Always overwrite scripts

Author: bbimber

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

@@ -237,20 +237,13 @@ protected void executeR(SequenceOutputHandler.JobContext ctx, File rmd, String o
     public static void executeR(SequenceOutputHandler.JobContext ctx, String dockerContainerName, String outputPrefix, List<String> lines) throws PipelineJobException
     {
         File localRScript = new File(ctx.getOutputDir(), outputPrefix + ".R");
-        if (!localRScript.exists())
+        try (PrintWriter writer = PrintWriters.getPrintWriter(localRScript))
         {
-            try (PrintWriter writer = PrintWriters.getPrintWriter(localRScript))
-            {
-                lines.forEach(writer::println);
-            }
-            catch (IOException e)
-            {
-                throw new PipelineJobException(e);
-            }
+            lines.forEach(writer::println);
         }
-        else
+        catch (IOException e)
         {
-            ctx.getLogger().info("R script exists, re-using: " + localRScript.getPath());
+            throw new PipelineJobException(e);
         }
 
         File localBashScript = new File(ctx.getOutputDir(), "dockerWrapper.sh");

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

@@ -1111,10 +1111,11 @@ public File ensureLocalCopy(File input, File outputDir, Logger log, Set<File> to
             try
             {
                 //needed for docker currently
-                log.debug("Copying file to working directory: " + input.getName());
+                log.debug("Copying file to working directory: " + input.getPath());
                 File dest = new File(outputDir, input.getName());
                 if (dest.exists())
                 {
+                    log.debug("deleting existing folder: " + dest.getPath());
                     if (input.isDirectory())
                     {
                         FileUtils.deleteDirectory(dest);
@@ -1224,33 +1225,26 @@ private File generateCellHashingCalls(File citeSeqCountOutDir, File outputDir, S
         File metricsFile = getMetricsFile(callsFile);
 
         File localRScript = new File(outputDir, "generateCallsWrapper.R");
-        if (!localRScript.exists())
+        try (PrintWriter writer = PrintWriters.getPrintWriter(localRScript))
         {
-            try (PrintWriter writer = PrintWriters.getPrintWriter(localRScript))
-            {
-                List<String> methodNames = parameters.methods.stream().map(Enum::name).collect(Collectors.toList());
+            List<String> methodNames = parameters.methods.stream().map(Enum::name).collect(Collectors.toList());
 
-                String cellbarcodeWhitelist = "";
-                if (cellBarcodeWhitelistFile != null)
-                {
-                    cellbarcodeWhitelist = "'/work/" + cellBarcodeWhitelistFile.getName() + "'";
-                }
+            String cellbarcodeWhitelist = "";
+            if (cellBarcodeWhitelistFile != null)
+            {
+                cellbarcodeWhitelist = "'/work/" + cellBarcodeWhitelistFile.getName() + "'";
+            }
 
-                Set<String> allowableBarcodes = parameters.getAllowableBarcodeNames();
-                String allowableBarcodeParam = allowableBarcodes != null ? "c('" + StringUtils.join(allowableBarcodes, "','") + "')" : "NULL";
+            Set<String> allowableBarcodes = parameters.getAllowableBarcodeNames();
+            String allowableBarcodeParam = allowableBarcodes != null ? "c('" + StringUtils.join(allowableBarcodes, "','") + "')" : "NULL";
 
-                writer.println("f <- cellhashR::CallAndGenerateReport(rawCountData = '/work/" + citeSeqCountOutDir.getName() + "', reportFile = '/work/" + htmlFile.getName() + "', callFile = '/work/" + callsFile.getName() + "', metricsFile = '/work/" + metricsFile.getName() + "', cellbarcodeWhitelist  = " + cellbarcodeWhitelist + ", barcodeWhitelist = " + allowableBarcodeParam + ", title = '" + parameters.getReportTitle() + "', methods = c('" + StringUtils.join(methodNames, "','") + "'))");
-                writer.println("print('Rmarkdown complete')");
+            writer.println("f <- cellhashR::CallAndGenerateReport(rawCountData = '/work/" + citeSeqCountOutDir.getName() + "', reportFile = '/work/" + htmlFile.getName() + "', callFile = '/work/" + callsFile.getName() + "', metricsFile = '/work/" + metricsFile.getName() + "', cellbarcodeWhitelist  = " + cellbarcodeWhitelist + ", barcodeWhitelist = " + allowableBarcodeParam + ", title = '" + parameters.getReportTitle() + "', methods = c('" + StringUtils.join(methodNames, "','") + "'))");
+            writer.println("print('Rmarkdown complete')");
 
-            }
-            catch (IOException e)
-            {
-                throw new PipelineJobException(e);
-            }
         }
-        else
+        catch (IOException e)
         {
-            log.info("script exists, re-using: " + localRScript.getPath());
+            throw new PipelineJobException(e);
         }
 
         File localBashScript = new File(outputDir, "generateCallsDockerWrapper.sh");