Merge discvr-20.7 to develop

mGAP/resources/etls/prime-seq.xml

@@ -87,6 +87,7 @@
                     <column>dbSnpId</column>
                     <column>jbrowseId</column>
                     <column>variantTable</column>
+                    <column>gtf/DataFileUrl</column>
                     <column>liftedVcfId/dataid/DataFileUrl</column>
                     <column>liftedVcfId/name</column>
                     <column>liftedVcfId/library_id/name</column>

mGAP/resources/views/geneSearch.html

@@ -136,7 +136,7 @@
                             }
 
                             this.searchNames(loc).then(function (loc, callee) {
-                                var url = loc.location ? loc.location.ref + ':' + loc.location.start + '..' + loc.location.end : null;
+                                var url = loc && loc.location ? loc.location.ref + ':' + loc.location.start + '..' + loc.location.end : null;
 
                                 if (!loc) {
                                     alert('Coordinates not found for this location.');

mGAP/src/org/labkey/mgap/mGAPController.java

@@ -478,47 +478,69 @@ public void setRequestIds(int[] requestIds)
         }
     }
 
+    private static Map<String, Object> getReleaseRow(User u, ReleaseForm form, Errors errors)
+    {
+        TableInfo ti = DbSchema.get(mGAPSchema.NAME, DbSchemaType.Module).getTable(mGAPSchema.TABLE_VARIANT_CATALOG_RELEASES);
+        Map<String, Object> row = new TableSelector(ti, new SimpleFilter(FieldKey.fromString("rowId"), form.getReleaseId()), null).getMap();
+        if (row == null)
+        {
+            errors.reject(ERROR_MSG, "Unknown release: " + form.getReleaseId());
+            return null;
+        }
+
+        Container rowContainer = ContainerManager.getForId((String)row.get("container"));
+        if (rowContainer == null)
+        {
+            errors.reject(ERROR_MSG, "Unknown row container: " + form.getReleaseId());
+            return null;
+        }
+        else if (!rowContainer.hasPermission(u, ReadPermission.class))
+        {
+            throw new UnauthorizedException("Cannot read the folder: " + rowContainer.getPath());
+        }
+
+        return row;
+    }
+
+    private static SequenceOutputFile getOutputFile(Map<String, Object> row, ReleaseForm form, Errors errors)
+    {
+        SequenceOutputFile so = SequenceOutputFile.getForId((Integer)row.get("vcfId"));
+        if (so == null)
+        {
+            errors.reject(ERROR_MSG, "Unknown VCF file ID: " + form.getReleaseId());
+            return null;
+        }
+        else if (so.getFile() == null || !so.getFile().exists())
+        {
+            errors.reject(ERROR_MSG, "VCF file does not exist: " + (so.getFile() == null ? form.getReleaseId() : so.getFile().getPath()));
+            return null;
+        }
+
+        return so;
+    }
+
     @RequiresPermission(ReadPermission.class)
     @IgnoresTermsOfUse
     public static class DownloadBundleAction extends ExportAction<DownloadBundleForm>
     {
         public void export(DownloadBundleForm form, HttpServletResponse response, BindException errors) throws Exception
         {
-            TableInfo ti = DbSchema.get(mGAPSchema.NAME, DbSchemaType.Module).getTable(mGAPSchema.TABLE_VARIANT_CATALOG_RELEASES);
-            Map<String, Object> row = new TableSelector(ti, new SimpleFilter(FieldKey.fromString("rowId"), form.getReleaseId()), null).getMap();
-            if (row == null)
+            Map<String, Object> row = getReleaseRow(getUser(), form, errors);
+            if (errors.hasErrors())
             {
-                errors.reject(ERROR_MSG, "Unknown release: " + form.getReleaseId());
                 return;
             }
 
