Bugfixes around JBrowse and lucene indexes

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/RestoreSraDataHandler.java

@@ -307,15 +307,18 @@ public void complete(PipelineJob job, List<Readset> readsets, List<SequenceOutpu
                     boolean hasMetrics = new TableSelector(SequenceAnalysisSchema.getTable(SequenceAnalysisSchema.TABLE_QUALITY_METRICS), PageFlowUtil.set("RowId"), filter, null).exists();
                     if (!hasMetrics)
                     {
+                        job.getLogger().debug("No existing metrics found for: " + rd.getFileId1());
                         List<Integer> toAdd = new ArrayList<>(rd.getFileId1());
                         if (rd.getFileId2() != null)
                         {
                             toAdd.add(rd.getFileId2());
                         }
 
+                        job.getLogger().debug("adding metrics for " + toAdd.size() + " total fastq files");
                         for (int dataId : toAdd)
                         {
                             //then delete/add:
+                            job.getLogger().debug("adding metrics for: " + dataId);
                             ReadsetCreationTask.addQualityMetricsForReadset(rs, dataId, job, true);
                         }
                     }
@@ -332,15 +335,22 @@ public void complete(PipelineJob job, List<Readset> readsets, List<SequenceOutpu
                 }
             }
 
-            Container target = job.getContainer().isWorkbook() ? job.getContainer().getParent() : job.getContainer();
-            TableInfo ti = QueryService.get().getUserSchema(job.getUser(), target, SequenceAnalysisSchema.SCHEMA_NAME).getTable(SequenceAnalysisSchema.TABLE_READ_DATA);
-            try
+            if (!rows.isEmpty())
             {
-                ti.getUpdateService().updateRows(job.getUser(), target, rows, rows, null, null);
+                Container target = job.getContainer().isWorkbook() ? job.getContainer().getParent() : job.getContainer();
+                TableInfo ti = QueryService.get().getUserSchema(job.getUser(), target, SequenceAnalysisSchema.SCHEMA_NAME).getTable(SequenceAnalysisSchema.TABLE_READ_DATA);
+                try
+                {
+                    ti.getUpdateService().updateRows(job.getUser(), target, rows, rows, null, null);
+                }
+                catch (InvalidKeyException | BatchValidationException | QueryUpdateServiceException | SQLException e)
+                {
+                    throw new PipelineJobException(e);
+                }
             }
-            catch (InvalidKeyException | BatchValidationException | QueryUpdateServiceException | SQLException e)
+            else
             {
-                throw new PipelineJobException(e);
+                job.getLogger().debug("There were no readdata rows to update");
             }
         }
 

jbrowse/src/org/labkey/jbrowse/model/JsonFile.java

@@ -964,7 +964,8 @@ public File prepareResource(User u, Logger log, boolean throwIfNotPrepared, bool
             }
             else if (existingLuceneDir != null && existingLuceneDir.exists())
             {
-                if (doesLuceneIndexExist())
+                // Note: this could exist, but be an empty folder:
+                if (luceneDir.exists())
                 {
                     log.info("Deleting existing lucene index dir: " + luceneDir.getPath());
                     try
@@ -978,8 +979,16 @@ else if (existingLuceneDir != null && existingLuceneDir.exists())
                 }
 
                 log.debug("Creating symlink to existing index: " + existingLuceneDir.getPath());
+                log.debug("Symlink target: " + luceneDir.getPath());
+
                 try
                 {
+                    if (!luceneDir.getParentFile().exists())
+                    {
+                        log.debug("Creating parent directories: " + luceneDir.getParentFile().getPath());
+                        FileUtil.mkdirs(luceneDir.getParentFile());
+                    }
+
                     Files.createSymbolicLink(luceneDir.toPath(), existingLuceneDir.toPath());
                 }
                 catch (IOException e)