Xmx5g" \ - docker.elastic.co/elasticsearch/elasticsearch:7.12.1 - diff --git a/JENA.md b/JENA.md index 97861e3aa..c5375ce11 100644 --- a/JENA.md +++ b/JENA.md @@ -8,7 +8,7 @@ Run the following command to build the Jena image: ```bash cd docker/fuseki -docker build -t evsrestapi/fuseki:5.1.0 . +docker build -t evsrestapi/fuseki:5.3.0 . ``` ### Running a Jena/Fuseki Container @@ -18,7 +18,7 @@ Note: you need the mount path to a local directory ($dir) of your choice to pers ```bash dir=c:/Users/carlsenbr/eclipse-workspace/data/fuseki -docker run -d --name=jena_evs --rm -p "3030:3030" -v "$dir":/opt/fuseki/run/databases evsrestapi/fuseki:5.1.0 +docker run -d --name=jena_evs --rm -p "3030:3030" -v "$dir":/opt/fuseki/run/databases evsrestapi/fuseki:5.3.0 ``` ### Running a sparql query (assumes jena/fuseki running on localhost and curl and jq are installed) diff --git a/Makefile b/Makefile index 82a1ed41f..82d6a5fb8 100644 --- a/Makefile +++ b/Makefile @@ -24,7 +24,7 @@ clean: # Build the library without tests # On Windows use: git config core.eol lf build: - ./gradlew clean spotlessApply build -x test + ./gradlew clean spotlessApply build -x test -x zipFile test: ./gradlew spotlessCheck -x test diff --git a/OPENSEARCH.md b/OPENSEARCH.md index 0af48a4e4..33e6d80dd 100644 --- a/OPENSEARCH.md +++ b/OPENSEARCH.md @@ -27,7 +27,35 @@ In a terminal, run the following to have an opensearch instance running on the b -v "$OS_DIR":/usr/share/opensearch/data \ -e DISABLE_SECURITY_PLUGIN=true \ --name opensearch-node -d opensearchproject/opensearch:2.18.0 - + +## Configure refresh interval globally + +To prevent "too many requests" issue from happening while loader is running, it may be useful +to set the refresh interval higher. Making it higher than 5s requires review of loader +code to ensure it is not trying to read back data earlier than 5s after a required prior +indexing operation completes (Review `Thread.sleep` calls in the code). + +``` +curl -X PUT $ES/_cluster/settings -H "Content-type: application/json" \ + -d '{ "persistent": { "index.refresh_interval": "60s" } } +``` + +A call like this in AWS needs to be done from a machine with an IAM role l + +``` +{ + "Effect": "Allow", + "Principal": { + "AWS": "arn:aws:iam:::user/" + }, + "Action": [ + "es:ESHttpPut", + "es:admin/cluster/settings/update" + ], + "Resource": "arn:aws:es:::domain//*" +} +``` + ## References * Documentation - https://opensearch.org/docs/latest/ diff --git a/build.gradle b/build.gradle index 8b04cf91c..0a8d24e8c 100644 --- a/build.gradle +++ b/build.gradle @@ -1,6 +1,6 @@ buildscript { ext { - springBootVersion = '3.3.5' + springBootVersion = '3.3.11' // Remove this line to see what version is favored by springBootVersion // and the version brought in by spring-data-elasticsearch set('elasticsearch.version', '7.12.1') @@ -56,7 +56,7 @@ ext { /* Version info */ group = "gov.nih.nci.evs.api" -version = "2.1.1.RELEASE" +version = "2.2.0.RELEASE" sourceCompatibility = 17 targetCompatibility = 17 @@ -72,6 +72,7 @@ java { toolchain { languageVersion = JavaLanguageVersion.of(17) } + } dependencies { @@ -89,7 +90,7 @@ dependencies { implementation "org.springframework:spring-aop" // For vulnerabilities - implementation "org.apache.tomcat.embed:tomcat-embed-core:10.1.40" + implementation "org.apache.tomcat.embed:tomcat-embed-core:10.1.42" //implementation "org.springframework.data:spring-data-elasticsearch:4.2.12" implementation "org.opensearch.client:spring-data-opensearch-starter:1.5.3" @@ -120,11 +121,11 @@ dependencies { implementation 'com.google.protobuf:protobuf-java:3.25.5' // fhir dependencies - implementation "ca.uhn.hapi.fhir:hapi-fhir-base:7.4.5"; - implementation "ca.uhn.hapi.fhir:hapi-fhir-structures-r4:7.4.5" - implementation "ca.uhn.hapi.fhir:hapi-fhir-structures-r5:7.4.5" - implementation "ca.uhn.hapi.fhir:hapi-fhir-server:7.4.5" - implementation("ca.uhn.hapi.fhir:hapi-fhir-jpaserver-base:7.4.5") { + implementation "ca.uhn.hapi.fhir:hapi-fhir-base:7.6.1"; + implementation "ca.uhn.hapi.fhir:hapi-fhir-structures-r4:7.6.1" + implementation "ca.uhn.hapi.fhir:hapi-fhir-structures-r5:7.6.1" + implementation "ca.uhn.hapi.fhir:hapi-fhir-server:7.6.1" + implementation("ca.uhn.hapi.fhir:hapi-fhir-jpaserver-base:7.6.1") { exclude group: "net.minidev", module: "json-smart" exclude group: "ca.uhn.hapi.fhir", module: "hapi-fhir-sql-migrate" exclude group: "org.elasticsearch.client", module: "elasticsearch-rest-high-level-client" @@ -136,19 +137,19 @@ dependencies { exclude group: "org.glassfish", module: "javax.el" exclude group: "org.apache.logging.log4j", module: "log4j-to-slf4j" } - implementation "ca.uhn.hapi.fhir:hapi-fhir-server-openapi:7.4.5" + implementation "ca.uhn.hapi.fhir:hapi-fhir-server-openapi:7.6.1" // For the moment, these require explicit 6.4.0 to resolve vulnerabilities (as 7.4.5 above is current) implementation "org.fhir:ucum:1.0.9" - implementation "ca.uhn.hapi.fhir:org.hl7.fhir.convertors:6.4.0" - implementation "ca.uhn.hapi.fhir:org.hl7.fhir.dstu2:6.4.0" - implementation "ca.uhn.hapi.fhir:org.hl7.fhir.dstu2016may:6.4.0" - implementation "ca.uhn.hapi.fhir:org.hl7.fhir.dstu3:6.4.0" - implementation "ca.uhn.hapi.fhir:org.hl7.fhir.r4:6.4.0" - implementation "ca.uhn.hapi.fhir:org.hl7.fhir.r4b:6.4.0" - implementation "ca.uhn.hapi.fhir:org.hl7.fhir.r5:6.4.0" - implementation "ca.uhn.hapi.fhir:org.hl7.fhir.utilities:6.4.0" - implementation "ca.uhn.hapi.fhir:org.hl7.fhir.validation:6.4.0" + //implementation "ca.uhn.hapi.fhir:org.hl7.fhir.convertors:6.4.0" + //implementation "ca.uhn.hapi.fhir:org.hl7.fhir.dstu2:6.4.0" + //implementation "ca.uhn.hapi.fhir:org.hl7.fhir.dstu2016may:6.4.0" + //implementation "ca.uhn.hapi.fhir:org.hl7.fhir.dstu3:6.4.0" + //implementation "ca.uhn.hapi.fhir:org.hl7.fhir.r4:6.4.0" + //implementation "ca.uhn.hapi.fhir:org.hl7.fhir.r4b:6.4.0" + //implementation "ca.uhn.hapi.fhir:org.hl7.fhir.r5:6.4.0" + //implementation "ca.uhn.hapi.fhir:org.hl7.fhir.utilities:6.4.0" + //implementation "ca.uhn.hapi.fhir:org.hl7.fhir.validation:6.4.0" // Lombok dependencies (avoid using lombok for now) //implementation "org.projectlombok:lombok:1.18.32" diff --git a/docker/fuseki/Dockerfile b/docker/fuseki/Dockerfile index 08e8deb22..d94b1164f 100644 --- a/docker/fuseki/Dockerfile +++ b/docker/fuseki/Dockerfile @@ -1,7 +1,7 @@ FROM bellsoft/liberica-openjre-alpine:17.0.13 # Set environment variables -ENV FUSEKI_VERSION=5.1.0 +ENV FUSEKI_VERSION=5.3.0 ENV JENA_HOME=/opt/jena ENV FUSEKI_HOME=/opt/fuseki ENV FUSEKI_BASE=/opt/fuseki/run diff --git a/software/NCIT.md b/software/NCIT.md deleted file mode 100644 index e386d8932..000000000 --- a/software/NCIT.md +++ /dev/null @@ -1,29 +0,0 @@ -# EVSRESTAPI - NCIT Maintenance Tasks - -Information on using evsrestapi-util for maintenance tasks. - -## Computing SPARQL queries for roles/subclasses - -The roles and subclasses queries in sparql-queries.properties -may need to change from time to time as patterns within NCIt OWL -change over time. Periodically (e.g. quarterly/bi-annually), -it is desirable to recompute the roles and subclasses sparql queries -to understand whether new patterns need to be supported. - -### Steps - -1. Build software/evsapi-util to create the evsrestapi-util.jar file (requires `ant` installation) - - -2. Generate roles - -java -d64 -Xms512m -Xmx4g -classpath evsrestapi-util.jar gov.nih.nci.evs.restapi.util.SPARQLQueryGenerator /path/to//ThesaurusInferred.owl roles - -Use the output to update all "roles" entries in `sparql-queries.properties`) - -3. Generate subclasses - -java -d64 -Xms512m -Xmx4g -classpath evsrestapi-util.jar gov.nih.nci.evs.restapi.util.SPARQLQueryGenerator /path/to//ThesaurusInferred.owl subclasses - -Use the output to update all "hierarchy" entries in `sparql-queries.properties`) - diff --git a/software/evsrestapi-client/build.properties b/software/evsrestapi-client/build.properties deleted file mode 100644 index a6942a212..000000000 --- a/software/evsrestapi-client/build.properties +++ /dev/null @@ -1,30 +0,0 @@ -# The project name will be the name of the jar file. -project.name = evsrestapi-client - -# CVS settings -cvs.root = -export.command = export -DNOW src - -# Where source files are found -src.dir = ./src - -# Classpath - -# Intermediate directory for building class files. -build.dir = ./build - -# Compiler options. -debug = on -optimize = on -deprecation = off -packagename = evsrestapi-client - -# Javadoc options. -javadoc.dir = ./api -#javadoc.style = -javadoc.author = true -javadoc.private = false -javadoc.use = true -javadoc.version = true -javadoc.window.title = evsrestapi-client -javadoc.doc.title = evsrestapi-client diff --git a/software/evsrestapi-client/build.xml b/software/evsrestapi-client/build.xml deleted file mode 100644 index 367e2991c..000000000 --- a/software/evsrestapi-client/build.xml +++ /dev/null @@ -1,61 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - JAVA_HOME: ${java.home} - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/software/evsrestapi-client/cmd.exe b/software/evsrestapi-client/cmd.exe deleted file mode 100644 index dca94f437..000000000 Binary files a/software/evsrestapi-client/cmd.exe and /dev/null differ diff --git a/software/evsrestapi-client/evsrestapi-client.jar b/software/evsrestapi-client/evsrestapi-client.jar deleted file mode 100644 index 9867b1acb..000000000 Binary files a/software/evsrestapi-client/evsrestapi-client.jar and /dev/null differ diff --git a/software/evsrestapi-client/lib/evsrestapi-util.jar b/software/evsrestapi-client/lib/evsrestapi-util.jar deleted file mode 100644 index 758e707ad..000000000 Binary files a/software/evsrestapi-client/lib/evsrestapi-util.jar and /dev/null differ diff --git a/software/evsrestapi-client/lib/gson-2.6.2.jar b/software/evsrestapi-client/lib/gson-2.6.2.jar deleted file mode 100644 index 9d78626d8..000000000 Binary files a/software/evsrestapi-client/lib/gson-2.6.2.jar and /dev/null differ diff --git a/software/evsrestapi-client/lib/jackson-annotations-2.9.0.jar b/software/evsrestapi-client/lib/jackson-annotations-2.9.0.jar deleted file mode 100644 index 624db9882..000000000 Binary files a/software/evsrestapi-client/lib/jackson-annotations-2.9.0.jar and /dev/null differ diff --git a/software/evsrestapi-client/lib/jackson-core-2.9.7.jar b/software/evsrestapi-client/lib/jackson-core-2.9.7.jar deleted file mode 100644 index 8211c6442..000000000 Binary files a/software/evsrestapi-client/lib/jackson-core-2.9.7.jar and /dev/null differ diff --git a/software/evsrestapi-client/lib/jackson-databind-2.9.7.jar b/software/evsrestapi-client/lib/jackson-databind-2.9.7.jar deleted file mode 100644 index 89b059975..000000000 Binary files a/software/evsrestapi-client/lib/jackson-databind-2.9.7.jar and /dev/null differ diff --git a/software/evsrestapi-client/lib/jackson-dataformat-yaml-2.9.7.jar b/software/evsrestapi-client/lib/jackson-dataformat-yaml-2.9.7.jar deleted file mode 100644 index 0bfba2eb3..000000000 Binary files a/software/evsrestapi-client/lib/jackson-dataformat-yaml-2.9.7.jar and /dev/null differ diff --git a/software/evsrestapi-client/lib/jackson-datatype-jdk8-2.9.7.jar b/software/evsrestapi-client/lib/jackson-datatype-jdk8-2.9.7.jar deleted file mode 100644 index 7e8c24e48..000000000 Binary files a/software/evsrestapi-client/lib/jackson-datatype-jdk8-2.9.7.jar and /dev/null differ diff --git a/software/evsrestapi-client/lib/jackson-datatype-jsr310-2.9.7.jar b/software/evsrestapi-client/lib/jackson-datatype-jsr310-2.9.7.jar deleted file mode 100644 index 1357a6a09..000000000 Binary files a/software/evsrestapi-client/lib/jackson-datatype-jsr310-2.9.7.jar and /dev/null differ diff --git a/software/evsrestapi-client/lib/jackson-module-parameter-names-2.9.7.jar b/software/evsrestapi-client/lib/jackson-module-parameter-names-2.9.7.jar deleted file mode 100644 index 8bd6a449d..000000000 Binary files a/software/evsrestapi-client/lib/jackson-module-parameter-names-2.9.7.jar and /dev/null differ diff --git a/software/evsrestapi-client/lib/xstream-1.2.2.jar b/software/evsrestapi-client/lib/xstream-1.2.2.jar deleted file mode 100644 index 2d813c229..000000000 Binary files a/software/evsrestapi-client/lib/xstream-1.2.2.jar and /dev/null differ diff --git a/software/evsrestapi-client/src/gov/nih/nci/evs/restapi/client/bean/Association.java b/software/evsrestapi-client/src/gov/nih/nci/evs/restapi/client/bean/Association.java deleted file mode 100644 index 0a747e778..000000000 --- a/software/evsrestapi-client/src/gov/nih/nci/evs/restapi/client/bean/Association.java +++ /dev/null @@ -1,93 +0,0 @@ -package gov.nih.nci.evs.restapi.client.bean; - -import java.io.*; -import java.util.*; -import java.net.*; - -import com.google.gson.*; -import com.google.gson.GsonBuilder; -import com.google.gson.reflect.TypeToken; -import com.thoughtworks.xstream.io.json.JettisonMappedXmlDriver; -import com.thoughtworks.xstream.io.xml.DomDriver; -import com.thoughtworks.xstream.XStream; - -public class Association -{ - -// Variable declaration - private String type; - private String relatedCode; - private String relatedName; - -// Default constructor - public Association() { - } - -// Constructor - public Association( - String type, - String relatedCode, - String relatedName) { - - this.type = type; - this.relatedCode = relatedCode; - this.relatedName = relatedName; - } - -// Set methods - public void setType(String type) { - this.type = type; - } - - public void setRelatedCode(String relatedCode) { - this.relatedCode = relatedCode; - } - - public void setRelatedName(String relatedName) { - this.relatedName = relatedName; - } - - -// Get methods - public String getType() { - return this.type; - } - - public String getRelatedCode() { - return this.relatedCode; - } - - public String getRelatedName() { - return this.relatedName; - } - - public String toXML() { - XStream xstream_xml = new XStream(new DomDriver()); - String xml = xstream_xml.toXML(this); - xml = escapeDoubleQuotes(xml); - StringBuffer buf = new StringBuffer(); - String XML_DECLARATION = ""; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i"; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i"; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i synonyms; - private List definitions; - private List properties; - private List parents; - private List children; - private List associations; - private List inverseAssociations; - private List roles; - private List inverseRoles; - private List maps; - -// Default constructor - public ConceptDetails() { - } - -// Constructor - public ConceptDetails( - String code, - String name, - String terminology, - String version, - boolean leaf, - List synonyms, - List definitions, - List properties, - List parents, - List children, - List associations, - List inverseAssociations, - List roles, - List inverseRoles, - List maps) { - - this.code = code; - this.name = name; - this.terminology = terminology; - this.version = version; - this.leaf = leaf; - this.synonyms = synonyms; - this.definitions = definitions; - this.properties = properties; - this.parents = parents; - this.children = children; - this.associations = associations; - this.inverseAssociations = inverseAssociations; - this.roles = roles; - this.inverseRoles = inverseRoles; - this.maps = maps; - } - -// Set methods - public void setCode(String code) { - this.code = code; - } - - public void setName(String name) { - this.name = name; - } - - public void setTerminology(String terminology) { - this.terminology = terminology; - } - - public void setVersion(String version) { - this.version = version; - } - - public void setLeaf(boolean leaf) { - this.leaf = leaf; - } - - public void setSynonyms(List synonyms) { - this.synonyms = synonyms; - } - - public void setDefinitions(List definitions) { - this.definitions = definitions; - } - - public void setProperties(List properties) { - this.properties = properties; - } - - public void setParents(List parents) { - this.parents = parents; - } - - public void setChildren(List children) { - this.children = children; - } - - public void setAssociations(List associations) { - this.associations = associations; - } - - public void setInverseAssociations(List inverseAssociations) { - this.inverseAssociations = inverseAssociations; - } - - public void setRoles(List roles) { - this.roles = roles; - } - - public void setInverseRoles(List inverseRoles) { - this.inverseRoles = inverseRoles; - } - - public void setMaps(List maps) { - this.maps = maps; - } - - -// Get methods - public String getCode() { - return this.code; - } - - public String getName() { - return this.name; - } - - public String getTerminology() { - return this.terminology; - } - - public String getVersion() { - return this.version; - } - - public boolean getLeaf() { - return this.leaf; - } - - public List getSynonyms() { - return this.synonyms; - } - - public List getDefinitions() { - return this.definitions; - } - - public List getProperties() { - return this.properties; - } - - public List getParents() { - return this.parents; - } - - public List getChildren() { - return this.children; - } - - public List getAssociations() { - return this.associations; - } - - public List getInverseAssociations() { - return this.inverseAssociations; - } - - public List getRoles() { - return this.roles; - } - - public List getInverseRoles() { - return this.inverseRoles; - } - - public List getMaps() { - return this.maps; - } - - public String toXML() { - XStream xstream_xml = new XStream(new DomDriver()); - String xml = xstream_xml.toXML(this); - xml = escapeDoubleQuotes(xml); - StringBuffer buf = new StringBuffer(); - String XML_DECLARATION = ""; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i qualifiers; - -// Default constructor - public Definition() { - } - -// Constructor - public Definition( - String type, - String definition, - String source, - List qualifiers) { - - this.type = type; - this.definition = definition; - this.source = source; - this.qualifiers = qualifiers; - } - -// Set methods - public void setType(String type) { - this.type = type; - } - - public void setDefinition(String definition) { - this.definition = definition; - } - - public void setSource(String source) { - this.source = source; - } - - public void setQualifiers(List qualifiers) { - this.qualifiers = qualifiers; - } - - -// Get methods - public String getType() { - return this.type; - } - - public String getDefinition() { - return this.definition; - } - - public String getSource() { - return this.source; - } - - public List getQualifiers() { - return this.qualifiers; - } - - public String toXML() { - XStream xstream_xml = new XStream(new DomDriver()); - String xml = xstream_xml.toXML(this); - xml = escapeDoubleQuotes(xml); - StringBuffer buf = new StringBuffer(); - String XML_DECLARATION = ""; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i"; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i"; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i"; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i"; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i"; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i"; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i property; - List synonymType; - private List terminology; - -// Default constructor - public Parameter() { - } - -// Constructor - public Parameter( - String term, - String type, - String include, - int fromRecord, - int pageSize, - List property, - List synonymType, - List terminology) { - - this.term = term; - this.type = type; - this.include = include; - this.fromRecord = fromRecord; - this.pageSize = pageSize; - this.property = property; - this.synonymType = synonymType; - this.terminology = terminology; - } - -// Set methods - public void setTerm(String term) { - this.term = term; - } - - public void setType(String type) { - this.type = type; - } - - public void setInclude(String include) { - this.include = include; - } - - public void setFromRecord(int fromRecord) { - this.fromRecord = fromRecord; - } - - public void setPageSize(int pageSize) { - this.pageSize = pageSize; - } - - public void setProperty(List property) { - this.property = property; - } - - public void setSynonymType(List synonymType) { - this.synonymType = synonymType; - } - - public void setTerminology(List terminology) { - this.terminology = terminology; - } - - -// Get methods - public String getTerm() { - return this.term; - } - - public String getType() { - return this.type; - } - - public String getInclude() { - return this.include; - } - - public int getFromRecord() { - return this.fromRecord; - } - - public int getPageSize() { - return this.pageSize; - } - - public List getProperty() { - return this.property; - } - - public List getSynonymType() { - return this.synonymType; - } - - public List getTerminology() { - return this.terminology; - } - - public String toXML() { - XStream xstream_xml = new XStream(new DomDriver()); - String xml = xstream_xml.toXML(this); - xml = escapeDoubleQuotes(xml); - StringBuffer buf = new StringBuffer(); - String XML_DECLARATION = ""; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i"; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i path; - -// Default constructor - public Path() { - } - -// Constructor - public Path( - List path) { - - this.path = path; - } - -// Set methods - public void setPath(List path) { - this.path = path; - } - - -// Get methods - public List getPath() { - return this.path; - } - - public String toXML() { - XStream xstream_xml = new XStream(new DomDriver()); - String xml = xstream_xml.toXML(this); - xml = escapeDoubleQuotes(xml); - StringBuffer buf = new StringBuffer(); - String XML_DECLARATION = ""; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i paths; - -// Default constructor - public Paths() { - } - -// Constructor - public Paths( - List paths) { - - this.paths = paths; - } - -// Set methods - public void setPaths(List paths) { - this.paths = paths; - } - - -// Get methods - public List getPaths() { - return this.paths; - } - - public String toXML() { - XStream xstream_xml = new XStream(new DomDriver()); - String xml = xstream_xml.toXML(this); - xml = escapeDoubleQuotes(xml); - StringBuffer buf = new StringBuffer(); - String XML_DECLARATION = ""; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i qualifiers; - -// Default constructor - public Property() { - } - -// Constructor - public Property( - String type, - String value, - List qualifiers) { - - this.type = type; - this.value = value; - this.qualifiers = qualifiers; - } - -// Set methods - public void setType(String type) { - this.type = type; - } - - public void setValue(String value) { - this.value = value; - } - - public void setQualifiers(List qualifiers) { - this.qualifiers = qualifiers; - } - - -// Get methods - public String getType() { - return this.type; - } - - public String getValue() { - return this.value; - } - - public List getQualifiers() { - return this.qualifiers; - } - - public String toXML() { - XStream xstream_xml = new XStream(new DomDriver()); - String xml = xstream_xml.toXML(this); - xml = escapeDoubleQuotes(xml); - StringBuffer buf = new StringBuffer(); - String XML_DECLARATION = ""; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i"; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i"; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i"; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i concepts; - -// Default constructor - public SearchResult() { - } - -// Constructor - public SearchResult( - int total, - int timeTaken, - Parameter parameters, - List concepts) { - - this.total = total; - this.timeTaken = timeTaken; - this.parameters = parameters; - this.concepts = concepts; - } - -// Set methods - public void setTotal(int total) { - this.total = total; - } - - public void setTimeTaken(int timeTaken) { - this.timeTaken = timeTaken; - } - - public void setParameters(Parameter parameters) { - this.parameters = parameters; - } - - public void setConcepts(List concepts) { - this.concepts = concepts; - } - - -// Get methods - public int getTotal() { - return this.total; - } - - public int getTimeTaken() { - return this.timeTaken; - } - - public Parameter getParameters() { - return this.parameters; - } - - public List getConcepts() { - return this.concepts; - } - - public String toXML() { - XStream xstream_xml = new XStream(new DomDriver()); - String xml = xstream_xml.toXML(this); - xml = escapeDoubleQuotes(xml); - StringBuffer buf = new StringBuffer(); - String XML_DECLARATION = ""; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i concepts; - -// Default constructor - public SearchResultDetails() { - } - -// Constructor - public SearchResultDetails( - int total, - int timeTaken, - Parameter parameters, - List concepts) { - - this.total = total; - this.timeTaken = timeTaken; - this.parameters = parameters; - this.concepts = concepts; - } - -// Set methods - public void setTotal(int total) { - this.total = total; - } - - public void setTimeTaken(int timeTaken) { - this.timeTaken = timeTaken; - } - - public void setParameters(Parameter parameters) { - this.parameters = parameters; - } - - public void setConcepts(List concepts) { - this.concepts = concepts; - } - - -// Get methods - public int getTotal() { - return this.total; - } - - public int getTimeTaken() { - return this.timeTaken; - } - - public Parameter getParameters() { - return this.parameters; - } - - public List getConcepts() { - return this.concepts; - } - - public String toXML() { - XStream xstream_xml = new XStream(new DomDriver()); - String xml = xstream_xml.toXML(this); - xml = escapeDoubleQuotes(xml); - StringBuffer buf = new StringBuffer(); - String XML_DECLARATION = ""; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i"; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i children; - -// Default constructor - public TreeNode() { - } - -// Constructor - public TreeNode( - String code, - String label, - boolean leaf, - boolean expanded, - List children) { - - this.code = code; - this.label = label; - this.leaf = leaf; - this.expanded = expanded; - this.children = children; - } - -// Set methods - public void setCode(String code) { - this.code = code; - } - - public void setLabel(String label) { - this.label = label; - } - - public void setLeaf(boolean leaf) { - this.leaf = leaf; - } - - public void setExpanded(boolean expanded) { - this.expanded = expanded; - } - - public void setChildren(List children) { - this.children = children; - } - - -// Get methods - public String getCode() { - return this.code; - } - - public String getLabel() { - return this.label; - } - - public boolean getLeaf() { - return this.leaf; - } - - public boolean getExpanded() { - return this.expanded; - } - - public List getChildren() { - return this.children; - } - - public String toXML() { - XStream xstream_xml = new XStream(new DomDriver()); - String xml = xstream_xml.toXML(this); - xml = escapeDoubleQuotes(xml); - StringBuffer buf = new StringBuffer(); - String XML_DECLARATION = ""; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i"; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i"); - out.println(""); - out.println(""); - out.println(""); - out.println(""); - out.println(""); - out.println("" + title + ""); - out.println(""); - out.println(""); - out.println(""); - out.println(""); - out.println(""); - } - - public void writeBody(PrintWriter out, String title, gov.nih.nci.evs.restapi.model.ConceptDetails c) { - out.println(""); - out.println("
"); - out.println("
"); - out.println(" "); - out.println("

" + title + "

"); - out.println("

"); - out.println("  Synonyms: none"); - } else { - out.println("
  Synonyms:
"); - out.println(" "); - out.println(" "); - - out.println(" "); - - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - - out.println(" "); - - for (int i=0; i"); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - } - - out.println(" "); - out.println("
NameTypeTerm GroupSourceSubsourceSource Code
 " + synonym.getName() + "" + synonym.getType() + "" + termgroup + "" + source + "" + subsource + "" + sourcecode + "
"); - } - out.println("

"); - - out.println("
"); - List defs = c.getDefinitions(); - if (defs == null || defs.size() == 0) { - out.println("
  Definitions: none
"); - } else { - out.println("
  Definitions:
"); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - - out.println(" "); - out.println(" "); - out.println(" "); - for (int i=0; i"); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - } - out.println(" "); - out.println("
TypeDescriptionSource
 " + type + "" + a.getDefinition() + "" + a.getSource() + "
"); - } - out.println("
"); - out.println("

"); - - out.println("
"); - List properties = c.getProperties(); - if (properties == null || properties.size() == 0) { - out.println("
  Properties: none
"); - } else { - out.println("
  Properties:
"); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - - out.println(" "); - out.println(" "); - out.println(" "); - for (int i=0; i"); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - } - out.println(" "); - out.println("
TypeValue
 " + a.getType() + "" + a.getValue() + "
"); - } - out.println("
"); - out.println("

"); - - out.println("
"); - - List superconcepts = c.getParents(); - if (superconcepts == null || superconcepts.size() == 0) { - out.println("
  Superconcepts: none
"); - } else { - out.println("
  Superconcepts:
"); - out.println(" "); - out.println(" "); - - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - - - for (int i=0; i"); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - } - out.println(" "); - out.println("
 CodeName
 " + superconcept.getCode() + "" + superconcept.getName() + "
"); - } - out.println("

"); - out.println("
"); - out.println("
"); - List subconcepts = c.getChildren(); - if (subconcepts == null || subconcepts.size() == 0) { - out.println("
  Subconcepts: none
"); - } else { - out.println("
  Subconcepts:
"); - out.println(" "); - out.println(" "); - - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - - for (int i=0; i"); - - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - } - out.println(" "); - out.println("
 CodeName
 " + subconcept.getCode() + "" + subconcept.getName() + "
"); - } - out.println("
"); - out.println("

"); - - out.println("
"); - ///////////////////////////////////////////////////////////////////////////////// - List associations = c.getAssociations(); - if (associations == null || associations.size() == 0) { - out.println("
  Associations: none
"); - } else { - out.println("
  Associations:
"); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - - - out.println(" "); - out.println(" "); - out.println(" "); - - out.println(" "); - out.println(" "); - out.println(" "); - for (int i=0; i"); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - } - out.println(" "); - out.println("
NameRelated NameRelated Code
 " + a.getType() + "" + a.getRelatedName() + "" + a.getRelatedCode() + "
"); - } - out.println("
"); - out.println("

"); - - out.println("
"); - List inv_associations = c.getInverseAssociations(); - if (inv_associations == null || inv_associations.size() == 0) { - out.println("
  Inverse Associations: none
"); - } else { - out.println("
  Inverse Associations:
"); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - - out.println(" "); - out.println(" "); - out.println(" "); - - out.println(" "); - out.println(" "); - out.println(" "); - for (int i=0; i"); - out.println(" "); - - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - - - out.println(" "); - } - out.println(" "); - out.println("
Related NameRelated CodeName
  " + a.getRelatedName() + "" + a.getRelatedCode() + "" + a.getType() + "
"); - } - - - out.println("
"); - out.println("

"); - List roles = c.getRoles(); - if (roles == null || roles.size() == 0) { - out.println("
  Roles: none
"); - } else { - out.println("
  Roles:
"); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - - out.println(" "); - out.println(" "); - out.println(" "); - - out.println(" "); - out.println(" "); - out.println(" "); - for (int i=0; i"); - - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - - out.println(" "); - } - out.println(" "); - out.println("
NameRelated NameRelated Code
 " + a.getType() + "" + a.getRelatedName() + "" + a.getRelatedCode() + "
"); - } - out.println("

"); - out.println("
"); - List inv_roles = c.getInverseRoles(); - if (inv_roles == null || inv_roles.size() == 0) { - out.println("
  Inverse Roles: none
"); - } else { - out.println("
  Inverse Roles:
"); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - - out.println(" "); - out.println(" "); - out.println(" "); - - out.println(" "); - out.println(" "); - out.println(" "); - for (int i=0; i"); - - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - - out.println(" "); - } - out.println(" "); - out.println("
Related NameRelated CodeName
 " + a.getRelatedName() + "" + a.getRelatedCode() + "" + a.getType() + "
"); - } - out.println("

"); - - out.println("
"); - List maps = c.getMaps(); - if (maps == null || maps.size() == 0) { - out.println("
  MapsTo: none
"); - } else { - out.println("
  MapsTo:
"); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - - out.println(" "); - out.println(" "); - out.println(" "); - for (int i=0; i"); - - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(" "); - - out.println(" "); - } - out.println(" "); - out.println("
TypeTarget NameTarget Term GroupTarget CodeTarget TermonologyTarget Termonology Version
 " + a.getType() + "" + a.getTargetName() + "" + a.getTargetTermGroup() + "" + a.getTargetCode() + "" + a.getTargetTerminology() + "" +version + "
"); - } - - out.println("
"); - out.println(""); - } - - public void writeFooter(PrintWriter out) { - out.println(""); - } - - public void generate(PrintWriter out, String title, gov.nih.nci.evs.restapi.model.ConceptDetails c) { - writeHeader(out, title); - writeBody(out, title, c); - writeFooter(out); - } - - public void generate(String outputfile, String title, gov.nih.nci.evs.restapi.model.ConceptDetails c) { - long ms = System.currentTimeMillis(); - PrintWriter pw = null; - try { - pw = new PrintWriter(outputfile, "UTF-8"); - generate(pw, title, c); - - } catch (Exception ex) { - - } finally { - try { - pw.close(); - System.out.println("Output file " + outputfile + " generated."); - } catch (Exception ex) { - ex.printStackTrace(); - } - } - System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms)); - } - - public static void main(String[] args) { - Vector v = null; - try { - //String terminology = "ncit"; - //String code = "C3224"; - String terminology = args[0]; - String code = args[1]; - - gov.nih.nci.evs.restapi.model.ConceptDetails c = EVSRESTAPIClient.getConceptDetails(terminology, code); - /* - String json = c.toJson(); - //System.out.println(c.toJson()); - String flattened_json = EVSRESTAPIClient.flattenJSON(json); - System.out.println(flattened_json); - gov.nih.nci.evs.restapi.model.ConceptDetails c2 = (gov.nih.nci.evs.restapi.model.ConceptDetails) EVSRESTAPIClient.deserialize("ConceptDetails", flattened_json); - System.out.println(c2.toJson()); - */ - - ConceptDetailsPageGenerator generator = new ConceptDetailsPageGenerator(); - String outputfile = "concept_details_" + code + ".html"; - String title = c.getName() + " (" + code + ")"; - generator.generate(outputfile, title, c); - - } catch (Exception ex) { - ex.printStackTrace(); - } - } -} - - -/* - private String code; - private String name; - private String terminology; - private String version; - private List synonyms; - private List definitions; - private List properties; - private List parents; - private List children; - private List associations; - private List inverseAssociations; - private List roles; - private List inverseRoles; - private List maps; -*/ \ No newline at end of file diff --git a/software/evsrestapi-client/src/gov/nih/nci/evs/restapi/util/EVSRESTAPIClient.java b/software/evsrestapi-client/src/gov/nih/nci/evs/restapi/util/EVSRESTAPIClient.java deleted file mode 100644 index 8228d08fc..000000000 --- a/software/evsrestapi-client/src/gov/nih/nci/evs/restapi/util/EVSRESTAPIClient.java +++ /dev/null @@ -1,478 +0,0 @@ -package gov.nih.nci.evs.restapi.util; - -import gov.nih.nci.evs.restapi.model.*; - -import java.io.*; -import java.io.BufferedReader; -import java.io.InputStream; -import java.io.InputStreamReader; -import java.net.*; -import java.net.HttpURLConnection; -import java.net.MalformedURLException; -import java.net.URL; -import java.net.URL; -import java.net.URLConnection; -import java.net.URLEncoder; -import java.util.*; -import java.util.regex.*; -import java.nio.charset.Charset; - -import com.fasterxml.jackson.core.JsonParseException; -import com.fasterxml.jackson.databind.JsonMappingException; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.fasterxml.jackson.databind.DeserializationFeature; - -public class EVSRESTAPIClient { - public static String ENDPOINT_PREFIX = "https://api-evsrest.nci.nih.gov"; - public static String ENDPOINT_CONCEPT = "/api/v1/concept/{terminology}/{code}"; - public static String[] TYPES = new String[]{"roles", "inverseRoles", "associations", "inverseAssociations", "parents"}; - public static HashMap EVSRESTAPI_URL_MAP = new HashMap(); - - static { - EVSRESTAPI_URL_MAP = new HashMap(); - EVSRESTAPI_URL_MAP.put("associations", "https://api-evsrest.nci.nih.gov/api/v1/concept/{terminology}/{code}/associations"); - EVSRESTAPI_URL_MAP.put("inverseAssociations", "https://api-evsrest.nci.nih.gov/api/v1/concept/{terminology}/{code}/inverseAssociations"); - EVSRESTAPI_URL_MAP.put("code", "https://api-evsrest.nci.nih.gov/api/v1/concept/{terminology}/{code}"); - EVSRESTAPI_URL_MAP.put("maps", "https://api-evsrest.nci.nih.gov/api/v1/concept/{terminology}/{code}/maps"); - EVSRESTAPI_URL_MAP.put("pathsToAncestor_ancestorCode", "https://api-evsrest.nci.nih.gov/api/v1/concept/{terminology}/{code}/pathsToAncestor/{ancestorCode}"); - EVSRESTAPI_URL_MAP.put("roles", "https://api-evsrest.nci.nih.gov/api/v1/concept/{terminology}/{code}/roles"); - EVSRESTAPI_URL_MAP.put("roots", "https://api-evsrest.nci.nih.gov/api/v1/concept/{terminology}/roots"); - EVSRESTAPI_URL_MAP.put("descendants", "https://api-evsrest.nci.nih.gov/api/v1/concept/{terminology}/{code}/descendants"); - EVSRESTAPI_URL_MAP.put("pathsToRoot", "https://api-evsrest.nci.nih.gov/api/v1/concept/{terminology}/{code}/pathsToRoot"); - EVSRESTAPI_URL_MAP.put("subtree", "https://api-evsrest.nci.nih.gov/api/v1/concept/{terminology}/{code}/subtree"); - EVSRESTAPI_URL_MAP.put("inverseAssociations", "https://api-evsrest.nci.nih.gov/api/v1/concept/{terminology}/{code}/inverseAssociations"); - EVSRESTAPI_URL_MAP.put("inverseRoles", "https://api-evsrest.nci.nih.gov/api/v1/concept/{terminology}/{code}/inverseRoles"); - EVSRESTAPI_URL_MAP.put("concept_terminology", "https://api-evsrest.nci.nih.gov/api/v1/concept/{terminology}"); - EVSRESTAPI_URL_MAP.put("children", "https://api-evsrest.nci.nih.gov/api/v1/concept/{terminology}/{code}/subtree/children"); - EVSRESTAPI_URL_MAP.put("disjointWith", "https://api-evsrest.nci.nih.gov/api/v1/concept/{terminology}/{code}/disjointWith"); - EVSRESTAPI_URL_MAP.put("pathsFromRoot", "https://api-evsrest.nci.nih.gov/api/v1/concept/{terminology}/{code}/pathsFromRoot"); - EVSRESTAPI_URL_MAP.put("parents", "https://api-evsrest.nci.nih.gov/api/v1/concept/{terminology}/{code}/parents"); - EVSRESTAPI_URL_MAP.put("concept", "https://api-evsrest.nci.nih.gov/api/v1/concept/{terminology}/{code}?include=full"); - - - EVSRESTAPI_URL_MAP.put("metadata_associations", "https://api-evsrest.nci.nih.gov/api/v1/metadata/{terminology}/associations"); - EVSRESTAPI_URL_MAP.put("metadata_terminologies", "https://api-evsrest.nci.nih.gov/api/v1/metadata/terminologies"); - EVSRESTAPI_URL_MAP.put("metadata_values", "https://api-evsrest.nci.nih.gov/api/v1/metadata/{terminology}/qualifier/{codeOrLabel}/values"); - EVSRESTAPI_URL_MAP.put("metadata_roles", "https://api-evsrest.nci.nih.gov/api/v1/metadata/{terminology}/roles"); - EVSRESTAPI_URL_MAP.put("metadata_role_codeOrLabel", "https://api-evsrest.nci.nih.gov/api/v1/metadata/{terminology}/role/{codeOrLabel}"); - EVSRESTAPI_URL_MAP.put("metadata_qualifiers", "https://api-evsrest.nci.nih.gov/api/v1/metadata/{terminology}/qualifiers"); - EVSRESTAPI_URL_MAP.put("metadata_definitionSources", "https://api-evsrest.nci.nih.gov/api/v1/metadata/{terminology}/definitionSources"); - EVSRESTAPI_URL_MAP.put("metadata_termTypes", "https://api-evsrest.nci.nih.gov/api/v1/metadata/{terminology}/termTypes"); - EVSRESTAPI_URL_MAP.put("metadata_synonymSources", "https://api-evsrest.nci.nih.gov/api/v1/metadata/{terminology}/synonymSources"); - EVSRESTAPI_URL_MAP.put("metadata_association_codeOrLabel", "https://api-evsrest.nci.nih.gov/api/v1/metadata/{terminology}/association/{codeOrLabel}"); - EVSRESTAPI_URL_MAP.put("metadata_property_codeOrLabel", "https://api-evsrest.nci.nih.gov/api/v1/metadata/{terminology}/property/{codeOrLabel}"); - EVSRESTAPI_URL_MAP.put("metadata_conceptStatuses", "https://api-evsrest.nci.nih.gov/api/v1/metadata/{terminology}/conceptStatuses"); - EVSRESTAPI_URL_MAP.put("metadata_properties", "https://api-evsrest.nci.nih.gov/api/v1/metadata/{terminology}/properties"); - EVSRESTAPI_URL_MAP.put("metadata_qualifier_codeOrLabel", "https://api-evsrest.nci.nih.gov/api/v1/metadata/{terminology}/qualifier/{codeOrLabel}"); - } - - - public EVSRESTAPIClient() { - - } - - public static HashMap get_evsrestapi_endpoint_map(String filename) { - HashMap hmap = new HashMap(); - String end_point_prefix = EVSRESTAPIClient.ENDPOINT_PREFIX; - Vector v = Utils.readFile(filename); - Vector w = new Vector(); - for (int i=0; i list = Arrays.asList(TYPES); - Vector end_points = get_evsrestapi_endpoints( filename, code); - Vector v = new Vector(); - int k = 0; - for (int i=0; i 0) { - Utils.saveToFile("failed_urls.txt", failed_urls); - } - System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms)); - return w; - } - - public static String getURL(String t, String terminology, String code) { - if (terminology != null) t = t.replace("{terminology}", terminology); - if (code != null) t = t.replace("{code}", code); - return t; - } - - public String code2Label(String code) { - return code2Label("ncit", code); - } - - public String code2Label(String terminology, String code) { - String t = (String) EVSRESTAPI_URL_MAP.get("code"); - String url = getURL(t, terminology, code); - String json = getJson(url); - if (json == null) return null; - try { - gov.nih.nci.evs.restapi.model.Concept c = (gov.nih.nci.evs.restapi.model.Concept) deserialize("Concept", json); - return c.getName(); - } catch (Exception ex) { - ex.printStackTrace(); - } - return null; - } - - public Vector extractHierarchyData(String parentCode, String parntLabel , gov.nih.nci.evs.restapi.model.TreeNode node) { - if (node == null) return null; - Vector w = new Vector(); - w.add(parntLabel + "|" + parentCode + "|" + node.getName() + "|" + node.getCode()); - List list = node.getChildren(); - if (list != null) { - for (int k=0; k codes = vs.getCodes(); - for (int i=0; i definitions) { - int hashcode = 0; - if (definitions == null || definitions.size() == 0) return 0; - for (int i=0; i superclasses) { - int hashcode = 0; - if (superclasses == null || superclasses.size() == 0) return 0; - for (int i=0; i subclasses) { - int hashcode = 0; - if (subclasses == null || subclasses.size() == 0) return 0; - for (int i=0; i maps) { - int hashcode = 0; - if (maps == null || maps.size() == 0) return 0; - for (int i=0; i synonyms) { - int hashcode = 0; - if (synonyms == null || synonyms.size() == 0) return 0; - for (int i=0; i roles) { - int hashcode = 0; - if (roles == null || roles.size() == 0) return 0; - for (int i=0; i inverseroles) { - int hashcode = 0; - if (inverseroles == null || inverseroles.size() == 0) return 0; - for (int i=0; i associations) { - int hashcode = 0; - if (associations == null || associations.size() == 0) return 0; - for (int i=0; i inverseassociation) { - int hashcode = 0; - if (inverseassociation == null || inverseassociation.size() == 0) return 0; - for (int i=0; i superclasses = cd.getParents(); - if (superclasses == null || superclasses.size() == 0) return null; - for (int i=0; i suberclasses = cd.getChildren(); - if (suberclasses == null || suberclasses.size() == 0) return null; - for (int i=0; i maps = cd.getMaps(); - if (maps == null || maps.size() == 0) return null; - for (int i=0; i properties = cd.getProperties(); - if (properties == null || properties.size() == 0) return null; - for (int i=0; i definitions = cd.getDefinitions(); - if (definitions == null || definitions.size() == 0) return null; - for (int i=0; i roles = cd.getRoles(); - if (roles == null || roles.size() == 0) return null; - for (int i=0; i roles = cd.getInverseRoles(); - if (roles == null || roles.size() == 0) return null; - for (int i=0; i roles = cd.getAssociations(); - if (roles == null || roles.size() == 0) return null; - for (int i=0; i roles = cd.getInverseAssociations(); - if (roles == null || roles.size() == 0) return null; - for (int i=0; i synonyms = cd.getSynonyms(); - if (synonyms == null || synonyms.size() == 0) return null; - for (int i=0; i properties) { - int hashcode = 0; - if (properties == null || properties.size() == 0) return 0; - for (int i=0; i 0) { - v1.add(t); - } - } - Vector v2 = new Vector(); - for (int i=0; i 0) { - v2.add(t); - } - } - Vector cd1 = new Vector(); - Vector cd2 = new Vector(); - Vector w1 = new Vector(); - Vector w2 = new Vector(); - Vector hashcd_1 = new Vector(); - Vector hashcd_2 = new Vector(); - HashMap code2CDMap1 = new HashMap(); - HashMap code2CDMap2 = new HashMap(); - - HashMap code2Label1 = new HashMap(); - HashMap code2Label2 = new HashMap(); - - Vector edit_history = new Vector(); - - for (int i=0; i loadEditHistory(String filename) { - Vector lines = Utils.readFile(filename); - return toEditActionList(lines); - } - - public static List toEditActionList(Vector lines) { - List list = new ArrayList(); - for (int i=0; i list = loadEditHistory("edit_history.txt"); - */ - List list = toEditActionList(edit_history); - for (int i=0; i"); - out.println(""); - out.println(" "); - out.println(" " + title + ""); - out.println(" "); - out.println(""); - out.println(" "); - out.println(" "); - out.println(" "); - out.println(""); - out.println(" "); - out.println(""); - out.println(" "); - out.println(" "); - out.println(" "); - out.println("

" + title + "

"); - out.println(" "); - out.println("

"); - out.println(" Options:"); - out.println(" "); - //out.println(" "); - out.println("

