Partial upgrade of libsedml, fixed cli plot bugs

.github/workflows/ci_cd.yml

@@ -184,9 +184,9 @@ jobs:
             mvn --batch-mode clean install dependency:copy-dependencies -Dgroups="${{ matrix.test-group }}"
           fi
 
-#      - name: Setup tmate session
-#        uses: mxschmitt/action-tmate@v3
-#        if: ${{ failure() }}
+      - name: Setup tmate session
+        uses: mxschmitt/action-tmate@v3
+        if: ${{ failure() }}
 
   CD:
     name: CD

vcell-api/src/main/java/org/vcell/rest/server/RestDatabaseService.java

@@ -40,7 +40,7 @@
 import org.vcell.sbml.OmexPythonUtils;
 import org.vcell.sedml.ModelFormat;
 import org.vcell.sedml.PublicationMetadata;
-import org.vcell.sedml.SEDMLExporter;
+import org.vcell.sedml.SedMLExporter;
 import org.vcell.util.*;
 import org.vcell.util.document.*;
 
@@ -466,7 +466,7 @@ public String query(BiomodelVCMLServerResource resource, User vcellUser) throws
 		return vcmlBigString.toString();
 	}
 
-	public ByteArrayRepresentation query(BiomodelOMEXServerResource resource, User vcellUser, boolean bSkipUnsupported, StringBuffer suggestedProjectName) throws SQLException, DataAccessException, XmlParseException, IOException, SEDMLExporter.SEDMLExportException, OmexPythonUtils.OmexValidationException {
+	public ByteArrayRepresentation query(BiomodelOMEXServerResource resource, User vcellUser, boolean bSkipUnsupported, StringBuffer suggestedProjectName) throws SQLException, DataAccessException, XmlParseException, IOException, SedMLExporter.SEDMLExportException, OmexPythonUtils.OmexValidationException {
 		if (vcellUser == null) {
 			vcellUser = VCellApiApplication.DUMMY_USER;
 		}
@@ -487,7 +487,7 @@ public ByteArrayRepresentation query(BiomodelOMEXServerResource resource, User v
 
 		Predicate<SimulationContext> simContextFilter = (SimulationContext sc) -> true;
 		if (bSkipUnsupported) {
-			Map<String, String> unsupportedApplications = SEDMLExporter.getUnsupportedApplicationMap(bioModel, modelFormat);
+			Map<String, String> unsupportedApplications = SedMLExporter.getUnsupportedApplicationMap(bioModel, modelFormat);
 			simContextFilter = (SimulationContext sc) -> !unsupportedApplications.containsKey(sc.getName());
 		}
 		String filenamePrefix = "VCDB_"+bioModelKey;
@@ -498,7 +498,7 @@ public ByteArrayRepresentation query(BiomodelOMEXServerResource resource, User v
 		suggestedProjectName.append(filenamePrefix);
 		try {
 			boolean bCreateOmexArchive = true;
-			SEDMLExporter.writeBioModel(bioModel, publicationMetadata, exportOmexFile, modelFormat, simContextFilter,
+			SedMLExporter.writeBioModel(bioModel, publicationMetadata, exportOmexFile, modelFormat, simContextFilter,
 					bHasPython, bRoundTripSBMLValidation, bCreateOmexArchive);
 			byte[] omexFileBytes = Files.readAllBytes(exportOmexFile.toPath());
 			return new ByteArrayRepresentation(omexFileBytes, BiomodelOMEXResource.OMEX_MEDIATYPE);

vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java

@@ -141,7 +141,8 @@ public void executeArchive(boolean isBioSimSedml) throws BiosimulationsHdfWriter
 
     private void executeSedmlDocument(String sedmlLocation, HDF5ExecutionResults cumulativeHdf5Results) throws IOException, PreProcessingException, ExecutionException {
         BiosimulationLog.instance().updateSedmlDocStatusYml(sedmlLocation, BiosimulationLog.Status.QUEUED);
-        SedmlJob job = new SedmlJob(sedmlLocation, this.omexHandler, this.inputFile, this.outputDir, this.sedmlPath2d3d.toString(), this.cliRecorder, this.bKeepTempFiles, this.bExactMatchOnly, this.bSmallMeshOverride, this.logOmexMessage);
+        SedMLJob job = new SedMLJob(sedmlLocation, this.omexHandler, this.inputFile, this.outputDir, this.sedmlPath2d3d.toString(), this.cliRecorder, this.bKeepTempFiles, this.bExactMatchOnly, this.bSmallMeshOverride);
+        this.logOmexMessage.append("Processing ").append(job.SEDML_NAME).append(". ");
         SedmlStatistics stats = job.preProcessDoc();
         boolean hasSucceeded = job.simulateSedml(cumulativeHdf5Results);
         this.anySedmlDocumentHasSucceeded |= hasSucceeded;

vcell-cli/src/main/java/org/vcell/cli/run/RunUtils.java

@@ -14,8 +14,15 @@
 import org.apache.commons.lang.StringUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
-import org.jlibsedml.DataSet;
+import org.jlibsedml.components.SId;
+import org.jlibsedml.components.SedBase;
+import org.jlibsedml.components.SedML;
+import org.jlibsedml.components.dataGenerator.DataGenerator;
+import org.jlibsedml.components.output.DataSet;
 import org.jlibsedml.*;
+import org.jlibsedml.components.output.Output;
+import org.jlibsedml.components.output.Report;
+import org.jlibsedml.components.simulation.UniformTimeCourse;
 import org.vcell.cli.run.results.ValueHolder;
 import org.vcell.sbml.vcell.lazy.LazySBMLNonSpatialDataAccessor;
 import org.vcell.util.DataAccessException;
@@ -146,10 +153,11 @@ public static double[] interpLinear(double[] x, double[] y, double[] xi) throws
         return yi;
     }
 
