Dap4 package purge

build.gradle

@@ -192,7 +192,7 @@ dependencies {
     providedCompile group: 'org.apache.tomcat', name: 'catalina', version: '6.0.53'
     providedCompile group: 'javax.servlet', name: 'javax.servlet-api', version: '3.0.1'
     providedCompile group: 'javax.servlet', name: 'javax.servlet-api', version: '3.1.0'
-    providedCompile group: 'javax.xml.bind', name: 'jaxb-api', version: '2.3.0'
+    // providedCompile group: 'javax.xml.bind', name: 'jaxb-api', version: '2.3.0'
 
     implementation group: 'org.jdom', name: 'jdom', version: '1.1.3'
 
@@ -246,16 +246,16 @@ dependencies {
 
 
     // implementation group: 'javax.xml.bind', name: 'jaxb-api', version: '2.3.1'
-    implementation group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '2.3.6'
-    implementation group: 'javax.annotation', name: 'javax.annotation-api', version: '1.3.2'
-    implementation group: 'javax.activation', name: 'activation', version: '1.1.1'
+    //implementation group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '2.3.6'
+    //implementation group: 'javax.annotation', name: 'javax.annotation-api', version: '1.3.2'
+    //implementation group: 'javax.activation', name: 'activation', version: '1.1.1'
 
-    implementation group: 'org.jvnet.jaxb2_commons', name: 'jaxb2-basics-runtime', version: '0.11.0'
-    implementation group: 'com.sun.xml.bind', name: 'jaxb-api', version: '2.3.1'
-    implementation group: 'com.sun.xml.bind', name: 'jaxb-core', version: '2.3.0-b170127.1453'
-    implementation group: 'com.sun.xml.bind', name: 'jaxb-impl', version: '2.3.0-b170127.1453'
+    //implementation group: 'org.jvnet.jaxb2_commons', name: 'jaxb2-basics-runtime', version: '0.11.0'
+    //implementation group: 'com.sun.xml.bind', name: 'jaxb-api', version: '2.3.1'
+    //implementation group: 'com.sun.xml.bind', name: 'jaxb-core', version: '2.3.0-b170127.1453'
+    //implementation group: 'com.sun.xml.bind', name: 'jaxb-impl', version: '2.3.0-b170127.1453'
 
-    implementation group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.10.5.1'
+    //implementation group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.10.5.1'
     implementation group: 'io.netty', name: 'netty-codec', version: '4.1.68.Final'
 
     implementation group: 'xerces', name: 'xercesImpl', version: '2.12.2'

build.xml

@@ -309,6 +309,7 @@
 
     <property name="joda-time.lib" value="joda-time-2.12.7.jar"/>
 
+    <!--
     <property name="jaxb-api.lib" value="jaxb-api-2.3.1.jar"/>
     <property name="jaxb-core.lib" value="jaxb-core-2.3.0-b170127.1453.jar"/>
     <property name="jaxb-impl.lib" value="jaxb-impl-2.3.0-b170127.1453.jar"/>
@@ -317,6 +318,7 @@
     <property name="javax.activation.lib" value="activation-1.1.1.jar"/>
 
     <property name="xlink.lib" value="xlink-v_1_0-1.4.0.jar"/>
+    -->
 
     <!-- Cloudwatch logback appender -->
     <property name="cloudwatch-logback-appender.lib" value="cloudwatch-logback-appender-3.11.jar"/>
@@ -358,24 +360,27 @@
         <include name="${aws-java-sdk-ec2.lib}"/>
         <include name="${aws-java-sdk-logs.lib}"/>
 
+        <!--
         <include name="${jackson-core.lib}"/>
         <include name="${jackson-databind.lib}"/>
         <include name="${jackson-annotations.lib}"/>
-
+        -->
         <include name="${java-jwt.lib}"/>
         <include name="${jwks-rsa.lib}"/>
 
         <include name="${joda-time.lib}"/>
 
         <include name="${urlRewrite.lib}"/>
 
+        <!--
         <include name="${jaxb-api.lib}"/>
         <include name="${jaxb-core.lib}"/>
         <include name="${jaxb-impl.lib}"/>
         <include name="${jaxb-runtime.lib}"/>
         <include name="${javax.annotation-api.lib}"/>
         <include name="${javax.activation.lib}"/>
         <include name="${xlink.lib}"/>
+        -->
     </fileset>
     <!--
         These are the library jars used by Hyrax.

dmrppJoinExisiting.xml

@@ -298,7 +298,7 @@ located identified in the arguments. Run this target with no arguments to see th
 Use -DARGS="..." to specify command line options."
              depends="compile ">
 
-        <java classname="opendap.dap4.DmrppJoinExistingAggregator"
+        <java classname="opendap.dap4.dmrpp.DmrppJoinExistingAggregator"
               fork="true"
               maxmemory="4096m"
               dir="${build.run}" >

src/opendap/dap4/DmrppAggException.java → src/opendap/dap4/dmrpp/DmrppAggException.java

@@ -1,6 +1,6 @@
-package opendap.dap4;
+package opendap.dap4.dmrpp;
 
 import java.lang.Exception;
 
 public class DmrppAggException extends Exception {
 

src/opendap/dap4/DmrppJoinExistingAggregator.java → src/opendap/dap4/dmrpp/DmrppJoinExistingAggregator.java