"); - //out.println(" "); - out.println(" "); - out.println(" 
");
-		out.println("  ");
-		out.println("");
-    }
-
-    public static void generate_html(String json, String title) {
-		long ms = System.currentTimeMillis();
-		String outputfile = title + ".html";
-		outputfile = outputfile.replace(" ","_");
-		System.out.println("Generating " + outputfile + " ...");
-		PrintWriter pw = null;
-		try {
-			pw = new PrintWriter(outputfile, "UTF-8");
-			generate(pw, title, json);
-
-		} catch (Exception ex) {
-
-		} finally {
-			try {
-				pw.close();
-				System.out.println("Output file " + outputfile + " generated.");
-			} catch (Exception ex) {
-				ex.printStackTrace();
-			}
-		}
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-
-
-    public static void generateHTML(String jsonfile) {
-		long ms = System.currentTimeMillis();
-		String json = readJSONFromFile(jsonfile);
-		int n = jsonfile.lastIndexOf(".");
-		String title = jsonfile.substring(0, n);
-		int m = title.lastIndexOf("\\");
-		if (m == -1) {
-			m = title.lastIndexOf("/");
-		}
-		if (m != -1) {
-			title = title.substring(m+1, title.length());
-		}
-		String outputfile = jsonfile.substring(0, n) + ".html";
-		System.out.println("Generating " + outputfile + " ...");
-		PrintWriter pw = null;
-		try {
-			pw = new PrintWriter(outputfile, "UTF-8");
-			generate(pw, title, json);
-
-		} catch (Exception ex) {
-
-		} finally {
-			try {
-				pw.close();
-				System.out.println("Output file " + outputfile + " generated.");
-			} catch (Exception ex) {
-				ex.printStackTrace();
-			}
-		}
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-
-    public static void main(String[] args) {
-		long ms = System.currentTimeMillis();
-		String jsonfile = args[0];
-		generateHTML(jsonfile);
-	}
-}
\ No newline at end of file
diff --git a/software/evsrestapi-client/src/gov/nih/nci/evs/restapi/util/ObjectMappingUtils.java b/software/evsrestapi-client/src/gov/nih/nci/evs/restapi/util/ObjectMappingUtils.java
deleted file mode 100644
index f9fdfa0df..000000000
--- a/software/evsrestapi-client/src/gov/nih/nci/evs/restapi/util/ObjectMappingUtils.java
+++ /dev/null
@@ -1,429 +0,0 @@
-package gov.nih.nci.evs.restapi.util;
-
-import gov.nih.nci.evs.restapi.client.bean.*;
-import java.io.*;
-import java.io.IOException;
-
-import java.math.BigDecimal;
-import java.util.ArrayList;
-import java.util.*;
-
-import com.fasterxml.jackson.core.JsonGenerationException;
-import com.fasterxml.jackson.databind.JsonMappingException;
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-
-public class ObjectMappingUtils {
-
-	static String BASE_URL = "https://api-evsrest.nci.nih.gov/api/v1/";
-
-	public static String ASSOCIATIONS = "associations";
-	public static String CHILDREN = "children";
-	public static String DESCENDANTS = "descendants";
-	public static String DISJOINTWITH = "disjointWith";
-	public static String INVERSEASSOCIATIONS = "inverseAssociations";
-	public static String INVERSEROLES = "inverseRoles";
-	public static String MAPS = "maps";
-	public static String PARENTS = "parents";
-	public static String ROLES = "roles";
-
-	public static String[] HIERARCHICAL_RELATIONSHIPS = new String[] {CHILDREN, PARENTS};
-
-	public static String[] RELATIONSHIPS = new String[] {ASSOCIATIONS, DISJOINTWITH, INVERSEASSOCIATIONS,
-	                                                    INVERSEROLES, MAPS, ROLES};
-
-    public static void setBASE_URL(String url) {
-		BASE_URL = url;
-	}
-
-	public static void run(String[] args) {
-		String inputfile = args[0];
-		run(inputfile);
-	}
-
-	public static Vector readFile(String filename)
-	{
-		Vector v = new Vector();
-		try {
-			BufferedReader in = new BufferedReader(
-			   new InputStreamReader(
-						  new FileInputStream(filename), "UTF8"));
-			String str;
-			while ((str = in.readLine()) != null) {
-				v.add(str);
-			}
-            in.close();
-		} catch (Exception ex) {
-            ex.printStackTrace();
-		}
-		return v;
-	}
-
-	 public static String replaceFilename(String filename) {
-	    return filename.replaceAll("[^a-zA-Z0-9\\.\\-]", "_");
-	 }
-
-	 public static void saveToFile(String outputfile, Vector v) {
-		outputfile = replaceFilename(outputfile);
-		PrintWriter pw = null;
-		try {
-			pw = new PrintWriter(outputfile, "UTF-8");
-			if (v != null && v.size() > 0) {
-				for (int i=0; i 0) {
-			for (int i=0; i
-    
- 
-    
-  
-    
-    
-    
-    
-      
-    
-        
-            
-        
-       
-
-    
-        
-            
-        
-        
-            
-                
-     
-      
-    
-        
-    
-    
-        JAVA_HOME: ${java.home}
-        
-    
-  
-    
-        
-            
-            
-        
-    
-
-    
-        
-    
-
-    
-        
-            
-                
-                
-            
-        
-    
-  
-  
-  
-
diff --git a/software/evsrestapi-util/evsrestapi-util.jar b/software/evsrestapi-util/evsrestapi-util.jar
deleted file mode 100644
index 758e707ad..000000000
Binary files a/software/evsrestapi-util/evsrestapi-util.jar and /dev/null differ
diff --git a/software/evsrestapi-util/jar/ncitqa.jar b/software/evsrestapi-util/jar/ncitqa.jar
deleted file mode 100644
index 037117d68..000000000
Binary files a/software/evsrestapi-util/jar/ncitqa.jar and /dev/null differ
diff --git a/software/evsrestapi-util/lib/application-thesaurus.yml b/software/evsrestapi-util/lib/application-thesaurus.yml
deleted file mode 100644
index 5a1077495..000000000
--- a/software/evsrestapi-util/lib/application-thesaurus.yml
+++ /dev/null
@@ -1,424 +0,0 @@
-thesaurus:
-       owl:
-        returnFields: { code: 'Code',
-                        nhc0: 'Code',
-                        label: 'Label',
-                        displayname: 'Display_Name',
-                        display_name: 'Display_Name',
-                        p107: 'Display_Name',
-                        preferredname: 'Preferred_Name',
-                        preferred_name: 'Preferred_Name',
-                        p108: 'Preferred_Name',
-                        definitions: 'DEFINITION',
-                        definition: 'DEFINITION',
-                        p97: 'DEFINITION',
-                        alt_definition: 'ALT_DEFINITION',
-                        alt_definitions: 'ALT_DEFINITION',
-                        p325: 'ALT_DEFINITION',
-                        semantictypes: 'Semantic_Type',
-                        semantictype: 'Semantic_Type',
-                        semantic_type: 'Semantic_Type',
-                        p106: 'Semantic_Type',
-                        synonyms: 'FULL_SYN',
-                        synonym: 'FULL_SYN',
-                        full_syn: 'FULL_SYN',
-                        p90: 'FULL_SYN',
-                        superconcepts: 'Superconcept',
-                        superconcept: 'Superconcept',
-                        subconcepts: 'Subconcept',
-                        subconcept: 'Subconcept',
-                        roles: 'Role',
-                        role: 'Role',
-                        inverseroles: 'InverseRole',
-                        inverserole: 'InverseRole',
-                        associations: 'Association',
-                        association: 'Association',
-                        inverseassociations: 'InverseAssociation',
-                        inverseassociation: 'InverseAssociation',
-                        conceptstatus: 'Concept_Status',
-                        concept_status: 'Concept_Status',
-                        p310: 'Concept_Status',
-                        neoplastic_status: 'Neoplastic_Status',
-                        p363: 'Neoplastic_Status',
-                        umls_cui: 'UMLS_CUI',
-                        p207: 'UMLS_CUI',
-                        nci_meta_cui: 'NCI_META_CUI',
-                        p208: 'NCI_META_CUI',
-                        cas_registry: 'CAS_Registry',
-                        p210: 'CAS_Registry',
-                        kegg_id:  'KEGG_ID',
-                        p215:  'KEGG_ID',
-                        biocarta_id:  'BioCarta_ID',
-                        p216:  'BioCarta_ID',
-                        accepted_therapeutic_use_for: 'Accepted_Therapeutic_Use_For',
-                        p302: 'Accepted_Therapeutic_Use_For',
-                        snp_id: 'SNP_ID',
-                        p315: 'SNP_ID',
-                        relative_enzyme_activity: 'Relative_Enzyme_Activity',
-                        p316: 'Relative_Enzyme_Activity',
-                        fda_table:  'FDA_Table',
-                        p317:  'FDA_Table',
-                        fda_unii_code:  'FDA_UNII_Code',
-                        p319:  'FDA_UNII_Code',
-                        oid:  'OID',
-                        p320:  'OID',
-                        legacy_concept_name:  'Legacy_Concept_Name',
-                        p366:  'Legacy_Concept_Name',
-                        nichd_hierarchy_term: 'NICHD_Hierarchy_Term',
-                        p371: 'NICHD_Hierarchy_Term',
-                        term_browser_value_set_description: 'Term_Browser_Value_Set_Description',
-                        p376: 'Term_Browser_Value_Set_Description',
-                        gene_encodes_product: 'Gene_Encodes_Product',
-                        p96: 'Gene_Encodes_Product',
-                        swiss_prot: 'Swiss_Prot',
-                        p93: 'Swiss_Prot',
-                        icd-o-3_code: 'ICD-O-3_Code',
-                        p334: 'ICD-O-3_Code',
-                        chemical_formula: 'Chemical_Formula',
-                        p350: 'Chemical_Formula',
-                        infoods:  'INFOODS',
-                        p353:  'INFOODS',
-                        usda_id:  'USDA_ID',
-                        p354:  'USDA_ID',
-                        essential_amino_acid: 'Essential_Amino_Acid',
-                        p356: 'Essential_Amino_Acid',
-                        essential_fatty_acid: 'Essential_Fatty_Acid',
-                        p357: 'Essential_Fatty_Acid',
-                        nutrient: 'Nutrient',
-                        p358: 'Nutrient',
-                        micronutrient:  'Micronutrient',
-                        p359:  'Micronutrient',
-                        macronutrient:  'Macronutrient',
-                        p360:  'Macronutrient',
-                        extensible_list:  'Extensible_List',
-                        p361:  'Extensible_List',
-                        mirbase_id: 'miRBase_ID',
-                        p362: 'miRBase_ID',
-                        hgnc_id:  'HGNC_ID',
-                        p369:  'HGNC_ID',
-                        pid_id: 'PID_ID',
-                        p367: 'PID_ID',
-                        chebi_id: 'CHEBI_ID',
-                        p368: 'CHEBI_ID',
-                        pdq_open_trial_search_id: 'PDQ_Open_Trial_Search_ID',
-                        p329: 'PDQ_Open_Trial_Search_ID',
-                        pdq_closed_trial_search_id: 'PDQ_Closed_Trial_Search_ID',
-                        p330: 'PDQ_Closed_Trial_Search_ID',
-                        ncbi_taxon_id:  'NCBI_Taxon_ID',
-                        p331:  'NCBI_Taxon_ID',
-                        mgi_accession_id: 'MGI_Accession_ID',
-                        p332: 'MGI_Accession_ID',
-                        contributing_source:  'Contributing_Source',
-                        p322:  'Contributing_Source',
-                        pubmedid_primary_reference: 'PubMedID_Primary_Reference',
-                        p171: 'PubMedID_Primary_Reference',
-                        nsc_code: 'NSC_Code',
-                        p175: 'NSC_Code',
-                        entrezgene_id:  'EntrezGene_ID',
-                        p321:  'EntrezGene_ID',
-                        omim_number:  'OMIM_Number',
-                        p100:  'OMIM_Number',
-                        homologous_gene:  'Homologous_Gene',
-                        p101:  'Homologous_Gene',
-                        genbank_accession_number: 'GenBank_Accession_Number',
-                        p102: 'GenBank_Accession_Number',
-                        maps_to:  'Maps_To',
-                        p375:  'Maps_To',
-                        go_annotation:  'GO_Annotation',
-                        p211:  'GO_Annotation'
-                       }
-        propertyNotConsidered:
-                       {
-                       NHC4: 'Split_From',
-                       P167: 'Image_Link',
-                       P200: 'OLD_PARENT',
-                       P201: 'OLD_CHILD',
-                       P203: 'OLD_KIND',
-                       P204: 'OLD_ROLE',
-                       P205: 'OLD_STATE',
-                       P333: 'Use_For',
-                       P351: 'US_Recommended_Intake',
-                       P352: 'Tolerable_Level',
-                       P355: 'Unit',
-                       P364: 'OLD_ASSOCIATION',
-                       P365: 'OLD_SOURCE_ASSOCIATION',
-                       P377: 'def-definition',
-                       P378: 'Definition_Source',
-                       P379: 'Definition_Reviewer_Name',
-                       P380: 'Definition_Review_Date',
-                       P381: 'attribution',
-                       P382: 'term-name',
-                       P383: 'Term_Type',
-                       P384: 'Term_Source',
-                       P385: 'Source_Code',
-                       P386: 'Subsource_Name',
-                       P387: 'go-id',
-                       P388: 'go-term',
-                       P389: 'go-evi',
-                       P390: 'go-source',
-                       P391: 'source-date',
-                       P392: 'Target_Term',
-                       P393: 'Relationship_to_Target',
-                       P394: 'Target_Term_Type',
-                       P395: 'Target_Code',
-                       P396: 'Target_Terminology',
-                       P92: 'Subsource',
-                       P98: 'DesignNote'
-                       }
-        conceptStatuses: {concept_pending_approval: 'Concept_Pending_Approval',
-                          deprecated_concept: 'Deprecated_Concept',
-                          header_concept: 'Header_Concept',
-                          obsolete_concept: 'Obsolete_Concept',
-                          provisional_concept: 'Provisional_Concept',
-                          retired_concept: 'Retired_Concept'
-                          }
-        contributingSources: {
-                            acc: 'ACC',
-                            bridg: 'BRIDG',
-                            carelex: 'CareLex',
-                            cdisc: 'CDISC',
-                            cdisc-gloss: 'CDISC-GLOSS',
-                            crch: 'CRCH',
-                            ctcae: 'CTCAE',
-                            ctep: 'CTEP',
-                            ctrp: 'CTRP',
-                            edqm-hc: 'EDQM-HC',
-                            fda: 'FDA',
-                            gaia: 'GAIA',
-                            hl7: 'HL7',
-                            ich: 'ICH',
-                            inc: 'INC',
-                            meddra: 'MedDRA',
-                            nccn: 'NCCN',
-                            ncpdp: 'NCPDP',
-                            ndc: 'NDC',
-                            nichd: 'NICHD',
-                            pi-rads: 'PI-RADS',
-                            ucum: 'UCUM'
-                         }
-        sourcesToBeRemoved: ['cadsr', 'CADSR', 'CAdsr','caDSR'
-                        ]
-        associations:  {a1: 'Role_Has_Domain',
-                        a10: 'Has_CDRH_Parent',
-                        a11: 'Has_NICHD_Parent',
-                        a12: 'Has_Data_Element',
-                        a13: 'Related_To_Genetic_Biomarker',
-                        a14: 'Neoplasm_Has_Special_Category',
-                        a15: 'Has_CTCAE_5_Parent',
-                        a2: 'Role_Has_Range',
-                        a3: 'Role_Has_Parent',
-                        a4: 'Qualifier_Applies_To',
-                        a5: 'Has_Salt_Form',
-                        a6: 'Has_Free_Acid_Or_Base_Form',
-                        a7: 'Has_Target',
-                        a8: 'Concept_In_Subset',
-                        a9: 'Is_Related_To_Endogenous_Product',
-                        role_has_domain: 'Role_Has_Domain',
-                        has_cdrh_parent: 'Has_CDRH_Parent',
-                        has_nichd_parent: 'Has_NICHD_Parent',
-                        has_data_element: 'Has_Data_Element',
-                        related_to_genetic_biomarker: 'Related_To_Genetic_Biomarker',
-                        neoplasm_has_special_category: 'Neoplasm_Has_Special_Category',
-                        has_ctcae_5_parent: 'Has_CTCAE_5_Parent',
-                        role_has_range: 'Role_Has_Range',
-                        role_has_parent: 'Role_Has_Parent',
-                        qualifier_applies_To: 'Qualifier_Applies_To',
-                        has_salt_form: 'Has_Salt_Form',
-                        has_free_acid_or_base_form: 'Has_Free_Acid_Or_Base_Form',
-                        has_target: 'Has_Target',
-                        concept_in_subset: 'Concept_In_Subset',
-                        is_related_to_endogenous_product: 'Is_Related_To_Endogenous_Product'}
-        roles: {r156: 'Allele_Absent_From_Wild-type_Chromosomal_Location',
-                r153: 'Allele_Has_Abnormality',
-                r159: 'Allele_Has_Activity',
-                r155: 'Allele_In_Chromosomal_Location',
-                r158: 'Allele_Plays_Altered_Role_In_Process',
-                r160: 'Allele_Plays_Role_In_Metabolism_Of_Chemical_Or_Drug',
-                r81: 'Anatomic_Structure_Has_Location',
-                r82: 'Anatomic_Structure_Is_Physical_Part_Of',
-                r30: 'Biological_Process_Has_Associated_Location',
-                r32: 'Biological_Process_Has_Initiator_Chemical_Or_Drug',
-                r28: 'Biological_Process_Has_Initiator_Process',
-                r31: 'Biological_Process_Has_Result_Anatomy',
-                r34: 'Biological_Process_Has_Result_Biological_Process',
-                r29: 'Biological_Process_Has_Result_Chemical_Or_Drug',
-                r35: 'Biological_Process_Is_Part_Of_Process',
-                r150: 'Chemical_Or_Drug_Affects_Abnormal_Cell',
-                r72: 'Chemical_Or_Drug_Affects_Cell_Type_Or_Tissue',
-                r146: 'Chemical_Or_Drug_Affects_Gene_Product',
-                r124: 'Chemical_Or_Drug_Has_Mechanism_Of_Action',
-                r125: 'Chemical_Or_Drug_Has_Physiologic_Effect',
-                r122: 'Chemical_Or_Drug_Is_Metabolized_By_Enzyme',
-                r66: 'Chemical_Or_Drug_Plays_Role_In_Biological_Process',
-                r123: 'Chemotherapy_Regimen_Has_Component',
-                r27: 'Conceptual_Part_Of',
-                r173: 'Cytogenetic_Abnormality_Involves_Chromosome',
-                r139: 'Disease_Excludes_Abnormal_Cell',
-                r141: 'Disease_Excludes_Cytogenetic_Abnormality',
-                r142: 'Disease_Excludes_Finding',
-                r136: 'Disease_Excludes_Metastatic_Anatomic_Site',
-                r140: 'Disease_Excludes_Molecular_Abnormality',
-                r138: 'Disease_Excludes_Normal_Cell_Origin',
-                r137: 'Disease_Excludes_Normal_Tissue_Origin',
-                r135: 'Disease_Excludes_Primary_Anatomic_Site',
-                r105: 'Disease_Has_Abnormal_Cell',
-                r100: 'Disease_Has_Associated_Anatomic_Site',
-                r126: 'Disease_Has_Associated_Disease',
-                r107: 'Disease_Has_Cytogenetic_Abnormality',
-                r108: 'Disease_Has_Finding',
-                r102: 'Disease_Has_Metastatic_Anatomic_Site',
-                r106: 'Disease_Has_Molecular_Abnormality',
-                r104: 'Disease_Has_Normal_Cell_Origin',
-                r103: 'Disease_Has_Normal_Tissue_Origin',
-                r101: 'Disease_Has_Primary_Anatomic_Site',
-                r110: 'Disease_Is_Grade',
-                r88: 'Disease_Is_Stage',
-                r174: 'Disease_Mapped_To_Chromosome',
-                r176: 'Disease_Mapped_To_Gene',
-                r113: 'Disease_May_Have_Abnormal_Cell',
-                r116: 'Disease_May_Have_Associated_Disease',
-                r114: 'Disease_May_Have_Cytogenetic_Abnormality',
-                r115: 'Disease_May_Have_Finding',
-                r89: 'Disease_May_Have_Molecular_Abnormality',
-                r112: 'Disease_May_Have_Normal_Cell_Origin',
-                r111: 'Disease_May_Have_Normal_Tissue_Origin',
-                r23: 'EO_Disease_Has_Associated_Cell_Type',
-                r25: 'EO_Disease_Has_Associated_EO_Anatomy',
-                r26: 'EO_Disease_Has_Property_Or_Attribute',
-                r24: 'EO_Disease_Maps_To_Human_Disease',
-                r38: 'Gene_Associated_With_Disease',
-                r41: 'Gene_Found_In_Organism',
-                r132: 'Gene_Has_Abnormality',
-                r145: 'Gene_Has_Physical_Location',
-                r40: 'Gene_In_Chromosomal_Location',
-                r175: 'Gene_Involved_In_Pathogenesis_Of_Disease',
-                r39: 'Gene_Is_Biomarker_Of',
-                r36: 'Gene_Is_Biomarker_Type',
-                r130: 'Gene_Is_Element_In_Pathway',
-                r178: 'Gene_Mutant_Encodes_Gene_Product_Sequence_Variation',
-                r37: 'Gene_Plays_Role_In_Process',
-                r54: 'Gene_Product_Encoded_By_Gene',
-                r49: 'Gene_Product_Expressed_In_Tissue',
-                r133: 'Gene_Product_Has_Abnormality',
-                r46: 'Gene_Product_Has_Associated_Anatomy',
-                r52: 'Gene_Product_Has_Biochemical_Function',
-                r44: 'Gene_Product_Has_Chemical_Classification',
-                r45: 'Gene_Product_Has_Organism_Source',
-                r50: 'Gene_Product_Has_Structural_Domain_Or_Motif',
-                r47: 'Gene_Product_Is_Biomarker_Of',
-                r42: 'Gene_Product_Is_Biomarker_Type',
-                r131: 'Gene_Product_Is_Element_In_Pathway',
-                r51: 'Gene_Product_Is_Physical_Part_Of',
-                r48: 'Gene_Product_Malfunction_Associated_With_Disease',
-                r53: 'Gene_Product_Plays_Role_In_Biological_Process',
-                r179: 'Gene_Product_Sequence_Variation_Encoded_By_Gene_Mutant',
-                r182: 'Gene_Product_Variant_Of_Gene_Product',
-                r177: 'Molecular_Abnormality_Involves_Gene',
-                r171: 'Procedure_Has_Completely_Excised_Anatomy',
-                r167: 'Procedure_Has_Excised_Anatomy',
-                r165: 'Procedure_Has_Imaged_Anatomy',
-                r169: 'Procedure_Has_Partially_Excised_Anatomy',
-                r163: 'Procedure_Has_Target_Anatomy',
-                r180: 'Procedure_Has_Target_Disease',
-                r170: 'Procedure_May_Have_Completely_Excised_Anatomy',
-                r166: 'Procedure_May_Have_Excised_Anatomy',
-                r168: 'Procedure_May_Have_Partially_Excised_Anatomy',
-                r181: 'Procedure_Uses_Manufactured_Object',
-                r172: 'Regimen_Has_Accepted_Use_For_Disease',
-                allele_absent_from_wild-type_chromosomal_location: 'Allele_Absent_From_Wild-type_Chromosomal_Location',
-                allele_has_abnormality: 'Allele_Has_Abnormality',
-                allele_has_activity: 'Allele_Has_Activity',
-                allele_in_chromosomal_location: 'Allele_In_Chromosomal_Location',
-                allele_plays_altered_role_in_process: 'Allele_Plays_Altered_Role_In_Process',
-                allele_plays_role_in_metabolism_of_chemical_or_drug: 'Allele_Plays_Role_In_Metabolism_Of_Chemical_Or_Drug',
-                anatomic_structure_has_location: 'Anatomic_Structure_Has_Location',
-                anatomic_structure_is_physical_part_of: 'Anatomic_Structure_Is_Physical_Part_Of',
-                biological_process_has_associated_location: 'Biological_Process_Has_Associated_Location',
-                biological_process_has_initiator_chemical_or_drug: 'Biological_Process_Has_Initiator_Chemical_Or_Drug',
-                biological_process_has_initiator_process: 'Biological_Process_Has_Initiator_Process',
-                biological_process_has_result_anatomy: 'Biological_Process_Has_Result_Anatomy',
-                biological_process_has_result_biological_process: 'Biological_Process_Has_Result_Biological_Process',
-                biological_process_has_result_chemical_or_drug: 'Biological_Process_Has_Result_Chemical_Or_Drug',
-                biological_process_is_part_of_process: 'Biological_Process_Is_Part_Of_Process',
-                chemical_or_drug_affects_abnormal_cell: 'Chemical_Or_Drug_Affects_Abnormal_Cell',
-                chemical_or_drug_affects_cell_type_or_tissue: 'Chemical_Or_Drug_Affects_Cell_Type_Or_Tissue',
-                chemical_or_drug_affects_gene_product: 'Chemical_Or_Drug_Affects_Gene_Product',
-                chemical_or_drug_has_mechanism_of_action: 'Chemical_Or_Drug_Has_Mechanism_Of_Action',
-                chemical_or_drug_has_physiologic_effect: 'Chemical_Or_Drug_Has_Physiologic_Effect',
-                chemical_or_drug_is_metabolized_by_enzyme: 'Chemical_Or_Drug_Is_Metabolized_By_Enzyme',
-                chemical_or_drug_plays_role_in_biological_process: 'Chemical_Or_Drug_Plays_Role_In_Biological_Process',
-                chemotherapy_regimen_has_component: 'Chemotherapy_Regimen_Has_Component',
-                conceptual_part_of: 'Conceptual_Part_Of',
-                cytogenetic_abnormality_involves_chromosome: 'Cytogenetic_Abnormality_Involves_Chromosome',
-                disease_excludes_abnormal_cell: 'Disease_Excludes_Abnormal_Cell',
-                disease_excludes_cytogenetic_abnormality: 'Disease_Excludes_Cytogenetic_Abnormality',
-                disease_excludes_finding: 'Disease_Excludes_Finding',
-                disease_excludes_metastatic_anatomic_site: 'Disease_Excludes_Metastatic_Anatomic_Site',
-                disease_excludes_molecular_abnormality: 'Disease_Excludes_Molecular_Abnormality',
-                disease_excludes_normal_cell_origin: 'Disease_Excludes_Normal_Cell_Origin',
-                disease_excludes_normal_tissue_origin: 'Disease_Excludes_Normal_Tissue_Origin',
-                disease_excludes_primary_anatomic_site: 'Disease_Excludes_Primary_Anatomic_Site',
-                disease_has_abnormal_cell: 'Disease_Has_Abnormal_Cell',
-                disease_has_associated_anatomic_site: 'Disease_Has_Associated_Anatomic_Site',
-                disease_has_associated_disease: 'Disease_Has_Associated_Disease',
-                disease_has_cytogenetic_abnormality: 'Disease_Has_Cytogenetic_Abnormality',
-                disease_has_finding: 'Disease_Has_Finding',
-                disease_has_metastatic_anatomic_site: 'Disease_Has_Metastatic_Anatomic_Site',
-                disease_has_molecular_abnormality: 'Disease_Has_Molecular_Abnormality',
-                disease_has_normal_cell_origin: 'Disease_Has_Normal_Cell_Origin',
-                disease_has_normal_tissue_origin: 'Disease_Has_Normal_Tissue_Origin',
-                disease_has_primary_anatomic_site: 'Disease_Has_Primary_Anatomic_Site',
-                disease_is_grade: 'Disease_Is_Grade',
-                disease_is_stage: 'Disease_Is_Stage',
-                disease_mapped_to_chromosome: 'Disease_Mapped_To_Chromosome',
-                disease_mapped_to_gene: 'Disease_Mapped_To_Gene',
-                disease_may_have_abnormal_cell: 'Disease_May_Have_Abnormal_Cell',
-                disease_may_have_associated_disease: 'Disease_May_Have_Associated_Disease',
-                disease_may_have_cytogenetic_abnormality: 'Disease_May_Have_Cytogenetic_Abnormality',
-                disease_may_have_finding: 'Disease_May_Have_Finding',
-                disease_may_have_molecular_abnormality: 'Disease_May_Have_Molecular_Abnormality',
-                disease_may_have_normal_cell_origin: 'Disease_May_Have_Normal_Cell_Origin',
-                disease_may_have_normal_tissue_origin: 'Disease_May_Have_Normal_Tissue_Origin',
-                eo_disease_has_associated_cell_type: 'EO_Disease_Has_Associated_Cell_Type',
-                eo_disease_has_associated_eo_anatomy: 'EO_Disease_Has_Associated_EO_Anatomy',
-                eo_disease_has_property_or_attribute: 'EO_Disease_Has_Property_Or_Attribute',
-                eo_disease_maps_to_human_disease: 'EO_Disease_Maps_To_Human_Disease',
-                gene_associated_with_disease: 'Gene_Associated_With_Disease',
-                gene_found_in_organism: 'Gene_Found_In_Organism',
-                gene_has_abnormality: 'Gene_Has_Abnormality',
-                gene_has_physical_location: 'Gene_Has_Physical_Location',
-                gene_in_chromosomal_location: 'Gene_In_Chromosomal_Location',
-                gene_involved_in_pathogenesis_of_disease: 'Gene_Involved_In_Pathogenesis_Of_Disease',
-                gene_is_biomarker_of: 'Gene_Is_Biomarker_Of',
-                gene_is_biomarker_type: 'Gene_Is_Biomarker_Type',
-                gene_is_element_in_pathway: 'Gene_Is_Element_In_Pathway',
-                gene_mutant_encodes_gene_product_sequence_variation: 'Gene_Mutant_Encodes_Gene_Product_Sequence_Variation',
-                gene_plays_role_in_process: 'Gene_Plays_Role_In_Process',
-                gene_product_encoded_by_gene: 'Gene_Product_Encoded_By_Gene',
-                gene_product_expressed_in_tissue: 'Gene_Product_Expressed_In_Tissue',
-                gene_product_has_abnormality: 'Gene_Product_Has_Abnormality',
-                gene_product_has_associated_anatomy: 'Gene_Product_Has_Associated_Anatomy',
-                gene_product_has_biochemical_function: 'Gene_Product_Has_Biochemical_Function',
-                gene_product_has_chemical_classification: 'Gene_Product_Has_Chemical_Classification',
-                gene_product_has_organism_source: 'Gene_Product_Has_Organism_Source',
-                gene_product_has_structural_domain_or_motif: 'Gene_Product_Has_Structural_Domain_Or_Motif',
-                gene_product_is_biomarker_of: 'Gene_Product_Is_Biomarker_Of',
-                gene_product_is_biomarker_type: 'Gene_Product_Is_Biomarker_Type',
-                gene_product_is_element_in_pathway: 'Gene_Product_Is_Element_In_Pathway',
-                gene_product_is_physical_part_of: 'Gene_Product_Is_Physical_Part_Of',
-                gene_product_malfunction_associated_with_disease: 'Gene_Product_Malfunction_Associated_With_Disease',
-                gene_product_plays_role_in_biological_process: 'Gene_Product_Plays_Role_In_Biological_Process',
-                gene_product_sequence_variation_encoded_by_gene_mutant: 'Gene_Product_Sequence_Variation_Encoded_By_Gene_Mutant',
-                gene_product_variant_of_gene_product: 'Gene_Product_Variant_Of_Gene_Product',
-                molecular_abnormality_involves_gene: 'Molecular_Abnormality_Involves_Gene',
-                procedure_has_completely_excised_anatomy: 'Procedure_Has_Completely_Excised_Anatomy',
-                procedure_has_excised_anatomy: 'Procedure_Has_Excised_Anatomy',
-                procedure_has_imaged_anatomy: 'Procedure_Has_Imaged_Anatomy',
-                procedure_has_partially_excised_anatomy: 'Procedure_Has_Partially_Excised_Anatomy',
-                procedure_has_target_anatomy: 'Procedure_Has_Target_Anatomy',
-                procedure_has_target_disease: 'Procedure_Has_Target_Disease',
-                procedure_may_have_completely_excised_anatomy: 'Procedure_May_Have_Completely_Excised_Anatomy',
-                procedure_may_have_excised_anatomy: 'Procedure_May_Have_Excised_Anatomy',
-                procedure_may_have_partially_excised_anatomy: 'Procedure_May_Have_Partially_Excised_Anatomy',
-                procedure_uses_manufactured_object: 'Procedure_Uses_Manufactured_Object',
-                regimen_has_accepted_use_for_disease: 'Regimen_Has_Accepted_Use_For_Disease'}
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diff --git a/software/evsrestapi-util/runEVSStat.bat b/software/evsrestapi-util/runEVSStat.bat
deleted file mode 100644
index a34199beb..000000000
--- a/software/evsrestapi-util/runEVSStat.bat
+++ /dev/null
@@ -1,10 +0,0 @@
-set OCP=%CLASSPATH%
-set lib1=.
-set lib2=lib
-set CLASSPATH=.
-set CLASSPATH=%CLASSPATH%;%lib1%\*
-set CLASSPATH=%CLASSPATH%;%lib2%\*
-
-java -d64 -Xms512m -Xmx4g -classpath %CLASSPATH% gov.nih.nci.evs.restapi.appl.EVSStatistics     
-
-set CLASSPATH=%OCP%
\ No newline at end of file
diff --git a/software/evsrestapi-util/runNCItWikiStat.bat b/software/evsrestapi-util/runNCItWikiStat.bat
deleted file mode 100644
index 31af59bea..000000000
--- a/software/evsrestapi-util/runNCItWikiStat.bat
+++ /dev/null
@@ -1,10 +0,0 @@
-set OCP=%CLASSPATH%
-set lib1=.
-set lib2=lib
-set CLASSPATH=.
-set CLASSPATH=%CLASSPATH%;%lib1%\*
-set CLASSPATH=%CLASSPATH%;%lib2%\*
-
-java -d64 -Xms512m -Xmx4g -classpath %CLASSPATH% gov.nih.nci.evs.restapi.appl.WiKiHomeStatistics ThesaurusInferred_forTS.owl
-
-set CLASSPATH=%OCP%
\ No newline at end of file
diff --git a/software/evsrestapi-util/runUNIIQA.bat b/software/evsrestapi-util/runUNIIQA.bat
deleted file mode 100644
index a4b1171f8..000000000
--- a/software/evsrestapi-util/runUNIIQA.bat
+++ /dev/null
@@ -1,10 +0,0 @@
-set OCP=%CLASSPATH%
-set lib1=.
-set lib2=lib
-set CLASSPATH=.
-set CLASSPATH=%CLASSPATH%;%lib1%\*
-set CLASSPATH=%CLASSPATH%;%lib2%\*
-
-java -d64 -Xms512m -Xmx4g -classpath %CLASSPATH% gov.nih.nci.evs.restapi.appl.UNIIProcessor https://sparql-evs.nci.nih.gov/sparql http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl UNII_Names_27Mar2020.txt UNII_Records_27Mar2020.txt  
-
-set CLASSPATH=%OCP%
\ No newline at end of file
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/AsciiApiUtils.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/AsciiApiUtils.java
deleted file mode 100644
index 8f0b606f5..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/AsciiApiUtils.java
+++ /dev/null
@@ -1,150 +0,0 @@
-package gov.nih.nci.evs.restapi.appl;
-
-import gov.nih.nci.evs.restapi.util.*;
-
-import java.io.*;
-import java.util.*;
-import java.nio.charset.StandardCharsets;
-
-import gov.nih.nlm.nls.lvg.Api.*;
-import gov.nih.nlm.nls.lvg.Lib.*;
-
-// This class uses ToAsciiApi to convert an input term to ASCII
-public class AsciiApiUtils
-{
-	private ToAsciiApi api = null;
-
-	public AsciiApiUtils() {
-		Hashtable properties = new Hashtable();
-		String currentDirectory = System.getProperty("user.dir");
-		properties.put("LVG_DIR", currentDirectory + "/");
-		api = new ToAsciiApi(properties);
-	}
-
-	public AsciiApiUtils(String currentDirectory) {
-		Hashtable properties = new Hashtable();
-		if (currentDirectory == null) {
-			currentDirectory = System.getProperty("user.dir");
-		}
-		properties.put("LVG_DIR", currentDirectory + "/");
-		api = new ToAsciiApi(properties);
-	}
-
-
-	public Vector readFromFile(String filename) {
-		Vector v = new Vector();
-		try {
-			BufferedReader in = new BufferedReader(
-			   new InputStreamReader(
-				  new FileInputStream(filename)));
-			String str;
-			while ((str = in.readLine()) != null) {
-				v.add(str);
-			}
-            in.close();
-		} catch (Exception ex) {
-            ex.printStackTrace();
-		}
-		return v;
-	}
-
-	public void writeToFile(String outputfile, String content) {
-		try {
-			File file = new File(outputfile);
-			if (!file.exists()) {
-				file.createNewFile();
-			}
-			FileWriter fw = new FileWriter(file.getAbsoluteFile());
-			BufferedWriter bw = new BufferedWriter(fw);
-			bw.write(content);
-			bw.close();
-
-		} catch (IOException e) {
-			e.printStackTrace();
-		}
-	}
-
-	public String toAscii(String inTerm) {
-		// mutate the inTerm
-		String outTerm = api.Mutate(inTerm);
-		return outTerm;
-	}
-
-	public String getFootNote() {
-		return "";
-	}
-
-    //scan non-ascii characters in a file
-	public void scan(String inputfile, String outputfile) {
-		try {
-			File file = new File(outputfile);
-			if (!file.exists()) {
-				file.createNewFile();
-			}
-			FileWriter fw = new FileWriter(file.getAbsoluteFile());
-			BufferedWriter bw = new BufferedWriter(fw);
-
-			Vector lines = readFromFile(inputfile);
-			for (int i=0; i");
-			System.exit(1);
-		}
-		AsciiApiUtils utils = new AsciiApiUtils();
-		String inputfile = args[0];
-		//Vector v = readFile(inputfile);
-		int n = inputfile.lastIndexOf(".");
-		String outputfile = inputfile.substring(0, n) + "_" + StringUtils.getToday() + inputfile.substring(n, inputfile.length());
-		String warning_file = "warning_" + outputfile;
-        new AsciiApiUtils().scan(inputfile, warning_file);
-		new AsciiApiUtils().run(inputfile, outputfile);
-	}
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/CASProcessor.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/CASProcessor.java
deleted file mode 100644
index ac41f36fd..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/CASProcessor.java
+++ /dev/null
@@ -1,417 +0,0 @@
-package gov.nih.nci.evs.restapi.appl;
-
-import gov.nih.nci.evs.restapi.util.*;
-import gov.nih.nci.evs.restapi.bean.*;
-import gov.nih.nci.evs.restapi.common.*;
-
-import java.io.*;
-//import java.math.*;
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.*;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
-import java.util.*;
-import java.util.regex.*;
-import org.apache.commons.codec.binary.Base64;
-import org.json.*;
-
-/**
- * 
- * Copyright 2020 MSC. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or MSC
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      MSC, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@nih.gov
- *
- */
-
-
-public class CASProcessor {
-    String named_graph = null;
-    String serviceUrl = null;
-
-    private OWLSPARQLUtils owlSPARQLUtils = null;
-    private Vector unii_link = null;
-	private Vector unii_data = null;
-	private String username = null;
-	private String password = null;
-	private String namedGraph = null;
-	private static String ncit_unii_txt_file = "ncit_unii.txt";
-    private HashMap code2LabelMap = null;
-    private HashMap code2CasRegistryMap = null;
-    private HashMap code2UNIIMap = null;
-    private String unii_file = "FDA_UNII_Code.txt";
-    private String case_registry_file = "CAS_Registry.txt";
-    private HashMap ncit_code2CasRegistryMap = null;
-    private HashMap ncit_code2UNIIMap = null;
-
-	public CASProcessor() {
-
-	}
-
-
-	public CASProcessor(String serviceUrl, String namedGraph) {
-		this.serviceUrl = serviceUrl;
-		this.namedGraph = namedGraph;
-		System.out.println("serviceUrl: " + this.serviceUrl);
-		System.out.println("namedGraph: " + this.namedGraph);
-		owlSPARQLUtils = new OWLSPARQLUtils(serviceUrl, null, null);
-		owlSPARQLUtils.set_named_graph(this.namedGraph);
-		new MetadataUtils(serviceUrl).dumpNameVersion2NamedGraphMap();
-
-    }
-
-    private void initialize() {
-		code2LabelMap = new HashMap();
-        code2CasRegistryMap = new HashMap();
-        code2UNIIMap = new HashMap();
-        // single valued
-        Vector v = null;
-        if (!new File(unii_file).exists()) {
-			System.out.println(unii_file + " does not exist.");
-			Vector w = owlSPARQLUtils.findConceptsWithProperty(this.namedGraph, "FDA_UNII_Code");
-			Utils.saveToFile(unii_file, w);
-		}
-		v = Utils.readFile(unii_file);
-        System.out.println("Number of records in " + unii_file + ": " + v.size());
-
-        code2LabelMap = gov.nih.nci.evs.restapi.util.StringUtils.constructHashMap(v, 1, 0, '|');
-        ncit_code2UNIIMap = gov.nih.nci.evs.restapi.util.StringUtils.constructHashMap(v, 1, 3, '|');
-
-        // multiple valued
-
-        if (!new File(case_registry_file).exists()) {
-			System.out.println(case_registry_file + " does not exist.");
-			Vector w = owlSPARQLUtils.findConceptsWithProperty(this.namedGraph, "CAS_Registry");
-			Utils.saveToFile(case_registry_file, w);
-		}
-        v = Utils.readFile(case_registry_file);
-        HashMap hmap = gov.nih.nci.evs.restapi.util.StringUtils.constructHashMap(v, 1, 0, '|');
-        Iterator it = hmap.keySet().iterator();
-        while (it.hasNext()) {
-			String key = (String) it.next();
-			if (!code2LabelMap.containsKey(key)) {
-				String value = (String) hmap.get(key);
-				code2LabelMap.put(key, value);
-			}
-		}
-
-
-		//String test_label = (String) code2LabelMap.get(test_code);
-		//System.out.println("**********" + test_code + " -> " + test_label);
-
-
-		//Utils.dumpHashMap("code2LabelMap", code2LabelMap);
-
-        System.out.println("Number of records in " + case_registry_file + ": " + v.size());
-        ncit_code2CasRegistryMap = gov.nih.nci.evs.restapi.util.StringUtils.constructMultiValuedHashMap(v, 1, 3, '|');
-
-		System.out.println(unii_file + ": " + ncit_code2UNIIMap.keySet().size());
-		System.out.println(case_registry_file + ": " + ncit_code2CasRegistryMap.keySet().size());
-
-
-	}
-
-
-
-    public void run() {
-		String property_name = "CAS_Registry";
-		String property_value = null;
-		Vector v = owlSPARQLUtils.findConceptsWithPropertyMatching(this.namedGraph, property_name, property_value);
-		v = new SortUtils().quickSort(v);
-		Utils.saveToFile(property_name + ".txt", v);
-
-		property_name = "FDA_UNII_Code";
-		property_value = null;
-		v = owlSPARQLUtils.findConceptsWithPropertyMatching(this.namedGraph, property_name, property_value);
-		v = new SortUtils().quickSort(v);
-		Utils.saveToFile(property_name + ".txt", v);
-	}
-
-
-/*
-        (1) NCIt Subset Code
-        (2) NCIt Subset Name
-        (3) NCIt Code
-        (4) NCIt PT
-        (5) NCIt Synonyms
-        (6) Definition
-        (7) CAS Registry
-        (8) FDA UNII Code
-*/
-
-
-	public static int countDelimiters(String line, char delim) {
-		int knt = 0;
-		for (int i=0; i 0 && w == null) {
-				if (values != null && values.length() > 0) {
-					for (int k=0; k
- * Copyright 2020 MSC. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or MSC
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      MSC, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@nih.gov
- *
- */
-
-
-public class CTRPProcessor {
-	static String CTRP_TERMINOLOGY_CODE = "C116977";
-	static String CTRP_TERMINOLOGY_LABEL = "CTRP terminology";
-
-    JSONUtils jsonUtils = null;
-    HTTPUtils httpUtils = null;
-    String named_graph = null;
-    String prefixes = null;
-    String sparql_endpoint = null;
-    String serviceUrl = null;
-    String named_graph_id = ":NHC0";
-    String base_uri = "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl";
-
-    OWLSPARQLUtils owlSPARQLUtils = null;
-
-	private static String NCI_THESAURUS = "NCI_Thesaurus";
-	private String namedGraph = null;
-
-	public Vector concepts_in_subset = null;
-
-	private TermSearchUtils termSearchUtils = null;
-	private HashSet ncit_code_hset = null;
-
-	private List synonyms = null;
-    private HashMap code2SynonymMap = null;
-    private HashMap ncitcode2labelMap = null;
-
-    private UNIIDataRetriever uniiDataRetriever = null;
-
-	public CTRPProcessor(String serviceUrl, String namedGraph) {
-		this.serviceUrl = serviceUrl;
-		this.namedGraph = namedGraph;
-		System.out.println("serviceUrl: " + this.serviceUrl);
-		System.out.println("namedGraph: " + this.namedGraph);
-
-		owlSPARQLUtils = new OWLSPARQLUtils(serviceUrl, null, null);
-		new MetadataUtils(serviceUrl).dumpNameVersion2NamedGraphMap();
-		uniiDataRetriever = new UNIIDataRetriever(this.serviceUrl, this.namedGraph);
-/*
-		if (!fileExists(FDA_UNII_Subset_Code + ".txt")) {
-			System.out.println("Retrieving supporting data from triple store server ...");
-			uniiDataRetriever = new UNIIDataRetriever(this.serviceUrl, this.namedGraph);
-			uniiDataRetriever.retrieveUNIISupportingData();
-			System.out.println("Completed retrieving supporting data.");
-		}
-
-		System.out.println("Initialized TermSearchUtils ...");
-*/
-		//termSearchUtils = new TermSearchUtils(serviceUrl, this.namedGraph);
-		synonyms = loadSynonyms();
-		System.out.println("createCode2SynonymMap ...");
-		code2SynonymMap = createCode2SynonymMap(synonyms);
-		System.out.println("createCode2SynonymMap done. " + code2SynonymMap.keySet().size());
-	}
-
-	public void dumpSynonymData() {
-		for (int i=0; i parseData(String line) {
-		if (line == null) return null;
-        char tab = '|';
-        return parseData(line, tab);
-    }
-
-	public void saveSynonyms() {
-		saveSynonyms(synonyms);
-	}
-
-
-	public void saveSynonyms(List synonyms) {
-	    Vector w = new Vector();
-	    for (int i=0; i
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class ConceptDetailsBatchRunner {
-    JSONUtils jsonUtils = null;
-    HTTPUtils httpUtils = null;
-
-    String prefixes = null;
-    //String sparql_endpoint = null;
-    String serviceUrl = null;
-    String named_graph = null;
-    String username = null;
-    String password = null;
-
-    String named_graph_id = ":NHC0";
-    String base_uri = "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl";
-    TreeBuilder treeBuilder = null;//new TreeBuilder(this);
-    ParserUtils parser = new ParserUtils();
-
-    gov.nih.nci.evs.restapi.util.OWLSPARQLUtils owlSPARQLUtils = null;
-    MainTypeHierarchy mth = null;
-    ExportUtils exportUtils = null;
-    String ncit_version = "17.07c";
-	HashSet main_type_set = null;
-	Vector category_vec = null;
-
-	HashSet ctrp_biomarker_set = null;
-	HashSet ctrp_reference_gene_set = null;
-
-
-	private Vector parent_child_vec = null;
-	private static String stage_file = "DISEASE_IS_STAGE.txt";
-	private static String grade_file = "DISEASE_IS_GRADE.txt";
-	private static String NCI_THESAURUS = "NCI_Thesaurus";
-
-	Vector disease_is_stage_vec = null;
-	Vector disease_is_grade_vec = null;
-
-	public ConceptDetailsBatchRunner(String serviceUrl, String named_graph, String username, String password) {
-        this.serviceUrl = serviceUrl;//"https://sparql-evs-dev.nci.nih.gov/ctrp/?query=";
-        this.named_graph = named_graph;
-        this.username = username;
-        this.password = password;
-        initialize();
-	}
-
-	public MainTypeHierarchy createMainTypeHierarchy() {
-        long ms = System.currentTimeMillis();
-        long ms0 = System.currentTimeMillis();
-		System.out.println("Instantiating MainTypeHierarchy. Please wait...");
-		MetadataUtils mdu = new MetadataUtils(serviceUrl, username, password);
-		//String named_graph = mdu.getNamedGraph(NCI_THESAURUS);
-		String ncit_version = mdu.getLatestVersion(NCI_THESAURUS);
-		gov.nih.nci.evs.restapi.util.OWLSPARQLUtils owlSPARQLUtils = new gov.nih.nci.evs.restapi.util.OWLSPARQLUtils(serviceUrl, username, password);
-		owlSPARQLUtils.set_named_graph(named_graph);
-
-		String parent_child_file = "parent_child.txt";
-		if (parent_child_vec == null) {
-			File file = new File(parent_child_file);
-			boolean exists = file.exists();
-			if (exists) {
-				System.out.println("Loading parent_child_vec...");
-				parent_child_vec = Utils.readFile("parent_child.txt");
-			} else {
-				System.out.println("Generating parent_child_vec...");
-				parent_child_vec = owlSPARQLUtils.getHierarchicalRelationships(named_graph);
-			}
-		}
-		File f = new File(stage_file);
-		if(f.exists() && !f.isDirectory()) {
-			disease_is_stage_vec = Utils.readFile(stage_file);
-			System.out.println(stage_file + " exists.");
-		}  else {
-			String association_name = "Disease_Is_Stage";
-			disease_is_stage_vec = owlSPARQLUtils.getAssociationSourceCodes(named_graph, association_name);
-			Utils.saveToFile(stage_file, disease_is_stage_vec);
-		}
-		HashMap stageConceptHashMap = new ParserUtils().getCode2LabelHashMap(disease_is_stage_vec);
-		System.out.println("Number of stage terms: " + stageConceptHashMap.keySet().size());
-
-		f = new File(grade_file);
-		if(f.exists() && !f.isDirectory()) {
-			disease_is_grade_vec = Utils.readFile(grade_file);
-			System.out.println(grade_file + " exists.");
-		}  else {
-			String association_name = "Disease_Is_Grade";
-			disease_is_grade_vec = owlSPARQLUtils.getAssociationSourceCodes(named_graph, association_name);
-			Utils.saveToFile(grade_file, disease_is_grade_vec);
-		}
-		HashMap gradeConceptHashMap = new ParserUtils().getCode2LabelHashMap(disease_is_grade_vec);
-		System.out.println("Number of grade terms: " + gradeConceptHashMap.keySet().size());
-
- 		MainTypeHierarchyData mthd = new MainTypeHierarchyData(serviceUrl, named_graph, username, password);
-
-		main_type_set = mthd.get_main_type_set();
-		ctrp_biomarker_set = mthd.get_ctrp_biomarker_set();
-		ctrp_reference_gene_set = mthd.get_ctrp_reference_gene_set();
-        category_vec = mthd.get_broad_category_vec();
-
-		System.out.println("main_type_set: " + main_type_set.size());
-		System.out.println("category_vec: " + category_vec.size());
-		System.out.println("ctrp_biomarker_set: " + ctrp_biomarker_set.size());
-		System.out.println("ctrp_reference_gene_set: " + ctrp_reference_gene_set.size());
-		System.out.println("Instantiating MainTypeHierarchy " + parent_child_vec.size());
-
-		MainTypeHierarchy mth = new MainTypeHierarchy(
-            ncit_version,
-            parent_child_vec,
-            main_type_set,
-            category_vec,
-            stageConceptHashMap,
-            gradeConceptHashMap,
-            ctrp_biomarker_set,
-            ctrp_reference_gene_set
-            );
-
-        System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms0));
-        return mth;
-	}
-
-    public void initialize() {
-		long ms = System.currentTimeMillis();
-        this.mth = createMainTypeHierarchy();
-		this.httpUtils = new HTTPUtils(serviceUrl, username, password);
-        this.jsonUtils = new JSONUtils();
-		MetadataUtils mdu = new MetadataUtils(serviceUrl, username, password);
-		this.named_graph = mdu.getNamedGraph(NCI_THESAURUS);
-		this.ncit_version = mdu.getLatestVersion(NCI_THESAURUS);
-		this.owlSPARQLUtils = new gov.nih.nci.evs.restapi.util.OWLSPARQLUtils(serviceUrl, username, password);
-		this.owlSPARQLUtils.set_named_graph(named_graph);
-        this.treeBuilder = new TreeBuilder(this.owlSPARQLUtils);
-        this.exportUtils = new ExportUtils(this.owlSPARQLUtils);
-        System.out.println("Total initialization run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-
-    public HashSet combineMainTypesAndCategories() {
-		HashSet hset = main_type_set;
-        for (int i=0; i
- * Copyright 2020 MSC. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or MSC
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      MSC, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@nih.gov
- *
- */
-
-
-public class EVSStatistics {
-	String serviceUrl = null;
-	String named_graph = null;
-	String username = null;
-	String password = null;
-	MetadataUtils metadataUtils = null;
-	OWLSPARQLUtils owlSPARQLUtils = null;
-	int table_number = 0;
-
-	HTTPUtils httpUtils = null;
-	String prefixes = null;
-	static String PUBLISH_VALUE_SET = "Publish_Value_Set";
-
-	static String[] ANNOTATED_TARGETS = null;
-	static String[] ANNOTATED_TARGET_CODES = null;
-	static List ANNOTATED_TARGET_LIST = null;
-	static HashMap ANNOTATED_TARGET_HASHMAP = null;
-
-	Vector properties = null;
-	HashMap propertyCode2NameHashMap = new HashMap();
-	HashMap propertyName2CodeHashMap = new HashMap();
-
-	HashMap roleCode2NameHashMap = new HashMap();
-	HashMap roleName2CodeHashMap = new HashMap();
-
-	Vector table_data = null;
-	String version = null;
-
-	String named_graph_id = ":NHC0";
-	Vector roots = null;
-
-	HierarchyHelper hh = null;
-    static String NCIT_OWL = "ThesaurusInferred_forTS.owl";
-	static String PARENT_CHILD_FILE = "parent_child.txt";
-	static String RESTRICTION_FILE = "roles.txt";
-
-	HashSet retired_concepts = new HashSet();
-	HashMap valueset2ContributingSourceMap = new HashMap();
-	HashMap valuesetCode2NameMap = new HashMap();
-	HashMap valuesetName2CodeMap = new HashMap();
-
-	static HashMap propertyCode2CountMap = null;
-
-    static {
-		ANNOTATED_TARGETS = new String[] {"term-name", "go-term", "TARGET TERM"};
-		ANNOTATED_TARGET_CODES = new String[] {"P382", "P388", "P392"};
-		ANNOTATED_TARGET_LIST = Arrays.asList(ANNOTATED_TARGET_CODES);
-		ANNOTATED_TARGET_HASHMAP = new HashMap();
-		ANNOTATED_TARGET_HASHMAP.put("P382", "P90");
-		ANNOTATED_TARGET_HASHMAP.put("P388", "P211");
-		ANNOTATED_TARGET_HASHMAP.put("P392", "P375");
-
-		OWLScanner scanner = new OWLScanner(NCIT_OWL);
-		propertyCode2CountMap = scanner.getPropertyCode2CountMap();
-		Vector roles = scanner.extractOWLRestrictions(scanner.get_owl_vec());
-		Utils.saveToFile(RESTRICTION_FILE, roles);
-		scanner.get_owl_vec().clear();
-	}
-
-	public String get_ncit_version() {
-		Vector v = owlSPARQLUtils.get_ontology_info(named_graph);
-		Utils.dumpVector("get_ncit_version", v);
-		String line = (String) v.elementAt(0);
-		Vector u = StringUtils.parseData(line, '|');
-		String ncit_version = (String) u.elementAt(0);
-		System.out.println(ncit_version);
-		return ncit_version;
-	}
-
-	public EVSStatistics(String serviceUrl, String named_graph, String username, String password) {
-		this.serviceUrl = serviceUrl;
-		this.named_graph = named_graph;
-		this.username = username;
-		this.password = password;
-		this.table_number = 0;
-
-		this.metadataUtils = new MetadataUtils(serviceUrl, username, password);
-
-		this.owlSPARQLUtils = new OWLSPARQLUtils(serviceUrl, username, password);
-		this.owlSPARQLUtils.set_named_graph(named_graph);
-		this.version  = get_ncit_version();//metadataUtils.getVocabularyVersion(named_graph);
-        System.out.println("NCI Thesaurus version: " + version);
-        try {
-			httpUtils = new HTTPUtils();
-		} catch (Exception ex) {
-			ex.printStackTrace();
-		}
-		System.out.println("httpUtils instantiated.");
-		System.out.println("getSupportedProperties ...");
-		properties = getSupportedProperties(named_graph);
-
-		System.out.println("properties: " + properties.size());
-		Utils.saveToFile("properties.txt", properties);
-
-		propertyCode2NameHashMap = new HashMap();
-		propertyName2CodeHashMap = new HashMap();
-        for (int i=0; i" + title);
-	}
-
-	public boolean is_retired(String code) {
-		return retired_concepts.contains(code);
-	}
-
-	public void addTable(String tableName, Vector th_vec, Vector data) {
-		table_data.add("" + tableName);
-		for (int i=0; i" + th);
-		}
-		table_data.add("");
-		table_data.addAll(data);
-		table_data.add("");
-        table_data.add("
");
-	}
-
-    public void addFooter() {
-		table_data.add("
(Source; NCI Thesaurus, version " + this.version + ")");
-	}
-
-    public boolean is_ANNOTATED_TARGET_CODES(String propertyCode) {
-		return ANNOTATED_TARGET_LIST.contains(propertyCode);
-	}
-
-	public static void dumpVector(String label, Vector v) {
-		System.out.println(label);
-		for (int i=0; i").append("\n");
-		buf.append("PREFIX base:").append("\n");
-		buf.append("PREFIX Thesaurus:").append("\n");
-		buf.append("PREFIX xml:").append("\n");
-		buf.append("PREFIX rdf:").append("\n");
-		buf.append("PREFIX owl:").append("\n");
-		buf.append("PREFIX owl2xml:").append("\n");
-		buf.append("PREFIX protege:").append("\n");
-		buf.append("PREFIX xsd:").append("\n");
-		buf.append("PREFIX rdfs:").append("\n");
-		buf.append("PREFIX ncicp:").append("\n");
-		buf.append("PREFIX dc:").append("\n");
-		return buf.toString();
-	}
-
-	public String loadQuery(String queryfile) {
-		return httpUtils.loadQuery(queryfile, false);
-	}
-
-    public Vector executeQuery(String query) {
-		//boolean parsevalues = true;
-		//Vector w = httpUtils.execute(serviceUrl, username, password, query, parsevalues);
-
-		//Vector w = HTTPUtils.runQuery(serviceUrl, username, password, query);
-		Vector w = owlSPARQLUtils.executeQuery(query);
-
-		return w;
-	}
-
-    public void run(String queryfile) {
-		String query = HTTPUtils.loadQuery(queryfile);
-		//boolean parsevalues = true;
-		//Vector w = httpUtils.execute(serviceUrl, username, password, query, parsevalues);
-		Vector w = HTTPUtils.runQuery(serviceUrl,  username, password, query);
-		if (w != null && w.size() > 0) {
-			int n = queryfile.lastIndexOf("_query");
-			if(n ==  -1) {
-				System.out.println("ERROR: Wrong query file naming.");
-				System.exit(1);
-			}
-			String t = queryfile.substring(0, n);
-			String methodSignature = "construct_get_" + t + "(String named_graph)";
-			SPARQLQueryGenerator.generateCode(queryfile, methodSignature);
-			Utils.dumpVector("w", w);
-		} else {
-			System.out.println("ERROR: Query failed.");
-            int n = queryfile.lastIndexOf("_query");
-			String t = queryfile.substring(0, n);
-			String methodSignature = "construct_get_" + t + "(String named_graph)";
-			SPARQLQueryGenerator.generateCode(queryfile, methodSignature);
-		}
-	}
-
-    public String construct_root_query(String named_graph) {
-        String prefixes = getPrefixes();
-        StringBuffer buf = new StringBuffer();
-        buf.append(prefixes);
-        buf.append("select ?s_label ?s_code").append("\n");
-        buf.append("from <" + named_graph + ">").append("\n");
-        buf.append("where  { ").append("\n");
-        buf.append("?s a owl:Class .").append("\n");
-        buf.append("?s rdfs:label ?s_label .").append("\n");
-        buf.append("?s :NHC0 ?s_code . ").append("\n");
-        buf.append("filter not exists { ?s rdfs:subClassOf|owl:equivalentClass ?o } ").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-    }
-
-	public Vector getRoots(String named_graph, boolean code_only) {
-		Vector w = new Vector();
-        String query = construct_root_query(named_graph);
-        Vector v = executeQuery(query);
-        if (!code_only) return v;
-        for (int i=0; i {").append("\n");
-		buf.append("            ?p a owl:ObjectProperty.").append("\n");
-		buf.append("            ?p :NHC0 ?p_code .").append("\n");
-		buf.append("            ?p rdfs:label ?p_label ").append("\n");
-		buf.append("    }").append("\n");
-		buf.append("}").append("\n");
-		return buf.toString();
-	}
-
-	public Vector getObjectProperties(String named_graph) {
-		return executeQuery(construct_get_object_properties(named_graph));
-	}
-
-	public String construct_get_object_properties_domain_range(String named_graph) {
-		String prefixes = getPrefixes();
-		StringBuffer buf = new StringBuffer();
-		buf.append(prefixes);
-		buf.append("SELECT distinct ?x_pt ?x_code ?x_domain_label ?x_range_label ").append("\n");
-		buf.append("{ ").append("\n");
-		buf.append("    graph <" + named_graph + ">").append("\n");
-		buf.append("    {").append("\n");
-		buf.append("	    {").append("\n");
-		buf.append("		?x a owl:ObjectProperty .").append("\n");
-		buf.append("		?x :NHC0 ?x_code .").append("\n");
-		buf.append("		?x rdfs:domain ?x_domain .").append("\n");
-		buf.append("		?x_domain rdfs:label ?x_domain_label .").append("\n");
-		buf.append("		?x rdfs:range ?x_range .").append("\n");
-		buf.append("		?x_range rdfs:label ?x_range_label .").append("\n");
-		buf.append("        ?x :P108 ?x_pt .").append("\n");
-		buf.append("	    }").append("\n");
-		buf.append("	    ").append("\n");
-		buf.append("    }").append("\n");
-		buf.append("}").append("\n");
-		return buf.toString();
-	}
-
-
-	public String construct_get_object_valued_annotation_properties(String named_graph) {
-		String prefixes = getPrefixes();
-		StringBuffer buf = new StringBuffer();
-		buf.append(prefixes);
-		buf.append("SELECT distinct ?x_label ?x_code ").append("\n");
-		buf.append("{ ").append("\n");
-		buf.append("    graph <" + named_graph + ">").append("\n");
-		buf.append("    {").append("\n");
-		buf.append("        ?x a owl:AnnotationProperty .").append("\n");
-		buf.append("        ?x :NHC0 ?x_code .").append("\n");
-		buf.append("        ?x rdfs:label ?x_label .").append("\n");
-		buf.append("        ?x rdfs:range ?x_range").append("\n");
-		buf.append("    }").append("\n");
-		buf.append("    FILTER (str(?x_range)=\"http://www.w3.org/2001/XMLSchema#anyURI\")").append("\n");
-		buf.append("}").append("\n");
-		return buf.toString();
-	}
-
-	public Vector getObjectValuedProperty(String named_graph) {
-        String query = construct_get_object_valued_annotation_properties(named_graph);
-        return executeQuery(query);
-	}
-
-	public String construct_get_supported_properties(String named_graph, String code, String propertyName, String propertyValue, boolean concept_only) {
-        String prefixes = getPrefixes();
-        StringBuffer buf = new StringBuffer();
-        buf.append(prefixes);
-        if (concept_only) {
-			buf.append("select distinct ?x_label ?x_code").append("\n");
-		} else {
-        	buf.append("select distinct ?x_label ?x_code ?p_label ?p_value").append("\n");
-		}
-        buf.append("from <" + named_graph + ">").append("\n");
-        buf.append("where  { ").append("\n");
-        buf.append("").append("\n");
-        buf.append("                ?x a owl:Class .").append("\n");
-        buf.append("                ?x :NHC0 ?x_code .").append("\n");
-        if (code != null) {
-        	buf.append("                ?x :NHC0 \"" + code + "\"^^xsd:string .").append("\n");
-		}
-        buf.append("                ?x rdfs:label ?x_label .").append("\n");
-        buf.append("").append("\n");
-        buf.append("                ?x ?p ?p_value .").append("\n");
-        if (propertyValue != null) {
-        	buf.append("                ?x ?p \"" + propertyValue + "\"^^xsd:string .").append("\n");
-	    }
-
-        buf.append("                ?p rdfs:label ?p_label .").append("\n");
-        buf.append("                ?p :NHC0 ?p_code .").append("\n");
-        buf.append("                ?p rdfs:label \"" + propertyName + "\"^^xsd:string .").append("\n");
-        buf.append("").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-	public Vector getSupportedProperties(String named_graph, String code, String propertyName, String propertyValue, boolean concept_only) {
-        String query = construct_get_supported_properties(named_graph, code, propertyName, propertyValue, concept_only);
-        return executeQuery(query);
-	}
-
-	public String construct_get_property_qualifier(String named_graph, String code, String propertyCode,
-	                                               String qualifierCode, String qualifierValue, boolean concept_only) {
-        String prefixes = getPrefixes();
-        StringBuffer buf = new StringBuffer();
-        buf.append(prefixes);
-
-        if (concept_only) {
-			buf.append("select distinct ?x_label ?x_code").append("\n");
-	    } else {
-        	buf.append("select ?x_label ?x_code ?p_label ?a_target ?q1_label ?q1_value").append("\n");
-		}
-
-        buf.append("from <" + named_graph + ">").append("\n");
-        buf.append("where { ").append("\n");
-        buf.append("                ?x a owl:Class .").append("\n");
-        buf.append("                ?x :NHC0 ?x_code .").append("\n");
-        if (code != null) {
-        	buf.append("                ?x :NHC0 \"" + code + "\"^^xsd:string .").append("\n");
-		}
-        buf.append("                ?x rdfs:label ?x_label .").append("\n");
-        buf.append("").append("\n");
-        buf.append("                ?a a owl:Axiom .").append("\n");
-        buf.append("                ?a owl:annotatedSource ?x .").append("\n");
-        buf.append("                ?a owl:annotatedProperty ?p .").append("\n");
-        buf.append("                ?a owl:annotatedTarget ?a_target .").append("\n");
-        buf.append("                ?p :NHC0 ?p_code .").append("\n");
-        buf.append("                ?p :NHC0 \"" + propertyCode + "\"^^xsd:string .").append("\n");
-        buf.append("                ?p rdfs:label ?p_label .").append("\n");
-        buf.append("").append("\n");
-        buf.append("                ?a ?q1 ?q1_value .").append("\n");
-        buf.append("                ?a ?q1 \"" + qualifierValue + "\"^^xsd:string .").append("\n");
-        buf.append("                ?q1 :NHC0 ?q1_code .").append("\n");
-        buf.append("                ?q1 :NHC0 \"" + qualifierCode + "\"^^xsd:string .").append("\n");
-        buf.append("                ?q1 rdfs:label ?q1_label .").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-
-	public Vector getPropertyQualifier(String named_graph, String code, String propertyCode,
-	    String qualifierCode, String qualifierValue, boolean concept_only) {
-        String query = construct_get_property_qualifier(named_graph, code, propertyCode, qualifierCode, qualifierValue, concept_only);
-        return executeQuery(query);
-	}
-
-	public String construct_get_associations(String named_graph) {
-		return construct_get_associations(named_graph, null);
-	}
-
-	public String construct_get_associations(String named_graph, String code) {
-		String prefixes = getPrefixes();
-		StringBuffer buf = new StringBuffer();
-		buf.append(prefixes);
-		buf.append("SELECT distinct ?x_label ?x_code ?y_label ?y_code ?z_label ?z_code").append("\n");
-		buf.append("{").append("\n");
-		buf.append("    graph <" + named_graph + ">").append("\n");
-		buf.append("    {").append("\n");
-		buf.append("	    ?x a owl:Class .").append("\n");
-		buf.append("	    ?x :NHC0 ?x_code .").append("\n");
-        if (code != null) {
-        	buf.append("                ?x :NHC0 \"" + code + "\"^^xsd:string .").append("\n");
-		}
-		buf.append("	    ?x rdfs:label ?x_label .").append("\n");
-		buf.append("	    ?y a owl:AnnotationProperty .").append("\n");
-		buf.append("	    ?x ?y ?z .").append("\n");
-		buf.append("	    ?z a owl:Class .").append("\n");
-		buf.append("	    ?z rdfs:label ?z_label .").append("\n");
-		buf.append("	    ?z :NHC0 ?z_code .").append("\n");
-		buf.append("	    ?y rdfs:label ?y_label .").append("\n");
-		buf.append("	    ?y :NHC0 ?y_code .").append("\n");
-		buf.append("	    ?y rdfs:range ?y_range").append("\n");
-		buf.append("    }").append("\n");
-		buf.append("    FILTER (str(?y_range)=\"http://www.w3.org/2001/XMLSchema#anyURI\")").append("\n");
-		buf.append("}").append("\n");
-		return buf.toString();
-	}
-
-	public Vector getAssociations(String named_graph) {
-        String query = construct_get_associations(named_graph);
-        return executeQuery(query);
-	}
-
-	public Vector getAssociations(String named_graph, String code) {
-        String query = construct_get_associations(named_graph, code);
-        return executeQuery(query);
-	}
-
-
-	public String construct_get_role_targets(String named_graph, String code, String roleName) {
-		String prefixes = getPrefixes();
-		StringBuffer buf = new StringBuffer();
-		buf.append(prefixes);
-		buf.append("").append("\n");
-		buf.append("SELECT distinct ?x_label ?x_code ?p_label ?p_code ?c_label ?c_code").append("\n");
-		buf.append("{").append("\n");
-		buf.append("    graph <" + named_graph + "> {").append("\n");
-		buf.append("            {").append("\n");
-		buf.append("            ?x a owl:Class .").append("\n");
-		buf.append("            ?x :NHC0 ?x_code .").append("\n");
-		if (code != null) {
-			buf.append("                ?x :NHC0 \"" + code + "\"^^xsd:string .").append("\n");
-		}
-		buf.append("            ?x rdfs:label ?x_label .").append("\n");
-		buf.append("").append("\n");
-		buf.append("            ?x owl:equivalentClass ?y .").append("\n");
-		buf.append("            ?y (rdfs:subClassOf|(owl:intersectionOf/rdf:rest*/rdf:first))* ?r1 .").append("\n");
-		buf.append("            ?r1 owl:onProperty ?p .").append("\n");
-		buf.append("").append("\n");
-		buf.append("            ?p :NHC0 ?p_code .").append("\n");
-		buf.append("            ?p rdfs:label ?p_label .").append("\n");
-		if (roleName != null) {
-			buf.append("            ?p rdfs:label \"" + roleName + "\"^^xsd:string .").append("\n");
-		}
-		buf.append("").append("\n");
-		buf.append("            ?r1 owl:someValuesFrom ?c .").append("\n");
-		buf.append("            ?c :NHC0 ?c_code .").append("\n");
-
-		buf.append("            ?c rdfs:label ?c_label .").append("\n");
-		buf.append("            }").append("\n");
-		buf.append("            UNION").append("\n");
-		buf.append("            {").append("\n");
-		buf.append("            ?x a owl:Class .").append("\n");
-		buf.append("            ?x :NHC0 ?x_code .").append("\n");
-
-		if (code != null) {
-			buf.append("                ?x :NHC0 \"" + code + "\"^^xsd:string .").append("\n");
-		}
-
-		buf.append("            ?x rdfs:label ?x_label .").append("\n");
-		buf.append("").append("\n");
-		buf.append("            ?x owl:equivalentClass ?y .").append("\n");
-		buf.append("            ?y (rdfs:subClassOf|(owl:unionOf/rdf:rest*/rdf:first))* ?r1 .").append("\n");
-		buf.append("            ?r1 owl:onProperty ?p .").append("\n");
-		buf.append("").append("\n");
-		buf.append("            ?p :NHC0 ?p_code .").append("\n");
-		buf.append("            ?p rdfs:label ?p_label .").append("\n");
-
-		if (roleName != null) {
-			buf.append("            ?p rdfs:label \"" + roleName + "\"^^xsd:string .").append("\n");
-		}
-
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("            ?r1 owl:someValuesFrom ?c .").append("\n");
-		buf.append("            ?c :NHC0 ?c_code .").append("\n");
-		buf.append("            ?c rdfs:label ?c_label .").append("\n");
-		buf.append("").append("\n");
-		buf.append("            }").append("\n");
-		buf.append("            UNION").append("\n");
-		buf.append("            {").append("\n");
-		buf.append("            ?x a owl:Class .").append("\n");
-		buf.append("            ?x :NHC0 ?x_code .").append("\n");
-
-		if (code != null) {
-			buf.append("                ?x :NHC0 \"" + code + "\"^^xsd:string .").append("\n");
-		}
-		buf.append("            ?x rdfs:label ?x_label .").append("\n");
-		buf.append("            ?x rdfs:subClassOf ?r .").append("\n");
-		buf.append("").append("\n");
-		buf.append("            ?r owl:onProperty ?p .").append("\n");
-		buf.append("            ?p :NHC0 ?p_code .").append("\n");
-		buf.append("            ?p rdfs:label ?p_label .").append("\n");
-
-		if (roleName != null) {
-			buf.append("            ?p rdfs:label \"" + roleName + "\"^^xsd:string .").append("\n");
-		}
-		buf.append("").append("\n");
-		buf.append("            ?r owl:someValuesFrom ?c .").append("\n");
-		buf.append("            ?c :NHC0 ?c_code .").append("\n");
-		buf.append("            ?c rdfs:label ?c_label .").append("\n");
-		buf.append("            }").append("\n");
-		buf.append("    }").append("\n");
-		buf.append("").append("\n");
-		buf.append("}").append("\n");
-		return buf.toString();
-	}
-
-	public Vector getRoleTargets(String named_graph) {
-		return getRoleTargets(named_graph, true);
-	}
-
-	public Vector getRoleTargets(String named_graph, boolean savefile) {
-        Vector v = getRoleTargets(named_graph, null, null);
-        if (savefile) {
-        	Utils.saveToFile(RESTRICTION_FILE, v);
-		}
-        return v;
-	}
-
-	public Vector getRoleTargets(String named_graph, String code, String roleName) {
-        String query = construct_get_role_targets(named_graph, code, roleName);
-        return executeQuery(query);
-	}
-
-
-	public String construct_get_hierarchical_relationships(String named_graph) {
-		String prefixes = getPrefixes();
-		StringBuffer buf = new StringBuffer();
-		buf.append(prefixes);
-		buf.append("SELECT ?z_label ?z_code ?x_label ?x_code").append("\n");
-		buf.append("{").append("\n");
-		buf.append("  graph <" + named_graph + ">").append("\n");
-		buf.append("  {").append("\n");
-		buf.append("	  {").append("\n");
-		buf.append("		  {").append("\n");
-		buf.append("		    ?x a owl:Class .").append("\n");
-		buf.append("		    ?x rdfs:label ?x_label .").append("\n");
-		buf.append("		    ?x " + named_graph_id + " ?x_code .").append("\n");
-		buf.append("		    ?x rdfs:subClassOf ?z .").append("\n");
-		buf.append("		    ?z a owl:Class .").append("\n");
-		buf.append("		    ?z rdfs:label ?z_label .").append("\n");
-		buf.append("		    ?z " + named_graph_id + " ?z_code").append("\n");
-		buf.append("		  }").append("\n");
-		buf.append("		  FILTER (?x != ?z)").append("\n");
-		buf.append("	  }").append("\n");
-		buf.append("  	  UNION").append("\n");
-		buf.append("	  {").append("\n");
-		buf.append("		  {").append("\n");
-		buf.append("		    ?x a owl:Class .").append("\n");
-		buf.append("		    ?x rdfs:label ?x_label .").append("\n");
-		buf.append("		    ?x " + named_graph_id + " ?x_code .").append("\n");
-		buf.append("		    ?x owl:equivalentClass ?y .").append("\n");
-		buf.append("		    ?y owl:intersectionOf ?list .").append("\n");
-		buf.append("		    ?list rdf:rest*/rdf:first ?z .").append("\n");
-		buf.append("		    ?z a owl:Class .").append("\n");
-		buf.append("		    ?z rdfs:label ?z_label .").append("\n");
-		buf.append("		    ?z " + named_graph_id + " ?z_code").append("\n");
-		buf.append("		  }").append("\n");
-		buf.append("		  FILTER (?x != ?z)").append("\n");
-		buf.append("	  }").append("\n");
-		buf.append("  }").append("\n");
-		buf.append("}").append("\n");
-		return buf.toString();
-	}
-
-	public Vector getHierarchicalRelationships(String named_graph) {
-		return executeQuery(construct_get_hierarchical_relationships(named_graph));
-	}
-
-
-	public Vector get_roots(String named_graph) {
-		return executeQuery(construct_root_query(named_graph));
-	}
-
-	public String construct_get_concepts_with_annotation_property(String named_graph, String propertyName) {
-		String prefixes = getPrefixes();
-		StringBuffer buf = new StringBuffer();
-		buf.append(prefixes);
-		buf.append("SELECT ?x_label ?x_code ?y_label ?z").append("\n");
-		buf.append("{").append("\n");
-		buf.append("    graph <" + named_graph + ">").append("\n");
-		buf.append("    {").append("\n");
-		buf.append("            ?x a owl:Class .").append("\n");
-		buf.append("            ?x rdfs:label ?x_label .").append("\n");
-		buf.append("		    ?x :NHC0 ?x_code .").append("\n");
-		buf.append("            ?y a owl:AnnotationProperty .").append("\n");
-		buf.append("            ?x ?y ?z .").append("\n");
-		buf.append("            ?y rdfs:label ?y_label .").append("\n");
-		buf.append("            ?y rdfs:label " + "\"" + propertyName + "\"^^xsd:string ").append("\n");
-		buf.append("    }").append("\n");
-		buf.append("}").append("\n");
-		return buf.toString();
-	}
-
-	public Vector getConceptsWithAnnotationProperty(String named_graph, String propertyName) {
-		String query = construct_get_concepts_with_annotation_property(named_graph, propertyName);
-		Vector v = executeQuery(query);
-		return v;
-	}
-
-	public String construct_get_concepts_with_annotation_property_matching(String named_graph,
-	    String propertyName, String propertyValue) {
-		String prefixes = getPrefixes();
-		StringBuffer buf = new StringBuffer();
-		buf.append(prefixes);
-		buf.append("SELECT ?x_label ?x_code ?y_label ?z").append("\n");
-		buf.append("{").append("\n");
-		buf.append("    graph <" + named_graph + ">").append("\n");
-		buf.append("    {").append("\n");
-		buf.append("            ?x a owl:Class .").append("\n");
-		buf.append("            ?x rdfs:label ?x_label .").append("\n");
-		buf.append("            ?x :NHC0 ?x_code .").append("\n");
-		buf.append("            ?y a owl:AnnotationProperty .").append("\n");
-		buf.append("            ?x ?y ?z .").append("\n");
-		buf.append("            ?y rdfs:label ?y_label .").append("\n");
-		buf.append("            ?y rdfs:label " + "\"" + propertyName + "\"^^xsd:string .").append("\n");
-		if (propertyValue != null) {
-		    buf.append("            ?x ?y " + "\"" + propertyValue + "\"^^xsd:string .").append("\n");
-		}
-
-		buf.append("    }").append("\n");
-		buf.append("}").append("\n");
-		return buf.toString();
-	}
-
-	public Vector getConceptsWithAnnotationPropertyMatching(String named_graph, String propertyName, String propertyValue) {
-		String query = construct_get_concepts_with_annotation_property_matching(named_graph, propertyName, propertyValue);
-		Vector v = executeQuery(query);
-		return v;
-	}
-
-
-	public String construct_get_supported_properties(String named_graph) {
-        String prefixes = getPrefixes();
-        StringBuffer buf = new StringBuffer();
-        buf.append(prefixes);
-        buf.append("select distinct ?p_label ?p_code ").append("\n");
-        buf.append("from <" + named_graph + ">").append("\n");
-        buf.append("where  { ").append("\n");
-        buf.append("                ?p :NHC0 ?p_code .").append("\n");
-        buf.append("                ?p rdfs:label ?p_label .").append("\n");
-        buf.append("                ?p a owl:AnnotationProperty .").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-
-	public Vector getSupportedProperties(String named_graph) {
-		String query = construct_get_supported_properties(named_graph);
-    	Vector v = executeQuery(query);
-		return v;
-	}
-
-	public String construct_get_concepts_with_property(String named_graph, String property_code) {
-		String prefixes = getPrefixes();
-		StringBuffer buf = new StringBuffer();
-		buf.append(prefixes);
-		buf.append("select distinct ?x_label ?x_code ?p_label ?p_value").append("\n");
-		buf.append("from <" + named_graph + ">").append("\n");
-		buf.append("where  { ").append("\n");
-		buf.append("                ?x a owl:Class .").append("\n");
-		buf.append("                ?x :NHC0 ?x_code .").append("\n");
-		buf.append("                ?x rdfs:label ?x_label .").append("\n");
-		buf.append("").append("\n");
-		buf.append("                ?p a owl:AnnotationProperty .").append("\n");
-		buf.append("                ?p :NHC0 ?p_code .").append("\n");
-		buf.append("                ?p rdfs:label ?p_label .").append("\n");
-		buf.append("                ?p :NHC0 \"" + property_code + "\"^^xsd:string .").append("\n");
-		buf.append("").append("\n");
-		buf.append("                ?x ?p ?p_value .").append("\n");
-		buf.append("}").append("\n");
-		return buf.toString();
-	}
-
-	public Vector getConceptsWithProperty(String named_graph, String property_code) {
-		String query = construct_get_concepts_with_property(named_graph, property_code);
-		Vector v = executeQuery(query);
-		v = removeDuplicates(v);
-		v = new SortUtils().quickSort(v);
-		return v;
-	}
-
-	public String construct_get_supported_qualifiers(String named_graph) {
-        String prefixes = getPrefixes();
-        StringBuffer buf = new StringBuffer();
-        buf.append(prefixes);
-        buf.append("select distinct ?p_label ?p_code ?q1_label ?q1_code").append("\n");
-        buf.append("from <" + named_graph + ">").append("\n");
-        buf.append("where  { ").append("\n");
-        buf.append("                ?x a owl:Class .").append("\n");
-        buf.append("                ?x :NHC0 ?x_code .").append("\n");
-        buf.append("                ?x rdfs:label ?x_label .").append("\n");
-        buf.append("").append("\n");
-        buf.append("                ?a a owl:Axiom .").append("\n");
-        buf.append("                ?a owl:annotatedSource ?x .").append("\n");
-        buf.append("                ?a owl:annotatedProperty ?p .").append("\n");
-        buf.append("                ?a owl:annotatedTarget ?a_target .").append("\n");
-        buf.append("                ").append("\n");
-        buf.append("                ?p :NHC0 ?p_code .").append("\n");
-        buf.append("                ?p rdfs:label ?p_label .").append("\n");
-        buf.append("").append("\n");
-        buf.append("                ?a ?q1 ?q1_value .").append("\n");
-        buf.append("                ?q1 :NHC0 ?q1_code .").append("\n");
-        buf.append("                ?q1 rdfs:label ?q1_label .").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-    public HashMap createQualifierCode2PropertyCodeHashMap(String named_graph) {
-		Vector v = getSupportedQualifiers(named_graph);
-		HashMap hmap = new HashMap();
-		for (int i=0; i").append("\n");
-        buf.append("where  { ").append("\n");
-        buf.append("                ?x a owl:Class .").append("\n");
-        buf.append("                ?x :NHC0 ?x_code .").append("\n");
-        buf.append("                ?x rdfs:label ?x_label .").append("\n");
-        buf.append("").append("\n");
-        buf.append("                ?a a owl:Axiom .").append("\n");
-        buf.append("                ?a owl:annotatedSource ?x .").append("\n");
-        buf.append("                ?a owl:annotatedProperty ?p .").append("\n");
-        buf.append("                ?a owl:annotatedTarget ?a_target .").append("\n");
-        buf.append("                ").append("\n");
-        buf.append("                ?p :NHC0 ?p_code .").append("\n");
-        buf.append("                ?p :NHC0 \"" + propertyCode + "\"^^xsd:string .").append("\n");
-        buf.append("                ?p rdfs:label ?p_label .").append("\n");
-        buf.append("").append("\n");
-        buf.append("                ?a ?q1 ?q1_value .").append("\n");
-        buf.append("                ?q1 :NHC0 ?q1_code .").append("\n");
-        buf.append("                ?q1 :NHC0 \"" + qualifierCode + "\"^^xsd:string .").append("\n");
-        buf.append("                ?q1 rdfs:label ?q1_label .").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-
-	public int getAnnotatedTargetCount(String named_graph, String propertyCode, String qualifierCode) {
-		String query = construct_get_annotated_target_count(named_graph, propertyCode, qualifierCode);
-		Vector v = executeQuery(query);
-		if (v == null || v.size() == 0) return 0;
-		return v.size();
-	}
-
-
-	public String construct_get_annotated_target_count(String named_graph, String propertyCode) {
-        String prefixes = getPrefixes();
-        StringBuffer buf = new StringBuffer();
-        buf.append(prefixes);
-        buf.append("SELECT ?a_target").append("\n");
-        buf.append("from <" + named_graph + ">").append("\n");
-        buf.append("where  { ").append("\n");
-        buf.append("                ?a a owl:Axiom .").append("\n");
-        buf.append("                ?a owl:annotatedSource ?x .").append("\n");
-        buf.append("                ?a owl:annotatedProperty ?p .").append("\n");
-        buf.append("                ?a owl:annotatedTarget ?a_target .").append("\n");
-        buf.append("                ").append("\n");
-        buf.append("                ?p :NHC0 ?p_code .").append("\n");
-        buf.append("                ?p :NHC0 \"" + propertyCode + "\"^^xsd:string .").append("\n");
-        buf.append("                ?p rdfs:label ?p_label .").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-	public int getAnnotatedTargetCount(String named_graph, String propertyCode) {
-		String query = construct_get_annotated_target_count(named_graph, propertyCode);
-		Vector v = executeQuery(query);
-		if (v == null || v.size() == 0) return 0;
-		return v.size();
-	}
-
-
-    public String construct_get_distinct_property_qualifier_values(String named_graph,
-        String code,
-        String propertyCode,
-        String qualifierCode) {
-        String prefixes = getPrefixes();
-        StringBuffer buf = new StringBuffer();
-        buf.append(prefixes);
-        buf.append("select distinct ?q1_value").append("\n");
-        buf.append("from <" + named_graph + ">").append("\n");
-        buf.append("where  { ").append("\n");
-        buf.append("                ?x a owl:Class .").append("\n");
-        buf.append("                ?x :NHC0 ?x_code .").append("\n");
-        if (code != null) {
-        	buf.append("                ?x :NHC0 \"" + code + "\"^^xsd:string .").append("\n");
-	    }
-        buf.append("                ?x rdfs:label ?x_label .").append("\n");
-        buf.append("").append("\n");
-        buf.append("                ?a a owl:Axiom .").append("\n");
-        buf.append("                ?a owl:annotatedSource ?x .").append("\n");
-        buf.append("                ?a owl:annotatedProperty ?p .").append("\n");
-        buf.append("                ?a owl:annotatedTarget ?a_target .").append("\n");
-        buf.append("                ?p :NHC0 ?p_code .").append("\n");
-        buf.append("                ?p :NHC0 \"" + propertyCode + "\"^^xsd:string .").append("\n");
-        buf.append("                ?p rdfs:label ?p_label .").append("\n");
-        buf.append("").append("\n");
-        buf.append("                ?a ?q1 ?q1_value .").append("\n");
-        buf.append("                ?q1 :NHC0 ?q1_code .").append("\n");
-        buf.append("                ?q1 :NHC0 \"" + qualifierCode + "\"^^xsd:string .").append("\n");
-        buf.append("                ?q1 rdfs:label ?q1_label .").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-
-	public Vector getDistinctPropertyQualifierValues(String named_graph, String code, String propertyCode, String qualifierCode) {
-		String query = construct_get_annotated_target_count(named_graph, propertyCode);
-		Vector v = executeQuery(query);
-		v = new SortUtils().quickSort(v);
-		return v;
-	}
-
-	public String construct_get_distinct_property_values(String named_graph, String propertyName) {
-        String prefixes = getPrefixes();
-        StringBuffer buf = new StringBuffer();
-        buf.append(prefixes);
-        buf.append("select distinct ?p_value").append("\n");
-        buf.append("from <" + named_graph + ">").append("\n");
-        buf.append("where  { ").append("\n");
-        buf.append("                ?x a owl:Class .").append("\n");
-        buf.append("                ?x :NHC0 ?x_code .").append("\n");
-        buf.append("                ?x rdfs:label ?x_label .").append("\n");
-        buf.append("").append("\n");
-        buf.append("                ?p :NHC0 ?p_code .").append("\n");
-        buf.append("                ?p rdfs:label ?p_label .").append("\n");
-        buf.append("                ?p rdfs:label \"" + propertyName + "\"^^xsd:string .").append("\n");
