Bugfix genome caching

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AlignerIndexUtil.java

@@ -184,7 +184,7 @@ public static void saveCachedIndex(boolean hasCachedIndex, PipelineContext ctx,
 
                 lockFile.delete();
 
-                ReferenceGenomeManager.get().markGenomeModified(genome);
+                ReferenceGenomeManager.get().markGenomeModified(genome, ctx.getLogger());
             }
             catch (IOException e)
             {

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/ReferenceGenomeManager.java

@@ -57,12 +57,13 @@ private boolean isUpToDate(ReferenceGenome genome)
         long lastUpdated = localFile.lastModified();
         long lastSync = remoteFile.lastModified();
 
-        return lastUpdated >= lastSync;
+        return lastSync >= lastUpdated;
     }
 
-    public void markGenomeModified(ReferenceGenome genome) throws IOException
+    public void markGenomeModified(ReferenceGenome genome, Logger log) throws IOException
     {
         File toUpdate = getLocalUpdateFile(genome);
+        log.info("Marking genome as modified: " + toUpdate.getPath());
         FileUtils.touch(toUpdate);
     }
 

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

@@ -384,7 +384,7 @@ public RecordedActionSet run() throws PipelineJobException
             getJob().getLogger().info("creation complete");
 
             ReferenceGenome rg = SequenceAnalysisService.get().getReferenceGenome(rowId, getJob().getUser());
-            ReferenceGenomeManager.get().markGenomeModified(rg);
+            ReferenceGenomeManager.get().markGenomeModified(rg, getJob().getLogger());
 
             Set<GenomeTrigger> triggers = new HashSet<>(getPipelineJob().getExtraTriggers());
             if (getPipelineJob().isSkipTriggers())

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

@@ -143,7 +143,7 @@ public RecordedActionSet run() throws PipelineJobException
             }
 
             final int trackId = addTrackForLibrary(getPipelineJob().getTrack(), getPipelineJob().getTrackName(), getPipelineJob().getTrackDescription(), action);
-            ReferenceGenomeManager.get().markGenomeModified(SequenceAnalysisService.get().getReferenceGenome(getPipelineJob().getLibraryId(), getJob().getUser()));
+            ReferenceGenomeManager.get().markGenomeModified(SequenceAnalysisService.get().getReferenceGenome(getPipelineJob().getLibraryId(), getJob().getUser()), getJob().getLogger());
 
             Set<GenomeTrigger> triggers = SequenceAnalysisServiceImpl.get().getGenomeTriggers();
             if (!triggers.isEmpty())