Cleanup getters on RefNtSequenceModel so InputStream not opened by Table.update()

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/RefNtSequenceModel.java

@@ -26,6 +26,7 @@
 import org.labkey.api.data.Table;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
+import org.labkey.api.data.Transient;
 import org.labkey.api.exp.api.DataType;
 import org.labkey.api.exp.api.ExpData;
 import org.labkey.api.exp.api.ExperimentService;
@@ -116,8 +117,8 @@ public void setName(String name)
         _name = name;
     }
 
-    public @Nullable
-    InputStream getSequenceInputStream() throws IOException
+    @Nullable @Transient
+    public InputStream getSequenceInputStream() throws IOException
     {
         if (_sequenceFile != null)
         {
@@ -150,6 +151,7 @@ public String getLegacySequence()
         return _sequence;
     }
 
+    @Transient
     public String getSequence()
     {
         //resolve from cached file
@@ -388,6 +390,7 @@ public void setDisabledby(String disabledby)
         _disabledby = disabledby;
     }
 
+    @Transient
     public byte[] getSequenceBases()
     {
         if (_sequenceBytes == null)

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceIntegrationTests.java

@@ -690,12 +690,12 @@ protected static void doCleanup(String projectName)
             Container project = ContainerManager.getForPath(projectName);
             if (project != null)
             {
-                File _pipelineRoot = PipelineService.get().getPipelineRootSetting(project).getRootPath();
+                File pipelineRoot = PipelineService.get().getPipelineRootSetting(project).getRootPath();
                 try
                 {
-                    if (_pipelineRoot.exists())
+                    if (pipelineRoot.exists())
                     {
-                        File[] contents = _pipelineRoot.listFiles();
+                        File[] contents = pipelineRoot.listFiles();
                         for (File f : contents)
                         {
                             if (f.exists())

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ProcessVariantsHandler.java

@@ -402,22 +402,16 @@ public static File processVCF(File input, Integer libraryId, JobContext ctx, Res
                 action.addInput(vcfIdx, "Input VCF Index");
             }
 
-            if (!currentVCF.equals(input))
+            if (!URIUtil.isDescendant(ctx.getOutputDir().toURI(), currentVCF.toURI()))
             {
-                if (!URIUtil.isDescendant(ctx.getOutputDir().toURI(), currentVCF.toURI()))
-                {
-                    ctx.getLogger().info("VCF is not a descendent of the output directory, will not add as intermediate file: " + currentVCF.getPath());
-                }
-                else
-                {
-                    resumer.getFileManager().addIntermediateFile(currentVCF);
-                    resumer.getFileManager().addIntermediateFile(vcfIdx);
-                }
+                ctx.getLogger().info("VCF is not a descendent of the output directory, will not add as intermediate file: " + currentVCF.getPath());
             }
             else
             {
-                ctx.getLogger().info("ending VCF same as input, will not add as intermediate file: " + input.getPath());
+                resumer.getFileManager().addIntermediateFile(currentVCF);
+                resumer.getFileManager().addIntermediateFile(vcfIdx);
             }
+
             ReferenceGenome genome = ctx.getSequenceSupport().getCachedGenome(libraryId);
             action.addInput(genome.getSourceFastaFile(), "Reference FASTA");