Gzip metadata for seurat objects

Author: bbimber

singlecell/resources/chunks/Functions.R

@@ -81,7 +81,7 @@ saveData <- function(seuratObj, datasetId) {
 
     logger::log_info(paste0('Saving RDS file: ', fn, ' with ', ncol(seuratObj), ' cells'))
     barcodeFile <- paste0(outputPrefix, '.', datasetIdForFile, '.cellBarcodes.csv')
-    metaFile <- paste0(outputPrefix, '.', datasetIdForFile, '.seurat.meta.txt')
+    metaFile <- paste0(outputPrefix, '.', datasetIdForFile, '.seurat.meta.txt.gz')
 
     saveRDS(seuratObj, file = fn)
 

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

@@ -1573,7 +1573,7 @@ public File getMetaTableFromSeurat(File seuratObj)
 
     public File getMetaTableFromSeurat(File seuratObj, boolean throwIfNotFound)
     {
-        File barcodes = new File(seuratObj.getParentFile(), seuratObj.getName().replaceAll("seurat.rds$", "seurat.meta.txt"));
+        File barcodes = new File(seuratObj.getParentFile(), seuratObj.getName().replaceAll("seurat.rds$", "seurat.meta.txt.gz"));
         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/pipeline/singlecell/UpdateSeuratPrototype.java

@@ -15,6 +15,7 @@
 import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler;
 import org.labkey.api.singlecell.pipeline.SeuratToolParameter;
 import org.labkey.api.singlecell.pipeline.SingleCellStep;
+import org.labkey.singlecell.CellHashingServiceImpl;
 import org.labkey.singlecell.SingleCellSchema;
 
 import java.io.File;
@@ -140,6 +141,24 @@ public Output execute(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWra
             }
 
             FileUtils.moveFile(wrapper.getFile(), toReplace);
+
+            // Also metadata:
+            File meta = CellHashingServiceImpl.get().getMetaTableFromSeurat(wrapper.getFile());
+            File metaOrig = CellHashingServiceImpl.get().getMetaTableFromSeurat(toReplace);
+            if (metaOrig.exists())
+            {
+                metaOrig.delete();
+            }
+            FileUtils.moveFile(meta, metaOrig);
+
+            // Also cellbarcodes:
+            File cellbarcodes = CellHashingServiceImpl.get().getCellBarcodesFromSeurat(wrapper.getFile());
+            File cellbarcodesOrig = CellHashingServiceImpl.get().getCellBarcodesFromSeurat(toReplace);
+            if (cellbarcodesOrig.exists())
+            {
+                cellbarcodesOrig.delete();
+            }
+            FileUtils.moveFile(cellbarcodes, cellbarcodesOrig);
         }
         catch (IOException e)
         {