Include analysis in cellranger download

bbimber · bbimber · commit 441c00ecdc47 · 2022-02-07T10:08:24.000-08:00
diff --git a/singlecell/src/org/labkey/singlecell/SingleCellController.java b/singlecell/src/org/labkey/singlecell/SingleCellController.java
@@ -113,7 +113,7 @@ public void export(OutputFilesForm form, HttpServletResponse response, BindExcep
 
                     String name = FileUtil.makeLegalName(so.getName());
                     Set<File> toAdd = toExport.getOrDefault(name, new HashSet<>());
-                    toAdd.addAll(CellRangerWrapper.getRawDataDirs(loupe.getParentFile(), false));
+                    toAdd.addAll(CellRangerWrapper.getRawDataDirs(loupe.getParentFile(), false, true));
 
                     toExport.put(name, toAdd);
                 }
diff --git a/singlecell/src/org/labkey/singlecell/run/CellRangerWrapper.java b/singlecell/src/org/labkey/singlecell/run/CellRangerWrapper.java
@@ -37,7 +37,7 @@ protected File getExe(boolean use31)
         return SequencePipelineService.get().getExeForPackage("CELLRANGERPATH", "cellranger" + (use31 ? "-31" : ""));
     }
 
-    public static Set<File> getRawDataDirs(File outputDir, boolean filteredOnly)
+    public static Set<File> getRawDataDirs(File outputDir, boolean filteredOnly, boolean includeAnalysis)
     {
         List<String> dirs = new ArrayList<>();
         dirs.add("filtered_feature_bc_matrix");
@@ -49,6 +49,11 @@ public static Set<File> getRawDataDirs(File outputDir, boolean filteredOnly)
             dirs.add("raw_feature_bc_matrix");
         }
 
+        if (includeAnalysis)
+        {
+            dirs.add("analysis");
+        }
+
         Set<File> toAdd = new HashSet<>();
         for (String dir : dirs)
         {

Original file line number	Diff line number	Diff line change
`@@ -113,7 +113,7 @@ public void export(OutputFilesForm form, HttpServletResponse response, BindExcep`
`113`	`113`
`114`	`114`	`String name = FileUtil.makeLegalName(so.getName());`
`115`	`115`	`Set<File> toAdd = toExport.getOrDefault(name, new HashSet<>());`
`116`		`- toAdd.addAll(CellRangerWrapper.getRawDataDirs(loupe.getParentFile(), false));`
	`116`	`+ toAdd.addAll(CellRangerWrapper.getRawDataDirs(loupe.getParentFile(), false, true));`
`117`	`117`
`118`	`118`	`toExport.put(name, toAdd);`
`119`	`119`	`}`
Original file line number	Diff line number	Diff line change
`@@ -37,7 +37,7 @@ protected File getExe(boolean use31)`
`37`	`37`	`return SequencePipelineService.get().getExeForPackage("CELLRANGERPATH", "cellranger" + (use31 ? "-31" : ""));`
`38`	`38`	`}`
`39`	`39`
`40`		`- public static Set<File> getRawDataDirs(File outputDir, boolean filteredOnly)`
	`40`	`+ public static Set<File> getRawDataDirs(File outputDir, boolean filteredOnly, boolean includeAnalysis)`
`41`	`41`	`{`
`42`	`42`	`List<String> dirs = new ArrayList<>();`
`43`	`43`	`dirs.add("filtered_feature_bc_matrix");`
`@@ -49,6 +49,11 @@ public static Set<File> getRawDataDirs(File outputDir, boolean filteredOnly)`
`49`	`49`	`dirs.add("raw_feature_bc_matrix");`
`50`	`50`	`}`
`51`	`51`
	`52`	`+ if (includeAnalysis)`
	`53`	`+ {`
	`54`	`+ dirs.add("analysis");`
	`55`	`+ }`
	`56`	`+`
`52`	`57`	`Set<File> toAdd = new HashSet<>();`
`53`	`58`	`for (String dir : dirs)`
`54`	`59`	`{`