Added new test and correlated helper classes; need to test prototype …

…and confirm everything's working.
virtualcell · Aug 15, 2023 · 44a10c2 · 44a10c2
1 parent 381cb7b
commit 44a10c2
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diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/hdf5/Hdf5Writer.java b/vcell-cli/src/main/java/org/vcell/cli/run/hdf5/Hdf5Writer.java
@@ -72,7 +72,7 @@ public static void writeHdf5(Hdf5DataContainer hdf5DataWrapper, File outDirForCu
                         masterHdf5.insertNumericAttributes(currentDatasetId, "times", Hdf5DataPreparer.getSpatialHdf5Attribute_Times(data));
                     }  
                     masterHdf5.insertFixedStringAttribute(currentDatasetId, "_type", data.datasetMetadata._type);
-                    masterHdf5.insertFixedStringAttributes(currentDatasetId, "scanParameterNames", Arrays.asList(data.dataSource.scanParameterNames));
+                    //masterHdf5.insertFixedStringAttributes(currentDatasetId, "scanParameterNames", Arrays.asList(data.dataSource.scanParameterNames));
                     masterHdf5.insertFixedStringAttributes(currentDatasetId, "sedmlDataSetDataTypes", data.datasetMetadata.sedmlDataSetDataTypes);
                     masterHdf5.insertFixedStringAttributes(currentDatasetId, "sedmlDataSetIds", data.datasetMetadata.sedmlDataSetIds);
 

diff --git a/vcell-core/src/test/java/org/vcell/sbml/NightlyRoundTripVCMLFilenameFilter.java b/vcell-core/src/test/java/org/vcell/sbml/NightlyRoundTripVCMLFilenameFilter.java
@@ -0,0 +1,63 @@
+package org.vcell.sbml;
+
+import java.io.File;
+import java.io.FilenameFilter;
+import java.util.HashSet;
+import java.util.Set;
+
+public class NightlyRoundTripVCMLFilenameFilter implements FilenameFilter {
+
+    private static Set<String> exemptTests;
+
+    // Static Initializer, equivalent to a static "contractor"
+    static {
+        Set<String> superSet = new HashSet<>();
+        superSet.addAll(NightlyRoundTripVCMLFilenameFilter.slowTestSet());
+        superSet.addAll(NightlyRoundTripVCMLFilenameFilter.outOfMemorySet());
+        superSet.addAll(NightlyRoundTripVCMLFilenameFilter.largeFileSet());
+        NightlyRoundTripVCMLFilenameFilter.exemptTests = superSet;
+    }
+    @Override
+    public boolean accept(File dir, String name) {
+        return name.endsWith(".vcml") && !NightlyRoundTripVCMLFilenameFilter.exemptTests.contains(name);
+    }
+
+    static Set<String> slowTestSet() {
+        Set<String> slowModels = new HashSet<>();
+        slowModels.add("biomodel_101981216.vcml");    // 29s
+        slowModels.add("biomodel_147699816.vcml");    // 23s
+        slowModels.add("biomodel_17326658.vcml");     // 24s
+        slowModels.add("biomodel_188880263.vcml");    // 89s
+        slowModels.add("biomodel_200301029.vcml");    // 124s (and fails with java.lang.OutOfMemoryError: GC overhead limit exceeded)
+        slowModels.add("biomodel_200301683.vcml");    // 37s
+        slowModels.add("biomodel_28625786.vcml");     // 57s
+        slowModels.add("biomodel_34826524.vcml");     // 129s
+        slowModels.add("biomodel_47429473.vcml");     // 194s
+        slowModels.add("biomodel_59361239.vcml");     // 116s
+        slowModels.add("biomodel_60799209.vcml");     // 41s
+        slowModels.add("biomodel_61699798.vcml");     // 69s
+        slowModels.add("biomodel_62467093.vcml");     // 23s
+        slowModels.add("biomodel_62477836.vcml");     // 30s
+        slowModels.add("biomodel_62585003.vcml");     // 24s
+        slowModels.add("biomodel_66264206.vcml");     // 45s
+        slowModels.add("biomodel_93313420.vcml");     // 137s
+        slowModels.add("biomodel_9590643.vcml");      // 40s
+        return slowModels;
+    }
+
+    static Set<String> outOfMemorySet() {
+        Set<String> outOfMemoryModels = new HashSet<>();
+        outOfMemoryModels.add("biomodel_101963252.vcml"); // FAULT.JAVA_HEAP_SPACE
+        outOfMemoryModels.add("biomodel_200301029.vcml"); // FAULT.OUT_OF_MEMORY - GC Overhead Limit Exceeded (and 124s)
+        outOfMemoryModels.add("biomodel_26455186.vcml");  // FAULT.OUT_OF_MEMORY - GC Overhead Limit Exceeded
+        outOfMemoryModels.add("biomodel_27192647.vcml");  // FAULT.OUT_OF_MEMORY - GC Overhead Limit Exceeded
+        outOfMemoryModels.add("biomodel_27192717.vcml");  // FAULT.OUT_OF_MEMORY) - Java heap space: failed reallocation of scalar replaced objects
+        return outOfMemoryModels;
+    }
+
+    public static Set<String> largeFileSet() {
+        Set<String> largeFiles = new HashSet<>();
+        largeFiles.add("biomodel_101963252.vcml");
+        return largeFiles;
+    }
+}