Misc debugging updates

Author: bbimber

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

@@ -307,7 +307,7 @@ public void liftOverVcf(JobContext ctx, ReferenceGenome targetGenome, ReferenceG
             else
             {
                 SelectVariantsWrapper wrapper = new SelectVariantsWrapper(job.getLogger());
-                wrapper.execute(sourceGenome.getWorkingFastaFile(), currentVCF, outputFile, List.of("--sites_only"));
+                wrapper.execute(sourceGenome.getWorkingFastaFile(), currentVCF, outputFile, List.of("--sites-only-vcf-output"));
             }
             currentVCF = outputFile;
 

SequenceAnalysis/src/org/labkey/sequenceanalysis/util/ChainFileValidator.java

@@ -301,11 +301,11 @@ public void exec(ResultSet rs) throws SQLException
                     // Always store the numeric version, if present:
                     if (name.startsWith("chr0"))
                     {
-                        cachedReferences.put(name.replaceAll("chr0", ""), name);
+                        cachedReferences.put(name.replaceFirst("chr0", ""), name);
                     }
                     else if (name.startsWith("chr"))
                     {
-                        cachedReferences.put(name.replaceAll("chr", ""), name);
+                        cachedReferences.put(name.replaceFirst("chr", ""), name);
                     }
 
                     if (StringUtils.trimToNull(rs.getString("genbank")) != null)

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

@@ -544,7 +544,7 @@ private JSONObject getVcfTrack(Logger log, ExpData targetFile, ReferenceGenome r
                 JSONObject json = getExtraTrackConfig();
                 if (json != null && json.has("additionalFeatureMsg"))
                 {
-                    getJSONObject("renderer").put("message", json.getString("message"));
+                    getJSONObject("renderer").put("message", json.getString("additionalFeatureMsg"));
                 }
             }});
         }});

singlecell/api-src/org/labkey/api/singlecell/pipeline/AbstractSingleCellPipelineStep.java

@@ -29,7 +29,9 @@
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 import java.util.stream.Collectors;
 
 abstract public class AbstractSingleCellPipelineStep extends AbstractPipelineStep implements SingleCellStep
@@ -89,6 +91,7 @@ public Output execute(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWra
         try (CSVReader reader = new CSVReader(Readers.getReader(tracker), '\t'))
         {
             String[] line;
+            Set<String> encounteredFiles = new HashSet<>();
             while ((line = reader.readNext()) != null)
             {
                 File f = new File(ctx.getOutputDir(), line[2]);
@@ -97,6 +100,14 @@ public Output execute(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWra
                     throw new PipelineJobException("File not found: " + f.getPath());
                 }
 
+                String key = line[0] + " / " + line[1] + " / "+ f.getName() + " / " + line[3] + " / " + line[4];
+                if (encounteredFiles.contains(key))
+                {
+                    ctx.getLogger().error("Duplicate output found: " + key);
+                    continue;
+                }
+                encounteredFiles.add(key);
+
                 getPipelineCtx().getLogger().debug("Output seurat: " + line[0] + " / " + line[1] + " / "+ f.getName() + " / " + line[3] + " / " + line[4]);
 
                 String outputIdVal = "NA".equals(line[3]) ? null : StringUtils.trimToNull(line[3]);

singlecell/resources/chunks/Functions.R

@@ -70,11 +70,13 @@ file.create('/work/savedSeuratObjects.txt')
 print(paste0('Total lines in savedSeuratObjects.txt on job start:', length(readLines('savedSeuratObjects.txt'))))
 
 saveData <- function(seuratObj, datasetId) {
+    message(paste0('Saving dataset: ', datasetId, ' with ', ncol(seuratObj), ' cells'))
     print(paste0('Saving dataset: ', datasetId))
     print(seuratObj)
 
     datasetIdForFile <- makeLegalFileName(datasetId)
     fn <- paste0(outputPrefix, '.', datasetIdForFile, '.seurat.rds')
+    message(paste0('Filename: ', fn))
 
     message(paste0('Saving RDS file: ', fn, ' with ', ncol(seuratObj), ' cells'))
     barcodeFile <- paste0(outputPrefix, '.', datasetIdForFile, '.cellBarcodes.csv')