Changeset 4982

Timestamp:

Sep 26, 2018, 9:10:59 AM (4 years ago)

Author:

Nicklas Nordborg

Message:

References #1054: Even more functionality in the Flagged alignment wizard

Added PreNormalizedRNA as an option for the DoNotUse annotation. The options is of course only available if the alignment has a pre-normalied RNA item in the parent chain.

A minor complication is present when filtering on a QiaCube. It is possible that alignments from both a pre-normalized and a regular RNA exists and that there is a mixup that only affects the pre-normalized RNA. But the "Resolve" options are grouped by QiaCube positions so there is only one set of options for the two alignments. If the PreNormalizedRNA option is selected, only the pre-normalized RNA is marked as DoNotUse and we rely on the auto-unflag option to fix the regular RNA as if the Ok checkbox had been selected.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/flaggedalignment/search.js (modified) (5 diffs)
• resources/flaggedalignment/search.jsp (modified) (2 diffs)
• src/net/sf/basedb/reggie/servlet/GenotypeServlet.java (modified) (6 diffs)
• src/net/sf/basedb/reggie/servlet/InstallServlet.java (modified) (1 diff)

extensions/net.sf.basedb.reggie/trunk/resources/flaggedalignment/search.js

@@ -444 +444 @@
       // Note! "mode-resolve" columns here to get the same order for grouping
       html += '<th class="mode-resolve dottedleft">Ok</th>';
-      html += '<th class="mode-resolve">DoNotUse</th>';
-      html += '<th class="mode-resolve">FutureGT</th>';
+      html += '<th class="mode-resolve" colspan="2">DoNotUse<span style="float:right;">FutureGT</span></th>';
       html += '<th class="mode-resolve comment-col">Comment</th>';
 
@@ -1135 +1134 @@
           if (okToUse.value == 'ok-rna')
           {
-            item = {'type': 'EXTRACT', 'id': aligned.rna.id, 'okToUse': true, 'sort': 5 };
+            item = {'type': 'EXTRACT', 'id': aligned.rna.id, 'okToUse': true, 'sort': 6 };
           }
           else if (okToUse.value == 'ok-library')
           {
-            item = {'type': 'EXTRACT', 'id': aligned.lib.id, 'okToUse': true, 'sort': 6 };
+            item = {'type': 'EXTRACT', 'id': aligned.lib.id, 'okToUse': true, 'sort': 7 };
           }
         }
@@ -1154 +1153 @@
           item = {'type': 'EXTRACT', 'id': aligned.rna.id, 'doNotUse': 'RNA', 'sort': 3 };
         }
+        else if (doNotUse.value == 'prenormalized')
+        {
+          item = {'type': 'EXTRACT', 'id': aligned.preNormalizedRna.id, 'doNotUse': 'PreNormalizedRNA', 'sort': 4 };
+        }
         else if (doNotUse.value == 'library')
         {
-          item = {'type': 'EXTRACT', 'id': aligned.lib.id, 'doNotUse': 'Library', 'sort': 4 };
+          item = {'type': 'EXTRACT', 'id': aligned.lib.id, 'doNotUse': 'Library', 'sort': 5 };
         }
         else if (aligned.flagged && doNotUse.classList.contains('required'))
@@ -1323 +1326 @@
     var posA = a.rna.QIACUBE_POSITION;
     var posB = b.rna.QIACUBE_POSITION;
-    return posA < posB ? -1 : 1;
+    if (posA != posB) return posA < posB ? -1 : 1;
+    
+    // Critical, sort pre-normalized RNA before regular RNA to
+    // enable the 'PreNormalizedRNA' option in the 'DoNotUse' selection list
+    if (a.preNormalizedRna && !b.preNormalizedRna) return -1;
+    if (b.preNormalizedRna && !a.preNormalizedRna) return 1;
+    
+    return sort.sortByName(a, b);
   }
   
@@ -1599 +1609 @@
         html += '<option value="library">Library';
       }
+      if (aligned.preNormalizedRna)
+      {
+        html += '<option value="prenormalized">PreNormalizedRNA';
+      }
       html += '<option value="rna">RNA';
       html += '<option value="lysate">Lysate';

extensions/net.sf.basedb.reggie/trunk/resources/flaggedalignment/search.jsp

@@ -117 +117 @@
 #itemTable .comment-col input
 {
-  width: 15em;
+  width: calc(100% - 12px);
 }
 
@@ -223 +223 @@
   border-right-width: 8px;
   border-right-color: #2288AA;
+}
+
+select.donotuse-options 
+{
+    width: calc(100% - 10px);
 }
 

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

@@ -504 +504 @@
         ItemSubtype lysateType = Subtype.LYSATE.get(dc);
         ItemSubtype rnaType = Subtype.RNA.get(dc);
+        ItemSubtype preNormalizedType = Subtype.RNA_NORMALIZED_ALIQUOT.get(dc);
         ItemSubtype libraryType = Subtype.LIBRARY.get(dc);
         ItemList flaggedAlignments = BiomaterialList.FLAGGED_ALIGNMENT.get(dc);
@@ -526 +527 @@
         int numLysate = 0;
         int numRna = 0;
+        int numPreNormalizedRna = 0;
         int numLibrary = 0;
         
@@ -614 +616 @@
                 else if (lysateType.equals(subtype)) numLysate++;
                 else if (rnaType.equals(subtype)) numRna++;
+                else if (preNormalizedType.equals(subtype)) numPreNormalizedRna++;
                 else if (libraryType.equals(subtype)) numLibrary++;
               }
@@ -716 +719 @@
             msg.append(countMessage(numRna, "RNA", "RNA"));
           }
+          if (numPreNormalizedRna > 0)
+          {
+            if (msg.length() > 0) msg.append(", ");
+            msg.append(countMessage(numPreNormalizedRna, "pre-normalized RNA", "pre-normalized RNA"));
+          }
           if (numLibrary > 0)
           {
@@ -953 +961 @@
       as.setAnnotation("flagged", checker.isFlagged(as.getItem()));
       Library lib = as.getLibrary(dc);
-      Rna rna = lib.getRna(dc, false);
+      Rna rna = lib.getRna(dc, true);
+      Rna prenormalizedRna = null;
+      if (rna != null && rna.isPreNormalized(dc))
+      {
+        prenormalizedRna = rna;
+        rna = Rna.get((Extract)rna.getExtract().getParent());
+      }
       Lysate lys = rna != null ? rna.getLysate() : null;
       SpecimenTube sp = lys != null ? lys.getSpecimen() : null;
@@ -975 +989 @@
       
       if (lib != null) as.setAnnotation("lib", lib.asJSONObject());
+      if (prenormalizedRna != null) as.setAnnotation("preNormalizedRna", prenormalizedRna.asJSONObject());
       if (rna != null) as.setAnnotation("rna", rna.asJSONObject());
       if (lys != null) as.setAnnotation("lysate", lys.asJSONObject());

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

@@ -588 +588 @@
         
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.DO_NOT_USE, 1, 
-            new ValueOptions("Specimen", "Lysate", "RNA", "Library"), 
+            new ValueOptions("Specimen", "Lysate", "RNA", "PreNormalizedRNA", "Library"), 
             createIfMissing, effectivePermissionsUse));
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.DO_NOT_USE_COMMENT, 1, null, createIfMissing, effectivePermissionsUse));