Changeset 5787

Timestamp:

Dec 13, 2019, 11:02:36 AM (2 years ago)

Author:

Nicklas Nordborg

Message:

References #1216: Finalize the "Confirm MIPs demux" wizard

Added the "MIPs alignment pipeline" item list.

Location:

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

Files:

• dao/BiomaterialList.java (modified) (1 diff)
• servlet/InstallServlet.java (modified) (3 diffs)

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

@@ -177 +177 @@
       "automatically, but it is possible to also manually add items.");
 
-    
+  /**
+    The definition of the list used for storing merged sequences that
+    should to be processed with the MIPs alignment pipeline.
+    @since 4.25
+  */
+  public static final BiomaterialList MIPS_ALIGN_PIPELINE = 
+    new BiomaterialList("MIPs Alignment Pipeline", "net.sf.basedb.reggie.pipeline.mips-align",
+      Item.DERIVEDBIOASSAY, Subtype.MERGED_SEQUENCES,
+      "This list contains merged sequences items that should be processed with the " +
+      "MIPs alignment pipeline. Items are normally added and removed from this list " +
+      "automatically, but it is possible to also manually add items.");
+
   /**
     Get the bioplate type by name of the static constant defined in this class.

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/InstallServlet.java

@@ -1108 +1108 @@
         jsonChecks.add(checkItemList(dc, BiomaterialList.MBAF_PIPELINE, effectivePermissionsWrite, createIfMissing));
         jsonChecks.add(checkItemList(dc, BiomaterialList.VARIANT_CALLING_PIPELINE, effectivePermissionsWrite, createIfMissing));
+        jsonChecks.add(checkItemList(dc, BiomaterialList.MIPS_ALIGN_PIPELINE, effectivePermissionsWrite, createIfMissing));
         jsonChecks.add(checkItemList(dc, BiomaterialList.FLAGGED_ALIGNMENT, effectivePermissionsWrite, createIfMissing));
         
@@ -1150 +1151 @@
         ItemList mBafPipeline = BiomaterialList.MBAF_PIPELINE.get(dc);
         ItemList variantCallingPipeline = BiomaterialList.VARIANT_CALLING_PIPELINE.get(dc);
+        ItemList mipsAlignPipeline = BiomaterialList.MIPS_ALIGN_PIPELINE.get(dc);
         AnnotationType autoProc = Annotationtype.AUTO_PROCESSING.get(dc);
         if (autoProc != null)
@@ -1158 +1160 @@
           json.put("mBafPipelineDisabled", "Disable".equals(Annotationtype.AUTO_PROCESSING.getAnnotationValue(dc, mBafPipeline)));
           json.put("variantCallingPipelineDisabled", "Disable".equals(Annotationtype.AUTO_PROCESSING.getAnnotationValue(dc, variantCallingPipeline)));
+          json.put("mipsAlignPipelineDisabled", "Disable".equals(Annotationtype.AUTO_PROCESSING.getAnnotationValue(dc, mipsAlignPipeline)));
         }
         dc.close();