Update rsync target folder

Author: bbimber

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

@@ -90,6 +90,7 @@ public void cacheGenomeLocally(ReferenceGenome genome, Logger log) throws Pipeli
 
         File sourceDir = genome.getSourceFastaFile().getParentFile();
 
+        //Note: neither source nor dest have trailing slashes, so the entire source (i.e '128', gets synced into a subdir of dest)
         new SimpleScriptWrapper(log).execute(Arrays.asList(
                 "rsync", "-r", "-vi", "-a", "--delete", "--delete-excluded", "--no-owner", "--no-group", sourceDir.getPath(), localCacheDir.getPath()
         ));

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/AbstractGenomicsDBImportHandler.java

@@ -335,7 +335,7 @@ Set<String> getContigsInInputs(List<File> inputVCFs, Logger log) throws Pipeline
 
     private void copyToLevelFiles(PipelineJob job, File sourceWorkspace, File destinationWorkspace) throws IOException
     {
-        job.getLogger().info("Copying top-level files");
+        job.getLogger().info("Copying top-level files from: " + sourceWorkspace.getPath());
         for (String fn : Arrays.asList("callset.json", "vidmap.json", "vcfheader.vcf", "__tiledb_workspace.tdb"))
         {
             File source = new File(sourceWorkspace, fn);
@@ -537,8 +537,9 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                         else
                         {
                             ctx.getLogger().debug("Copying directory with rsync: " + sourceFolder.getPath());
+                            //NOTE: since neither path will end in slashes, rsync to the parent folder should result in the correct placement
                             new SimpleScriptWrapper(ctx.getLogger()).execute(Arrays.asList(
-                                    "rsync", "-r", "-vi", "-a", "--delete", "--delete-excluded", "--no-owner", "--no-group", sourceFolder.getPath(), destContigFolder.getPath()
+                                    "rsync", "-r", "-vi", "-a", "--delete", "--delete-excluded", "--no-owner", "--no-group", sourceFolder.getPath(), destContigFolder.getParentFile().getPath()
                             ));
                         }
 

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/GenotypeGVCFsWrapper.java

@@ -195,9 +195,10 @@ else if (f.isDirectory() && doneFile.exists())
                             }
                             else
                             {
+                                //NOTE: since neither path will end in slashes, rsync to the parent folder should result in the correct placement
                                 ctx.getLogger().debug("Copying directory with rsync: " + movedFile.getPath());
                                 new SimpleScriptWrapper(ctx.getLogger()).execute(Arrays.asList(
-                                    "rsync", "-r", "-vi", "-a", "--delete", "--delete-excluded", "--no-owner", "--no-group", f.getPath(), movedFile.getPath()
+                                    "rsync", "-r", "-vi", "-a", "--delete", "--delete-excluded", "--no-owner", "--no-group", f.getPath(), movedFile.getParentFile().getPath()
                                 ));
                             }