Prevent unnecessary exception when seurat pipeline doesnt create new outputs

Author: bbimber

singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java

@@ -1440,9 +1440,14 @@ public File subsetBarcodes(File allCellBarcodes, @Nullable String barcodePrefix)
     }
 
     public File getCellBarcodesFromSeurat(File seuratObj)
+    {
+        return getCellBarcodesFromSeurat(seuratObj, true);
+    }
+
+    public File getCellBarcodesFromSeurat(File seuratObj, boolean throwIfNotFound)
     {
         File barcodes = new File(seuratObj.getParentFile(), seuratObj.getName().replaceAll("seurat.rds", "cellBarcodes.csv"));
-        if (!barcodes.exists())
+        if (throwIfNotFound && !barcodes.exists())
         {
             throw new IllegalArgumentException("Unable to find expected cell barcodes file.  This might indicate the seurat object was created with an older version of the pipeline.  Expected: " + barcodes.getPath());
         }
@@ -1451,9 +1456,14 @@ public File getCellBarcodesFromSeurat(File seuratObj)
     }
 
     public File getMetaTableFromSeurat(File seuratObj)
+    {
+        return getCellBarcodesFromSeurat(seuratObj, true);
+    }
+
+    public File getMetaTableFromSeurat(File seuratObj, boolean throwIfNotFound)
     {
         File barcodes = new File(seuratObj.getParentFile(), seuratObj.getName().replaceAll("seurat.rds", "seurat.meta.txt"));
-        if (!barcodes.exists())
+        if (throwIfNotFound && !barcodes.exists())
         {
             throw new IllegalArgumentException("Unable to find expected metadata file.  This might indicate the seurat object was created with an older version of the pipeline.  Expected: " + barcodes.getPath());
         }

singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java

@@ -516,8 +516,8 @@ else if (step.createsSeuratObjects())
                     ctx.getLogger().debug("Removing intermediate file: " + seurat.getFile().getPath());
                     ctx.getFileManager().removeIntermediateFile(seurat.getFile());
                     _resumer.getFileManager().removeIntermediateFile(seurat.getFile());
-                    _resumer.getFileManager().removeIntermediateFile(CellHashingServiceImpl.get().getCellBarcodesFromSeurat(seurat.getFile()));
-                    _resumer.getFileManager().removeIntermediateFile(CellHashingServiceImpl.get().getMetaTableFromSeurat(seurat.getFile()));
+                    _resumer.getFileManager().removeIntermediateFile(CellHashingServiceImpl.get().getCellBarcodesFromSeurat(seurat.getFile(), false));
+                    _resumer.getFileManager().removeIntermediateFile(CellHashingServiceImpl.get().getMetaTableFromSeurat(seurat.getFile(), false));
                 }
             }