-    public static HashMap<String, File> generateReportsAsCSV(SedML sedml, Map<DataGenerator, ValueHolder<LazySBMLNonSpatialDataAccessor>> organizedNonSpatialResults, File outDirForCurrentSedml) {
+    public static HashMap<SId, File> generateReportsAsCSV(SedMLDataContainer sedmlContainer, Map<DataGenerator, ValueHolder<LazySBMLNonSpatialDataAccessor>> organizedNonSpatialResults, File outDirForCurrentSedml) {
         // finally, the real work
-        HashMap<String, File> reportsHash = new HashMap<>();
-        for (Output sedmlOutput : sedml.getOutputs()) {
+        SedML sedML = sedmlContainer.getSedML();
+        HashMap<SId, File> reportsHash = new HashMap<>();
+        for (Output sedmlOutput : sedML.getOutputs()) {
             // We only want Reports
             if (!(sedmlOutput instanceof Report sedmlReport)) {
                 if (logger.isDebugEnabled()) logger.info("Ignoring unsupported output `" + sedmlOutput.getId() + "` while CSV generation.");
@@ -168,11 +176,11 @@ public static HashMap<String, File> generateReportsAsCSV(SedML sedml, Map<DataGe
              * * we search the sbml model to find the vcell variable name associated with the urn
              */
             try {
-                List<DataSet> datasets = sedmlReport.getListOfDataSets();
+                List<DataSet> datasets = sedmlReport.getDataSets();
                 Map<DataSet, DataGenerator> dataGeneratorMapping = new LinkedHashMap<>();
                 for (DataSet dataset : datasets) {
-                    DataGenerator referencedGenerator = sedml.getDataGeneratorWithId(dataset.getDataReference());
-                    if (referencedGenerator == null) throw new NullPointerException("SedML DataGenerator referenced by report is missing!");
+                    DataGenerator referencedGenerator = sedmlContainer.findDataGeneratorById(dataset.getDataReference());
+                    if (null == referencedGenerator) throw new IllegalArgumentException("Unable to find data generator referenced in dataset: " + dataset.getDataReference());
                     if (!organizedNonSpatialResults.containsKey(referencedGenerator)) break;
                     dataGeneratorMapping.put(dataset, referencedGenerator);
                 }
@@ -184,22 +192,22 @@ public static HashMap<String, File> generateReportsAsCSV(SedML sedml, Map<DataGe
 
                 for (DataSet validDataSet: dataGeneratorMapping.keySet()) {
                     DataGenerator referencedGenerator = dataGeneratorMapping.get(validDataSet);
-                    boolean isReservedVCellPrefix = validDataSet.getId().startsWith("__vcell_reserved_data_set_prefix__");
+                    boolean isReservedVCellPrefix = validDataSet.getId().string().startsWith("__vcell_reserved_data_set_prefix__");
                     ValueHolder<LazySBMLNonSpatialDataAccessor> dataHolder = organizedNonSpatialResults.get(referencedGenerator);
 
 
                     boolean timeAlreadyIncluded = false;
                     int numTrials = dataHolder.listOfResultSets.size();
                     for(int i = 0; i < numTrials; i++) {
                         if (timeAlreadyIncluded) break;
-                        if (validDataSet.getId().contains("time_")) timeAlreadyIncluded = true;
+                        if (validDataSet.getId().string().contains("time_")) timeAlreadyIncluded = true;
                         LazySBMLNonSpatialDataAccessor data = dataHolder.listOfResultSets.get(i);
 
-                        String formattedId = isReservedVCellPrefix ? "VCell::" + validDataSet.getId().substring(34) : validDataSet.getId();
+                        String formattedId = isReservedVCellPrefix ? "VCell::" + validDataSet.getId().string().substring(34) : validDataSet.getId().string();
                         sb.append(RunUtils.generateCsvItem(formattedId, ',', false, i, numTrials));
                         sb.append(RunUtils.generateCsvItem(validDataSet.getLabel(), ',', true, i, numTrials));
                         String referencedGeneratorName = referencedGenerator.getName() == null ? "" : referencedGenerator.getName();
-                        sb.append(RunUtils.generateCsvItem(referencedGeneratorName.isEmpty() ? referencedGenerator.getId() : referencedGenerator.getName(), ',', true, i, numTrials));
+                        sb.append(RunUtils.generateCsvItem(referencedGeneratorName.isEmpty() ? referencedGenerator.getId().string() : referencedGenerator.getName(), ',', true, i, numTrials));
                         String[] dataStrings = Arrays.stream(data.getData().data()).boxed().map(String::valueOf).toArray(String[]::new);
                         sb.append(String.join(",", dataStrings)).append('\n');
                     } // end of trials loop
@@ -240,9 +248,9 @@ public static void zipResFiles(File dirFile) throws IOException {
 
         // TODO: Add SED-ML name as base dirFile to avoid zipping all available CSV, PDF
         // Map for naming to extension
-        Map<String, String> extensionListMap = new HashMap<String, String>() {{
-            put("csv", "reports.zip");
-            put("pdf", "plots.zip");
+        Map<String, String> extensionListMap = new HashMap<>() {{
+            this.put("csv", "reports.zip");
+            this.put("pdf", "plots.zip");
         }};
 
         for (String ext : extensionListMap.keySet()) {