Changeset 5785


Ignore:
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:
2 edited

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.reggie/trunk/resources/sampleproc/extraction_registration.js

    r5607 r5785  
    458458  }
    459459 
    460   exreg.qiacubeDateOnChange = function()
     460  exreg.qiacubeDateOnChange = function(event)
    461461  {
    462462    var frm = document.forms['reggie'];
     
    477477
    478478    qiacubeDateIsAfterLysisDate = true;
    479    
    480479    Wizard.setInputStatus('qiacubeDate', 'valid');
    481     var url = '../Extraction.servlet?ID='+App.getSessionId();
    482     url += '&cmd=GetNextQiacubeRunNo&qiacubeDate='+encodeURIComponent(frm.qiacubeDate.value);
    483     Wizard.showLoadingAnimation('Loading Qiacube run number...');
    484     Wizard.asyncJsonRequest(url, exreg.gotNextRunNumber);
     480   
     481    if (event.target.id == 'qiacubeDate')
     482    {
     483      var url = '../Extraction.servlet?ID='+App.getSessionId();
     484      url += '&cmd=GetNextQiacubeRunNo&qiacubeDate='+encodeURIComponent(frm.qiacubeDate.value);
     485      Wizard.showLoadingAnimation('Loading Qiacube run number...');
     486      Wizard.asyncJsonRequest(url, exreg.gotNextRunNumber);
     487    }
    485488  }
    486489
     
    743746      frm['dnaPreNormalize'+id].disabled = !enoughQuantity;
    744747      Doc.element('dnaQuantity'+id).innerHTML = Reggie.formatNumber(lysate.dna.quantity || null, null, 2) || '-';
    745       frm['dnaPreNormalize'+id].checked = enoughQuantity && ENABLE_DNA_PRENORMALIZE;
     748      frm['dnaPreNormalize'+id].checked = enoughQuantity && ENABLE_DNA_PRENORMALIZE && !Reggie.isExternal(lysate.name);
    746749      var warning = lysate.dna.quantity && !enoughQuantity;
    747750      Wizard.setInputStatus('dnaPreNormalize'+id, warning ? 'flag' : '', warning ? 'Not enough quantity' : '');
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/ExtractionServlet.java

    r5601 r5785  
    737737            flaggedRna.add(rna);
    738738          }
     739          else if (Reggie.isExternalItem(rna.getName()))
     740          {
     741            // External items are paused at this stage
     742            Annotationtype.AUTO_PROCESSING.setAnnotationValue(dc, rna, "Disable");
     743          }
    739744          Annotationtype.QIACUBE_DATE.setAnnotationValue(dc, rna, qiacubeDate);
    740745          Annotationtype.QIACUBE_RUN_NO.setAnnotationValue(dc, rna, qiacubeRunNo);
     
    878883            Annotationtype.AUTO_PROCESSING.setAnnotationValue(dc, parentRna, "Disable");
    879884           
    880             // Create a child RNAQC extract
     885            // Create a child RNANormalizedAliquot extract
    881886            Extract normalizedRna = Extract.getNew(dc);
    882887            normalizedRna.setItemSubtype(subtypeNormalized);
     
    886891            Annotationtype.DILUTION_OPERATOR.setAnnotationValue(dc, normalizedRna, operator);
    887892 
     893            if (Reggie.isExternalItem(normalizedRna.getName()))
     894            {
     895              // External items are paused at this stage
     896              Annotationtype.AUTO_PROCESSING.setAnnotationValue(dc, normalizedRna, "Disable");
     897            }
     898           
    888899            BioMaterialEvent creationEvent = normalizedRna.getCreationEvent();
    889900            creationEvent.setEventDate(normalizationDate);
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