@@ -23,7 +23,7 @@
  * // You can contact OPeNDAP, Inc. at PO Box 112, Saunderstown, RI. 02874-0112.
  * /////////////////////////////////////////////////////////////////////////////
  */
-package opendap.dap4;
+package opendap.dap4.dmrpp;
 
 import ch.qos.logback.classic.Level;
 import opendap.logging.LogUtil;
@@ -152,7 +152,7 @@
             else {
                 log.debug("Ingesting ListFile: {}", listFileName);
                 BufferedReader reader=null;
                 try{
                     reader = new BufferedReader(new FileReader(listFileName));
                     String value = reader.readLine();
                     while(value!=null){
@@ -179,7 +179,7 @@
      * @throws MalformedURLException
      * @throws DmrppAggException
      */
     public void ingestDmrppList(ArrayList<String> dmrpp_urls) throws IOException, DmrppAggException {
 
         for(String dmrppUrl: dmrpp_urls){
             String targetUrl;
@@ -213,7 +213,7 @@
         }
 
             /*
         if(dmrpp_urls.size()>1) {
         }
         else if(dmrpp_urls.size()==1){
             File arg0 = new File(dmrpp_urls.iterator().next());
@@ -290,8 +290,8 @@
 
         if(log.isDebugEnabled()) {
             XMLOutputter xmlo = new XMLOutputter(Format.getPrettyFormat());
             for (String aggVarName : templateVars.keySet()) {
                 Element aggVarElement = templateVars.get(aggVarName);
                 log.debug("aggVar:\n{}", xmlo.outputString(aggVarElement));
             }
         }
@@ -304,7 +304,7 @@
      * @param chunkIndex
      * @throws DmrppAggException
      */
     public void ingestAggDataset(Document datasetDoc, int chunkIndex) throws DmrppAggException, IOException {
 
         Element datasetElement = datasetDoc.getRootElement();
         String s = datasetElement.getAttributeValue(DMRPP.HREF,DMRPP.NS);
@@ -327,7 +327,7 @@
         @SuppressWarnings("unchecked")
         List<Element> dapObjects = container.getChildren();
         for(Element dapObject:dapObjects){
             String aggVarName = getFQN(dapObject);
             log.debug("Begin processing {}",aggVarName);
             if (dapObject.getName().equals(DAP4.GROUP)){
                 aggContainer(dapObject, dataURL, chunkIndex);
@@ -584,7 +584,7 @@
             while(dims.hasNext()){
                 Element dim = dims.next();
                 String dimName = dim.getAttributeValue(DAP4.NAME);
                 String dimSize = dim.getAttributeValue(DAP4.SIZE);
 
                 if(dimName==null){
                     // Handle anonymous dimensions
@@ -755,14 +755,14 @@
 
                         if (tChunkDimSizesElement == null) {
                             // This is a simple hack one dimensional variables with a single chunk.
                             tChunkDimSizesElement = hack_simple_var_chunks(childFQN, chunksElement);
                             //chunksElement.addContent(0, tChunkDimSizesElement);
                         }
                         for (Element chunkElement : chunkElements) {
                             String chunkPositionInArray = chunkElement.getAttributeValue(DMRPP.CHUNK_POSITION_IN_ARRAY);
                             if (chunkPositionInArray != null) {
                                 // Took this out, looks like a no-op
                                 // chunkElement.setAttribute(DMRPP.CHUNK_POSITION_IN_ARRAY, chunkPositionInArray.replaceFirst("\\[0,", "[0,"));
                                 String href = chunkElement.getAttributeValue(DMRPP.HREF);
                                 if (href == null) {
                                     if (dataURL == null) {
@@ -770,7 +770,7 @@
                                                 "Both the Dataset and the Chunk are missing a " + DMRPP.HREF + " attribute.";
                                         throw new DmrppAggException(sb);
                                     }
                                     chunkElement.setAttribute(DMRPP.HREF, dataURL.toString());
                                 }
                             }
                             else if(chunkElements.size()==1){
@@ -811,7 +811,7 @@
      * @param var
      * @return
      */
     public String getFQN(Element var){
 
         if(var.getName().equals(DAP4.DIM) && var.getNamespace()==DAP4.NS){
             String name = var.getAttributeValue(DAP4.NAME);
@@ -821,7 +821,7 @@
             return name;
         }
 
         ArrayList<String> name_fields = new ArrayList<>();
         name_fields.add(var.getAttributeValue(DAP4.NAME));
 
         Element parentElement = var.getParentElement();
@@ -862,7 +862,7 @@
         log = (Logger) LoggerFactory.getLogger(opendap.xml.Util.class);
         log.setLevel(Level.ERROR);
         /*
         Iterator<Appender<ILoggingEvent>> it = log.iteratorForAppenders();
         while (it.hasNext()) {
             Appender<ILoggingEvent> app = it.next();
             System.out.println( app.getName() );

src/opendap/dap4/DmrppJoinNewAggregator.java → src/opendap/dap4/dmrpp/DmrppJoinNewAggregator.java

@@ -23,7 +23,7 @@
  * // You can contact OPeNDAP, Inc. at PO Box 112, Saunderstown, RI. 02874-0112.
  * /////////////////////////////////////////////////////////////////////////////
  */
-package opendap.dap4;
+package opendap.dap4.dmrpp;
 
 import ch.qos.logback.classic.Level;
 import opendap.bes.BadConfigurationException;
@@ -116,7 +116,7 @@
             }
             else {
                 BufferedReader reader=null;
                 try{
                     reader = new BufferedReader(new FileReader(listFileName));
                     String value = reader.readLine();
                     while(value!=null){
@@ -628,9 +628,9 @@
      * @param var
      * @return
      */
     public String getFQN(Element var){
 
         ArrayList<String> name_fields = new ArrayList<>();
         name_fields.add(var.getAttributeValue(DAP4.NAME));
 
         Element parentElement = var.getParentElement();
@@ -680,7 +680,7 @@
             //---------------------------
             // Debug control
             if (cmd.hasOption("d")) {
                 debugLevel = Level.ALL;
             }
 
             //---------------------------