Merge 26.3 to 26.7

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

@@ -44,6 +44,7 @@
 import java.nio.file.DirectoryStream;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.time.LocalDate;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -81,25 +82,32 @@ public String getName()
         return "DeleteSequenceAnalysisArtifacts";
     }
 
+    private int _jobId = -1;
+
     // NOTE: if there is a more direct way to locate the JobID this hack should be replaced
     private void checkJobCancelled(Logger log)
     {
-        // Make the assumption there is only one active maintenance job at a time:
-        SimpleFilter filter = new SimpleFilter(FieldKey.fromString("description"), SYSTEM_MAINTENANCE_DESCRIPTION).
-                addCondition(FieldKey.fromString("container"), ContainerManager.getRoot().getId()).
-                addCondition(FieldKey.fromString("modified"), new Date(), CompareType.DATE_EQUAL);
-        int rowId = new TableSelector(DbSchema.get("pipeline", DbSchemaType.Module).getTable(JOB_TABLE), PageFlowUtil.set("RowId", "Status"), filter, null).getMapCollection().stream().filter(map -> {
-            String val = String.valueOf(map.get("status"));
-            return val != null && (val.toLowerCase().startsWith(PipelineJob.TaskStatus.cancelling.name()) || val.toLowerCase().startsWith(PipelineJob.TaskStatus.running.name()));
-        }).map(rs -> Integer.parseInt(String.valueOf(rs.get("rowid")))).max(Integer::compareTo).orElse(-1);
-
-        if (rowId == -1)
+        if (_jobId == -1)
         {
-            log.warn("Unable to find rowId for job", new Exception("Unable to find rowId for job"));
-            return;
+            // Make the assumption there is only one active maintenance job at a time:
+            SimpleFilter filter = new SimpleFilter(FieldKey.fromString("description"), SYSTEM_MAINTENANCE_DESCRIPTION).
+                    addCondition(FieldKey.fromString("container"), ContainerManager.getRoot().getId()).
+                    addCondition(FieldKey.fromString("modified"), LocalDate.now().minusDays(2), CompareType.DATE_GTE);
+            int rowId = new TableSelector(DbSchema.get("pipeline", DbSchemaType.Module).getTable(JOB_TABLE), PageFlowUtil.set("RowId", "Status"), filter, null).getMapCollection().stream().filter(map -> {
+                String val = String.valueOf(map.get("status"));
+                return val != null && (val.toLowerCase().startsWith(PipelineJob.TaskStatus.cancelling.name()) || val.toLowerCase().startsWith(PipelineJob.TaskStatus.running.name()));
+            }).map(rs -> Integer.parseInt(String.valueOf(rs.get("rowid")))).max(Integer::compareTo).orElse(-1);
+
+            if (rowId == -1)
+            {
+                log.warn("Unable to find rowId for job", new Exception("Unable to find rowId for job"));
+                return;
+            }
+
+            _jobId = rowId;
         }
 
-        PipelineStatusFile sf = PipelineService.get().getStatusFile(rowId);
+        PipelineStatusFile sf = PipelineService.get().getStatusFile(_jobId);
         if (PipelineJob.TaskStatus.cancelling.name().equalsIgnoreCase(sf.getStatus()))
         {
             throw new CancelledException();

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/PrintReadBackedHaplotypesHandler.java

@@ -90,6 +90,12 @@ public boolean doSplitJobs()
         return true;
     }
 
+    @Override
+    public boolean supportsSraArchivedData()
+    {
+        return true;
+    }
+
     public class Processor implements SequenceOutputProcessor
     {
         @Override
@@ -99,7 +105,7 @@ public void init(JobContext ctx, List<SequenceOutputFile> inputFiles, List<Recor
             {
                 if (so.getReadset() != null)
                 {
-                    ctx.getSequenceSupport().cacheReadset(so.getReadset(), ctx.getJob().getUser());
+                    ctx.getSequenceSupport().cacheReadset(so.getReadset(), ctx.getJob().getUser(), true);
                 }
                 else
                 {
@@ -148,7 +154,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                     args.addAll(extraArgs);
                 }
 
-                File output = new File(ctx.getWorkingDirectory(), FileUtil.getBaseName(input) + ".txt");
+                File output = FileUtil.appendName(ctx.getWorkingDirectory(), FileUtil.getBaseName(input) + ".txt");
                 Wrapper wrapper = new Wrapper(ctx.getLogger());
                 wrapper.execute(input, ctx.getSequenceSupport().getCachedGenome(so.getLibrary_id()).getWorkingFastaFile(), output, args);
 

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/SnpEffWrapper.java

@@ -145,8 +145,14 @@ else if ("gbk".equalsIgnoreCase(ext))
 
         try
         {
-            Files.createSymbolicLink(FileUtil.appendName(genomeDir, "sequences.fa").toPath(), genome.getSourceFastaFile().toPath());
-            Files.createSymbolicLink(FileUtil.appendName(genomeDir, "genes." + ext).toPath(), genes.toPath());
+            if (!FileUtil.appendName(genomeDir, "sequences.fa").exists())
+            {
+                Files.createSymbolicLink(FileUtil.appendName(genomeDir, "sequences.fa").toPath(), genome.getSourceFastaFile().toPath());
+            }
+            if (!FileUtil.appendName(genomeDir, "genes." + ext).exists())
+            {
+                Files.createSymbolicLink(FileUtil.appendName(genomeDir, "genes." + ext).toPath(), genes.toPath());
+            }
         }
         catch (IOException e)
         {