-        buf.append("                ?p a owl:AnnotationProperty .").append("\n");
-        buf.append("                ").append("\n");
-        buf.append("                ?x ?p ?p_value .").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-	public Vector getDistinctPropertyValues(String named_graph, String propertyName) {
-        String query = construct_get_distinct_property_values(named_graph, propertyName);
-        Vector v = executeQuery(query);
-        v = new SortUtils().quickSort(v);
-        return v;
-	}
-
-
-	public String construct_get_concepts_with_property_value(String named_graph, String propertyName, String propertyValue) {
-        String prefixes = getPrefixes();
-        StringBuffer buf = new StringBuffer();
-        buf.append(prefixes);
-        buf.append("select distinct ?x_label ?x_code ?p_label ?p_value").append("\n");
-        buf.append("from <" + named_graph + ">").append("\n");
-        buf.append("where  { ").append("\n");
-        buf.append("                ?x a owl:Class .").append("\n");
-        buf.append("                ?x :NHC0 ?x_code .").append("\n");
-        buf.append("                ?x rdfs:label ?x_label .").append("\n");
-        buf.append("").append("\n");
-        buf.append("                ?p :NHC0 ?p_code .").append("\n");
-        buf.append("                ?p rdfs:label ?p_label .").append("\n");
-        buf.append("                ?p rdfs:label \"" + propertyName + "\"^^xsd:string .").append("\n");
-        buf.append("                ?p a owl:AnnotationProperty .").append("\n");
-        buf.append("                ").append("\n");
-        buf.append("                ?x ?p ?p_value .").append("\n");
-        buf.append("                ?x ?p  \"" + propertyValue + "\"^^xsd:string .").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-
-	public Vector getConceptsWithPropertyValue(String named_graph, String propertyName, String propertyValue) {
-		String query = construct_get_concepts_with_property_value(named_graph, propertyName, propertyValue);
-		Vector v = executeQuery(query);
-		v = removeDuplicates(v);
-		return v;
-	}
-
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-	public static HashMap getPropertyCountHashMap(String owlfile) {
-		OWLScanner owlscanner = new OWLScanner(owlfile);
-		Vector v = owlscanner.extractProperties(owlscanner.get_owl_vec());
-		HashMap propertyCountHashMap = new HashMap();
-		for (int i=0; i").append("\n");
-        buf.append("where  { ").append("\n");
-        buf.append("                ?x a owl:Class .").append("\n");
-        buf.append("                ?x :NHC0 ?x_code .").append("\n");
-        buf.append("                ?x rdfs:label ?x_label .").append("\n");
-        buf.append("").append("\n");
-        buf.append("                ?p2 a owl:AnnotationProperty .").append("\n");
-        buf.append("                ?p2 :NHC0 ?p2_code .").append("\n");
-        buf.append("                ?p2 rdfs:label ?p2_label .").append("\n");
-        buf.append("                ?p2 rdfs:label \"Publish_Value_Set\"^^xsd:string .").append("\n");
-        buf.append("                ").append("\n");
-        buf.append("                ?x ?p2 ?p2_value .").append("\n");
-        if (publishedOnly) {
-       	    buf.append("                ?x ?p2 \"Yes\"^^xsd:string .").append("\n");
-		}
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-	public Vector getValueSets(String named_graph) {
-		boolean publishedOnly = true;
-		String query = construct_get_value_sets(named_graph, publishedOnly);
-		Vector v = executeQuery(query);
-		return v;
-	}
-
-	public Vector getValueSets(String named_graph, boolean publishedOnly) {
-		String query = construct_get_value_sets(named_graph, publishedOnly);
-		Vector v = executeQuery(query);
-		return v;
-	}
-
-	public String construct_get_value_sets_with_contributing_source(String named_graph) {
-		boolean publishedOnly = true;
-		return construct_get_value_sets_with_contributing_source(named_graph, publishedOnly);
-	}
-
-	public String construct_get_value_sets_with_contributing_source(String named_graph, boolean publishedOnly) {
-        String prefixes = getPrefixes();
-        StringBuffer buf = new StringBuffer();
-        buf.append(prefixes);
-        buf.append("select distinct ?x_label ?x_code ?p1_label ?p1_value ").append("\n");
-        //buf.append("select distinct ?x_label ?x_code ?p1_value ?p2_value ").append("\n");
-        buf.append("from <" + named_graph + ">").append("\n");
-        buf.append("where  { ").append("\n");
-        buf.append("                ?x a owl:Class .").append("\n");
-        buf.append("                ?x :NHC0 ?x_code .").append("\n");
-        buf.append("                ?x rdfs:label ?x_label .").append("\n");
-        buf.append("").append("\n");
-        buf.append("                ?p1 a owl:AnnotationProperty .").append("\n");
-        buf.append("                ?p1 :NHC0 ?p1_code .").append("\n");
-        buf.append("                ?p1 rdfs:label ?p1_label .").append("\n");
-        buf.append("                ?p1 rdfs:label \"Contributing_Source\"^^xsd:string .").append("\n");
-        buf.append("                ?x  ?p1 ?p1_value .").append("\n");
-        buf.append("").append("\n");
-        buf.append("                ?p2 a owl:AnnotationProperty .").append("\n");
-        buf.append("                ?p2 :NHC0 ?p2_code .").append("\n");
-        buf.append("                ?p2 rdfs:label ?p2_label .").append("\n");
-        buf.append("                ?p2 rdfs:label \"Publish_Value_Set\"^^xsd:string .").append("\n");
-        buf.append("                ").append("\n");
-        buf.append("                ?x ?p2 ?p2_value .").append("\n");
-        if (publishedOnly) {
-        	buf.append("                ?x ?p2 \"Yes\"^^xsd:string .").append("\n");
-		}
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-	public Vector getValueSetsWithContributingSource(String named_graph) {
-		boolean publishedOnly = true;
-		String query = construct_get_value_sets_with_contributing_source(named_graph, publishedOnly);
-		Vector v = executeQuery(query);
-		return v;
-	}
-
-	public Vector getValueSetsWithContributingSource(String named_graph, boolean publishedOnly) {
-		String query = construct_get_value_sets_with_contributing_source(named_graph, publishedOnly);
-		Vector v = executeQuery(query);
-		return v;
-	}
-
-	public String construct_get_concepts_in_subset(String named_graph, String subset_code, boolean codeOnly) {
-		String prefixes = getPrefixes();
-		StringBuffer buf = new StringBuffer();
-		buf.append(prefixes);
-		if (codeOnly) {
-			buf.append("SELECT ?x_code").append("\n");
-		} else {
-			buf.append("SELECT ?x_label ?x_code").append("\n");
-	    }
-		buf.append("{").append("\n");
-		buf.append("    graph <" + named_graph + ">").append("\n");
-		buf.append("    {").append("\n");
-		buf.append("            ?x a owl:Class .").append("\n");
-		buf.append("            ?x rdfs:label ?x_label .").append("\n");
-		buf.append("            ?x " + named_graph_id + " ?x_code .").append("\n");
-		buf.append("            ?y a owl:AnnotationProperty .").append("\n");
-		buf.append("            ?x ?y ?z .").append("\n");
-		buf.append("            ?z " + named_graph_id + " \"" + subset_code + "\"^^xsd:string .").append("\n");
-		buf.append("            ?y rdfs:label " + "\"" + "Concept_In_Subset" + "\"^^xsd:string ").append("\n");
-		buf.append("    }").append("\n");
-		buf.append("}").append("\n");
-		return buf.toString();
-	}
-
-	public Vector getConceptsInSubset(String named_graph, String code, boolean codeOnly) {
-		return executeQuery(construct_get_concepts_in_subset(named_graph, code, codeOnly));
-	}
-
-	public String construct_get_value_set_data(String named_graph) {
-		boolean publishedOnly = true;
-		return construct_get_value_set_data(named_graph, publishedOnly);
-	}
-
-	public String construct_get_value_set_data(String named_graph, boolean publishedOnly) {
-		String prefixes = getPrefixes();
-		StringBuffer buf = new StringBuffer();
-		buf.append(prefixes);
-		buf.append("select distinct ?y_label ?y_code ?p0_label ?x_label ?x_code ?p1_label ?p1_value ?p2_label ?p2_value ").append("\n");
-		buf.append("from <" + named_graph + ">").append("\n");
-		buf.append("where  { ").append("\n");
-		buf.append("                ?y a owl:Class .").append("\n");
-		buf.append("                ?y :NHC0 ?y_code .").append("\n");
-		buf.append("                ?y rdfs:label ?y_label .").append("\n");
-		buf.append("").append("\n");
-		buf.append("                ?p0 a owl:AnnotationProperty .").append("\n");
-		buf.append("                ?p0 :NHC0 ?p0_code .").append("\n");
-		buf.append("                ?p0 rdfs:label ?p0_label .").append("\n");
-		buf.append("                ?p0 rdfs:label \"Concept_In_Subset\"^^xsd:string .  ").append("\n");
-		buf.append(" ").append("\n");
-		buf.append("                ?x a owl:Class .").append("\n");
-		buf.append("                ?x :NHC0 ?x_code .").append("\n");
-		buf.append("                ?x rdfs:label ?x_label .").append("\n");
-		buf.append("").append("\n");
-		buf.append("                ?y ?p0 ?x .   ").append("\n");
-		buf.append("").append("\n");
-		buf.append("                ?p1 a owl:AnnotationProperty .").append("\n");
-		buf.append("                ?p1 :NHC0 ?p1_code .").append("\n");
-		buf.append("                ?p1 rdfs:label ?p1_label .").append("\n");
-		buf.append("                ?p1 rdfs:label \"Contributing_Source\"^^xsd:string .").append("\n");
-
-		buf.append("                OPTIONAL {").append("\n");
-		buf.append("                ?x  ?p1 ?p1_value .").append("\n");
-		buf.append("                }").append("\n");
-		buf.append("").append("\n");
-		buf.append("                ?p2 a owl:AnnotationProperty .").append("\n");
-		buf.append("                ?p2 :NHC0 ?p2_code .").append("\n");
-		buf.append("                ?p2 rdfs:label ?p2_label .").append("\n");
-		buf.append("                ?p2 rdfs:label \"Publish_Value_Set\"^^xsd:string .").append("\n");
-		buf.append("                ").append("\n");
-		buf.append("                ?x ?p2 ?p2_value .").append("\n");
-		if (publishedOnly) {
-			buf.append("                ?x ?p2 \"Yes\"^^xsd:string .").append("\n");
-		}
-		buf.append("}").append("\n");
-		return buf.toString();
-	}
-
-
-//	(221972) CTRP Disease Finding|C173902|Concept_In_Subset|CTS-API Disease Broad Category Terminology|C138189|Contributing_Source|Publish_Value_Set|null|Yes
-
-	public Vector getValueSetData(String named_graph) {
-		boolean publishedOnly = true;
-		return getValueSetData(named_graph, publishedOnly);
-	}
-
-	public Vector getValueSetData(String named_graph, boolean publishedOnly) {
-		Vector v = executeQuery(construct_get_value_set_data(named_graph, publishedOnly));
-
-		Utils.saveToFile("value_set_data.txt", v);
-
-		Vector w = new Vector();
-		for (int i=0; i " + Integer.valueOf(value));
-        }
-	}
-
-
-	public HashMap getPropertyValueHashMap(Vector v) {
-		HashMap hmap = new HashMap();
-		if (v == null) return hmap;
-		for (int i=0; i
- * Copyright 2020 MSC. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or MSC
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      MSC, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@nih.gov
- *
- */
-
-
-public class EVSStatisticsRunner {
-	String serviceUrl = null;
-	String named_graph = null;
-	String username = null;
-	String password = null;
-
-	public static void main(String[] args) {
-		long ms = System.currentTimeMillis();
-
-System.out.println("Downloading NCI Thesaurus...");
-		//Download NCI Thesaurus
-		String currentWorkingDirectory = System.getProperty("user.dir");
-        NCItDownload.download(NCItDownload.NCIt_URI + NCItDownload.NCIT_ZIP_FILE, NCItDownload.NCIT_ZIP_FILE);
-        String zipFilePath = currentWorkingDirectory + "/" + NCItDownload.NCIT_ZIP_FILE;
-        NCItDownload.unzip(zipFilePath, currentWorkingDirectory);
-
-System.out.println("Running OWLScanner ...");
-		//Run scanner for extracting roles.txt
-        String owlfile = "ThesaurusInferred_forTS.owl";
-		OWLScanner scanner = new OWLScanner(owlfile);
-        String RESTRICTION_FILE = "roles.txt";
-		Vector v = scanner.extractOWLRestrictions(scanner.get_owl_vec());
-		Utils.saveToFile(RESTRICTION_FILE, v);
-		v.clear();
-		scanner.get_owl_vec().clear();
-
-System.out.println("Running EVSStatistics ...");
-        //Run EVSStatistics
-		String serviceUrl = args[0];
-		String named_graph = args[1];
-		String username = args[2];
-		String password = args[3];
-		EVSStatistics evsStatistics = new EVSStatistics(serviceUrl, named_graph, username, password);
-	    evsStatistics.generate();
-        System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-}
-
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/FlatFileGenerator.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/FlatFileGenerator.java
deleted file mode 100644
index 050a7e4a9..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/FlatFileGenerator.java
+++ /dev/null
@@ -1,387 +0,0 @@
-package gov.nih.nci.evs.restapi.appl;
-import gov.nih.nci.evs.restapi.util.*;
-import gov.nih.nci.evs.restapi.bean.*;
-import gov.nih.nci.evs.restapi.common.*;
-
-import java.io.*;
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.*;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
-import java.util.*;
-import java.util.regex.*;
-import org.json.*;
-
-/**
- * 
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@nih.gov
- *
- */
-
-
-public class FlatFileGenerator {
-    JSONUtils jsonUtils = null;
-    HTTPUtils httpUtils = null;
-    String named_graph = null;
-    String prefixes = null;
-    String serviceUrl = null;
-    String restURL = null;
-    String named_graph_id = ":NHC0";
-    String BASE_URI = "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl";
-
-    ParserUtils parser = new ParserUtils();
-    HashMap nameVersion2NamedGraphMap = null;
-    HashMap ontologyUri2LabelMap = null;
-    String version = null;
-    String username = null;
-    String password = null;
-    OWLSPARQLUtils owlSPARQLUtils = null;
-
-    static String CONCEPT_MEMBESHIP_FILE = "concept_membership_results.txt";
-
-    public FlatFileGenerator(String serviceUrl, String named_graph, String username, String password) {
-		this.serviceUrl = serviceUrl;
-    	this.named_graph = named_graph;
-    	this.username = username;
-    	this.password = password;
-        this.owlSPARQLUtils = new OWLSPARQLUtils(serviceUrl, username, password);
-        this.owlSPARQLUtils.set_named_graph(named_graph);
-    }
-
-    public OWLSPARQLUtils getOWLSPARQLUtils() {
-		return this.owlSPARQLUtils;
-	}
-
-	public String construct_get_class_uris(String named_graph) {
-		String prefixes = owlSPARQLUtils.getPrefixes();
-		StringBuffer buf = new StringBuffer();
-		buf.append(prefixes);
-		buf.append("select distinct ?x_code ?x").append("\n");
-		buf.append("{").append("\n");
-		buf.append("	graph <" + named_graph + "> ").append("\n");
-		buf.append("	{").append("\n");
-		buf.append("				?x a owl:Class .").append("\n");
-		buf.append("				?x :NHC0 ?x_code .").append("\n");
-		buf.append("	}").append("\n");
-		buf.append("}").append("\n");
-		return buf.toString();
-	}
-
-	public Vector getClassURIs(String named_graph) {
-		String query = construct_get_class_uris(named_graph);
-
-		System.out.println(query);
-
-		Vector v = owlSPARQLUtils.executeQuery(query);
-		if (v == null) return null;
-		if (v.size() == 0) return v;
-		v = new ParserUtils().getResponseValues(v);
-		return new SortUtils().quickSort(v);
-	}
-
-
-	public String construct_get_hierarchical_relationships(String named_graph) {
-        String prefixes = owlSPARQLUtils.getPrefixes();
-        StringBuffer buf = new StringBuffer();
-        buf.append(prefixes);
-        buf.append("select distinct ?x_code ?y_code").append("\n");
-        buf.append("from <" + named_graph + ">").append("\n");
-        buf.append("where  { ").append("\n");
-        buf.append("    {").append("\n");
-        buf.append("                ?x a owl:Class .").append("\n");
-        buf.append("                ?x :NHC0 ?x_code .").append("\n");
-        buf.append("                ?x rdfs:label ?x_label .").append("\n");
-        buf.append("").append("\n");
-        buf.append("                ?y a owl:Class .").append("\n");
-        buf.append("                ?y :NHC0 ?y_code .").append("\n");
-        buf.append("                ?y rdfs:label ?y_label .").append("\n");
-        buf.append("                ").append("\n");
-        buf.append("                ?x (rdfs:subClassOf|owl:equivalentClass/owl:intersectionOf/rdf:rest*/rdf:first) ?y .  ").append("\n");
-        buf.append("    } ").append("\n");
-        buf.append("}").append("\n");
-        buf.append("").append("\n");
-        return buf.toString();
-	}
-
-	public Vector getHierarchicalRelationships(String named_graph) {
-        String query = construct_get_hierarchical_relationships(named_graph);
-        Vector v = owlSPARQLUtils.executeQuery(query);
-        if (v == null) return null;
-        if (v.size() == 0) return v;
-        v = new ParserUtils().getResponseValues(v);
-        return new SortUtils().quickSort(v);
-	}
-
-	public String construct_get_prop(String named_graph, String propertyCode) {
-        String prefixes = owlSPARQLUtils.getPrefixes();
-        StringBuffer buf = new StringBuffer();
-        buf.append(prefixes);
-        buf.append("SELECT distinct ?x_code ?p_value").append("\n");
-        buf.append("from <" + named_graph + "> ").append("\n");
-        buf.append("where { ").append("\n");
-        buf.append("                    ?x a owl:Class .").append("\n");
-        buf.append("                    ?x :NHC0 ?x_code .").append("\n");
-        //buf.append("                    ?x rdfs:label ?x_label .").append("\n");
-        buf.append("                    ?p :NHC0 \"" + propertyCode + "\"^^xsd:string .").append("\n");
-        //buf.append("                    ?p rdfs:label ?p_label .").append("\n");
-        buf.append("                    ?x ?p ?p_value .").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-	public Vector getProp(String named_graph, String propertyCode) {
-        String query = construct_get_prop(named_graph, propertyCode);
-        Vector v = owlSPARQLUtils.executeQuery(query);
-        if (v == null) return null;
-        if (v.size() == 0) return v;
-        v = new ParserUtils().getResponseValues(v);
-        return new SortUtils().quickSort(v);
-	}
-
-	public Vector getSynonyms(String named_graph) {
-        String propertyCode = "P90";
-        return getProp(named_graph, propertyCode);
-	}
-
-	public String construct_get_labels(String named_graph) {
-        String prefixes = owlSPARQLUtils.getPrefixes();
-        StringBuffer buf = new StringBuffer();
-        buf.append(prefixes);
-        buf.append("select distinct ?x_code ?x_label").append("\n");
-        buf.append("{").append("\n");
-        buf.append("    graph <" + named_graph + "> ").append("\n");
-        buf.append("    {").append("\n");
-        buf.append("            {").append("\n");
-        buf.append("            ?x a owl:Class .").append("\n");
-        buf.append("            ?x :NHC0 ?x_code .").append("\n");
-        buf.append("            ?x rdfs:label ?x_label .").append("\n");
-        buf.append("            }").append("\n");
-        buf.append("    }").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-
-	public Vector getLabels(String named_graph) {
-        String query = construct_get_labels(named_graph);
-        Vector v = owlSPARQLUtils.executeQuery(query);
-        if (v == null) return null;
-        if (v.size() == 0) return v;
-        v = new ParserUtils().getResponseValues(v);
-        return new SortUtils().quickSort(v);
-	}
-
-	public String getClassUri(String code) {
-		return "";
-	}
-
-	public String construct_get_concept_membership(String named_graph) {
-        String prefixes = owlSPARQLUtils.getPrefixes();
-        StringBuffer buf = new StringBuffer();
-        buf.append(prefixes);
-        buf.append("").append("\n");
-        buf.append("SELECT distinct ?x_label ?x_code ?p_label ?y_label ?y_code ").append("\n");
-        buf.append("{").append("\n");
-        buf.append("    graph <" + named_graph + "> {").append("\n");
-        buf.append("            ?x a owl:Class .").append("\n");
-        buf.append("            ?x :NHC0 ?x_code .").append("\n");
-        buf.append("            ?x rdfs:label ?x_label .").append("\n");
-        buf.append("").append("\n");
-        buf.append("            ?y a owl:Class .").append("\n");
-        buf.append("            ?y :NHC0 ?y_code .").append("\n");
-        buf.append("            ?y rdfs:label ?y_label .").append("\n");
-        buf.append("").append("\n");
-        buf.append("            ?x ?p ?y .").append("\n");
-        buf.append("            ?p rdfs:label ?p_label .").append("\n");
-        buf.append("            ?p rdfs:label \"Concept_In_Subset\"^^xsd:string .").append("\n");
-        buf.append("").append("\n");
-        buf.append("    }").append("\n");
-        buf.append("}").append("\n");
-        buf.append("").append("\n");
-        return buf.toString();
-	}
-
-    public HashMap createMultiValuedHashMap(Vector data) {
-		HashMap hmap = new HashMap();
-        for (int i=0; i
- * Copyright 2022 Guidehouse. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by Guidehouse and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "Guidehouse" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or Guidehouse
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class FlatFileGeneratorRunner {
-    static String CONCEPT_MEMBESHIP_FILE = "concept_in_subset_data.txt";
-	public static void run(String restURL, String named_graph, String username, String password) {
-		System.out.println("Generating NCI Thesaurus flat file ...");
-        FlatFileGenerator generator = new FlatFileGenerator(restURL, named_graph, username, password);
-		String flatfile = generator.generate();
-		Vector v = generator.getConceptMembership(named_graph);
-		HashMap code2LabelMap = new HashMap();
-        HashMap hmap = new HashMap();
-		for (int i=0; i 0) {
-			System.out.println("\nWARNING: Codes in " + CONCEPT_MEMBESHIP_FILE + " not found in " + flatfile + ".");
-			it = missing_codes.iterator();
-			int lcv = 0;
-			while (it.hasNext()) {
-				lcv++;
-				String code = (String) it.next();
-				String label = (String) code2LabelMap.get(code);
-				System.out.println("(" + lcv + ") " + label + " (" + code + ")");
-			}
-		}
-	}
-
-	public static void main(String[] args) {
-		long ms = System.currentTimeMillis();
-		String restURL = args[0];
-		String named_graph = args[1];
-		String username = args[2];
-		String password = args[3];
-		run(restURL, named_graph, username, password);
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-}
-
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/MainTypeHierarchy.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/MainTypeHierarchy.java
deleted file mode 100644
index 6d1fff7f4..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/MainTypeHierarchy.java
+++ /dev/null
@@ -1,1338 +0,0 @@
-package gov.nih.nci.evs.restapi.appl;
-
-import gov.nih.nci.evs.restapi.util.*;
-import gov.nih.nci.evs.restapi.bean.*;
-import gov.nih.nci.evs.restapi.common.*;
-
-import java.io.*;
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.*;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
-import java.util.*;
-import java.util.regex.*;
-
-public class MainTypeHierarchy {
-	public int multiple_count = 0;
-	static String MAIN_TYPE_TREE = "main_type_tree";
-	static String SUBTYPE_TREE = "subtype_tree";
-	static String STAGE_TREE = "stage_tree";
-	public static String DISEASE_DISORDER_OR_FINDING_CODE = "C7057";
-
-
-	static String FINDING_CODE = "C3367";
-
-	public static String DISEASES_AND_DISORDERS_CODE = "C2991";
-	public static String NEOPLASM_CODE = "C3262";
-	static Vector main_type_hierarchy_data = null;
-
-	static String RECURRENT = "recurrent";
-
-    Vector parent_child_vec = null;
-    HierarchyHelper hh = null;
-    HierarchyHelper mth_hh = null;
-    HierarchyHelper mth_hh_without_categories = null;
-
-    PathFinder pathFinder = null;
-
-    String ctrp_classification_data = null;
-    Vector main_types = null;
-    Vector main_type_leaves = null;
-    HashSet main_type_set = null;
-	HashSet ctrp_biomarker_set = null;
-	HashSet ctrp_reference_gene_set = null;
-
-
-    Vector subtype_terms = null;
-    Vector stage_terms = null;
-
-    HashSet subtype_set = null;
-    HashSet stage_set = null;
-
-    HashMap label2CodeMap = new HashMap();
-    HashSet ctrp_codes = new HashSet();
-
-    HashMap levelMap = null;
-    HashMap stageConceptHashMap = null;
-    HashMap gradeConceptHashMap = null;
-    Vector category_vec = null;
-    HashSet category_hset = null;
-
-    static String NCI_THESAURUS = "NCI_Thesaurus";
-
-    public MainTypeHierarchy() {
-
-    }
-
-    public MainTypeHierarchy(Vector parent_child_vec) {
-		this.parent_child_vec = parent_child_vec;
-		this.hh = new HierarchyHelper(parent_child_vec);
-    }
-
-    public MainTypeHierarchy(String ncit_version, Vector parent_child_vec, HashSet main_type_set, Vector category_vec,
-        Vector stageConcepts, Vector gradeConcepts, HashSet ctrp_biomarker_set, HashSet ctrp_reference_gene_set) {
-
-		this.parent_child_vec = parent_child_vec;
-		this.hh = new HierarchyHelper(parent_child_vec);
-
-        this.stageConceptHashMap = new HashMap();
-        for (int i=0; i 0) {
-					return true;
-				} else {
-					return false;
-				}
-			}
-
-			if (isDiseaseGrade(code)) {
-				String name = (String) gradeConceptHashMap.get(code);
-				name = name.toLowerCase();
-				if (name.indexOf("grade") == -1) {
-					return true;
-				}
-				return false;
-			}
-
-		} catch (Exception ex) {
-			ex.printStackTrace();
-		}
-		return true;
-	}
-
-    public Vector generate_main_type_hierarchy() {
-		if (main_type_set == null) {
-			return null;
-		}
-		return generate_embedded_hierarchy(DISEASES_AND_DISORDERS_CODE, main_type_set);
-	}
-
-	public Vector generate_embedded_hierarchy(String rootCode, HashSet nodeSet) {
-		return generate_embedded_hierarchy(rootCode, nodeSet, true);
-	}
-
-	public Vector generate_embedded_hierarchy(String rootCode, HashSet nodeSet, boolean trim) {
-		Vector v = generateEmbeddedHierarchy(rootCode, nodeSet, trim);
-        HierarchyHelper hh = new HierarchyHelper(v);
-        Vector w = hh.exportTree();
-        w = new ASCIITreeUtils().removeRootNode(w);
-        return w;
-	}
-
-    public void generateMainTypeHierarchy(String outputfile) {
-		generateEmbeddedHierarchy(outputfile, DISEASES_AND_DISORDERS_CODE, main_type_set);
-	}
-
-	public void generateEmbeddedHierarchy(String treefile, String rootCode, HashSet nodeSet) {
-		generateEmbeddedHierarchy(treefile, rootCode, nodeSet, true);
-	}
-
-	public void generateEmbeddedHierarchy(String treefile, String rootCode, HashSet nodeSet, boolean trim) {
-		Vector v = generateEmbeddedHierarchy(rootCode, nodeSet, trim);
-        HierarchyHelper hh = new HierarchyHelper(v);
-        Vector w = hh.exportTree();
-        //KLO
-        w = new ASCIITreeUtils().removeRootNode(w);
-        Utils.saveToFile(treefile, w);
-	}
-
-	public Vector createEmbeddedHierarchy(String rootCode, HashSet nodeSet) {
-		return createEmbeddedHierarchy(rootCode, nodeSet, true);
-	}
-
-	public Vector createEmbeddedHierarchy(String rootCode, HashSet nodeSet, boolean trim) {
-		Vector v = generateEmbeddedHierarchy(rootCode, nodeSet, trim);
-        HierarchyHelper hh = new HierarchyHelper(v);
-        Vector w = hh.exportTree();
-        return w;
-	}
-
-	public TreeItem trimTree(TreeItem ti, int level, String code, int maxLevel) {
-		if (level >= maxLevel) return ti;
-        if (ti._code.compareTo(code) == 0 && level < maxLevel) {
-			return null;
-		}
-
-		List children = ti._assocToChildMap.get(Constants.ASSOCIATION_NAME);
-		if (children != null && children.size() > 0) {
-			List new_children = new ArrayList();
-			for (int i=0; i= maxLevel) {
-							new_children.add(child_ti);
-						}
-					}
-				}
-			}
-			ti._assocToChildMap.put(Constants.ASSOCIATION_NAME, new_children);
-		}
-		return ti;
-	}
-
-	public HashMap create_level_hashmap(Vector v) {
-		ASCIITreeUtils utils = new ASCIITreeUtils();
-	    HashMap hmap = new HashMap();
-	    for (int i=0; i 1) {
-				int maxLevel = findMaximumLevel(w);
-				w2.add(key + "|" + maxLevel);
-			}
-		}
-		return w2;
-	}
-
-	public int findMaximumLevel(Vector v) {
-		int max = -1;
-		for (int i=0; i max) {
-				max = value;
-			}
-		}
-		return max;
-	}
-
-	public HashMap createLevelHashMap(Vector parent_child_vec) {
-		HierarchyHelper hh = new HierarchyHelper(parent_child_vec);
-		ASCIITreeUtils utils = new ASCIITreeUtils();
-	    HashMap hmap = new HashMap();
-	    Vector v = hh.exportTree();//(Vector) parent_child_vec.clone();
-	    for (int i=0; i maxLevel) {
-						maxLevel = i1;
-						w = new Vector();
-						w.add(parent_label + "|" + parent_code + "|" + maxLevel);
-					} else if (i1 == maxLevel) {
-						String t = parent_label + "|" + parent_code + "|" + maxLevel;
-						if (!w.contains(t)) {
-							w.add(t);
-						}
-					}
-				}
-			}
-
-			if (child_code.compareTo(rootCode) != 0) {
-				Integer n2 = (Integer) levelMap.get(child_code);
-				if (n2 != null) {
-					int i2 = n2.intValue();
-					if (i2 > maxLevel) {
-						maxLevel = i2;
-						w = new Vector();
-						w.add(child_label + "|" + child_code + "|" + maxLevel);
-					} else if (i2 == maxLevel) {
-						String t = child_label + "|" + child_code + "|" + maxLevel;
-						if (!w.contains(t)) {
-							w.add(t);
-						}
-					}
-				}
-		    }
-		}
-		return w;
-	}
-
-	public List getMainMenuAncestors(String code) {
-		if (!isSubtype(code) && !isDiseaseStage(code) && !isDiseaseGrade(code)) {
-			return null;
-		}
-        String label = hh.getLabel(code);
-        if (label == null) return null;
-		List list = new ArrayList();
-	    Vector v = findMainMenuAncestors(code);
-        for (int i=0; i 0) {
-				for (int i=0; i 0) {
-			for (int i=0; i 0) {
-				w.addAll(u);
-			}
-		}
-		w = removeDuplicates(w);
-		return w;
-	}
-
-	public Vector removeDuplicates(Vector codes) {
-		HashSet hset = new HashSet();
-		Vector w = new Vector();
-		for (int i=0; i 0) {
-
-					System.out.println("\t(10) sups != null && sups.size() > 0 -- isSubtype: true");
-					return true;
-				} else {
-
-					System.out.println("\t(11) sups == null -- isSubtype: false");
-					return false;
-				}
-			}
-
-            System.out.println("\t(12)" + " isDiseaseGrade? " + isDiseaseGrade(code));
-			if (isDiseaseGrade(code)) {
-				System.out.println("\t(13)" + " isDiseaseGrade "  + isDiseaseGrade(code));
-				String label = name;
-				label = label.toLowerCase();
-				if (label.indexOf("grade") == -1) {
-					System.out.println("\t(14)" + " isSubtype? true (does not contains the word grade.)" );
-					return true;
-				}
-				System.out.println("\t(15)" + " isSubtype? false -- contains the word grade." );
-				return false;
-			}
-		} catch (Exception ex) {
-			ex.printStackTrace();
-		}
-
-		System.out.println("\t(16)" + " isSubtype: true");
-		return true;
-	}
-
-
-
-    public static void save_main_type_hierarchy() {
-        String today = StringUtils.getToday();
-        Utils.saveToFile("main_type_hierarchy_" + today + ".txt", main_type_hierarchy_data);
-    }
-
-    public void generate_main_type_label_code_file(HashSet main_type_set) {
-		Vector w = new Vector();
-		Iterator it = main_type_set.iterator();
-		while (it.hasNext()) {
-			String code = (String) it.next();
-			String label = hh.getLabel(code);
-			w.add(label + "|" + code);
-		}
-
-		w = new SortUtils().quickSort(w);
-		String today = StringUtils.getToday();
-		Utils.saveToFile("main_type_label_and_code_" + today + ".txt", w);
-	}
-
-
-    public static void generate_data_files(String serviceUrl, String named_graph) {
-		OWLSPARQLUtils owlSPARQLUtils = new OWLSPARQLUtils(serviceUrl, null, null);
-		System.out.println("getHierarchicalRelationships ...");
-		Vector v = owlSPARQLUtils.getHierarchicalRelationships(named_graph);
-		Vector parent_child_vec = new ParserUtils().toDelimited(v, 4, '|');
-		String today = StringUtils.getToday();
-		Utils.saveToFile("parent_child_" + today + ".txt", parent_child_vec);
-
-		System.out.println("getDiseaseIsStageSourceCodes ...");
-	    v = owlSPARQLUtils.getDiseaseIsStageSourceCodes(named_graph);
-	    Utils.saveToFile("DISEASE_IS_STAGE_" + today + ".txt", v);
-
-	    System.out.println("getDiseaseIsGradeSourceCodes ...");
-	    v = owlSPARQLUtils.getDiseaseIsGradeSourceCodes(named_graph);
-	    Utils.saveToFile("DISEASE_IS_GRADE_" + today + ".txt", v);
-	}
-
-
-	public void testIsSubtype(Vector codes) {
-		for (int i=0; i 0) {
-			//remove all path_to_category
-			Iterator it = hmap.keySet().iterator();
-			while (it.hasNext()) {
-				String key = (String) it.next();
-				Vector u = StringUtils.parseData(key);
-				String code_1 = (String) u.elementAt(1);
-				if (!category_vec.contains(code_1)) {
-					hmap2.put(key, (Path) hmap.get(key));
-				}
-			}
-		}
-		HashMap hmap3 = new HashMap();
-		//code_0 --> List
-		Iterator it = hmap2.keySet().iterator();
-		while (it.hasNext()) {
-			String key = (String) it.next();
-			Vector u = StringUtils.parseData(key);
-			String code_0 = (String) u.elementAt(0);
-			Path path = (Path) hmap2.get(key);
-			List path_list = new ArrayList();
-			if (hmap3.containsKey(code_0)) {
-				path_list = (List) hmap3.get(code_0);
-			}
-			path_list.add(path);
-			hmap3.put(code_0, path_list);
-		}
-        List paths_list = new ArrayList();
-		it = hmap3.keySet().iterator();
-		while (it.hasNext()) {
-			String code_0 = (String) it.next();
-			List path_list = (List) hmap3.get(code_0);
-            Paths paths = new Paths(path_list);
-            paths_list.add(paths);
-		}
-        return paths_list;
-	}
-
-
-	public static String dumpMainTypeHierarchyCodes() {
-		Vector codes = new Vector();
-		Vector w = (Vector) main_type_hierarchy_data.clone();
-		Vector v = new Vector();
-		for (int i=0; i 0) {
-				for (int i=0; i parent_child_vec = mthd.get_parent_child_vec(named_graph);
-		Vector v1 = mthd.getDiseaseIsStageSourceCodes(named_graph);
-		Vector v2 = mthd.getDiseaseIsGradeSourceCodes(named_graph);
-        HashMap stageConceptHashMap = mthd.generateStageConceptHashMap(v1);
-        HashMap gradeConceptHashMap = mthd.generateGradeConceptHashMap(v2);
-
-	    HashSet ctrp_biomarker_set = mthd.get_ctrp_biomarker_set();
-	    HashSet ctrp_reference_gene_set = mthd.get_ctrp_reference_gene_set();
-
-        MainTypeHierarchy mth = new MainTypeHierarchy(ncit_version, parent_child_vec, main_type_set, broad_category_vec,
-             stageConceptHashMap, gradeConceptHashMap, ctrp_biomarker_set, ctrp_reference_gene_set);
-        Vector mth_vec = mth.generate_main_type_hierarchy();
-        Utils.saveToFile("MainTypeHierarchy_" + StringUtils.getToday() + ".txt", mth_vec);
-
-        //AIDS-Related Primary Central Nervous System Lymphoma (C8284)
-        String code = "C8284";
-        System.out.println("get_ctrp_response: " + code);
-        Vector v = mth.findMainMenuAncestors(code);
-        StringUtils.dumpVector("findMainMenuAncestors", v);
-
-		String outputfile = mth.DISEASES_AND_DISORDERS_CODE + "_multiple.txt";
-		PrintWriter pw = null;
-		try {
-			pw = new PrintWriter(outputfile, "UTF-8");
-            Vector codes = mth.getTransitiveClosure(mth.DISEASES_AND_DISORDERS_CODE);
-            mth.searchMultiplePaths(pw, codes);
-		} catch (Exception ex) {
-
-		} finally {
-			try {
-				pw.close();
-				System.out.println("Output file " + outputfile + " generated.");
-			} catch (Exception ex) {
-				ex.printStackTrace();
-			}
-		}
-		System.out.println("Multiple cases: " + mth.multiple_count);
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-}
-
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/MainTypeHierarchyData.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/MainTypeHierarchyData.java
deleted file mode 100644
index 2fdea15da..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/MainTypeHierarchyData.java
+++ /dev/null
@@ -1,309 +0,0 @@
-package gov.nih.nci.evs.restapi.appl;
-
-import gov.nih.nci.evs.restapi.util.*;
-import gov.nih.nci.evs.restapi.bean.*;
-import gov.nih.nci.evs.restapi.common.*;
-
-import java.io.*;
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.*;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
-import java.util.*;
-import java.util.regex.*;
-
-public class MainTypeHierarchyData {
-	static String DISEASES_AND_DISORDERS_CODE = "C2991";
-	static String CTS_API_Disease_Broad_Category_Terminology_Code = "C138189";
-	static String CTS_API_Disease_Main_Type_Terminology_Code = "C138190";
-
-    static String CTRP_BIOMARKER_TERMINOLOGY_CODE = "C142799";
-    static String CTRP_REFERENCE_GENE_TERMINOLOGY_CODE = "C142801";
-
-	String[] disease_main_types = null;
-	String[] disease_broad_categories = null;
-
-	String[] ctrp_biomarkers = null;
-	String[] ctrp_reference_genes = null;
-
-	HashSet main_type_set = null;
-	HashSet ctrp_biomarker_set = null;
-	HashSet ctrp_reference_gene_set = null;
-
-	Vector broad_category_vec = null;
-	ArrayList broad_category_list = null;
-	OWLSPARQLUtils owlSPARQLUtils = null;
-	HierarchyHelper hh = null;
-
-	Vector parent_child_vec = null;
-	Vector disease_is_stage_code_vec = null;
-	Vector disease_is_grade_code_vec = null;
-	String serviceUrl = null;
-	String version = null;
-	String named_graph = null;
-
-    public MainTypeHierarchyData(String serviceUrl, String named_graph, String username, String password) {
-		owlSPARQLUtils = new OWLSPARQLUtils(serviceUrl, username, password);
-        this.named_graph = named_graph;
-        owlSPARQLUtils.set_named_graph(named_graph);
-		this.disease_main_types = owlSPARQLUtils.get_concept_in_subset_codes(named_graph, CTS_API_Disease_Main_Type_Terminology_Code);
-		System.out.println("disease_main_types: "+ disease_main_types.length);
-
-		this.disease_broad_categories = owlSPARQLUtils.get_concept_in_subset_codes(named_graph, CTS_API_Disease_Broad_Category_Terminology_Code);
-		System.out.println("disease_broad_categories: "+ disease_broad_categories.length);
-
-		this.ctrp_biomarkers = owlSPARQLUtils.get_concept_in_subset_codes(named_graph, CTRP_BIOMARKER_TERMINOLOGY_CODE);
-		System.out.println("ctrp_biomarkers: "+ ctrp_biomarkers.length);
-
-		this.ctrp_reference_genes = owlSPARQLUtils.get_concept_in_subset_codes(named_graph, CTRP_REFERENCE_GENE_TERMINOLOGY_CODE);
-		System.out.println("ctrp_reference_genes: "+ ctrp_reference_genes.length);
-
-        main_type_set = new HashSet();
-        for (int i=0; i();
-		broad_category_vec = new Vector();
-        for (int i=0; i get_broad_category_list() {
-		return this.broad_category_list;
-	}
-
-	public Vector get_broad_category_vec() {
-		return this.broad_category_vec;
-	}
-
-	public Vector getHierarchicalRelationships(String named_graph) {
-        String query = construct_get_hierarchical_relationships(named_graph);
-        Vector v = owlSPARQLUtils.executeQuery(query);
-        if (v == null) return null;
-        if (v.size() == 0) return v;
-        v = new ParserUtils().getResponseValues(v);
-        return new SortUtils().quickSort(v);
-	}
-
-	public Vector getHierarchicalRelationships(String named_graph, boolean raw_data) {
-		Vector v = owlSPARQLUtils.executeQuery(construct_get_hierarchical_relationships(named_graph));
-		if (raw_data) return v;
-        v = new ParserUtils().getResponseValues(v);
-        v = new SortUtils().quickSort(v);
-        return v;
-	}
-
-	public String construct_get_hierarchical_relationships(String named_graph) {
-        String prefixes = owlSPARQLUtils.getPrefixes();
-        StringBuffer buf = new StringBuffer();
-        buf.append(prefixes);
-        //buf.append("select distinct ?x_label ?x_code ?y_label ?y_code").append("\n");
-        //buf.append("select distinct ?x_code ?y_code").append("\n");
-        buf.append("select distinct ?y_label ?y_code ?x_label ?x_code ").append("\n");
-        buf.append("from <" + named_graph + ">").append("\n");
-        buf.append("where  { ").append("\n");
-        buf.append("    {").append("\n");
-        buf.append("                ?x a owl:Class .").append("\n");
-        buf.append("                ?x :NHC0 ?x_code .").append("\n");
-        buf.append("                ?x rdfs:label ?x_label .").append("\n");
-        buf.append("").append("\n");
-        buf.append("                ?y a owl:Class .").append("\n");
-        buf.append("                ?y :NHC0 ?y_code .").append("\n");
-        buf.append("                ?y rdfs:label ?y_label .").append("\n");
-        buf.append("                ").append("\n");
-        buf.append("                ?x (rdfs:subClassOf|owl:equivalentClass/owl:intersectionOf/rdf:rest*/rdf:first) ?y .  ").append("\n");
-        buf.append("    } UNION {").append("\n");
-        buf.append("    ").append("\n");
-        buf.append("                ?x a owl:Class .").append("\n");
-        buf.append("                ?x :NHC0 ?x_code .").append("\n");
-        buf.append("").append("\n");
-        buf.append("                ?x rdfs:label ?x_label .").append("\n");
-        buf.append("").append("\n");
-        buf.append("                ?y a owl:Class .").append("\n");
-        buf.append("                ?y :NHC0 ?y_code .").append("\n");
-        buf.append("                ?y rdfs:label ?y_label .").append("\n");
-        buf.append("                ").append("\n");
-        buf.append("                ?x (rdfs:subClassOf/owl:intersectionOf/rdf:rest*/rdf:first) ?y .  ").append("\n");
-        buf.append("    }").append("\n");
-        buf.append("}").append("\n");
-        buf.append("").append("\n");
-        return buf.toString();
-	}
-
-	public Vector generate_parent_child_vec(String named_graph) {
-		Vector parent_child_vec = null;
-        File f = new File("parent_child.txt");
-		if(f.exists() && !f.isDirectory()) {
-		    parent_child_vec = Utils.readFile("parent_child.txt");
-		} else {
-			Vector parent_child_data = owlSPARQLUtils.getHierarchicalRelationships(named_graph);
-			Utils.saveToFile("parent_child.txt", parent_child_vec);
-		}
-		return parent_child_vec;
-	}
-
-    public Vector generateDiseaseIsStageSourceCodes(String named_graph) {
-		Vector v1 = owlSPARQLUtils.getDiseaseIsStageSourceCodes(named_graph);
-		//v1 = new ParserUtils().getResponseValues(v1);
-		//v1 = new SortUtils().quickSort(v1);
-		return v1;
-	}
-
-    public Vector generateDiseaseIsGradeSourceCodes(String named_graph) {
-		Vector v2 = owlSPARQLUtils.getDiseaseIsGradeSourceCodes(named_graph);
-		//v2 = new ParserUtils().getResponseValues(v2);
-		//v2 = new SortUtils().quickSort(v2);
-		return v2;
-	}
-
-	public Vector get_parent_child_vec(String named_graph) {
-		if (this.named_graph.compareTo(named_graph) != 0) {
-			return generate_parent_child_vec(named_graph);
-		}
-		return parent_child_vec;
-	}
-
-	public Vector getDiseaseIsStageSourceCodes(String named_graph) {
-		if (this.named_graph.compareTo(named_graph) != 0) {
-			return getDiseaseIsStageSourceCodes(named_graph);
-		}
-		return disease_is_stage_code_vec;
-	}
-
-	public Vector getDiseaseIsGradeSourceCodes(String named_graph) {
-		if (this.named_graph.compareTo(named_graph) != 0) {
-			return getDiseaseIsGradeSourceCodes(named_graph);
-		}
-		return disease_is_grade_code_vec;
-	}
-
-    public HashMap generateStageConceptHashMap(Vector stageConcepts) {
-        HashMap stageConceptHashMap = new HashMap();
-        for (int i=0; i v = mthd.get_parent_child_vec(named_graph);
-		System.out.println("get_parent_child_vec: " + v.size());
-
-		Vector v1 = mthd.getDiseaseIsStageSourceCodes(named_graph);
-		StringUtils.dumpVector("getDiseaseIsStageSourceCodes", v1);
-
-		Vector v2 = mthd.getDiseaseIsGradeSourceCodes(named_graph);
-		StringUtils.dumpVector("getDiseaseIsGradeSourceCodes", v2);
-	}
-}
\ No newline at end of file
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/MainTypeHierarchyRunner.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/MainTypeHierarchyRunner.java
deleted file mode 100644
index 1b50ff170..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/MainTypeHierarchyRunner.java
+++ /dev/null
@@ -1,107 +0,0 @@
-package gov.nih.nci.evs.restapi.appl;
-
-import gov.nih.nci.evs.restapi.util.*;
-import gov.nih.nci.evs.restapi.bean.*;
-import gov.nih.nci.evs.restapi.common.*;
-
-import java.io.*;
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.*;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
-import java.util.*;
-import java.util.regex.*;
-
-public class MainTypeHierarchyRunner {
-
-	public static void countColumn(String filename, int column) {
-		int knt = 0;
-
-		Vector v = gov.nih.nci.evs.restapi.util.Utils.readFile(filename);
-		int total = v.size()-1;
-
-		String firstLine = (String) v.elementAt(0);
-		Vector u = gov.nih.nci.evs.restapi.util.StringUtils.parseData(firstLine, '\t');
-		String columnLabel = (String) u.elementAt(column);
-
-		for (int i=1; i parent_child_vec = mthd.get_parent_child_vec(named_graph);
-
-		System.out.println(	"parent_child_vec: " + parent_child_vec.size());
-
-		Vector v1 = mthd.getDiseaseIsStageSourceCodes(named_graph);
-		Vector v2 = mthd.getDiseaseIsGradeSourceCodes(named_graph);
-        HashMap stageConceptHashMap = mthd.generateStageConceptHashMap(v1);
-        HashMap gradeConceptHashMap = mthd.generateGradeConceptHashMap(v2);
-
-	    HashSet ctrp_biomarker_set = mthd.get_ctrp_biomarker_set();
-	    HashSet ctrp_reference_gene_set = mthd.get_ctrp_reference_gene_set();
-
-
-System.out.println("====================== Instantiating MainTypeHierarchy ======================");
-
-        MainTypeHierarchy mth = new MainTypeHierarchy(ncit_version, parent_child_vec, main_type_set, broad_category_vec,
-             stageConceptHashMap, gradeConceptHashMap, ctrp_biomarker_set, ctrp_reference_gene_set);
-System.out.println("main_type_set: " +  main_type_set.size());
-
-        Vector mth_vec = mth.generate_main_type_hierarchy();
-        Utils.saveToFile("MainTypeHierarchy_" + StringUtils.getToday() + ".txt", mth_vec);
-
-        String outputfile = mth.DISEASES_AND_DISORDERS_CODE + ".txt";
-        try {
-			Vector codes = mth.getTransitiveClosure(mth.DISEASES_AND_DISORDERS_CODE);
-			boolean flatFormat = true;
-			mth.run(codes, outputfile, flatFormat);
-		} catch (Exception ex) {
-			ex.printStackTrace();
-		}
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-
-}
-
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/MapsToReportWriter.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/MapsToReportWriter.java
deleted file mode 100644
index b04c85575..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/MapsToReportWriter.java
+++ /dev/null
@@ -1,452 +0,0 @@
-package gov.nih.nci.evs.restapi.appl;
-
-import gov.nih.nci.evs.restapi.util.*;
-import gov.nih.nci.evs.restapi.bean.*;
-import gov.nih.nci.evs.restapi.common.*;
-
-import java.io.*;
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.*;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
-import java.util.*;
-import java.util.regex.*;
-import org.apache.commons.codec.binary.Base64;
-import org.json.*;
-
-
-public class MapsToReportWriter {
-
-    public static String MAPS_TO_HEADING = "Subset Code|Subset Name|Concept Code|NCIt Preferred Term|Relationship To Target|Target Code|Target Term|Target Term Type|Target Terminology|Target Terminology Version";
-
-	public static String MAPS_TO = "Maps_To";
-	public static int NUMER_OF_FIELDS = 8;
-    JSONUtils jsonUtils = null;
-    HTTPUtils httpUtils = null;
-    String named_graph = null;
-    String prefixes = null;
-    String serviceUrl = null;
-    String named_graph_id = ":NHC0";
-    String BASE_URI = "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl";
-    String OWLFILE = "ThesaurusInferred_forTS.owl";
-
-    OWLSPARQLUtils owlSPARQLUtils = null;
-    MetadataUtils metadataUtils = null;
-    String namedGraph = null;
-
-	String username = null;
-	String password = null;
-
-    Vector raw_maps_to_data = null;
-    Vector mapsToEntries = null;
-    String ncit_version = null;
-    HashSet retired = null;
-
-    public MapsToReportWriter(String serviceUrl, String namedGraph, String username, String password) {
-		this.serviceUrl = serviceUrl;
-		this.namedGraph = namedGraph;
-		this.username = username;
-		this.password = password;
-
-		System.out.println("serviceUrl: " + serviceUrl);
-		System.out.println("namedGraph: " + namedGraph);
-
-		owlSPARQLUtils = new OWLSPARQLUtils(serviceUrl, username, password);
-		if (owlSPARQLUtils == null) {
-			System.out.println("WARNING: unable to instantiate owlSPARQLUtils???");
-		}
-
-        long ms = System.currentTimeMillis();
-        owlSPARQLUtils.set_named_graph(namedGraph);
-        Vector concept_status_vec = owlSPARQLUtils.getPropertyValues(namedGraph, "Concept_Status");
-        if (concept_status_vec == null) {
-			System.out.println("namedGraph: " + namedGraph);
-			System.out.println("WARNING: concept_status_vec == null???");
-		} else {
-			//concept_status_vec = new ParserUtils().getResponseValues(concept_status_vec);
-			retired = new HashSet();
-			for (int i=0; iNCIt_Properties_and_Relationships");
-			pw.println("Supported Properties");
-			pw.println("
Name");
-			pw.println("Code");
-			pw.println("");
-			Vector v = owlSPARQLUtils.getSupportedProperties(named_graph);
-			for (int i=0; i");
-			pw.println("
");
-
-			pw.println("Supported Roles");
-			pw.println("
Name");
-			pw.println("Code");
-			pw.println("");
-			v = owlSPARQLUtils.getSupportedRoles(named_graph);
-			for (int i=0; i");
-			pw.println("
");
-
-			pw.println("Supported Associations");
-			pw.println("
Name");
-			pw.println("Code");
-			pw.println("");
-			v = owlSPARQLUtils.getSupportedAssociations(named_graph);
-			for (int i=0; i");
-			pw.println("
");
-
-			pw.println("Supported Property Qualifiers");
-			pw.println("
Property Name");
-			pw.println("Property Code");
-			pw.println("Qualifier Name");
-			pw.println("QualifierCode");
-			pw.println("");
-			v = owlSPARQLUtils.getSupportedPropertyQualifiers(named_graph);
-			for (int i=0; i");
-			pw.println("
");
-
-			pw.println("
(Source: NCI Thesaurus, version " + this.version + ")");
-		} catch (Exception ex) {
-			ex.printStackTrace();
-		} finally {
-			try {
-				pw.close();
-			} catch (Exception ex) {
-				ex.printStackTrace();
-			}
-		}
-	}
-
-	public static void main(String[] args) {
-		String serviceUrl = args[0];
-		String named_graph = args[1];
-		String username = args[2];
-		String password = args[3];
-        MetadataGenerator metadataGenerator = new MetadataGenerator(serviceUrl, named_graph, username, password);
-        String filename = "metadata.txt";
-        metadataGenerator.generate(filename);
-        metadataGenerator.generateHTML(filename);
-	}
-}
\ No newline at end of file
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/NCItQA.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/NCItQA.java
deleted file mode 100644
index c943db70a..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/NCItQA.java
+++ /dev/null
@@ -1,906 +0,0 @@
-package gov.nih.nci.evs.restapi.appl;
-
-import gov.nih.nci.evs.restapi.model.*;
-import gov.nih.nci.evs.restapi.util.*;
-import gov.nih.nci.evs.restapi.bean.*;
-
-import java.io.*;
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.*;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
-import java.util.*;
-import java.util.regex.*;
-import java.nio.charset.Charset;
-import java.io.PrintWriter;
-
-public class NCItQA {
-    //ThesaurusInferred_forTS
-    public static String NCIT_OWL = "ThesaurusInferred_forTS.owl";
-    public static String SEMANTIC_TYPE_URL = "https://metamap.nlm.nih.gov/Docs/SemanticTypes_2018AB.txt";
-    public static String UMLS_SEMANTIC_TYPE_URL = "https://www.nlm.nih.gov/research/umls/META3_current_semantic_types.html";
-
-    public static String PROPERTY_FILE = "properties.txt";
-    public static String ROLE_FILE = "roles.txt";
-    public static String SEMANTIC_TYPE_FILE = "semantictypes.txt";
-    public static String FULLSYN_FILE = "FULLSYN.txt";
-
-    public static String OBJECT_PROPERTY_FILE = "objectProperties.txt";
-    public static String DEPRECATED_FILE = "deprecated.txt";
-    public static String ANNOTATION_PROPERTY_FILE = "annotationProperties.txt";
-
-    public static String SEMANTIC_TYPE_PROP_CODE = "P106";
-    public static String PREFERRED_NAME_PROP_CODE = "P108";
-    public static String CONCEPT_STATUS_PROP_CODE = "P310";
-
-
-
-    public Vector semantic_types = null;
-    Vector objectProperties = null;
-    Vector association_vec = null;
-
-    Vector deprecated_vec = null;
-    Vector property_vec = null;
-    Vector role_vec = null;
-    private PrintWriter pw = null;
-
-    HashMap code2LabelMap = null;//getCode2LabelMap
-    HashMap roleCode2LabelMap = null;
-
-    public static String AXIOM_FILE = "axioms.txt";
-
-    public HashMap concept_status_map = null;
-    public String owlfile = null;
-    OWLScanner owlScanner = null;
-    List full_syn_list = null;
-    List active_full_syn_list = null;
-
-    Vector annotationProperties = null;
-    public boolean saveOption = false;
-
-    public NCItQA() {
-
-	}
-
-	public NCItQA(String owlfile) {
-		this.owlfile = owlfile;
-		//initialize();
-	}
-
-	public void setSaveOption(boolean saveOption) {
-		this.saveOption = saveOption;
-	}
-
-	public void initialize() {
-		if (owlfile == null) {
-			if (FileUtils.fileExists(NCIT_OWL)) {
-				System.out.println(NCIT_OWL + " exists.");
-			} else {
-				System.out.println(NCIT_OWL + " does not exist.");
-				NCItDownload.download();
-				Vector files = NCItDownload.listFilesInDirectory();
-				Utils.dumpVector("listFilesInDirectory", files);
-			}
-			this.owlfile = NCIT_OWL;
-	    }
-
-		owlScanner = new OWLScanner(NCIT_OWL);
-		if (FileUtils.fileExists(FULLSYN_FILE)) {
-			System.out.println(FULLSYN_FILE + " exists.");
-			Vector w = Utils.readFile(FULLSYN_FILE);
-            full_syn_list = new AxiomUtils().getSynonyms(w);
-		} else {
-		    full_syn_list = extractFULLSyns();
-		}
-
-		semantic_types = owlScanner.extractSemanticTypes(owlScanner.get_owl_vec());
-
-		property_vec = null;
-		if (!FileUtils.fileExists(PROPERTY_FILE)) {
-			property_vec = owlScanner.extractProperties(owlScanner.get_owl_vec());
-			if (saveOption) Utils.saveToFile(PROPERTY_FILE, property_vec);
-		} else {
-			property_vec = Utils.readFile(PROPERTY_FILE);
-		}
-
-		Vector w = null;
-		if (!FileUtils.fileExists(ROLE_FILE)) {
-			role_vec = owlScanner.extractOWLRestrictions(owlScanner.get_owl_vec());
-			if (saveOption)  Utils.saveToFile(ROLE_FILE, role_vec);
-		} else {
-			role_vec = Utils.readFile(ROLE_FILE);
-		}
-
-		if (!FileUtils.fileExists(OBJECT_PROPERTY_FILE)) {
-			objectProperties = owlScanner.extractObjectProperties(owlScanner.get_owl_vec());
-			if (saveOption)  Utils.saveToFile(OBJECT_PROPERTY_FILE, objectProperties);
-		} else {
-			objectProperties = Utils.readFile(OBJECT_PROPERTY_FILE);
-		}
-
-		roleCode2LabelMap = new HashMap();
-		for (int i=0; i 0) {
-					pw.println("WARNING: multiple Preferred names detected for " + code);
-					error_count++;
-				}
-				v.add(name);
-				pt_map.put(code, v);
-			}
-		}
-        String methodName = "QA_PreferredNames";
-	    dump_QA_error_counts(pw, methodName, error_count);
-	}
-
-	public void QA_NCIPT(PrintWriter pw) {
-		pw.println("\n5.	Verify exactly one NCI PT per concept.");
-		int num_errors = 0;
-		//System.out.println("active_full_syn_list: " + active_full_syn_list.size());
-		HashMap hmap = new HashMap();
-		for (int i=0; i 0) {
-				key = syn.getTermName() + "|" + syn.getTermGroup() + "|" + syn.getTermSource() + "|" + syn.getCode();
-				String sourceCode = syn.getSourceCode();
-				if (sourceCode == null) {
-					sourceCode = "null";
-				}
-				key = key + "|" + sourceCode;
-				Vector v = new Vector();
-				if (hmap.containsKey(key)) {
-
-pw.println("JSON: " + syn.toJson());
-
-System.out.println("KEY: " + key);
-pw.println("KEY: " + key);
-
-					v = (Vector) hmap.get(key);
-					num_errors++;
-					for (int k=0; k 0) {
-				key = syn.getTermName() + "|" + syn.getTermGroup() + "|" + syn.getTermSource() + "|" + syn.getSourceCode();
-				String subSourceName = syn.getSubSourceName();
-				if (subSourceName == null) {
-					subSourceName = "null";
-				}
-				key = key + "|" + subSourceName;
-
-				Vector v = new Vector();
-				if (hmap.containsKey(key)) {
-					//System.out.println("\nWARNING: Duplicated Atoms in multipe concepts identified.");
-					v = (Vector) hmap.get(key);
-					for (int k=0; k") != -1) {
-				break;
-			}
-
-			if (t.indexOf("") != -1) {
-				switch_off = true;
-			}
-			if (t.indexOf("") != -1) {
-				switch_off = false;
-			}
-
-			if (t.indexOf("")) {
-				int n = t.lastIndexOf("#");
-				t = t.substring(n, t.length());
-				n = t.lastIndexOf(" ");
-				classId = t.substring(1, n);
-				if (istart0) {
-					istart = true;
-				}
-			}
-			if (istart) {
-				t = t.trim();
-				if (t.startsWith("<") && t.indexOf("rdf:resource=") != -1 && t.indexOf("owl:") == -1 && t.indexOf("rdfs:subClassOf") == -1) {
-					int n = t.indexOf(">");
-                    if (n != -1) {
-						String s = t.substring(1, n-1);
-						if (!switch_off) {
-							w.add(classId + "|" + new OWLScanner().parseProperty(t));
-					    }
-					}
-				} else if (t.startsWith("<") && t.indexOf("rdf:resource=") == -1 && t.indexOf("owl:") == -1 && t.indexOf("rdfs:subClassOf") == -1
-				    && t.indexOf("rdf:Description") == -1 && t.indexOf("rdfs:subClassOf") == -1) {
-					int n = t.indexOf(">");
-                    if (n != -1) {
-						String s = t.substring(1, n-1);
-						if (!switch_off) {
-						    w.add(classId + "|" + new OWLScanner().parseProperty(t));
-						}
-					}
-				}
-		    }
-		}
-		return w;
-	}
-
-    public void QA_SemanticTypes(PrintWriter pw) {
-		pw.println("\n4.	Invalid STYs.");
-        int number_of_errors = 0;
-        for (int i=0; i " +
-		       targetLabel + " (" + targetCode + ")";
-	}
-
-    public void QA_conflicting_RELAs(PrintWriter pw) {
-		pw.println("\n15.	Conflicting RELAs between same concept pairs.");
-
-		int num_errors = 0;
-		HashSet hset = new HashSet();
-		for (int i=0; i 0) {
-			owlfile = (String) args[0];
-		}
-		if (args.length > 1) {
-			String saveOptionStr = (String) args[1];
-			if (saveOptionStr.compareTo("true") == 0) {
-				saveOption = true;
-			}
-		}
-		NCItQA ncitQA = new NCItQA(owlfile);
-		ncitQA.setSaveOption(saveOption);
-		ncitQA.initialize();
-        ncitQA.runQA();
-	}
-}
-
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/NCItWikiUtils.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/NCItWikiUtils.java
deleted file mode 100644
index 5349bb1aa..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/NCItWikiUtils.java
+++ /dev/null
@@ -1,325 +0,0 @@
-package gov.nih.nci.evs.restapi.appl;
-import gov.nih.nci.evs.restapi.util.*;
-import gov.nih.nci.evs.restapi.config.*;
-
-import java.io.*;
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.*;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
-import java.util.*;
-import java.util.regex.*;
-import org.apache.commons.codec.binary.Base64;
-import java.nio.charset.Charset;
-
-import java.time.Duration;
-/**
- * 
- * Copyright 2020 MSC. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
-6 * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or MSC
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      MSC, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@nih.gov
- *
- */
-
-
-public class NCItWikiUtils {
-	String restURL = null;
-	String namedGraph = null;
-	String username = null;
-	String password = null;
-	MetadataUtils metadataUtils = null;
-	OWLSPARQLUtils owlSPARQLUtils = null;
-	HashSet retired_concepts = new HashSet();
-
-    public NCItWikiUtils(String restURL, String namedGraph, String username, String password) {
-		this.restURL = restURL;
-		this.namedGraph = namedGraph;
-		this.username = username;
-		this.password = password;
-
-System.out.println(	"restURL: " + restURL);
-System.out.println(	"namedGraph: " + namedGraph);
-System.out.println(	"username: " + username);
-System.out.println(	"password: " + password);
-
-		metadataUtils = new MetadataUtils(restURL, username, password);
-		owlSPARQLUtils = new OWLSPARQLUtils(restURL, username, password);
-		owlSPARQLUtils.set_named_graph(namedGraph);
-
-		String ncit_version = getVersion();
-		System.out.println(ncit_version);
-
-	    String property_name = "Concept_Status";
-	    String property_value = "Retired_Concept";
-		Vector w = findConceptsWithPropertyMatching(namedGraph, property_name, property_value);
-		for (int i=0; i").append("\n");
-		buf.append("where  { ").append("\n");
-		buf.append("            	?x a owl:Class .").append("\n");
-		buf.append("            	?x :NHC0 ?x_code .").append("\n");
-		buf.append("            	?x rdfs:label ?x_label .").append("\n");
-		buf.append("").append("\n");
-		buf.append("                ?p2 a owl:AnnotationProperty .").append("\n");
-		buf.append(" ").append("\n");
-		buf.append("                ?a1 a owl:Axiom .").append("\n");
-		buf.append("                ?a1 owl:annotatedSource ?x .").append("\n");
-		buf.append("                ?a1 owl:annotatedProperty ?p2 .").append("\n");
-		buf.append("                ?p2 :NHC0 \"P90\"^^xsd:string .").append("\n");
-		buf.append("                ?a1 owl:annotatedTarget ?a_target .").append("\n");
-		buf.append("").append("\n");
-		buf.append("                ?q1 :NHC0 \"P384\"^^xsd:string .").append("\n");
-		buf.append("                ?q1 rdfs:label ?q1_label .").append("\n");
-		buf.append("                ?a1 ?q1 ?q1_value .").append("\n");
-		buf.append("").append("\n");
-		buf.append("                ?q2 :NHC0 \"P383\"^^xsd:string .  ").append("\n");
-		buf.append("                ?q2 rdfs:label ?q2_label . ").append("\n");
-		buf.append("                ?a1 ?q2 ?q2_value .").append("\n");
-		buf.append("").append("\n");
-		buf.append("}").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		return buf.toString();
-	}
-
-	public Vector getAxiomData(String named_graph) {
-		String query = cnstruct_get_axiom_data(named_graph);
-		Vector v = owlSPARQLUtils.executeQuery(query);
-		if (v == null) return null;
-		if (v.size() == 0) return v;
-		//v = new ParserUtils().getResponseValues(v);
-		return new SortUtils().quickSort(v);
-	}
-
-
-	public String construct_get_contributing_source(String named_graph) {
-		String prefixes = owlSPARQLUtils.getPrefixes();
-		StringBuffer buf = new StringBuffer();
-		buf.append(prefixes);
-		buf.append("select distinct ?x1_label ?x1_code ?p_label ?p_value ").append("\n");
-		buf.append("from <" + named_graph + ">").append("\n");
-		buf.append("where  { ").append("\n");
-		buf.append("            	?x1 a owl:Class .").append("\n");
-		buf.append("            	?x1 :NHC0 ?x1_code .").append("\n");
-		buf.append("             	?x1 rdfs:label ?x1_label .").append("\n");
-		buf.append(" ").append("\n");
-		buf.append("                ?x1 ?p ?p_value .").append("\n");
-		buf.append("                ?p :NHC0 ?p_code .").append("\n");
-		buf.append("                ?p :NHC0 \"P322\"^^xsd:string .").append("\n");
-		buf.append("                ?p rdfs:label ?p_label .").append("\n");
-		buf.append("}").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		return buf.toString();
-	}
-
-
-	public Vector getContributingSource(String named_graph) {
-
-		System.out.println("************************ getContributingSource ");
-		String query = construct_get_contributing_source(named_graph);
-		Vector v = owlSPARQLUtils.executeQuery(query);
-
-		if (v == null) {
-			//System.out.println("************************ v=null??? ");
-			return null;
-		}
-		//System.out.println("************************ v: " + v.size());
-		//Utils.dumpVector("getContributingSource", v);
-
-		if (v.size() == 0) return v;
-		//????????????????????????????????????????????????????????????????
-		//v = new ParserUtils().getResponseValues(v);
-
-		Utils.saveToFile("debug_cs.txt", v);
-
-		return new SortUtils().quickSort(v);
-	}
-
-	public String getVersion() {
-		Vector v = owlSPARQLUtils.get_ontology_info(namedGraph);
-		Utils.dumpVector("get_ncit_version", v);
-		String line = (String) v.elementAt(0);
-		Vector u = StringUtils.parseData(line, '|');
-		String ncit_version = (String) u.elementAt(0);
-		System.out.println(ncit_version);
-		return ncit_version;
-	}
-
-//Activity|C43431|Contributing_Source|BRIDG
-	public Vector removedRetired(Vector w) {
-		Vector v = new Vector();
-		for (int i=0; i
- * Copyright 2020, MSC. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@nih.gov
- *
- */
-
-
-public class OWLDiffUtils {
-    //OWLSPARQLUtils owlSPARQLUtils = null;
-    //String serviceUrl = null;
-    //String namedGraph = null;
-    Vector properties = null;
-    Vector qualifiers = null;
-    HashMap qualifierMap = null;
-    HashMap propertyMap = null;
-    Vector propertyCountVec = null;
-    String owlfile = null;
-    Vector owl_vec = null;
-    static PrintWriter pw = null;
-
-    public OWLDiffUtils() {
-
-    }
-
-    public static boolean fileExists(String filename) {
-		File file = new File(filename);
-		return file.exists();
-	}
-
-	public static void dumpHashSet(HashSet hset) {
-		Iterator it = hset.iterator();
-		while (it.hasNext()) {
-			String t = (String) it.next();
-			System.out.println(t);
-		}
-	}
-
-	public static Vector hashSet2Vector(HashSet hset) {
-		Vector w = new Vector();
-		Iterator it = hset.iterator();
-		while (it.hasNext()) {
-			String t = (String) it.next();
-			w.add(t);
-		}
-		return w;
-	}
-
-    public static void compute(String owlfile1, String owlfile2) {
-        long ms = System.currentTimeMillis();
-        //String owlfile = "ThesaurusInferred_20.04d.owl";
-        System.out.println("owlfile1: " + owlfile1);
-        OWLScanner owlScanner = new OWLScanner(owlfile1);
-        Vector w1 = owlScanner.getAllOWLClassHashCode();
-        String hashfile_1 = "hash_" + owlfile1;
-        Utils.saveToFile(hashfile_1, w1);
-        System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-        owlScanner.clear();
-
-        System.out.println("owlfile2: " + owlfile2);
-        ms = System.currentTimeMillis();
-        owlScanner = new OWLScanner(owlfile2);
-        Vector w2 = owlScanner.getAllOWLClassHashCode();
-        String hashfile_2 = "hash_" + owlfile2;
-        Utils.saveToFile(hashfile_2, w2);
-        System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-        owlScanner.clear();
-
-        //w2 versus w1
-        ms = System.currentTimeMillis();
-        w2.removeAll(w1);
-        w1.clear();
-        String hash_2_rm_1 = "hash_2_rm_1.txt";
-        Utils.saveToFile(hash_2_rm_1, w2);
-        System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-
-        w1 = Utils.readFile(hashfile_1);
-        w2 = Utils.readFile(hashfile_2);
-        w1.removeAll(w2);
-        w2.clear();
-        String hash_1_rm_2 = "hash_1_rm_2.txt";
-        Utils.saveToFile(hash_1_rm_2, w1);
-        System.out.println("RM Total run time (ms): " + (System.currentTimeMillis() - ms));
-
-        ms = System.currentTimeMillis();
-        Vector hash_2_rm_1_vec = Utils.readFile(hash_2_rm_1);
-        System.out.println("hash_2_rm_1_vec: " + hash_2_rm_1_vec.size());
-        Vector codes = new Vector();
-        for (int i=0; i
- * Copyright 2020, MSC. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@nih.gov
- *
- */
-
-
-public class OWLDiffUtilsRunner {
-
-    public OWLDiffUtilsRunner() {
-
-    }
-
-    public static void clear(String outfile1, String outfile2) {
-		Utils.deleteFile("hash_1_rm_2.txt");
-		Utils.deleteFile("hash_2_rm_1.txt");
-		Utils.deleteFile("hash_" + outfile1);
-		Utils.deleteFile("hash_" + outfile2);
-		Utils.deleteFile("partial_" + outfile1);
-		Utils.deleteFile("partial_" + outfile2);
-	}
-
-    public static void main(String[] args) {
-		long ms = System.currentTimeMillis();
-		/*
-		String version1 = args[0];
-		String owlfile1 = FTPUtils.downloadNCItInferredOWL(version1);
-		System.out.println("owlfile1: " + owlfile1);
-
-		String version2 = args[1];
-		String owlfile2 = FTPUtils.downloadNCItInferredOWL(version2);
-		System.out.println("owlfile2: " + owlfile2);
-		*/
-		String owlfile1 = args[0];
-		String owlfile2 = args[1];
-
-		System.out.println(owlfile1);
-		System.out.println(owlfile2);
-
-		String diff_file = OWLDiffUtils.run(owlfile1, owlfile2);
-		System.out.println("Total diff run time (ms): " + (System.currentTimeMillis() - ms));
-
-		HistoryUtils hist = new HistoryUtils(owlfile2, diff_file);
-		hist.run();
-
-        clear(owlfile1, owlfile2);
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-}
-
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/OWLDisjointWithAnalyzer.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/OWLDisjointWithAnalyzer.java
deleted file mode 100644
index fe882021d..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/OWLDisjointWithAnalyzer.java
+++ /dev/null
@@ -1,164 +0,0 @@
-package gov.nih.nci.evs.restapi.appl;
-
-import gov.nih.nci.evs.restapi.util.*;
-
-import java.io.*;
-import java.util.*;
-
-
-/**
- * 
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class OWLDisjointWithAnalyzer {
-
-    HierarchyHelper hh = null;
-    static int CODE_ONLY = 1;
-    static int LABEL_AND_CODE = 2;
-    static int LABEL_WITH_CODE_IN_BRACKET = 3;
-
-
-    public OWLDisjointWithAnalyzer() {
-	}
-
-    public OWLDisjointWithAnalyzer(Vector v) {
-        hh = new HierarchyHelper(v);
-	}
-
-	public HierarchyHelper getHierarchyHelper() {
-		return this.hh;
-	}
-
-	public Vector getRoots(int format) {
-		Vector roots = hh.getRoots();
-		Vector w = new Vector();
-		for (int i=0; i [" + "owl:disjointWith" + "} --> " +  label_2 + " (" + c2 + ")");
-		}
-		output_vec = new SortUtils().quickSort(output_vec);
-		branch_vec.addAll(output_vec);
-		return branch_vec;
-	}
-
-    public static void main(String[] args) {
-		String owlfile = "20.05d_disjoint-test-export_200601.owl";
-        Vector output_vec = test(owlfile);
-        Utils.saveToFile("output_vec_1.txt", output_vec);
-
- 		owlfile = "ThesaurusInferred_forTS.owl";
-        output_vec = test(owlfile);
-        Utils.saveToFile("output_vec_2.txt", output_vec);
-
-    }
-
-}
-
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/PostOWLScrubber.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/PostOWLScrubber.java
deleted file mode 100644
index 703b090d1..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/PostOWLScrubber.java
+++ /dev/null
@@ -1,558 +0,0 @@
-package gov.nih.nci.evs.restapi.appl;
-
-import java.io.*;
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.*;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
-import java.util.*;
-import java.text.*;
-
-/**
- * 
- * Copyright 2020 MSC. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or MSC
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      MSC, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@nih.gov
- *
- */
-
-
-public class PostOWLScrubber {
-    String owlfile = null;
-    Vector owl_vec = null;
-    Vector disjointwith_classes = null;
-    HashMap subclassOfHashMap = null;
-
-    static String NCIT_NAMESPACE_TARGET = "";
-		boolean istart = false;
-		for (int i=0; i";
-	}
-
-    public boolean hasOwlDisjointWith(Vector v) {
-		for (int i=0; i 0) {
-					if (hasOwlDisjointWith(v)) {
-						class_line = getClassLine(v);
-						String code = getCode(class_line);
-						w.add(code);
-					}
-				}
-				v = new Vector();
-				istart = true;
-			} else if (istart && line.indexOf(OWL_CLS_TARGET) != -1 && line.indexOf("enum") == -1) {
-                istart = false;
-			}
-			if (istart) {
-				v.add(line);
-			}
-			i++;
-		}
-		return w;
-	}
-
-    public String getCode(String line) {
-		int n = line.lastIndexOf("#");
-		String t = line.substring(n+1, line.length());
-		n = t.indexOf("\"");
-		t = t.substring(0, n);
-		return t;
-	}
-
-	public void getModifiedClasses(PrintWriter pw) {
-        for (int i=0; i 0) {
-					if (hasOwlDisjointWith(v)) {
-						class_line = getClassLine(v);
-						String code = getCode(class_line);
-						v = removeOwlDisjointWith(v);
-						if (!subclassOfHashMap.containsKey(code)) {
-							v = addOwlDisjointWith(v, code);
-						}
-						for (int k=0; k 0) {
-			if (hasOwlDisjointWith(v)) {
-				class_line = getClassLine(v);
-				String code = getCode(class_line);
-				v = removeOwlDisjointWith(v);
-				if (!subclassOfHashMap.containsKey(code)) {
-					v = addOwlDisjointWith(v, code);
-				}
-				for (int k=0; k");
-    }
-
-
-    public static void main(String[] args) {
-		long ms = System.currentTimeMillis();
-        String owlfile = args[0];
-		PostOWLScrubber postOWLScrubber = new PostOWLScrubber(owlfile);
-		int n = owlfile.lastIndexOf(".");
-		String outputfile = owlfile.substring(0, n) + "_" + getToday() + ".owl";
-		postOWLScrubber.run(outputfile);
-		String changefile = "owlDisjointWith_mod_" + getToday() + ".txt";
-		postOWLScrubber.getModifiedClasses(changefile);
-
-
-/*
-	(1) Abnormal Cell (C12913)
-	(2) Activity (C43431)
-	(3) Anatomic Structure, System, or Substance (C12219)
-	(4) Biochemical Pathway (C20633)
-	(5) Biological Process (C17828)
-	(6) Chemotherapy Regimen or Agent Combination (C12218)
-	(7) Conceptual Entity (C20181)
-	(8) Diagnostic or Prognostic Factor (C20047)
-	(9) Diagnostic, Therapeutic, or Research Equipment (C19238)
-	(10) Disease, Disorder or Finding (C7057)
-	(11) Drug, Food, Chemical or Biomedical Material (C1908)
-	(12) Experimental Organism Anatomical Concept (C22188)
-	(13) Experimental Organism Diagnosis (C22187)
-	(14) Gene (C16612)
-	(15) Gene Product (C26548)
-	(16) Manufactured Object (C97325)
-	(17) Molecular Abnormality (C3910)
-	(18) Organism (C14250)
-	(19) Property or Attribute (C20189)
-	(20) Retired Concept (C28428)
-
-*/
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-    }
-}
-
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/PropertyQAProcessor.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/PropertyQAProcessor.java
deleted file mode 100644
index 6f7139f04..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/PropertyQAProcessor.java
+++ /dev/null
@@ -1,339 +0,0 @@
-package gov.nih.nci.evs.restapi.appl;
-
-import gov.nih.nci.evs.restapi.util.*;
-import gov.nih.nci.evs.restapi.bean.*;
-import gov.nih.nci.evs.restapi.common.*;
-
-import java.io.*;
-//import java.math.*;
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.*;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
-import java.util.*;
-import java.util.regex.*;
-import org.apache.commons.codec.binary.Base64;
-import org.json.*;
-
-/**
- * 
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class PropertyQAProcessor {
-    String named_graph = null;
-    String serviceUrl = null;
-
-    private OWLSPARQLUtils owlSPARQLUtils = null;
-	private String username = null;
-	private String password = null;
-	private String namedGraph = null;
-	private static String ncit_unii_txt_file = "ncit_unii.txt";
-    private HashMap code2LabelMap = null;
-    private HashMap code2PropertyMap = null;
-    private String property_file = null;
-    private HashMap ncit_code2PropertyMap = null;
-    private Vector supported_properties = null;
-    private HashMap supported_properties_hmap = null;
-    private String propertyName = null;
-
-	public PropertyQAProcessor() {
-
-	}
-
-
-	public PropertyQAProcessor(String serviceUrl, String namedGraph) {
-		this.serviceUrl = serviceUrl;
-		this.namedGraph = namedGraph;
-		System.out.println("serviceUrl: " + this.serviceUrl);
-		System.out.println("namedGraph: " + this.namedGraph);
-		owlSPARQLUtils = new OWLSPARQLUtils(serviceUrl, null, null);
-		owlSPARQLUtils.set_named_graph(this.namedGraph);
-		new MetadataUtils(serviceUrl).dumpNameVersion2NamedGraphMap();
-		supported_properties = owlSPARQLUtils.getSupportedProperties(this.namedGraph);
-		supported_properties_hmap = gov.nih.nci.evs.restapi.util.StringUtils.constructHashMap(supported_properties, 0, 1, '|');
-    }
-
-    private void initialize(String propertyName) {
-        if (!supported_properties_hmap.containsKey(propertyName)) {
-			System.out.println("Unidentifiable property name: " + propertyName + ". Program aborts.");
-			System.exit(1);
-		}
-		this.propertyName = propertyName;
-		property_file = propertyName + ".txt";
-		code2LabelMap = new HashMap();
-        code2PropertyMap = new HashMap();
-
-        // single valued
-        Vector v = null;
-        if (!new File(property_file).exists()) {
-			System.out.println(property_file + " does not exist.");
-			Vector w = owlSPARQLUtils.findConceptsWithProperty(this.namedGraph, propertyName);
-			Utils.saveToFile(property_file, w);
-		}
-		v = Utils.readFile(property_file);
-        System.out.println("Number of records in " + property_file + ": " + v.size());
-        code2LabelMap = gov.nih.nci.evs.restapi.util.StringUtils.constructHashMap(v, 1, 0, '|');
-        // use multiple valued
-        ncit_code2PropertyMap = gov.nih.nci.evs.restapi.util.StringUtils.constructMultiValuedHashMap(v, 1, 3, '|');
-
-        Iterator it = ncit_code2PropertyMap.keySet().iterator();
-        while (it.hasNext()) {
-			String key = (String) it.next();
-			if (!code2LabelMap.containsKey(key)) {
-				String value = (String) ncit_code2PropertyMap.get(key);
-				code2LabelMap.put(key, value);
-			}
-		}
-
-        System.out.println("Number of records in " + property_file + ": " + v.size());
-    }
-
-	public static int countDelimiters(String line, char delim) {
-		int knt = 0;
-		for (int i=0; i 0 && w == null) {
-				if (values != null && values.length() > 0) {
-					for (int k=0; k
- * Copyright 2020, MSC. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIT
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIT, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- *          Modification history Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class SRSDownload {
-
-	public static void download(String uri, String outputfile) {
-		try (BufferedInputStream in = new BufferedInputStream(new URL(uri).openStream());
-		  FileOutputStream fileOutputStream = new FileOutputStream(outputfile)) {
-			byte dataBuffer[] = new byte[1024];
-			int bytesRead;
-			while ((bytesRead = in.read(dataBuffer, 0, 1024)) != -1) {
-				fileOutputStream.write(dataBuffer, 0, bytesRead);
-			}
-		} catch (IOException e) {
-			// handle exception
-		}
-	}
-
-    private static void unzip(String zipFilePath, String destDir) {
-        File dir = new File(destDir);
-        // create output directory if it doesn't exist
-        if(!dir.exists()) dir.mkdirs();
-        FileInputStream fis;
-        //buffer for read and write data to file
-        byte[] buffer = new byte[1024];
-        try {
-            fis = new FileInputStream(zipFilePath);
-            ZipInputStream zis = new ZipInputStream(fis);
-            ZipEntry ze = zis.getNextEntry();
-            while(ze != null){
-                String fileName = ze.getName();
-                File newFile = new File(destDir + File.separator + fileName);
-                System.out.println("Unzipping to "+newFile.getAbsolutePath());
-                //create directories for sub directories in zip
-                new File(newFile.getParent()).mkdirs();
-                FileOutputStream fos = new FileOutputStream(newFile);
-                int len;
-                while ((len = zis.read(buffer)) > 0) {
-                fos.write(buffer, 0, len);
-                }
-                fos.close();
-                //close this ZipEntry
-                zis.closeEntry();
-                ze = zis.getNextEntry();
-            }
-            //close last ZipEntry
-            zis.closeEntry();
-            zis.close();
-            fis.close();
-        } catch (IOException e) {
-            e.printStackTrace();
-        }
-
-    }
-
-    public static Vector listUNIITextFilesInDirectory() {
-		String dirName = null;
-		return listUNIITextFilesInDirectory(dirName);
-	}
-
-
-    public static Vector listUNIITextFilesInDirectory(String dirName) {
-		Vector v = new Vector();
-		if (dirName == null) {
-			dirName = System.getProperty("user.dir");;
-		}
-        File f = new File(dirName);
-        String[] pathnames = f.list();
-        for (String pathname : pathnames) {
-			if (pathname.indexOf("UNII") != -1) {
-				if (pathname.endsWith(".txt") && pathname.indexOf("READ ME") == -1) {
-					System.out.println(pathname);
-					v.add(pathname);
-				}
-			}
-        }
-        return v;
-	}
-
-    public static Vector run(String SRS_URI) {
-		String currentWorkingDirectory = System.getProperty("user.dir");
-        String UNII_DATA_FILE = "UNII_Data.zip";
-        download(SRS_URI + UNII_DATA_FILE, UNII_DATA_FILE);
-
-        String UNIIS_FILE = "UNIIs.zip";
-        download(SRS_URI + UNIIS_FILE, UNIIS_FILE);
-
-        String zipFilePath = currentWorkingDirectory + "/" + UNII_DATA_FILE;
-        unzip(zipFilePath, currentWorkingDirectory);
-
-        zipFilePath = currentWorkingDirectory + "/" + UNIIS_FILE;
-        unzip(zipFilePath, currentWorkingDirectory);
-
-        Vector files = listUNIITextFilesInDirectory();
-        return files;
-	}
-
-    public static void main(String[] args) {
-        String SRS_URI = "https://fdasis.nlm.nih.gov/srs/download/srs/";
-        Vector files = run(SRS_URI);
-        Utils.dumpVector("listUNIITextFilesInDirectory", files);
-	}
-
-}
-
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/SemanticTypeQA.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/SemanticTypeQA.java
deleted file mode 100644
index b71c42057..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/SemanticTypeQA.java
+++ /dev/null
@@ -1,214 +0,0 @@
-package gov.nih.nci.evs.restapi.appl;
-import gov.nih.nci.evs.restapi.util.*;
-
-import gov.nih.nci.evs.restapi.bean.*;
-import java.io.*;
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.*;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
-import java.util.*;
-import java.text.*;
-
-/**
- * 
- * Copyright 2020 MSC. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or MSC
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      MSC, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@nih.gov
- *
- */
-
-
-public class SemanticTypeQA {
-    String owlfile = null;
-    OWLScanner scanner = null;
-    static String DISEASE_ROOT = "C2991"; //Disease or Disorder (Code C2991)
-    static String FINDING_ROOT = "C3367";
-    static String SEMANTIC_TYPE_PROP_CODE = "P106";
-
-    HierarchyHelper hh = null;
-    Vector parent_child_vec = null;
-    Vector semantic_type_vec = null;
-    HashMap semantic_type_hashmap = null;
-    Vector roots = null;
-
-    public SemanticTypeQA(String owlfile) {
-		long ms = System.currentTimeMillis();
-		this.owlfile = owlfile;
-		scanner = new OWLScanner(owlfile);
-		parent_child_vec = scanner.extractHierarchicalRelationships();
-
-		//C100003|P106|Therapeutic or Preventive Procedure
-		semantic_type_vec  = scanner.extractProperties(scanner.get_owl_vec(), SEMANTIC_TYPE_PROP_CODE);
-		semantic_type_hashmap = new HashMap();
-		for (int i=0; i
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-public class ServerMonitor {
-    public static String SERVER_STATUS = "server_status.txt";
-
-	public static void query(String version) throws Exception {
-		query("NCI_Thesaurus", version);
-	}
-
-	public static void query(String codingScheme, String version) throws Exception {
-		if (version == null) {
-			version = DateUtils.getNCItMonthlyVersion();
-		}
-		Vector v = Utils.readFile(SERVER_STATUS);
-		Vector w = new Vector();
-        String serviceUrl = null;
-		for (int i=0; i 0) {
-			System.out.println(version + " available at");
-			for (int i=0; i " + value);
-					w.add(key + "|" + key2 + "|" + value);
-				}
-			}
-		}
-		Utils.saveToFile("stardog_server_status_" + StringUtils.getToday() + ".txt", w);
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-
-}
-
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/TransitiveClosureRunner.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/TransitiveClosureRunner.java
deleted file mode 100644
index 0ccc521d0..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/TransitiveClosureRunner.java
+++ /dev/null
@@ -1,139 +0,0 @@
-package gov.nih.nci.evs.restapi.appl;
-
-import gov.nih.nci.evs.restapi.util.*;
-import gov.nih.nci.evs.restapi.bean.*;
-import gov.nih.nci.evs.restapi.common.*;
-
-import java.io.*;
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.*;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
-import java.util.*;
-import java.util.regex.*;
-
-public class TransitiveClosureRunner {
-	private MainTypeHierarchy mth = null;
-	private HierarchyHelper hh = null;
-	private Vector parent_child_vec = null;
-
-    public TransitiveClosureRunner(MainTypeHierarchy mth) {
-		this.mth = mth;
-		this.hh = mth.getHierarchyHelper();
-    }
-
-    public HierarchyHelper getHierarchyHelper() {
-		return hh;
-	}
-
-    public TransitiveClosureRunner(Vector parent_child_vec) {
-		this.parent_child_vec = parent_child_vec;
-		hh = new HierarchyHelper(parent_child_vec);
-    }
-
-	public Vector removeDuplicates(Vector codes) {
-		HashSet hset = new HashSet();
-		Vector w = new Vector();
-		for (int i=0; i 0) {
-				w.addAll(u);
-			}
-		}
-		w = removeDuplicates(w);
-		return w;
-	}
-
-
-    public Vector run(Vector codes) {
-		Vector v = new Vector();
-        for (int i=0; i 1) {
-        	named_graph = args[1];
-		}
-		*/
-
-		/*
-		String serviceUrl = args[0];
-		System.out.println(serviceUrl);
-
-		String named_graph = args[1];
-		String inputfile = args[2];
-		String outputfile = args[3];
