Merge 2.2.0 changes into master

.gitignore

@@ -29,3 +29,5 @@ log
 src/main/bin/NCIT_HISTORY/
 report.html
 gradle.lockfile
+/.apt_generated/
+/.apt_generated_tests/

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

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)

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 

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::<YOUR_AWS_ACCOUNT_ID>:user/<YOUR_IAM_USERNAME>"
+  },
+  "Action": [
+    "es:ESHttpPut",
+    "es:admin/cluster/settings/update"
+  ],
+  "Resource": "arn:aws:es:<YOUR_AWS_REGION>:<YOUR_AWS_ACCOUNT_ID>:domain/<YOUR_DOMAIN_NAME>/*"
+}
+```
+
 ## References
 
 * Documentation - https://opensearch.org/docs/latest/

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"

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