Revert "Changes to fix nonspatial data set in biosim mode"

This reverts commit 429aee0.

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

@@ -389,7 +389,7 @@ private void generateHDF5(SolverHandler solverHandler, HDF5ExecutionResults mast
 
         Hdf5DataExtractor hdf5Extractor = new Hdf5DataExtractor(this.sedml, solverHandler.taskToTempSimulationMap, this.RESULTS_DIRECTORY_PATH);
 
-        Hdf5DataContainer partialHdf5File = hdf5Extractor.extractHdf5RelevantData(solverHandler.nonSpatialResults, solverHandler.spatialResults, masterHdf5File.isBioSimHdf5);
+        Hdf5DataContainer partialHdf5File = hdf5Extractor.extractHdf5RelevantData(solverHandler.nonSpatialResults, solverHandler.spatialResults);
         masterHdf5File.addResults(this.sedml, partialHdf5File);
 
         for (File tempH5File : solverHandler.spatialResults.values()) {

vcell-cli/src/main/java/org/vcell/cli/run/hdf5/Hdf5DataPreparer.java

@@ -124,7 +124,7 @@ public static Hdf5PreparedData prepareNonspatialData(Hdf5SedmlResults datasetWra
         List<Long> dataDimensionList = new LinkedList<>();
 
         Hdf5SedmlResultsNonspatial dataSourceNonspatial = (Hdf5SedmlResultsNonspatial) datasetWrapper.dataSource;
-        Map<DataSet, List<double[]>> dataSetMap = dataSourceNonspatial.dataItems.getDataSetMappings(report);
+        Map<DataSet, List<double[]>> dataSetMap = dataSourceNonspatial.allJobResults;
         numDataSets = dataSetMap.keySet().size();
 
         for (DataSet dataSet : dataSetMap.keySet()){
@@ -150,7 +150,7 @@ public static Hdf5PreparedData prepareNonspatialData(Hdf5SedmlResults datasetWra
         int bufferOffset = 0;
 
         for (DataSet dataSet : dataSetMap.keySet()) {
-            List<double[]> dataArrays = dataSourceNonspatial.dataItems.get(report, dataSet);
+            List<double[]> dataArrays = dataSourceNonspatial.allJobResults.get(dataSet);
             for (double[] dataArray : dataArrays){
                 if (dataArray.length < numTimePoints){
                     double[] paddedArray = new double[Math.toIntExact(numTimePoints)];

vcell-cli/src/main/java/org/vcell/cli/run/hdf5/Hdf5SedmlResultsNonspatial.java

@@ -14,6 +14,6 @@ public Hdf5SedmlResultsNonspatial() {}
     /**
      * Map of all data contained within a job relevant to HDF5 formatted files
      */
-    public NonspatialDataMapping dataItems = new NonspatialDataMapping();
+    public Map<DataSet, List<double[]>> allJobResults = new LinkedHashMap<>();
 
 }

vcell-cli/src/main/java/org/vcell/cli/run/hdf5/NonspatialResultsConverter.java

@@ -174,11 +174,11 @@ public static Map<Report, List<Hdf5SedmlResults>> convertNonspatialResultsToSedm
             for (DataSet dataSet : dataSetValues.keySet()){
                 NonspatialValueHolder dataSetValuesSource = dataSetValues.get(dataSet);
 
-                dataSourceNonspatial.dataItems.put(report, dataSet, new LinkedList<>());
+                dataSourceNonspatial.allJobResults.put(dataSet, new LinkedList<>());
                 dataSourceNonspatial.scanBounds = dataSetValuesSource.vcSimulation.getMathOverrides().getScanBounds();
                 dataSourceNonspatial.scanParameterNames = dataSetValuesSource.vcSimulation.getMathOverrides().getScannedConstantNames();
                 for (double[] data : dataSetValuesSource.listOfResultSets) {
-                    dataSourceNonspatial.dataItems.get(report, dataSet).add(data);
+                    dataSourceNonspatial.allJobResults.get(dataSet).add(data);
                     shapes.add(Integer.toString(data.length));
                 }
 

vcell-cli/src/test/java/org/vcell/cli/run/hdf5/Hdf5WriterTest.java

@@ -20,14 +20,9 @@ public class Hdf5WriterTest {
 
     public static HDF5ExecutionResults createExampleData() {
 
-        Report plotReport = new Report("report0", "Plot Report");
-        Report reportReport = new Report("report1", "Report Report");
-
         DataSet t = new DataSet("t","t","t","#null");
         DataSet s0 = new DataSet("s0","s0","s0","#null");
         DataSet s1 = new DataSet("s1", "s1", "s1","#null");
-        plotReport.addDataSet(t); plotReport.addDataSet(s0); plotReport.addDataSet(s1);
-        reportReport.addDataSet(t); reportReport.addDataSet(s0); reportReport.addDataSet(s1);
 