-
-		MainTypeHierarchyData mthd = new MainTypeHierarchyData(serviceUrl, named_graph);
-		String ncit_version = mthd.getVersion();
-		System.out.println("version " + ncit_version);
-		Vector broad_category_vec = mthd.get_broad_category_vec();
-		HashSet main_type_set = mthd.get_main_type_set();
-		Vector parent_child_vec = mthd.get_parent_child_vec(named_graph);
-		Vector v1 = mthd.getDiseaseIsStageSourceCodes(named_graph);
-		Vector v2 = mthd.getDiseaseIsGradeSourceCodes(named_graph);
-        HashMap stageConceptHashMap = mthd.generateStageConceptHashMap(v1);
-        HashMap gradeConceptHashMap = mthd.generateGradeConceptHashMap(v2);
-
-	    HashSet ctrp_biomarker_set = mthd.get_ctrp_biomarker_set();
-	    HashSet ctrp_reference_gene_set = mthd.get_ctrp_reference_gene_set();
-
-        MainTypeHierarchy mth = new MainTypeHierarchy(ncit_version, parent_child_vec, main_type_set, broad_category_vec,
-             stageConceptHashMap, gradeConceptHashMap, ctrp_biomarker_set, ctrp_reference_gene_set);
-
-        TransitiveClosureRunner runner = new TransitiveClosureRunner(mth);
-        */
-
-        String parent_child_file = args[0];
-        Vector parent_child_vec = Utils.readFile(parent_child_file);
-        String root = args[1];
-        Vector codes = new Vector();
-        codes.add(root);
-        TransitiveClosureRunner runner = new TransitiveClosureRunner(parent_child_vec);
-        Vector v = runner.run(codes);
-        String outputfile = "parent_child_" + root + ".txt";
-        Utils.saveToFile(outputfile, v);
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-}
-
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/UNIIDataRetriever.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/UNIIDataRetriever.java
deleted file mode 100644
index c4d7a3fee..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/UNIIDataRetriever.java
+++ /dev/null
@@ -1,325 +0,0 @@
-package gov.nih.nci.evs.restapi.appl;
-
-import gov.nih.nci.evs.restapi.util.*;
-import gov.nih.nci.evs.restapi.bean.*;
-import gov.nih.nci.evs.restapi.common.*;
-
-import java.io.*;
-//import java.math.*;
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.*;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
-import java.util.*;
-import java.util.regex.*;
-import org.apache.commons.codec.binary.Base64;
-import org.json.*;
-
-/**
- * 
- * Copyright Copyright 2020 MSC.. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or MSC
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      MSC, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class UNIIDataRetriever {
-	static String UNIDENTIFIABLE_SRS_UNII_CODE = "Unknown SRS UNII code";
-	static String UNIDENTIFIABLE_NCIT_UNII_CODE = "UNII code not found in NCIt";
-	static String MISSING_NCIT_CODE = "NCIT code not given";
-	static String UNKNOWN_NCIT_CODE = "Unknown NCIt code";
-	static String FDA_UNII_Subset_Code = "C63923";
-	static String FDA_UNII_Subset = "FDA Established Names and Unique Ingredient Identifier Codes Terminology";
-	static String FDA_UNII_Code = "FDA_UNII_Code";
-
-    public Vector term_source_fda_vec = null;
-    public Vector fda_unii_subset_vec = null;
-    public Vector ncit_concepts_with_unii_code_vec = null;
-    public Vector ncit_retired_concepts_vec = null;
-    public Vector term_source_vec = null;
-    public Vector term_source_code_vec = null;
-    public Vector full_syn_vec = null;
-
-    JSONUtils jsonUtils = null;
-    HTTPUtils httpUtils = null;
-    String named_graph = null;
-    String prefixes = null;
-    String sparql_endpoint = null;
-    String serviceUrl = null;
-    String named_graph_id = ":NHC0";
-    String base_uri = "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl";
-
-    OWLSPARQLUtils owlSPARQLUtils = null;
-
-	private static String NCI_THESAURUS = "NCI_Thesaurus";
-	private Vector unii_link = null;
-	private Vector unii_data = null;
-	private String username = null;
-	private String password = null;
-	private String namedGraph = null;
-
-	HashMap unii2ncitcode_map = new HashMap();
-	HashMap ncitcode2unii_map = new HashMap();
-	HashMap ncitcode2pt_map = new HashMap();
-
-	static String term_source_fda_file = "term-source-fda.txt";
-	static String subsource_name_file = "subsource-name.txt";
-	static String source_code_file = "source-code.txt";
-
-	static String obsolete_concept_file = "retired_and_obsolete_concepts.txt";
-	static String ncit_unii_file = "ncit_unii.txt";
-	static String FDA_UNII_Subset_file = FDA_UNII_Subset_Code + ".txt";
-	static String full_syn_file = "FULL_SYN.txt";
-
-	public Vector concepts_in_subset = null;
-
-	public String unii_link_file = null;
-	public String unii_data_file = null;
-
-	private TermSearchUtils termSearchUtils = null;
-	private HashSet ncit_code_hset = null;
-
-	private List synonyms = null;
-    private HashMap code2SynonymMap = null;
-    private HashMap ncitcode2labelMap = null;
-
-
-    public UNIIDataRetriever(String serviceUrl, String namedGraph) {
-		this.serviceUrl = serviceUrl;
-		if (serviceUrl.indexOf("?") == -1) {
-			if (!serviceUrl.endsWith("/")) {
-				this.serviceUrl = serviceUrl + "/";
-			}
-	    }
-		this.namedGraph = namedGraph;
-		owlSPARQLUtils = new OWLSPARQLUtils(serviceUrl, null, null);
-    }
-
-    public Vector get_term_source_vec(String source) {
-		return retrieveTermSourceData(source);
-	}
-
-    public Vector get_term_source_fda_vec() {
-		if (term_source_fda_vec == null) {
-			term_source_fda_vec = retrieveTermSourceFDAdata();
-		}
-		return term_source_fda_vec;
-	}
-
-    public Vector get_fda_unii_subset_vec() {
-		if (fda_unii_subset_vec == null) {
-			fda_unii_subset_vec = retrieveUNIIConceptsInSubsetData();
-		}
-		return fda_unii_subset_vec;
-	}
-
-    public Vector get_ncit_concepts_with_unii_code_vec() {
-		if (ncit_concepts_with_unii_code_vec == null) {
-			ncit_concepts_with_unii_code_vec = retrieveConceptsWithUNIICode();
-		}
-		return ncit_concepts_with_unii_code_vec;
-	}
-
-    public Vector get_ncit_retired_concepts_vec() {
-		if (ncit_retired_concepts_vec == null) {
-			ncit_retired_concepts_vec = retrieveRetiredConceptData();
-		}
-		return ncit_retired_concepts_vec;
-	}
-
-    public Vector get_term_source_vec() {
-		if (term_source_vec == null) {
-			term_source_vec = retrieveTermSourceData();
-		}
-		return term_source_vec;
-	}
-
-    public Vector get_term_source_code_vec() {
-		if (term_source_code_vec == null) {
-			term_source_code_vec = retrieveSourceCodeData();
-		}
-		return term_source_code_vec;
-	}
-
-    public Vector get_full_syn_vec() {
-		if (full_syn_vec == null) {
-			full_syn_vec = retrievePropertyData("FULL_SYN");
-		}
-		return full_syn_vec;
-	}
-
-    public void retrieveUNIISupportingData() {
-		Vector v = null;
-		v = retrieveTermSourceFDAdata();
-		Utils.saveToFile(term_source_fda_file, v);
-
-		v = retrieveUNIIConceptsInSubsetData();
-		Utils.saveToFile(FDA_UNII_Subset_Code + ".txt", v);
-
-	    v = retrieveConceptsWithUNIICode();
-	    Utils.saveToFile(ncit_unii_file, v);
-
-		v = retrieveRetiredConceptData();
-		Utils.saveToFile(obsolete_concept_file, v);
-
-		v = retrieveTermSourceData();
-		Utils.saveToFile(subsource_name_file, v);
-
-		v = retrieveSourceCodeData();
-		Utils.saveToFile(source_code_file, v);
-
-        if (!FileUtils.fileExists(full_syn_file)) {
-			v = retrievePropertyData("FULL_SYN");
-			Utils.saveToFile(full_syn_file, v);
-		}
-	}
-
-	public Vector retrievePropertyData(String propertyName) {
-		Vector v = owlSPARQLUtils.get_property_query(this.namedGraph, propertyName);
-        return v;
-	}
-
-	public Vector retrieveTermSourceFDAdata() {
-		String prop_label = "FULL_SYN";
-		String qualifier_label = "Term Source";
-		String qualifier_value = "FDA";
-		Vector v = owlSPARQLUtils.getAxiomsWithQualifierMatching(this.namedGraph, null, prop_label, qualifier_label, qualifier_value);
-        return v;
-	}
-
-	public Vector retrieveTermSourceData(String qualifier_value) {
-		String prop_label = "FULL_SYN";
-		String qualifier_label = "Term Source";
-		Vector v = owlSPARQLUtils.getAxiomsWithQualifierMatching(this.namedGraph, null, prop_label, qualifier_label, qualifier_value);
-        return v;
-	}
-
-/*
-bnode_301c03a7_663e_49c8_be4e_8726b4fc92ea_800112|Molecular Abnormality|C3910|FULL_SYN|P90|Molecular Alteration|Subsource Name|P386|caDSR
-bnode_301c03a7_663e_49c8_be4e_8726b4fc92ea_800110|Molecular Abnormality|C3910|FULL_SYN|P90|Molecular Abnormality|Subsource Name|P386|caDSR
-*/
-
-	public Vector retrieveTermSourceData() {
-		String prop_label = "FULL_SYN";
-		String qualifier_label = "Subsource Name";
-		String qualifier_value = null;
-		Vector v = owlSPARQLUtils.getAxiomsWithQualifierMatching(this.namedGraph, null, prop_label, qualifier_label, qualifier_value);
-        return v;
-	}
-
-/*
-bnode_301c03a7_663e_49c8_be4e_8726b4fc92ea_800110|Molecular Abnormality|C3910|FULL_SYN|P90|Molecular Abnormality|Source Code|P385|TCGA
-bnode_301c03a7_663e_49c8_be4e_8726b4fc92ea_550723|Gene|C16612|FULL_SYN|P90|Gene|Source Code|P385|TCGA
-*/
-
-	public Vector get_term_type_data(String term_type) {
-        return retrieveTermTypeData(term_type);
-	}
-
-	public Vector retrieveTermTypeData(String term_type) {
-		String prop_label = "FULL_SYN";
-		String qualifier_label = "Term Type";
-		String qualifier_value = term_type;
-		Vector v = owlSPARQLUtils.getAxiomsWithQualifierMatching(this.namedGraph, null, prop_label, qualifier_label, qualifier_value);
-        return v;
-	}
-
-	public Vector retrieveTermTypeData() {
-		String prop_label = "FULL_SYN";
-		String qualifier_label = "Term Type";
-		String qualifier_value = null;
-		Vector v = owlSPARQLUtils.getAxiomsWithQualifierMatching(this.namedGraph, null, prop_label, qualifier_label, qualifier_value);
-        return v;
-	}
-
-	public Vector retrieveSourceCodeData() {
-		String prop_label = "FULL_SYN";
-		String qualifier_label = "Source Code";
-		String qualifier_value = null;
-		Vector v = owlSPARQLUtils.getAxiomsWithQualifierMatching(this.namedGraph, null, prop_label, qualifier_label, qualifier_value);
-        return v;
-	}
-
-	public Vector retrieveUNIIConceptsInSubsetData() {
-        Vector v = owlSPARQLUtils.getConceptsInSubset(this.namedGraph, FDA_UNII_Subset_Code);
-	    v = new ParserUtils().getResponseValues(v);
-	    v = new SortUtils().quickSort(v);
-        return v;
-	}
-
-	public Vector retrieveConceptsWithUNIICode() {
-		Vector v = owlSPARQLUtils.findConceptsWithProperty(this.namedGraph, FDA_UNII_Code);
-        return v;
-	}
-
-/*
-Cyclophosphamide/Fluoxymesterone/Mitolactol/Prednisone/Tamoxifen|C10000|Concept_Status|Obsolete_Concept
-Agent Combination Indexed in Open Clinical Trials|C61007|Concept_Status|Obsolete_Concept
-*/
-
-	public Vector retrieveRetiredConceptData() {
-		String property_name = "Concept_Status";
-		String property_value = "Obsolete_Concept";
-		Vector v = owlSPARQLUtils.findConceptsWithPropertyMatching(this.namedGraph, property_name, property_value);
-		property_value = "Retired_Concept";
-		Vector v2 = owlSPARQLUtils.findConceptsWithPropertyMatching(this.namedGraph, property_name, property_value);
-		v.addAll(v2);
-        return v;
-	}
-
-    public static void main(String[] args) {
-		String serviceUrl = args[0];
-		String namedGraph = args[1];
-		UNIIDataRetriever test = new UNIIDataRetriever(serviceUrl, namedGraph);
-		test.retrieveUNIISupportingData();
-	}
-}
\ No newline at end of file
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/UNIIProcessor.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/UNIIProcessor.java
deleted file mode 100644
index 66c0d95cf..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/UNIIProcessor.java
+++ /dev/null
@@ -1,812 +0,0 @@
-package gov.nih.nci.evs.restapi.appl;
-
-import gov.nih.nci.evs.restapi.util.*;
-import gov.nih.nci.evs.restapi.bean.*;
-import gov.nih.nci.evs.restapi.common.*;
-
-import java.io.*;
-//import java.math.*;
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.*;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
-import java.util.*;
-import java.util.regex.*;
-import org.apache.commons.codec.binary.Base64;
-import org.json.*;
-
-/**
- * 
- * Copyright Copyright 2020 MSC.. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or MSC
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      MSC, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@nih.gov
- *
- */
-
-
-public class UNIIProcessor {
-	static String UNIDENTIFIABLE_SRS_UNII_CODE = "Unknown SRS UNII code";
-	static String UNIDENTIFIABLE_NCIT_UNII_CODE = "UNII code not found in NCIt";
-	static String MISSING_NCIT_CODE = "NCIT code not given";
-	static String UNKNOWN_NCIT_CODE = "Unknown NCIt code";
-
-    JSONUtils jsonUtils = null;
-    HTTPUtils httpUtils = null;
-    String named_graph = null;
-    String prefixes = null;
-    String sparql_endpoint = null;
-    String serviceUrl = null;
-    String named_graph_id = ":NHC0";
-    String base_uri = "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl";
-
-    OWLSPARQLUtils owlSPARQLUtils = null;
-
-	private static String NCI_THESAURUS = "NCI_Thesaurus";
-	private Vector unii_link = null;
-	private Vector unii_data = null;
-	private String username = null;
-	private String password = null;
-	private String namedGraph = null;
-	private static String ncit_unii_txt_file = "ncit_unii.txt";
-
-	HashMap unii2ncitcode_map = new HashMap();
-	HashMap ncitcode2unii_map = new HashMap();
-	HashMap ncitcode2pt_map = new HashMap();
-	public static String FDA_UNII_Subset_Code = "C63923";
-	public static String FDA_UNII_Subset = "FDA Established Names and Unique Ingredient Identifier Codes Terminology";
-
-	public Vector concepts_in_subset = null;
-
-	public String unii_link_file = null;
-	public String unii_data_file = null;
-
-	private TermSearchUtils termSearchUtils = null;
-	private HashSet ncit_code_hset = null;
-
-	private List synonyms = null;
-    private HashMap code2SynonymMap = null;
-    private HashMap ncitcode2labelMap = null;
-
-    private MetadataUtils metadataUtils = null;
-    private UNIIDataRetriever uniiDataRetriever = null;
-
-    public Vector term_source_fda_vec = null;
-    public Vector fda_unii_subset_vec = null;
-    public Vector ncit_concepts_with_unii_code_vec = null;
-    public Vector ncit_retired_concepts_vec = null;
-    public Vector term_source_vec = null;
-    public Vector term_source_code_vec = null;
-    public Vector full_syn_vec = null;
-
-	public UNIIProcessor(String serviceUrl, String namedGraph) {
-		this.serviceUrl = serviceUrl;
-		this.namedGraph = namedGraph;
-		System.out.println("serviceUrl: " + this.serviceUrl);
-		System.out.println("namedGraph: " + this.namedGraph);
-
-		owlSPARQLUtils = new OWLSPARQLUtils(serviceUrl, null, null);
-		metadataUtils = new MetadataUtils(serviceUrl);
-		metadataUtils.dumpNameVersion2NamedGraphMap();
-		uniiDataRetriever = new UNIIDataRetriever(this.serviceUrl, this.namedGraph);
-
-		System.out.println("Initialized TermSearchUtils ...");
-		termSearchUtils = new TermSearchUtils(serviceUrl, this.namedGraph);
-
-		synonyms = loadSynonyms();
-		code2SynonymMap = createCode2SynonymMap(synonyms);
-		System.out.println("TermSearchUtils initialized.");
-	}
-
-    public boolean fileExists(String filename) {
-		File file = new File(filename);
-		return file.exists();
-	}
-
-	public void initialize() {
-		concepts_in_subset = uniiDataRetriever.get_fda_unii_subset_vec();
-        ncitcode2labelMap = createNCItCode2LabelMap();
-	}
-
-	public void loadSRSData(String unii_link_file, String unii_data_file) {
-		this.unii_link_file = unii_link_file;
-		this.unii_data_file = unii_data_file;
-        unii_link = Utils.readFile(unii_link_file);
-        unii_data = Utils.readFile(unii_data_file);
-        if (ncit_concepts_with_unii_code_vec == null) {
-			ncit_concepts_with_unii_code_vec = uniiDataRetriever.get_ncit_concepts_with_unii_code_vec();
-		}
-
-        create_unii_hashmaps(ncit_concepts_with_unii_code_vec);
-	}
-
-/*
-Name	TYPE	UNII	Display Name
-(R)-2-(5-CYANO-2-(6-(METHOXYCARBONYL)-7-METHYL-3-OXO-8-(3-(TRIFLUOROMETHYL)PHENYL)-2,3,5,8-TETRAHYDRO-(1,2,4)TRIAZOLO(4,3-A)PYRIMIDIN-5-YL)PHENYL)-N,N,N-TRIMETHYLETHANAMINIUM	sys	00174624E2	CHF-6333 CATION
-(R)-2-(5-CYANO-2-(6-(METHOXYCARBONYL)-7-METHYL-3-OXO-8-(3-(TRIFLUOROMETHYL)PHENYL)-2,3,5,8-TETRAHYDRO-(1,2,4)TRIAZOLO(4,3-A)PYRIMIDIN-5-YL)PHENYL)-N,N,N-TRIMETHYLETHANAMINIUM ION	cn	00174624E2	CHF-6333 CATION
-*/
-
-	public void create_unii_hashmaps(Vector v) {
-        unii2ncitcode_map = new HashMap();
-        ncitcode2unii_map = new HashMap();
-        ncitcode2pt_map = new HashMap();
-		for (int i=0; i parseData(String line) {
-		if (line == null) return null;
-        char tab = '|';
-        return parseData(line, tab);
-    }
-
-
-	public Vector findConceptsWithPropertyMatching(String property_name, String property_value) {
-		return owlSPARQLUtils.findConceptsWithPropertyMatching(this.namedGraph, property_name, property_value);
-	}
-
-
-
-    public void runFDASubstanceRegistrationSystemFilesQA(String unii_link_file, String unii_data_file) {
-		if (ncit_code_hset == null) {
-			HashMap hmap = createSynonymHashMap();
-		}
-
-		this.unii_link_file = unii_link_file;
-		this.unii_data_file = unii_data_file;
-		loadSRSData(unii_link_file, unii_data_file);
-        initialize();
-        char demiliter = '|';
-        char comma = ',';
-
-        // STEP 1: Name	TYPE	UNII	Display Name
-        String unii_link_file_heading = null;
-        String line = (String) unii_link.elementAt(0);
-		Vector u = StringUtils.parseData(line, '\t');
-		String name = (String) u.elementAt(0);
-		String unii = (String) u.elementAt(2);
-		String display_name = (String) u.elementAt(3);
-
-		Vector headings = new Vector();
-		headings.add(name);
-		headings.add(unii);
-		headings.add(display_name);
-
-		headings.add("Comment (" + unii + ")");
-		headings.add("Matched NCIt Concepts");
-
-		String new_unii_link_file_heading = FormatHelper.toCSVLine(headings);
-
-		int count = 0;
-
-        Vector w = new Vector();
-        w.add(new_unii_link_file_heading);
-        HashSet hset = new HashSet();
-		for (int i=1; i= 1
-        at java.util.Vector.elementAt(Vector.java:474)
-        at UNIIProcessor.runFDASubstanceRegistrationSystemFilesQA(UNIIProcessor.java:554)
-        at UNIIProcessor.main(UNIIProcessor.java:862)
-
-*/
\ No newline at end of file
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/ValueSetColumnAppender.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/ValueSetColumnAppender.java
deleted file mode 100644
index 93d674367..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/appl/ValueSetColumnAppender.java
+++ /dev/null
@@ -1,139 +0,0 @@
-package gov.nih.nci.evs.restapi.appl;
-import gov.nih.nci.evs.restapi.util.*;
-import java.io.*;
-import java.text.*;
-import java.net.*;
-import java.util.*;
-import java.nio.file.*;
-import java.nio.charset.Charset;
-
-/**
- * 
- * Copyright 2022 Guidehouse. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by Guidehouse and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "Guidehouse" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or Guidehouse
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class ValueSetColumnAppender {
-
-	public static void run(String restURL, String named_graph, String username, String password, String flatfile) {
-        FlatFileGenerator generator = new FlatFileGenerator(restURL, named_graph, username, password);
-		//flatfile = generator.generate();
-		Vector v = generator.getConceptMembership(named_graph);
-		HashMap code2LabelMap = new HashMap();
-        HashMap hmap = new HashMap();
-		for (int i=0; i
- * Copyright 2020 MSC. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or MSC
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      MSC, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@nih.gov
- *
- */
-
-
-public class WiKiHomeStatistics {
-	String serviceUrl = null;
-	String named_graph = null;
-	String username = null;
-	String password = null;
-
-	int councept_cocunt= -1;
-	int def_count = -1;
-	int relationship_count = -1;
-
-	OWLScanner owlScanner = null;
-	static String NCI_THESAURUS_OWL = "ThesaurusInferred_forTS.owl";
-
-	public WiKiHomeStatistics(String owlfile) {
-        owlScanner = new OWLScanner(owlfile);
-	}
-
-    public String wikiStat() {
-        HashMap hmap = owlScanner.getCode2LabelMap();
-        int n1 = hmap.keySet().size();
-        System.out.println("Number of concepts: " + n1);
-
-        Vector v1 = owlScanner.extractProperties(owlScanner.get_owl_vec(), "P97");
-        int n2 = v1.size();
-        System.out.println("Number of DEFINITION: " + n2);
-        Vector v2 = owlScanner.extractProperties(owlScanner.get_owl_vec(), "P325");
-        int n3 = v2.size();
-        System.out.println("Number of ALT_DEFINITION: " + n3);
-        int total = v1.size() + v2.size();
-        int n4 = n2 + n3;
-        System.out.println("Total number of textual definitions: " + n4);
-
-        Vector v3 = owlScanner.extractAssociations(owlScanner.get_owl_vec());
-        int n5 = v3.size();
-        System.out.println("Number of associations: " + n5);
-        Vector v4 = owlScanner.extractOWLRestrictions(owlScanner.get_owl_vec());
-        int n6 = v4.size();
-        total = v3.size() + v4.size();
-        int n7 = n5 + n6;
-        System.out.println("Number of roles: " + n6);
-        System.out.println("Total number of inter-concept relationships: " + n7);
-
-        StringBuffer buf = new StringBuffer();
-
- String stat = "NCI Thesaurus (NCIt) is NCI's reference terminology and core biomedical ontology, covering some "
- + n1
- + " key biomedical concepts with a rich set of terms, codes, "
- + n4
- + " textual definitions, and over "
- + n7 +
- " inter-concept relationships. NCIt combined and extended core NCI terminologies within a scientifically and technically rigorous framework. NCIt is now a broadly shared coding and semantic infrastructure resource - over half of NCIt concepts include content explicitly tagged by one or more EVS partners (see the shared terminology development wiki page ).";
-         return stat;
-	}
-
-	public static void main(String[] args) {
-		String owlfile = NCI_THESAURUS_OWL;
-		if (args.length == 1) {
-			owlfile = args[0];
-		}
-		WiKiHomeStatistics test = new WiKiHomeStatistics(owlfile);
-		String stat = test.wikiStat();
-		System.out.println("\n" + stat);
-	}
-}
-
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/AltDefinition.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/AltDefinition.java
deleted file mode 100644
index a6b69e53c..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/AltDefinition.java
+++ /dev/null
@@ -1,137 +0,0 @@
-package gov.nih.nci.evs.restapi.bean;
-
-import java.io.*;
-import java.util.*;
-import java.net.*;
-
-import com.google.gson.*;
-import com.google.gson.GsonBuilder;
-import com.google.gson.reflect.TypeToken;
-import com.thoughtworks.xstream.io.json.JettisonMappedXmlDriver;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-import com.thoughtworks.xstream.XStream;
-
-public class AltDefinition
-{
-
-// Variable declaration
-	private String code;
-	private String label;
-	private String propertyLabel;
-	private String description;
-	private String attribution;
-	private String source;
-
-// Default constructor
-	public AltDefinition() {
-	}
-
-// Constructor
-	public AltDefinition(
-		String code,
-		String label,
-		String description,
-		String attribution,
-		String source) {
-
-		this.code = code;
-		this.label = label;
-		this.propertyLabel = "ALT_DEFINITION";
-		this.description = description;
-		this.attribution = attribution;
-		this.source = source;
-	}
-
-// Set methods
-	public void setCode(String code) {
-		this.code = code;
-	}
-
-	public void setLabel(String label) {
-		this.label = label;
-	}
-/*
-	public void setPropertyLabel(String propertyLabel) {
-		this.propertyLabel = propertyLabel;
-	}
-*/
-	public void setDescription(String description) {
-		this.description = description;
-	}
-
-	public void setAttribution(String attribution) {
-		this.attribution = attribution;
-	}
-
-	public void setSource(String source) {
-		this.source = source;
-	}
-
-
-// Get methods
-	public String getCode() {
-		return this.code;
-	}
-
-	public String getLabel() {
-		return this.label;
-	}
-
-	public String getPropertyLabel() {
-		return this.propertyLabel;
-	}
-
-	public String getDescription() {
-		return this.description;
-	}
-
-	public String getAttribution() {
-		return this.attribution;
-	}
-
-	public String getSource() {
-		return this.source;
-	}
-
-	public String toXML() {
-		XStream xstream_xml = new XStream(new DomDriver());
-		String xml = xstream_xml.toXML(this);
-		xml = escapeDoubleQuotes(xml);
-		StringBuffer buf = new StringBuffer();
-		String XML_DECLARATION = "";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-public class Association
-{
-
-// Variable declaration
-	private String relationship;
-	private String relatedConceptCode;
-	private String relatedConceptLabel;
-
-// Default constructor
-	public Association() {
-	}
-
-// Constructor
-	public Association(
-		String relationship,
-		String relatedConceptCode,
-		String relatedConceptLabel) {
-
-		this.relationship = relationship;
-		this.relatedConceptCode = relatedConceptCode;
-		this.relatedConceptLabel = relatedConceptLabel;
-	}
-
-// Set methods
-	public void setRelationship(String relationship) {
-		this.relationship = relationship;
-	}
-
-	public void setRelatedConceptCode(String relatedConceptCode) {
-		this.relatedConceptCode = relatedConceptCode;
-	}
-
-	public void setRelatedConceptLabel(String relatedConceptLabel) {
-		this.relatedConceptLabel = relatedConceptLabel;
-	}
-
-
-// Get methods
-	public String getRelationship() {
-		return this.relationship;
-	}
-
-	public String getRelatedConceptCode() {
-		return this.relatedConceptCode;
-	}
-
-	public String getRelatedConceptLabel() {
-		return this.relatedConceptLabel;
-	}
-
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Atom.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Atom.java
deleted file mode 100644
index e603892b0..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Atom.java
+++ /dev/null
@@ -1,208 +0,0 @@
-package gov.nih.nci.evs.restapi.bean;
-
-import java.io.*;
-import java.util.*;
-import java.net.*;
-
-import com.google.gson.*;
-import com.google.gson.GsonBuilder;
-import com.google.gson.reflect.TypeToken;
-import com.thoughtworks.xstream.io.json.JettisonMappedXmlDriver;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-import com.thoughtworks.xstream.XStream;
-
-public class Atom
-{
-
-// Variable declaration
-	private String code;
-	private String str;
-	private String aui;
-	private String sab;
-	private String cui;
-	private String ispref;
-	private String lat;
-	private String stt;
-	private String ts;
-	private String tty;
-
-// Default constructor
-	public Atom() {
-	}
-
-// Constructor
-	public Atom(
-		String code,
-		String str,
-		String aui,
-		String sab,
-		String cui,
-		String ispref,
-		String lat,
-		String stt,
-		String ts,
-		String tty) {
-
-		this.code = code;
-		this.str = str;
-		this.aui = aui;
-		this.sab = sab;
-		this.cui = cui;
-		this.ispref = ispref;
-		this.lat = lat;
-		this.stt = stt;
-		this.ts = ts;
-		this.tty = tty;
-	}
-
-	public Atom(
-		String code,
-		String str,
-		String aui,
-		String sab,
-		String cui
-        ) {
-		this.code = code;
-		this.str = str;
-		this.aui = aui;
-		this.sab = sab;
-		this.cui = cui;
-		this.ispref = null;
-		this.lat = null;
-		this.stt = null;
-		this.ts = null;
-		this.tty = null;
-	}
-
-	public Atom(
-		String code,
-		String str,
-		String aui,
-		String sab,
-		String cui,
-		String tty) {
-		this.code = code;
-		this.str = str;
-		this.aui = aui;
-		this.sab = sab;
-		this.cui = cui;
-		this.ispref = "Y";
-		this.lat = "ENG";
-		this.stt = "PF";
-		this.ts = "P";
-		this.tty = tty;
-	}
-
-// Set methods
-	public void setCode(String code) {
-		this.code = code;
-	}
-
-	public void setStr(String str) {
-		this.str = str;
-	}
-
-	public void setAui(String aui) {
-		this.aui = aui;
-	}
-
-	public void setSab(String sab) {
-		this.sab = sab;
-	}
-
-	public void setCui(String cui) {
-		this.cui = cui;
-	}
-
-	public void setIspref(String ispref) {
-		this.ispref = ispref;
-	}
-
-	public void setLat(String lat) {
-		this.lat = lat;
-	}
-
-	public void setStt(String stt) {
-		this.stt = stt;
-	}
-
-	public void setTs(String ts) {
-		this.ts = ts;
-	}
-
-	public void setTty(String tty) {
-		this.tty = tty;
-	}
-
-
-// Get methods
-	public String getCode() {
-		return this.code;
-	}
-
-	public String getStr() {
-		return this.str;
-	}
-
-	public String getAui() {
-		return this.aui;
-	}
-
-	public String getSab() {
-		return this.sab;
-	}
-
-	public String getCui() {
-		return this.cui;
-	}
-
-	public String getIspref() {
-		return this.ispref;
-	}
-
-	public String getLat() {
-		return this.lat;
-	}
-
-	public String getStt() {
-		return this.stt;
-	}
-
-	public String getTs() {
-		return this.ts;
-	}
-
-	public String getTty() {
-		return this.tty;
-	}
-
-	public String toXML() {
-		XStream xstream_xml = new XStream(new DomDriver());
-		String xml = xstream_xml.toXML(this);
-		xml = escapeDoubleQuotes(xml);
-		StringBuffer buf = new StringBuffer();
-		String XML_DECLARATION = "";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class Biomarker
-{
-
-// Variable declaration
-	private String code;
-	private String label;
-
-// Default constructor
-	public Biomarker() {
-	}
-
-// Constructor
-	public Biomarker(
-		String code,
-		String label) {
-
-		this.code = code;
-		this.label = label;
-	}
-
-// Set methods
-	public void setCode(String code) {
-		this.code = code;
-	}
-
-	public void setLabel(String label) {
-		this.label = label;
-	}
-
-
-// Get methods
-	public String getCode() {
-		return this.code;
-	}
-
-	public String getLabel() {
-		return this.label;
-	}
-
-
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/ComplexDefinition.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/ComplexDefinition.java
deleted file mode 100644
index 18346054e..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/ComplexDefinition.java
+++ /dev/null
@@ -1,61 +0,0 @@
-package gov.nih.nci.evs.restapi.bean;
-
-import java.io.*;
-import java.util.*;
-import java.net.*;
-
-import com.thoughtworks.xstream.XStream;
-import com.thoughtworks.xstream.annotations.XStreamAlias;
-import com.thoughtworks.xstream.annotations.XStreamImplicit;
-
-@XStreamAlias("ComplexDefinition")
-public class ComplexDefinition implements java.io.Serializable
-{
-
-// Variable declaration
-    @XStreamImplicit
-	private String definition;
-	private String source;
-
-// Default constructor
-	public ComplexDefinition() {
-	}
-
-// Constructor
-	public ComplexDefinition(
-		String definition,
-		String source) {
-
-		this.definition = definition;
-		this.source = source;
-	}
-
-// Set methods
-	public void setDefinition(String definition) {
-		this.definition = definition;
-	}
-
-	public void setSource(String source) {
-		this.source = source;
-	}
-
-
-// Get methods
-	public String getDefinition() {
-		return this.definition;
-	}
-
-	public String getSource() {
-		return this.source;
-	}
-
-
-	public String getDisplayForm() {
-		return definition + " (source: " + source + ")";
-	}
-
-    @Override
-    public String toString() {
-        return "ComplexDefinition [definition=" + definition + "]" + "[source=" + source + "]";
-    }
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/ComplexProperty.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/ComplexProperty.java
deleted file mode 100644
index 2e9830a3b..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/ComplexProperty.java
+++ /dev/null
@@ -1,92 +0,0 @@
-package gov.nih.nci.evs.restapi.bean;
-
-import java.io.*;
-import java.util.*;
-import java.net.*;
-
-import com.google.gson.*;
-import com.google.gson.GsonBuilder;
-import com.google.gson.reflect.TypeToken;
-import com.thoughtworks.xstream.io.json.JettisonMappedXmlDriver;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-import com.thoughtworks.xstream.XStream;
-
-public class ComplexProperty extends Property
-{
-
-// Variable declaration
-	private String name;
-	private String value;
-	private List qualifiers;
-
-// Default constructor
-	public ComplexProperty() {
-	}
-
-// Constructor
-	public ComplexProperty(
-		String name,
-		String value,
-		List qualifiers) {
-
		this.name = name;
-		this.value = value;
-		this.qualifiers = qualifiers;
-	}
-
-// Set methods
-	public void setName(String name) {
-		this.name = name;
-	}
-
-	public void setValue(String value) {
-		this.value = value;
-	}
-
-	public void setQualifiers(List qualifiers) {
-		this.qualifiers = qualifiers;
-	}
-
-
-// Get methods
-	public String getName() {
-		return this.name;
-	}
-
-	public String getValue() {
-		return this.value;
-	}
-
-	public List getQualifiers() {
-		return this.qualifiers;
-	}
-
-	public String toXML() {
-		XStream xstream_xml = new XStream(new DomDriver());
-		String xml = xstream_xml.toXML(this);
-		xml = escapeDoubleQuotes(xml);
-		StringBuffer buf = new StringBuffer();
-		String XML_DECLARATION = "";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  iAcinar CellSYNCITCGA
-
-
-Acinar CellSY<
-/ncicp:term-group>NCIT
-CGA
-Acinar CellSY<
-/ncicp:term-group>NCIT
-CGAcaDSR
-Acinar CellSYNCITCGAcaDSR
-*/
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Concept.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Concept.java
deleted file mode 100644
index fea9fbfc6..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Concept.java
+++ /dev/null
@@ -1,203 +0,0 @@
-package gov.nih.nci.evs.restapi.bean;
-
-
-import java.io.*;
-import java.net.*;
-import java.util.*;
-
-
-/**
- * 
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class Concept
-{
-
-// Variable declaration
-	private int idx;
-	private String codingScheme;
-	private String version;
-	private String label;
-	private String code;
-
-	private String cui;
-	private String aui;
-	private String sab;
-
-
-// Default constructor
-	public Concept() {
-	}
-
-// Constructor
-	public Concept(
-		int idx,
-		String codingScheme,
-		String version,
-		String label,
-		String code) {
-
-		this.idx = idx;
-		this.codingScheme = codingScheme;
-		this.version = version;
-		this.label = label;
-		this.code = code;
-		this.cui = null;
-		this.aui = null;
-		this.sab = null;
-	}
-
-	public Concept(
-		int idx,
-		String label,
-		String code,
-		String cui,
-		String aui,
-		String sab
-		) {
-
-		this.idx = idx;
-		this.codingScheme = null;
-		this.version = null;
-		this.label = label;
-		this.code = code;
-		this.cui = cui;
-		this.aui = aui;
-		this.sab = sab;
-	}
-
-	public Concept(
-		int idx,
-		String codingScheme,
-		String version,
-		String label,
-		String code,
-		String cui,
-		String aui,
-		String sab
-		) {
-
-		this.idx = idx;
-		this.codingScheme = codingScheme;
-		this.version = version;
-		this.label = label;
-		this.code = code;
-		this.cui = cui;
-		this.aui = aui;
-		this.sab = sab;
-	}
-
-// Set methods
-	public void setIdx(int idx) {
-		this.idx = idx;
-	}
-
-	public void setCodingScheme(String codingScheme) {
-		this.codingScheme = codingScheme;
-	}
-
-	public void setVersion(String version) {
-		this.version = version;
-	}
-
-	public void setLabel(String label) {
-		this.label = label;
-	}
-
-	public void setCode(String code) {
-		this.code = code;
-	}
-
-	public void setCui(String cui) {
-		this.cui = cui;
-	}
-
-	public void setAui(String aui) {
-		this.aui = aui;
-	}
-
-	public void setSab(String sab) {
-		this.sab = sab;
-	}
-
-// Get methods
-	public int getIdx() {
-		return this.idx;
-	}
-
-	public String getCodingScheme() {
-		return this.codingScheme;
-	}
-
-	public String getVersion() {
-		return this.version;
-	}
-
-	public String getLabel() {
-		return this.label;
-	}
-
-	public String getCode() {
-		return this.code;
-	}
-
-	public String getCui() {
-		return this.cui;
-	}
-
-	public String getAui() {
-		return this.aui;
-	}
-	public String getSab() {
-		return this.sab;
-	}
-
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/ConceptDetails.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/ConceptDetails.java
deleted file mode 100644
index 8e8b338ac..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/ConceptDetails.java
+++ /dev/null
@@ -1,350 +0,0 @@
-package gov.nih.nci.evs.restapi.bean;
-
-import gov.nih.nci.evs.restapi.common.*;
-
-import gov.nih.nci.evs.restapi.util.*;
-
-import com.google.gson.*;
-import com.google.gson.GsonBuilder;
-import com.google.gson.reflect.TypeToken;
-import com.thoughtworks.xstream.io.json.JettisonMappedXmlDriver;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-import com.thoughtworks.xstream.XStream;
-
-import java.io.*;
-import java.net.*;
-import java.util.*;
-
-public class ConceptDetails
-{
-
-// Variable declaration
-	private String code;
-	private String label;
-	private String preferredName;
-	private String displayName;
-	private Boolean isMainType;
-	private Boolean isSubtype;
-	private Boolean isDiseaseStage;
-	private Boolean isDiseaseGrade;
-	private Boolean isDisease;
-	private Boolean isBiomarker;
-	private Boolean isReferenceGene;
-	private List mainMenuAncestors;
-	private List definitions;
-	private List synonyms;
-	private List conceptStatus;
-	private List semanticTypes;
-	private List superconcepts;
-	private List subconcepts;
-	private List additionalProperties;
-
-// Default constructor
-	public ConceptDetails() {
-	}
-
-// Constructor
-	public ConceptDetails(
-		String code,
-		String label,
-		String preferredName,
-		String displayName,
-		Boolean isMainType,
-		Boolean isSubtype,
-		Boolean isDiseaseStage,
-		Boolean isDiseaseGrade,
-		Boolean isDisease,
-		List mainMenuAncestors,
-		List definitions,
-		List synonyms,
-		List conceptStatus,
-		List semanticTypes,
-		List superconcepts,
-		List subconcepts,
-		List additionalProperties) {
-
-		this.code = code;
-		this.label = label;
-		this.preferredName = preferredName;
-		this.displayName = displayName;
-		this.isMainType = isMainType;
-		this.isSubtype = isSubtype;
-		this.isDiseaseStage = isDiseaseStage;
-		this.isDiseaseGrade = isDiseaseGrade;
-		this.isDisease = isDisease;
-		this.mainMenuAncestors = mainMenuAncestors;
-		this.definitions = definitions;
-		this.synonyms = synonyms;
-		this.conceptStatus = conceptStatus;
-		this.semanticTypes = semanticTypes;
-		this.superconcepts = superconcepts;
-		this.subconcepts = subconcepts;
-		this.additionalProperties = additionalProperties;
-	}
-
-    public static List vector2List(Vector v) {
-		if (v == null) return null;
-		return new ArrayList(v);
-	}
-
-// Set methods
-	public void setCode(String code) {
-		this.code = code;
-	}
-
-	public void setLabel(String label) {
-		this.label = label;
-	}
-
-	public void setPreferredName(String preferredName) {
-		this.preferredName = preferredName;
-	}
-
-	public void setDisplayName(String displayName) {
-		this.displayName = displayName;
-	}
-
-	public void setIsMainType(Boolean isMainType) {
-		this.isMainType = isMainType;
-	}
-
-	public void setIsSubtype(Boolean isSubtype) {
-		this.isSubtype = isSubtype;
-	}
-
-	public void setIsDiseaseStage(Boolean isDiseaseStage) {
-		this.isDiseaseStage = isDiseaseStage;
-	}
-
-	public void setIsDiseaseGrade(Boolean isDiseaseGrade) {
-		this.isDiseaseGrade = isDiseaseGrade;
-	}
-
-	public void setIsDisease(Boolean isDisease) {
-		this.isDisease = isDisease;
-	}
-
-	public void setmainMenuAncestors(List mainMenuAncestors) {
-		this.mainMenuAncestors = mainMenuAncestors;
-	}
-
-	public void setDefinitions(List definitions) {
-		this.definitions = definitions;
-	}
-
-	public void setSynonyms(List synonyms) {
-		this.synonyms = synonyms;
-	}
-
-	public void setConceptStatus(List conceptStatus) {
-		this.conceptStatus = conceptStatus;
-	}
-
-	public void setSemanticTypes(List semanticTypes) {
-		this.semanticTypes = semanticTypes;
-	}
-
-	public void setSuperconcepts(List superconcepts) {
-		this.superconcepts = superconcepts;
-	}
-
-	public void setSubconcepts(List subconcepts) {
-		this.subconcepts = subconcepts;
-	}
-
-	public void setAdditionalProperties(List additionalProperties) {
-		this.additionalProperties = additionalProperties;
-	}
-
-
-// Get methods
-	public String getCode() {
-		return this.code;
-	}
-
-	public String getLabel() {
-		return this.label;
-	}
-
-	public String getPreferredName() {
-		return this.preferredName;
-	}
-
-	public String getDisplayName() {
-		return this.displayName;
-	}
-
-	public Boolean getIsMainType() {
-		return this.isMainType;
-	}
-
-	public Boolean getIsSubtype() {
-		return this.isSubtype;
-	}
-
-	public Boolean getIsDiseaseStage() {
-		return this.isDiseaseStage;
-	}
-
-	public Boolean getIsDiseaseGrade() {
-		return this.isDiseaseGrade;
-	}
-
-	public Boolean getIsDisease() {
-		return this.isDisease;
-	}
-	public List getmainMenuAncestors() {
-		return this.mainMenuAncestors;
-	}
-
-	public List getDefinitions() {
-		return this.definitions;
-	}
-
-	public List getSynonyms() {
-		return this.synonyms;
-	}
-
-	public List getConceptStatus() {
-		return this.conceptStatus;
-	}
-
-	public List getSemanticTypes() {
-		return this.semanticTypes;
-	}
-
-	public List getSuperconcepts() {
-		return this.superconcepts;
-	}
-
-	public List getSubconcepts() {
-		return this.subconcepts;
-	}
-
-	public List getAdditionalProperties() {
-		return this.additionalProperties;
-	}
-
-	public ConceptDetails(
-		Vector label_vec,
-		Vector property_vec,
-		Vector property_qualifier_vec,
-		Vector synonym_vec,
-		Vector superclass_vec,
-		Vector subclass_vec,
-		List mainMenuAncestors,
-	    Boolean isMainType,
-	    Boolean isSubtype,
-	    Boolean isDiseaseStage,
-	    Boolean isDiseaseGrade,
-	    Boolean isDisease,
-	    Boolean isBiomarker,
-	    Boolean isReferenceGene
-		) {
-		ParserUtils parser = new ParserUtils();
-        HashMap prop_hmap = parser.parseProperties(property_vec);
-        Vector code_vec = (Vector) prop_hmap.get("code");
-
-		String code = null;
-		if (code_vec != null) {
-				code = (String) code_vec.elementAt(0);
-		}
-        String label = parser.parseLabel(label_vec);
-        Vector displayNames = (Vector) prop_hmap.get("Display_Name");
-        if (displayNames != null) {
-        	displayName = (String) displayNames.elementAt(0);
-		}
-        Vector preferredName_vec = (Vector) prop_hmap.get("Preferred_Name");
-        String preferredName = null;
-        if (preferredName_vec != null) {
-        	preferredName = (String) preferredName_vec.elementAt(0);
-		}
-
-        Vector displayName_vec = (Vector) prop_hmap.get("Display_Name");
-        if (displayName_vec != null) {
-        	displayName = (String) displayName_vec.elementAt(0);
-		}
-
-        List synonyms = parser.getSynonyms(synonym_vec);
-		List list = new ParserUtils().getSynonyms(synonym_vec);
-
-        Vector conceptStatus_vec = (Vector) prop_hmap.get("Concept_Status");
-        Vector semanticType_vec = (Vector) prop_hmap.get("Semantic_Type");
-
-        HashMap superclasses_hmap = parser.parseSuperclasses(superclass_vec);
-        List superconcepts = new ArrayList();
-        Iterator it = superclasses_hmap.keySet().iterator();
-        while (it.hasNext()) {
-			String cd = (String) it.next();
-			Vector w = (Vector) superclasses_hmap.get(cd);
-			String name = null;
-			if (w != null) {
-				name = (String) w.elementAt(0);
-			}
-			superconcepts.add(new Superconcept(cd, name));
-		}
-
-        HashMap subclasses_hmap = parser.parseSubclasses(subclass_vec);
-        List subconcepts = new ArrayList();
-        it = subclasses_hmap.keySet().iterator();
-        while (it.hasNext()) {
-			String cd = (String) it.next();
-			Vector w = (Vector) subclasses_hmap.get(cd);
-			String name = null;
-			if (w != null) {
-				name = (String) w.elementAt(0);
-			}
-			subconcepts.add(new Subconcept(cd, name));
-		}
-		this.code = code;
-		this.label = label;
-		this.preferredName = preferredName;
-		this.displayName = displayName;
-		this.synonyms =synonyms;
-
-		this.conceptStatus = vector2List(conceptStatus_vec);
-		this.semanticTypes = vector2List(semanticType_vec);
-		this.superconcepts = superconcepts;
-		this.subconcepts = subconcepts;
-
-		List definitions = new ArrayList();
-        Vector def_vec = parser.filterPropertyQualifiers(property_qualifier_vec, Constants.DEFINITION);//) { //type: FULL_SYN, DEFINITION, ALT_DEFINITION
-        definitions = parser.getDefinitions(def_vec);
-		Vector alt_def_vec = parser.filterPropertyQualifiers(property_qualifier_vec, Constants.ALT_DEFINITION);//) { //type: FULL_SYN, DEFINITION, ALT_DEFINITION
-		List alt_definitions = parser.getDefinitions(alt_def_vec);//) { //type: FULL_SYN, DEFINITION, ALT_DEFINITION
-		if (alt_definitions != null && alt_definitions.size() > 0) {
-			for (int j=0; j";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i
- * Copyright 2008,2009 NGIT. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIT and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIT" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIT
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIT, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- *          Modification history Initial implementation kim.ong@ngc.com
- *
- */
-
-public class DisplayItem {
-    private String _propertyName;
-    private String _itemLabel;
-    private String _url;
-    private String _hyperlinkText;
-    private boolean _isExternalCode;
-
-    public DisplayItem() {
-    }
-
-    public DisplayItem(String propertyName, String itemLabel, String url,
-        String hyperlinkText) {
-        _propertyName = propertyName;
-        _itemLabel = itemLabel;
-        _url = url;
-        _hyperlinkText = hyperlinkText;
-        _isExternalCode = false;
-    }
-
-    public DisplayItem(String propertyName, String itemLabel, String url,
-        String hyperlinkText, boolean isExternalCode) {
-        _propertyName = propertyName;
-        _itemLabel = itemLabel;
-        _url = url;
-        _hyperlinkText = hyperlinkText;
-        _isExternalCode = isExternalCode;
-    }
-
-    public String getPropertyName() {
-        return _propertyName;
-    }
-
-    public void setPropertyName(String propertyName) {
-        _propertyName = propertyName;
-    }
-
-    public String getItemLabel() {
-        return _itemLabel;
-    }
-
-    public void setItemLabel(String itemLabel) {
-        _itemLabel = itemLabel;
-    }
-
-    public String getUrl() {
-        return _url;
-    }
-
-    public void setUrl(String url) {
-        _url = url;
-    }
-
-    public String getHyperlinkText() {
-        return _hyperlinkText;
-    }
-
-    public void setHyperlinkText(String hyperlinkText) {
-        _hyperlinkText = hyperlinkText;
-    }
-
-    public boolean getIsExternalCode() {
-        return _isExternalCode;
-    }
-
-    public void setIsExternalCode(String isExternalCode) {
-        _hyperlinkText = isExternalCode;
-    }
-
-    public String toString() {
-        StringBuffer sb = new StringBuffer();
-        sb.append("DisplayItem ");
-        sb.append("\n");
-        sb.append("\tpropertyName: " + getPropertyName());
-        sb.append("\n");
-        sb.append("\titemLabel: " + getItemLabel());
-        sb.append("\n");
-        sb.append("\turl: " + getUrl());
-        sb.append("\n");
-        sb.append("\thyperlinkText: " + getHyperlinkText());
-        sb.append("\n");
-        sb.append("\tisExternalCode: " + getIsExternalCode());
-        sb.append("\n");
-        return sb.toString();
-    }
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/EditAction.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/EditAction.java
deleted file mode 100644
index 0432b9924..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/EditAction.java
+++ /dev/null
@@ -1,119 +0,0 @@
-package gov.nih.nci.evs.restapi.bean;
-
-import java.io.*;
-import java.util.*;
-import java.net.*;
-
-import com.google.gson.*;
-import com.google.gson.GsonBuilder;
-import com.google.gson.reflect.TypeToken;
-import com.thoughtworks.xstream.io.json.JettisonMappedXmlDriver;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-import com.thoughtworks.xstream.XStream;
-
-public class EditAction
-{
-
-// Variable declaration
-	private String label;
-	private String code;
-	private String action;
-	private String type;
-	private String value;
-
-// Default constructor
-	public EditAction() {
-	}
-
-// Constructor
-	public EditAction(
-		String label,
-		String code,
-		String action,
-		String type,
-		String value) {
-
-		this.label = label;
-		this.code = code;
-		this.action = action;
-		this.type = type;
-		this.value = value;
-	}
-
-// Set methods
-	public void setLabel(String label) {
-		this.label = label;
-	}
-
-	public void setCode(String code) {
-		this.code = code;
-	}
-
-	public void setAction(String action) {
-		this.action = action;
-	}
-
-	public void setType(String type) {
-		this.type = type;
-	}
-
-	public void setValue(String value) {
-		this.value = value;
-	}
-
-
-// Get methods
-	public String getLabel() {
-		return this.label;
-	}
-
-	public String getCode() {
-		return this.code;
-	}
-
-	public String getAction() {
-		return this.action;
-	}
-
-	public String getType() {
-		return this.type;
-	}
-
-	public String getValue() {
-		return this.value;
-	}
-
-	public String toXML() {
-		XStream xstream_xml = new XStream(new DomDriver());
-		String xml = xstream_xml.toXML(this);
-		xml = escapeDoubleQuotes(xml);
-		StringBuffer buf = new StringBuffer();
-		String XML_DECLARATION = "";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-public class InverseAssociation
-{
-
-// Variable declaration
-	private String relationship;
-	private String relatedConceptCode;
-	private String relatedConceptLabel;
-
-// Default constructor
-	public InverseAssociation() {
-	}
-
-// Constructor
-	public InverseAssociation(
-		String relationship,
-		String relatedConceptCode,
-		String relatedConceptLabel) {
-
-		this.relationship = relationship;
-		this.relatedConceptCode = relatedConceptCode;
-		this.relatedConceptLabel = relatedConceptLabel;
-	}
-
-// Set methods
-	public void setRelationship(String relationship) {
-		this.relationship = relationship;
-	}
-
-	public void setRelatedConceptCode(String relatedConceptCode) {
-		this.relatedConceptCode = relatedConceptCode;
-	}
-
-	public void setRelatedConceptLabel(String relatedConceptLabel) {
-		this.relatedConceptLabel = relatedConceptLabel;
-	}
-
-
-// Get methods
-	public String getRelationship() {
-		return this.relationship;
-	}
-
-	public String getRelatedConceptCode() {
-		return this.relatedConceptCode;
-	}
-
-	public String getRelatedConceptLabel() {
-		return this.relatedConceptLabel;
-	}
-
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/InverseRole.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/InverseRole.java
deleted file mode 100644
index d4f9cf9a9..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/InverseRole.java
+++ /dev/null
@@ -1,111 +0,0 @@
-package gov.nih.nci.evs.restapi.bean;
-
-import java.io.*;
-import java.util.*;
-import java.net.*;
-
-/**
- * 
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-public class InverseRole
-{
-
-// Variable declaration
-	private String relationship;
-	private String relatedConceptCode;
-	private String relatedConceptLabel;
-
-// Default constructor
-	public InverseRole() {
-	}
-
-// Constructor
-	public InverseRole(
-		String relationship,
-		String relatedConceptCode,
-		String relatedConceptLabel) {
-
-		this.relationship = relationship;
-		this.relatedConceptCode = relatedConceptCode;
-		this.relatedConceptLabel = relatedConceptLabel;
-	}
-
-// Set methods
-	public void setRelationship(String relationship) {
-		this.relationship = relationship;
-	}
-
-	public void setRelatedConceptCode(String relatedConceptCode) {
-		this.relatedConceptCode = relatedConceptCode;
-	}
-
-	public void setRelatedConceptLabel(String relatedConceptLabel) {
-		this.relatedConceptLabel = relatedConceptLabel;
-	}
-
-
-// Get methods
-	public String getRelationship() {
-		return this.relationship;
-	}
-
-	public String getRelatedConceptCode() {
-		return this.relatedConceptCode;
-	}
-
-	public String getRelatedConceptLabel() {
-		return this.relatedConceptLabel;
-	}
-
-	public String toString() {
-		return "[" + relatedConceptLabel + " (" + relatedConceptCode + ")] --> (" + relationship + ")";
-    }
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Link.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Link.java
deleted file mode 100644
index a71fc9db0..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Link.java
+++ /dev/null
@@ -1,136 +0,0 @@
-package gov.nih.nci.evs.restapi.bean;
-
-
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-
-
-/**
- * 
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class Link {
-	int id;
-	String sourceCode;
-	String sourceName;
-	String targetCode;
-	String targetName;
-
-
-// Default constructor
-	public Link() {
-	}
-
-// Constructor
-	public Link(
-		int id,
-		String sourceCode,
-		String sourceName,
-		String targetCode,
-		String targetName) {
-		this.id = id;
-		this.sourceCode = sourceCode;
-		this.sourceName = sourceName;
-		this.targetCode = targetCode;
-		this.targetName = targetName;
-	}
-
-	public int getId() {
-		return id;
-	}
-
-	public String getSourceCode() {
-		return sourceCode;
-	}
-
-	public String getSourceName() {
-		return sourceName;
-	}
-
-	public String getTargetCode() {
-		return targetCode;
-	}
-
-	public String getTargetName() {
-		return targetName;
-	}
-
-
-	@XmlAttribute
-	public void setId(int id) {
-		this.id = id;
-	}
-
-	@XmlElement
-	public void setSourceCode(String sourceCode) {
-		this.sourceCode = sourceCode;
-	}
-
-	@XmlElement
-	public void setSourceName(String sourceName) {
-		this.sourceName = sourceName;
-	}
-
-	@XmlElement
-	public void setTargetCode(String targetCode) {
-		this.targetCode = targetCode;
-	}
-
-	@XmlElement
-	public void setTargetName(String targetName) {
-		this.targetName = targetName;
-	}
-
-	public String toString() {
-		return "Id: " + this.id + "\n\t" + "SourceCode: " + this.sourceCode + "\n\t" + "SourceName: " + this.sourceName + "\n\t" + "TargetCode: " + this.targetCode + "\n\t" + "TargetName: " + this.targetName;
-	}
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Links.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Links.java
deleted file mode 100644
index d190f40e5..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Links.java
+++ /dev/null
@@ -1,105 +0,0 @@
-package gov.nih.nci.evs.restapi.bean;
-
-import java.util.List;
-import gov.nih.nci.evs.restapi.common.*;
-import gov.nih.nci.evs.restapi.util.*;
-/*
-import com.thoughtworks.xstream.io.json.JettisonMappedXmlDriver;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-import com.thoughtworks.xstream.XStream;
-import gov.nih.nci.evs.restapi.common.*;
-
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-*/
-
-import com.google.gson.*;
-import com.google.gson.GsonBuilder;
-import com.google.gson.reflect.TypeToken;
-import com.thoughtworks.xstream.io.json.JettisonMappedXmlDriver;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-import com.thoughtworks.xstream.XStream;
-
-/**
- * 
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class Links
-{
-	//@XmlElement(name = "Link")
-	private List links = null;
-
-	public List getLinks() {
-		return links;
-	}
-
-	public void setLinks(List links) {
-		this.links = links;
-	}
-
-	public String toXML() {
-		XStream xstream_xml = new XStream(new DomDriver());
-		String xml = xstream_xml.toXML(this);
-		xml = StringUtils.escapeDoubleQuotes(xml);
-		xml = Constants.XML_DECLARATION + "\n" + xml;
-		xml = StringUtils.removePackageNames(Constants.EVSRESTAPI_BEAN, xml);
-        return xml;
-	}
-
-	public String toJson() {
-		//return new Gson().toJson(this);
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/MapEntry.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/MapEntry.java
deleted file mode 100644
index ddae7d590..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/MapEntry.java
+++ /dev/null
@@ -1,203 +0,0 @@
-package gov.nih.nci.evs.restapi.bean;
-
-import java.io.*;
-import java.util.*;
-import java.net.*;
-
-import com.google.gson.*;
-import com.google.gson.GsonBuilder;
-import com.google.gson.reflect.TypeToken;
-import com.thoughtworks.xstream.io.json.JettisonMappedXmlDriver;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-import com.thoughtworks.xstream.XStream;
-
-public class MapEntry
-{
-
-// Variable declaration
-	private String sourceCode;
-	private String sourceName;
-	private String sourceCodingScheme;
-	private String sourceCodingSchemeVersion;
-	private String sourceCodingSchemeNamespace;
-	private String associationName;
-	private String rel;
-	private String mapRank;
-	private String targetCode;
-	private String targetName;
-	private String targetCodingScheme;
-	private String targetCodingSchemeVersion;
-	private String targetCodingSchemeNamespace;
-
-// Default constructor
-	public MapEntry() {
-	}
-
-// Constructor
-	public MapEntry(
-		String sourceCode,
-		String sourceName,
-		String sourceCodingScheme,
-		String sourceCodingSchemeVersion,
-		String sourceCodingSchemeNamespace,
-		String associationName,
-		String rel,
-		String mapRank,
-		String targetCode,
-		String targetName,
-		String targetCodingScheme,
-		String targetCodingSchemeVersion,
-		String targetCodingSchemeNamespace) {
-
-		this.sourceCode = sourceCode;
-		this.sourceName = sourceName;
-		this.sourceCodingScheme = sourceCodingScheme;
-		this.sourceCodingSchemeVersion = sourceCodingSchemeVersion;
-		this.sourceCodingSchemeNamespace = sourceCodingSchemeNamespace;
-		this.associationName = associationName;
-		this.rel = rel;
-		this.mapRank = mapRank;
-		this.targetCode = targetCode;
-		this.targetName = targetName;
-		this.targetCodingScheme = targetCodingScheme;
-		this.targetCodingSchemeVersion = targetCodingSchemeVersion;
-		this.targetCodingSchemeNamespace = targetCodingSchemeNamespace;
-	}
-
-// Set methods
-	public void setSourceCode(String sourceCode) { 
-		this.sourceCode = sourceCode;
-	}
-
-	public void setSourceName(String sourceName) { 
-		this.sourceName = sourceName;
-	}
-
-	public void setSourceCodingScheme(String sourceCodingScheme) { 
-		this.sourceCodingScheme = sourceCodingScheme;
-	}
-
-	public void setSourceCodingSchemeVersion(String sourceCodingSchemeVersion) { 
-		this.sourceCodingSchemeVersion = sourceCodingSchemeVersion;
-	}
-
-	public void setSourceCodingSchemeNamespace(String sourceCodingSchemeNamespace) { 
-		this.sourceCodingSchemeNamespace = sourceCodingSchemeNamespace;
-	}
-
-	public void setAssociationName(String associationName) { 
-		this.associationName = associationName;
-	}
-
-	public void setRel(String rel) { 
-		this.rel = rel;
-	}
-
-	public void setMapRank(String mapRank) { 
-		this.mapRank = mapRank;
-	}
-
-	public void setTargetCode(String targetCode) { 
-		this.targetCode = targetCode;
-	}
-
-	public void setTargetName(String targetName) { 
-		this.targetName = targetName;
-	}
-
-	public void setTargetCodingScheme(String targetCodingScheme) { 
-		this.targetCodingScheme = targetCodingScheme;
-	}
-
-	public void setTargetCodingSchemeVersion(String targetCodingSchemeVersion) { 
-		this.targetCodingSchemeVersion = targetCodingSchemeVersion;
-	}
-
-	public void setTargetCodingSchemeNamespace(String targetCodingSchemeNamespace) { 
-		this.targetCodingSchemeNamespace = targetCodingSchemeNamespace;
-	}
-
-
-// Get methods
-	public String getSourceCode() { 
-		return this.sourceCode;
-	}
-
-	public String getSourceName() { 
-		return this.sourceName;
-	}
-
-	public String getSourceCodingScheme() { 
-		return this.sourceCodingScheme;
-	}
-
-	public String getSourceCodingSchemeVersion() { 
-		return this.sourceCodingSchemeVersion;
-	}
-
-	public String getSourceCodingSchemeNamespace() { 
-		return this.sourceCodingSchemeNamespace;
-	}
-
-	public String getAssociationName() { 
-		return this.associationName;
-	}
-
-	public String getRel() { 
-		return this.rel;
-	}
-
-	public String getMapRank() { 
-		return this.mapRank;
-	}
-
-	public String getTargetCode() { 
-		return this.targetCode;
-	}
-
-	public String getTargetName() { 
-		return this.targetName;
-	}
-
-	public String getTargetCodingScheme() { 
-		return this.targetCodingScheme;
-	}
-
-	public String getTargetCodingSchemeVersion() { 
-		return this.targetCodingSchemeVersion;
-	}
-
-	public String getTargetCodingSchemeNamespace() { 
-		return this.targetCodingSchemeNamespace;
-	}
-
-	public String toXML() {
-		XStream xstream_xml = new XStream(new DomDriver());
-		String xml = xstream_xml.toXML(this);
-		xml = escapeDoubleQuotes(xml);
-		StringBuffer buf = new StringBuffer();
-		String XML_DECLARATION = "";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class Parameter
-{
-
-// Variable declaration
-	private String name;
-	private String type;
-	private String nodeType;
-
-// Default constructor
-	public Parameter() {
-	}
-
-// Constructor
-	public Parameter(
-		String name,
-		String type,
-		String nodeType) {
-
-		this.name = name;
-		this.type = type;
-		this.nodeType = nodeType;
-	}
-
-// Set methods
-	public void setName(String name) {
-		this.name = name;
-	}
-
-	public void setType(String type) {
-		this.type = type;
-	}
-
-	public void setNodeType(String nodeType) {
-		this.nodeType = nodeType;
-	}
-
-
-// Get methods
-	public String getName() {
-		return this.name;
-	}
-
-	public String getType() {
-		return this.type;
-	}
-
-	public String getNodeType() {
-		return this.nodeType;
-	}
-
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Path.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Path.java
deleted file mode 100644
index d6f4e3cb0..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Path.java
+++ /dev/null
@@ -1,101 +0,0 @@
-package gov.nih.nci.evs.restapi.bean;
-
-
-import java.io.*;
-import java.net.*;
-import java.util.*;
-
-
-/**
- * 
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class Path
-{
-// Variable declaration
-	private int direction;
-	private List concepts;
-
-// Default constructor
-	public Path() {
-	}
-
-// Constructor
-	public Path(
-		int direction,
-		List concepts) {
-
-		this.direction = direction;
-		this.concepts = concepts;
-	}
-
-// Set methods
-	public void setDirection(int direction) {
-		this.direction = direction;
-	}
-
-
-	public void setConcepts(List concepts) {
-		this.concepts = concepts;
-	}
-
-
-// Get methods
-	public int getDirection() {
-		return this.direction;
-	}
-
-	public List getConcepts() {
-		return this.concepts;
-	}
-
-
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Paths.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Paths.java
deleted file mode 100644
index 0511ecca7..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Paths.java
+++ /dev/null
@@ -1,161 +0,0 @@
-package gov.nih.nci.evs.restapi.bean;
-import gov.nih.nci.evs.restapi.common.*;
-
-import gov.nih.nci.evs.restapi.util.*;
-
-import com.google.gson.*;
-import com.google.gson.GsonBuilder;
-import com.google.gson.reflect.TypeToken;
-import com.thoughtworks.xstream.io.json.JettisonMappedXmlDriver;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-import com.thoughtworks.xstream.XStream;
-
-import java.io.*;
-import java.net.*;
-import java.util.*;
-
-
-/**
- * 
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class Paths
-{
-// Variable declaration
-	private List paths;
-
-// Default constructor
-	public Paths() {
-		paths = new ArrayList();
-	}
-
-// Constructor
-	public Paths(
-		List paths) {
-
-		this.paths = paths;
-	}
-
-// Set methods
-	public void setPath(List paths) {
-		this.paths = paths;
-	}
-
-
-	public void add(Path path) {
-		this.paths.add(path);
-	}
-
-
-// Get methods
-	public List getPaths() {
-		return this.paths;
-	}
-
-
-	public int getPathCount() {
-		return this.paths.size();
-	}
-
-
-	public static String getIndentation(int n) {
-		StringBuffer buf = new StringBuffer();
-		for (int i=0; i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-public class RelatedConcepts
-{
-
-// Variable declaration
-	private List superconcepts;
-	private List subconcepts;
-	private List associations;
-	private List inverseAssoications;
-	private List roles;
-	private List inverseRoles;
-
-// Default constructor
-	public RelatedConcepts() {
-	}
-
-// Constructor
-	public RelatedConcepts(
-		List superconcepts,
-		List subconcepts,
-		List associations,
-		List inverseAssoications,
-		List roles,
-		List inverseRoles) {
-
-		this.superconcepts = superconcepts;
-		this.subconcepts = subconcepts;
-		this.associations = associations;
-		this.inverseAssoications = inverseAssoications;
-		this.roles = roles;
-		this.inverseRoles = inverseRoles;
-	}
-
-// Set methods
-	public void setSuperconcepts(List superconcepts) {
-		this.superconcepts = superconcepts;
-	}
-
-	public void setSubconcepts(List subconcepts) {
-		this.subconcepts = subconcepts;
-	}
-
-	public void setAssociations(List associations) {
-		this.associations = associations;
-	}
-
-	public void setInverseAssoications(List inverseAssoications) {
-		this.inverseAssoications = inverseAssoications;
-	}
-
-	public void setRoles(List roles) {
-		this.roles = roles;
-	}
-
-	public void setInverseRoles(List inverseRoles) {
-		this.inverseRoles = inverseRoles;
-	}
-
-
-// Get methods
-	public List getSuperconcepts() {
-		return this.superconcepts;
-	}
-
-	public List getSubconcepts() {
-		return this.subconcepts;
-	}
-
-	public List getAssociations() {
-		return this.associations;
-	}
-
-	public List getInverseAssoications() {
-		return this.inverseAssoications;
-	}
-
-	public List getRoles() {
-		return this.roles;
-	}
-
-	public List getInverseRoles() {
-		return this.inverseRoles;
-	}
-
-
-	public String toXML() {
-		XStream xstream_xml = new XStream(new DomDriver());
-		String xml = xstream_xml.toXML(this);
-		xml = StringUtils.escapeDoubleQuotes(xml);
-		xml = Constants.XML_DECLARATION + "\n" + xml;
-		xml = StringUtils.removePackageNames(Constants.EVSRESTAPI_BEAN, xml);
-        return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Relationship.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Relationship.java
deleted file mode 100644
index 160a03d51..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Relationship.java
+++ /dev/null
@@ -1,147 +0,0 @@
-package gov.nih.nci.evs.restapi.bean;
-
-import java.io.*;
-import java.util.*;
-import java.net.*;
-
-/**
- * 
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-public class Relationship
-{
-// Variable declaration
-	private String type;
-	private String name;
-	private String sourceCode;
-	private String sourceLabel;
-	private String targetCode;
-	private String targetLabel;
-
-// Default constructor
-	public Relationship() {
-	}
-
-// Constructor
-	public Relationship(
-		String type,
-		String name,
-		String sourceCode,
-		String sourceLabel,
-		String targetCode,
-		String targetLabel) {
-
-		this.type = type;
-		this.name = name;
-		this.sourceCode = sourceCode;
-		this.sourceLabel = sourceLabel;
-		this.targetCode = targetCode;
-		this.targetLabel = targetLabel;
-	}
-
-// Set methods
-	public void setType(String type) {
-		this.type = type;
-	}
-
-	public void setName(String name) {
-		this.name = name;
-	}
-
-	public void setSourceCode(String sourceCode) {
-		this.sourceCode = sourceCode;
-	}
-
-	public void setSourceLabel(String sourceLabel) {
-		this.sourceLabel = sourceLabel;
-	}
-
-	public void setTargetCode(String targetCode) {
-		this.targetCode = targetCode;
-	}
-
-	public void setTargetLabel(String targetLabel) {
-		this.targetLabel = targetLabel;
-	}
-
-
-// Get methods
-	public String getType() {
-		return this.type;
-	}
-
-	public String getName() {
-		return this.name;
-	}
-
-	public String getSourceCode() {
-		return this.sourceCode;
-	}
-
-	public String getSourceLabel() {
-		return this.sourceLabel;
-	}
-
-	public String getTargetCode() {
-		return this.targetCode;
-	}
-
-	public String getTargetLabel() {
-		return this.targetLabel;
-	}
-
-
-	public String toString() {
-		return "[" + sourceLabel + " (" + sourceCode + ")] -- (" + name + ") --> "
-		           + "[" + targetLabel + " (" + targetCode + ")]";
-
-	}
-
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/ResolvedConceptReference.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/ResolvedConceptReference.java
deleted file mode 100644
index 9ca5aca1d..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/ResolvedConceptReference.java
+++ /dev/null
@@ -1,79 +0,0 @@
-package gov.nih.nci.evs.restapi.bean;
-
-import java.io.*;
-import java.util.*;
-import java.net.*;
-
-public class ResolvedConceptReference implements java.io.Serializable
-{
-
-// Variable declaration
-	private String codingScheme;
-	private String version;
-	private String code;
-	private String namespace;
-	private String name;
-
-// Default constructor
-	public ResolvedConceptReference() {
-	}
-
-// Constructor
-	public ResolvedConceptReference(
-		String codingScheme,
-		String version,
-		String code,
-		String namespace,
-		String name) {
-
-		this.codingScheme = codingScheme;
-		this.version = version;
-		this.code = code;
-		this.namespace = namespace;
-		this.name = name;
-	}
-
-// Set methods
-	public void setCodingScheme(String codingScheme) {
-		this.codingScheme = codingScheme;
-	}
-
-	public void setVersion(String version) {
-		this.version = version;
-	}
-
-	public void setCode(String code) {
-		this.code = code;
-	}
-
-	public void setNamespace(String namespace) {
-		this.namespace = namespace;
-	}
-
-	public void setName(String name) {
-		this.name = name;
-	}
-
-
-// Get methods
-	public String getCodingScheme() {
-		return this.codingScheme;
-	}
-
-	public String getVersion() {
-		return this.version;
-	}
-
-	public String getCode() {
-		return this.code;
-	}
-
-	public String getNamespace() {
-		return this.namespace;
-	}
-
-	public String getName() {
-		return this.name;
-	}
-
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/ResolvedConceptReferenceList.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/ResolvedConceptReferenceList.java
deleted file mode 100644
index 13d3c61ec..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/ResolvedConceptReferenceList.java
+++ /dev/null
@@ -1,114 +0,0 @@
-package gov.nih.nci.evs.restapi.bean;
-
-import java.io.*;
-import java.util.*;
-
-
-public class ResolvedConceptReferenceList implements java.io.Serializable {
-
-    private Boolean _incomplete = Boolean.valueOf("false");
-    private java.util.List _resolvedConceptReferenceList;
-
-
-    public ResolvedConceptReferenceList() {
-        super();
-        this._resolvedConceptReferenceList = new java.util.ArrayList();
-    }
-
-
-    public void addResolvedConceptReference(
-            final ResolvedConceptReference vResolvedConceptReference)
-    throws java.lang.IndexOutOfBoundsException {
-        this._resolvedConceptReferenceList.add(vResolvedConceptReference);
-    }
-
-    public void addResolvedConceptReference(
-            final int index,
-            final ResolvedConceptReference vResolvedConceptReference)
-    throws java.lang.IndexOutOfBoundsException {
-        this._resolvedConceptReferenceList.add(index, vResolvedConceptReference);
-    }
-
-    public java.util.Enumeration enumerateResolvedConceptReference(
-    ) {
-        return java.util.Collections.enumeration(this._resolvedConceptReferenceList);
-    }
-
-    public java.lang.Boolean getIncomplete(
-    ) {
-        return this._incomplete;
-    }
-
-    public ResolvedConceptReference getResolvedConceptReference(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._resolvedConceptReferenceList.size()) {
-            throw new IndexOutOfBoundsException("getResolvedConceptReference: Index value '" + index + "' not in range [0.." + (this._resolvedConceptReferenceList.size() - 1) + "]");
-        }
-        return (ResolvedConceptReference) _resolvedConceptReferenceList.get(index);
-    }
-
-    public ResolvedConceptReference[] getResolvedConceptReference(
-    ) {
-        ResolvedConceptReference[] array = new ResolvedConceptReference[0];
-        return (ResolvedConceptReference[]) this._resolvedConceptReferenceList.toArray(array);
-    }
-
-    public int getResolvedConceptReferenceCount(
-    ) {
-        return this._resolvedConceptReferenceList.size();
-    }
-
-    public java.lang.Boolean isIncomplete(
-    ) {
-        return this._incomplete;
-    }
-
-    public java.util.Iterator iterateResolvedConceptReference(
-    ) {
-        return this._resolvedConceptReferenceList.iterator();
-    }
-
-    public void removeAllResolvedConceptReference(
-    ) {
-        this._resolvedConceptReferenceList.clear();
-    }
-
-    public boolean removeResolvedConceptReference(
-            final ResolvedConceptReference vResolvedConceptReference) {
-        boolean removed = _resolvedConceptReferenceList.remove(vResolvedConceptReference);
-        return removed;
-    }
-
-    public ResolvedConceptReference removeResolvedConceptReferenceAt(
-            final int index) {
-        java.lang.Object obj = this._resolvedConceptReferenceList.remove(index);
-        return (ResolvedConceptReference) obj;
-    }
-
-    public void setIncomplete(
-            final java.lang.Boolean incomplete) {
-        this._incomplete = incomplete;
-    }
-
-    public void setResolvedConceptReference(
-            final int index,
-            final ResolvedConceptReference vResolvedConceptReference)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._resolvedConceptReferenceList.size()) {
-            throw new IndexOutOfBoundsException("setResolvedConceptReference: Index value '" + index + "' not in range [0.." + (this._resolvedConceptReferenceList.size() - 1) + "]");
-        }
-        this._resolvedConceptReferenceList.set(index, vResolvedConceptReference);
-    }
-
-    public void setResolvedConceptReference(
-            final ResolvedConceptReference[] vResolvedConceptReferenceArray) {
-        _resolvedConceptReferenceList.clear();
-
-        for (int i = 0; i < vResolvedConceptReferenceArray.length; i++) {
-                this._resolvedConceptReferenceList.add(vResolvedConceptReferenceArray[i]);
-        }
-    }
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/ResolvedValueSet.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/ResolvedValueSet.java
deleted file mode 100644
index 2dbcec07e..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/ResolvedValueSet.java
+++ /dev/null
@@ -1,93 +0,0 @@
-package gov.nih.nci.evs.restapi.bean;
-
-import java.io.*;
-import java.util.*;
-import java.net.*;
-
-import com.google.gson.*;
-import com.google.gson.GsonBuilder;
-import com.google.gson.reflect.TypeToken;
-import com.thoughtworks.xstream.io.json.JettisonMappedXmlDriver;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-import com.thoughtworks.xstream.XStream;
-
-public class ResolvedValueSet
-{
-
-// Variable declaration
-	private String uri;
-	private String name;
-	private List concepts;
-
-// Default constructor
-	public ResolvedValueSet() {
-	}
-
-// Constructor
-	public ResolvedValueSet(
-		String uri,
-		String name,
-		List concepts) {
-
-		this.uri = uri;
-		this.name = name;
-		this.concepts = concepts;
-	}
-
-// Set methods
-	public void setUri(String uri) { 
-		this.uri = uri;
-	}
-
-	public void setName(String name) { 
-		this.name = name;
-	}
-
-	public void setConcepts(List concepts) { 
-		this.concepts = concepts;
-	}
-
-
-// Get methods
-	public String getUri() { 
-		return this.uri;
-	}
-
-	public String getName() { 
-		return this.name;
-	}
-
-	public List getConcepts() { 
-		return this.concepts;
-	}
-
-	public String toXML() {
-		XStream xstream_xml = new XStream(new DomDriver());
-		String xml = xstream_xml.toXML(this);
-		xml = escapeDoubleQuotes(xml);
-		StringBuffer buf = new StringBuffer();
-		String XML_DECLARATION = "";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i editActions;
-
-// Default constructor
-	public Revision() {
-	}
-
-// Constructor
-	public Revision(
-		String codingScheme,
-		String version,
-		String date,
-		List editActions) {
-
-		this.codingScheme = codingScheme;
-		this.version = version;
-		this.date = date;
-		this.editActions = editActions;
-	}
-
-// Set methods
-	public void setCodingScheme(String codingScheme) {
-		this.codingScheme = codingScheme;
-	}
-
-	public void setVersion(String version) {
-		this.version = version;
-	}
-
-	public void setDate(String date) {
-		this.date = date;
-	}
-
-	public void setEditActions(List editActions) {
-		this.editActions = editActions;
-	}
-
-
-// Get methods
-	public String getCodingScheme() {
-		return this.codingScheme;
-	}
-
-	public String getVersion() {
-		return this.version;
-	}
-
-	public String getDate() {
-		return this.date;
-	}
-
-	public List getEditActions() {
-		return this.editActions;
-	}
-
-	public String toXML() {
-		XStream xstream_xml = new XStream(new DomDriver());
-		String xml = xstream_xml.toXML(this);
-		xml = escapeDoubleQuotes(xml);
-		StringBuffer buf = new StringBuffer();
-		String XML_DECLARATION = "";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-public class Role
-{
-
-// Variable declaration
-	private String relationship;
-	private String relatedConceptCode;
-	private String relatedConceptLabel;
-
-// Default constructor
-	public Role() {
-	}
-
-// Constructor
-	public Role(
-		String relationship,
-		String relatedConceptCode,
-		String relatedConceptLabel) {
-
-		this.relationship = relationship;
-		this.relatedConceptCode = relatedConceptCode;
-		this.relatedConceptLabel = relatedConceptLabel;
-	}
-
-// Set methods
-	public void setRelationship(String relationship) {
-		this.relationship = relationship;
-	}
-
-	public void setRelatedConceptCode(String relatedConceptCode) {
-		this.relatedConceptCode = relatedConceptCode;
-	}
-
-	public void setRelatedConceptLabel(String relatedConceptLabel) {
-		this.relatedConceptLabel = relatedConceptLabel;
-	}
-
-
-// Get methods
-	public String getRelationship() {
-		return this.relationship;
-	}
-
-	public String getRelatedConceptCode() {
-		return this.relatedConceptCode;
-	}
-
-	public String getRelatedConceptLabel() {
-		return this.relatedConceptLabel;
-	}
-
-	public String toString() {
-		return "(" + relationship + ") --> [" + relatedConceptLabel + " (" + relatedConceptCode + ")]";
-
-	}
-
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Row.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Row.java
deleted file mode 100644
index 2f42bcfe6..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Row.java
+++ /dev/null
@@ -1,70 +0,0 @@
-package gov.nih.nci.evs.restapi.bean;
-
-import java.io.*;
-import java.util.*;
-import java.net.*;
-
-import com.google.gson.*;
-import com.google.gson.GsonBuilder;
-import com.google.gson.reflect.TypeToken;
-import com.thoughtworks.xstream.io.json.JettisonMappedXmlDriver;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-import com.thoughtworks.xstream.XStream;
-
-public class Row
-{
-
-// Variable declaration
-	private List row;
-
-// Default constructor
-	public Row() {
-	}
-
-// Constructor
-	public Row(
-		List row) {
-
		this.row = row;
-	}
-
-// Set methods
-	public void setrow(List row) {
-		this.row = row;
-	}
-
-
-// Get methods
-	public List getrow() {
-		return this.row;
-	}
-
-	public String toXML() {
-		XStream xstream_xml = new XStream(new DomDriver());
-		String xml = xstream_xml.toXML(this);
-		xml = escapeDoubleQuotes(xml);
-		StringBuffer buf = new StringBuffer();
-		String XML_DECLARATION = "";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class SearchResult
-{
-	public static final String XML_DECLARATION = "";
-
-// Variable declaration
-	private List matchedConcepts;
-
-// Default constructor
-	public SearchResult() {
-	}
-
-// Constructor
-	public SearchResult(
-		List matchedConcepts) {
-
-		this.matchedConcepts = matchedConcepts;
-	}
-
-// Set methods
-	public void setMatchedConcepts(List matchedConcepts) {
-		this.matchedConcepts = matchedConcepts;
-	}
-
-
-// Get methods
-	public List getMatchedConcepts() {
-		return this.matchedConcepts;
-	}
-
-
-	public String toXML() {
-		XStream xstream_xml = new XStream(new DomDriver());
-		String xml = xstream_xml.toXML(this);
-		xml = StringUtils.escapeDoubleQuotes(xml);
-		xml = XML_DECLARATION + "\n" + xml;
-		xml = StringUtils.removePackageNames(Constants.EVSRESTAPI_BEAN, xml);
-        return xml;
-	}
-
-	public String toJson() {
-		//return new Gson().toJson(this);
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-    public static Vector searchResult2DelimitedStrings(SearchResult sr) {
-		if (sr == null) return null;
-		Vector v = new Vector();
-		List matchedConcepts = sr.getMatchedConcepts();
-		for (int i=0; i
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class ServerInfo
-{
-
-// Variable declaration
-	private String name;
-	private String serviceUrl;
-	private String username;
-	private String password;
-	private String defaultGraph;
-
-// Default constructor
-	public ServerInfo() {
-	}
-
-// Constructor
-	public ServerInfo(
-		String name,
-		String serviceUrl,
-		String username,
-		String password) {
-
-		this.name = name;
-		this.serviceUrl = serviceUrl;
-		this.username = username;
-		this.password = password;
-		this.defaultGraph = null;
-	}
-
-	public ServerInfo(
-		String name,
-		String serviceUrl,
-		String username,
-		String password,
-		String defaultGraph) {
-
-		this.name = name;
-		this.serviceUrl = serviceUrl;
-		this.username = username;
-		this.password = password;
-		this.defaultGraph = defaultGraph;
-	}
-
-// Set methods
-	public void setName(String name) {
-		this.name = name;
-	}
-
-	public void setServiceUrl(String serviceUrl) {
-		this.serviceUrl = serviceUrl;
-	}
-
-	public void setUsername(String username) {
-		this.username = username;
-	}
-
-	public void setPassword(String password) {
-		this.password = password;
-	}
-
-	public void setDefaultGraph(String defaultGraph) {
-		this.defaultGraph = defaultGraph;
-	}
-
-
-// Get methods
-	public String getName() {
-		return this.name;
-	}
-
-	public String getServiceUrl() {
-		return this.serviceUrl;
-	}
-
-	public String getUsername() {
-		return this.username;
-	}
-
-	public String getPassword() {
-		return this.password;
-	}
-
-	public String getDefaultGraph() {
-		return this.defaultGraph;
-	}
-
-
-	public String toString() {
-		StringBuffer buf = new StringBuffer();
-		buf.append("Name: " + name).append("\n");
-		buf.append("URL: " + serviceUrl).append("\n");
-		buf.append("Username: " + username).append("\n");
-		buf.append("Password: " + password).append("\n");
-		buf.append("DefaultGraph: " + defaultGraph);
-		return buf.toString();
-	}
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Subconcept.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Subconcept.java
deleted file mode 100644
index ba7aa5f6b..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Subconcept.java
+++ /dev/null
@@ -1,101 +0,0 @@
-package gov.nih.nci.evs.restapi.bean;
-
-
-import java.io.*;
-import java.net.*;
-import java.util.*;
-
-
-/**
- * 
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class Subconcept
-{
-
-// Variable declaration
-	private String code;
-	private String label;
-
-// Default constructor
-	public Subconcept() {
-	}
-
-// Constructor
-	public Subconcept(
-		String code,
-		String label) {
-
-		this.code = code;
-		this.label = label;
-	}
-
-// Set methods
-	public void setCode(String code) {
-		this.code = code;
-	}
-
-	public void setLabel(String label) {
-		this.label = label;
-	}
-
-
-// Get methods
-	public String getCode() {
-		return this.code;
-	}
-
-	public String getLabel() {
-		return this.label;
-	}
-
-
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Subset.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Subset.java
deleted file mode 100644
index 9dd3401cb..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Subset.java
+++ /dev/null
@@ -1,71 +0,0 @@
-package gov.nih.nci.evs.restapi.bean;
-
-import java.io.*;
-import java.util.*;
-import java.net.*;
-
-import com.google.gson.*;
-import com.google.gson.GsonBuilder;
-import com.google.gson.reflect.TypeToken;
-import com.thoughtworks.xstream.io.json.JettisonMappedXmlDriver;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-import com.thoughtworks.xstream.XStream;
-
-public class Subset
-{
-
-// Variable declaration
-	private List entities;
-
-// Default constructor
-	public Subset() {
-	}
-
-// Constructor
-	public Subset(
-		List entities) {
-
-		this.entities = entities;
-	}
-
-// Set methods
-	public void setEntities(List entities) {
-		this.entities = entities;
-	}
-
-
-// Get methods
-	public List getEntities() {
-		return this.entities;
-	}
-
-	public String toXML() {
-		XStream xstream_xml = new XStream(new DomDriver());
-		String xml = xstream_xml.toXML(this);
-		xml = escapeDoubleQuotes(xml);
-		StringBuffer buf = new StringBuffer();
-		String XML_DECLARATION = "";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class Superconcept
-{
-
-// Variable declaration
-	private String code;
-	private String label;
-
-// Default constructor
-	public Superconcept() {
-	}
-
-// Constructor
-	public Superconcept(
-		String code,
-		String label) {
-
-		this.code = code;
-		this.label = label;
-	}
-
-// Set methods
-	public void setCode(String code) {
-		this.code = code;
-	}
-
-	public void setLabel(String label) {
-		this.label = label;
-	}
-
-
-// Get methods
-	public String getCode() {
-		return this.code;
-	}
-
-	public String getLabel() {
-		return this.label;
-	}
-
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Synonym.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Synonym.java
deleted file mode 100644
index 74295cd84..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/Synonym.java
+++ /dev/null
@@ -1,243 +0,0 @@
-package gov.nih.nci.evs.restapi.bean;
-
-
-import java.io.*;
-import java.net.*;
-import java.util.*;
-
-import com.google.gson.*;
-import com.google.gson.GsonBuilder;