-            Container rowContainer = ContainerManager.getForId((String)row.get("container"));
-            if (rowContainer == null)
+            SequenceOutputFile so = getOutputFile(row, form, errors);
+            if (errors.hasErrors())
             {
-                errors.reject(ERROR_MSG, "Unknown row container: " + form.getReleaseId());
                 return;
             }
-            else if (!rowContainer.hasPermission(getUser(), ReadPermission.class))
-            {
-                throw new UnauthorizedException("Cannot read the folder: " + rowContainer.getPath());
-            }
 
             Set<File> toZip = new HashSet<>();
             String zipName = "mGap_VariantCatalog_v" + FileUtil.makeLegalName((String)row.get("version"));
             zipName = zipName.replaceAll(" ", "_");
 
-            SequenceOutputFile so = SequenceOutputFile.getForId((Integer)row.get("vcfId"));
-            if (so == null)
-            {
-                errors.reject(ERROR_MSG, "Unknown VCF file ID: " + form.getReleaseId());
-                return;
-            }
-            else if (so.getFile() == null || !so.getFile().exists())
-            {
-                errors.reject(ERROR_MSG, "VCF file does not exist: " + (so.getFile() == null ? form.getReleaseId() : so.getFile().getPath()));
-                return;
-            }
-
             toZip.add(so.getFile());
             toZip.add(new File(so.getFile().getPath() + ".tbi"));
 
@@ -558,10 +580,9 @@ else if (so.getFile() == null || !so.getFile().exists())
         }
     }
 
-    public static class DownloadBundleForm
+    public static class ReleaseForm
     {
         private Integer _releaseId;
-        private Boolean _includeGenome;
 
         public Integer getReleaseId()
         {
@@ -572,6 +593,11 @@ public void setReleaseId(Integer releaseId)
         {
             _releaseId = releaseId;
         }
+    }
+
+    public static class DownloadBundleForm extends ReleaseForm
+    {
+        private Boolean _includeGenome;
 
         public Boolean getIncludeGenome()
         {

mGAP/src/org/labkey/mgap/pipeline/AnnotationStep.java

@@ -439,6 +439,7 @@ private File runCassandra(File liftedToGRCh37, File finalOutput, VariantProcessi
         }
 
         output.addIntermediateFile(liftedToGRCh37Unzipped);
+        output.addIntermediateFile(new File(liftedToGRCh37Unzipped.getPath() + ".idx"));
         output.addIntermediateFile(liftedToGRCh37UnzippedDone);
 
         cassRunner.execute(liftedToGRCh37Unzipped, finalOutput, extraArgs);

tcrdb/resources/web/tcrdb/panel/PoolImportPanel.js

@@ -1008,7 +1008,7 @@ Ext4.define('TCRdb.panel.PoolImportPanel', {
     },
 
     getStimKey: function(data){
-        return [data.stimId, data.animalId, data.stim, data.treatment, data.tissue].join('|');
+        return [data.stimId, data.animalId, data.stim, data.treatment, data.tissue, (Ext4.isDate(data.sampleDate) ? Ext4.Date.format(data.sampleDate, 'Y-m-d') : data.sampleDate)].join('|');
     },
 
     getSortKey: function(data){

tcrdb/src/org/labkey/tcrdb/TCRdbTableCustomizer.java

@@ -101,6 +101,7 @@ private void customizeCdnas(AbstractTableInfo ti)
     private void customizeSorts(AbstractTableInfo ti)
     {
         LDKService.get().applyNaturalSort(ti, "plateId");
+        LDKService.get().applyNaturalSort(ti, "hto");
 
         String name = "numLibraries";
         if (ti.getColumn(name) == null)

tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerSeuratHandler.java

@@ -415,7 +415,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                 IOUtil.copyFile(gtfFile, gtfCopy);
                 ctx.getFileManager().addIntermediateFile(gtfCopy);
 
-                writer.println("gtfFile <- " + gtfCopy.getName());
+                writer.println("gtfFile <- '" + gtfCopy.getName() + "'");
 
                 String mergeMethod = StringUtils.trimToNull(ctx.getParams().optString("mergeMethod"));
                 mergeMethod = mergeMethod == null ? "NULL" : "'" + mergeMethod + "'";