Changeset 5064

Timestamp:

Oct 31, 2018, 8:44:21 AM (4 years ago)

Author:

Nicklas Nordborg

Message:

References #1068: Add mBAF analysis step to the Hisat/StringTie? pipeline

File links should be created 'soft' links so that they can be easier removed or replaced if we want to.

Location:

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie

Files:

• grid/MBafJobCreator.java (modified) (4 diffs)
• plugins/MBafPlotterPlugin.java (modified) (2 diffs)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/MBafJobCreator.java

@@ -182 +182 @@
       if (autoConfirm)
       {
-        AnyToAny link = AnyToAny.getNewOrExisting(dc, aligned, "mbaf_genotype.vcf", mBafJob, true);
+        AnyToAny link = AnyToAny.getNewOrExisting(dc, aligned, "mbaf_genotype.vcf", mBafJob, false);
         if (!link.isInDatabase()) dc.saveItem(link);
       }
@@ -322 +322 @@
           }
           
-          AnyToAny link = AnyToAny.getNewOrExisting(dc, aligned, f.getName(), f, true);
+          AnyToAny link = AnyToAny.getNewOrExisting(dc, aligned, f.getName(), f, false);
           if (!link.isInDatabase()) dc.saveItem(link);
           
@@ -331 +331 @@
             {
               link.setDescription("Created with " + software.getName());
-              AnyToAny swLink = AnyToAny.getNewOrExisting(dc, f, "software", software, true);
+              AnyToAny swLink = AnyToAny.getNewOrExisting(dc, f, "software", software, false);
               if (!swLink.isInDatabase()) dc.saveItem(swLink);
             }
@@ -365 +365 @@
                 png.setMimeTypeAuto("image/png", null);
                 if (!png.isInDatabase()) dc.saveItem(png);
-                AnyToAny pngLink = AnyToAny.getNewOrExisting(dc, aligned, png.getName(), png, true);
+                AnyToAny pngLink = AnyToAny.getNewOrExisting(dc, aligned, png.getName(), png, false);
                 if (!pngLink.isInDatabase()) dc.saveItem(pngLink);
 

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/MBafPlotterPlugin.java

@@ -545 +545 @@
   private void linkFileAndSoftware(DbControl dc, DerivedBioAssay alignment, File file, Software software)
   {
-    AnyToAny link = AnyToAny.getNewOrExisting(dc, alignment, file.getName(), file, true);
+    AnyToAny link = AnyToAny.getNewOrExisting(dc, alignment, file.getName(), file, false);
     if (!link.isInDatabase()) dc.saveItem(link);
     
@@ -551 +551 @@
     {
       link.setDescription("Created with " + software.getName());
-      AnyToAny swLink = AnyToAny.getNewOrExisting(dc, file, "software", software, true);
+      AnyToAny swLink = AnyToAny.getNewOrExisting(dc, file, "software", software, false);
       if (!swLink.isInDatabase()) dc.saveItem(swLink);
     }