-import com.google.gson.reflect.TypeToken;
-import com.thoughtworks.xstream.io.json.JettisonMappedXmlDriver;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-import com.thoughtworks.xstream.XStream;
-
-/**
- * 
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class Synonym
-{
-
-// Variable declaration
-	private String code;
-	private String label;
-	private String termName;
-	private String termGroup;
-	private String termSource;
-	private String sourceCode;
-	private String subSourceName;
-	private String subSourceCode;
-
-// Default constructor
-	public Synonym() {
-	}
-
-// Constructor
-	public Synonym(
-		String code,
-		String label,
-		String termName,
-		String termGroup,
-		String termSource,
-		String sourceCode,
-		String subSourceName,
-		String subSourceCode) {
-
-		this.code = code;
-		this.label = label;
-		this.termName = termName;
-		this.termGroup = termGroup;
-		this.termSource = termSource;
-		this.sourceCode = sourceCode;
-		this.subSourceName = subSourceName;
-		this.subSourceCode = subSourceCode;
-	}
-
-	public Synonym(
-		String termName,
-		String termGroup,
-		String termSource,
-		String sourceCode) {
-		this.code = null;
-		this.label = null;
-		this.termName = termName;
-		this.termGroup = termGroup;
-		this.termSource = termSource;
-		this.sourceCode = sourceCode;
-		this.subSourceName = null;
-		this.subSourceCode = null;
-	}
-
-// Set methods
-	public void setCode(String code) {
-		this.code = code;
-	}
-
-	public void setLabel(String label) {
-		this.label = label;
-	}
-
-	public void setTermName(String termName) {
-		this.termName = termName;
-	}
-
-	public void setTermGroup(String termGroup) {
-		this.termGroup = termGroup;
-	}
-
-	public void setTermSource(String termSource) {
-		this.termSource = termSource;
-	}
-
-	public void setSourceCode(String sourceCode) {
-		this.sourceCode = sourceCode;
-	}
-
-	public void setSubSourceName(String subSourceName) {
-		this.subSourceName = subSourceName;
-	}
-
-	public void setSubSourceCode(String subSourceCode) {
-		this.subSourceCode = subSourceCode;
-	}
-
-
-// Get methods
-	public String getCode() {
-		return this.code;
-	}
-
-	public String getLabel() {
-		return this.label;
-	}
-
-	public String getTermName() {
-		return this.termName;
-	}
-
-	public String getTermGroup() {
-		return this.termGroup;
-	}
-
-	public String getTermSource() {
-		return this.termSource;
-	}
-
-	public String getSourceCode() {
-		return this.sourceCode;
-	}
-
-	public String getSubSourceName() {
-		return this.subSourceName;
-	}
-
-	public String getSubSourceCode() {
-		return this.subSourceCode;
-	}
-
-	public String toXML() {
-		XStream xstream_xml = new XStream(new DomDriver());
-		String xml = xstream_xml.toXML(this);
-		xml = escapeDoubleQuotes(xml);
-		StringBuffer buf = new StringBuffer();
-		String XML_DECLARATION = "";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i headings;
-	private List rows;
-
-// Default constructor
-	public Table() {
-	}
-
-// Constructor
-	public Table(
-		String label,
-		List headings,
-		List rows) {
-
-		this.label = label;
-		this.headings = headings;
-		this.rows = rows;
-	}
-
-
-	public Table(
-		String label,
-		Vector heading_vec,
-		Vector data_vec) {
-		this.label = label;
-		this.headings = new ArrayList();
-		for (int i=0; i headings) {
-		this.headings = headings;
-	}
-
-	public void setRows(List rows) {
-		this.rows = rows;
-	}
-
-
-// Get methods
-	public String getLabel() {
-		return this.label;
-	}
-
-	public List getHeadings() {
-		return this.headings;
-	}
-
-	public List getRows() {
-		return this.rows;
-	}
-
-	public String toXML() {
-		XStream xstream_xml = new XStream(new DomDriver());
-		String xml = xstream_xml.toXML(this);
-		xml = escapeDoubleQuotes(xml);
-		StringBuffer buf = new StringBuffer();
-		String XML_DECLARATION = "";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i").append("\n");
-		buf.append("
").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		List headings = table.getHeadings();
-		for (int i=0; i").append("\n");
-			buf.append(heading).append("\n");
-			buf.append("").append("\n");
-		}
-		buf.append("").append("\n");
-		List rows = table.getRows();
-		for (int i=0; i").append("\n");
-			Row row = rows.get(i);
-			List cell_values = row.getrow();
-			for (int j=0; j").append("\n");
-				buf.append(cell_value).append("\n");
-				buf.append("").append("\n");
-			}
-			buf.append("").append("\n");
-		}
-		buf.append("
").append("\n");
-		buf.append("
").append("\n");
-		return buf.toString();
-	}
-
-
-	public static Table construct_table(
-		String label,
-		Vector heading_vec,
-		Vector data_vec) {
-		List headings = new ArrayList();
-		for (int i=0; i rows = new ArrayList();
-		for (int i=0; i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i nodes;
-
-// Default constructor
-	public Tree() {
-	}
-
-// Constructor
-	public Tree(
-		String root,
-		List nodes) {
-
-		this.root = root;
-		this.nodes = nodes;
-	}
-
-// Set methods
-	public void setRoot(String root) {
-		this.root = root;
-	}
-
-	public void setNodes(List nodes) {
-		this.nodes = nodes;
-	}
-
-
-// Get methods
-	public String getRoot() {
-		return this.root;
-	}
-
-	public List getNodes() {
-		return this.nodes;
-	}
-
-	public String toXML() {
-		XStream xstream_xml = new XStream(new DomDriver());
-		String xml = xstream_xml.toXML(this);
-		xml = escapeDoubleQuotes(xml);
-		StringBuffer buf = new StringBuffer();
-		String XML_DECLARATION = "";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class TreeItem implements Serializable, Comparable {
-    public String _code = null;
-    public String _text = null;
-
-    public String _ns = null;//"na";
-    public String _id = null;  // tree_node_id
-
-    public String _auis = null;
-    public boolean _expandable = false;
-
-    public static String ROOT = "Root";
-    public static String ROOT_CODE = "";
-
-    public Map> _assocToChildMap =
-        new TreeMap>();
-
-    public boolean equals(Object o) {
-		if (o == null) return false;
-		if (!(o instanceof TreeItem)) return false;
-		TreeItem item = (TreeItem) o;
-		if (_ns == null) {
-			return _text.compareTo(item._text) == 0 && _code.compareTo(item._code) == 0;
-		} else {
-			if (item._ns == null) return false;
-			return _text.compareTo(item._text) == 0 && _code.compareTo(item._code) == 0 && _ns.compareTo(item._ns) == 0;
-		}
-    }
-
-    public int compareTo(TreeItem ti) {
-        String c1 = _code;
-        String c2 = ti._code;
-        if (c1.startsWith("@"))
-            return 1;
-        if (c2.startsWith("@"))
-            return -1;
-        int i = c1.compareTo(c2);
-        return i != 0 ? i : _text.compareTo(ti._text);
-    }
-
-    public TreeItem(String code, String text) {
-        super();
-        _code = code;
-        _text = text;
-        _auis = null;
-        _ns = null;
-    }
-
-    public TreeItem(String code, String text, String auiText) {
-        super();
-        _code = code;
-        _text = text;
-        _auis = auiText;
-        _ns = null;
-    }
-
-    public TreeItem(String code, String text, String ns, String auiText) {
-        super();
-        _code = code;
-        _ns = ns;
-        _text = text;
-        _auis = auiText;
-    }
-
-    public TreeItem(String code, String text, String ns, String id, String auiText) {
-        super();
-        _code = code;
-        _ns = ns;
-        _text = text;
-        _id = id;
-        _auis = auiText;
-    }
-
-    public void setNs(String ns) {
-		_ns = ns;
-	}
-
-    public void setId(String id) {
-		_id = id;
-	}
-
-    public void addAll(String assocText, List children) {
-        for (TreeItem item : children)
-            addChild(assocText, item);
-    }
-
-    public void addChild(String assocText, TreeItem child) {
-        List children = _assocToChildMap.get(assocText);
-        if (children == null) {
-            children = new ArrayList();
-            _assocToChildMap.put(assocText, children);
-        }
-        int i;
-        if ((i = children.indexOf(child)) >= 0) {
-            TreeItem existingTreeItem = children.get(i);
-            for (String assoc : child._assocToChildMap.keySet()) {
-                List toAdd = child._assocToChildMap.get(assoc);
-                if (!toAdd.isEmpty()) {
-                    existingTreeItem.addAll(assoc, toAdd);
-                    existingTreeItem._expandable = false;
-                }
-            }
-        } else
-            children.add(child);
-    }
-
-    public int hashCode() {
-		int hashcode = 0;
-		if (_code != null) hashcode = hashcode + _code.hashCode();
-		if (_ns != null && _ns.compareTo("na") != 0) hashcode = hashcode + _ns.hashCode();
-		if (_id != null) hashcode = hashcode + _id.hashCode();
-		if (_text != null) hashcode = hashcode + _text.hashCode();
-		if (_auis != null) hashcode = hashcode + _auis.hashCode();
-		if (_expandable) {
-			hashcode = hashcode + "expandable".hashCode();
-		}
-	    return hashcode;
-	}
-
-    public String toString() {
-    	String s = _text;
-    	if (_code != null && _code.length() > 0)
-    		s += " (" + _code + ")";
-
-    	if (_ns != null && _ns.length() > 0 && _ns.compareTo("na") != 0)
-    		s += " (" + _ns + ")";
-
-    	return s;
-    }
-
-    public static void printTree(TreeItem ti, int depth) {
-		printTree(ti, depth, true);
-	}
-
-    public static void printTree(TreeItem ti, int depth, boolean print_code_first) {
-		if (ti == null) return;
-
-        StringBuffer indent = new StringBuffer();
-        for (int i = 0; i < depth; i++) {
-            indent.append("\t");
-		}
-
-        StringBuffer codeAndText = new StringBuffer();
-
-        codeAndText.append(indent);
-
-        if (print_code_first) {
-			codeAndText.append("").append(ti._code)
-					.append(':').append(ti._text).append(ti._expandable ? " [+]" : "");
-		} else {
-			codeAndText.append("").append(ti._text).append(" (").append(ti._code).append(")");
-		}
-        System.out.println(codeAndText);
-
-        for (String association : ti._assocToChildMap.keySet()) {
-            List children = ti._assocToChildMap.get(association);
-            new SortUtils().quickSort(children);
-            for (int i=0; i children = ti._assocToChildMap.get(association);
-            new SortUtils().quickSort(children);
-            for (int i=0; i") != 0) return ti;
-		List children = ti._assocToChildMap.get(getAssociation(ti));
-		return (TreeItem) children.get(0);
-	}
-
-	public static TreeItem searchTree(TreeItem ti, String text) {
-		if (ti._text.compareTo(text) == 0) return ti;
-		TreeItem node = null;
-        for (String association : ti._assocToChildMap.keySet()) {
-            List children = ti._assocToChildMap.get(association);
-            if (children != null) {
-				for (int i=0; i
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class TypeAndValue
-{
-
-// Variable declaration
-	private String type;
-	private String value;
-
-// Default constructor
-	public TypeAndValue() {
-	}
-
-// Constructor
-	public TypeAndValue(
-		String type,
-		String value) {
-
-		this.type = type;
-		this.value = value;
-	}
-
-// Set methods
-	public void setType(String type) {
-		this.type = type;
-	}
-
-	public void setValue(String value) {
-		this.value = value;
-	}
-
-
-// Get methods
-	public String getType() {
-		return this.type;
-	}
-
-	public String getValue() {
-		return this.value;
-	}
-
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/ValueSetConfig.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/ValueSetConfig.java
deleted file mode 100644
index a1a6b18b3..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/ValueSetConfig.java
+++ /dev/null
@@ -1,132 +0,0 @@
-package gov.nih.nci.evs.restapi.bean;
-
-import java.io.*;
-import java.net.*;
-import java.util.*;
-
-
-/**
- * 
- * Copyright 2008,2009 NGIT. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIT and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIT" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIT
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIT, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- *          Modification history Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class ValueSetConfig
-{
-
-// Variable declaration
-	private String name;
-	private String uri;
-	private String reportURI;
-	private String extractionRule;
-
-// Default constructor
-	public ValueSetConfig() {
-	}
-
-// Constructor
-	public ValueSetConfig(
-		String name,
-		String uri,
-		String reportURI,
-		String extractionRule) {
-
-		this.name = name;
-		this.uri = uri;
-		this.reportURI = reportURI;
-		this.extractionRule = extractionRule;
-	}
-
-// Set methods
-	public void setName(String name) {
-		this.name = name;
-	}
-
-	public void setUri(String uri) {
-		this.uri = uri;
-	}
-
-	public void setReportURI(String reportURI) {
-		this.reportURI = reportURI;
-	}
-
-	public void setExtractionRule(String extractionRule) {
-		this.extractionRule = extractionRule;
-	}
-
-
-// Get methods
-	public String getName() {
-		return this.name;
-	}
-
-	public String getUri() {
-		return this.uri;
-	}
-
-	public String getReportURI() {
-		return this.reportURI;
-	}
-
-	public String getExtractionRule() {
-		return this.extractionRule;
-	}
-
-	public String toString() {
-		StringBuffer buf = new StringBuffer();
-		buf.append("name: ").append(name);
-		buf.append("\n\turi: ").append(uri);
-		String report_uri = reportURI;
-		if (report_uri != null) {
-			report_uri = reportURI.replaceAll(" ", "%20");
-		}
-		buf.append("\n\treportURI: ").append(report_uri);
-		buf.append("\n\textractionRule: ").append(extractionRule);
-		return buf.toString();
-	}
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/ValueSetDefinition.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/ValueSetDefinition.java
deleted file mode 100644
index 2f678627f..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/ValueSetDefinition.java
+++ /dev/null
@@ -1,126 +0,0 @@
-package gov.nih.nci.evs.restapi.bean;
-
-import java.io.*;
-import java.util.*;
-import java.net.*;
-
-import com.google.gson.*;
-import com.google.gson.GsonBuilder;
-import com.google.gson.reflect.TypeToken;
-import com.thoughtworks.xstream.io.json.JettisonMappedXmlDriver;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-import com.thoughtworks.xstream.XStream;
-
-public class ValueSetDefinition
-{
-
-// Variable declaration
-	private String uri;
-	private String defaultCodingScheme;
-	private String conceptDomain;
-	private String name;
-	private String code;
-	private List sources;
-
-// Default constructor
-	public ValueSetDefinition() {
-	}
-
-// Constructor
-	public ValueSetDefinition(
-		String uri,
-		String defaultCodingScheme,
-		String conceptDomain,
-		String name,
-		String code,
-		List sources) {
-
-		this.uri = uri;
-		this.defaultCodingScheme = defaultCodingScheme;
-		this.conceptDomain = conceptDomain;
-		this.name = name;
-		this.code = code;
-		this.sources = sources;
-	}
-
-// Set methods
-	public void setUri(String uri) { 
-		this.uri = uri;
-	}
-
-	public void setDefaultCodingScheme(String defaultCodingScheme) { 
-		this.defaultCodingScheme = defaultCodingScheme;
-	}
-
-	public void setConceptDomain(String conceptDomain) { 
-		this.conceptDomain = conceptDomain;
-	}
-
-	public void setName(String name) { 
-		this.name = name;
-	}
-
-	public void setCode(String code) { 
-		this.code = code;
-	}
-
-	public void setSources(List sources) { 
-		this.sources = sources;
-	}
-
-
-// Get methods
-	public String getUri() { 
-		return this.uri;
-	}
-
-	public String getDefaultCodingScheme() { 
-		return this.defaultCodingScheme;
-	}
-
-	public String getConceptDomain() { 
-		return this.conceptDomain;
-	}
-
-	public String getName() { 
-		return this.name;
-	}
-
-	public String getCode() { 
-		return this.code;
-	}
-
-	public List getSources() { 
-		return this.sources;
-	}
-
-	public String toXML() {
-		XStream xstream_xml = new XStream(new DomDriver());
-		String xml = xstream_xml.toXML(this);
-		xml = escapeDoubleQuotes(xml);
-		StringBuffer buf = new StringBuffer();
-		String XML_DECLARATION = "";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class Constants {
-	public static final  String INVERSE_IS_A = "inverse_is_a";
-	public static final int TRAVERSE_UP = 1;
-	public static final int TRAVERSE_DOWN = 0;
-    public static final String NEW_CODE = "NHC0";
-    public static final String NCIT_NS = "";
-
-	public static final String XML_DECLARATION = "";
-	public static final String INVERSE_IS_OF = "inverseIsA";
-	public static final String ROLE = "Role";
-	public static final String ASSOCIATION = "Association";
-	public static final String HIERARCHICAL = "Hierarchical";
-
-    public static final String FULL_SYN = "FULL_SYN";
-    public static final String DEFINITION = "DEFINITION";
-    public static final String ALT_DEFINITION = "ALT_DEFINITION";
-
-	public static final String EXACT_MATCH = "exactMatch";
-	public static final String STARTS_MATCH = "startsWith";
-	public static final String ENDS_MATCH = "endsWith";
-	public static final String CONTAINS = "contains";
-	public static String DISEASE_IS_STAGE  = "Disease_Is_Stage";
-    public static int MAXIMUM_LEVEL  = 1000;
-
-	public static final String EVSRESTAPI_BEAN = "gov.nih.nci.evs.restapi.bean";
-
-    public static String[] COMMON_PROPERTIES = {"code", "label", "Preferred_Name", "Display_Name", "DEFINITION", "ALT_DEFINITION",
-                                                "FULL_SYN", "Concept_Status", "Semantic_Type"};
-
-	public static String DEFAULT_VERSION_PREDICATE = "owl:versionInfo";
-	public static String OBO_VERSION_PREDICATE = "oboInOwl:hasOBOFormatVersion";
-
-	public static String[] VERSION_PREDICATE = new String[] {DEFAULT_VERSION_PREDICATE, OBO_VERSION_PREDICATE};
-
-    public static String ASSOCIATION_NAME = "inverse_is_a";
-
-    public static final String TYPE_ROLE = "type_role";
-    public static final String TYPE_ASSOCIATION = "type_association";
-    public static final String TYPE_SUPERCONCEPT = "type_superconcept";
-    public static final String TYPE_SUBCONCEPT = "type_subconcept";
-    public static final String TYPE_INVERSE_ROLE = "type_inverse_role";
-    public static final String TYPE_INVERSE_ASSOCIATION = "type_inverse_association";
-
-    public static String STARTS_WITH = "startsWith";
-    public static String ENDS_WITH = "endsWith";
-
-    public static String TERMINOLOGY_SUBSET_CODE = "C54443"; //Terminology Subset (Code C54443)
-
-	public static String CONCEPT_IN_SUBSET = "Concept_In_Subset";
-	public static String CONTRIBUTING_SOURCE = "Contributing_Source";
-	public static String NCI_THESAURUS = "NCI_Thesaurus";
-
-	public static int DEFAULT_LIMIT = 15000;
-
-    public static final String VALUE_SET_REPORT_CONFIG = "gov.nih.nci.evs.browser.ValueSetReportConfig";
-
-    public static final String VALUE_SET_URI_PREFIX = "http://evs.nci.nih.gov/valueset/";
-    public static final String VALUE_SET_URI_PREFIX_OLD = "http://ncit";
-
-
-    /**
-     * Constructor
-     */
-    private Constants() {
-
-    }
-
-} // Class Constants
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/config/ConfigurationController.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/config/ConfigurationController.java
deleted file mode 100644
index e0b7fbdbe..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/config/ConfigurationController.java
+++ /dev/null
@@ -1,132 +0,0 @@
-package gov.nih.nci.evs.restapi.config;
-
-import gov.nih.nci.evs.restapi.util.*;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.util.Iterator;
-import java.util.Properties;
-import java.util.Vector;
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-import org.w3c.dom.NodeList;
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@nih.gov
- *
- */
-
-abstract public class ConfigurationController {
-	/** The sys prop. */
-	private static Properties sysProp = System.getProperties();
-
-	/** The dom. */
-	private static Document dom;
-
-	/** The properties. */
-	private static Properties properties = loadProperties();
-
-	/** The Constants. */
-	public final static String owlfile = properties.getProperty("owlfile");
-
-	public final static String username = properties.getProperty("username");
-	public final static String password = properties.getProperty("password");
-	public final static String serviceUrl = properties.getProperty("serviceUrl");
-	public final static String namedGraph = properties.getProperty("namedGraph");
-	public final static String restURL = properties.getProperty("restURL");
-	public final static String serviceUrl_ctrp = properties.getProperty("serviceUrl_ctrp");
-	public final static String serviceUrls = properties.getProperty("serviceUrls");
-
-	public final static String masterSubsetCodeColumnNumber = properties.getProperty("masterSubsetCodeColumnNumber");
-	public final static String masterConceptCodeColumnNumber = properties.getProperty("masterConceptCodeColumnNumber");
-	public final static String subsetCodeColumnNumber = properties.getProperty("subsetCodeColumnNumber");
-	public final static String conceptCodeColumnNumber = properties.getProperty("conceptCodeColumnNumber");
-
-	public final static String compositeFile = properties.getProperty("compositeFile");
-	public final static String projectFile = properties.getProperty("projectFile");
-
-	public final static String mapping_source_shortname = properties.getProperty("mapping_source_shortname");
-	public final static String mapping_target_shortname = properties.getProperty("mapping_target_shortname");
-	public final static String mapping_source_graphname = properties.getProperty("mapping_source_graphname");
-	public final static String mapping_target_graphname = properties.getProperty("mapping_target_graphname");
-	public final static String mapping_datafile = properties.getProperty("mapping_datafile");
-    public final static String mapping_filename = properties.getProperty("mapping_filename");
-	public final static String mapping_source_id = properties.getProperty("mapping_source_id");
-    public final static String mapping_target_id = properties.getProperty("mapping_target_id");
-
-	public final static String source_coding_scheme = properties.getProperty("source_coding_scheme");
-	public final static String source_coding_scheme_version = properties.getProperty("source_coding_scheme_version");
-	public final static String target_coding_scheme =  properties.getProperty("target_coding_scheme");
-	public final static String target_coding_scheme_version = properties.getProperty("target_coding_scheme_version");
-	public final static String mapping_name = properties.getProperty("mapping_name");
-	public final static String mapping_version = properties.getProperty("mapping_version");
-
-	public final static String source_ns = properties.getProperty("source_ns");
-	public final static String target_ns = properties.getProperty("target_ns");
-
-	public final static String ontology_display_label = properties.getProperty("ontology_display_label");
-	public final static String ontology_version_info = properties.getProperty("ontology_version_info");
-	public final static String ontology_release_date = properties.getProperty("ontology_release_date");
-	public final static String ontology_description = properties.getProperty("ontology_description");
-
-	public final static String termfiles = properties.getProperty("termfiles");
-	public final static String term_file_heading = properties.getProperty("term_file_heading");
-	public final static String term_file_delim = properties.getProperty("term_file_delim");
-	public final static String match_file_heading = properties.getProperty("match_file_heading");
-	public final static String term_column = properties.getProperty("term_column");
-
-	/**
-	 * To be implemented by each descendant testcase.
-	 *
-	 * @return String
-	 */
-	protected String getTestID(){
-		return "Test Case";
-	}
-
-
-	/**
-	 * Load properties.
-	 *
-	 * @return the properties
-	 */
-	private static Properties loadProperties() {
-		try{
-			String propertyFile = "resources/Test.properties";
-			Properties lproperties = new Properties();
-			FileInputStream fis = new FileInputStream(new File(propertyFile));
-			lproperties.load(fis);
-			return lproperties;
-		} catch (Exception e){
-			System.out.println("Error reading properties file");
-			e.printStackTrace();
-			return null;
-		}
-	}
-
-	/**
-	 * Parses the xml file.
-	 *
-	 * @param filename the filename
-	 */
-	private static void parseXMLFile(String filename)
-	{
-		DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
-		try{
-			DocumentBuilder db = dbf.newDocumentBuilder();
-			dom=db.parse(filename);
-		}
-		catch (Exception e){
-			e.printStackTrace();
-		}
-	}
-
-}
-
-
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/model/Association.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/model/Association.java
deleted file mode 100644
index 487547490..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/model/Association.java
+++ /dev/null
@@ -1,94 +0,0 @@
-package gov.nih.nci.evs.restapi.model;
-
-import java.io.*;
-import java.util.*;
-import java.net.*;
-
-import com.google.gson.*;
-import com.google.gson.GsonBuilder;
-import com.google.gson.reflect.TypeToken;
-import com.thoughtworks.xstream.io.json.JettisonMappedXmlDriver;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-import com.thoughtworks.xstream.XStream;
-
-
-public class Association
-{
-
-// Variable declaration
-	private String type;
-	private String relatedCode;
-	private String relatedName;
-
-// Default constructor
-	public Association() {
-	}
-
-// Constructor
-	public Association(
-		String type,
-		String relatedCode,
-		String relatedName) {
-
-		this.type = type;
-		this.relatedCode = relatedCode;
-		this.relatedName = relatedName;
-	}
-
-// Set methods
-	public void setType(String type) {
-		this.type = type;
-	}
-
-	public void setRelatedCode(String relatedCode) {
-		this.relatedCode = relatedCode;
-	}
-
-	public void setRelatedName(String relatedName) {
-		this.relatedName = relatedName;
-	}
-
-
-// Get methods
-	public String getType() {
-		return this.type;
-	}
-
-	public String getRelatedCode() {
-		return this.relatedCode;
-	}
-
-	public String getRelatedName() {
-		return this.relatedName;
-	}
-
-	public String toXML() {
-		XStream xstream_xml = new XStream(new DomDriver());
-		String xml = xstream_xml.toXML(this);
-		xml = escapeDoubleQuotes(xml);
-		StringBuffer buf = new StringBuffer();
-		String XML_DECLARATION = "";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i synonyms;
-	private List definitions;
-	private List properties;
-
-// Default constructor
-	public Concept() {
-	}
-
-// Constructor
-	public Concept(
-		String code,
-		String name,
-		String terminology,
-		String version,
-		List synonyms,
-		List definitions,
-		List properties) {
-
-		this.code = code;
-		this.name = name;
-		this.terminology = terminology;
-		this.version = version;
-		this.synonyms = synonyms;
-		this.definitions = definitions;
-		this.properties = properties;
-	}
-
-// Set methods
-	public void setCode(String code) {
-		this.code = code;
-	}
-
-	public void setName(String name) {
-		this.name = name;
-	}
-
-	public void setTerminology(String terminology) {
-		this.terminology = terminology;
-	}
-
-	public void setVersion(String version) {
-		this.version = version;
-	}
-
-	public void setSynonyms(List synonyms) {
-		this.synonyms = synonyms;
-	}
-
-	public void setDefinitions(List definitions) {
-		this.definitions = definitions;
-	}
-
-	public void setProperties(List properties) {
-		this.properties = properties;
-	}
-
-
-// Get methods
-	public String getCode() {
-		return this.code;
-	}
-
-	public String getName() {
-		return this.name;
-	}
-
-	public String getTerminology() {
-		return this.terminology;
-	}
-
-	public String getVersion() {
-		return this.version;
-	}
-
-	public List getSynonyms() {
-		return this.synonyms;
-	}
-
-	public List getDefinitions() {
-		return this.definitions;
-	}
-
-	public List getProperties() {
-		return this.properties;
-	}
-
-	public String toXML() {
-		XStream xstream_xml = new XStream(new DomDriver());
-		String xml = xstream_xml.toXML(this);
-		xml = escapeDoubleQuotes(xml);
-		StringBuffer buf = new StringBuffer();
-		String XML_DECLARATION = "";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i parents;
-	private List children;
-	private List roles;
-	private List inverseRoles;
-	private List associations;
-	private List inverseAssociations;
-	private List maps;
-
-// Default constructor
-	public ConceptDetails() {
-	}
-
-// Constructor
-	public ConceptDetails(
-		List parents,
-		List children,
-		List roles,
-		List inverseRoles,
-		List associations,
-		List inverseAssociations,
-		List maps) {
-
-		this.parents = parents;
-		this.children = children;
-		this.roles = roles;
-		this.inverseRoles = inverseRoles;
-		this.associations = associations;
-		this.inverseAssociations = inverseAssociations;
-		this.maps = maps;
-	}
-
-// Set methods
-	public void setParents(List parents) {
-		this.parents = parents;
-	}
-
-	public void setChildren(List children) {
-		this.children = children;
-	}
-
-	public void setRoles(List roles) {
-		this.roles = roles;
-	}
-
-	public void setInverseRoles(List inverseRoles) {
-		this.inverseRoles = inverseRoles;
-	}
-
-	public void setAssociations(List associations) {
-		this.associations = associations;
-	}
-
-	public void setInverseAssociations(List inverseAssociations) {
-		this.inverseAssociations = inverseAssociations;
-	}
-
-	public void setMaps(List maps) {
-		this.maps = maps;
-	}
-
-
-// Get methods
-	public List getParents() {
-		return this.parents;
-	}
-
-	public List getChildren() {
-		return this.children;
-	}
-
-	public List getRoles() {
-		return this.roles;
-	}
-
-	public List getInverseRoles() {
-		return this.inverseRoles;
-	}
-
-	public List getAssociations() {
-		return this.associations;
-	}
-
-	public List getInverseAssociations() {
-		return this.inverseAssociations;
-	}
-
-	public List getMaps() {
-		return this.maps;
-	}
-
-	public String toXML() {
-		XStream xstream_xml = new XStream(new DomDriver());
-		String xml = xstream_xml.toXML(this);
-		xml = escapeDoubleQuotes(xml);
-		StringBuffer buf = new StringBuffer();
-		String XML_DECLARATION = "";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i descendants;
-
-// Default constructor
-	public Descendant() {
-	}
-
-// Constructor
-	public Descendant(
-		List descendants) {
-
-		this.descendants = descendants;
-	}
-
-// Set methods
-	public void setDescendants(List descendants) { 
-		this.descendants = descendants;
-	}
-
-
-// Get methods
-	public List getDescendants() { 
-		return this.descendants;
-	}
-
-	public String toXML() {
-		XStream xstream_xml = new XStream(new DomDriver());
-		String xml = xstream_xml.toXML(this);
-		xml = escapeDoubleQuotes(xml);
-		StringBuffer buf = new StringBuffer();
-		String XML_DECLARATION = "";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i children;
-
-// Default constructor
-	public Subtree() {
-	}
-
-// Constructor
-	public Subtree(
-		String code,
-		String label,
-		boolean leaf,
-		List children) {
-
-		this.code = code;
-		this.label = label;
-		this.leaf = leaf;
-		this.children = children;
-	}
-
-// Set methods
-	public void setCode(String code) {
-		this.code = code;
-	}
-
-	public void setLabel(String label) {
-		this.label = label;
-	}
-
-	public void setLeaf(boolean leaf) {
-		this.leaf = leaf;
-	}
-
-	public void setChildren(List children) {
-		this.children = children;
-	}
-
-
-// Get methods
-	public String getCode() {
-		return this.code;
-	}
-
-	public String getLabel() {
-		return this.label;
-	}
-
-	public boolean getLeaf() {
-		return this.leaf;
-	}
-
-	public List getChildren() {
-		return this.children;
-	}
-
-	public String toXML() {
-		XStream xstream_xml = new XStream(new DomDriver());
-		String xml = xstream_xml.toXML(this);
-		xml = escapeDoubleQuotes(xml);
-		StringBuffer buf = new StringBuffer();
-		String XML_DECLARATION = "";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i subtrees;
-
-// Default constructor
-	public Tree() {
-	}
-
-// Constructor
-	public Tree(
-		List subtrees) {
-
-		this.subtrees = subtrees;
-	}
-
-// Set methods
-	public void setSubtrees(List subtrees) {
-		this.subtrees = subtrees;
-	}
-
-
-// Get methods
-	public List getSubtrees() {
-		return this.subtrees;
-	}
-
-	public String toXML() {
-		XStream xstream_xml = new XStream(new DomDriver());
-		String xml = xstream_xml.toXML(this);
-		xml = escapeDoubleQuotes(xml);
-		StringBuffer buf = new StringBuffer();
-		String XML_DECLARATION = "";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i children;
-
-// Default constructor
-	public TreeNode() {
-	}
-
-// Constructor
-	public TreeNode(
-		String code,
-		String name,
-		int level,
-		boolean leaf,
-		List children) {
-
-		this.code = code;
-		this.name = name;
-		this.level = level;
-		this.leaf = leaf;
-		this.children = children;
-	}
-
-// Set methods
-	public void setCode(String code) {
-		this.code = code;
-	}
-
-	public void setName(String name) {
-		this.name = name;
-	}
-
-	public void setLevel(int level) {
-		this.level = level;
-	}
-
-	public void setLeaf(boolean leaf) {
-		this.leaf = leaf;
-	}
-
-	public void setChildren(List children) {
-		this.children = children;
-	}
-
-// Get methods
-	public String getCode() {
-		return this.code;
-	}
-
-	public String getName() {
-		return this.name;
-	}
-
-	public int getLevel() {
-		return this.level;
-	}
-
-	public boolean getLeaf() {
-		return this.leaf;
-	}
-
-	public List getChildren() {
-		return this.children;
-	}
-
-	public String toXML() {
-		XStream xstream_xml = new XStream(new DomDriver());
-		String xml = xstream_xml.toXML(this);
-		xml = escapeDoubleQuotes(xml);
-		StringBuffer buf = new StringBuffer();
-		String XML_DECLARATION = "";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i codes;
-
-// Default constructor
-	public ValueSet() {
-	}
-
-// Constructor
-	public ValueSet(
-		String code,
-		String name,
-		String terminology,
-		String version,
-		List codes) {
-
-		this.code = code;
-		this.name = name;
-		this.terminology = terminology;
-		this.version = version;
-		this.codes = codes;
-	}
-
-// Set methods
-	public void setCode(String code) {
-		this.code = code;
-	}
-
-	public void setName(String name) {
-		this.name = name;
-	}
-
-	public void setTerminology(String terminology) {
-		this.terminology = terminology;
-	}
-
-	public void setVersion(String version) {
-		this.version = version;
-	}
-
-	public void setCodes(List codes) {
-		this.codes = codes;
-	}
-
-// Get methods
-	public String getCode() {
-		return this.code;
-	}
-
-	public String getName() {
-		return this.name;
-	}
-
-	public String getTerminology() {
-		return this.terminology;
-	}
-
-	public String getVersion() {
-		return this.version;
-	}
-
-	public List getCodes() {
-		return this.codes;
-	}
-
-	public String toXML() {
-		XStream xstream_xml = new XStream(new DomDriver());
-		String xml = xstream_xml.toXML(this);
-		xml = escapeDoubleQuotes(xml);
-		StringBuffer buf = new StringBuffer();
-		String XML_DECLARATION = "";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i";
-		buf.append(XML_DECLARATION).append("\n").append(xml);
-		xml = buf.toString();
-		return xml;
-	}
-
-	public String toJson() {
-		JsonParser parser = new JsonParser();
-		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(this);
-	}
-
-	public String escapeDoubleQuotes(String inputStr) {
-		char doubleQ = '"';
-		StringBuffer buf = new StringBuffer();
-		for (int i=0;  i
- * Copyright 2020 MSC. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or MSC
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      MSC, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@nih.gov
- *
- */
-
-
-public class OBOScannerTest {
-
-	public static void extractHierarchicalRelationships(String[] args) {
-		String owlfile = args[0];
-		long ms = System.currentTimeMillis();
-		Vector w = new OBOScanner(owlfile).extractHierarchicalRelationships();
-		String hierfile = "hier_" + owlfile + ".txt";
-		Utils.saveToFile(hierfile, w);
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-
-	public static void extractAxiomData(String[] args) {
-		String owlfile = args[0];
-		long ms = System.currentTimeMillis();
-		String outputfile = "axiom_" + owlfile;
-		Vector w = new OBOScanner(owlfile).extractAxiomData();
-		Utils.saveToFile(outputfile, w);
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-
-	public static void extractOWLRestrictions(String[] args) {
-		String owlfile = args[0];
-		long ms = System.currentTimeMillis();
-		String outputfile = "role_" + owlfile;
-		OBOScanner scanner = new OBOScanner(owlfile);
-		Vector w = scanner.extractOWLRestrictions(scanner.get_owl_vec());
-		Utils.saveToFile(outputfile, w);
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-
-	public static void extractProperties(String[] args) {
-		String owlfile = args[0];
-		OBOScanner scanner = new OBOScanner(owlfile);
-
-		long ms = System.currentTimeMillis();
-		String outputfile = "properties_" + owlfile;
-		Vector w = null;
-		w = scanner.extractProperties();
-		Utils.saveToFile(outputfile, w);
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-
-	public static void extractAssociations(String[] args) {
-		String owlfile = args[0];
-		long ms = System.currentTimeMillis();
-		String outputfile = "association_" + owlfile;
-		OBOScanner scanner = new OBOScanner(owlfile);
-		Vector w = scanner.extractAssociations();
-		Utils.saveToFile(outputfile, w);
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-
-	public static void extractRDFSLabels(String[] args) {
-		String owlfile = args[0];
-		long ms = System.currentTimeMillis();
-		String outputfile = "label_" + owlfile;
-		OBOScanner scanner = new OBOScanner(owlfile);
-		if (args.length > 1) {
-			String namespace = args[1];
-			OBOScanner.set_NAMESPACE(namespace);
-		}
-		Vector w = scanner.extractRDFSLabels(scanner.get_owl_vec());
-		Utils.saveToFile(outputfile, w);
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-
-
-	public static void extractSynonymsFromAxiomData(String filename){
-		Vector v = Utils.readFile(filename);
-		Vector w = new Vector();
-		for (int i=0; i " + ns);
-			}
-		}
-		return hmap;
-	}
-
-	public static void extractAnnotationProperties(String[] args) {
-		String owlfile = args[0];
-		long ms = System.currentTimeMillis();
-		String outputfile = "annotation_properties_" + owlfile;
-		OBOScanner scanner = new OBOScanner(owlfile);
-		Vector w = scanner.extractAnnotationProperties();
-		Utils.saveToFile(outputfile, w);
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-
-	public static void extractObjectProperties(String[] args) {
-		String owlfile = args[0];
-		long ms = System.currentTimeMillis();
-		String outputfile = "object_properties_" + owlfile;
-		OBOScanner scanner = new OBOScanner(owlfile);
-		Vector w = scanner.extractObjectProperties();
-		Utils.saveToFile(outputfile, w);
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-
-	public static void generateTermFile(String[] args) {
-		String owlfile = args[0];
-		long ms = System.currentTimeMillis();
-		String outputfile = "term_" + owlfile;
-		OBOScanner scanner = new OBOScanner(owlfile);
-		Vector v = scanner.extractAxiomData();
-		Vector w = new Vector();
-		for (int i=0; i";
-		String outputfile = "mod_" + termfile;
-		Vector v = Utils.readFile(termfile);
-		HashSet hset = new HashSet();
-		Vector w = new Vector();
-		for (int i=0; i
- * Copyright 2020 MSC. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or MSC
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      MSC, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@nih.gov
- *
- */
-
-
-public class OWLScannerTest {
-	public static String[] AXIOM_PROP_CODES = new String[] {
-		"P325", "P97", "P90", "P211", "P375"};
-
-	public static void extractHierarchicalRelationships(String[] args) {
-		String owlfile = args[0];
-		long ms = System.currentTimeMillis();
-		Vector w = new OWLScanner(owlfile).extractHierarchicalRelationships();
-		String hierfile = "hier_" + owlfile + ".txt";
-		Utils.saveToFile(hierfile, w);
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-
-	public static void extractAxiomData(String[] args) {
-		String owlfile = args[0];
-		String prop_code = null;//args[1];
-		long ms = System.currentTimeMillis();
-		String outputfile = "axiom_" + owlfile;
-		if (prop_code != null) {
-			outputfile = "axiom_" + prop_code + "_" + owlfile;
-		}
-		Vector w = new OWLScanner(owlfile).extractAxiomData(prop_code);
-		Utils.saveToFile(outputfile, w);
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-
-	public static void extractOWLRestrictions(String[] args) {
-		String owlfile = args[0];
-		long ms = System.currentTimeMillis();
-		String outputfile = "role_" + owlfile;
-		OWLScanner scanner = new OWLScanner(owlfile);
-		Vector w = scanner.extractOWLRestrictions(scanner.get_owl_vec());
-		Utils.saveToFile(outputfile, w);
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-
-	public static void extractProperties(String[] args) {
-		String owlfile = args[0];
-		OWLScanner scanner = new OWLScanner(owlfile);
-		String prop_code = null;
-		if (args.length > 1) {
-			prop_code = args[1];
-			//OWLScanner.set_NAMESPACE(namespace);
-		}
-		long ms = System.currentTimeMillis();
-		String outputfile = "properties_" + owlfile;
-		Vector w = null;
-		if (prop_code != null) {
-			outputfile = prop_code + "_" + owlfile;
-			w = scanner.extractProperties(scanner.get_owl_vec(), prop_code);
-		} else {
-			w = scanner.extractProperties(scanner.get_owl_vec());
-		}
-		Utils.saveToFile(outputfile, w);
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-
-	public static void extractAssociations(String[] args) {
-		String owlfile = args[0];
-		long ms = System.currentTimeMillis();
-		String outputfile = "association_" + owlfile;
-		OWLScanner scanner = new OWLScanner(owlfile);
-		Vector w = scanner.extractAssociations(scanner.get_owl_vec());
-		Utils.saveToFile(outputfile, w);
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-
-	public static void extractRDFSLabels(String[] args) {
-		String owlfile = args[0];
-		long ms = System.currentTimeMillis();
-		String outputfile = "label_" + owlfile;
-		OWLScanner scanner = new OWLScanner(owlfile);
-		if (args.length > 1) {
-			String namespace = args[1];
-			OWLScanner.set_NAMESPACE(namespace);
-		}
-		Vector w = scanner.extractRDFSLabels(scanner.get_owl_vec());
-		Utils.saveToFile(outputfile, w);
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-
-	public static void generate_FULL_SYN(String[] args) {
-		String owlfile = args[0];
-		long ms = System.currentTimeMillis();
-		OWLScanner scanner = new OWLScanner(owlfile);
-		scanner.generate_FULL_SYN();
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-
-	public static void test(String[] args) {
-		long ms = System.currentTimeMillis();
-		System.out.println("extractHierarchicalRelationships ...");
-		extractHierarchicalRelationships(args);
-		System.out.println("extractAxiomData ...");
-		extractAxiomData(args);
-		System.out.println("extractOWLRestrictions ...");
-		extractOWLRestrictions(args);
-		System.out.println("extractAssociations ...");
-		extractAssociations(args);
-		System.out.println("extractProperties ...");
-		extractProperties(args);
-		System.out.println("extractRDFSLabels ...");
-		extractRDFSLabels(args);
-		System.out.println("generate_FULL_SYN ...");
-		generate_FULL_SYN(args);
-		System.out.println("Grand total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-
-	public static void main(String[] args) {
-		test(args);
-	}
-}
-
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/test/RandomVariateGenerator.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/test/RandomVariateGenerator.java
deleted file mode 100644
index afae05ce2..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/test/RandomVariateGenerator.java
+++ /dev/null
@@ -1,129 +0,0 @@
-package gov.nih.nci.evs.restapi.test;
-
-import java.io.*;
-import java.util.*;
-
-
-/**
- * 
- * Copyright 2008-2015 NGIT. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIT and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIT" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIT
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIT, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class RandomVariateGenerator {
-
-    public RandomVariateGenerator() {
-
-    }
-
-    public int uniform(int min, int max) {
- 	   Random random = new Random();
- 	   int k = max - min + 1;
- 	   if (k <= 0) k = 1;
- 	   return random.nextInt(k) + min;
-    }
-
-    public boolean verifyFrequencies(int[] frequencies) {
-        int sum = 0;
-        for (int i=0; i < frequencies.length; i++) {
-            if (frequencies[i] < 0) return false;
-            sum = sum + frequencies[i];
-        }
-
-        if (sum != 100) return false;
-        return true;
-	}
-
-    public int discreteRamdomVariate(int[] frequencies) {
-        int rand = new Random().nextInt(100);
-        int begin = 0, end = 0;
-        for (int i=0; i < frequencies.length; i++) {
-            end += frequencies[i];
-            if (rand >= begin && rand < end)
-                return i;
-            begin = end;
-        }
-        return 0;
-    }
-
-    public void testDiscreteRamdomVariate(int knt) {
-		int[] frequencies = {10, 10, 80};
-		for (int i=0; i arrayList = new ArrayList();
-		for (int i=0; i targetList = new ArrayList();
-		for (int j=0; j
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class TreeTraversal {
-    String serviceUrl = null;
-    String named_graph = null;
-    String username = null;
-    String password = null;
-    OWLSPARQLUtils owlSPARQLUtils = null;
-    MetadataUtils metadataUtils = null;
-    String version = null;
-
-    public TreeTraversal(String serviceUrl, String named_graph, String username, String password) {
-		this.serviceUrl = serviceUrl;
-		this.named_graph = named_graph;
-		this.username = username;
-		this.password = password;
-		this.metadataUtils = new MetadataUtils(serviceUrl, username, password);
-        this.version = 	metadataUtils.getLatestVersion("NCI_Thesaurus");
-        System.out.println(this.version);
-
-		this.owlSPARQLUtils = new OWLSPARQLUtils(serviceUrl, username, password);
-		this.owlSPARQLUtils.set_named_graph(named_graph);
-    }
-
-    public OWLSPARQLUtils getOWLSPARQLUtils() {
-		return owlSPARQLUtils;
-	}
-
-	public Vector get_roots(String named_graph) {
-		return this.owlSPARQLUtils.get_roots(named_graph);
-	}
-
-
-	public Vector getAncestors(String namedGraph, String root) {
-		ParserUtils parser = new ParserUtils();
-	    Vector w = new Vector();
-	    Stack stack = new Stack();
-	    stack.push(root + "|" + "0");
-	    while (!stack.isEmpty()) {
-			String codeAndLevel = (String) stack.pop();
-			Vector u0 = StringUtils.parseData(codeAndLevel, '|');
-			String code = (String) u0.elementAt(0);
-			String level_str = (String) u0.elementAt(1);
-			Integer int_obj = Integer.valueOf(Integer.parseInt(level_str));
-			int k = Integer.valueOf(int_obj);
-			w.add(codeAndLevel);
-			Vector u = this.owlSPARQLUtils.getSuperclassesByCode(namedGraph, code);
-			if (u != null && u.size() > 0) {
-				int n = u.size()/2;
-				for (int i=0; i " + rel_node_label).append("\n");
-				buf.append("[label=" + rel_label + "];").append("\n");
-			}
-		}
-
-		key = "type_subconcept";
-		list = (ArrayList) relMap.get(key);
-		if (list != null) {
-			for (int i=0; i " + rel_node_label).append("\n");
-				buf.append("[label=" + rel_label + "];").append("\n");
-			}
-		}
-
-		key = "type_role";
-		list = (ArrayList) relMap.get(key);
-		if (list != null) {
-			for (int i=0; i " + rel_node_label).append("\n");
-				buf.append("[label=" + rel_label + "];").append("\n");
-			}
-		}
-
-		key = "type_inverse_role";
-		list = (ArrayList) relMap.get(key);
-		if (list != null) {
-			for (int i=0; i " + focused_node_label).append("\n");
-				buf.append("[label=" + rel_label + "];").append("\n");
-			}
-		}
-
-		key = "type_association";
-		list = (ArrayList) relMap.get(key);
-		if (list != null) {
-			for (int i=0; i " + rel_node_label).append("\n");
-				buf.append("[label=" + rel_label + "];").append("\n");
-			}
-		}
-
-		key = "type_inverse_association";
-		list = (ArrayList) relMap.get(key);
-		if (list != null) {
-			for (int i=0; i " + focused_node_label).append("\n");
-				buf.append("[label=" + rel_label + "];").append("\n");
-			}
-		}
-
-        buf.append(focused_node_label + " [").append("\n");
-        buf.append("fontcolor=white,").append("\n");
-        buf.append("color=red,").append("\n");
-        buf.append("]").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-
-    public Vector generateGraphScriptVector(String scheme, String version, String namespace, String code, String[] types, int option, HashMap hmap) {
-        if (types == null) {
-			types = ALL_RELATIONSHIP_TYPES;
-		}
-        Vector graphData = generateGraphData(scheme, version, namespace, code, types, option, hmap);
-        return GraphUtils.generateGraphScriptVector(graphData, option);
-	}
-
-	public Vector treeItem2GraphData(TreeItem root) {
-	    Vector graphData = treeItem2GraphData(root, new Vector());
-	    return graphData;
-    }
-
-	public Vector treeItem2GraphData(TreeItem ti, Vector v) {
-		String focused_node_label = getLabel(ti._text, ti._code);
-		for (String association : ti._assocToChildMap.keySet()) {
-			List children = ti._assocToChildMap.get(association);
-			for (TreeItem childItem : children) {
-				String code = childItem._code;
-				String text = childItem._text;
-				String rel_node_label = getLabel(text, code);
-				v.add(focused_node_label + "|" + rel_node_label + "|" + association + "|7");
-				v = treeItem2GraphData(childItem, v);
-			}
-		}
-	    return v;
-    }
-
-    public Vector generateGraphData(String scheme, String version, String namespace, String code, String[] types, int option, HashMap hmap) {
-		Vector graphData = new Vector();
-		List typeList = null;
-		if (types != null) {
-			typeList = Arrays.asList(types);
-		} else {
-			typeList = new ArrayList();
-			typeList.add("type_superconcept");
-			typeList.add("type_subconcept");
-    	}
-
-		boolean useNamespace = true;
-		if (gov.nih.nci.evs.restapi.util.StringUtils.isNullOrBlank(namespace)) {
-			useNamespace = false;
-		}
-
-		String name = "";
-		String retstr = getEntityDescriptionByCode(code);
-		if (retstr != null) {
-			name = retstr;
-		}
-		name = encode(name);
-
-		if (gov.nih.nci.evs.restapi.util.StringUtils.isNullOrBlank(namespace)) {
-			namespace = "";
-		}
-		if (!gov.nih.nci.evs.restapi.util.StringUtils.isNullOrBlank(namespace)) {
-			useNamespace = true;
-		}
-        String focused_node_label = getLabel(name, code);
-
-        HashMap relMap = null;
-        if (hmap == null) {
-			//RelationshipHelper relUtils = new RelationshipHelper(sparql_service);
-			relMap = relationshipHelper.getRelationshipHashMap(scheme, version, code, namespace, useNamespace);
-	    } else {
-			relMap = hmap;
-		}
-
-        HashSet nodes = new HashSet();
-        nodes.add(focused_node_label);
-
-        ArrayList list = null;
-
-		String key = null;
-
-		key = "type_superconcept";
-		if (typeList.contains(key)) {
-			list = (ArrayList) relMap.get(key);
-			if (list != null) {
-				for (int i=0; i graphReductionUtils.MINIMUM_REDUCED_GRAPH_SIZE) {
-
-		  group_node_id = graphReductionUtils.getGroupNodeId(v);
-		  int group_node_id_int = Integer.parseInt(group_node_id);
-		  group_node_id_2 = Integer.valueOf(group_node_id_int+1).toString();
-		  Vector w = graphReductionUtils.reduce_graph(v, direction);
-
-		  boolean graph_reduced = graphReductionUtils.graph_reduced(v, w);
-		  if (graph_reduced) {
-			  group_node_data = graphReductionUtils.get_removed_node_str(v, direction);
-			  Vector group_node_ids = graphReductionUtils.get_group_node_ids(w);
-			  for (int k=0; k");
-		out.println("");
-		out.println("");
-		out.println("  View Graph");
-		out.println("");
-		out.println("  ");
-		out.println("");
-		out.println("  ");
-		out.println("  ");
-		out.println("  ");
-
-		out.println("");
-		out.println("  ");
-		out.println("");
-		out.println("");
-		out.println("");
-
-		out.println("
");
-		out.println("       ");
-		out.println("    \"National");
-		out.println("  ");
-		out.println("       ");
-		out.println("    \"National");
-		out.println("  ");
-		out.println("        ");
-		out.println("    \"U.S.");
-		out.println("  ");
-		out.println("        ");
-		out.println("    \"www.cancer.gov\"/");
-		out.println("  ");
-		out.println("
");
-		out.println("
");
-
-		if (!graph_available) {
-		  out.println("
 No graph data is available.
");
-		}
-
-		out.println("
");
-
-		out.println("Relationships");
-		out.println("");
-		out.println("");
-		out.println("");
-		out.println("");
-		out.println("");
-		out.println("");
-		out.println("  ");
-		out.println("");
-		out.println("
");
-		out.println("");
-
-		if (type.endsWith("path")) {
-
-		out.println("
");
-		out.println("    ");
-		out.println("    ");
-		out.println("    ");
-		out.println("    ");
-		out.println("    ");
-		out.println("
");
-		out.println("");
-		}
-
-		out.println("
");
-		out.println("
");
-		out.println("");
-		out.println("
");
-		out.println("");
-		out.println("
");
-		out.println("");
-		out.println("");
-
-		out.flush();
-
-		if (response != null) {
-			request.getSession().setAttribute("scheme", scheme);
-			request.getSession().setAttribute("version", version);
-			request.getSession().setAttribute("ns", namespace);
-			request.getSession().setAttribute("code", code);
-			request.getSession().setAttribute("nodes_and_edges", nodes_and_edges);
-			request.getSession().setAttribute("RelationshipHashMap", hmap);
-		}
-
-		try {
-			out.close();
-		} catch (Exception e) {
-			e.printStackTrace();
-		}
-	}
-
-
-    public static String endPoint2ServiceUrl(String sparql_endpoint) {
-		int n = sparql_endpoint.indexOf("?");
-		if (n == -1) return sparql_endpoint;
-		return sparql_endpoint.substring(0, n);
-	}
-
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-	public static void main(String[] args) {
-		boolean testurl = false;
-		String serviceUrl = args[0];
-		String named_graph = args[1];
-		String username = args[2];
-		String password = args[3];
-		String code = args [4];
-
-        long ms = System.currentTimeMillis();
-
-
-		MetadataUtils test = new MetadataUtils(serviceUrl, username, password);
-		String codingScheme = "NCI_Thesaurus";
-		String version = test.getLatestVersion(codingScheme);
-		System.out.println(codingScheme);
-		System.out.println(version);
-
-		String scheme = codingScheme;
-
-GraphDrawer gd = new GraphDrawer(serviceUrl, named_graph, username, password);
-
-		//System.out.println(version);
-		//String named_graph = test.getNamedGraph(scheme);
-		//System.out.println(named_graph);
-
-		PrintWriter pw = null;
-		String namespace = codingScheme;
-		//String code = "C12365";
-		String type = "type_superconcept";
-		String outputfile = "graph.html";
-
-		try {
-			pw = new PrintWriter(outputfile, "UTF-8");
-        	gd.view_graph(pw, named_graph, scheme, version, namespace, code, type);
-
-		} catch (Exception ex) {
-			ex.printStackTrace();
-		} finally {
-			try {
-				pw.close();
-				System.out.println("Output file " + outputfile + " generated.");
-			} catch (Exception ex) {
-				ex.printStackTrace();
-			}
-		}
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-}
\ No newline at end of file
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/ui/GraphReductionUtils.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/ui/GraphReductionUtils.java
deleted file mode 100644
index 785d1a82b..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/ui/GraphReductionUtils.java
+++ /dev/null
@@ -1,885 +0,0 @@
-package gov.nih.nci.evs.restapi.ui;
-
-import java.io.*;
-import java.util.*;
-
-public class GraphReductionUtils {
-	static String POP_UP_MSG = "Click to view node content.";
-    Vector data_vec = null;
-    HashMap sourceEdge2TargetsMap = null;
-    HashMap targetEdge2SourcesMap = null;
-    public int MINIMUM_REDUCED_GRAPH_SIZE = 25;
-    private int MINIMUM_GRAPH_NODE_ID = 1000;
-
-    int group_node_id = 0;
-
-    static boolean FORWARD = true;
-
-    public GraphReductionUtils() {
-
-	}
-
-	public void initialize_group_node_id(int n) {
-		MINIMUM_GRAPH_NODE_ID = n;
-	}
-
-	private int getGroupNodeID() {
-		MINIMUM_GRAPH_NODE_ID++;
-		return MINIMUM_GRAPH_NODE_ID;
-	}
-
-    public GraphReductionUtils(Vector data_vec) {
-		this.data_vec = data_vec;
-		sourceEdge2TargetsMap = createSourceEdge2TargetsMap(data_vec);
-		targetEdge2SourcesMap = getInverseHashMap(sourceEdge2TargetsMap);
-	}
-
-
-    public HashMap getInverseHashMap(HashMap hmap) {
-		HashMap inv_hmap = new HashMap();
-        Iterator it = hmap.keySet().iterator();
-        while (it.hasNext()) {
-			String key = (String) it.next();
-			Vector node_edge = parseData(key);
-			String node = (String) node_edge.elementAt(0);
-			String edge = (String) node_edge.elementAt(1);
-			Vector w = (Vector) hmap.get(key);
-			for (int i=0; i max) {
-				max = w.size();
-				max_key = key;
-			}
-		}
-		return max_key;
-    }
-
-   	public String getHighestFreqTargetEdge(HashMap targetEdge2SourcesMap) {
-		return getHighestFreqSourceEdge(targetEdge2SourcesMap);
-	}
-
-
-	public int getHighestFreqSourceEdgeCount(HashMap sourceEdge2TargetsMap) {
-		int max = -1;
-		String max_key = null;
-        Iterator it = sourceEdge2TargetsMap.keySet().iterator();
-        while (it.hasNext()) {
-			String key = (String) it.next();
-			Vector w = (Vector) sourceEdge2TargetsMap.get(key);
-			if (w.size() > max) {
-				max = w.size();
-				max_key = key;
-			}
-		}
-		return max;
-    }
-
-	public int getHighestFreqTargetEdgeCount(HashMap targetEdge2SourcesMap) {
-		return getHighestFreqSourceEdgeCount(targetEdge2SourcesMap);
-	}
-
-	public Vector getCandidateTargetNodesToRemove(HashMap sourceEdge2TargetsMap) {
-		String key = getHighestFreqSourceEdge(sourceEdge2TargetsMap);
-		return (Vector) sourceEdge2TargetsMap.get(key);
-	}
-
-	public Vector getCandidateSourceNodesToRemove(HashMap targetEdge2SourcesMap) {
-		return getCandidateTargetNodesToRemove(targetEdge2SourcesMap);
-	}
-
-    public boolean isSourceNodeRemovable(Vector v, String targetEdge, String nodeId) {
-		Vector u = parseData(targetEdge);
-		String max_id = (String) u.elementAt(0);
-		String max_edge = (String) u.elementAt(1);
-		for (int i=0; i parseData(String line) {
-		if (line == null) return null;
-        String tab = "|";
-        return parseData(line, tab);
-    }
-
-    public Vector parseData(String line, String tab) {
-		if (line == null) return null;
-        Vector data_vec = new Vector();
-        StringTokenizer st = new StringTokenizer(line, tab);
-        while (st.hasMoreTokens()) {
-            String value = st.nextToken();
-            data_vec.add(value);
-        }
-        return data_vec;
-    }
-
-	public static Vector readFile(String filename)
-	{
-		Vector v = new Vector();
-		try {
-
-            FileReader a = new FileReader(filename);
-            BufferedReader br = new BufferedReader(a);
-            String line;
-            line = br.readLine();
-            while(line != null){
-                v.add(line);
-                line = br.readLine();
-            }
-            br.close();
-		} catch (Exception ex) {
-            ex.printStackTrace();
-		}
-		return v;
-	}
-
-	//{id: 1, label: 'Adenocarcinoma of the Gastroesophageal Junction (C9296)', shape: 'dot', size: 5},
-    public boolean isNode(String line) {
-		if (line.indexOf("id:") != -1 && line.indexOf("label:") != -1) {
-			return true;
-		}
-		return false;
-	}
-
-    //{from: 44, to: 33, arrows:'to', label: 'Gene_Involved_In_Pathogenesis_Of_Disease', length: 400},
-    public boolean isEdge(String line) {
-		if (line.indexOf("from:") != -1 && line.indexOf("to:") != -1) {
-			return true;
-		}
-		return false;
-	}
-
-	//{id: 1, label: 'Adenocarcinoma of the Gastroesophageal Junction (C9296)', shape: 'dot', size: 5},
-	public String getNodeId(String line) {
-		int n = line.indexOf("id:");
-		String t = line.substring(n+3, line.length());
-		n = t.indexOf(",");
-		t = t.substring(1, n);
-		return t;
-	}
-
-	//{id: 1, label: 'Adenocarcinoma of the Gastroesophageal Junction (C9296)', shape: 'dot', size: 5},
-	public String getNodeLabel(String line) {
-		int n = line.indexOf("label:");
-		String t = line.substring(n+6, line.length());
-		n = t.indexOf(",");
-		t = t.substring(2, n-1);
-		return t;
-	}
-
-//    //{from: 44, to: 33, arrows:'to', label: 'Gene_Involved_In_Pathogenesis_Of_Disease', length: 400},
-    public String getSourceId(String line) {
-		int n = line.indexOf("from:");
-		String t = line.substring(n+5, line.length());
-		n = t.indexOf(",");
-		t = t.substring(1, n);
-		return t;
-	}
-
-    public String getTargetId(String line) {
-		int n = line.indexOf("to:");
-		String t = line.substring(n+3, line.length());
-		n = t.indexOf(",");
-		t = t.substring(1, n);
-		return t;
-	}
-
-	public String getEdgeLabel(String line) {
-		int n = line.indexOf("label:");
-		String t = line.substring(n+6, line.length());
-		n = t.indexOf(",");
-		t = t.substring(2, n-1);
-		return t;
-	}
-
-	public void dumpVector(Vector v) {
-		for (int i=0; i 0) {
-				System.out.println("(" + j + ")" + t);
-			} else {
-				System.out.println(t);
-			}
-		}
-	}
-
-	public void dumpHashMap(String label, HashMap hmap) {
-		if (hmap == null) return;
-		System.out.println(label);
-		Iterator it = hmap.keySet().iterator();
-		while (it.hasNext()) {
-			String key = (String) it.next();
-			Vector v = (Vector) hmap.get(key);
-			StringBuffer buf = new StringBuffer();
-			for (int i=0; i " + buf.toString());
-		}
-	}
-
-	public Vector extractNodeIDs(Vector v) {
-	    Vector w = new Vector();
-	    for (int i=0; i");
-		String groupNodeContent = "Node " + groupNodeId + " content:";
-		buf.append("");
-		buf.append("" + groupNodeContent + "");
-		buf.append("");
-		int j = 0;
-		for (int i=0; i");
-			buf.append("(" + j + ") " + t);
-			buf.append("");
-		}
-		buf.append("");
-		return buf.toString();
-	}
-
-/*
-    //PrintWriter out = response.getWriter();
-	public void generateResponse(PrintWriter out, Vector v, String group_node_id, String group_node_data) {
-      out.println("");
-      out.println("");
-      out.println("");
-      out.println("  View Graph");
-      out.println("");
-      out.println("  ");
-      out.println("");
-      out.println("  ");
-      out.println("  ");
-      out.println("  ");
-      out.println("");
-      out.println("  ");
-      out.println("");
-      out.println("");
-      out.println("");
-      out.println("
");
-      out.println("  ");
-      out.println("    \"National");
-      out.println("  ");
-      out.println("  ");
-      out.println("    \"National");
-      out.println("  ");
-      out.println("  ");
-      out.println("    \"U.S.");
-      out.println("  ");
-      out.println("  ");
-      out.println("    \"www.cancer.gov\"/");
-      out.println("  ");
-      out.println("
");
-      out.println("
");
-      out.println("
");
-      out.println("Relationships");
-      out.println("");
-      out.println("");
-      out.println("");
-      out.println("");
-      out.println("");
-      out.println("");
-      out.println("  ");
-      out.println("");
-      out.println("
");
-      out.println("");
-      out.println("
");
-      out.println("
");
-      out.println("");
-      out.println("
");
-      out.println("");
-      out.println("
");
-      out.println("");
-      out.println("");
-   }
-*/
-    public Vector get_nodes_to_remove(Vector v, HashMap hmap) {
-		int source_max = getHighestFreqSourceEdgeCount(hmap);
-		String max_source_edge_str = getHighestFreqSourceEdge(hmap);
-		Vector v1 = getCandidateTargetNodesToRemove(hmap);
-		//dumpVector("CandidateTargetNodesToRemove:", v1);
-		Vector nodes_to_remove = getTargetNodesToRemove(v, max_source_edge_str, v1);
-		return nodes_to_remove;
-	}
-
-
-	public String get_removed_node_str(Vector v, HashMap hmap) {
-		int n1 = getNodeCount(v);
-		String groupNodeId = Integer.valueOf(n1+1).toString();
-		Vector w = null;
-		String removed_nodes_str = "";
-		Vector nodes_to_remove = get_nodes_to_remove(v, hmap);
-		if (nodes_to_remove.size() == 0) return removed_nodes_str;
-		String max_source_edge_str =  getHighestFreqSourceEdge(hmap);
-		w = removeNodes(v, nodes_to_remove);
-		Vector removed_nodes = vec_difference(v, w);
-		Vector removed_node_ids = extractNodeIDs(removed_nodes);
-		removed_nodes_str = get_removed_node_str(removed_node_ids, groupNodeId);
-		return removed_nodes_str;
-	}
-
-	public Vector reduceGraph(Vector v, HashMap hmap) {
-		return reduceGraph(v, hmap, true);
-	}
-
-	public Vector reduceGraph(Vector v, HashMap hmap, boolean forward) {
-
-		//int n1 = getNodeCount(v);
-		//String groupNodeId = Integer.valueOf(n1+1).toString();
-		int n1 = getGroupNodeID();
-		String groupNodeId = Integer.valueOf(n1).toString();
-		String groupNodeLabel = "Node " + groupNodeId;
-		Vector w = null;
-		try {
-			Vector nodes_to_remove = get_nodes_to_remove(v, hmap);
-			String removed_nodes_str = null;
-			if (nodes_to_remove.size() > 0) {
-				String max_source_edge_str =  getHighestFreqSourceEdge(hmap);
-				w = removeNodes(v, nodes_to_remove);
-				Vector removed_nodes = vec_difference(v, w);
-				Vector removed_node_ids = extractNodeIDs(removed_nodes);
-				removed_nodes_str = get_removed_node_str(removed_node_ids, groupNodeId);
-				w = removeEdges(w, nodes_to_remove);
-				Vector u = parseData(max_source_edge_str);
-				String max_node = (String) u.elementAt(0);
-				String max_edge = (String) u.elementAt(1);
-				String sourceNodeId = max_node;
-				w = insert_group_node(w, groupNodeId, groupNodeLabel);
-				w = insert_edge_to_group_node(w, sourceNodeId, groupNodeId, max_edge, forward);
-				return w;
-		    }
-		} catch (Exception ex) {
-			ex.printStackTrace();
-		}
-		return v;
-	}
-
-	public String getGroupNodeId(Vector v) {
-		int n1 = getNodeCount(v);
-		return Integer.valueOf(n1+1).toString();
-	}
-
-	public Vector reduce_graph(Vector v, boolean direction) {
-		int n = getNodeCount(v);
-		HashMap hmap = createSourceEdge2TargetsMap(v);
-		if (!direction) {
-			hmap = getInverseHashMap(hmap);
-		}
-		return reduceGraph(v, hmap, direction);
-	}
-
-	public boolean graph_reduced(Vector v, Vector w) {
-		int n1 = getNodeCount(v);
-		int n2 = getNodeCount(w);
-		//if (n1 > n2 * 2) {
-		if (n1 > n2) {
-			return true;
-		}
-		return false;
-	}
-
-/*
-	public Vector reduce_graph(Vector v) {
-		Vector w = reduce_graph(v, true);
-		if (graph_reduced(v, w)) {
-		    return w;
-		}
-		w = reduce_graph(v, false);
-		if (graph_reduced(v, w)) {
-		    return w;
-		}
-		return v;
-	}
-*/
-
-	public String get_removed_node_str(Vector v, boolean direction) {
-		HashMap hmap = createSourceEdge2TargetsMap(v);
-		if (!direction) {
-			hmap = getInverseHashMap(hmap);
-		}
-		return get_removed_node_str(v, hmap);
-	}
-
-	public Vector get_group_node_ids(Vector v) {
-		Vector w = new Vector();
-		if (v == null) return w;
-		for (int i=0; i n2 * 2) {
-				graph_reduced = true;
-				String removed_nodes_str = get_removed_node_str(v, hmap);
-				generateResponse(pw, w, groupNodeId, removed_nodes_str);
-				System.out.println("Outputfile " + outputfile + " generated.");
-			} else {
-				System.out.println("No reduction at the forward direction.");
-				System.out.println("Attempting the reverse direction...");
-				hmap = getInverseHashMap(hmap);
-				w = reduceGraph(v, hmap, false);
-				n2 = getNodeCount(w);
-				if (n1 > n2 * 2) {
-					graph_reduced = true;
-					String removed_nodes_str = get_removed_node_str(v, hmap);
-
-					System.out.println("********** removed_nodes_str: " + removed_nodes_str);
-
-					generateResponse(pw, w, groupNodeId, removed_nodes_str);
-					System.out.println("Outputfile " + outputfile + " generated.");
-				}
-			}
-			if (!graph_reduced) {
-				System.out.println("No graph reduction is made.");
-			}
-
-		} catch (Exception ex) {
-			ex.printStackTrace();
-		} finally {
-			try {
-				pw.close();
-			} catch (Exception e) {
-                e.printStackTrace();
-			}
-		}
-    }
-
-	public static void main(String args[])
-	{
-		String filename = args[0];
-		Vector v = readFile(filename);
-		GraphReductionUtils util = new GraphReductionUtils(v);
-
-		//test.reduceGraph(v);
-		int n = filename.lastIndexOf(".");
-
-		String outputfile = filename.substring(0, n) + ".html";
-		System.out.println("outputfile " + outputfile);
-		//test.reduceGraph2(v, outputfile);
-
-		util.test(filename, outputfile);
-
-	}
-*/
-}
-
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/ui/GraphUtils.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/ui/GraphUtils.java
deleted file mode 100644
index 82a846443..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/ui/GraphUtils.java
+++ /dev/null
@@ -1,322 +0,0 @@
-package gov.nih.nci.evs.restapi.ui;
-
-import gov.nih.nci.evs.restapi.util.*;
-import java.util.*;
-import java.io.*;
-import java.util.Map.Entry;
-
-public class GraphUtils {
-    public static final int NODES_ONLY = 1;
-    public static final int EDGES_ONLY = 2;
-    public static final int NODES_AND_EDGES = 3;
-
-    public static final int NODE_COUNT_THRESHOLD = 25;
-    public static final int MIN_EDGE_LENGTH = 200;
-    public static final int EDGE_LENGTH = 400;
-
-    public static final String NO_DATA_AVAILABLE = "No data available.";
-
-	public static Vector readFile(String filename)
-	{
-		Vector v = new Vector();
-		try {
-            FileReader a = new FileReader(filename);
-            BufferedReader br = new BufferedReader(a);
-            String line;
-            line = br.readLine();
-            while(line != null){
-                v.add(line);
-                line = br.readLine();
-            }
-            br.close();
-		} catch (Exception ex) {
-            ex.printStackTrace();
-		}
-		return v;
-	}
-
-    public static String generateGraphScript(Vector v) {
-		StringBuffer buf = new StringBuffer();
-		for (int i=0; i
- * Copyright 2008,2009 NGIT. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIT and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIT" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIT
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIT, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * SimpleSearchUtils (uses LexEVSAPI 6.1 SearchExtension)
- *
- * @author kimong
- *
- */
-
-
-public class SimpleTreeUtils {
-    int node_counter = 0;
-    static int MAXIMUM = 5;
-    static int MINIMUM = 0;
-    static String ASSOCIATION = "has_sub";
-    static String TAB = "";
-    private String URL = null;
-    private int tabindex = 0;
-    private String basePath = "/sparql/";
-    private HashMap checkboxid2NodeIdMap = null;
-
-    private String focusNodeId = null;
-    private boolean checkAll = false;
-
-    private Vector selected_nodes = null;
-    private Set vocabularyNameSet = null;
-
-    public SimpleTreeUtils(Set vocabularyNameSet) {
-        this.checkboxid2NodeIdMap = new HashMap();
-        this.vocabularyNameSet = vocabularyNameSet;
-    }
-
-    public void setBasePath(String basePath) {
-		this.basePath = basePath;
-	}
-
-    public void setVocabularyNameSet(Set vocabularyNameSet) {
-		this.vocabularyNameSet = vocabularyNameSet;
-	}
-
-	public boolean isFormalName(String name) {
-		if (vocabularyNameSet != null && vocabularyNameSet.contains(name)) return true;
-		return false;
-	}
-
-    public void setFocusNodeId(String focusNodeId) {
-		this.focusNodeId = focusNodeId;
-	}
-
-    public void setCheckAll(boolean checkAll) {
-		this.checkAll = checkAll;
-	}
-
-	public String getCheckBoxStatus() {
-		if (this.checkAll) {
-			return "checked";
-		}
-		return "";
-	}
-
-	public String getCheckBoxStatus(String node_id) {
-		if (this.selected_nodes == null) {
-			return getCheckBoxStatus();
-		} else {
-			if (this.selected_nodes.contains(node_id)) {
-				return "checked";
-			}
-		}
-		return "";
-	}
-
-
-	public void setSelectedNodes(Vector selected_nodes) {
-		this.selected_nodes = selected_nodes;
-	}
-
-
-    public void setUrl(String url) {
-		this.URL = url;
-	}
-
-    private String getIndentation(int level) {
-		if (level <= 0) return "";
-		StringBuffer buf = new StringBuffer();
-		for (int i=0; i 0) return true;
-		return false;
-	}
-
-    private int getChildrenCount(TreeItem tree_node) {
-		int knt = 0;
-		for (String asso_name : tree_node._assocToChildMap.keySet()) {
-			List cs_vs_children = tree_node._assocToChildMap.get(asso_name);
-			knt = knt + cs_vs_children.size();
-		}
-		return knt;
-	}
-
-    private Vector getChildren(TreeItem tree_node) {
-		Vector sub_vec = new Vector();
-		for (String asso_name : tree_node._assocToChildMap.keySet()) {
-			List cs_vs_children = tree_node._assocToChildMap.get(asso_name);
-			for (TreeItem child_item : cs_vs_children) {
-				sub_vec.add(child_item);
-			}
-		}
-		return sub_vec;
-	}
-
-    public StringBuffer getValueSetTreeStringBuffer(HashMap tree_map) {
-		if (tree_map == null) return null;
-
-		TreeItem root = (TreeItem) tree_map.get("");
-		int knt = 0;
-		for (String asso_name : root._assocToChildMap.keySet()) {
-			List cs_vs_children = root._assocToChildMap.get(asso_name);
-			for (TreeItem child_item : cs_vs_children) {
-				knt++;
-				assignNodeId(null, child_item, knt);
-			}
-		}
-
-
-		Vector v = treeHashMap2StringBuffer(tree_map);
-		if (v == null) return null;
-		StringBuffer buf = new StringBuffer();
-		if (v.size() == 0) {
-		    return buf;
-		}
-
-		for (int i=0; i");
-		return treeItem2StringBuffer(root);
-	}
-
-
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-	public void printFormHeader(PrintWriter out) {
-      //out.println("	    ");
-      out.println("	    ");
-      out.println("	    
");
-    }
-
-	public void printFormHeader(Vector v) {
-      v.add("	    ");
-      //v.add("	    ");
-    }
-
-	public void printPageHeader(PrintWriter out) {
-      out.println("");
-      out.println("");
-      out.println("	");
-      out.println("		");
-      out.println("		");
-      out.println("		");
-      out.println("		Value Set Hierarchy");
-
-      out.println("	");
-      out.println("	");
-
-	  out.println("	");
-	  out.println("	");
-
-      out.println("	    ");
-      out.println("	    ");
-  }
-
-
-//Expand all Collapse all Check all Uncheck all
-  public void printSelectAllOrNoneLinks(PrintWriter out) {
-      out.println("");
-      out.println("
");
-      out.println("Expand all");
-      out.println(" ");
-      out.println("Collapse all");
-      out.println(" ");
-      out.println("Check all");
-      out.println(" ");
-      out.println("Uncheck all");
-      out.println("
");
-      out.println("");
-  }
-
-  public String getTabIndex() {
-	  tabindex++;
-	  return "tabindex=\"" + tabindex + "\"";
-  }
-
-  public static void printFormFooter(PrintWriter out) {
-	  out.println("	    ");
-	  out.println("	    ");
-  }
-
-
-  public static void printFormFooter(Vector v) {
-	  v.add("	    ");
-	  v.add("	    
");
-  }
-
-
-
-  public static void printPageFooter(PrintWriter out) {
-	  out.println("	    ");
-	  out.println("	    ");
-      out.println("	");
-      out.println("");
-  }
-
-  public HashMap getCheckboxid2NodeIdMap() {
-	  return checkboxid2NodeIdMap;
-  }
-
-  public void printNode(PrintWriter pw, TreeItem ti, int level) {
-	  boolean expandAll = true;
-	  printNode(pw, ti, level, expandAll);
- }
-
-
-  public void printNode(PrintWriter pw, TreeItem ti, int level, boolean expandAll) {
-	    if (ti == null) return;
-	    String display_text = ti._text;
-		String indentation = getIndentation(level);
-		pw.println(indentation + "
  • ");
-		String checkbox_id = ti._id;
-		if (checkbox_id == null) {
-			checkbox_id = ti._code;
-		}
-		checkboxid2NodeIdMap.put(checkbox_id, ti._code);
-		String img_id = "IMG_" + checkbox_id;
-		if (ti._expandable) {
-			String div_id = "DIV_" + checkbox_id;
- 			pw.println("\"show_hide\""
- 			    + ""
- 			    + getHyperLink(ti));
-
-            if (expandAll) {
-				pw.println(indentation + "
    ");
-				pw.println(indentation + "
      ");
-
-				for (String asso_name : ti._assocToChildMap.keySet()) {
-					List cs_vs_children = ti._assocToChildMap.get(asso_name);
-					for (TreeItem child_item : cs_vs_children) {
-						printNode(pw, child_item, level+1, expandAll);
-						pw.flush();
-					}
-				}
-				pw.println(indentation + "
    ");
-				pw.println(indentation + "
    ");
-		    }
-
-		    pw.flush();
-	    } else {
-			pw.println("\"show_hide\""
-			+ ""
-			+ getHyperLink(ti));
-		}
-		pw.println(indentation + "
    • ");
-		pw.flush();
-	}
-
-  public void printNode(Vector v, TreeItem ti, int level) {
-	  boolean expandAll = true;
-	  printNode(v, ti, level, expandAll);
-  }
-
-  public void printNode(Vector v, TreeItem ti, int level, boolean expandAll) {
-	    String display_text = ti._text;
-		String indentation = getIndentation(level);
-		v.add(indentation + "
  • ");
-		String checkbox_id = ti._id;
-		if (checkbox_id == null) {
-			checkbox_id = ti._code;
-		}
-		checkboxid2NodeIdMap.put(checkbox_id, ti._code);
-
-		String img_id = "IMG_" + checkbox_id;
-
-		if (ti._expandable) {
-			String div_id = "DIV_" + checkbox_id;
- 			v.add("\"show_hide\""
- 			    + ""
- 			    + getHyperLink(ti));
-
-            if (expandAll) {
-				v.add(indentation + "
    ");
-				v.add(indentation + "
      ");
-
-				for (String asso_name : ti._assocToChildMap.keySet()) {
-					List cs_vs_children = ti._assocToChildMap.get(asso_name);
-					for (TreeItem child_item : cs_vs_children) {
-						printNode(v, child_item, level+1);
-						//pw.flush();
-					}
-				}
-				v.add(indentation + "
    ");
-				v.add(indentation + "
    ");
-		    }
-		    //pw.flush();
-	    } else {
-			v.add("\"show_hide\""
-			+ ""
-			+ getHyperLink(ti));
-		}
-		v.add(indentation + "
    • ");
-	}
-
-
-    // Make root node clickable:
-	private String getHyperLink(TreeItem ti) {
-		//if (ti._code.startsWith("TVS_")) {
-		//	return ti._text;
-		//}
-
-		//if (!ti._code.startsWith("http:")) {
-		//	return ti._text;
-		//}
-
-		//if (DataUtils.getFormalName(ti._code) != null || DataUtils.getFormalName(ti._text) != null) {
-		if (isFormalName(ti._code) || isFormalName(ti._text)) {
-			return ti._text;
-		}
-
-		if (focusNodeId != null && ti._code.compareTo(focusNodeId) == 0) {
-			return ti._text;
-		}
-
-	    return "" + ti._text + "";
-    }
-
-
-// Collapse nodes at initialization.
-    public void printTree(PrintWriter pw, HashMap tree_map) {
-		boolean expandAll = true;
-		printTree(pw, tree_map, expandAll);
-	}
-
-
-    public void printTree(PrintWriter pw, HashMap tree_map, boolean expandAll) {
-		if (tree_map == null) return;
-		//checkboxid2NodeIdMap = new HashMap();
-
-		TreeItem root = (TreeItem) tree_map.get("");
-		if (root == null) {
-			System.out.println("ERROR in printTree -- root is null.");
-			return;
-		}
-
-		if (root._assocToChildMap == null) {
-			System.out.println("ERROR in printTree -- root._assocToChildMap is null.");
-			return;
-		}
-
-		int knt = 0;
-		for (String asso_name : root._assocToChildMap.keySet()) {
-			List cs_vs_children = root._assocToChildMap.get(asso_name);
-			for (TreeItem child_item : cs_vs_children) {
-				if (child_item != null) {
-				    knt++;
-					assignNodeId(null, child_item, knt);
-				}
-			}
-		}
-		printTree(pw, root, expandAll);
-	}
-
-    public void printTree(Vector v, HashMap tree_map) {
-         boolean expandAll = true;
-         printTree(v, tree_map, expandAll);
-	}
-
-    public void printTree(Vector v, HashMap tree_map, boolean expandAll) {
-		if (tree_map == null) return;
-		TreeItem root = (TreeItem) tree_map.get("");
-		int knt = 0;
-		for (String asso_name : root._assocToChildMap.keySet()) {
-			List cs_vs_children = root._assocToChildMap.get(asso_name);
-			for (TreeItem child_item : cs_vs_children) {
-				knt++;
-				assignNodeId(null, child_item, knt);
-			}
-		}
-		v = new Vector();
-		printTree(v, root, expandAll);
-	}
-
-	public void printTree(PrintWriter pw, TreeItem root) {
-		boolean expandAll = true;
-		printTree(pw, root, true);
-	}
-
-    public void printTree(PrintWriter pw, TreeItem root, boolean expandAll) {
-		if (root == null) return;
-		pw.println("
      ");
-		for (String asso_name : root._assocToChildMap.keySet()) {
-			List cs_vs_children = root._assocToChildMap.get(asso_name);
-			for (TreeItem child_item : cs_vs_children) {
-				printNode(pw, child_item, 0, expandAll);
-			}
-		}
-        pw.println("
    ");
-	}
-
-
-    public void printTree(TreeItem root) {
-        boolean expandAll = true;
-        printTree(root, expandAll);
-	}
-
-    public void printTree(TreeItem root, boolean expandAll) {
-		PrintWriter pw = new PrintWriter(System.out);
-        printTree(pw, root, expandAll);
-	}
-
-    public void printTree(Vector v, TreeItem root) {
-        boolean expandAll = true;
-        printTree(v, root, expandAll);
-	}
-
-    public void printTree(Vector v, TreeItem root, boolean expandAll) {
-		if (root == null) return;
-		v.add("
      ");
-		for (String asso_name : root._assocToChildMap.keySet()) {
-			List cs_vs_children = root._assocToChildMap.get(asso_name);
-			for (TreeItem child_item : cs_vs_children) {
-				printNode(v, child_item, 0, expandAll);
-			}
-		}
-        v.add("
    ");
-	}
-
-
-///////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-	public void assignNodeId(String parent_id, TreeItem ti, int index) {
-		String id = null;
-		if (parent_id == null) {
-			id = "N_" + index;
-		} else {
-			id = parent_id + "_" + index;
-		}
-		ti.setId(id);
-
-		int lcv = 0;
-		for (String asso_name : ti._assocToChildMap.keySet()) {
-			List cs_vs_children = ti._assocToChildMap.get(asso_name);
-			for (TreeItem child_item : cs_vs_children) {
-				lcv++;
-				assignNodeId(id, child_item, lcv);
-			}
-		}
-	}
-
-
-	public void assignNodeId(TreeItem root) {
-		node_counter = 0;
-		if (root._text.compareTo("") == 0) {
-			int knt = 0;
-			for (String asso_name : root._assocToChildMap.keySet()) {
-				List cs_vs_children = root._assocToChildMap.get(asso_name);
-				for (TreeItem child_item : cs_vs_children) {
-					knt++;
-					assignNodeId(null, child_item, knt);
-				}
-			}
-		} else {
-			assignNodeId(null, root, 1);
-		}
-	}
-
-    public void writeTree2HTML(HashMap hmap, String basePath, String htmlfile) {
-		setBasePath(basePath);
-		tabindex = 0;
-        TreeItem root = (TreeItem) hmap.get("");
-		int knt = 0;
-		for (String asso_name : root._assocToChildMap.keySet()) {
-			List cs_vs_children = root._assocToChildMap.get(asso_name);
-			for (TreeItem child_item : cs_vs_children) {
-				knt++;
-				assignNodeId(null, child_item, knt);
-			}
-		}
-
-        try {
-			PrintWriter pw = new PrintWriter(htmlfile, "UTF-8");
-			printPageHeader(pw);
-			printSelectAllOrNoneLinks(pw);
-			printTree(pw, root);
-			printPageFooter(pw);
-			pw.close();
-
-		} catch (Exception ex) {
-			ex.printStackTrace();
-		}
-	}
-
-    public static String getValueSetTreeKey(String uri, String name) {
-		return uri + "$" + name;
-	}
-
-    public static HashMap createValueSetTreeKey2TreeItemMap(TreeItem ti) {
-		return createValueSetTreeKey2TreeItemMap(ti, new HashMap());
-	}
-
-    private static HashMap createValueSetTreeKey2TreeItemMap(TreeItem ti, HashMap map) {
-        String key = ti._code + "$" + ti._text;
-        map.put(key, ti);
-		for (String association : ti._assocToChildMap.keySet()) {
-			 List children = ti._assocToChildMap.get(association);
-			 for (TreeItem childItem : children) {
-				 map = createValueSetTreeKey2TreeItemMap(childItem, map);
-			 }
-		}
-		return map;
-    }
-}
-
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/ui/UICodeGenerator.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/ui/UICodeGenerator.java
deleted file mode 100644
index b0457a2f1..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/ui/UICodeGenerator.java
+++ /dev/null
@@ -1,863 +0,0 @@
-package gov.nih.nci.evs.restapi.ui;
-
-import gov.nih.nci.evs.restapi.util.*;
-import gov.nih.nci.evs.restapi.bean.*;
-
-
-import java.io.*;
-import java.util.*;
-import java.text.*;
-import java.sql.*;
-import java.net.*;
-
-import org.apache.commons.lang.*;
-//import org.apache.log4j.*;
-import java.util.Map;
-import java.util.Map.Entry;
-
-/**
- * 
- * Copyright 2008,2009 NGIT. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIT and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIT" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIT
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIT, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- *          Modification history Initial implementation kim.ong@ngc.com
- *
- */
-
- public class UICodeGenerator {
-	 public String application_name = "ncimbrowser";
-	 public String bookmark_url = null;
-
-	 public UICodeGenerator() {
-
-	 }
-
-	 public void set_application_name(String application_name) {
-		 this.application_name = application_name;
-	 }
-
-	 public String get_application_name() {
-		 return this.application_name;
-	 }
-
-	 public void set_bookmark_url(String bookmark_url) {
-		 this.bookmark_url = bookmark_url;
-	 }
-
-	 public static String escapeDoubleQuotes(String inputStr) {
-		 char doubleQ = '"';
-		 StringBuffer buf = new StringBuffer();
-		 for (int i=0;  i").append("\n");
-		buf.append("").append("\n");
-		buf.append("Synonym Details:").append("\n");
-		buf.append("").append("\n");
-		buf.append(" ").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-if (syn_vec != null) {
-		for (int i=0; i").append("\n");
-			buf.append("               ").append("\n");
-			buf.append("").append("\n");
-			buf.append("").append("\n");
-			buf.append("").append("\n");
-			buf.append("").append("\n");
-		}
-}
-		buf.append("
          
