Changeset 3517

Timestamp:

Oct 1, 2015, 1:57:26 PM (7 years ago)

Author:

olle

Message:

Refs #815. Bug fix: The wizard "DNA/RNA registration/quantification" only updates lot numbers for DNA and RNA extracts that were extracted from a MeLuDI specimen, but not extract source items, since they were not extracted in the MeLuDI lab. However, while this is correct for extraction and QIAcube reagents, lot number for quality control reagents should be stored for all extracts in the start item list, since the quality control procedure is performed at the MeLuDI lab:

1. Java servlet class/file ExtractionServlet.java in src/net/sf/basedb/meludi/servlet/ updated in protected method void doPost(HttpServletRequest req, HttpServletResponse resp) for command "RegisterDnaRna" to update lot numbers for quality control reagents for all extracts related to the start item list, including extract source items. Also removal of some code, that were commented out, and fix of code for special cases, that will normally never occur.

File:

• extensions/net.sf.basedb.meludi/trunk/src/net/sf/basedb/meludi/servlet/ExtractionServlet.java (modified) (6 diffs)

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

@@ -2329 +2329 @@
             if (Meludi.itemIsSpecimen(itemName))
             {
-/*
-              dna = Extract.getNew(dc);
-              dna.setName((String)jsonDna.get("name"));
-*/
               Dna d = Dna.findByName(dc, itemName + ".d");
               dna = d.getExtract();
@@ -2341 +2337 @@
               if (dna == null)
               {
-                Dna d = Dna.findByName(dc, itemName + ".d");
+                Dna d = Dna.findByName(dc, itemName);
                 dna = d.getExtract();
               }
@@ -2404 +2400 @@
               Annotationtype.RNEASY_MIN_ELUTE_SPIN_COL.setAnnotationValue(dc, dna, rneasyMinEluteSpinColumn);         
               Annotationtype.QIAAMP_MIN_ELUTE_SPIN_COL.setAnnotationValue(dc, dna, qiaampMinEluteSpinColumn);
-              
-              // Quality control reagents
-              Annotationtype.KAPA_SYBR_FAST.setAnnotationValue(dc, dna, kapaSybrFast);          
-              Annotationtype.QUALITY_CONTROL_PRIMERS_QCP_RGT.setAnnotationValue(dc, dna, qualityControlPrimersQcpRgt);          
-              Annotationtype.QUALITY_CONTROL_TEMPLATE_QCT.setAnnotationValue(dc, dna, qualityControlTemplateQct);         
-              Annotationtype.QUBIT_DNA_HIGH_SENS.setAnnotationValue(dc, dna, qubitDnaHighSens);         
-              Annotationtype.QUBIT_DNA_BROAD_RANGE.setAnnotationValue(dc, dna, qubitDnaBroadRange);         
-            }
-/*
-            if (itemIsSpecimen(itemName))
-            {
-              dc.saveItem(dna);
-              newDna.add(dna);
-            }
-*/
+            }
+            // Quality control reagents
+            Annotationtype.KAPA_SYBR_FAST.setAnnotationValue(dc, dna, kapaSybrFast);          
+            Annotationtype.QUALITY_CONTROL_PRIMERS_QCP_RGT.setAnnotationValue(dc, dna, qualityControlPrimersQcpRgt);          
+            Annotationtype.QUALITY_CONTROL_TEMPLATE_QCT.setAnnotationValue(dc, dna, qualityControlTemplateQct);         
+            Annotationtype.QUBIT_DNA_HIGH_SENS.setAnnotationValue(dc, dna, qubitDnaHighSens);         
+            Annotationtype.QUBIT_DNA_BROAD_RANGE.setAnnotationValue(dc, dna, qubitDnaBroadRange);         
           }
           
@@ -2428 +2416 @@
             if (Meludi.itemIsSpecimen(itemName))
             {
-/*
-              rna = Extract.getNew(dc);
-              rna.setName((String)jsonRna.get("name"));
-*/
               Rna r = Rna.findByName(dc, itemName + ".r");
               rna = r.getExtract();
@@ -2515 +2499 @@
               Annotationtype.RNEASY_MIN_ELUTE_SPIN_COL.setAnnotationValue(dc, rna, rneasyMinEluteSpinColumn);         
               Annotationtype.QIAAMP_MIN_ELUTE_SPIN_COL.setAnnotationValue(dc, rna, qiaampMinEluteSpinColumn);
-              
-              // Quality control reagents
-              Annotationtype.KAPA_SYBR_FAST.setAnnotationValue(dc, rna, kapaSybrFast);          
-              Annotationtype.QUALITY_CONTROL_PRIMERS_QCP_RGT.setAnnotationValue(dc, rna, qualityControlPrimersQcpRgt);          
-              Annotationtype.QUALITY_CONTROL_TEMPLATE_QCT.setAnnotationValue(dc, rna, qualityControlTemplateQct);         
-              Annotationtype.QUBIT_DNA_HIGH_SENS.setAnnotationValue(dc, rna, qubitDnaHighSens);         
-              Annotationtype.QUBIT_DNA_BROAD_RANGE.setAnnotationValue(dc, rna, qubitDnaBroadRange);         
-            }
-/*
-            if (itemIsSpecimen(itemName))
-            {
-              dc.saveItem(rna);
-              newRna.add(rna);
-            }
-*/
+            }
+            // Quality control reagents
+            Annotationtype.KAPA_SYBR_FAST.setAnnotationValue(dc, rna, kapaSybrFast);          
+            Annotationtype.QUALITY_CONTROL_PRIMERS_QCP_RGT.setAnnotationValue(dc, rna, qualityControlPrimersQcpRgt);          
+            Annotationtype.QUALITY_CONTROL_TEMPLATE_QCT.setAnnotationValue(dc, rna, qualityControlTemplateQct);         
+            Annotationtype.QUBIT_DNA_HIGH_SENS.setAnnotationValue(dc, rna, qubitDnaHighSens);         
+            Annotationtype.QUBIT_DNA_BROAD_RANGE.setAnnotationValue(dc, rna, qubitDnaBroadRange);         
           }
           
@@ -2535 +2511 @@
           if (Meludi.itemIsSpecimen(itemName))
           {
-/*
-            msg += "RNA and DNA created from " + itemName;
-*/
             msg += "RNA and DNA updated for " + itemName;
           }