Changeset 5785

Timestamp:

Dec 12, 2019, 2:26:52 PM (3 years ago)

Author:

Nicklas Nordborg

Message:

References #1214: Add support for external specimen

When an external specimen has been extracted either the RNA or the pre-normalized RNA is marked with AutoProcessing=Disable since the library preparation of external RNA should always be a manual action.

The DNA from external specimen are by default NOT pre-normalized since a pre-normalized DNA always get a specific location on the next MIPs plate.

If DNA from external specimen should go into the MIPs pipeline they can be selected for pre-normalization at a later time.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/sampleproc/extraction_registration.js (modified) (3 diffs)
• src/net/sf/basedb/reggie/servlet/ExtractionServlet.java (modified) (3 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/sampleproc/extraction_registration.js

@@ -458 +458 @@
   }
   
-  exreg.qiacubeDateOnChange = function()
+  exreg.qiacubeDateOnChange = function(event)
   {
     var frm = document.forms['reggie'];
@@ -477 +477 @@
 
     qiacubeDateIsAfterLysisDate = true;
-    
     Wizard.setInputStatus('qiacubeDate', 'valid');
-    var url = '../Extraction.servlet?ID='+App.getSessionId();
-    url += '&cmd=GetNextQiacubeRunNo&qiacubeDate='+encodeURIComponent(frm.qiacubeDate.value);
-    Wizard.showLoadingAnimation('Loading Qiacube run number...');
-    Wizard.asyncJsonRequest(url, exreg.gotNextRunNumber);
+    
+    if (event.target.id == 'qiacubeDate')
+    {
+      var url = '../Extraction.servlet?ID='+App.getSessionId();
+      url += '&cmd=GetNextQiacubeRunNo&qiacubeDate='+encodeURIComponent(frm.qiacubeDate.value);
+      Wizard.showLoadingAnimation('Loading Qiacube run number...');
+      Wizard.asyncJsonRequest(url, exreg.gotNextRunNumber);
+    }
   }
 
@@ -743 +746 @@
       frm['dnaPreNormalize'+id].disabled = !enoughQuantity;
       Doc.element('dnaQuantity'+id).innerHTML = Reggie.formatNumber(lysate.dna.quantity || null, null, 2) || '-';
-      frm['dnaPreNormalize'+id].checked = enoughQuantity && ENABLE_DNA_PRENORMALIZE;
+      frm['dnaPreNormalize'+id].checked = enoughQuantity && ENABLE_DNA_PRENORMALIZE && !Reggie.isExternal(lysate.name);
       var warning = lysate.dna.quantity && !enoughQuantity;
       Wizard.setInputStatus('dnaPreNormalize'+id, warning ? 'flag' : '', warning ? 'Not enough quantity' : '');

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

@@ -737 +737 @@
             flaggedRna.add(rna);
           }
+          else if (Reggie.isExternalItem(rna.getName()))
+          {
+            // External items are paused at this stage
+            Annotationtype.AUTO_PROCESSING.setAnnotationValue(dc, rna, "Disable");
+          }
           Annotationtype.QIACUBE_DATE.setAnnotationValue(dc, rna, qiacubeDate);
           Annotationtype.QIACUBE_RUN_NO.setAnnotationValue(dc, rna, qiacubeRunNo);
@@ -878 +883 @@
             Annotationtype.AUTO_PROCESSING.setAnnotationValue(dc, parentRna, "Disable");
             
-            // Create a child RNAQC extract
+            // Create a child RNANormalizedAliquot extract
             Extract normalizedRna = Extract.getNew(dc);
             normalizedRna.setItemSubtype(subtypeNormalized);
@@ -886 +891 @@
             Annotationtype.DILUTION_OPERATOR.setAnnotationValue(dc, normalizedRna, operator);
   
+            if (Reggie.isExternalItem(normalizedRna.getName())) 
+            {
+              // External items are paused at this stage
+              Annotationtype.AUTO_PROCESSING.setAnnotationValue(dc, normalizedRna, "Disable");
+            }
+            
             BioMaterialEvent creationEvent = normalizedRna.getCreationEvent();
             creationEvent.setEventDate(normalizationDate);