    ").append("\n");
-		buf.append("Term").append("\n");
-		buf.append("").append("\n");
-		buf.append("Source").append("\n");
-		buf.append("").append("\n");
-		buf.append("\"Source").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("Type").append("\n");
-		buf.append("").append("\n");
-		buf.append("\"Term").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("Code").append("\n");
-		buf.append("
    ").append("\n");
-			buf.append("
    ").append("\n");
-
-			Synonym syn = (Synonym) syn_vec.elementAt(i);
-	        String ncit_code = null;
-			String term = syn.getTermName();
-			String sab = syn.getTermSource();
-
-			String type = syn.getTermGroup();
-			String src_code = syn.getSourceCode();
-			buf.append("" + term + "").append("\n");
-			buf.append("
    ").append("\n");
-			buf.append("    		" + sab + "" + type + "").append("\n");
-
-            if (codingSchemes != null && codingSchemes.contains(sab)) {
-                buf.append(getCodeHyperlink(src_code, sab));
-			} else {
-				buf.append(src_code);
-			}
-			if (sourcesWithHierarchy_vec != null && sourcesWithHierarchy_vec.contains(sab)) {
-				buf.append("  " + getViewInSourceHierarchyLink(code, sab));
-			}
-            buf.append("\n");
-			buf.append("
    ").append("\n");
-		return buf.toString();
-	 }
-
-     public String generateRelationshipTable(String table_name, Vector rel_vec) {
-		StringBuffer buf = new StringBuffer();
-		buf.append("" + table_name + " Concepts:").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("    ").append("\n");
-
-if (rel_vec != null) {
-		for (int i=0; i").append("\n");
-
-			String rela = (String) u.elementAt(1);
-			String name = (String) u.elementAt(4);
-			String cui = (String) u.elementAt(2);
-			String sab = (String) u.elementAt(6);
-
-			buf.append("").append("\n");
-			buf.append("").append("\n");
-			buf.append("").append("\n");
-			buf.append("").append("\n");
-			buf.append("").append("\n");
-		}
-		buf.append("
    Relationship").append("\n");
-		buf.append("").append("\n");
-		buf.append("\"Relationship").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("Rel. Attribute").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("\"Relationship").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("Name").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("Rel. Source").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("\"Source").append("\n");
-		buf.append("").append("\n");
-		buf.append("" + table_name + "" + rela + "").append("\n");
-			buf.append("").append("\n");
-			buf.append("" + name + "").append("\n");
-			buf.append("").append("\n");
-			buf.append("" + sab + "
    ").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("
    ").append("\n");
-}
-		return buf.toString();
-	 }
-
-     public String generateRelationshipTable(HashMap rel_hashmap) {
-		StringBuffer buf = new StringBuffer();
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("Relationships with other NCI Metathesaurus Concepts:").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("").append("\n");
-		buf.append("Parents |").append("\n");
-		buf.append("Children |").append("\n");
-		buf.append("Broader |").append("\n");
-		buf.append("Narrower |").append("\n");
-		buf.append("Siblings |").append("\n");
-		buf.append("Other").append("\n");
-		buf.append("").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("
    ").append("\n");
-
-if (rel_hashmap != null) {
-		String table_name = "Parent";
-		String content = generateRelationshipTable(table_name, (Vector) rel_hashmap.get("PAR"));
-		buf.append(content);
-		table_name = "Child";
-		content = generateRelationshipTable(table_name, (Vector) rel_hashmap.get("CHD"));
-		buf.append(content);
-		table_name = "Broader";
-		content = generateRelationshipTable(table_name, (Vector) rel_hashmap.get("RB"));
-		buf.append(content);
-		table_name = "Narrower";
-		content = generateRelationshipTable(table_name, (Vector) rel_hashmap.get("RN"));
-		buf.append(content);
-		table_name = "Sibling";
-		content = generateRelationshipTable(table_name, (Vector) rel_hashmap.get("SIB"));
-		buf.append(content);
-		table_name = "Other";
-		content = generateRelationshipTable(table_name, (Vector) rel_hashmap.get("OTH"));
-		buf.append(content);
-}
-		return buf.toString();
-	}
-
-    public String generateSourceTable(String cui, String source, Vector source_vec) {
-		StringBuffer buf = new StringBuffer();
-		String str = generateSourceSynonymTable(cui, source, source_vec);
-		buf.append(str);
-
-		buf.append("Relationships").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-
-
-        if (source_vec != null) {
-
-			int lcv = 0;
-			for (int i=0; i").append("\n");
-					buf.append("").append("\n");
-					buf.append("").append("\n");
-					buf.append("").append("\n");
-					buf.append("").append("\n");
-					buf.append("").append("\n");
-					buf.append("").append("\n");
-					buf.append("").append("\n");
-					buf.append("").append("\n");
-					lcv++;
-				}
-			}
-
-
-        }
-		buf.append("
    ").append("\n");
-		buf.append("Relationship").append("\n");
-		buf.append("").append("\n");
-		buf.append("\"Relationship").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("Rel. Attribute").append("\n");
-		buf.append("").append("\n");
-		buf.append("\"Relationship").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("CUI").append("\n");
-		buf.append("").append("\n");
-		buf.append("Term").append("\n");
-		buf.append("").append("\n");
-		buf.append("Source").append("\n");
-		buf.append("").append("\n");
-		buf.append("\"Source").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("Type").append("\n");
-		buf.append("").append("\n");
-		buf.append("\"Term").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("Code").append("\n");
-		buf.append("
    " + rel + "" + rela + "").append("\n");
-					buf.append("").append("\n");
-					buf.append("" + cui2 + "").append("\n");
-					buf.append("").append("\n");
-					buf.append("" + term + "" + sab + "" + type + "" + code + "
    ").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("
    ").append("\n");
-
-		return buf.toString();
-	 }
-
-     public String generateSourceSynonymTable(String cui, String source, Vector source_vec) {
-		StringBuffer buf = new StringBuffer();
-		buf.append("Synonyms").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-
-if (source_vec != null) {
-        int lcv = 0;
-		for (int i=0; i").append("\n");
-				buf.append("").append("\n");
-				buf.append("").append("\n");
-				buf.append("").append("\n");
-				buf.append("").append("\n");
-				buf.append("").append("\n");
-				lcv++;
-			}
-		}
-		buf.append("
    ").append("\n");
-		buf.append("Term").append("\n");
-		buf.append("").append("\n");
-		buf.append("Source").append("\n");
-		buf.append("").append("\n");
-		buf.append("\"Source").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("Type").append("\n");
-		buf.append("").append("\n");
-		buf.append("\"Term").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("Code").append("\n");
-		buf.append("
    " + term + "" + sab + "" + type + "" + code + "
    ").append("\n");
-		buf.append("
    ").append("\n");
-}
-		return buf.toString();
-	 }
-
-     public String generatePropertyTable(String cui, HashMap property_hashmap) {
-		StringBuffer buf = new StringBuffer();
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("Terms & Properties").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("
    Concept Unique Identifier (CUI): " + cui + "
    ").append("\n");
-		buf.append("
    ").append("\n");
-
-if(property_hashmap != null) {
-		String ncit_code = null;
-		Vector v = (Vector) property_hashmap.get("Synonym");
-		int lcv = 0;
-		for (int i=0; iNCI Thesaurus Code: " + ncit_code + " ").append("\n");
-		buf.append("(see NCI Thesaurus info)").append("\n");
-		buf.append("
    ").append("\n");
-
-		v = (Vector) property_hashmap.get("Property");
-		for (int i=0; iSemantic Type: " + semantic_type + "
    ").append("\n");
-			}
-		}
-		buf.append("
    ").append("\n");
-
-		v = (Vector) property_hashmap.get("Definition");
-		for (int i=0; i" + source + " Definition: " + description + "
    ").append("\n");
-		}
-
-		buf.append("
    ").append("\n");
-		buf.append("Synonyms & Abbreviations:").append("\n");
-		buf.append("(see Synonym Details)").append("\n");
-		buf.append("").append("\n");
-		v = (Vector) property_hashmap.get("Synonym");
-		lcv = 0;
-		HashSet syn_hset = new HashSet();
-		int k = 0;
-		for (int i=0; i").append("\n");
-				buf.append("").append("\n");
-				buf.append("").append("\n");
-				lcv++;
-			}
-		}
-		buf.append("
    " + termname + "
    ").append("\n");
-		buf.append("
    ").append("\n");
-
-		buf.append("
    ").append("\n");
-		buf.append("Other Properties:").append("\n");
-		buf.append("").append("\n");
-		buf.append("\"Property").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-
-		v = (Vector) property_hashmap.get("Property");
-		lcv = 0;
-		for (int i=0; i").append("\n");
-			buf.append("").append("\n");
-			buf.append("").append("\n");
-			buf.append("").append("\n");
-			buf.append("").append("\n");
-		}
-}
-		buf.append("
    ").append("\n");
-		buf.append("Name").append("\n");
-		buf.append("").append("\n");
-		buf.append("Value").append("\n");
-		buf.append("").append("\n");
-		buf.append("Source").append("\n");
-		buf.append("" + prop_name + "" + prop_value + "" + prop_source + "
    ").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("Additional Concept Data:  (none)").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("URL to Bookmark:").append("\n");
-		//https://ncim65.nci.nih.gov/sparqlncim/ConceptReport.jsp?dictionary=NCI Metathesaurus&code=
-		buf.append("").append("\n");
-        buf.append(bookmark_url + cui).append("\n");
-		buf.append("").append("\n");
-		return buf.toString();
-	 }
-
-	 public String generateSourceSelection(String code, String label, String sab, Vector sab_vec) {
-		StringBuffer buf = new StringBuffer();
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("
    '" + label + "' By Source: " + sab + "
    ").append("\n");
-		buf.append("
          ").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("Select source:  ").append("\n");
-
-		for (int i=0; i").append("\n");
-			buf.append(source).append("\n");
-			buf.append(" ").append("\n");
-		}
-		buf.append("
    ");
-		return buf.toString();
-	}
-
-
-	public String generatePaginationForm(int total_count, String matchText) {
-        StringBuffer buf = new StringBuffer();
-		buf.append("
    ").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("Results 1-50 of " + total_count + "").append("\n");
-		buf.append("").append("\n");
-		buf.append("      ").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("1 ").append("\n");
-		buf.append("").append("\n");
-		buf.append("2").append("\n");
-		buf.append(" ").append("\n");
-		buf.append("").append("\n");
-		buf.append(" ").append("\n");
-		buf.append("").append("\n");
-		buf.append("Next").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append(" results per page").append("\n");
-		buf.append("").append("\n");
-		buf.append("  ").append("\n");
-		buf.append("").append("\n");
-		buf.append(" ").append("\n");
-		buf.append("
    ").append("\n");
-		return buf.toString();
-	}
-
-	public String generateSearchResultsTable(int total_count, String matchText, Vector search_results_vec) {
-		StringBuffer buf = new StringBuffer();
-		buf.append("").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-
-		buf.append("
    ").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("
    Result for:cell aging
    ").append("\n");
-
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("").append("\n");
-
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("Results 1-50 of " + total_count + " for: " + matchText + "").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-
-		if (search_results_vec != null) {
-			String line = (String) search_results_vec.elementAt(0);
-			Vector u0 = gov.nih.nci.evs.restapi.util.StringUtils.parseData(line, '|');
-			if (u0.size() > 2) {
-				buf.append("").append("\n");
-			}
-		}
-		buf.append("").append("\n");
-		if (search_results_vec != null) {
-			int lcv = 0;
-			for (int i=0; i 2) {
-					semantic_type = (String) u.elementAt(2);
-				}
-				String dataRowColor = "dataRowDark";
-				if (!isEven(lcv).equals(Boolean.TRUE)) {
-					dataRowColor = "dataRowLight";
-				}
-				buf.append("").append("\n");
-				buf.append("").append("\n");
-				if (u.size() > 2) {
-					buf.append("").append("\n");
-			    }
-				buf.append("").append("\n");
-			}
-		}
-		buf.append("
    ConceptSemantic Type
    ").append("\n");
-				buf.append("" + label + "").append("\n");
-				buf.append("").append("\n");
-					buf.append(semantic_type).append("\n");
-					buf.append("
    ").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		return buf.toString();
-	}
-
-	public String generateAdvancedSearchForm(Vector source_vec) {
-		StringBuffer buf = new StringBuffer();
-		buf.append("
    ").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("
    Advanced Search
    ").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("  ").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("Concepts with this value in:").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("
    ").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		buf.append("
    ").append("\n");
-		return buf.toString();
-	}
-
-
-    public String getViewInSourceHierarchyLink(String cui, String sab) {
-		StringBuffer buf = new StringBuffer();
-		buf.append("").append("\n");
-		buf.append("\"View").append("\n");
-		buf.append("").append("\n");
-		return buf.toString();
-	}
-
-    public String getCodeHyperlink(String code, String sab) {
-		StringBuffer buf = new StringBuffer();
-	    buf.append("			  ").append("\n");
-	    buf.append(code);
-	    buf.append("			  ").append("\n");
-		return buf.toString();
-	}
-
-	public static void main(String[] args) {
-
-		 String filename = args[0];
-		 Vector v = Utils.readFile(filename);
-		 String t = vector2String(v);
-		 Vector w = new Vector();
-		 w.add(t);
-		 Utils.saveToFile("test_" + filename, w);
-         /*
-		 Vector w = new Vector();
-		 w.add(test());
-		 Utils.saveToFile("test_" + filename, w);
-		 */
-		 String s = "Cell aging";
-		 //s = encode(s);
-		 //System.out.println(s);
-	 }
-
- }
\ No newline at end of file
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/ui/UIUtils.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/ui/UIUtils.java
deleted file mode 100644
index 9c19d8d52..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/ui/UIUtils.java
+++ /dev/null
@@ -1,200 +0,0 @@
-package gov.nih.nci.evs.restapi.ui;
-
-import gov.nih.nci.evs.restapi.bean.*;
-import gov.nih.nci.evs.restapi.common.*;
-import gov.nih.nci.evs.restapi.util.*;
-
-import java.io.*;
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.*;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
-import java.util.*;
-import java.util.regex.*;
-import org.apache.commons.codec.binary.Base64;
-import org.json.*;
-
-/**
- * 
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-public class UIUtils {
-
-    public static String getConceptReportHyperlink(String applicationName, String named_graph, String name, String code) {
-		StringBuffer buf = new StringBuffer();
-		buf.append("").append("\n");
-		buf.append(name).append("\n");
-		buf.append("").append("\n");
-		return buf.toString();
-    }
-
-
-//sparql/ConceptReport.jsp
-    public static String getHyperlink(String named_graph, String name, String code) {
-		return getConceptReportHyperlink("sparqlncim", named_graph, name, code);
-    }
-
-    public static String getHyperlink(String jsp, String named_graph, String name, String code) {
-		StringBuffer buf = new StringBuffer();
-		buf.append("").append("\n");
-		buf.append(name).append("\n");
-		buf.append("").append("\n");
-		return buf.toString();
-    }
-
-
-    public static void generateTestPage(String outputfile, String serviceUrl) {
-		PrintWriter pw = null;
-		try {
-			pw = new PrintWriter(outputfile, "UTF-8");
-			generateTestPage(pw, serviceUrl);
-
-		} catch (Exception ex) {
-
-		} finally {
-			try {
-				pw.close();
-				System.out.println("Output file " + outputfile + " generated.");
-			} catch (Exception ex) {
-				ex.printStackTrace();
-			}
-		}
-	}
-
-	public static String generateCartContent(String applicationName, Vector label_vec, Vector semtype_vec) {
-		StringBuffer buf = new StringBuffer();
-		buf.append("      ").append("\n");
-		buf.append("            ").append("\n");
-		buf.append("              ").append("\n");
-		buf.append("              ").append("\n");
-		buf.append("              ").append("\n");
-		buf.append("            ").append("\n");
-		for (int i=0; i").append("\n");
-			buf.append("              ").append("\n");
-			buf.append("              ").append("\n");
-			buf.append("              ").append("\n");
-			buf.append("            ").append("\n");
-		}		buf.append("").append("\n");
-		buf.append("      
     ConceptSemantic Type
    ").append("\n");
-			String hyperlink = getConceptReportHyperlink(applicationName, null, name, code);
-			buf.append("                   ").append("\n");
-			buf.append("              " + semtype + "
    ").append("\n");
-		//buf.append("      ").append("\n");
-		//buf.append("").append("\n");
-        return buf.toString();
-	}
-
-
-    public static void generateTestPage(PrintWriter out, String serviceUrl) {
-		out.println("");
-		out.println("");
-		out.println("");
-		out.println("");
-		out.println("");
-		out.println("");
-		out.println("");
-		out.println("");
-		out.println("");
-		out.println("");
-		out.println("
    ");
-		out.println("    
    ");
-		out.println("
    ");
-		out.println("
    ");
-		out.println("Code: ");
-		out.println("");
-		out.println("");
-		out.println("");
-		out.println("");
-		out.println("");
-	}
-
-	public static StringBuffer treeItem2StringBuffer(String applicationName, gov.nih.nci.evs.restapi.bean.TreeItem ti) {
-        HashSet _vocabularyNameSet = null;
-        gov.nih.nci.evs.restapi.util.SimpleTreeUtils stu = new gov.nih.nci.evs.restapi.util.SimpleTreeUtils(_vocabularyNameSet);
-        stu.setBasePath("/" + applicationName + "/");
-		HashMap sourceValueSetTree = new HashMap();
-		sourceValueSetTree.put("", ti);
-		return stu.getValueSetTreeStringBuffer(sourceValueSetTree);
-	}
-
-}
\ No newline at end of file
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/ui/VisUtils.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/ui/VisUtils.java
deleted file mode 100644
index 805ccb2b6..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/ui/VisUtils.java
+++ /dev/null
@@ -1,612 +0,0 @@
-package gov.nih.nci.evs.restapi.ui;
-
-import gov.nih.nci.evs.restapi.bean.*;
-import gov.nih.nci.evs.restapi.common.*;
-import gov.nih.nci.evs.restapi.util.*;
-
-import java.util.*;
-import java.io.*;
-import java.util.Map.Entry;
-//import org.apache.log4j.*;
-
-public class VisUtils {
-    //private static Logger _logger = Logger.getLogger(VisualizationUtils.class);
-
-    private OWLSPARQLUtils owlSPARQLUtils = null;//(String sparql_service) {
-    private String sparql_service = null;
-    private String prefixes = null;
-
-    public static int NODES_ONLY = 1;
-    public static int EDGES_ONLY = 2;
-    public static int NODES_AND_EDGES = 3;
-
-    public static String ROOT = "";
-    public static String PART_OF = "part_of";
-
-    public static final String[] ALL_RELATIONSHIP_TYPES = {"type_superconcept",
-                                                           "type_subconcept",
-                                                           "type_role",
-                                                           "type_inverse_role",
-                                                           "type_association",
-                                                           "type_inverse_association"};
-    public static HashMap RELATIONSHIP_LABEL_MAP;
-    String serviceUrl = null;
-    String named_graph = null;
-    String username = null;
-    String password = null;
-
-    static {
-		RELATIONSHIP_LABEL_MAP = new HashMap();
-		RELATIONSHIP_LABEL_MAP.put("ALL", "ALL");
-		RELATIONSHIP_LABEL_MAP.put("type_superconcept", "Superconcept");
-		RELATIONSHIP_LABEL_MAP.put("type_subconcept", "Subconcept");
-		RELATIONSHIP_LABEL_MAP.put("type_role", "Role");
-		RELATIONSHIP_LABEL_MAP.put("type_inverse_role", "Inverse Role");
-		RELATIONSHIP_LABEL_MAP.put("type_association", "Association");
-		RELATIONSHIP_LABEL_MAP.put("type_inverse_association", "Inverse Association");
-		RELATIONSHIP_LABEL_MAP.put("type_part_of", "Part Of");
-		RELATIONSHIP_LABEL_MAP.put("type_part_of_path", "Part Of (Path to Roots)");
-	};
-
-	public static String getRelatinshipLabel(String option_label) {
-	    if (!RELATIONSHIP_LABEL_MAP.containsKey(option_label)) return option_label;
-	    return (String) RELATIONSHIP_LABEL_MAP.get(option_label);
-	}
-
-	public VisUtils() {
-
-	}
-
-	public VisUtils(String serviceUrl, String named_graph, String username, String password) {
-        this.serviceUrl = serviceUrl;
-        this.sparql_service = serviceUrl;
-        this.username = username;
-        this.password = password;
-
-        owlSPARQLUtils = new OWLSPARQLUtils(serviceUrl, username, password);
-        owlSPARQLUtils.set_named_graph(named_graph);
-
-        /*
-        String serviceUrl = sparql_service;
-        int n = sparql_service.lastIndexOf("?");
-        if (n != -1) {
-			serviceUrl = sparql_service.substring(0, n);
-		}
-
-		System.out.println("serviceUrl: " + serviceUrl);
-		*/
-
-		MetadataUtils metadataUtils = new MetadataUtils(serviceUrl, username, password);
-		String codingScheme = "NCI_Thesaurus";
-		long ms = System.currentTimeMillis();
-		String version = metadataUtils.getLatestVersion(codingScheme);
-		System.out.println(codingScheme);
-		System.out.println(version);
-		this.named_graph = metadataUtils.getNamedGraph(codingScheme);
-
-
-	}
-
-    public String getLabel(String name, String code) {
-		name = encode(name);
-		StringBuffer buf = new StringBuffer();
-		buf.append(name + " (" + code + ")");
-		return buf.toString();
-	}
-
-    public String getLabel(String line) {
-        Vector u = gov.nih.nci.evs.restapi.util.StringUtils.parseData(line);
-        String name = (String) u.elementAt(0);
-        name = encode(name);
-        String code = (String) u.elementAt(1);
-        return getLabel(name, code);
-	}
-
-    public String getFieldValue(String line, int index) {
-        Vector u = gov.nih.nci.evs.restapi.util.StringUtils.parseData(line);
-        return (String) u.elementAt(index);
-	}
-
-	public String encode(String t) {
-		if (t == null) return null;
-		t = t.replaceAll("'", "\'");
-		return t;
-	}
-
-    public String getEntityDescriptionByCode(String code) {
-		Vector v = owlSPARQLUtils.getLabelByCode(named_graph, code);
-		v = new ParserUtils().getResponseValues(v);
-		return (String) v.elementAt(0);
-	}
-
-    public String generateDiGraph(String scheme, String version, String namespace, String code) {
-		boolean useNamespace = false;
-		if (namespace != null) useNamespace = true;
-		String name = "";
-		String retstr = getEntityDescriptionByCode(code);
-		/*
-		Vector v = owlSPARQLUtils.getLabelByCode(named_graph, code);
-		v = new ParserUtils().getResponseValues(v);
-		String retstr = (String) v.elementAt(0);
-		*/
-
-		if (retstr != null) {
-			name = retstr;
-		}
-		name = encode(name);
-		if (gov.nih.nci.evs.restapi.util.StringUtils.isNullOrBlank(namespace)) {
-			namespace = "";
-		}
-
-		StringBuffer buf = new StringBuffer();
-        buf.append("\ndigraph {").append("\n");
-        buf.append("node [shape=oval fontsize=16]").append("\n");
-        buf.append("edge [length=100, color=gray, fontcolor=black]").append("\n");
-
-        String focused_node_label = "\"" + getLabel(name, code) + "\"" ;
-
-        RelationshipHelper relUtils = new RelationshipHelper(serviceUrl, named_graph, username, password);
-        HashMap relMap = relUtils.getRelationshipHashMap(scheme, version, code, namespace, useNamespace);
-
-		String key = "type_superconcept";
-		ArrayList list = (ArrayList) relMap.get(key);
-		if (list != null) {
-			for (int i=0; i " + rel_node_label).append("\n");
-				buf.append("[label=" + rel_label + "];").append("\n");
-			}
-		}
-
-		key = "type_subconcept";
-		list = (ArrayList) relMap.get(key);
-		if (list != null) {
-			for (int i=0; i " + rel_node_label).append("\n");
-				buf.append("[label=" + rel_label + "];").append("\n");
-			}
-		}
-
-		key = "type_role";
-		list = (ArrayList) relMap.get(key);
-		if (list != null) {
-			for (int i=0; i " + rel_node_label).append("\n");
-				buf.append("[label=" + rel_label + "];").append("\n");
-			}
-		}
-
-		key = "type_inverse_role";
-		list = (ArrayList) relMap.get(key);
-		if (list != null) {
-			for (int i=0; i " + focused_node_label).append("\n");
-				buf.append("[label=" + rel_label + "];").append("\n");
-			}
-		}
-
-		key = "type_association";
-		list = (ArrayList) relMap.get(key);
-		if (list != null) {
-			for (int i=0; i " + rel_node_label).append("\n");
-				buf.append("[label=" + rel_label + "];").append("\n");
-			}
-		}
-
-		key = "type_inverse_association";
-		list = (ArrayList) relMap.get(key);
-		if (list != null) {
-			for (int i=0; i " + focused_node_label).append("\n");
-				buf.append("[label=" + rel_label + "];").append("\n");
-			}
-		}
-
-        buf.append(focused_node_label + " [").append("\n");
-        buf.append("fontcolor=white,").append("\n");
-        buf.append("color=red,").append("\n");
-        buf.append("]").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-
-    public String generateGraphScript(String scheme, String version, String namespace, String code) {
-		return generateGraphScript(scheme, version, namespace, code, null);
-	}
-
-
-    public String generateGraphScript(String scheme, String version, String namespace, String code, String[] types) {
-		return generateGraphScript(scheme, version, namespace, code, types, NODES_AND_EDGES, null);
-	}
-
-
-
-    public String generateGraphScript(String scheme, String version, String namespace, String code, String[] types, int option, HashMap hmap) {
-        if (types == null) {
-			types = ALL_RELATIONSHIP_TYPES;
-		}
-        Vector graphData = generateGraphData(scheme, version, namespace, code, types, option, hmap);
-        return GraphUtils.generateGraphScript(graphData, option);
-	}
-
-
-    public Vector generateGraphScriptVector(String scheme, String version, String namespace, String code, String[] types, int option, HashMap hmap) {
-        if (types == null) {
-			types = ALL_RELATIONSHIP_TYPES;
-		}
-		System.out.println("generateGraphData ...");
-        Vector graphData = generateGraphData(scheme, version, namespace, code, types, option, hmap);
-
-        return GraphUtils.generateGraphScriptVector(graphData, option);
-	}
-
-	public Vector treeItem2GraphData(TreeItem root) {
-	    Vector graphData = treeItem2GraphData(root, new Vector());
-	    return graphData;
-    }
-
-	public Vector treeItem2GraphData(TreeItem ti, Vector v) {
-		String focused_node_label = getLabel(ti._text, ti._code);
-		for (String association : ti._assocToChildMap.keySet()) {
-			List children = ti._assocToChildMap.get(association);
-			for (TreeItem childItem : children) {
-				String code = childItem._code;
-				String text = childItem._text;
-				String rel_node_label = getLabel(text, code);
-				v.add(focused_node_label + "|" + rel_node_label + "|" + association + "|7");
-				v = treeItem2GraphData(childItem, v);
-			}
-		}
-	    return v;
-    }
-
-/*
-    public Vector generatePartonomyGraphData(String scheme, String version, String namespace, String code, String type, int option, HashMap hmap) {
-		Vector graphData = new Vector();
-		boolean useNamespace = true;
-		if (gov.nih.nci.evs.restapi.util.StringUtils.isNullOrBlank(namespace)) {
-			useNamespace = false;
-		}
-
-		String name = "";
-		String retstr = owlSPARQLUtils.getEntityDescriptionByCode(code);
-		if (retstr != null) {
-			name = retstr;
-		}
-		name = encode(name);
-		if (gov.nih.nci.evs.restapi.util.StringUtils.isNullOrBlank(namespace)) {
-			namespace = "";
-		}
-
-		if (gov.nih.nci.evs.restapi.util.StringUtils.isNullOrBlank(namespace)) {
-			namespace = "";
-		}
-		if (!gov.nih.nci.evs.restapi.util.StringUtils.isNullOrBlank(namespace)) {
-			useNamespace = true;
-		}
-        String focused_node_label = getLabel(name, code);
-
-        HashMap relMap = null;
-        if (hmap == null) {
-			RelationshipHelper relUtils = new RelationshipHelper(sparql_service);
-			relMap = relUtils.getRelationshipHashMap(scheme, version, code, namespace, useNamespace);
-	    } else {
-			relMap = hmap;
-		}
-
-        HashSet nodes = new HashSet();
-        nodes.add(focused_node_label);
-
-        PartonomyUtils partUtils = new PartonomyUtils(sparql_service);
-
-        if (type.compareTo("type_part_of") == 0) {
-			ArrayList list = null;
-
-			List part_of_list = partUtils.getPartOfData(relMap);
-			for (int i=0; i " + rel_node_label).append("\n");
-				buf.append("[label=" + rel_label + "];").append("\n");
-			}
-		}
-
-		key = "type_subconcept";
-		list = (ArrayList) relMap.get(key);
-		if (list != null) {
-			for (int i=0; i " + rel_node_label).append("\n");
-				buf.append("[label=" + rel_label + "];").append("\n");
-			}
-		}
-
-		key = "type_role";
-		list = (ArrayList) relMap.get(key);
-		if (list != null) {
-			for (int i=0; i " + rel_node_label).append("\n");
-				buf.append("[label=" + rel_label + "];").append("\n");
-			}
-		}
-
-		key = "type_inverse_role";
-		list = (ArrayList) relMap.get(key);
-		if (list != null) {
-			for (int i=0; i " + focused_node_label).append("\n");
-				buf.append("[label=" + rel_label + "];").append("\n");
-			}
-		}
-
-		key = "type_association";
-		list = (ArrayList) relMap.get(key);
-		if (list != null) {
-			for (int i=0; i " + rel_node_label).append("\n");
-				buf.append("[label=" + rel_label + "];").append("\n");
-			}
-		}
-
-		key = "type_inverse_association";
-		list = (ArrayList) relMap.get(key);
-		if (list != null) {
-			for (int i=0; i " + focused_node_label).append("\n");
-				buf.append("[label=" + rel_label + "];").append("\n");
-			}
-		}
-
-        buf.append(focused_node_label + " [").append("\n");
-        buf.append("fontcolor=white,").append("\n");
-        buf.append("color=red,").append("\n");
-        buf.append("]").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-
-    public String generateGraphScript(String scheme, String version, String namespace, String code) {
-		return generateGraphScript(scheme, version, namespace, code, null);
-	}
-
-
-    public String generateGraphScript(String scheme, String version, String namespace, String code, String[] types) {
-		return generateGraphScript(scheme, version, namespace, code, types, NODES_AND_EDGES, null);
-	}
-
-
-    public String generateGraphScript(String scheme, String version, String namespace, String code, String[] types, int option, HashMap hmap) {
-        if (types == null) {
-			types = ALL_RELATIONSHIP_TYPES;
-		}
-        Vector graphData = generateGraphData(scheme, version, namespace, code, types, option, hmap);
-        return GraphUtils.generateGraphScript(graphData, option);
-	}
-
-
-	public Vector treeItem2GraphData(TreeItem root) {
-	    Vector graphData = treeItem2GraphData(root, new Vector());
-	    return graphData;
-    }
-
-	public Vector treeItem2GraphData(TreeItem ti, Vector v) {
-		String focused_node_label = getLabel(ti._text, ti._code);
-		for (String association : ti._assocToChildMap.keySet()) {
-			List children = ti._assocToChildMap.get(association);
-			for (TreeItem childItem : children) {
-				String code = childItem._code;
-				String text = childItem._text;
-				String rel_node_label = getLabel(text, code);
-				v.add(focused_node_label + "|" + rel_node_label + "|" + association + "|7");
-				v = treeItem2GraphData(childItem, v);
-			}
-		}
-	    return v;
-    }
-
-/*
-    public Vector generatePartonomyGraphData(String scheme, String version, String namespace, String code, String type, int option, HashMap hmap) {
-		Vector graphData = new Vector();
-		boolean useNamespace = true;
-		if (gov.nih.nci.evs.restapi.util.StringUtils.isNullOrBlank(namespace)) {
-			useNamespace = false;
-		}
-
-		String name = "";
-		String retstr = OWLSPARQLUtils.getEntityDescriptionByCode(code);
-		if (retstr != null) {
-			name = retstr;
-		}
-		name = encode(name);
-		if (gov.nih.nci.evs.restapi.util.StringUtils.isNullOrBlank(namespace)) {
-			namespace = "";
-		}
-
-		if (gov.nih.nci.evs.restapi.util.StringUtils.isNullOrBlank(namespace)) {
-			namespace = "";
-		}
-		if (!gov.nih.nci.evs.restapi.util.StringUtils.isNullOrBlank(namespace)) {
-			useNamespace = true;
-		}
-        String focused_node_label = getLabel(name, code);
-
-        HashMap relMap = null;
-        if (hmap == null) {
-			RelationshipHelper relUtils = new RelationshipHelper(sparql_service);
-			relMap = relUtils.getRelationshipHashMap(scheme, version, code, namespace, useNamespace);
-	    } else {
-			relMap = hmap;
-		}
-
-        HashSet nodes = new HashSet();
-        nodes.add(focused_node_label);
-
-        PartonomyUtils partUtils = new PartonomyUtils(sparql_service);
-
-        if (type.compareTo("type_part_of") == 0) {
-			ArrayList list = null;
-
-			List part_of_list = partUtils.getPartOfData(relMap);
-			for (int i=0; i", ti);
-        String url = "https://nciterms.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=";
-        new SimpleTreeUtils().writeTree2HTML(hmap, url, htmlfile);
-    }
-
-    public static void main(String[] args) {
-        String parent_child_file = args[0];
-        Vector parent_child_vec = Utils.readFile(parent_child_file);
-        String nodefile = args[1];
-        Vector v = Utils.readFile(nodefile);
-        HashSet nodeSet = new HashSet();
-        for (int i=0; i
- * Copyright 2008-2016 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class ASCIITreeUtils {
-
-    public ASCIITreeUtils() {
-
-	}
-
-	public int getLevel(String t) {
-		int level = 0;
-		for (int i=0; i children = ti._assocToChildMap.get(association);
-            for (int i=0; i children = ti._assocToChildMap.get(association);
-            for (int i=0; i", "Root node");
-		root._expandable = false;
-		int child_count = 0;
-		try {
-			for (int i=0; i children = root._assocToChildMap.get(Constants.ASSOCIATION_NAME);
-		if (children != null && children.size() > 0) {
-			TreeItem child_ti = null;
-			for (int i=0; i children = root._assocToChildMap.get(Constants.ASSOCIATION_NAME);
-		if (children != null && children.size() > 0) {
-			List new_children = new ArrayList();
-			for (int i=0; i)") != 0) return v;
-		Vector w = new Vector();
-		for (int i=1; i");
-		out.println("");
-		out.println("");
-		out.println("    ");
-		out.println("    " + title + "");
-		out.println("    ");
-		out.println("");
-		out.println("");
-		out.println("    
    ");
-		out.println("");
-		out.println("");
-	}
-
-	public void run(String title, String url, String outputfile) {
-		PrintWriter pw = null;
-		try {
-			pw = new PrintWriter(outputfile, "UTF-8");
-			run(pw, title, url);
-
-		} catch (Exception ex) {
-
-		} finally {
-			try {
-				pw.close();
-				System.out.println("Output file " + outputfile + " generated.");
-			} catch (Exception ex) {
-				ex.printStackTrace();
-			}
-		}
-	}
-
-	public static void main(String[] args) {
-        long ms = System.currentTimeMillis();
-        String title = args[0];
-        String url = args[1];
-        AjaxUtils ajaxUtils = new AjaxUtils();
-        String outputfile = title + ".html";
-        outputfile = outputfile.replace(" ", "_");
-        ajaxUtils.run(title, url, outputfile);
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-
-}
\ No newline at end of file
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/ApachePoiPieChartCS.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/ApachePoiPieChartCS.java
deleted file mode 100644
index a794b293c..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/ApachePoiPieChartCS.java
+++ /dev/null
@@ -1,183 +0,0 @@
-package gov.nih.nci.evs.restapi.util;
-
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-
-import org.apache.poi.ss.usermodel.Cell;
-import org.apache.poi.ss.usermodel.Row;
-import org.apache.poi.ss.util.CellRangeAddress;
-import org.apache.poi.xddf.usermodel.chart.ChartTypes;
-import org.apache.poi.xddf.usermodel.chart.LegendPosition;
-import org.apache.poi.xddf.usermodel.chart.XDDFChartData;
-import org.apache.poi.xddf.usermodel.chart.XDDFChartLegend;
-import org.apache.poi.xddf.usermodel.chart.XDDFDataSource;
-import org.apache.poi.xddf.usermodel.chart.XDDFDataSourcesFactory;
-import org.apache.poi.xddf.usermodel.chart.XDDFNumericalDataSource;
-import org.apache.poi.xssf.usermodel.XSSFChart;
-import org.apache.poi.xssf.usermodel.XSSFClientAnchor;
-import org.apache.poi.xssf.usermodel.XSSFDrawing;
-import org.apache.poi.xssf.usermodel.XSSFSheet;
-import org.apache.poi.xssf.usermodel.XSSFWorkbook;
-
-import java.io.*;
-import java.util.*;
-import java.text.*;
-
-public class ApachePoiPieChartCS {
-	static HashSet retired_concepts = null;
-//1,1-Dimethylhydrazine|C1072|Contributing_Source|FDA
-	static {
-		retired_concepts = new HashSet();
-		Vector w = Utils.readFile("Retired_Concept.txt");
-		for (int i=0; i sources = XDDFDataSourcesFactory.fromStringCellRange(sheet,
-					new CellRangeAddress(1, src_vec.size(), 0, 0));
-
-			XDDFNumericalDataSource values = XDDFDataSourcesFactory.fromNumericCellRange(sheet,
-					new CellRangeAddress(1, count_vec.size(), 1, 1));
-
-			//XDDFChartData data = chart.createData(ChartTypes.PIE3D, null, null);
-			XDDFChartData data = chart.createData(ChartTypes.PIE, null, null);
-
-			data.setVaryColors(true);
-			data.addSeries(sources, values);
-			chart.plot(data);
-            String exceloutputfile = "NCIT_Concept_Stats_By_Contributing_Source.xlsx";
-			try (FileOutputStream fileOut = new FileOutputStream(exceloutputfile)) {
-				wb.write(fileOut);
-				fileOut.close();
-				wb.close();
-				System.out.println(exceloutputfile + " generated.");
-			} catch (Exception ex) {
-				ex.printStackTrace();
-			}
-		} catch (Exception ex) {
-			ex.printStackTrace();
-		}
-	}
-
-
-}
-
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/AxiomParser.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/AxiomParser.java
deleted file mode 100644
index 96ac7c656..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/AxiomParser.java
+++ /dev/null
@@ -1,387 +0,0 @@
-package gov.nih.nci.evs.restapi.util;
-import gov.nih.nci.evs.restapi.bean.*;
-import gov.nih.nci.evs.restapi.common.*;
-
-import java.io.*;
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.*;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
-import java.util.*;
-import java.util.regex.*;
-import org.json.*;
-
-/**
- * 
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class AxiomParser {
-    JSONUtils jsonUtils = null;
-    HTTPUtils httpUtils = null;
-    String named_graph = null;
-    String prefixes = null;
-    String serviceUrl = null;
-    String restURL = null;
-    String named_graph_id = ":NHC0";
-    String BASE_URI = "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl";
-
-    ParserUtils parser = new ParserUtils();
-    HashMap nameVersion2NamedGraphMap = null;
-    HashMap ontologyUri2LabelMap = null;
-    String version = null;
-    String username = null;
-    String password = null;
-    OWLSPARQLUtils owlSPARQLUtils = null;
-
-    public AxiomParser() {
-
-	}
-
-    public AxiomParser(String serviceUrl, String named_graph, String username, String password) {
-    	this.named_graph = named_graph;
-        this.owlSPARQLUtils = new OWLSPARQLUtils(serviceUrl, username, password);
-        this.owlSPARQLUtils.set_named_graph(named_graph);
-    }
-
-    public OWLSPARQLUtils getOWLSPARQLUtils() {
-		return this.owlSPARQLUtils;
-	}
-
-
-	public static HashSet getDistinctAxiomIds(Vector v) {
-		HashSet hset = new HashSet();
-		for (int i=0; i
- * Copyright 2011, MSC. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or MSC.
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      MSC, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation ongki@nih.gov
- *
- */
-
-public class AxiomRetrieval {
-    String owlfile = null;
-    OWLScanner owlscanner = null;
-    Vector owl_vec = null;
-
-    HashMap synonymMap = null;
-    HashMap sourceDefinitionMap = null;
-    HashMap definitionMap = null;
-    HashMap mapsToMap = null;
-
-    String source = null;
-
-    public AxiomRetrieval(String owlfile) {
-		this.owlfile = owlfile;
-		this.source = null;
-		initialize();
-    }
-
-    public AxiomRetrieval(String owlfile, String source) {
-		this.owlfile = owlfile;
-		this.source = source;
-		initialize();
-    }
-
-    public HashMap getSynonymMap() {
-		return this.synonymMap;
-	}
-
-    public HashMap getSourceDefinitionMap() {
-		return this.sourceDefinitionMap;
-	}
-
-    public HashMap getDefinitionMap() {
-		return this.definitionMap;
-	}
-
-    public HashMap getMapsToMap() {
-		return this.mapsToMap;
-	}
-
-	public void initialize() {
-		owlscanner = new OWLScanner(owlfile);
-		owl_vec = owlscanner.get_owl_vec();
-		String propertyCode = "P325";
-		Vector defs = owlscanner.extractAxiomData(propertyCode);
-        sourceDefinitionMap = new HashMap();
-        for (int i=0; i");
-		line = line.replace(""", "\"");
-		return line;
-	}
-
-    public static Synonym string2Synonym(String line) {
-		Vector u = parseData(line, '|');
-		String label = (String) u.elementAt(0);
-		String code = (String) u.elementAt(1);
-		String termName = (String) u.elementAt(3);
-		String termGroup = null;
-		String termSource = null;
-		String sourceCode = null;
-		String subSourceName = null;
-		String subSourceCode = null;
-		String qualifierCode = null;
-        String qualifierName = null;
-		if (u.size() > 4) {
-			for (int i=4; i 4) {
-			for (int i=4; i 0) {
-			s = s.substring(0, s.length()-4);
-		}
-		return s;
-	}
-
-
-    public String getDefinition(String code) {
-		if (definitionMap.containsKey(code)) {
-			return (String) definitionMap.get(code);
-		}
-		return "";
-	}
-
-    public String getSourceDefinition(String code) {
-		if (sourceDefinitionMap.containsKey(code)) {
-			return (String) sourceDefinitionMap.get(code);
-		}
-		return "";
-	}
-
-    public static Vector parseData(String line, char delimiter) {
-		if(line == null) return null;
-		Vector w = new Vector();
-		StringBuffer buf = new StringBuffer();
-		for (int i=0; i 0) {
-			t = t.substring(0, t.length()-1);
-		}
-		return t;
-	}
-
-    public String findMatchedSourcecodes(String code, String source, String type) {
-		StringBuffer buf = new StringBuffer();
-		Vector w = (Vector) synonymMap.get(code);
-		for (int i=0; i 0) {
-			t = t.substring(0, t.length()-1);
-		}
-		return t;
-	}
-
-	public Vector extractAxiomData(String propertyCode) {
-		return owlscanner.extractAxiomData(propertyCode);
-	}
-
-	public void test(String code) {
-		Vector w = (Vector) mapsToMap.get(code);
-		for (int i=0; i
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class AxiomUtils {
-	String serviceUrl = null;
-    OWLSPARQLUtils owlSPARQLUtils = null;
-    String username = null;
-    String password = null;
-
-    public AxiomUtils() {
-
-	}
-
-/*
-    public AxiomUtils(String serviceUrl) {
-        this.serviceUrl = serviceUrl;
-        this.owlSPARQLUtils = new OWLSPARQLUtils(this.serviceUrl, null, null);
-    }
-*/
-    public AxiomUtils(String serviceUrl, String username, String password) {
-        this.serviceUrl = serviceUrl;
-        this.username = username;
-        this.password = password;
-        this.owlSPARQLUtils = new OWLSPARQLUtils(this.serviceUrl, username, password);
-    }
-
-    public Vector getAxioms(String named_graph, String code, String propertyName) {
-		return owlSPARQLUtils.getAxioms(named_graph, code, propertyName);
-	}
-
-	public List getSynonyms(String named_graph, String code, String propertyName) {
-		Vector v = getAxioms(named_graph, code, propertyName);
-		return getSynonyms(v);
-	}
-
-    public Vector getAxioms(String named_graph, String code, String propertyName, String qualifierName) {
-		Vector w = owlSPARQLUtils.getAxioms(named_graph, code, propertyName, qualifierName);
-		return w;
-	}
-
-	public List getSynonyms(String named_graph, String code, String propertyName, String qualifierName) {
-		Vector v = getAxioms(named_graph, code, propertyName, qualifierName);
-		return getSynonyms(v);
-	}
-
-    public List getSynonyms(Vector axiom_data) {
-		if (axiom_data == null) return null;
-		HashMap hmap = new HashMap();
-		for (int i=0; i getSynonymWithQualifierMatching(String named_graph, String qualifierName, String qualifierValue) {
-		Vector syn_vec = new Vector();
-		String propertyName = "FULL_SYN";
-		List list = getSynonyms(named_graph, null, propertyName, qualifierName);
-		Vector codes = new Vector();
-		for (int i=0; i
- * Copyright 2020 MSC. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or MSC
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      MSC, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@nih.gov
- *
- */
-
-
-public class BasicQueryUtils {
-    String named_graph = null;
-    String prefixes = null;
-    String serviceUrl = null;
-    String username = null;
-    String password = null;
-    OWLSPARQLUtils owlSPARQLUtils = null;
-
-    public BasicQueryUtils(String serviceUrl, String named_graph, String username, String password) {
-		this.serviceUrl = serviceUrl;
-    	this.named_graph = named_graph;
-    	this.username = username;
-    	this.password = password;
-    	initialize();
-    }
-
-    public void initialize() {
-		owlSPARQLUtils = new OWLSPARQLUtils(serviceUrl, username, password);
-		owlSPARQLUtils.set_named_graph(named_graph);
-	}
-
-	public String getPrefixes() {
-		return owlSPARQLUtils.getPrefixes();
-	}
-
-	public Vector executeQuery(String query) {
-		return owlSPARQLUtils.executeQuery(query);
-	}
-
-	public String construct_get_hierarchical_relationships(String named_graph) {
-        String prefixes = owlSPARQLUtils.getPrefixes();
-        StringBuffer buf = new StringBuffer();
-        buf.append(prefixes);
-        buf.append("select distinct ?y_label ?y_code ?x_label ?x_code").append("\n");
-        buf.append("{").append("\n");
-        buf.append("    graph <" + named_graph + ">").append("\n");
-        buf.append("    {").append("\n");
-        buf.append("                ?x a owl:Class .").append("\n");
-        buf.append("                ?x :NHC0 ?x_code .").append("\n");
-        buf.append("                ?x rdfs:label ?x_label .").append("\n");
-        buf.append("").append("\n");
-        buf.append("                ?y a owl:Class .").append("\n");
-        buf.append("                ?y :NHC0 ?y_code .").append("\n");
-        buf.append("                ?y rdfs:label ?y_label .").append("\n");
-        buf.append("").append("\n");
-        buf.append("                ?x (rdfs:subClassOf|(owl:equivalentClass/owl:intersectionOf/rdf:rest*/rdf:first)) ?y .").append("\n");
-        buf.append("    } ").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-	public Vector getHierarchicalRelationships(String named_graph) {
-        String query = construct_get_hierarchical_relationships(named_graph);
-        Vector v = owlSPARQLUtils.executeQuery(query);
-        if (v == null) return null;
-        if (v.size() == 0) return v;
-        return new SortUtils().quickSort(v);
-	}
-
-	public String construct_get_subsets(String named_graph, String code) {
-        String prefixes = owlSPARQLUtils.getPrefixes();
-        StringBuffer buf = new StringBuffer();
-        buf.append(prefixes);
-        buf.append("SELECT ?x_label ?x_code ?p_label ?y_label ?y_code ").append("\n");
-        buf.append("{").append("\n");
-        buf.append("    graph <" + named_graph + ">").append("\n");
-        buf.append("{").append("\n");
-        buf.append("        ?x a owl:Class .  ").append("\n");
-        buf.append("    	?x :NHC0 ?x_code .").append("\n");
-        buf.append("    	?x rdfs:label ?x_label . ").append("\n");
-        buf.append("        ?p a owl:AnnotationProperty .       ").append("\n");
-        buf.append("        ?p :NHC0 \"A8\"^^xsd:string .").append("\n");
-        buf.append("        ?p rdfs:label ?p_label . ").append("\n");
-        buf.append("        ?y a owl:Class .  ").append("\n");
-        buf.append("   	    ?y :NHC0 ?y_code .").append("\n");
-        if (code != null) {
-        	buf.append("        ?y :NHC0 \"" + code + "\"^^xsd:string .").append("\n");
-		}
-        buf.append("    	?y rdfs:label ?y_label . ").append("\n");
-        buf.append("        ?x ?p ?y").append("\n");
-        buf.append("}").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-	public Vector getSubsets(String named_graph, String code) {
-        String query = construct_get_subsets(named_graph, code);
-        Vector v = owlSPARQLUtils.executeQuery(query);
-        if (v == null) return null;
-        if (v.size() == 0) return v;
-        return new SortUtils().quickSort(v);
-	}
-
-	public Vector getSubsets(String named_graph) {
-		return getSubsets(named_graph, null);
-	}
-
-	public String construct_get_published_subset(String named_graph) {
-        String prefixes = owlSPARQLUtils.getPrefixes();
-        StringBuffer buf = new StringBuffer();
-        buf.append(prefixes);
-        buf.append("SELECT ?x_label ?x_code ?p_label ?p_value").append("\n");
-        buf.append("{").append("\n");
-        buf.append("    graph <" + named_graph + ">").append("\n");
-        buf.append("   {").append("\n");
-        buf.append("        ?x a owl:Class .  ").append("\n");
-        buf.append("        ?x rdfs:label ?x_label .").append("\n");
-        buf.append("    	?x :NHC0 ?x_code .").append("\n");
-        buf.append("        ?p a owl:AnnotationProperty .      ").append("\n");
-        buf.append("        ?p rdfs:label ?p_label . ").append("\n");
-        buf.append("        ?p rdfs:label \"Publish_Value_Set\"^^xsd:string . ").append("\n");
-        buf.append("        ?x ?p ?p_value").append("\n");
-        buf.append("   }").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-
-	public Vector getPublishedSubset(String named_graph) {
-        String query = construct_get_published_subset(named_graph);
-        Vector v = owlSPARQLUtils.executeQuery(query);
-        if (v == null) return null;
-        if (v.size() == 0) return v;
-        return new SortUtils().quickSort(v);
-	}
-
-	public static void main(String[] args) {
-		String serviceUrl = ConfigurationController.serviceUrl;
-		String namedGraph = ConfigurationController.namedGraph;
-		String username = ConfigurationController.username;
-		String password = ConfigurationController.password;
-        BasicQueryUtils generator = new BasicQueryUtils(serviceUrl, namedGraph, username, password);
-
-	}
-}
\ No newline at end of file
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/CSV2HTMLTable.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/CSV2HTMLTable.java
deleted file mode 100644
index 14ddc1926..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/CSV2HTMLTable.java
+++ /dev/null
@@ -1,60 +0,0 @@
-package gov.nih.nci.evs.restapi.util;
-
-import java.io.*;
-import java.text.*;
-import java.util.*;
-
-public class CSV2HTMLTable {
-
-    public static Vector addHyperlinks(String datafile, int columnIndex, String url) {
-		Vector w = new Vector();
-		Vector v = Utils.readFile(datafile);
-		w.add((String) v.elementAt(0));
-
-		for (int i=1; i 5) {
-			String columnIndexStr = args[5];
-			int columnIndex = Integer.parseInt(columnIndexStr);
-			String url = args[6];
-			Vector w = addHyperlinks(inputfile, columnIndex, url);
-			Utils.saveToFile(inputfile, w);
-		}
-
-        Utils.saveToFile(inputfile, v);
-		String outputfile = new HTMLTableDataConverter(serviceUrl, named_graph, username, password).convert(inputfile);
-		System.out.println(outputfile + " generated.");
-		v = Utils.readFile(outputfile);
-		outputfile = new HTMLTable().generate(v);
-		System.out.println(outputfile + " generated.");
-	}
-}
\ No newline at end of file
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/CSVFileConverter.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/CSVFileConverter.java
deleted file mode 100644
index edfb26cea..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/CSVFileConverter.java
+++ /dev/null
@@ -1,81 +0,0 @@
-package gov.nih.nci.evs.restapi.util;
-
-import com.opencsv.CSVReader;
-import java.io.*;
-import java.util.*;
-
-
-/**
- * 
- * Copyright 2008-2016 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class CSVFileConverter {
-
-	public static void main(String[] args) {
-		String csvfile = args[0];
-        Vector v = Utils.readFile(csvfile);
-        String heading = (String) v.elementAt(0);
-        heading = heading.replace("REL", "rel");
-        heading = heading.replaceAll(" ", "");
-        heading = heading.replaceAll(",", "|");
-        Vector u = new Vector();
-        u.add(heading);
-        Vector w = CSVFileReader.csv2Delimited(v, true, "|");
-        w = new SortUtils().quickSort(w);
-        for (int j=0; j
- * Copyright 2008-2016 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class CSVFileReader {
-
-/*
-
-    public static void sortCSV(String inputfile, int[] sort_options, boolean skip_heading) {
-		Vector v = readCSV(inputfile, skip_heading, "$");
-		String header = null;
-		if (skip_heading) {
-			String[] a = extractHeadings(inputfile);
-			header = convertToDelimitedValue(a, "$");
-		}
-        v = quickSort(v, sort_options, "$");
-        if (skip_heading) {
-            v.add(0, header);
-		}
-        PrintWriter pw = null;
-        try {
- 			pw = new PrintWriter(inputfile, "UTF-8");
- 			for (int i=0; i 0) {
-				v.add(s);
-			}
-		}
-		return v;
-	}
-
-    public static String convertToDelimitedValue(String[] a, String delim) {
-		StringBuffer buf = new StringBuffer();
-		String s = null;
-		for (int j=0; j 0) {
-					for (int i=0; i
- * Copyright 2020 MSC. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or MSC
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      MSC, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class CalendarUtils {
-
-    public CalendarUtils() {
-
-	}
-
-	public static void test() {
-		Calendar calendar = Calendar.getInstance();
-		System.out.println(calendar.getActualMaximum(Calendar.WEEK_OF_MONTH));
-	}
-
-	public static int getNumberOfWeeksInMonth(String year_month) throws Exception {
-		SimpleDateFormat format = new SimpleDateFormat("yyyy-MM");
-		Date date = format.parse(year_month);
-		Calendar c = Calendar.getInstance();
-		c.setTime(date);
-		int start = c.get(Calendar.WEEK_OF_MONTH);
-		c.add(Calendar.MONTH, 1);
-		c.add(Calendar.DATE, -1);
-		int end = c.get(Calendar.WEEK_OF_MONTH);
-		int num_weeks = end - start + 1;
-		System.out.println(" # of weeks in " + format.format(c.getTime()) + ": " + (end - start + 1));
-		return num_weeks;
-	}
-
-    public static int getReleaseWeek(char c) {
-		int int_c = (int) c;
-		return int_c - 96;
-	}
-
-	public static char getReleaseChar(int int_c) {
-		char c = (char) (int_c + 96);
-		return c;
-	}
-
-	public static String getReleaseVersion(int year, int month, int week) {
-		String year_str = Integer.valueOf(year).toString().substring(2, 4);
-		//System.out.println(year_str);
-		String month_str = Integer.valueOf(month).toString();
-		if (month_str.length() == 1) {
-			month_str = "0" + month_str;
-		}
-		return year_str + "." + month_str + getReleaseChar(week);
-	}
-
-	public static String getLatestMonthlyHistoryFile() {
-		String today = StringUtils.getToday();
-		Vector u = StringUtils.parseData(today, '-');
-		String month_str = (String) u.elementAt(0);
-		String day_str = (String) u.elementAt(1);
-		String year_str = (String) u.elementAt(2);
-		if (month_str.startsWith("0")) {
-			month_str = month_str.substring(1, month_str.length());
-		}
-		System.out.println(year_str + " " + month_str + " " + day_str);
-		int year = Integer.parseInt(year_str);
-		int month = Integer.parseInt(month_str) - 1;
-		try {
-			String year_month = year_str + "-" + month;
-			System.out.println("year_month: " + year_month);
-			int week = CalendarUtils.getNumberOfWeeksInMonth(year_month);
-			String s = getReleaseVersion(year, month, week-1);
-			return s;
-		} catch (Exception ex) {
-            ex.printStackTrace();
-		}
-		return null;
-	}
-
-	public static void main(String[] args) throws Exception {
-		try {
-			String year_month = "2020-08";
-			int num_weeks = getNumberOfWeeksInMonth(year_month);
-
-			System.out.println(" # of weeks in " + year_month + ": " + num_weeks);
-
-		} catch (Exception ex) {
-			ex.printStackTrace();
-		}
-	}
-}
\ No newline at end of file
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/CodeGenerator.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/CodeGenerator.java
deleted file mode 100644
index 9cf530cf5..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/CodeGenerator.java
+++ /dev/null
@@ -1,206 +0,0 @@
-package gov.nih.nci.evs.restapi.util;
-
-import java.io.*;
-import java.text.*;
-import java.util.*;
-import javax.servlet.*;
-import javax.servlet.http.*;
-import java.sql.*;
-
-
-public class CodeGenerator {
-    static String BASE_URL = "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl";
-
-    public CodeGenerator(String serviceUrl, String namedGraph, String username, String password) {
-	}
-
-    public static Vector generateCode(String queryfile) {
-		int n = queryfile.lastIndexOf("_query");
-		if(n ==  -1) {
-			System.out.println("queryfile: " + queryfile);
-			System.out.println("ERROR: Incorrect naming of query file (example: sparql_query.txt.)");
-			return null;
-		}
-		String t = queryfile.substring(0, n);
-		String methodSignature = "construct_get_" + t + "(String named_graph)";
-
-		Vector v = Utils.readFile(queryfile);
-		Vector w = new Vector();
-		w.addAll(SPARQLQueryGenerator.createConstrcQueryMethod(methodSignature, v));
-		w.add("\n");
-		w.addAll(SPARQLQueryGenerator.createQueryMethod(methodSignature));
-        //w.addAll(SPARQLQueryGenerator.findHardCodedVariables(v));
-        return w;
-	}
-
-
-	public static void run(PrintWriter out, String queryfile, String className) {
-		out.println("import gov.nih.nci.evs.restapi.util.*;");
-		out.println("import gov.nih.nci.evs.restapi.bean.*;");
-		out.println("import gov.nih.nci.evs.restapi.common.*;");
-		out.println("");
-		out.println("import java.io.*;");
-		out.println("import java.io.BufferedReader;");
-		out.println("import java.io.InputStream;");
-		out.println("import java.io.InputStreamReader;");
-		out.println("import java.net.*;");
-		out.println("import java.net.HttpURLConnection;");
-		out.println("import java.net.MalformedURLException;");
-		out.println("import java.net.URL;");
-		out.println("import java.net.URLConnection;");
-		out.println("import java.net.URLEncoder;");
-		out.println("import java.util.*;");
-		out.println("import java.util.regex.*;");
-		out.println("import org.json.*;");
-		out.println("");
-		out.println("/**");
-		out.println(" * ");
-		out.println(" * Copyright 2008-2017 NGIS. This software was developed in conjunction");
-		out.println(" * with the National Cancer Institute, and so to the extent government");
-		out.println(" * employees are co-authors, any rights in such works shall be subject");
-		out.println(" * to Title 17 of the United States Code, section 105.");
-		out.println(" * Redistribution and use in source and binary forms, with or without");
-		out.println(" * modification, are permitted provided that the following conditions");
-		out.println(" * are met:");
-		out.println(" *   1. Redistributions of source code must retain the above copyright");
-		out.println(" *      notice, this list of conditions and the disclaimer of Article 3,");
-		out.println(" *      below. Redistributions in binary form must reproduce the above");
-		out.println(" *      copyright notice, this list of conditions and the following");
-		out.println(" *      disclaimer in the documentation and/or other materials provided");
-		out.println(" *      with the distribution.");
-		out.println(" *   2. The end-user documentation included with the redistribution,");
-		out.println(" *      if any, must include the following acknowledgment:");
-		out.println(" *      \"This product includes software developed by NGIS and the National");
-		out.println(" *      Cancer Institute.\"   If no such end-user documentation is to be");
-		out.println(" *      included, this acknowledgment shall appear in the software itself,");
-		out.println(" *      wherever such third-party acknowledgments normally appear.");
-		out.println(" *   3. The names \"The National Cancer Institute\", \"NCI\" and \"NGIS\" must");
-		out.println(" *      not be used to endorse or promote products derived from this software.");
-		out.println(" *   4. This license does not authorize the incorporation of this software");
-		out.println(" *      into any third party proprietary programs. This license does not");
-		out.println(" *      authorize the recipient to use any trademarks owned by either NCI");
-		out.println(" *      or NGIS");
-		out.println(" *   5. THIS SOFTWARE IS PROVIDED \"AS IS,\" AND ANY EXPRESSED OR IMPLIED");
-		out.println(" *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES");
-		out.println(" *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE");
-		out.println(" *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,");
-		out.println(" *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,");
-		out.println(" *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,");
-		out.println(" *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;");
-		out.println(" *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER");
-		out.println(" *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT");
-		out.println(" *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN");
-		out.println(" *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE");
-		out.println(" *      POSSIBILITY OF SUCH DAMAGE.");
-		out.println(" * ");
-		out.println(" */");
-		out.println("");
-		out.println("/**");
-		out.println(" * @author EVS Team");
-		out.println(" * @version 1.0");
-		out.println(" *");
-		out.println(" * Modification history:");
-		out.println(" *     Initial implementation kim.ong@ngc.com");
-		out.println(" *");
-		out.println(" */");
-		out.println("");
-		out.println("");
-		out.println("public class " + className + " {");
-		out.println("    JSONUtils jsonUtils = null;");
-		out.println("    HTTPUtils httpUtils = null;");
-		out.println("    String named_graph = null;");
-		out.println("    String prefixes = null;");
-		out.println("    String serviceUrl = null;");
-		out.println("    String restURL = null;");
-		out.println("    String named_graph_id = \":NHC0\";");
-		out.println("    String BASE_URI = \"http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl\";");
-		out.println("");
-		out.println("    ParserUtils parser = new ParserUtils();");
-		out.println("    HashMap nameVersion2NamedGraphMap = null;");
-		out.println("    HashMap ontologyUri2LabelMap = null;");
-		out.println("    String version = null;");
-		out.println("    String username = null;");
-		out.println("    String password = null;");
-		out.println("    OWLSPARQLUtils owlSPARQLUtils = null;");
-		out.println("");
-		out.println("    public " + className + "(String serviceUrl, String named_graph, String username, String password) {");
-		out.println("		this.serviceUrl = serviceUrl;");
-		out.println("    	this.named_graph = named_graph;");
-		out.println("    	this.username = username;");
-		out.println("    	this.password = password;");
-		out.println("        this.owlSPARQLUtils = new OWLSPARQLUtils(serviceUrl, username, password);");
-		out.println("        this.owlSPARQLUtils.set_named_graph(named_graph);");
-		out.println("    }");
-		out.println("");
-		out.println("    public OWLSPARQLUtils getOWLSPARQLUtils() {");
-		out.println("		return this.owlSPARQLUtils;");
-		out.println("	}");
-        out.println("\n");
-
-		Vector w = generateCode(queryfile);
-		String invokingMethod = null;
-
-		for (int i=0; iAcinar CellSYNCITCGAcaDSR
-*/
-
-public class ComplexPropertyParser {
-    public static String reformat(String str) {
-		str = str.replaceAll("< ncicp", "ActivityPTBRIDG";
-		ComplexTerm term = convertToComplexTerm(full_syn);
-		System.out.println(term.toString());
-    }
-
-}
-
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/ConceptData.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/ConceptData.java
deleted file mode 100644
index 104fca1c9..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/ConceptData.java
+++ /dev/null
@@ -1,290 +0,0 @@
-package gov.nih.nci.evs.restapi.util;
-import gov.nih.nci.evs.restapi.bean.*;
-import gov.nih.nci.evs.restapi.common.*;
-
-import java.io.*;
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.*;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
-import java.util.*;
-import java.util.regex.*;
-import org.json.*;
-
-/**
- * 
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class ConceptData {
-    JSONUtils jsonUtils = null;
-    HTTPUtils httpUtils = null;
-    String named_graph = null;
-    String prefixes = null;
-    String serviceUrl = null;
-    String restURL = null;
-    String named_graph_id = ":NHC0";
-    String BASE_URI = "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl";
-
-    ParserUtils parser = new ParserUtils();
-    HashMap nameVersion2NamedGraphMap = null;
-    HashMap ontologyUri2LabelMap = null;
-    String version = null;
-    String username = null;
-    String password = null;
-    OWLSPARQLUtils owlSPARQLUtils = null;
-    MetadataUtils metadataUtils = null;
-    AxiomParser axiomParser = null;// (String serviceUrl, String named_graph, String username, String password)
-
-    public ConceptData(String serviceUrl, String named_graph, String username, String password) {
-		this.serviceUrl = serviceUrl;
-    	this.named_graph = named_graph;
-    	this.username = username;
-    	this.password = password;
-        this.owlSPARQLUtils = new OWLSPARQLUtils(serviceUrl, username, password);
-        this.owlSPARQLUtils.set_named_graph(named_graph);
-		this.metadataUtils = new MetadataUtils(serviceUrl, username, password);
-		this.version = metadataUtils.getVocabularyVersion(named_graph);
-		this.axiomParser = new AxiomParser(serviceUrl, named_graph, username, password);
-    }
-
-    public OWLSPARQLUtils getOWLSPARQLUtils() {
-		return this.owlSPARQLUtils;
-	}
-
-
