Add action to manually create ExpData for file

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java

@@ -5293,4 +5293,62 @@ public void setDoNotRequireSra(boolean doNotRequireSra)
             _doNotRequireSra = doNotRequireSra;
         }
     }
+
+    @RequiresSiteAdmin
+    public static class CreateExpDataForFileAction extends ConfirmAction<CreateExpDataForFileForm>
+    {
+        @Override
+        public void validateCommand(CreateExpDataForFileForm form, Errors errors)
+        {
+
+        }
+
+        @Override
+        public URLHelper getSuccessURL(CreateExpDataForFileForm form)
+        {
+            return getContainer().getStartURL(getUser());
+        }
+
+        @Override
+        public ModelAndView getConfirmView(CreateExpDataForFileForm form, BindException errors) throws Exception
+        {
+            return new HtmlView(HtmlString.unsafe("This will create a new ExpData with a DataFileUrl pointing to the provided URI. This should be a full URI, such as file:///my/path/myFile.txt." +
+                    "<br><br>" +
+                    "<label>DataFileUrl </label><input name=\"dataFileUrl\" value = \"" + HtmlString.of(form.getDataFileUrl()) + "\"><br>"));
+        }
+
+        @Override
+        public boolean handlePost(CreateExpDataForFileForm form, BindException errors) throws Exception
+        {
+            URI newUri = URI.create(form.getDataFileUrl());
+            File f = new File(newUri);
+            if (!f.exists())
+            {
+                throw new PipelineJobException("Missing file: " + form.getDataFileUrl());
+            }
+
+            DataType dataType = new DataType("File");
+
+            ExpData d = ExperimentService.get().createData(getContainer(), dataType, f.getName());
+            d.setDataFileURI(newUri);
+            d.save(getUser());
+
+            return true;
+        }
+    }
+
+    public static class CreateExpDataForFileForm
+    {
+        private String _dataFileUrl;
+
+        public String getDataFileUrl()
+        {
+            return _dataFileUrl;
+        }
+
+        public void setDataFileUrl(String dataFileUrl)
+        {
+            _dataFileUrl = dataFileUrl;
+        }
+    }
 }

singlecell/src/org/labkey/singlecell/run/CellRangerVDJWrapper.java

@@ -3,7 +3,6 @@
 import au.com.bytecode.opencsv.CSVReader;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.lang3.stream.IntStreams;
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
@@ -524,9 +523,26 @@ private File processOutputsForType(String sampleId, Readset rs, ReferenceGenome
                 {
                     throw new PipelineJobException("Unable to find file: " + outputVloupe.getPath());
                 }
+                else
+                {
+                    if (isPrimaryDir)
+                    {
+                        try
+                        {
+
+                            getPipelineCtx().getLogger().debug("Creating empty vloupe file as placeholder: " + outputVloupe.getPath());
+                            FileUtils.touch(outputVloupe);
+                        }
+                        catch (IOException e)
+                        {
+                            throw new PipelineJobException(e);
+                        }
+                    }
+                }
             }
+
             // NOTE: only tag the vloupe file for a/b:
-            else if (isPrimaryDir)
+            if (isPrimaryDir)
             {
                 String versionString = "Version: " + getWrapper().getVersionString();
                 output.addSequenceOutput(outputVloupe, rs.getName() + " 10x VLoupe", VLOUPE_CATEGORY, rs.getRowId(), null, referenceGenome.getGenomeId(), versionString);