         Hdf5SedmlMetadata plotMetadata = new Hdf5SedmlMetadata();
         plotMetadata._type = "SedPlot2D";
@@ -63,31 +58,33 @@ public static HDF5ExecutionResults createExampleData() {
         plotDataSourceNonspatial.scanBounds = new int[0];
         plotDataSourceNonspatial.scanParameterNames = new String[0];
         plotDatasetWrapper.dataSource = plotDataSourceNonspatial;
-        plotDataSourceNonspatial.dataItems.put(plotReport, t, Arrays.asList(row_t));
-        plotDataSourceNonspatial.dataItems.put(plotReport, s0, Arrays.asList(row_S0_0));
-        plotDataSourceNonspatial.dataItems.put(plotReport, s1, Arrays.asList(row_S1));
+        Map<DataSet, List<double[]>> plotJob = new LinkedHashMap<>();
+        plotJob.put(t, Arrays.asList(row_t));
+        plotJob.put(s0, Arrays.asList(row_S0_0));
+        plotJob.put(s1, Arrays.asList(row_S1));
+        plotDataSourceNonspatial.allJobResults = plotJob;
+
 
         Hdf5SedmlResults reportDatasetWrapper = new Hdf5SedmlResults();
         reportDatasetWrapper.datasetMetadata = reportMetadata;
         Hdf5SedmlResultsNonspatial reportDataSourceNonspatial = new Hdf5SedmlResultsNonspatial();
         reportDataSourceNonspatial.scanBounds = new int[] { 2 }; // zero indexed? 
         reportDataSourceNonspatial.scanParameterNames = new String[] { "k1" };
         reportDatasetWrapper.dataSource = reportDataSourceNonspatial;
-        reportDataSourceNonspatial.dataItems.put(reportReport, t, Arrays.asList(row_t, row_t, row_t));
-        reportDataSourceNonspatial.dataItems.put(reportReport, s0, Arrays.asList(row_S0_0, row_S0_1, row_S0_2));
-        reportDataSourceNonspatial.dataItems.put(reportReport, s1, Arrays.asList(row_S1, row_S1, row_S1));
+        Map<DataSet, List<double[]>> reportJob = new LinkedHashMap<>();
+        reportJob.put(t, Arrays.asList(row_t, row_t, row_t));
+        reportJob.put(s0, Arrays.asList(row_S0_0, row_S0_1, row_S0_2));
+        reportJob.put(s1, Arrays.asList(row_S1, row_S1, row_S1));
+        reportDataSourceNonspatial.allJobResults = reportJob;
 
         Hdf5DataContainer hdf5FileWrapper = new Hdf5DataContainer();
-        String uri1 = "___0_export_NO_scan_test_1.sedml";
-        String uri2 = "___0_export_NO_scan_test_2.sedml";
-        List<Hdf5SedmlResults> wrappers1 = new ArrayList<>();
-        List<Hdf5SedmlResults> wrappers2 = new ArrayList<>();
-        wrappers1.add(plotDatasetWrapper);
-        wrappers2.add(reportDatasetWrapper);
-        hdf5FileWrapper.reportToUriMap.put(plotReport, uri1);
-        hdf5FileWrapper.reportToUriMap.put(reportReport, uri2);
-        hdf5FileWrapper.reportToResultsMap.put(plotReport, wrappers1);
-        hdf5FileWrapper.reportToResultsMap.put(reportReport, wrappers2);
+        Report report = new Report("simId","simName");
+        String uri = "___0_export_NO_scan_test.sedml";
+        List<Hdf5SedmlResults> wrappers = new ArrayList<>();
+        wrappers.add(plotDatasetWrapper);
+        wrappers.add(reportDatasetWrapper);
+        hdf5FileWrapper.reportToUriMap.put(report, uri);
+        hdf5FileWrapper.reportToResultsMap.put(report, wrappers);
 
         HDF5ExecutionResults results = new HDF5ExecutionResults(true);
         results.addResults(null, hdf5FileWrapper);