-	public String construct_get_concept_properties(String named_graph, String code) {
-		String prefixes = owlSPARQLUtils.getPrefixes();
-		StringBuffer buf = new StringBuffer();
-		buf.append(prefixes);
-		buf.append("").append("\n");
-		buf.append("SELECT distinct ?p_label ?p_value").append("\n");
-		buf.append("{").append("\n");
-		buf.append("    graph <" + named_graph + "> {").append("\n");
-		buf.append("            ?x a owl:Class .").append("\n");
-		buf.append("            ?x :NHC0 ?x_code .").append("\n");
-		buf.append("            ?x :NHC0 \"" + code + "\"^^xsd:string .").append("\n");
-		buf.append("            ?x rdfs:label ?x_label .").append("\n");
-		buf.append("").append("\n");
-		buf.append("            ?p a owl:AnnotationProperty .").append("\n");
-		buf.append("            ?x ?p ?p_value .").append("\n");
-		buf.append("            ?p rdfs:label ?p_label .").append("\n");
-		buf.append("      }").append("\n");
-		buf.append("}").append("\n");
-		return buf.toString();
-	}
-
-	public Vector getConceptProperties(String named_graph, String code) {
-		String query = construct_get_concept_properties(named_graph, code);
-		Vector v = owlSPARQLUtils.executeQuery(query);
-		if (v == null) return null;
-		if (v.size() == 0) return v;
-		v = new ParserUtils().getResponseValues(v);
-		return new SortUtils().quickSort(v);
-	}
-
-    public void generate(String named_graph, String code) {
-        Vector qualifiers = owlSPARQLUtils.getSupportedPropertyQualifiers(named_graph);
-        Vector properties = new Vector();
-        for (int i=0; i" + label + " (" + code + ")");
-		w.add("Terms & Properties");
-		w.add("
    Name");
-		w.add("Value");
-		w.add("");
-		for (int i=0; i");
-		w.add("
    ");
-		Vector axiomData = axiomParser.getAxioms(named_graph, code);
-		for (int i=0; i" + property);
-			w.add("Value");
-			for (int j=0; j" + s);
-				}
-			}
-			w.add("");
-			Vector w1 = filterAxiomData(axiomData, property);
-			w.addAll(w1);
-		    w.add("");
-    		w.add("");
-		}
-
-		w.add("
    (Source: NCI Thesaurus, version " + version + ")");
-
-		HTMLTable.generate(w);
-	}
-
-	public Vector filterAxiomData(Vector axiomData, String propertyName) {
-	    Vector w = new Vector();
-	    if (propertyName.compareTo("FULL_SYN") == 0) {
-			for (int i=0; i 126) {
-				buf.append(" ");
-			} else {
-				String s = "" + c;
-				if (s.compareTo("'") == 0) {
-					buf.append("\\'");
-				} else {
-					buf.append(s);
-				}
-			}
-		}
-		return buf.toString();
-	}
-
-    public void writeHeader(PrintWriter out, String title) {
-      out.println("");
-      out.println("");
-      out.println("");
-      out.println("	");
-      out.println("	" + title + "");
-      out.println("	");
-      writeFunction(out);
-      out.println("");
-	}
-
-
-    public void writeFunction(PrintWriter out) {
-		out.println("	");
-		out.println("	");
-		out.println("    ");
-		out.println("	");
-    }
-
-
-	public String getIndentation(int level) {
-		StringBuffer buf = new StringBuffer();
-		for (int i=0; i").append("\n");
-		buf.append("").append("\n");
-		buf.append("   Source Code").append("\n");
-		buf.append("   Source Term").append("\n");
-		buf.append("   Target Code").append("\n");
-		buf.append("   Target Term").append("\n");
-		buf.append("   Property").append("\n");
-		buf.append("   Property Value").append("\n");
-		buf.append("").append("\n");
-		buf.append("   ").append("\n");
-		buf.append("   ").append("\n");
-		buf.append("   ").append("\n");
-		buf.append("   ").append("\n");
-		buf.append("   ").append("\n");
-		buf.append("   ").append("\n");
-
-		Iterator it = propertyHashMap.keySet().iterator();
-		while (it.hasNext()) {
-			String key = (String) it.next();
-			String line = CSVFileReader.csv2Delimited(key, "|");
-			Vector u = StringUtils.parseData(line, '|');
-			String source_code = (String) u.elementAt(0);
-			String source_term = (String) u.elementAt(1);
-			String target_code = (String) u.elementAt(2);
-			String target_term = (String) u.elementAt(3);
-			StringBuffer property_buf = new StringBuffer();
-			HashMap hmap = (HashMap) propertyHashMap.get(key);
-			Vector properties = new Vector();
-			Iterator it2 = hmap.keySet().iterator();
-			while (it2.hasNext()) {
-				String key2 = (String) it2.next();
-				properties.add(key2);
-			}
-			properties = new gov.nih.nci.evs.restapi.util.SortUtils().quickSort(properties);
-			int line_num = 0;
-			for (int k=0; k").append("\n");
-					if (line_num == 0) {
-						line_buf.append("").append(source_code).append("").append("\n");
-						line_buf.append("").append(source_term).append("").append("\n");
-						line_buf.append("").append("").append(target_code).append("").append("").append("\n");
-						line_buf.append("").append(target_term).append("").append("\n");
-
-					} else {
-						line_buf.append("").append("").append("").append("\n");
-						line_buf.append("").append("").append("").append("\n");
-						line_buf.append("").append("").append("").append("\n");
-						line_buf.append("").append("").append("").append("\n");
-					}
-					String value = (String) values.elementAt(k2);
-					String col1 = property;
-					String col2 = value;
-					if (k2 != 0) {
-						col1 = "";
-					}
-					line_buf.append("").append(col1).append("").append("\n");
-					line_buf.append("").append(col2).append("").append("\n");
-
-					buf.append(line_buf.toString()).append("\n");
-					buf.append("").append("\n");
-					line_num++;
-					line_buf = new StringBuffer();
-				}
-
-			}
-
-		}
-		buf.append("").append("\n");
-		return buf.toString();
-	}
-
-	public void writeBody(PrintWriter out, String title) {
-		out.println("");
-		out.println("	
    " + title + "
    ");
-		out.println("	
    ");
-		String content = null;
-		try {
-			content = propertyHashMap2HTML(this.propertyHashMap);
-		} catch (Exception ex) {
-			ex.printStackTrace();
-		}
-		out.println(content);
-		out.println("");
-	}
-
-	public void writeFooter(PrintWriter out) {
-		out.println("");
-	}
-
-	public Vector sortByLabel(Vector codes) {
-		if (codes == null || codes.size()<=1) return codes;
-		Vector w = new Vector();
-		HashMap hmap = new HashMap();
-		for (int i=0; i|") == -1) {
-				w.add(line);
-			}
-		}
-		return w;
-	}
-
-
-    public HashMap appendPropertiesToMappingEntries(String serviceUrl, String namedGraph, Vector mapping_entries) {
-		HashMap propertyHashMap = new HashMap();
-		OWLSPARQLUtils owlSPARQLUtils = new OWLSPARQLUtils(serviceUrl);
-		ParserUtils parserUtils = new ParserUtils();
-        Vector v = mapping_entries;
-        for (int i=1; i 0) {
-				String query = owlSPARQLUtils.construct_get_properties_by_code(namedGraph, target_code);
-				Vector w = owlSPARQLUtils.getPropertiesByCode(namedGraph, target_code);
-				if (w == null || w.size() == 0) {
-					//System.out.println("\tgetPropertiesByCode returns null???");
-				} else {
-					w = parserUtils.getResponseValues(w);
-					HashMap hmap = createPropertyHashMap(w);
-					propertyHashMap.put(line, hmap);
-				}
-			}
-		}
-		return propertyHashMap;
-	}
-
-	public void dumpPropertyHashMap(HashMap propertyHashMap) {
-		Iterator it = propertyHashMap.keySet().iterator();
-		while (it.hasNext()) {
-			String key = (String) it.next();
-
-			HashMap hmap = (HashMap) propertyHashMap.get(key);
-			System.out.println(key);
-			Vector properties = new Vector();
-			Iterator it2 = hmap.keySet().iterator();
-			while (it2.hasNext()) {
-				String key2 = (String) it2.next();
-				properties.add(key2);
-			}
-			properties = new gov.nih.nci.evs.restapi.util.SortUtils().quickSort(properties);
-			for (int k=0; k
- * Copyright 2020 MSC. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or MSC
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      MSC, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@nih.gov
- *
- */
-
-
-public class ConceptHelper {
-	String serviceUrl = null;
-	String namedGraph = null;
-	String username = null;
-	String password = null;
-	OWLSPARQLUtils owlSPARQLUtils = null;
-
-    public ConceptHelper(String serviceUrl,
-                          String namedGraph,
-                          String username,
-                          String password) {
-		this.serviceUrl = serviceUrl;
-		this.namedGraph = namedGraph;
-		this.username = username;
-		this.password = password;
-	    this.owlSPARQLUtils = new OWLSPARQLUtils(serviceUrl, username, password);
-	    this.owlSPARQLUtils.set_named_graph(namedGraph);
-	}
-
-	public String construct_get_label(String named_graph, String code) {
-		String prefixes = owlSPARQLUtils.getPrefixes();
-		StringBuffer buf = new StringBuffer();
-		buf.append(prefixes);
-		buf.append("select distinct ?x_label ?x_code").append("\n");
-		buf.append("from ").append("\n");
-		buf.append("where  { ").append("\n");
-		buf.append("                ?x a owl:Class .").append("\n");
-		buf.append("                ?x :NHC0 ?x_code .").append("\n");
-		if (code != null) {
-			buf.append("                ?x :NHC0 \"" + code + "\"^^xsd:string .").append("\n");
-		}
-		buf.append("                ?x rdfs:label ?x_label .").append("\n");
-		buf.append("}").append("\n");
-		buf.append("").append("\n");
-		return buf.toString();
-	}
-
-	public Vector getLabel(String named_graph, String code) {
-        String query = construct_get_label(named_graph, code);
-        Vector v = owlSPARQLUtils.executeQuery(query);
-        if (v == null) return null;
-        if (v.size() == 0) return v;
-        v = new ParserUtils().getResponseValues(v);
-        return new SortUtils().quickSort(v);
-	}
-
-	public String construct_get_roles(String named_graph, String code) {
-        String prefixes = owlSPARQLUtils.getPrefixes();
-        StringBuffer buf = new StringBuffer();
-        buf.append(prefixes);
-        buf.append("select distinct ?x_code ?x_label ?p_code ?p_label ?y_code ?y_label").append("\n");
-        buf.append("{").append("\n");
-        buf.append("    graph <" + named_graph + "> ").append("\n");
-        buf.append("    {").append("\n");
-        buf.append("            ?x :NHC0 ?x_code .").append("\n");
-        buf.append("            ?x :NHC0 \"" + code + "\"^^xsd:string .").append("\n");
-        buf.append("            ?x rdfs:label ?x_label .").append("\n");
-        buf.append("            ?y :NHC0 ?y_code .").append("\n");
-        buf.append("            ?y rdfs:label ?y_label .").append("\n");
-        buf.append("            ?p :NHC0 ?p_code .").append("\n");
-        buf.append("            ?p rdfs:label ?p_label .").append("\n");
-        buf.append("            ?x (rdfs:subClassOf|owl:equivalentClass|owl:unionOf/rdf:rest*/rdf:first|owl:intersectionOf/rdf:rest*/rdf:first)* ?rs .  ").append("\n");
-        buf.append("            ?rs a owl:Restriction .").append("\n");
-        buf.append("            ?rs owl:onProperty ?p .").append("\n");
-        buf.append("            ?rs owl:someValuesFrom ?y .").append("\n");
-        buf.append("    }").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-
-	public Vector getRoles(String named_graph, String code) {
-        String query = construct_get_roles(named_graph, code);
-        Vector v = owlSPARQLUtils.executeQuery(query);
-        if (v == null) return null;
-        if (v.size() == 0) return v;
-        v = new ParserUtils().getResponseValues(v);
-        return new SortUtils().quickSort(v);
-	}
-
-	public String construct_get_proproperties(String named_graph, String code) {
-        String prefixes = owlSPARQLUtils.getPrefixes();
-        StringBuffer buf = new StringBuffer();
-        buf.append(prefixes);
-        buf.append("SELECT distinct ?x1_code ?x1_label ?p_label ?p_value").append("\n");
-        buf.append("from <" + named_graph + ">").append("\n");
-        buf.append("where { ").append("\n");
-        buf.append("                    ?x1 a owl:Class .").append("\n");
-        buf.append("                    ?x1 :NHC0 ?x1_code .").append("\n");
-        buf.append("                ?x1 :NHC0 \"" + code + "\"^^xsd:string .").append("\n");
-        buf.append("                    ?x1 rdfs:label ?x1_label .").append("\n");
-        buf.append("                    ?p rdfs:label ?p_label .").append("\n");
-        buf.append("                    ?x1 ?p ?p_value .               ").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-
-	public Vector getProperties(String named_graph, String code) {
-        String query = construct_get_proproperties(named_graph, code);
-        Vector v = owlSPARQLUtils.executeQuery(query);
-        if (v == null) return null;
-        if (v.size() == 0) return v;
-        v = new ParserUtils().getResponseValues(v);
-        return new SortUtils().quickSort(v);
-	}
-
-	public String construct_get_subclasses(String named_graph, String code) {
-		String prefixes = owlSPARQLUtils.getPrefixes();
-		StringBuffer buf = new StringBuffer();
-		buf.append(prefixes);
-		buf.append("select distinct ?x_label ?x_code ").append("\n");
-		buf.append("{").append("\n");
-		buf.append("    graph <" + named_graph + "> ").append("\n");
-		buf.append("    {").append("\n");
-		buf.append("      ?x :NHC0 ?x_code .").append("\n");
-		buf.append("      ?x rdfs:label ?x_label .").append("\n");
-		buf.append("      ?y :NHC0 ?y_code .").append("\n");
-		buf.append("      ?y rdfs:label ?y_label .").append("\n");
-		buf.append("      ?y :NHC0 \"" + code + "\"^^xsd:string .").append("\n");
-		buf.append("      ?x (rdfs:subClassOf|(owl:equivalentClass/owl:intersectionOf/rdf:rest*/rdf:first)) ?y . ").append("\n");
-		buf.append("    }").append("\n");
-		buf.append("}").append("\n");
-		return buf.toString();
-	}
-
-	public Vector getSubclasses(String named_graph, String code) {
-		String query = construct_get_subclasses(named_graph, code);
-		Vector v = owlSPARQLUtils.executeQuery(query);
-		if (v == null) return null;
-		if (v.size() == 0) return v;
-		v = new ParserUtils().getResponseValues(v);
-		return new SortUtils().quickSort(v);
-	}
-
-	public String construct_get_superclasses(String named_graph, String code) {
-		String prefixes = owlSPARQLUtils.getPrefixes();
-		StringBuffer buf = new StringBuffer();
-		buf.append(prefixes);
-		buf.append("select distinct ?y_label ?y_code ").append("\n");
-		buf.append("{").append("\n");
-		buf.append("    graph <" + named_graph + "> ").append("\n");
-		buf.append("    {").append("\n");
-		buf.append("      ?x :NHC0 ?x_code .").append("\n");
-		buf.append("      ?x rdfs:label ?x_label .").append("\n");
-		buf.append("      ?x :NHC0 \"" + code + "\"^^xsd:string .").append("\n");
-		buf.append("      ?y :NHC0 ?y_code .").append("\n");
-		buf.append("      ?y rdfs:label ?y_label .").append("\n");
-		buf.append("      ?x (rdfs:subClassOf|(owl:equivalentClass/owl:intersectionOf/rdf:rest*/rdf:first)) ?y . ").append("\n");
-		buf.append("    }").append("\n");
-		buf.append("}").append("\n");
-		return buf.toString();
-	}
-
-	public Vector getSuperclasses(String named_graph, String code) {
-		String query = construct_get_superclasses(named_graph, code);
-		Vector v = owlSPARQLUtils.executeQuery(query);
-		if (v == null) return null;
-		if (v.size() == 0) return v;
-		v = new ParserUtils().getResponseValues(v);
-		return new SortUtils().quickSort(v);
-	}
-
-	public String construct_get_axioms(String named_graph, String code) {
-        String prefixes = owlSPARQLUtils.getPrefixes();
-        StringBuffer buf = new StringBuffer();
-        buf.append(prefixes);
-        buf.append("select distinct ?a1 ?x1_label ?x1_code ?p_label ?a1_target ?q1_label ?q1_value").append("\n");
-        buf.append("from <" + named_graph + ">").append("\n");
-        buf.append("where  { ").append("\n");
-        buf.append("                    ?x1 a owl:Class .").append("\n");
-        buf.append("                    ?x1 :NHC0 ?x1_code .").append("\n");
-        buf.append("                ?x1 :NHC0 \"" + code + "\"^^xsd:string .").append("\n");
-        buf.append("                    ?x1 rdfs:label ?x1_label .").append("\n");
-        buf.append("").append("\n");
-        buf.append("                ?a1 a owl:Axiom .").append("\n");
-        buf.append("                ?a1 owl:annotatedSource ?x1 .").append("\n");
-        buf.append("                ?a1 owl:annotatedProperty ?p .").append("\n");
-        buf.append("                ?a1 owl:annotatedTarget ?a1_target .").append("\n");
-        buf.append("                ?p :NHC0 ?p_code .").append("\n");
-        buf.append("                ?p rdfs:label ?p_label .").append("\n");
-        buf.append("").append("\n");
-        buf.append("                ?q1 :NHC0 ?q1_code .").append("\n");
-        buf.append("                ?q1 rdfs:label ?q1_label .").append("\n");
-        buf.append("                ?a1 ?q1 ?q1_value .").append("\n");
-        buf.append("").append("\n");
-        buf.append("                             ").append("\n");
-        buf.append("").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-	public Vector getAxioms(String named_graph, String code) {
-        String query = construct_get_axioms(named_graph, code);
-        Vector v = owlSPARQLUtils.executeQuery(query);
-        if (v == null) return null;
-        if (v.size() == 0) return v;
-        v = new ParserUtils().getResponseValues(v);
-        return new SortUtils().quickSort(v);
-	}
-
-	public Vector getAxiomData(Vector w, String prop_label) {
-		Vector v = new Vector();
-		for (int i=0; i
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class DateUtils {
-	static String ALPHABETICS = "abcdefg";
-	static String NCI_THESAURUS_URI = "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus";
-
-	public static String getToday() {
-		return getToday("yyyy-MM");
-	}
-
-	public static String getToday(String format) {
-		java.util.Date date = Calendar.getInstance().getTime();
-		SimpleDateFormat sdf = new SimpleDateFormat(format);
-		return sdf.format(date);
-	}
-
-	public static int getNumberOfWeeks() {
-		String m = getToday();
-		SimpleDateFormat format = new SimpleDateFormat("yyyy-MM");
-		try {
-			Date date = format.parse(m);
-			Calendar c = Calendar.getInstance();
-			c.setTime(date);
-
-			int start = c.get(Calendar.WEEK_OF_MONTH);
-
-			c.add(Calendar.MONTH, 1);
-			c.add(Calendar.DATE, -1);
-			int end = c.get(Calendar.WEEK_OF_MONTH);
-			return end - start + 1;
-		} catch (Exception ex) {
-			return -1;
-		}
-	}
-
-	public static int getDayNumberNew(LocalDate date) {
-		DayOfWeek day = date.getDayOfWeek();
-		return day.getValue();
-	}
-
-    public static LocalDate getLocalDate() {
-		//Current Date
-		LocalDate today = LocalDate.now();
-		System.out.println("Current Date="+today);
-		return today;
-	}
-
-
-    public static LocalDate getLocalDate(int year, int month, int day) { // month: Month.JANUARY
-		//Creating LocalDate by providing input arguments
-		LocalDate local_date = LocalDate.of(year, month, day);
-		return local_date;
-    }
-
-    public static int getDayNumber(LocalDate date) {
-		DayOfWeek day = date.getDayOfWeek();
-		printDayOfWeek(day);
-		return day.getValue();
-	}
-
-    public static void printDayOfWeek(DayOfWeek dow) {
-		Locale locale = Locale.getDefault();
-		System.out.println(dow.getDisplayName(TextStyle.FULL, locale));
-		System.out.println(dow.getDisplayName(TextStyle.NARROW, locale));
-		System.out.println(dow.getDisplayName(TextStyle.SHORT, locale));
-	}
-
-
-
-    public static int getDaysInMonth(int year, int month) {
-		YearMonth yearMonthObject = YearMonth.of(year, month);
-		int daysInMonth = yearMonthObject.lengthOfMonth();
-		return daysInMonth;
-	}
-
-	public static int getNumberOfMondaysInAMonth(int year, int month) {
-		String weekDay = "Monday";
-		return getNumberOfWeekDaysInAMonth(year, month, weekDay);
-	}
-
-	public static int getNumberOfWeekDaysInAMonth(int year, int month, String weekDay) {
-		int m = 0;
-		Locale locale = Locale.getDefault();
-		int num_days = getDaysInMonth(year, month);
-		for (int day=1; day<=num_days; day++) {
-			LocalDate date = getLocalDate(year, month, day);
-			DayOfWeek dow = date.getDayOfWeek();
-			String fullName = dow.getDisplayName(TextStyle.FULL, locale);
-			if (fullName.compareTo(weekDay) == 0) {
-				m++;
-			}
-		}
-		return m;
-	}
-
-	public static String getNCItMonthlyVersion(int year, int month) {
-		int n = getNumberOfMondaysInAMonth(year, month);
-		char c = ALPHABETICS.charAt(n-1);
-		StringBuffer buf = new StringBuffer();
-		String year_str = "" + year;
-		String t = year_str.substring(2, 4);
-		buf.append(t).append(".");
-		if (month < 10) {
-			buf.append("0").append("" + month);
-			buf.append(c);
-		} else {
-			buf.append("" + month);
-			buf.append(c);
-		}
-		return buf.toString();
-	}
-
-	public static String getNCItMonthlyVersion() {
-		int currentYear = getCurrentYear();
-		int currentMonth = getCurrentMonth();
-		return getNCItMonthlyVersion(currentYear, currentMonth);
-	}
-
-    public static String getNCIThesaurusGraphName(int year, int month) {
-		 String version = getNCItMonthlyVersion(year, month);
-		 return NCI_THESAURUS_URI + version + ".owl";
-	}
-
-    public static String getNCIThesaurusGraphName() {
-		int currentYear = getCurrentYear();
-		int currentMonth = getCurrentMonth();
-		String version = getNCItMonthlyVersion(currentYear, currentMonth);
-		return NCI_THESAURUS_URI + version + ".owl";
-	}
-
-	public static int getCurrentMonth() {
-		 return Calendar.getInstance().get(Calendar.MONTH) + 1;
-	}
-
-	public static int getCurrentYear() {
-		 return Calendar.getInstance().get(Calendar.YEAR);
-	}
-
-	public static Vector getNCItReleaseSchedule(int year) {
-		Vector w = new Vector();
-		w.add("Year|Month|Version|Graph Name|Release Data");
-		for (int i=1; i<=12; i++) {
-			String version = getNCItMonthlyVersion(year, i);
-			String graphName = getNCIThesaurusGraphName(year, i);
-			w.add("" + year + "|" + getMonthString(i) + "|" + version + "|" + graphName + "|" + getMonthlyNCItReleaseDate(year, i));
-		}
-		return w;
-	}
-
-	public static int getLastWeekdayOfAMonth(int year, int month, String weekDay) {
-		int m = 0;
-		Locale locale = Locale.getDefault();
-		int num_days = getDaysInMonth(year, month);
-		for (int day=1; day<=num_days; day++) {
-			int j = num_days-day+1;
-			LocalDate date = getLocalDate(year, month, j);
-			DayOfWeek dow = date.getDayOfWeek();
-			String fullName = dow.getDisplayName(TextStyle.FULL, locale);
-			if (fullName.compareTo(weekDay) == 0) {
-				return j;
-			}
-		}
-		return 0;
-	}
-
-	public static String getMonthlyNCItReleaseDate(int year, int month) {
-		int n = getLastWeekdayOfAMonth(year, month, "Monday");
-		StringBuffer buf = new StringBuffer();
-		if (month < 10) {
-			buf.append("0");
-		}
-        buf.append(month).append("/");
-		if (n < 10) {
-			buf.append("0");
-		}
-        buf.append(n).append("/");
-        buf.append(year);
-        return buf.toString();
-	}
-
-    public static String getMonthString(int month) {
-		return new DateFormatSymbols().getMonths()[month-1];
-	}
-
-	public static HashMap getReleaseScheduleHashMap(int year) {
-		Vector w = getNCItReleaseSchedule(year);
-		HashMap hmap = new HashMap();
-		for (int i=1; i columns, char delim) {
-		Vector w = Utils.readFile(filename);
-		Vector v = new Vector();
-		for (int i=0; i columns, char delim) {
-		Vector v = new Vector();
-		for (int i=0; i= 0) {
-				bufferOut.write(buffer,0,readbyte);
-				TotalDownload += readbyte;
-				percentOfDownload = (TotalDownload*100)/filesize;
-				String percent = String.format("%.2f", percentOfDownload);
-				System.out.println("Downloaded "+ percent + "%");
-			}
-
-			System.out.println("Download is complete.");
-			bufferOut.close();
-			input.close();
-		}
-		catch(IOException e){
-			e.printStackTrace();
-		}
-	}
-
-	 // trusting all certificate
-	 public static void doTrustToCertificates() throws Exception {
-        //Security.addProvider(new com.sun.net.ssl.internal.ssl.Provider());
-        TrustManager[] trustAllCerts = new TrustManager[]{
-			new X509TrustManager() {
-				public X509Certificate[] getAcceptedIssuers() {
-					return null;
-				}
-
-				public void checkServerTrusted(X509Certificate[] certs, String authType) throws CertificateException {
-					return;
-				}
-
-				public void checkClientTrusted(X509Certificate[] certs, String authType) throws CertificateException {
-					return;
-				}
-			}
-        };
-
-        SSLContext sc = SSLContext.getInstance("SSL");
-        sc.init(null, trustAllCerts, new SecureRandom());
-        HttpsURLConnection.setDefaultSSLSocketFactory(sc.getSocketFactory());
-        HostnameVerifier hv = new HostnameVerifier() {
-            public boolean verify(String urlHostName, SSLSession session) {
-                if (!urlHostName.equalsIgnoreCase(session.getPeerHost())) {
-                    System.out.println("Warning: URL host '" + urlHostName + "' is different to SSLSession host '" + session.getPeerHost() + "'.");
-                }
-                return true;
-            }
-        };
-        HttpsURLConnection.setDefaultHostnameVerifier(hv);
-    }
-
-	public static void main(String[] args) {
-		String link = "https://www.africau.edu/images/default/sample.pdf";
-		File file = new File("sample.pdf");
-		download(link, file);
-	}
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/EmbeddedHierarchy.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/EmbeddedHierarchy.java
deleted file mode 100644
index 2a359c7cc..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/EmbeddedHierarchy.java
+++ /dev/null
@@ -1,674 +0,0 @@
-package gov.nih.nci.evs.restapi.util;
-
-import gov.nih.nci.evs.restapi.appl.*;
-import gov.nih.nci.evs.restapi.bean.*;
-import gov.nih.nci.evs.restapi.common.*;
-
-import java.io.*;
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.*;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
-import java.util.*;
-import java.util.regex.*;
-
-public class EmbeddedHierarchy {
-	static final String ROOT_NODE = "Root node";
-	static final String ROOT_NODE_CODE = "";
-
-	static final String UNUSED_SUBSET_CONCEPT_CODE = "C103175";
-	static final String TERMINOLOGY_SUBSET_CODE = "C54443";
-
-	static final String parent_child_file = "parent_child.txt";
-	static final String vs_header_concept_file = "P372.txt";
-
-	int multiple_count = 0;
-
-    Vector parent_child_vec = null;
-    HashSet node_set = null;
-
-    HierarchyHelper hh = null;
-    HierarchyHelper eh_hh = null;
-
-    PathFinder pathFinder = null;
-
-    HashMap label2CodeMap = new HashMap();
-
-    HashMap levelMap = null;
-
-    HashMap embeddedHierarchyCode2LabelHashMap = null;
-
-    static int TRAVERSE_UP = 1;
-    static int TRAVERSE_DOWN = 2;
-
-    public EmbeddedHierarchy() {
-
-    }
-
-    public EmbeddedHierarchy(Vector parent_child_vec) {
-		this.parent_child_vec = parent_child_vec;
-		this.hh = new HierarchyHelper(parent_child_vec);
-	}
-
-	public void set_embedded_hierarchy(HierarchyHelper hh) {
-		this.eh_hh = hh;
-	}
-
-    public HashMap createEmbeddedHierarchyCode2LabelHashMap(Vector v) {
-		//GAIA Terminology|C125481|GAIA Preeclampsia Level of Diagnostic Certainty Terminology|C126860
-		//CDISC Questionnaire Terminology|C100110|CDISC Questionnaire ADAS-Cog CDISC Version Test Code Terminology|C100132
-		HashMap hmap = new HashMap();
-        for (int k=0; k= maxLevel) return ti;
-        if (ti._code.compareTo(code) == 0 && level < maxLevel) {
-			return null;
-		}
-
-		List children = ti._assocToChildMap.get(Constants.ASSOCIATION_NAME);
-		if (children != null && children.size() > 0) {
-			List new_children = new ArrayList();
-			for (int i=0; i= maxLevel) {
-							new_children.add(child_ti);
-						}
-					}
-				}
-			}
-			ti._assocToChildMap.put(Constants.ASSOCIATION_NAME, new_children);
-		}
-		return ti;
-	}
-
-	public HashMap create_level_hashmap(Vector v) {
-		ASCIITreeUtils utils = new ASCIITreeUtils();
-	    HashMap hmap = new HashMap();
-	    for (int i=0; i 1) {
-				int maxLevel = findMaximumLevel(w);
-				w2.add(key + "|" + maxLevel);
-			}
-		}
-		return w2;
-	}
-
-	public int findMaximumLevel(Vector v) {
-		int max = -1;
-		for (int i=0; i max) {
-				max = value;
-			}
-		}
-		return max;
-	}
-
-	public HashMap createLevelHashMap(Vector parent_child_vec) {
-		HierarchyHelper hh = new HierarchyHelper(parent_child_vec);
-		ASCIITreeUtils utils = new ASCIITreeUtils();
-	    HashMap hmap = new HashMap();
-	    Vector v = hh.exportTree();//(Vector) parent_child_vec.clone();
-	    for (int i=0; i 0) {
-				w.addAll(u);
-			}
-		}
-		w = removeDuplicates(w);
-		return w;
-	}
-
-	public Vector removeDuplicates(Vector codes) {
-		HashSet hset = new HashSet();
-		Vector w = new Vector();
-		for (int i=0; i
- * Copyright 2020 MSC. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or MSC
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      MSC, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@nih.gov
- *
- */
-
-
-public class ExcelDiffUtils {
-    public String datafile1 = null;
-    public String datafile2 = null;
-    Vector headings = null;
-    boolean NORMALIZE = true;
-
-    public ExcelDiffUtils(String datafile1, String datafile2) {
-		this.datafile1 = datafile1;
-		this.datafile2 = datafile2;
-	}
-
-	public Vector split(String line) {
-		return StringUtils.parseData(line, '\t');
-	}
-
-	public Vector split(String line, char delim) {
-		return StringUtils.parseData(line, delim);
-	}
-
-
-	public void run(PrintWriter pw) {
-		Vector v1 = Utils.readFile(datafile1);
-		String heading = (String) v1.elementAt(0);
-		headings = split(heading);
-		HashSet codes_1 = new HashSet();
-		HashMap hmap_1 = new HashMap();
-		for (int i=1; i  0) {
-				Vector u = split(line, '\t');
-				String code = (String) u.elementAt(2);
-				if (!codes_1.contains(code)) {
-					codes_1.add(code);
-				}
-				HashMap hmap = new HashMap();
-				for (int j=0; j 0) {
-				Vector u = split(line, '\t');
-				String code = (String) u.elementAt(2);
-				if (!codes_2.contains(code)) {
-					codes_2.add(code);
-				}
-				HashMap hmap = new HashMap();
-				for (int j=0; j " + value);
-			}
-		}
-	}
-
-	public String normalize(String t) {
-		if (t.indexOf("||") == -1) return t;
-		t = t.replace(" || ", "|");
-		Vector u = StringUtils.parseData(t, '|');
-		u = new SortUtils().quickSort(u);
-		StringBuffer buf = new StringBuffer();
-		for (int i=0; i 0) {
-				for (int i=0; i 0) {
-			for (int i=0; i
- * Copyright 2011, MSC. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or MSC.
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      MSC, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation ongki@nih.gov
- *
- */
-
-
-public class ExcelReadWriteUtils {
-
-	 public static void saveToFile(String outputfile, String t) {
-		 Vector v = new Vector();
-		 v.add(t);
-		 saveToFile(outputfile, v);
-	 }
-
-	 public static void saveToFile(String outputfile, Vector v) {
-
-		PrintWriter pw = null;
-		try {
-			pw = new PrintWriter(outputfile, "UTF-8");
-			if (v != null && v.size() > 0) {
-				for (int i=0; i 0) {
-			for (int i=0; i parseData(String line) {
-		if (line == null) return null;
-        char delim = '|';
-        return parseData(line, delim);
-    }
-
-
-	public static String tab2CSV(String line, char delim) {
-		Vector u = parseData(line, delim);
-		StringBuffer buf = new StringBuffer();
-		for (int i=0; i getXLSXSheetNames(String xslxfile) {
-		File file = new File(xslxfile);
-		List sheetNames = null;
-		try {
-			XSSFWorkbook wb = new XSSFWorkbook(file);
-			sheetNames = new ArrayList();
-			for (int i=0; i getXLSSheetNames(String xlsfile) {
-		List sheetNames = null;
-		try {
-			InputStream is = new FileInputStream(xlsfile);
-			HSSFWorkbook wb = new HSSFWorkbook(is);
-			sheetNames = new ArrayList();
-			for (int i=0; i textfiles, Vector sheetNames, char delim) throws IOException {
-		XSSFWorkbook wb = new XSSFWorkbook();
-		for (int i=0; i textfiles, Vector sheetNames, char delim) throws IOException {
-		HSSFWorkbook wb = new HSSFWorkbook();
-		for (int i=0; i rowIterator = sheet.rowIterator();
-        while (rowIterator.hasNext()) {
-            Row row = rowIterator.next();
-            Iterator cellIterator = row.cellIterator();
-            StringBuffer buf = new StringBuffer();
-            while (cellIterator.hasNext()) {
-                Cell cell = cellIterator.next();
-                String cellValue = dataFormatter.formatCellValue(cell);
-                buf.append(cellValue + "\t");
-            }
-            String t = buf.toString();
-            t = t.substring(0, t.length()-1);
-            w.add(t);
-        }
-        ip.close();
-        return w;
-    }
-
-    public static int getNumberOfSheets(String excelfile) {
-		try {
-			Workbook workbook = WorkbookFactory.create(new File(excelfile));
-			return workbook.getNumberOfSheets();
-		} catch (Exception ex) {
-			//return -1;
-		}
-		return -1;
-	}
-
-    public static Workbook openWorkbook(String excelfile) {
-		try {
-			Workbook workbook = WorkbookFactory.create(new File(excelfile));
-			return workbook;
-		} catch (Exception ex) {
-			//return -1;
-		}
-		return null;
-	}
-
-    public static int getNumberOfSheets(Workbook workbook) {
-        return workbook.getNumberOfSheets();
-	}
-
-    public static Vector getSheetNames(String excelfile) {
-		try {
-			Workbook workbook = WorkbookFactory.create(new File(excelfile));
-			return getSheetNames(workbook);
-		} catch (Exception ex) {
-			//return -1;
-		}
-		return null;
-	}
-
-
-    public static Vector getSheetNames(Workbook workbook) {
-		Vector v = new Vector();
-        Iterator sheetIterator = workbook.sheetIterator();
-        System.out.println("Retrieving Sheets using Iterator");
-        while (sheetIterator.hasNext()) {
-            Sheet sheet = sheetIterator.next();
-            v.add(sheet.getSheetName());
-        }
-        return v;
-	}
-
-    public Sheet getSheet(Workbook workbook, int sheetNumber) {
-		return workbook.getSheetAt(sheetNumber);
-	}
-
-
-    public Sheet getSheet(String excelfile, int sheetNumber) {
-		try {
-		     Workbook workbook = openWorkbook(excelfile);
- 		     return getSheet(workbook, sheetNumber);
-		} catch (Exception e) {
-
-		}
-		return null;
-	}
-
-    public static Vector toDelimited(String excelfile, char delim) {
-		return toDelimited(excelfile, 0, delim);
-	}
-
-
-    private static void printCellValue(Cell cell) {
-        //switch (cell.getCellTypeEnum()) {
-		switch (cell.getCellType()) {
-            case BOOLEAN:
-                System.out.print(cell.getBooleanCellValue());
-                break;
-            case STRING:
-                System.out.print(cell.getRichStringCellValue().getString());
-                break;
-            case NUMERIC:
-                if (DateUtil.isCellDateFormatted(cell)) {
-                    System.out.print(cell.getDateCellValue());
-                } else {
-                    System.out.print(cell.getNumericCellValue());
-                }
-                break;
-            case FORMULA:
-                System.out.print(cell.getCellFormula());
-                break;
-            case BLANK:
-                System.out.print("");
-                break;
-            default:
-                System.out.print("");
-        }
-        System.out.print("\t");
-    }
-
-
-    public static Vector toDelimited(String excelfile, int sheetNumber, char delim) {
-		Vector w = new Vector();
-		Workbook workbook = openWorkbook(excelfile);
-        Sheet sheet = workbook.getSheetAt(sheetNumber);
-        Iterator rowIterator = sheet.rowIterator();
-        while (rowIterator.hasNext()) {
-			StringBuffer buf = new StringBuffer();
-			Row row = rowIterator.next();
-            List list = getRowData(row);
-            for (int i=0; i 0) {
-				for (int i=0; i maxColumn )
-                maxColumn = lastColumn;
-
-            if (lastColumn < columnToDelete )
-                continue;
-
-            for (int x=columnToDelete+1; x < lastColumn + 1; x++){
-                Cell oldCell    = row.getCell(x-1);
-                if ( oldCell != null ) {
-                    row.removeCell( oldCell );
-				}
-                Cell nextCell = row.getCell(x);
-                if ( nextCell != null ){
-                    Cell newCell    = row.createCell( x-1, nextCell.getCellType());
-                    cloneCell(newCell, nextCell);
-                }
-            }
-        }
-        // Adjust the column widths
-        for ( int c=0; c < maxColumn; c++ ){
-            sheet.setColumnWidth( c, sheet.getColumnWidth(c+1) );
-        }
-        return workbook;
-    }
-
-/*
-	private static void cloneCell( Cell cNew, Cell cOld ){
-		cNew.setCellComment( cOld.getCellComment() );
-		cNew.setCellStyle( cOld.getCellStyle() );
-		switch ( cNew.getCellType() ){
-			case Cell.CELL_TYPE_BOOLEAN:{
-				cNew.setCellValue( cOld.getBooleanCellValue() );
-				break;
-			}
-			case Cell.CELL_TYPE_NUMERIC:{
-				cNew.setCellValue( cOld.getNumericCellValue() );
-				break;
-			}
-			case Cell.CELL_TYPE_STRING:{
-				cNew.setCellValue( cOld.getStringCellValue() );
-				break;
-			}
-			case Cell.CELL_TYPE_ERROR:{
-				cNew.setCellValue( cOld.getErrorCellValue() );
-				break;
-			}
-			case Cell.CELL_TYPE_FORMULA:{
-				cNew.setCellFormula( cOld.getCellFormula() );
-			   break;
-			}
-		}
-
-	}
-*/
-
-	private static void cloneCell( Cell cNew, Cell cOld ){
-		cNew.setCellComment( cOld.getCellComment() );
-		cNew.setCellStyle( cOld.getCellStyle() );
-		switch ( cNew.getCellType() ){
-			case BOOLEAN:{
-				cNew.setCellValue( cOld.getBooleanCellValue() );
-				break;
-			}
-			case NUMERIC:{
-				cNew.setCellValue( cOld.getNumericCellValue() );
-				break;
-			}
-			case STRING:{
-				cNew.setCellValue( cOld.getStringCellValue() );
-				break;
-			}
-			case ERROR:{
-				cNew.setCellValue( cOld.getErrorCellValue() );
-				break;
-			}
-			case FORMULA:{
-				cNew.setCellFormula( cOld.getCellFormula() );
-			   break;
-			}
-		}
-	}
-
-	public static boolean isInteger(String input) {
-		try {
-			Integer.parseInt( input );
-			return true;
-		}
-			catch( Exception e ) {
-			return false;
-		}
-	}
-
-	public static Workbook addRow(Workbook workbook, int sheetIndex, Vector rowData){
-		Sheet sheet = workbook.getSheetAt(sheetIndex);
-		int lastRowNumber = sheet.getLastRowNum();
-		Row row = sheet.createRow(lastRowNumber+1);
-		for (int i=0; i= 1; i--)
-        {
-			Row row = sheet.getRow(i);
-            if (row != null)
-            {
-                sheet.removeRow(row);
-            }
-        }
-        int numOfColumns = getNumberOfRows(sheet);
-        for (int j = numOfColumns; j >= 1; j--)
-        {
-            workbook = deleteColumn(workbook, sheetIndex, j);
-        }
-        return workbook;
-	}
-
-    private String getFileType(File file) {
-		String fileName = file.getName();
-		String folderName = file.getParent();
-		if (fileName.toLowerCase().endsWith(FILE_TYPES[0])) {
-			return FILE_TYPES[0];
-		}
-		return FILE_TYPES[1];
-	}
-
-
-    public static String getExcelHeader(String filename, int sheet) {
-		if (filename.toLowerCase().endsWith(FILE_TYPES[0])) {
-			return getHSSFHeader(filename, sheet);
-		} else {
-			return getXSSFHeader(filename, sheet);
-		}
-	}
-
-    public static String getHSSFHeader(String file, int sheet) {
-		StringBuffer buf = new StringBuffer();
-		try {
-			FileInputStream fis = new FileInputStream(new File(file));
-			//Get the workbook instance for XLS file
-			HSSFWorkbook workbook = new HSSFWorkbook(fis);
-			try {
-				fis.close();
-			} catch (Exception ex) {
-                ex.printStackTrace();
-			}
-
-			//Get first sheet from the workbook
-			HSSFSheet hSSFSheet = workbook.getSheetAt(sheet);
-			HSSFRow row = hSSFSheet.getRow(0);
-
-			int cells = row.getPhysicalNumberOfCells();
-			for (int c = 0; c < cells; c++) {
-				HSSFCell cell = row.getCell(c);
-				String value = null;
-				/*
-
-				switch (cell.getCellType()) {
-					case HSSFCell.CELL_TYPE_FORMULA:
-						value = cell.getCellFormula();
-						break;
-
-					case HSSFCell.CELL_TYPE_NUMERIC:
-						value = "" + cell.getNumericCellValue();
-						break;
-
-					case HSSFCell.CELL_TYPE_STRING:
-						value = cell.getStringCellValue();
-						break;
-
-					default:
-				}
-				*/
-				value = getCellData(cell);
-				buf.append(value);
-				if (c < cells-1) {
-					buf.append("|");
-				}
-			}
-		} catch (Exception ex) {
-			ex.printStackTrace();
-		}
-		return buf.toString();
-	}
-
-    public static int getExcelStartRow(String filename, int sheet, int col, String code) {
-		if (filename.toLowerCase().endsWith(FILE_TYPES[0])) {
-			return getHSSFStartRow(filename, sheet, col, code);
-		} else {
-			return getXSSFStartRow(filename, sheet, col, code);
-		}
-	}
-
-     public static int getHSSFStartRow(String file, int sheet, int col, String code) {
-		try {
-			FileInputStream fis = new FileInputStream(new File(file));
-			//Get the workbook instance for XLS file
-			HSSFWorkbook workbook = new HSSFWorkbook(fis);
-			try {
-				fis.close();
-			} catch (Exception ex) {
-                ex.printStackTrace();
-			}
-
-			//Get first sheet from the workbook
-			HSSFSheet hSSFSheet = workbook.getSheetAt(sheet);
-
-			if (col == -1) {
-				return 1;
-			}
-
-			//Get iterator to all the rows in current sheet
-			Iterator rowIterator = hSSFSheet.iterator();
-
-			//Get iterator to all cells of current row
-			int lcv = 0;
-			while (rowIterator.hasNext()) {
-				Row row = rowIterator.next();
-				if (row == null) return -1;
-				//if (row.getCell(0).getStringCellValue().compareTo(code) == 0 ||
-				if (row.getCell(col).getStringCellValue().compareTo(code) == 0) {
-					return lcv;
-				}
-
-				lcv++;
-			}
-		} catch (Exception ex) {
-			ex.printStackTrace();
-		}
-		return -1;
-	 }
-
-    public static int getExcelEndRow(String filename, int sheet, int col, String code) {
-		if (filename.toLowerCase().endsWith(FILE_TYPES[0])) {
-			return getHSSFEndRow(filename, sheet, col, code);
-		} else {
-			return getXSSFEndRow(filename, sheet, col, code);
-		}
-	}
-
-     public static int getHSSFEndRow(String file, int sheet, int col, String code) {
-		int num = -1;
-		try {
-			FileInputStream fis = new FileInputStream(new File(file));
-			//Get the workbook instance for XLS file
-			HSSFWorkbook workbook = new HSSFWorkbook(fis);
-			try {
-				fis.close();
-			} catch (Exception ex) {
-                ex.printStackTrace();
-			}
-
-			//Get first sheet from the workbook
-			HSSFSheet hSSFSheet = workbook.getSheetAt(sheet);
-
-			if (col == -1) {
-				return hSSFSheet.getLastRowNum();
-			}
-
-			//Get iterator to all the rows in current sheet
-			Iterator rowIterator = hSSFSheet.iterator();
-
-			//Get iterator to all cells of current row
-			int lcv = 0;
-
-			while (rowIterator.hasNext()) {
-				Row row = rowIterator.next();
-				if (row == null) return -1;
-				//if (row.getCell(0).getStringCellValue().compareTo(code) == 0 ||
-				if (row.getCell(col).getStringCellValue().compareTo(code) == 0) {
-					num = lcv;
-				}
-				lcv++;
-			}
-		} catch (Exception ex) {
-			ex.printStackTrace();
-		}
-		return num;
-	}
-
-
-	private static String getCellData(Cell cell) {
-		String value = null;
-		if (cell == null) {
-			return null;
-		}
-		switch (cell.getCellType()) {
-			case STRING:
-				value = cell.getStringCellValue();
-				break;
-			case FORMULA:
-				value = cell.getCellFormula();
-				break;
-			case NUMERIC:
-				HSSFDataFormatter dataFormatter = new HSSFDataFormatter();
-				value = dataFormatter.formatCellValue(cell);
-				break;
-			case BLANK:
-				value = null;
-				break;
-			case ERROR:
-				value = "#ERROR#";
-				break;
-		}
-		return value;
-	}
-
-
-     public static String getXSSFHeader(String file, int sheet) {
-		StringBuffer buf = new StringBuffer();
-		try {
-			FileInputStream fis = new FileInputStream(new File(file));
-			//Get the workbook instance for XLS file
-			XSSFWorkbook workbook = new XSSFWorkbook(fis);
-			try {
-				fis.close();
-			} catch (Exception ex) {
-                ex.printStackTrace();
-			}
-
-			//Get first sheet from the workbook
-			XSSFSheet hSSFSheet = workbook.getSheetAt(sheet);
-			XSSFRow row = hSSFSheet.getRow(0);
-
-			int cells = row.getPhysicalNumberOfCells();
-			for (int c = 0; c < cells; c++) {
-				XSSFCell cell = row.getCell(c);
-
-				/*
-				String value = null;
-
-				switch (cell.getCellType()) {
-
-					case XSSFCell.CELL_TYPE_FORMULA:
-						value = cell.getCellFormula();
-						break;
-
-					case XSSFCell.CELL_TYPE_NUMERIC:
-						value = "" + cell.getNumericCellValue();
-						break;
-
-					case XSSFCell.CELL_TYPE_STRING:
-						value = cell.getStringCellValue();
-						break;
-
-					default:
-				}
-				*/
-				String value = getCellData(cell);
-				buf.append(value);
-				if (c < cells-1) {
-					buf.append("|");
-				}
-			}
-		} catch (Exception ex) {
-			ex.printStackTrace();
-		}
-		return buf.toString();
-	 }
-
-     public static int getXSSFStartRow(String file, int sheet, int col, String code) {
-		try {
-			FileInputStream fis = new FileInputStream(new File(file));
-			//Get the workbook instance for XLS file
-			XSSFWorkbook workbook = new XSSFWorkbook(fis);
-			try {
-				fis.close();
-			} catch (Exception ex) {
-                ex.printStackTrace();
-			}
-
-			//Get first sheet from the workbook
-			XSSFSheet hSSFSheet = workbook.getSheetAt(sheet);
-
-			if (col == -1) {
-				return 1;
-			}
-
-			//Get iterator to all the rows in current sheet
-			Iterator rowIterator = hSSFSheet.iterator();
-
-			//Get iterator to all cells of current row
-			int lcv = 0;
-			while (rowIterator.hasNext()) {
-				Row row = rowIterator.next();
-				if (row == null) return -1;
-				//if (row.getCell(0).getStringCellValue().compareTo(code) == 0 ||
-				if (row.getCell(col).getStringCellValue().compareTo(code) == 0) {
-					return lcv;
-				}
-
-				lcv++;
-			}
-		} catch (Exception ex) {
-			ex.printStackTrace();
-		}
-		return -1;
-	 }
-
-     public static int getXSSFEndRow(String file, int sheet, int col, String code) {
-		int num = -1;
-		try {
-			FileInputStream fis = new FileInputStream(new File(file));
-			//Get the workbook instance for XLS file
-			XSSFWorkbook workbook = new XSSFWorkbook(fis);
-			try {
-				fis.close();
-			} catch (Exception ex) {
-                ex.printStackTrace();
-			}
-
-			//Get first sheet from the workbook
-			XSSFSheet hSSFSheet = workbook.getSheetAt(sheet);
-
-			if (col == -1) {
-				return hSSFSheet.getLastRowNum();
-			}
-
-			//Get iterator to all the rows in current sheet
-			Iterator rowIterator = hSSFSheet.iterator();
-
-			//Get iterator to all cells of current row
-			int lcv = 0;
-
-			while (rowIterator.hasNext()) {
-				Row row = rowIterator.next();
-				if (row == null) return -1;
-				if (row.getCell(col).getStringCellValue().compareTo(code) == 0) {
-					num = lcv;
-				}
-				lcv++;
-			}
-		} catch (Exception ex) {
-			ex.printStackTrace();
-		}
-		return num;
-	}
-
-    public static void test(String excelfile, int sheet, int col, String code) {
-		System.out.println("excelfile: " + excelfile);
-		System.out.println("sheet: " + sheet);
-		System.out.println("col: " + col);
-		System.out.println("code: " + code);
-
-		String header = getExcelHeader(excelfile, sheet);
-		System.out.println(header);
-
-		int start_row = getExcelStartRow(excelfile, sheet, col, code);
-		System.out.println("getExcelStartRow: " + start_row);
-
-		int end_row = getExcelEndRow(excelfile, sheet, col, code);
-		System.out.println("getExcelEndRow: " + end_row);
-	}
-
-	public static void csvToXLSX(String csvfile, String xlsxfile, String sheet_name) {
-		try {
-			String csvFileAddress = csvfile;
-			String xlsxFileAddress = xlsxfile;
-			XSSFWorkbook workBook = new XSSFWorkbook();
-			XSSFSheet sheet = workBook.createSheet(sheet_name);
-			String currentLine=null;
-			int RowNum=0;
-			BufferedReader br = new BufferedReader(new FileReader(csvFileAddress));
-			while ((currentLine = br.readLine()) != null) {
-				String str[] = currentLine.split(",");
-
-				XSSFRow currentRow=sheet.createRow(RowNum);
-				for(int i=0;i 0) {
-					String heading = (String) lines.elementAt(0);
-					String[] columns = getColumnHeadings(heading, delim);
-
-					Row headerRow = sheet.createRow(0);
-
-					for(int i = 0; i < columns.length; i++) {
-						Cell cell = headerRow.createCell(i);
-						cell.setCellValue(columns[i]);
-						cell.setCellStyle(headerCellStyle);
-					}
-					if (lines.size() > 1) {
-						for (int i=1;i
- * Copyright 2020 MSC. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or MSC
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      MSC, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@nih.gov
- *
- */
-
-
-public class ExtendedPropertyQuery {
-    JSONUtils jsonUtils = null;
-    HTTPUtils httpUtils = null;
-    String named_graph = null;
-    String prefixes = null;
-    String serviceUrl = null;
-    HashMap nameVersion2NamedGraphMap = null;
-    HashMap ontologyUri2LabelMap = null;
-    String version = null;
-    String username = null;
-    String password = null;
-    OWLSPARQLUtils owlSPARQLUtils = null;
-    static Vector states = null;
-    static int MAX_LENGTH = 7;
-
-    static {
-		states = new Vector();
-		states.add("H"); //hierarchical
-		states.add("S"); //subset
-		states.add("R"); //role
-		states.add("A"); //asociation
-		states.add("P"); //property
-		states.add("C"); //class
-	}
-
-    public ExtendedPropertyQuery(String serviceUrl, String named_graph, String username, String password) {
-		this.serviceUrl = serviceUrl;
-    	this.named_graph = named_graph;
-    	this.username = username;
-    	this.password = password;
-        this.owlSPARQLUtils = new OWLSPARQLUtils(serviceUrl, username, password);
-        this.owlSPARQLUtils.set_named_graph(named_graph);
-    }
-
-    public OWLSPARQLUtils getOWLSPARQLUtils() {
-		return this.owlSPARQLUtils;
-	}
-
-    public String getPropSelectStmt(Vector path) {
-		StringBuffer buf = new StringBuffer();
-		if (path.size() > 1) {
-			buf.append("select distinct ?x_code ?x_label ?y_code ?y_label ?p_label ?p_value");
-		} else {
-			buf.append("select distinct ?y_code ?y_label ?p_label ?p_value");
-		}
-		String s = buf.toString();
-		s = s.trim();
-		return s;
-	}
-
-    public String getPropertyQuery(String named_graph, String code, Vector path) {
-        String prefixes = owlSPARQLUtils.getPrefixes();
-        StringBuffer buf = new StringBuffer();
-        buf.append(prefixes);
-        String selectStmt = getPropSelectStmt(path);
-        buf.append(selectStmt).append("\n");
-        buf.append("{").append("\n");
-        buf.append("    graph <" + named_graph + ">").append("\n");
-        buf.append("    {").append("\n");
-        if (path.size() > 1) {
-			buf.append("            ?x :NHC0 ?x_code .").append("\n");
-			buf.append("            ?x rdfs:label ?x_label .").append("\n");
-			if (code != null) {
-				buf.append("            ?x :NHC0 \"" + code + "\"^^xsd:string .").append("\n");
-			}
-		}
-		buf.append("            ?y rdfs:label ?y_label .").append("\n");
-		buf.append("            ?y :NHC0 ?y_code .").append("\n");
-
-		for (int i=0; i
- * Copyright 2020 MSC. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
-6 * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or MSC
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      MSC, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@nih.gov
- *
- */
-
-public class ExternalLinkPageGenerator {
-	static String NCI_BROWSER_PROPERTYES_XML = "NCItBrowserProperties.xml";
-	String restURL = null;
-	String namedGraph = null;
-	String username = null;
-	String password = null;
-	OWLSPARQLUtils owlSPARQLUtils = null;
-	HashMap propertyCode2labelHashMap = null;
-
-    public ExternalLinkPageGenerator() {
-
-	}
-
-    public ExternalLinkPageGenerator(String restURL, String namedGraph, String username, String password) {
-		this.restURL = restURL;
-		this.namedGraph = namedGraph;
-		this.username = username;
-		this.password = password;
-		owlSPARQLUtils = new OWLSPARQLUtils(restURL, username, password);
-		owlSPARQLUtils.set_named_graph(namedGraph);
-
-		propertyCode2labelHashMap = new HashMap();
-		Vector supportedProperties = owlSPARQLUtils.getSupportedProperties(namedGraph);
-		for (int i=0; i ").append("\n");
-		buf.append("    {").append("\n");
-		buf.append("            ?x a owl:Class .").append("\n");
-		buf.append("                ?x :NHC0 ?x_code .").append("\n");
-		buf.append("                ?x rdfs:label ?x_label .").append("\n");
-		buf.append("            ?x ?p1 ?y1 .").append("\n");
-		buf.append("").append("\n");
-		buf.append("                ?p1 :NHC0 \"" + propertyCode + "\"^^xsd:string .").append("\n");
-		buf.append("                ?p1 :NHC0 ?p1_code .").append("\n");
-		buf.append("                ?p1 rdfs:label ?p1_label .").append("\n");
-		buf.append("").append("\n");
-		buf.append("        }").append("\n");
-		buf.append("}").append("\n");
-		buf.append("").append("\n");
-		buf.append("").append("\n");
-		return buf.toString();
-	}
-
-	public Vector getConceptsWithProperty(String named_graph, String propertyCode) {
-		String query = construct_get_concepts_with_property(named_graph, propertyCode);
-		Vector v = executeQuery(query);
-		if (v == null) return null;
-		if (v.size() == 0) return v;
-		v = new ParserUtils().getResponseValues(v);
-		return new SortUtils().quickSort(v);
-	}
-
-    public static String hyperlink(String url, String code) {
-		return "" + code + "";
-	}
-
-    public void run(String propertyCode) {
-		run(NCI_BROWSER_PROPERTYES_XML, propertyCode);
-	}
-
-	public String external_hyperlink_url = null;
-
-	public String get_external_hyperlink_url() {
-		return external_hyperlink_url;
-	}
-
-	public void set_external_hyperlink_url(String external_hyperlink_url) {
-		System.out.println("external_hyperlink_url: " + external_hyperlink_url);
-		this.external_hyperlink_url = external_hyperlink_url;
-	}
-
-    public void run(String xmlfile, String propertyCode) {
-		String propertyName = getPropertyLabel(propertyCode);
-		String url = getUri(propertyName);
-
-        Vector w = getConceptsWithProperty(namedGraph, propertyCode);
-        Vector w1 = new Vector();
-		for (int i=0; i
- * Copyright 2008,2009 NGIT. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIT and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIT" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIT
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIT, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- *          Modification history Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class FTPCrawler {
-   public static String NCIT_FTP_SITE = "https://evs.nci.nih.gov/ftp1/";
-   public static String ABOUT_PAGE = "About.html";
-   public static String MAPPINGS = "Mappings";
-   public static String NCI_THESAURUS = "NCI_Thesaurus";
-   public static String NCIT_MAPPINGS_SITE = NCIT_FTP_SITE + NCI_THESAURUS + "/" + MAPPINGS + "/";
-   public static String NCIT_ABOUT_SITE = NCIT_MAPPINGS_SITE + ABOUT_PAGE;
-   public static String ICDO3_MAPPIGNS_SITE = NCIT_MAPPINGS_SITE + "ICD-O-3_Mappings/";
-   public static String ICDO3_ABOUT_SITE   = ICDO3_MAPPIGNS_SITE + "About.html";
-   public static String[] MAPPING_SITES = new String[] {NCIT_MAPPINGS_SITE, NCIT_ABOUT_SITE, ICDO3_MAPPIGNS_SITE, ICDO3_ABOUT_SITE};
-
-   public static HashMap lastUpdatedHashMap = null;
-
-   public static Vector otherMappingData = null;
-
-   public static Vector getOtherMappingData() {
-	   return otherMappingData;
-   }
-
-   public static void dumpMappingSites() {
-       for (int i=0; i
- * Copyright 2020, MSC. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIT
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIT, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- *          Modification history Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class FTPUtils {
-	static String NCIT_FTP_URL = "https://evs.nci.nih.gov/ftp1/NCI_Thesaurus/";
-    static String currentWorkingDirectory;
-    static {
-		currentWorkingDirectory = System.getProperty("user.dir");
-	}
-
-	public static void download(String uri, String outputfile) {
-		try (BufferedInputStream in = new BufferedInputStream(new URL(uri).openStream());
-		  FileOutputStream fileOutputStream = new FileOutputStream(outputfile)) {
-			byte dataBuffer[] = new byte[1024];
-			int bytesRead;
-			while ((bytesRead = in.read(dataBuffer, 0, 1024)) != -1) {
-				fileOutputStream.write(dataBuffer, 0, bytesRead);
-			}
-		} catch (IOException e) {
-			// handle exception
-		}
-	}
-
-    private static void unzip(String zipFilePath, String destDir) {
-		System.out.println("zipFilePath: " + zipFilePath);
-		System.out.println("destDir: " + destDir);
-
-        File dir = new File(destDir);
-        // create output directory if it doesn't exist
-        if(!dir.exists()) dir.mkdirs();
-        FileInputStream fis;
-        //buffer for read and write data to file
-        byte[] buffer = new byte[1024];
-        try {
-            fis = new FileInputStream(zipFilePath);
-            ZipInputStream zis = new ZipInputStream(fis);
-            ZipEntry ze = zis.getNextEntry();
-            while(ze != null){
-                String fileName = ze.getName();
-                File newFile = new File(destDir + File.separator + fileName);
-                System.out.println("Unzipping to "+newFile.getAbsolutePath());
-                //create directories for sub directories in zip
-                new File(newFile.getParent()).mkdirs();
-                FileOutputStream fos = new FileOutputStream(newFile);
-                int len;
-                while ((len = zis.read(buffer)) > 0) {
-                   fos.write(buffer, 0, len);
-                }
-                fos.close();
-                zis.closeEntry();
-                ze = zis.getNextEntry();
-            }
-            //close last ZipEntry
-            zis.closeEntry();
-            zis.close();
-            fis.close();
-        } catch (IOException e) {
-            e.printStackTrace();
-        }
-    }
-
-    public static void run(String NCIT_FTP_URL, String zipfile) {
-		String currentWorkingDirectory = System.getProperty("user.dir");
-		System.out.println("currentWorkingDirectory: " + currentWorkingDirectory);
-
-        download(NCIT_FTP_URL + zipfile, zipfile);
-        String zipFilePath = currentWorkingDirectory + "/" + zipfile;
-        unzip(zipFilePath, currentWorkingDirectory);
-	}
-
-    public static boolean rename(String old_file, String new_file) {
-		File oldfile = new File(old_file);
-		File newfile = new File(new_file);
-
-		if (!oldfile.exists()) {
-			System.out.println("File " + old_file + " does not existis.");
-			return false;
-		}
-
-		if (oldfile.renameTo(newfile)){
-			return true;
-		}
-		return false;
-	}
-
-    public static String downloadNCItInferredOWL(String version) {
-        //String zipfile = args[0];//"ThesaurusInf_20.05d.OWL.zip";
-        String zipfile = "ThesaurusInf_" + version + ".OWL.zip";
-        System.out.println("NCIT_FTP_URL: " + NCIT_FTP_URL);
-        System.out.println("zipfile: " + zipfile);
-        run(NCIT_FTP_URL, zipfile);
-        int n = zipfile.indexOf("_");
-        String old_file = zipfile.substring(0, n) + "erred.owl";
-        int m = zipfile.indexOf("OWL");
-        String new_file = zipfile.substring(0, m-1) + ".owl";
-        System.out.println("oldfile: " + old_file);
-        System.out.println("newfile: " + new_file);
-        boolean bool = rename(old_file, new_file);
-        if (bool) {
-        	System.out.println("File rename successful? " + bool);
-        	new File(zipfile).delete();
-        	return new_file;
-		}
-        return null;
-	}
-
-    public static void main(String[] args) {
-		long ms = System.currentTimeMillis();
-		String version = args[0];
-		String owlfile = downloadNCItInferredOWL(version);
-		System.out.println("owlfile: " + owlfile);
-		System.out.println("Total edit history run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-}
-
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/FileUtils.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/FileUtils.java
deleted file mode 100644
index c9326e624..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/FileUtils.java
+++ /dev/null
@@ -1,134 +0,0 @@
-package gov.nih.nci.evs.restapi.util;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStream;
-import java.util.*;
-import java.text.*;
-import java.nio.file.*;
-
-public class FileUtils
-{
-    public static void copyfile(String src_file, String target_file) {
-    	InputStream inStream = null;
-	    OutputStream outStream = null;
-    	try{
-    	    File afile =new File(src_file);
-    	    File bfile =new File(target_file);
-    	    inStream = new FileInputStream(afile);
-    	    outStream = new FileOutputStream(bfile);
-    	    byte[] buffer = new byte[1024];
-    	    int length;
-    	    while ((length = inStream.read(buffer)) > 0){
-    	    	outStream.write(buffer, 0, length);
-    	    }
-    	    inStream.close();
-    	    outStream.close();
-    	    System.out.println("File copied from " + src_file + " to " + target_file);
-    	}catch(IOException e){
-    		e.printStackTrace();
-    	}
-    }
-
-    public static boolean fileExists(String filename) {
-		File f = new File(filename);
-		if(f.exists() && !f.isDirectory()) {
-            return true;
-		}
-		return false;
-	}
-
-    public static boolean directoryExists(String filename) {
-		File f = new File(filename);
-		if(f.exists()) {
-            return true;
-		}
-		return false;
-	}
-
-	public static String getCurrentWorkingDirectory() {
-		return System.getProperty("user.dir");
-	}
-
-	public static String getToday() {
-		return getToday("MM-dd-yyyy");
-	}
-
-	public static String getToday(String format) {
-		java.util.Date date = Calendar.getInstance().getTime();
-		SimpleDateFormat sdf = new SimpleDateFormat(format);
-		return sdf.format(date);
-	}
-
-    public static boolean createDirectory(String pathname) {
-		Path path = Paths.get(pathname);
-		try {
-			Files.createDirectory(path);
-			return true;
-		} catch (Exception ex) {
-			return false;
-		}
-	}
-
-    public static void copyFile(String sourceDir, String targetDir, Vector filesToCopy) {
-		for (int i=0; i {
-		Path destination = Paths.get(destinationDirectoryLocation, source.toString().substring(sourceDirectoryLocation.length()));
-		try {
-			Files.copy(source, destination);
-		} catch (IOException e) {
-			e.printStackTrace();
-		}
-		});
-	}
-
-    public static void main(String[] args) {
-		String currentWorkingDir = getCurrentWorkingDirectory();
-		System.out.println("getCurrentWorkingDirectory: " + currentWorkingDir);
-		String today = getToday("MMddyy");
-		System.out.println("getToday: " + today);
-		boolean exists = directoryExists(today);
-		System.out.println("directory exist? " + exists);
-		String dirname = currentWorkingDir + File.separator + today + File.separator;
-		if (!exists) {
-			System.out.println(dirname);
-    		boolean created = createDirectory(dirname);
-    		System.out.println("directory created? " + created);
-		}
-		exists = directoryExists(dirname);
-		System.out.println("directory exist? " + exists);
-		Vector filesToCopy = new Vector();
-		filesToCopy.add("cmd.exe");
-		filesToCopy.add("run.bat");
-		copyFile(currentWorkingDir, dirname, filesToCopy);
-	}
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/FirstInFirstOutQueue.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/FirstInFirstOutQueue.java
deleted file mode 100644
index 4bd1d27d6..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/FirstInFirstOutQueue.java
+++ /dev/null
@@ -1,43 +0,0 @@
-package gov.nih.nci.evs.restapi.util;
-
-import java.util.LinkedList;
-import java.util.Queue;
-
-public class FirstInFirstOutQueue {
-	Queue fifo = null;
-
-	public FirstInFirstOutQueue() {
-		fifo = new LinkedList();
-	}
-
-	public void add(String link) {
-		fifo.add(link);
-	}
-
-	public String remove() {
-		String link = fifo.remove();
-		return link;
-	}
-
-	public boolean isEmpty() {
-		return fifo.isEmpty();
-	}
-
-    public static void main(String args[]) {
-        char arr[] = {'3','1','4','1','5','9','2','6','5','3','5','8','9'};
-        Queue fifo = new LinkedList();
-
-        for (int i = 0; i < arr.length; i++) {
-			String s = "" + arr[i];
-            fifo.add(s);
-		}
-
-        System.out.print (fifo.remove() + ".");
-        while (!fifo.isEmpty()) {
-			String link = fifo.remove();
-            System.out.print(link);
-		}
-        System.out.println();
-
-    }
-}
\ No newline at end of file
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/FormatHelper.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/FormatHelper.java
deleted file mode 100644
index 85a9f853f..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/FormatHelper.java
+++ /dev/null
@@ -1,177 +0,0 @@
-package gov.nih.nci.evs.restapi.util;
-
-import gov.nih.nci.evs.restapi.bean.*;
-import gov.nih.nci.evs.restapi.common.*;
-
-import java.io.*;
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.*;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
-import java.util.*;
-import java.util.regex.*;
-import org.apache.commons.codec.binary.Base64;
-import org.json.*;
-
-/**
- * 
- * Copyright Copyright 2020 MSC.. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by MSC and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "MSC" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or MSC
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      MSC, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class FormatHelper {
-
-    public FormatHelper() {
-
-
-    }
-
-	public static boolean isInteger(Object object) {
-		if(object instanceof Integer) {
-			return true;
-		} else {
-			String string = object.toString();
-
-			try {
-				Integer.parseInt(string);
-			} catch(Exception e) {
-				return false;
-			}
-		}
-		return true;
-	}
-
-    public static String escapeComma(String field) {
-		char ch = ',';
-		return escapeChar(field, ch);
-	}
-
-
-    public static String escapeChar(String field, char ch) {
-		if (field == null) return "";
-		StringBuffer buf = new StringBuffer();
-		for (int i=0; i
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-public class FormatUtils {
-    ParserUtils parserUtils = null;
-    String applicationName = "sparql";
-
-	public FormatUtils() {
-        parserUtils = new ParserUtils();
-	}
-
-	public void setApplicationName(String applicationName) {
-		this.applicationName = applicationName;
-	}
-
-	public Vector toDelimited(Vector v) {
-		return parserUtils.getResponseValues(v);
-	}
-
-	public PrintWriter systemOut2PrintWriter() {
-		return new PrintWriter(System.out, true);
-	}
-
-	public Vector formatRelationships(Vector v, String label, String code) {
-		if (v == null || v.size() == 0) return new Vector();
-		Vector w = new Vector();
