Changeset 5790

Timestamp:

Dec 13, 2019, 2:26:35 PM (3 years ago)

Author:

Nicklas Nordborg

Message:

References #1217: DoNotUse? flags and comments should be copied to new child items

Moved the helper method from ReggieItem.copyDoNotUseAnnotations() to a separate utility class DoNotUse since it easier to use two regular BASE items instead of one ReggieItem and one BASE item.

Fixed the implementation in the Cufflinks, StringTie and VariantCalling pipelines.

Location:

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

Files:

• dao/DoNotUse.java (added)
• dao/ReggieItem.java (modified) (1 diff)
• grid/CufflinksJobCreator.java (modified) (4 diffs)
• grid/StringTieJobCreator.java (modified) (2 diffs)
• grid/VariantCallingJobCreator.java (modified) (2 diffs)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/ReggieItem.java

@@ -249 +249 @@
   
   /**
-    Helper method to copy all DoNotUse-related annotations from this item to the other.
-    @param force TRUE to overwrite existing annotations, FALSE to not
-    @return TRUE if any of the information was changed, FALSE if not
-    @since 4.25
-  */
-  public boolean copyDoNotUseAnnotations(DbControl dc, Annotatable to, boolean force)
-  {
-    boolean copiedFlag = Annotationtype.DO_NOT_USE.copyAnnotationValues(dc, item, to, force);
-    boolean copiedComment = Annotationtype.DO_NOT_USE_COMMENT.copyAnnotationValues(dc, item, to, force);
-    return copiedFlag || copiedComment;
-  }
-
-  
-  /**
     Utility method for finding parent biomaterial of the specified subtypes
     by following the chain of parent items up to biosource.

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

@@ -48 +48 @@
 import net.sf.basedb.reggie.dao.Datafiletype;
 import net.sf.basedb.reggie.dao.DemuxedSequences;
+import net.sf.basedb.reggie.dao.DoNotUse;
 import net.sf.basedb.reggie.dao.Fileserver;
 import net.sf.basedb.reggie.dao.Library;
@@ -315 +316 @@
       masked.setProtocol(maskingProtocol);
       masked.addParent(merged);
+      DoNotUse.copyDoNotUseAnnotations(dc, merged, masked, false);
       dc.saveItem(masked);
       
@@ -327 +329 @@
       aligned.setProtocol(alignProtocol);
       aligned.addParent(masked);
+      DoNotUse.copyDoNotUseAnnotations(dc, merged, aligned, false);
       dc.saveItem(aligned);
 
@@ -340 +343 @@
       raw.setProtocol(protocol);
       raw.setParentBioAssay(aligned);
+      DoNotUse.copyDoNotUseAnnotations(dc, merged, raw, false);
       dc.saveItem(raw);
       

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

@@ -45 +45 @@
 import net.sf.basedb.reggie.dao.BiomaterialList;
 import net.sf.basedb.reggie.dao.Datafiletype;
+import net.sf.basedb.reggie.dao.DoNotUse;
 import net.sf.basedb.reggie.dao.Fileserver;
 import net.sf.basedb.reggie.dao.Library;
@@ -227 +228 @@
       raw.setProtocol(protocol);
       raw.setParentBioAssay(aligned);
+      DoNotUse.copyDoNotUseAnnotations(dc, aligned, raw, false);
       dc.saveItem(raw);
 

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

@@ -47 +47 @@
 import net.sf.basedb.reggie.dao.BiomaterialList;
 import net.sf.basedb.reggie.dao.Datafiletype;
+import net.sf.basedb.reggie.dao.DoNotUse;
 import net.sf.basedb.reggie.dao.Fileserver;
 import net.sf.basedb.reggie.dao.Library;
@@ -280 +281 @@
         raw.setArrayDesign(null); // To prevent the default hg38
         raw.setParentBioAssay(aligned);
+        DoNotUse.copyDoNotUseAnnotations(dc, aligned, raw, false);
         dc.saveItem(raw);