-		for (int i=0; i (" + role_name + ") --> [" + role_target + " (" + role_target_code + ")]");
-		}
-		return w;
-	}
-
-	public Vector formatInverseRelationships(Vector v, String label, String code) {
-		if (v == null || v.size() == 0) return new Vector();
-		Vector w = new Vector();
-		for (int i=0; i (" + role_name + ") --> [" + label + " (" + code + ")]");
-		}
-		return w;
-	}
-
-	public Vector formatSuperclasses(Vector v, String label, String code) {
-		if (v == null || v.size() == 0) return new Vector();
-		Vector w = new Vector();
-		for (int i=0; i (" + role_name + ") --> [" + role_target + " (" + role_target_code + ")]");
-		}
-		return w;
-	}
-
-	public Vector formatSubclasses(Vector v, String label, String code) {
-		if (v == null || v.size() == 0) return new Vector();
-		Vector w = new Vector();
-		for (int i=0; i (" + role_name + ") --> [" + label + " (" + code + ")]");
-		}
-		return w;
-	}
-
-	//formatSynonyms
-	public String formatSynonyms(Vector v) {
-		StringBuffer buf = new StringBuffer();
-		if (v == null || v.size() == 0) return "";
-		List list = new ParserUtils().getSynonyms(v);
-		Synonym first_syn = (Synonym) list.get(0);
-		String label = first_syn.getLabel();
-		String code = first_syn.getCode();
-		buf.append(label + " (" + code + ")").append("\n");
-		buf.append("\tTerm\tSource\tType\tSource Code\tSubsource Name").append("\n");
-		for (int i=0; i").append("\n");
-		} else {
-			buf.append("").append("\n");
-		}
-		buf.append(name).append("\n");
-		buf.append("").append("\n");
-		return buf.toString();
-     }
-
-     public String getHyperlink(String named_graph, String name, String code) {
-		StringBuffer buf = new StringBuffer();
-		buf.append("").append("\n");
-		buf.append(name).append("\n");
-		buf.append("").append("\n");
-		return buf.toString();
-     }
-
-	 public String getRelationshipTableLabel(String defaultLabel, String type, boolean isEmpty) {
-		String NONE = "(none)";
-		StringBuffer buf = new StringBuffer();
-
-		if (type.compareTo(Constants.TYPE_SUPERCONCEPT) == 0) {
-			buf.append("Parent Concepts:");
-			if (isEmpty) {
-				buf.append(" ").append(NONE).append("\n");
-			}
-		} else if (type.compareTo(Constants.TYPE_SUBCONCEPT) == 0) {
-			buf.append("Child Concepts:");
-			if (isEmpty) {
-				buf.append(" ").append(NONE).append("\n");
-			}
-		} else if (type.compareTo(Constants.TYPE_ROLE) == 0) {
-			buf.append("Role Relationships pointing from the current concept to other concepts:");
-			if (isEmpty) {
-				buf.append(" ").append(NONE).append("\n");
-			} else {
-				buf.append("
    ").append("\n");
-				buf.append("(True for the current concept.)").append("\n");
-			}
-
-		} else if (type.compareTo(Constants.TYPE_ASSOCIATION) == 0) {
-			buf.append("Associations pointing from the current concept to other concepts:");
-			if (isEmpty) {
-				buf.append(" ").append(NONE).append("\n");
-			} else {
-				buf.append("
    ").append("\n");
-				buf.append("(True for the current concept.)").append("\n");
-			}
-		} else if (type.compareTo(Constants.TYPE_INVERSE_ROLE) == 0) {
-			buf.append("Incoming Role Relationships pointing from other concepts to the current concept:");
-			if (isEmpty) {
-				buf.append(" ").append(NONE).append("\n");
-			}
-		} else if (type.compareTo(Constants.TYPE_INVERSE_ASSOCIATION) == 0) {
-			buf.append("Incoming Associations pointing from other concepts to the current concept:");
-			if (isEmpty) {
-				buf.append(" ").append(NONE).append("\n");
-			}
-		} else {
-			buf.append("" + type + ":");
-			if (isEmpty) {
-				buf.append(" ").append(NONE).append("\n");
-			}
-		}
-
-
-		String label = buf.toString();
-		if (label.length() == 0) {
-			label = defaultLabel;
-		}
-	    return label;
-    }
-
-     public Vector getSortedKeys(HashMap map) {
-		 if (map == null) return null;
-         Vector v = new Vector();
-         Iterator it = map.keySet().iterator();
-         while (it.hasNext()) {
-             String t = (String) it.next();
-             v.add(t);
-         }
-         v = new SortUtils().quickSort(v);
-         return v;
-	 }
-
-     public String formatTable(HashMap map, String firstColumnHeading, String secondColumnHeading,
-        int firstPercentColumnWidth, int secondPercentColumnWidth) {
-
-         return formatTable(map, firstColumnHeading, secondColumnHeading,
-         firstPercentColumnWidth, secondPercentColumnWidth, false);
-		}
-
-
-     public String formatTable(HashMap map, String firstColumnHeading, String secondColumnHeading,
-        int firstPercentColumnWidth, int secondPercentColumnWidth, boolean encode) {
-		Vector prop_names = getSortedKeys(map);
-        StringBuffer buf = new StringBuffer();
-		buf.append("").append("\n");
-
-        if (firstColumnHeading != null && secondColumnHeading != null) {
-			buf.append("").append("\n");
-			buf.append("   ").append("\n");
-			buf.append("   ").append("\n");
-			buf.append("").append("\n");
-	    }
-
-        if (firstPercentColumnWidth <= 0 || firstPercentColumnWidth <= 0) {
-			buf.append("   ").append("\n");
-			buf.append("   ").append("\n");
-		} else {
-			String w1 = Integer.toString(firstPercentColumnWidth);
-			String w2 = Integer.toString(secondPercentColumnWidth);
-			buf.append("   ").append("\n");
-			buf.append("   ").append("\n");
-	    }
-
-		int n = 0;
-        for (int i=0; i").append("\n");
-				} else {
-					  buf.append("	").append("\n");
-				}
-			    buf.append("").append("\n");
-                if (encode) {
-					value = formatComplexProperties(name, value);
-			    	value = StringUtils.encode_term(value);
-				}
-			    buf.append("").append("\n");
-			}
-			buf.append("	").append("\n");
-		}
-		buf.append("
    " + firstColumnHeading  + "" + secondColumnHeading + "
    ").append("\n");
-			    buf.append(name).append("\n");
-			    buf.append("" + value + "
    ").append("\n");
-        return buf.toString();
-    }
-
-
-     public String formatTable(Vector v, String firstColumnHeading, String secondColumnHeading,
-        int firstPercentColumnWidth, int secondPercentColumnWidth) {
-        StringBuffer buf = new StringBuffer();
-		buf.append("").append("\n");
-
-        if (firstColumnHeading != null && secondColumnHeading != null) {
-			buf.append("").append("\n");
-			buf.append("   ").append("\n");
-			buf.append("   ").append("\n");
-			buf.append("").append("\n");
-	    }
-
-        if (firstPercentColumnWidth <= 0 || firstPercentColumnWidth <= 0) {
-			buf.append("   ").append("\n");
-			buf.append("   ").append("\n");
-		} else {
-			String w1 = Integer.toString(firstPercentColumnWidth);
-			String w2 = Integer.toString(secondPercentColumnWidth);
-			buf.append("   ").append("\n");
-			buf.append("   ").append("\n");
-	    }
-
-		int n = 0;
-        for (int i=0; i").append("\n");
-			} else {
-				  buf.append("	").append("\n");
-			}
-			buf.append("").append("\n");
-
-			buf.append("").append("\n");
-			buf.append("	").append("\n");
-		}
-		buf.append("
    " + firstColumnHeading  + "" + secondColumnHeading + "
    ").append("\n");
-			buf.append(name).append("\n");
-			buf.append("" + value + "
    ").append("\n");
-        return buf.toString();
-    }
-}
\ No newline at end of file
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/GeneralizedQueryUtils.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/GeneralizedQueryUtils.java
deleted file mode 100644
index 996958d01..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/GeneralizedQueryUtils.java
+++ /dev/null
@@ -1,1224 +0,0 @@
-package gov.nih.nci.evs.restapi.util;
-
-import gov.nih.nci.evs.restapi.bean.*;
-import gov.nih.nci.evs.restapi.common.*;
-
-import java.io.*;
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.*;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
-import java.util.*;
-import java.util.regex.*;
-import org.apache.commons.codec.binary.Base64;
-import org.json.*;
-
-import java.util.StringTokenizer;
-
-/**
- * 
- * Copyright 2008-2017 NGIS. This software was developed in conjunction
- * with the National Cancer Institute, and so to the extent government
- * employees are co-authors, any rights in such works shall be subject
- * to Title 17 of the United States Code, section 105.
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *   1. Redistributions of source code must retain the above copyright
- *      notice, this list of conditions and the disclaimer of Article 3,
- *      below. Redistributions in binary form must reproduce the above
- *      copyright notice, this list of conditions and the following
- *      disclaimer in the documentation and/or other materials provided
- *      with the distribution.
- *   2. The end-user documentation included with the redistribution,
- *      if any, must include the following acknowledgment:
- *      "This product includes software developed by NGIS and the National
- *      Cancer Institute."   If no such end-user documentation is to be
- *      included, this acknowledgment shall appear in the software itself,
- *      wherever such third-party acknowledgments normally appear.
- *   3. The names "The National Cancer Institute", "NCI" and "NGIS" must
- *      not be used to endorse or promote products derived from this software.
- *   4. This license does not authorize the incorporation of this software
- *      into any third party proprietary programs. This license does not
- *      authorize the recipient to use any trademarks owned by either NCI
- *      or NGIS
- *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
- *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
- *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
- *      NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
- *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *      POSSIBILITY OF SUCH DAMAGE.
- * 
- */
-
-/**
- * @author EVS Team
- * @version 1.0
- *
- * Modification history:
- *     Initial implementation kim.ong@ngc.com
- *
- */
-
-
-public class GeneralizedQueryUtils {
-	OWLSPARQLUtils owlSPARQLUtils = null;
-	String serviceUrl = null;
-	String named_graph = null;
-	String ncit_version = null;
-	String sparql_endpoint = null;
-	HashMap nameVersion2NamedGraphMap = null;
-	gov.nih.nci.evs.restapi.util.MetadataUtils mdu = null;
-	HashMap uriBaseHashMap = null;
-	HashMap nameGraph2PredicateHashMap = null;
-	Vector supportedNamedGraphs = null;
-
-	SPARQLSearchUtils sparqlSearchUtils = null;
-	//ConceptDetailsPageGenerator cdpg = null;
-
-    static int FORWARD = 1;
-    static int BACKWARD = 2;
-
-    HierarchyHelper hh = null;
-
-    HashMap namedGraph2UIDPredicateHashMap = null;
-    HashMap basePrefixUIDHashMap = null;
-    static String PARENT_CHILD_FILE = "parent_child.txt";
-
-    static String[] COMMON_PREFIXES = new String[] {
-		"PREFIX xml:",
-		"PREFIX rdf:",
-		"PREFIX owl:",
-		"PREFIX owl2xml:",
-		"PREFIX protege:",
-		"PREFIX xsd:",
-        "PREFIX rdfs:"
-	};
-
-	public GeneralizedQueryUtils(String serviceUrl, HashMap nameVersion2NamedGraphMap, HashMap basePrefixUIDHashMap) {
-		this.serviceUrl = serviceUrl;
-		this.nameVersion2NamedGraphMap = nameVersion2NamedGraphMap;
-		this.basePrefixUIDHashMap = basePrefixUIDHashMap;
-		this.owlSPARQLUtils = new OWLSPARQLUtils(serviceUrl, null, null);
-	}
-
-	public String getServiceUrl() {
-		return this.serviceUrl;
-	}
-
-	public HashMap getNameVersion2NamedGraphMap() {
-		return this.nameVersion2NamedGraphMap;
-	}
-
-	public HashMap getBasePrefixUIDHashMap() {
-		return this.basePrefixUIDHashMap;
-	}
-
-	public gov.nih.nci.evs.restapi.util.MetadataUtils getMetadataUrils() {
-		return this.mdu;
-	}
-
-	public GeneralizedQueryUtils(String serviceUrl) {
-		long ms = System.currentTimeMillis();
-
-		int n = serviceUrl.indexOf("?");
-		if (n != -1) {
-			serviceUrl = serviceUrl.substring(0, n);
-		}
-		this.serviceUrl = serviceUrl;
-		this.sparql_endpoint = serviceUrl + "?query=";
-
-		mdu = new gov.nih.nci.evs.restapi.util.MetadataUtils(serviceUrl);
-		nameVersion2NamedGraphMap = mdu.getNameVersion2NamedGraphMap();
-		uriBaseHashMap = mdu.getURIBaseHashMap();
-
-		this.supportedNamedGraphs = mdu.getSupportedNamedGraphs();
-
-		this.named_graph = mdu.getNamedGraph(gov.nih.nci.evs.restapi.common.Constants.NCI_THESAURUS);
-		this.ncit_version = mdu.getLatestVersion(gov.nih.nci.evs.restapi.common.Constants.NCI_THESAURUS);
-
-		System.out.println("sparql_endpoint: " + sparql_endpoint);
-		System.out.println("named_graph: " + named_graph);
-		System.out.println("ncit_version: " + ncit_version);
-
-		this.owlSPARQLUtils = new OWLSPARQLUtils(serviceUrl, null, null);
-		this.sparqlSearchUtils = new SPARQLSearchUtils(serviceUrl);
-
-        if (FileUtils.fileExists(PARENT_CHILD_FILE)) {
-			Vector parent_child_vec = Utils.readFile(PARENT_CHILD_FILE);
-			hh = new HierarchyHelper(parent_child_vec);
-		}
-		namedGraph2UIDPredicateHashMap = createNamedGraph2UIDPredicateHashMap();
-		basePrefixUIDHashMap = createBasePrefixUIDHashMap();
-		System.out.println("Total initialization run time (ms): " + (System.currentTimeMillis() - ms));
-	}
-
-	public MetadataUtils getMetadataUtils() {
-		return this.mdu;
-	}
-
-
-    public HashMap createNamedGraph2UIDPredicateHashMap() {
-		HashMap namedGraph2UIDPredicateHashMap = new HashMap();;
-        HashMap hmap = getNameVersion2NamedGraphMap();
-        Iterator it = hmap.keySet().iterator();
-        while (it.hasNext()) {
-			String key = (String) it.next();
-			Vector ng_vec = (Vector) hmap.get(key);
-			for (int j=0; j").append("\n");
-		buf.append("{").append("\n");
-		buf.append("?x a owl:Class .").append("\n");
-		buf.append("?x ?y ?z .").append("\n");
-		buf.append("?x rdfs:label ?x_label .").append("\n");
-		buf.append("?y rdfs:label ?y_label .").append("\n");
-		buf.append("?x " + identifier + " ?x_code .").append("\n");
-		if (by_code) {
-			buf.append("?x " + identifier + " \"" + code + "\"^^ .").append("\n");
-		}
-		buf.append("}").append("\n");
-		if (!by_code) {
-			buf.append("FILTER (str(?x) = \"" + ns + code + "\"^^xsd:string)").append("\n");
-		}
-		buf.append("}").append("\n");
-		return buf.toString();
-	}
-
-
-	public Vector getOWLClassData(String named_graph, String identifier, String code, String ns, boolean by_code) {
-		String q = owlSPARQLUtils.construct_get_owl_class_data(named_graph, identifier, code, ns, by_code);
-        //System.out.println(q);
-		Vector v = owlSPARQLUtils.getOWLClassData(named_graph, identifier, code, ns, by_code);
-		return v;
-	}
-
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-	public String construct_simple_tuple_query(String named_graph, int limit) {
-		StringBuffer buf = new StringBuffer();
-		buf.append("PREFIX xml:").append("\n");
-		buf.append("PREFIX rdf:").append("\n");
-		buf.append("PREFIX owl:").append("\n");
-		buf.append("PREFIX owl2xml:").append("\n");
-		buf.append("PREFIX protege:").append("\n");
-		buf.append("PREFIX xsd:").append("\n");
-		buf.append("PREFIX rdfs:").append("\n");
-		buf.append("SELECT distinct ?x ?p ?y").append("\n");
-		buf.append("{ ").append("\n");
-		buf.append("graph <" + named_graph + ">").append("\n");
-		buf.append("{").append("\n");
-		buf.append("{").append("\n");
-		//buf.append("?x a owl:Class .").append("\n");
-		buf.append("?x ?p ?y ").append("\n");
-		buf.append("}").append("\n");
-		buf.append("}").append("\n");
-		buf.append("} ").append("\n");
-		buf.append("").append("\n");
-		buf.append("LIMIT " + limit).append("\n");
-		return buf.toString();
-	}
-
-	public Vector simple_tuple_query(String named_graph, int limit) {
-		String query = construct_simple_tuple_query(named_graph, limit);
-
-//System.out.println(query);
-
-
-		Vector v = owlSPARQLUtils.executeQuery(query);
-		if (v != null && v.size() > 0) {
-			v = new ParserUtils().getResponseValues(v);
-			v = new SortUtils().quickSort(v);
-			return v;
-		}
-		return null;
-	}
-
-
-	public String findNamedGraphIdentifierLine(Vector v) {
-		if (v == null) {
-			return null;
-		}
-		String id_line = null;
-		int n0 = 0;
-		for (int i=0; i n0 && n > 1) {
-					id_line = line;
-					n0 = n;
-				}
-			}
-		}
-		return id_line;
-	}
-
-    public String getNamedGraphBasePrefix(String line) {
-		Vector u = StringUtils.parseData(line, '|');
-		String t = (String) u.elementAt(1);
-		int n = t.lastIndexOf("#");
-		if (n == -1) {
-			n = t.lastIndexOf("/");
-		}
-		return "<" + t.substring(0, n+1) + ">";
-	}
-
-    public String getNamedGraphUniqueIdentifier(String line) {
-		Vector u = StringUtils.parseData(line, '|');
-		String t = (String) u.elementAt(1);
-		int n = t.lastIndexOf("#");
-		if (n == -1) {
-			n = t.lastIndexOf("/");
-		}
-		return t.substring(n+1, t.length());
-	}
-
-	public String getNamespace(String ng) {
-		Vector w = simple_tuple_query(ng, 1000);
-
-		String id_line = findNamedGraphIdentifierLine(w);
-		Vector u = StringUtils.parseData(id_line, '|');
-		String t = (String) u.elementAt(0);
-		int n = t.lastIndexOf("#");
-		if (n == -1) {
-			n = t.lastIndexOf("/");
-		}
-		//return t.substring(n+1, t.length());
-		return t.substring(0, n+1);
-	}
-
-    public String getNamedGraphUIDPredicate(String named_graph) {
-		String s = getNamedGraphBasePrefixAndUniqueIdentifier(named_graph);
-		Vector u = StringUtils.parseData(s);
-		String basePrefix = (String) u.elementAt(0);
-		String uid = (String) u.elementAt(1);
-		//System.out.println("\nnamed_graph: " + named_graph);
-		//System.out.println("\tbasePrefix: " + basePrefix);
-		//System.out.println("\tid: " + uid);
-		return basePrefix.substring(1, basePrefix.length()-1) + uid;
-	}
-
-
-	public String getNamedGraphBasePrefixAndUniqueIdentifier(String ng) {
-		Vector w = simple_tuple_query(ng, 1000);
-		String id_line = findNamedGraphIdentifierLine(w);
-		return getNamedGraphBasePrefixAndUniqueIdentifier(ng, id_line);
-	}
-
-	public String getNamedGraphBasePrefixAndUniqueIdentifier(String named_graph, String line) {
-		if (named_graph.compareTo("http://purl.obolibrary.org/obo/obi/2017-09-03/obi.owl") == 0) {
-			return "|IAO_0000111";
-		}
-		String basePrefix = getNamedGraphBasePrefix(line);
-		String uid = getNamedGraphUniqueIdentifier(line);
-		return basePrefix + "|" + uid;
-	}
-
-
-    public String generate_sample_id(String named_graph, String basePrefix, String uid) {
-		int knt = 0;
-		Vector w = simple_tuple_query(named_graph, 1000);
-		String target = get_named_graph_predicate(named_graph);
-
-		int rand = 500;//new RandomVariateGenerator().uniform(0, 999);
-		String line = (String) w.elementAt(rand);
-		Vector u = StringUtils.parseData(line, '|');
-		String s = (String) u.elementAt(0);
-		String p = (String) u.elementAt(1);
-		String o = (String) u.elementAt(2);
-		return o;
-
-	}
-
-
-    public String construct_class_uri_query(String named_graph, String code) {
-		//String p = getNamedGraphUIDPredicate(named_graph);
-		String p = get_named_graph_predicate(named_graph);
-		StringBuffer buf = new StringBuffer();
-
-        buf.append("PREFIX xml:").append("\n");
-        buf.append("PREFIX rdf:").append("\n");
-        buf.append("PREFIX owl:").append("\n");
-        buf.append("PREFIX owl2xml:").append("\n");
-        buf.append("PREFIX protege:").append("\n");
-        buf.append("PREFIX xsd:").append("\n");
-        buf.append("PREFIX rdfs:").append("\n");
-
-        buf.append("SELECT distinct ?x").append("\n");
-        buf.append("{ ").append("\n");
-        buf.append("graph <" + named_graph + ">").append("\n");
-        buf.append("{").append("\n");
-        buf.append("{").append("\n");
-        buf.append("?x a owl:Class .").append("\n");
-        buf.append("?x ?p ?y ").append("\n");
-        buf.append("}").append("\n");
-        buf.append("}").append("\n");
-        buf.append("FILTER ((str(?p) = \"" + p + "\"^^xsd:string) && (str(?y) = \"" + code + "\"^^xsd:string))").append("\n");
-        buf.append("} ").append("\n");
-        return buf.toString();
-    }
-
-
-	public String get_class_URI(String named_graph, String code) {
-		String query = construct_class_uri_query(named_graph, code);
-		System.out.println(query);
-
-		Vector v = owlSPARQLUtils.executeQuery(query);
-		if (v != null && v.size() > 0) {
-			v = new ParserUtils().getResponseValues(v);
-			v = new SortUtils().quickSort(v);
-			return (String) v.elementAt(0);
-		}
-		return null;
-	}
-
-
-    public String construct_class_query_by_cui(String named_graph, String cui) {
-		//String cui = get_class_URI(named_graph, code);
-		System.out.println("cui: " + cui);
-		StringBuffer buf = new StringBuffer();
-        buf.append("PREFIX xml:").append("\n");
-        buf.append("PREFIX rdf:").append("\n");
-        buf.append("PREFIX owl:").append("\n");
-        buf.append("PREFIX owl2xml:").append("\n");
-        buf.append("PREFIX protege:").append("\n");
-        buf.append("PREFIX xsd:").append("\n");
-        buf.append("PREFIX rdfs:").append("\n");
-        buf.append("SELECT distinct ?x ?p ?y").append("\n");
-        buf.append("{ ").append("\n");
-        buf.append("graph <" + named_graph + ">").append("\n");
-        buf.append("{").append("\n");
-        buf.append("{").append("\n");
-        buf.append("?x a owl:Class .").append("\n");
-        buf.append("?x ?p ?y ").append("\n");
-        buf.append("}").append("\n");
-        buf.append("}").append("\n");
-        buf.append("FILTER (str(?x) = \"" + cui + "\"^^xsd:string)").append("\n");
-        buf.append("} ").append("\n");
-        return buf.toString();
-    }
-
-	public Vector class_query(String named_graph, String code) {
-		String query = construct_class_query_by_cui(named_graph, code);
-		Vector v = owlSPARQLUtils.executeQuery(query);
-		if (v != null && v.size() > 0) {
-			v = new ParserUtils().getResponseValues(v);
-			v = new SortUtils().quickSort(v);
-			return v;
-		}
-		return null;
-	}
-
-
-    public String construct_class_query_by_id(String named_graph, String id) {
-		String cui = get_class_URI(named_graph, id);
-		System.out.println("cui: " + cui);
-		StringBuffer buf = new StringBuffer();
-        buf.append("PREFIX xml:").append("\n");
-        buf.append("PREFIX rdf:").append("\n");
-        buf.append("PREFIX owl:").append("\n");
-        buf.append("PREFIX owl2xml:").append("\n");
-        buf.append("PREFIX protege:").append("\n");
-        buf.append("PREFIX xsd:").append("\n");
-        buf.append("PREFIX rdfs:").append("\n");
-        buf.append("SELECT distinct ?x ?p ?y").append("\n");
-        buf.append("{ ").append("\n");
-        buf.append("graph <" + named_graph + ">").append("\n");
-        buf.append("{").append("\n");
-        buf.append("{").append("\n");
-        buf.append("?x a owl:Class .").append("\n");
-        buf.append("?x ?p ?y ").append("\n");
-        buf.append("}").append("\n");
-        buf.append("}").append("\n");
-        buf.append("FILTER (str(?x) = \"" + cui + "\"^^xsd:string)").append("\n");
-        buf.append("} ").append("\n");
-        return buf.toString();
-    }
-
-	public Vector class_query_by_id(String named_graph, String id) {
-		String query = construct_class_query_by_id(named_graph, id);
-		Vector v = owlSPARQLUtils.executeQuery(query);
-		if (v != null && v.size() > 0) {
-			v = new ParserUtils().getResponseValues(v);
-			v = new SortUtils().quickSort(v);
-			return v;
-		}
-		return null;
-	}
-
-    public String construct_class_query_by_code(String named_graph, String code) {
-		StringBuffer buf = new StringBuffer();
-        String line = (String) basePrefixUIDHashMap.get(named_graph);
-        Vector u = StringUtils.parseData(line, '|');
-        String basePrefix = (String) u.elementAt(0);
-        String uid = (String) u.elementAt(1);
-		buf.append("PREFIX :" + basePrefix).append("\n");
-        buf.append("PREFIX xml:").append("\n");
-        buf.append("PREFIX rdf:").append("\n");
-        buf.append("PREFIX owl:").append("\n");
-        buf.append("PREFIX owl2xml:").append("\n");
-        buf.append("PREFIX protege:").append("\n");
-        buf.append("PREFIX xsd:").append("\n");
-        buf.append("PREFIX rdfs:").append("\n");
-        buf.append("SELECT distinct ?x ?p ?y").append("\n");
-        buf.append("{ ").append("\n");
-        buf.append("graph <" + named_graph + ">").append("\n");
-        buf.append("{").append("\n");
-        buf.append("{").append("\n");
-        buf.append("?x :" + uid + " ?x_code .").append("\n");
-        buf.append("?x :" + uid + " \"" + code + "\"^^xsd:string .").append("\n");
-        buf.append("?x ?p ?y ").append("\n");
-        buf.append("}").append("\n");
-        buf.append("}").append("\n");
-        buf.append("} ").append("\n");
-        return buf.toString();
-    }
-
-	public Vector class_query_by_code(String named_graph, String code) {
-		String query = construct_class_query_by_code(named_graph, code);
-
-		//System.out.println(query);
-
-		Vector v = owlSPARQLUtils.executeQuery(query);
-		if (v != null && v.size() > 0) {
-			v = new ParserUtils().getResponseValues(v);
-			v = new SortUtils().quickSort(v);
-			return v;
-		}
-		return null;
-	}
-
-
-	public String getPrefixes() {
-		return owlSPARQLUtils.getPrefixes();
-	}
-
-    public String construct_annotation_property_query(String named_graph) {
-        StringBuffer buf = new StringBuffer();
-        buf.append("PREFIX xml:").append("\n");
-        buf.append("PREFIX rdf:").append("\n");
-        buf.append("PREFIX owl:").append("\n");
-        buf.append("PREFIX owl2xml:").append("\n");
-        buf.append("PREFIX protege:").append("\n");
-        buf.append("PREFIX xsd:").append("\n");
-        buf.append("PREFIX rdfs:").append("\n");
-        buf.append("").append("\n");
-        buf.append("SELECT distinct ?p ?prop ?prop_value").append("\n");
-        buf.append("{").append("\n");
-        buf.append("graph <" + named_graph + "> {").append("\n");
-        buf.append("?p a owl:AnnotationProperty .").append("\n");
-        buf.append("?p ?prop ?prop_value ").append("\n");
-        buf.append("}").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-    }
-
-	public Vector annotation_property_query(String named_graph) {
-		String query = construct_annotation_property_query(named_graph);
-		Vector v = owlSPARQLUtils.executeQuery(query);
-		if (v != null && v.size() > 0) {
-			v = new ParserUtils().getResponseValues(v);
-			v = new SortUtils().quickSort(v);
-			return v;
-		}
-		return null;
-	}
-
-/*
-	(73) http://purl.obolibrary.org/obo/IAO_0000115|http://www.w3.org/1999/02/22-rdf-syntax-ns#type|http://www.w3.org/2002/07/owl#AnnotationProperty
-	(74) http://purl.obolibrary.org/obo/IAO_0000115|http://www.w3.org/2000/01/rdf-schema#label|definition
-	(75) http://purl.obolibrary.org/obo/IAO_0000231|http://www.w3.org/1999/02/22-rdf-syntax-ns#type|http://www.w3.org/2002/07/owl#AnnotationProperty
-	(76) http://purl.obolibrary.org/obo/IAO_0000425|http://www.w3.org/1999/02/22-rdf-syntax-ns#type|http://www.w3.org/2002/07/owl#AnnotationProperty
-	(77) http://purl.obolibrary.org/obo/IAO_0000425|http://www.w3.org/2000/01/rdf-schema#label|expand assertion to
-*/
-
-	public HashMap createPropertyHashMap(String named_graph) {
-		Vector w = annotation_property_query(named_graph);
-		HashMap hmap = new HashMap();
-		for (int i=0; i").append("\n");
-		buf.append("PREFIX rdf:").append("\n");
-		buf.append("PREFIX owl:").append("\n");
-		buf.append("PREFIX owl2xml:").append("\n");
-		buf.append("PREFIX protege:").append("\n");
-		buf.append("PREFIX xsd:").append("\n");
-		buf.append("PREFIX rdfs:").append("\n");
-		buf.append("").append("\n");
-		buf.append("SELECT distinct ?x_code").append("\n");
-		buf.append("{").append("\n");
-		buf.append("graph <" + named_graph + "> {").append("\n");
-		buf.append("?x a owl:Class .").append("\n");
-		buf.append("?x :" + uid + " ?x_code .").append("\n");
-		buf.append("}").append("\n");
-		buf.append("}").append("\n");
-		buf.append("LIMIT " + limit).append("\n");
-		buf.append("").append("\n");
-		return buf.toString();
-	}
-
-	public Vector class_id_query(String named_graph, int limit) {
-		String query = construct_class_id_query(named_graph, limit);
-		Vector v = owlSPARQLUtils.executeQuery(query);
-		if (v != null && v.size() > 0) {
-			v = new ParserUtils().getResponseValues(v);
-			v = new SortUtils().quickSort(v);
-			return v;
-		}
-		return null;
-	}
-
-    public HashMap createBasePrefixUIDHashMap(){
-        HashMap hmap = getNameVersion2NamedGraphMap();
-        Iterator it = hmap.keySet().iterator();
-        HashMap basePrefixUIDHashMap = new HashMap();
-        while (it.hasNext()) {
-			String key = (String) it.next();
-			Vector ng_vec = (Vector) hmap.get(key);
-			for (int j=0; j")) {
-					uid = "id";
-				}
-				basePrefixUIDHashMap.put(ng, basePrefix + "|" + uid);
-			}
-		}
-		return basePrefixUIDHashMap;
-	}
-
-////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-	public String construct_mapping_query(String named_graph, String code) {
-		StringBuffer buf = new StringBuffer();
-        buf.append("PREFIX xml:").append("\n");
-        buf.append("PREFIX rdf:").append("\n");
-        buf.append("PREFIX owl:").append("\n");
-        buf.append("PREFIX owl2xml:").append("\n");
-        buf.append("PREFIX protege:").append("\n");
-        buf.append("PREFIX xsd:").append("\n");
-        buf.append("PREFIX rdfs:").append("\n");
-        buf.append("SELECT distinct ?x ?p ?y").append("\n");
-        buf.append("{ ").append("\n");
-        buf.append("graph <" + named_graph + ">").append("\n");
-        //buf.append("{").append("\n");
-        buf.append("{").append("\n");
-        buf.append("?x ?p ?y .").append("\n");
-        if (code != null) {
-        	buf.append("FILTER (contains(str(?y), \"" + code + "\") || contains(str(?x), \"" + code + "\"))").append("\n");
-		}
-        //buf.append("}").append("\n");
-        buf.append("}").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-	public Vector mapping_query(String named_graph) {
-		return mapping_query(named_graph, null);
-	}
-
-
-	public Vector mapping_query(String named_graph, String code) {
-		String query = construct_mapping_query(named_graph, code);
-		Vector v = owlSPARQLUtils.executeQuery(query);
-		if (v != null && v.size() > 0) {
-			v = new ParserUtils().getResponseValues(v);
-			Vector w = new Vector();
-			for (int i=0; i").append("\n");
-        buf.append("PREFIX rdf:").append("\n");
-        buf.append("PREFIX owl:").append("\n");
-        buf.append("PREFIX owl2xml:").append("\n");
-        buf.append("PREFIX protege:").append("\n");
-        buf.append("PREFIX xsd:").append("\n");
-        buf.append("PREFIX rdfs:").append("\n");
-
-        buf.append("SELECT distinct ?x ?p ?y").append("\n");
-
-        buf.append("{ ").append("\n");
-        buf.append("graph <" + named_graph + ">").append("\n");
-        buf.append("{").append("\n");
-        buf.append("{").append("\n");
-        buf.append("?y :" + uid + " ?y_code .").append("\n");
-        buf.append("?y :" + uid + " \"" + code + "\"^^xsd:string .").append("\n");
-        buf.append("?x ?p ?y ").append("\n");
-        buf.append("}").append("\n");
-        buf.append("}").append("\n");
-        buf.append("} ").append("\n");
-        return buf.toString();
-    }
-
-	public Vector inverse_class_query_by_code(String named_graph, String code) {
-		String query = construct_inverse_class_query_by_code(named_graph, code);
-		Vector v = owlSPARQLUtils.executeQuery(query);
-		if (v != null && v.size() > 0) {
-			v = new ParserUtils().getResponseValues(v);
-			v = new SortUtils().quickSort(v);
-			return v;
-		}
-		return null;
-	}
-
-	public String construct_search_by_code(String code) {
-        StringBuffer buf = new StringBuffer();
-        buf.append("PREFIX xsd:").append("\n");
-        buf.append("SELECT distinct ?g ?x ?p ?z ").append("\n");
-        buf.append("{").append("\n");
-        buf.append("graph ?g {").append("\n");
-        buf.append("?x ?p \"" + code + "\"^^xsd:string .").append("\n");
-        buf.append("?x ?p ?z").append("\n");
-        buf.append("}").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-	public Vector search_by_code(String code) {
-		String query = construct_search_by_code(code);
-		Vector v = owlSPARQLUtils.executeQuery(query);
-		if (v != null && v.size() > 0) {
-			v = new ParserUtils().getResponseValues(v);
-			v = new SortUtils().quickSort(v);
-			return v;
-		} else {
-			System.out.println("executeQuery returns NULL");
-		}
-		return null;
-	}
-
-
-	public String construct_search_by_property(String matchText, int maxReturn) {
-		String prefixes = getPrefixes();
-		StringBuffer buf = new StringBuffer();
-		buf.append(prefixes);
-		buf.append("PREFIX owl:").append("\n");
-		buf.append("SELECT distinct ?g ?x ?p ?y").append("\n");
-		buf.append("{").append("\n");
-		buf.append("graph ?g").append("\n");
-		buf.append("{").append("\n");
-		buf.append("?x a owl:Class .").append("\n");
-		buf.append("?x ?p ?y .").append("\n");
-		buf.append("FILTER contains(lcase(str(?y)), \"" + matchText + "\")").append("\n");
-		buf.append("}").append("\n");
-		buf.append("}").append("\n");
-		buf.append("LIMIT " + maxReturn).append("\n");
-		return buf.toString();
-	}
-
-	public Vector search_by_property(String mathText, int maxReturn) {
-		String query = construct_search_by_property(mathText, maxReturn);
-		Vector v = owlSPARQLUtils.executeQuery(query);
-		if (v != null && v.size() > 0) {
-			v = new ParserUtils().getResponseValues(v);
-			v = new SortUtils().quickSort(v);
-			return v;
-		} else {
-			System.out.println("executeQuery returns NULL");
-		}
-		return null;
-	}
-
-
-	public String construct_superclass_query(String named_graph, String code) {
-        HashMap hmap = getBasePrefixUIDHashMap();
-		String value = (String) hmap.get(named_graph);
-		Vector u = StringUtils.parseData(value);
-		String basePrefix = (String) u.elementAt(0);
-		String uid = (String) u.elementAt(1);
-
-        StringBuffer buf = new StringBuffer();
-        buf.append("PREFIX :" + basePrefix).append("\n");
-        buf.append("PREFIX owl:").append("\n");
-        buf.append("PREFIX rdfs:").append("\n");
-        buf.append("SELECT ?y_label ?y_code").append("\n");
-        buf.append("{").append("\n");
-        buf.append("graph <" + named_graph + ">").append("\n");
-        buf.append("{").append("\n");
-        //buf.append("?x a owl:Class .").append("\n");
-        buf.append("?x :" + uid + " \"" + code + "\"^^xsd:string .").append("\n");
-
-        buf.append("?x rdfs:subClassOf ?y .").append("\n");
-
-        //buf.append("?y a owl:Class .").append("\n");
-        buf.append("?y :" + uid + " ?y_code .").append("\n");
-        buf.append("?y rdfs:label ?y_label .").append("\n");
-
-        buf.append("}").append("\n");
-        buf.append("}").append("\n");
-
-        return buf.toString();
-	}
-
-	public Vector get_superclasses(String named_graph, String code) {
-		String query = construct_superclass_query(named_graph, code);
-		Vector v = owlSPARQLUtils.executeQuery(query);
-		if (v != null && v.size() > 0) {
-			v = new ParserUtils().getResponseValues(v);
-			v = new SortUtils().quickSort(v);
-			return v;
-		} else {
-			System.out.println("executeQuery returns NULL");
-		}
-		return null;
-	}
-
-
-	public String construct_subclass_query(String named_graph, String code) {
-        HashMap hmap = getBasePrefixUIDHashMap();
-		String value = (String) hmap.get(named_graph);
-		Vector u = StringUtils.parseData(value);
-		String basePrefix = (String) u.elementAt(0);
-		String uid = (String) u.elementAt(1);
-
-        StringBuffer buf = new StringBuffer();
-        buf.append("PREFIX :" + basePrefix).append("\n");
-        buf.append("PREFIX owl:").append("\n");
-        buf.append("PREFIX rdfs:").append("\n");
-        buf.append("SELECT ?x_label ?x_code").append("\n");
-        buf.append("{").append("\n");
-        buf.append("graph <" + named_graph + ">").append("\n");
-        buf.append("{").append("\n");
-        //buf.append("?x a owl:Class .").append("\n");
-        buf.append("?x :" + uid + " ?x_code .").append("\n");
-        buf.append("?x rdfs:label ?x_label .").append("\n");
-
-        //buf.append("?y a owl:Class .").append("\n");
-        buf.append("?y :" + uid + " ?y_code .").append("\n");
-        buf.append("?y :" + uid + " \"" + code + "\"^^xsd:string .").append("\n");
-
-        buf.append("?x rdfs:subClassOf ?y .").append("\n");
-        buf.append("}").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-	public Vector get_subclasses(String named_graph, String code) {
-		String query = construct_subclass_query(named_graph, code);
-		Vector v = owlSPARQLUtils.executeQuery(query);
-		if (v != null && v.size() > 0) {
-			v = new ParserUtils().getResponseValues(v);
-			v = new SortUtils().quickSort(v);
-			return v;
-		} else {
-			System.out.println("executeQuery returns NULL");
-		}
-		return null;
-	}
-
-	public String construct_label_query(String named_graph, String code) {
-        HashMap hmap = getBasePrefixUIDHashMap();
-		String value = (String) hmap.get(named_graph);
-		Vector u = StringUtils.parseData(value);
-		String basePrefix = (String) u.elementAt(0);
-		String uid = (String) u.elementAt(1);
-
-        StringBuffer buf = new StringBuffer();
-        buf.append("PREFIX :" + basePrefix).append("\n");
-        buf.append("PREFIX owl:").append("\n");
-        buf.append("PREFIX rdfs:").append("\n");
-        buf.append("SELECT ?x_label").append("\n");
-        buf.append("{").append("\n");
-        buf.append("graph <" + named_graph + ">").append("\n");
-        buf.append("{").append("\n");
-        //buf.append("?x a owl:Class .").append("\n");
-        buf.append("?x :" + uid + " ?x_code .").append("\n");
-        buf.append("?x :" + uid + " \"" + code + "\"^^xsd:string .").append("\n");
-        buf.append("?x rdfs:label ?x_label .").append("\n");
-        buf.append("}").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-	public String get_label(String named_graph, String code) {
-		String query = construct_label_query(named_graph, code);
-		Vector v = owlSPARQLUtils.executeQuery(query);
-		if (v != null && v.size() > 0) {
-			v = new ParserUtils().getResponseValues(v);
-			v = new SortUtils().quickSort(v);
-			return (String) v.elementAt(0);
-		} else {
-			System.out.println("executeQuery returns NULL");
-		}
-		return null;
-	}
-
-	public String construct_hierarchical_relationship_query(String named_graph, int maxReturn) {
-
-        HashMap hmap = getBasePrefixUIDHashMap();
-		String value = (String) hmap.get(named_graph);
-		Vector u = StringUtils.parseData(value);
-		String basePrefix = (String) u.elementAt(0);
-		String uid = (String) u.elementAt(1);
-
-        StringBuffer buf = new StringBuffer();
-        buf.append("PREFIX :" + basePrefix).append("\n");
-        buf.append("PREFIX owl:").append("\n");
-        buf.append("PREFIX rdfs:").append("\n");
-        buf.append("SELECT ?y_label ?y_code ?x_label ?x_code").append("\n");
-        buf.append("{").append("\n");
-        buf.append("graph <" + named_graph + ">").append("\n");
-        buf.append("{").append("\n");
-        buf.append("?x a owl:Class .").append("\n");
-        buf.append("?x rdfs:label ?x_label .").append("\n");
-        buf.append("?x :" + uid + " ?x_code .").append("\n");
-        buf.append("?y a owl:Class .").append("\n");
-        buf.append("?y rdfs:label ?y_label .").append("\n");
-        buf.append("?y :" + uid + " ?y_code .").append("\n");
-        buf.append("?x rdfs:subClassOf ?y .").append("\n");
-        buf.append("}").append("\n");
-        buf.append("}").append("\n");
-        if (maxReturn != -1) {
-        	buf.append("LIMIT " + maxReturn).append("\n");
-		}
-        return buf.toString();
-	}
-
-	public Vector get_hierarchical_relationships(String named_graph, int maxReturn) {
-		String query = construct_hierarchical_relationship_query(named_graph, maxReturn);
-		Vector v = owlSPARQLUtils.executeQuery(query);
-		if (v != null && v.size() > 0) {
-			v = new ParserUtils().getResponseValues(v);
-			v = new SortUtils().quickSort(v);
-			return v;
-		} else {
-			System.out.println("executeQuery returns NULL");
-		}
-		return null;
-	}
-
-
-	public Vector get_hierarchical_relationships(String named_graph) {
-		return get_hierarchical_relationships(named_graph, -1);
-	}
-
-
-    public String formatLabelCodeString(String line) {
-		//Eye Part|C13019
-		int n = line.indexOf("|");
-		String label = line.substring(0, n);
-		String code = line.substring(n+1, line.length());
-		return label + " (" + code + ")";
-	}
-
-	public String construct_search_by_name_query(String matchText, int maxReturn) {
-		StringBuffer buf = new StringBuffer();
-		buf.append("PREFIX owl:").append("\n");
-		buf.append("PREFIX rdfs:").append("\n");
-		buf.append("SELECT distinct ?g ?x ?x_label").append("\n");
-		buf.append("{").append("\n");
-		buf.append("graph ?g").append("\n");
-		buf.append("{").append("\n");
-		buf.append("?x a owl:Class .").append("\n");
-		buf.append("?x rdfs:label ?x_label .").append("\n");
-		String matchText_lc = matchText.toLowerCase();
-		buf.append("FILTER contains(lcase(str(?x_label)), \"" + matchText_lc + "\")").append("\n");
-		buf.append("}").append("\n");
-		buf.append("}").append("\n");
-		if (maxReturn != -1 && maxReturn > 0) {
-			buf.append("LIMIT " + maxReturn).append("\n");
-		}
-		return buf.toString();
-	}
-
-	public Vector search_by_name(String matchText, int maxReturn) {
-		String query = construct_search_by_name_query(matchText, maxReturn);
-		Vector v = owlSPARQLUtils.executeQuery(query);
-		if (v != null && v.size() > 0) {
-			v = new ParserUtils().getResponseValues(v);
-			v = new SortUtils().quickSort(v);
-			return v;
-		} else {
-			System.out.println("executeQuery returns NULL");
-		}
-		return null;
-	}
-
-	public String construct_search_by_name_query(String named_graph, String matchText, int maxReturn) {
-        HashMap hmap = getBasePrefixUIDHashMap();
-		String value = (String) hmap.get(named_graph);
-		Vector u = StringUtils.parseData(value);
-		String basePrefix = (String) u.elementAt(0);
-		String uid = (String) u.elementAt(1);
-
-		StringBuffer buf = new StringBuffer();
-		buf.append("PREFIX :" + basePrefix).append("\n");
-		buf.append("PREFIX owl:").append("\n");
-		buf.append("PREFIX rdfs:").append("\n");
-		buf.append("SELECT distinct ?x_label ?x_code").append("\n");
-		buf.append("{").append("\n");
-		buf.append("graph <" + named_graph + ">").append("\n");
-		buf.append("{").append("\n");
-		buf.append("?x a owl:Class .").append("\n");
-		buf.append("?x :" + uid + " ?x_code .").append("\n");
-		buf.append("?x rdfs:label ?x_label .").append("\n");
-
-		String matchText_lc = matchText.toLowerCase();
-		buf.append("FILTER contains(lcase(str(?x_label)), \"" + matchText_lc + "\")").append("\n");
-		buf.append("}").append("\n");
-		buf.append("}").append("\n");
-		if (maxReturn != -1 && maxReturn > 0) {
-			buf.append("LIMIT " + maxReturn).append("\n");
-		}
-		return buf.toString();
-	}
-
-	public Vector search_by_name(String named_graph, String matchText, int maxReturn) {
-		String query = construct_search_by_name_query(named_graph, matchText, maxReturn);
-		Vector v = owlSPARQLUtils.executeQuery(query);
-		if (v != null && v.size() > 0) {
-			v = new ParserUtils().getResponseValues(v);
-			v = new SortUtils().quickSort(v);
-			return v;
-		} else {
-			System.out.println("executeQuery returns NULL");
-		}
-		return null;
-	}
-
-
-	public String construct_search_by_code(String named_graph, String code) {
-        HashMap hmap = getBasePrefixUIDHashMap();
-		String value = (String) hmap.get(named_graph);
-		Vector u = StringUtils.parseData(value);
-		String basePrefix = (String) u.elementAt(0);
-		String uid = (String) u.elementAt(1);
-
-		StringBuffer buf = new StringBuffer();
-		buf.append("PREFIX :" + basePrefix).append("\n");
-        buf.append("PREFIX xsd:").append("\n");
-        buf.append("SELECT distinct ?x_label ?x_code ").append("\n");
-        buf.append("{").append("\n");
-        buf.append("graph <" + named_graph + ">").append("\n");
-        buf.append("?x rdfs:label ?x_label .").append("\n");
-        buf.append("?x :" + uid + " ?x_code .").append("\n");
-        buf.append("?x :" + uid + " \"" + code + "\"^^xsd:string").append("\n");
-        buf.append("}").append("\n");
-        buf.append("}").append("\n");
-        return buf.toString();
-	}
-
-	public Vector search_by_code(String named_graph, String code) {
-		String query = construct_search_by_code(named_graph, code);
-		Vector v = owlSPARQLUtils.executeQuery(query);
-		if (v != null && v.size() > 0) {
-			v = new ParserUtils().getResponseValues(v);
-			v = new SortUtils().quickSort(v);
-			return v;
-		} else {
-			System.out.println("executeQuery returns NULL");
-		}
-		return null;
-	}
-
-    public static void main(String[] args) {
-		String serviceUrl = args[0];
-		System.out.println(serviceUrl);
-		GeneralizedQueryUtils test = new GeneralizedQueryUtils(serviceUrl+"?query=");
-        long ms = System.currentTimeMillis();
-
-		String named_graph = args[1];
-		named_graph = "http://ncicb.nci.nih.gov/trix/NCIt-HGNC";
-		/*
-		test.set_named_graph(named_graph);
-
-		String queryfile = args[2];
-		System.out.println(queryfile);
-		//test.runQuery(queryfile);
-
-		String code = "2002093";
-		named_graph = "http://cbiit.nci.nih.gov/caDSR";
-		String label = test.get_label(named_graph, code);
-
-		System.out.println(named_graph);
-		System.out.println(code);
-
-		System.out.println("label: " + label);
-		*/
-		Vector w = test.mapping_query(named_graph);
-		if (w != null) {
-			System.out.println(w.size());
-		}
-    }
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/GraphGenerator.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/GraphGenerator.java
deleted file mode 100644
index b012869db..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/GraphGenerator.java
+++ /dev/null
@@ -1,392 +0,0 @@
-package gov.nih.nci.evs.restapi.util;
-import gov.nih.nci.evs.restapi.bean.*;
-import gov.nih.nci.evs.restapi.test.*;
-
-import java.io.*;
-import java.util.*;
-import java.text.DecimalFormat;
-
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.DataInputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.FileWriter;
-import java.io.InputStreamReader;
-
-public class GraphGenerator {
-	static float default_ranksep = (float) 1.0;
-	static float default_nodesep = (float) 1.5;
-
-	static Vector COLORS = new Vector();
-	static {
-		COLORS.add("black");
-		COLORS.add("blue");
-		COLORS.add("blueviolet");
-		COLORS.add("brown");
-		COLORS.add("brown4");
-		COLORS.add("burlywood");
-		COLORS.add("cadetblue4");
-		COLORS.add("chocolate4");
-		COLORS.add("coral3");
-		COLORS.add("cyan4");
-		COLORS.add("crimson");
-		COLORS.add("darkgreen");
-		COLORS.add("darkolivegreen");
-		COLORS.add("darkgoldenrod");
-		COLORS.add("darkorchid");
-		COLORS.add("darklategray");
-		COLORS.add("darkviolet");
-		COLORS.add("deeppink3");
-		COLORS.add("firebrick2");
-		COLORS.add("forestgreen");
-		COLORS.add("gold");
-		COLORS.add("grey6");
-		COLORS.add("green3");
-		COLORS.add("green4");
-		COLORS.add("lawngreen");
-		COLORS.add("lightblue");
-		COLORS.add("lightslateblue");
-		COLORS.add("limegreen");
-		COLORS.add("maroon");
-		COLORS.add("magenta");
-		COLORS.add("maroon");
-		COLORS.add("midnightblue");
-		COLORS.add("navyblue");
-		COLORS.add("orange");
-		COLORS.add("orangered");
-		COLORS.add("orangered4");
-		COLORS.add("orchid");
-		COLORS.add("palevioletred");
-		COLORS.add("pink");
-		COLORS.add("purple");
-		COLORS.add("red");
-		COLORS.add("saddlebrown");
-		COLORS.add("sienna");
-		COLORS.add("slateblue");
-		COLORS.add("snow");
-		COLORS.add("springgreen");
-		COLORS.add("tan");
-		COLORS.add("turquoise3");
-		COLORS.add("tomato");
-		COLORS.add("violet");
-		COLORS.add("wheat");
-		COLORS.add("yellowgreen");
-	}
-
-    public GraphGenerator() {
-
-	}
-
-	public static String generateColor() {
-		int n = new RandomVariateGenerator().uniform(0, COLORS.size()-1);
-		return (String) COLORS.elementAt(n);
-	}
-
-	public static String toString(Vector v) {
-		StringBuffer buf = new StringBuffer();
-		for (int i=0; i " + range_id
-				   + " [label=" + "\"" + role + "\"" + " fontcolor=" + color + ", color=" + color + "];");
-			} else {
-				if (selected_nodes.contains(domain_label) && selected_nodes.contains(range_label)) {
-					pw.println(domain_id + " -> " + range_id
-					   + " [label=" + "\"" + role + "\"" + " fontcolor=" + color + ", color=" + color + "];");
-				}
-			}
-		}
-    }
-
-
-	public static void generateGraphvizDataFile(Vector nodes, Vector edges, Vector selected_nodes, String outputfile) {
-        float ranksep = (float) 1.0;
-        float nodesep = (float) 1.5;
-        generateGraphvizDataFile(nodes, edges, selected_nodes, outputfile, ranksep, nodesep);
-	}
-
-	public static void generateGraphvizDataFile(Vector nodes, Vector edges, Vector selected_nodes, String outputfile, float ranksep, float nodesep) {
-         PrintWriter pw = null;
-         try {
- 			pw = new PrintWriter(outputfile, "UTF-8");
-			pw.println("ranksep = \"" + ranksep + "\";");
-			pw.println("nodesep = \"" + nodesep + "\";");
-			pw.println("ratio=fill;");
-			pw.println("overlap=scale;");
-			pw.println("concentrate=true;");
-			pw.println("ratio=auto;");
-			pw.println("overlap = false;");
-			pw.println("splines = true;");
-			pw.println("node [style=filled,color=lightblue,shape=box];");
-			pw.println("style=filled;");
-			pw.println("color=lightgrey;");
-            generateGraph(pw, nodes, edges, selected_nodes);
-
- 		} catch (Exception ex) {
-
- 		} finally {
- 			try {
- 				pw.close();
- 				System.out.println("Output file " + outputfile + " generated.");
- 		    } catch (Exception ex) {
- 				ex.printStackTrace();
- 			}
-		}
-	}
-
-
-
-	public static GraphData createGraphData(String inputfile, String format) { //source|edge label|target
-	    Vector data_vec = Utils.readFile(inputfile);
-	    float ranksep = default_ranksep;
-	    float nodesep = default_nodesep;
-	    String filename = "graph_" + inputfile;
-	    return createGraphData(data_vec, ranksep, nodesep, format, filename);
-	}
-
-	public static GraphData createGraphData(Vector data_vec, float ranksep, float nodesep, String format, String filename) { //source|edge label|target
-		GraphData gd = new GraphData();
-        Vector nodes = new Vector();
-        Vector edges = new Vector();
-        for (int i=0; i 0) {
-            --this.currentDpiPos;
-        }
-    }
-
-    public int getImageDpi() {
-        return this.dpiSizes[this.currentDpiPos];
-    }
-
-    private StringBuilder graph = new StringBuilder();
-
-    public GraphViz() {
-		//String os = System.getProperty("os.name");
-		//System.out.println(os);
-    }
-
-    public String getDotSource() {
-        return this.graph.toString();
-    }
-
-    public void add(String line) {
-        this.graph.append(line);
-    }
-
-    public void addln(String line) {
-        this.graph.append(line + "\n");
-    }
-
-    public void addln() {
-        this.graph.append('\n');
-    }
-
-    public void clearGraph(){
-        this.graph = new StringBuilder();
-    }
-
-    public byte[] getGraph(String dot_source, String type)
-    {
-        File dot;
-        byte[] img_stream = null;
-
-        try {
-            dot = writeDotSourceToFile(dot_source);
-            if (dot != null)
-            {
-                img_stream = get_img_stream(dot, type);
-                if (dot.delete() == false)
-                    System.err.println("Warning: " + dot.getAbsolutePath() + " could not be deleted!");
-                return img_stream;
-            }
-            return null;
-        } catch (java.io.IOException ioe) { return null; }
-    }
-
-
-    public byte[] getGraph(String dot_source, String type, String dotsourcefile) {
-        File dot;
-        byte[] img_stream = null;
-
-        try {
-            dot = writeDotSourceToFile(dot_source, dotsourcefile);
-            if (dot != null)
-            {
-                img_stream = get_img_stream(dot, type);
-                if (dot.delete() == false)
-                    System.err.println("Warning: " + dot.getAbsolutePath() + " could not be deleted!");
-                return img_stream;
-            }
-            return null;
-        } catch (java.io.IOException ioe) { return null; }
-    }
-
-    public int writeGraphToFile(byte[] img, String file)
-    {
-        File to = new File(file);
-        return writeGraphToFile(img, to);
-    }
-
-    public int writeGraphToFile(byte[] img, File to)
-    {
-        try {
-            FileOutputStream fos = new FileOutputStream(to);
-            fos.write(img);
-            fos.close();
-        } catch (java.io.IOException ioe) { return -1; }
-        return 1;
-    }
-
-    private byte[] get_img_stream(File dot, String type)
-    {
-        File img;
-        byte[] img_stream = null;
-
-        try {
-            img = File.createTempFile("graph_", "."+type, new File(GraphViz.TEMP_DIR));
-            Runtime rt = Runtime.getRuntime();
-            String[] args = {DOT, "-T"+type, "-Gdpi="+dpiSizes[this.currentDpiPos], dot.getAbsolutePath(), "-o", img.getAbsolutePath()};
-            Process p = rt.exec(args);
-            p.waitFor();
-            FileInputStream in = new FileInputStream(img.getAbsolutePath());
-            img_stream = new byte[in.available()];
-            in.read(img_stream);
-            if( in != null ) in.close();
-            if (img.delete() == false)
-                System.err.println("Warning: " + img.getAbsolutePath() + " could not be deleted!");
-        }
-        catch (java.io.IOException ioe) {
-            System.err.println("Error:    in I/O processing of tempfile in dir " + GraphViz.TEMP_DIR+"\n");
-            System.err.println("       or in calling external command");
-            ioe.printStackTrace();
-        }
-        catch (java.lang.InterruptedException ie) {
-            System.err.println("Error: the execution of the external program was interrupted");
-            ie.printStackTrace();
-        }
-        return img_stream;
-    }
-
-    private File writeDotSourceToFile(String str, String dotfilename) throws java.io.IOException
-    {
-        File temp;
-        try {
-            temp = File.createTempFile("dorrr",".dot", new File(GraphViz.TEMP_DIR));
-            FileWriter fout = new FileWriter(temp);
-            fout.write(str);
-                       BufferedWriter br=new BufferedWriter(new FileWriter(dotfilename));
-                       br.write(str);
-                       br.flush();
-                       br.close();
-            fout.close();
-        }
-        catch (Exception e) {
-            System.err.println("Error: I/O error while writing the dot source to temp file!");
-            return null;
-        }
-        return temp;
-    }
-
-    private File writeDotSourceToFile(String str) throws java.io.IOException
-    {
-        File temp;
-        try {
-            temp = File.createTempFile("dorrr",".dot", new File(GraphViz.TEMP_DIR));
-            FileWriter fout = new FileWriter(temp);
-            fout.write(str);
-                       BufferedWriter br=new BufferedWriter(new FileWriter("dotsource.dot"));
-                       br.write(str);
-                       br.flush();
-                       br.close();
-            fout.close();
-        }
-        catch (Exception e) {
-            System.err.println("Error: I/O error while writing the dot source to temp file!");
-            return null;
-        }
-        return temp;
-    }
-
-    public String start_graph() {
-        return "digraph G {";
-    }
-
-    public String end_graph() {
-        return "}";
-    }
-
-    public String start_subgraph(int clusterid) {
-        return "subgraph cluster_" + clusterid + " {";
-    }
-
-    public String end_subgraph() {
-        return "}";
-    }
-
-    public void readSource(String input)
-    {
-        StringBuilder sb = new StringBuilder();
-        try
-        {
-            FileInputStream fis = new FileInputStream(input);
-            DataInputStream dis = new DataInputStream(fis);
-            BufferedReader br = new BufferedReader(new InputStreamReader(dis));
-            String line;
-            while ((line = br.readLine()) != null) {
-                sb.append(line);
-            }
-            dis.close();
-        }
-        catch (Exception e) {
-            System.err.println("Error: " + e.getMessage());
-        }
-        this.graph = sb;
-    }
-}
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/HTMLHierarchy.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/HTMLHierarchy.java
deleted file mode 100644
index 331fb88c4..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/HTMLHierarchy.java
+++ /dev/null
@@ -1,189 +0,0 @@
-package gov.nih.nci.evs.restapi.util;
-
-import java.io.*;
-import java.text.*;
-import java.util.*;
-
-
-public class HTMLHierarchy {
-	HashMap code2NodeMap = new HashMap();
-    HierarchyHelper hh = null;
-
-    public String title = "NCI Thesaurus";
-
-    String datafile = null;
-
-    public HTMLHierarchy(String datafile) {
-        this.datafile = datafile;
-        initialize();
-	}
-
-    public void initialize() {
-		Vector parent_child_vec = Utils.readFile(datafile);
-		System.out.println("parent_child_vec: " + parent_child_vec.size());
-
-		hh = new HierarchyHelper(parent_child_vec);
-	}
-
-	public Vector sortByLabel(Vector codes) {
-		HashMap label2CodeMap = new HashMap();
-		Vector w = new Vector();
-		Vector labels = new Vector();
-		for (int i=0; i" + title + "");
-		out.println("	
    ");
-
-
-		out.println("		
      ");
-		out.println("			
    • NCI Thesaurus");
-		out.println("				
        ");
-		out.println("					
      • Child node 1
        • ");
-		out.println("					
      • Child node 2
        • ");
-		out.println("				
      ");
-		out.println("			
      • ");
-		out.println("		
    ");
-
-
-		out.println("	
    ");
-	}
-
-
-	public void writeNode(PrintWriter out, String code) {
-		String label = (String) hh.getLabel(code);
-		String link_code = HyperlinkHelper.toHyperlink(code);
-		String display = label + " (" + link_code + ")";
-		out.println("		
      ");
-		out.println("			
    • " + display);
-
-		Vector subs = hh.getSubclassCodes(code);
-		if (subs != null) {
-			//subs = sortByLabel(subs);
-			for (int j=0; j");
-		out.println("		
    ");
-	}
-
-	public void write_data(PrintWriter out, String title, String root) {
-		Stack stack = new Stack();
-		if (root != null) {
-			stack.push(root);
-		} else {
-			Vector codes = hh.getRoots();
-			codes = sortByLabel(codes);
-
-			for (int i=0; i");
-		out.println("");
-		out.println("");
-		out.println("	");
-		out.println("	NCI Thesaurus");
-		out.println("	");
-		out.println("	");
-		out.println("");
-		out.println("");
-		out.println("");
-
-		write_data(out, title, root);
-
-		out.println("");
-		out.println("");
-		out.println("	");
-		out.println("	");
-		out.println("");
-		out.println("	");
-		out.println("");
-		out.println("");
-    }
-
-    public static void run(String datafile, String title, String root) {
-        long ms = System.currentTimeMillis();
-		PrintWriter pw = null;
-		int n = datafile.lastIndexOf(".");
-		String outputfile = datafile.substring(0, n) + ".html";
-		try {
-			pw = new PrintWriter(outputfile, "UTF-8");
-            HTMLHierarchy htmlHierarchy = new HTMLHierarchy(datafile);
-            htmlHierarchy.run(pw, title, root);
-
-		} catch (Exception ex) {
-
-		} finally {
-			try {
-				pw.close();
-				System.out.println("Output file " + outputfile + " generated.");
-			} catch (Exception ex) {
-				ex.printStackTrace();
-			}
-		}
-		System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
-
-	}
-
-    public static void main(String[] args) {
-		String datafile = args[0];
-		String title = args[1];
-		String root = args[2];
-		HTMLHierarchy.run(datafile, title, root);
-	}
-}
\ No newline at end of file
diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/HTMLTable.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/HTMLTable.java
deleted file mode 100644
index e5844c0c0..000000000
--- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/util/HTMLTable.java
+++ /dev/null
@@ -1,348 +0,0 @@
-package gov.nih.nci.evs.restapi.util;
-
-import java.io.*;
-import java.text.*;
-import java.util.*;
-
-public class HTMLTable {
-    static String NCIT_URL = "https://nciterms.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=NCI_Thesaurus&&ns=ncit&code=";
-
-    public static String hyperlink(String url, String code) {
-		return "" + code + "";
-	}
-
-	public static String generate(Vector v) {
-		char delim = searchDelimiter(v);
-		return generate(v, delim);
-	}
-
-	public static String generate(Vector v, char delim) {
-		String title = null;
-		String table = null;
-		String outputfile = null;
-		PrintWriter pw = null;
-		Vector th_vec = null;
-		String th = null;
-		Vector data_vec = new Vector();
-		String footer = null;
-		for (int i=0; i") != -1) {
-				int n = t.indexOf("");
-				title = t.substring(n + "<title>".length(), t.length());
-				outputfile = title + ".html";
-				outputfile = outputfile.replace("/", "_");
-				try {
-					pw = new PrintWriter(outputfile, "UTF-8");
-				} catch (Exception ex) {
-				    ex.printStackTrace();
-				}
-                printHeader(pw, title);
-				table = null;
-			} else if (t.startsWith("<table>")) {
-				table = t.substring("<table>".length(), t.length());
-				th_vec = new Vector();
-			} else if (t.startsWith("<th>")) {
-				th = t.substring("<th>".length(), t.length());
-				th_vec.add(th);
-			} else if (t.startsWith("<data>")) {
-				data_vec = new Vector();
-			} else if (t.startsWith("</table>")) {
-				printTable(pw, table, th_vec, data_vec, delim);
-				table = null;
-                th_vec = new Vector();
-				data_vec = new Vector();
-			} else if (t.startsWith("<footer>")) {
-				footer = t.substring("<footer>".length(), t.length());
-			} else {
-				if (t.indexOf("</data>") == -1) {
-					data_vec.add(t);
-				}
-			}
-		}
-		try {
-			printFooter(pw, footer);
-			pw.close();
-			System.out.println("Output file " + outputfile + " generated.");
-		} catch (Exception ex) {
-			ex.printStackTrace();
-		}
-
-		return outputfile;
-	}
-
-	public static void printBanner(PrintWriter out) {
-		out.println("<div>");
-		out.println("  <img");
-		out.println("      src=\"https://nciterms.nci.nih.gov/ncitbrowser/images/evs-logo-swapped.gif\"");
-		out.println("      alt=\"EVS Logo\"");
-		out.println("      width=\"100%\"");
-		out.println("      height=\"26\"");
-		out.println("      border=\"0\"");
-		out.println("      usemap=\"#external-evs\"");
-		out.println("  />");
-		out.println("  <map id=\"external-evs\" name=\"external-evs\">");
-		out.println("    <area");
-		out.println("        shape=\"rect\"");
-		out.println("        coords=\"0,0,140,26\"");
-		out.println("        href=\"/ncitbrowser/start.jsf\"");
-		out.println("        target=\"_self\"");
-		out.println("        alt=\"NCI Term Browser\"");
-		out.println("    />");
-		out.println("    <area");
-		out.println("        shape=\"rect\"");
-		out.println("        coords=\"520,0,941,26\"");
-		out.println("        href=\"http://evs.nci.nih.gov/\"");
-		out.println("        target=\"_blank\"");
-		out.println("        alt=\"Enterprise Vocabulary Services\"");
-		out.println("    />");
-		out.println("  </map>");
-		out.println("</div>");
-	}
-
-    public static void printHeader(PrintWriter out, String pageTitle) {
-		out.println("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\">");
-		out.println("<html xmlns:c=\"http://java.sun.com/jsp/jstl/core\">");
-		out.println("<head>");
-		out.println("<title>" + pageTitle + "");
-		out.println("");
-		out.println("");
-		out.println("");
-		out.println("");
-		out.println("");
-		out.println("");
-		out.println("");
-		out.println(" ");
-		out.println("
    ");
-		out.println("  ");
-		out.println("    ");
-		out.println("  ");
-		out.println("
    ");
-		out.println("");
-		out.println("");
-
-		printBanner(out);
-
-		out.println("");
-		out.println("");
-		out.println("
    ");
-		out.println("
    " + pageTitle + "
    ");
-		out.println("
    ");
-		String today = StringUtils.getToday("MM-dd-yyyy");
-		out.println("
    (Last modified: " + today + ")
    ");
-		out.println("
    ");
-		out.println("
    ");
-	}
-
-	public static boolean isWideField(String th) {
-		th = th.toLowerCase();
-		if (th.indexOf("label") != -1 || th.indexOf("term") != -1
-		   || th.indexOf("name") != -1 || th.indexOf("description") != -1
-		   || th.indexOf("definition") != -1) {
-			return true;
-		}
-		return false;
-	}
-
-	public static int calculateWideFieldWidth(int numFields, int numWideFields) {
-		int total = 100;
-		int width = 10;
-		int remaining_width = 100 - 10 * (numFields - numWideFields);
-		return (int) (remaining_width / numWideFields + 0.5);
-	}
-
-	public static int getWidth(int numFields, int numWideFields, String th) {
-		if (!isWideField(th)) return 10;
-		return calculateWideFieldWidth(numFields, numWideFields);
-	}
-
-	public static char searchDelimiter(Vector data_vec) {
-		for (int i=0; i");
-		out.println("
    ");
-		out.println("
    " + tableLabel + "
    ");
-		out.println("");
-        out.println("");
-		for (int i=0; i");
-			out.println(th);
-			out.println("");
-		}
-		out.println("");
-
-		for (int i=0; i");
-			//Vector u = StringUtils.parseData(data, '\t');
-			Vector u = StringUtils.parseData(data, delim);
-
-			for (int j=0; j");
-				out.println(value);
-				out.println("");
-			}
-			out.println("");
-		}
-		out.println("
    ");
-		out.println("
    ");
-		out.println("");
-	}
-
-
-    public static void printFooter(PrintWriter out) {
-		printFooter(out, null);
-	}
-
-	public static boolean isCode(String t) {
-		if (t == null) return false;
-		if (t.length() == 0) return false;
-		char c = t.charAt(0);
-		if (c != 'C') return false;
-		String s = t.substring(1, t.length());
-		try {
-			int value = Integer.parseInt(s);
-		} catch (Exception ex) {
-			return false;
-		}
-		return true;
-	}
-
-
-    public static void printFooter(PrintWriter out, String footer) {
-		out.println("
    ");
-        out.println("

    ");
-        out.println("

    ");
-        out.println("
    ");
-		if(footer != null) {
-			out.println(footer);
-		}
-		out.println("
    ");
-		out.println("");
-		out.println("");
-    }
-
-	public void generateHTMLPage(String filename) {
-		String hyperlink_url = NCIT_URL;
-		generateHTMLPage(filename, hyperlink_url);
-	}
-
-	public void generateHTMLPage(String filename, String hyperlink_url) {
-        Vector w1 = Utils.readFile(filename);
-        Vector w = new Vector();
-		for (int i=1; i" + title);
-			pw.println("" + table);
-			for (int i=0; i" + th);
-			}
-			pw.println("");
-			for (int i=1; i");
-			pw.println("
    ");
-
-			pw.println("