Changeset 2065

Timestamp:

Oct 15, 2013, 8:02:38 AM (9 years ago)

Author:

olle

Message:

Refs #471. Library preparation information in 'Case Summary' updated regarding "extraction date" for mRNA, cDNA, Library, and PooledLibrary items:

• The dates currently denoted as "Extraction date" for the different items, are exchanged for the following dates:

Item	Date name	Definition
mRNA	Cleanup date	BioPlate annotation CleanupDate
cDNA	Synthesis date	BioPlate annotation SynthesisDate
Library	Cleanup date	BioPlate annotation CleanupDate
PooledLibrary	Pool date	´Date of the creation event of the real extract that represents the pooled library (current definition)

1. Class/file CaseSummaryServlet.java in reggie/src/net/sf/basedb/reggie/servlet/ updated in private methods
   void loadMRnaInfo(DbControl dc, MRna mrna),
   void loadCDnaInfo(DbControl dc, CDna cdna), and
   void loadLibraryInfo(DbControl dc, Library lib)
   
2. JSP script case_summary.jsp in reggie/resources/reports/ updated in the header titles in the HTML section.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/reports/case_summary.jsp (modified) (4 diffs)
• src/net/sf/basedb/reggie/servlet/CaseSummaryServlet.java (modified) (3 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/reports/case_summary.jsp

@@ -1122 +1122 @@
             </tr>
             <tr id="mrna.extractionDate">
-              <th>Extraction date</th>
+              <th>Cleanup date</th>
             </tr>
             <tr id="mrna.usedQuantity">
@@ -1148 +1148 @@
             </tr>
             <tr id="cdna.extractionDate">
-              <th>Extraction date</th>
+              <th>Synthesis date</th>
             </tr>
           </tbody>
@@ -1171 +1171 @@
             </tr>
             <tr id="lib.extractionDate">
-              <th>Extraction date</th>
+              <th>Cleanup date</th>
             </tr>
             <tr id="lib.remainingQuantity">
@@ -1209 +1209 @@
             </tr>
             <tr id="pooledlib.extractionDate">
-              <th>Extraction date</th>
+              <th>Pool date</th>
             </tr>
             <tr id="pooledlib.remainingQuantity">

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

@@ -516 +516 @@
     mrna.setAnnotation("editable", e.hasPermission(Permission.WRITE));  
     mrna.setAnnotation("usedQuantity", created.getUsedQuantity((Extract)e.getParent()));
-    mrna.setAnnotation("extractionDate", Reggie.CONVERTER_DATE_TO_STRING.convert(created.getEventDate()));
+    // Get BioPlate CleanupDate annotation
+    BioPlate plate = mrna.getItem().getBioWell().getPlate();
+    Date cleanupDate = (Date) Annotationtype.CLEANUP_DATE.getAnnotationValue(dc, plate);
+    mrna.setAnnotation("extractionDate", Reggie.CONVERTER_DATE_TO_STRING.convert(cleanupDate));
   }
 
@@ -522 +525 @@
   {
     Extract e = cdna.getExtract();
-    BioMaterialEvent created = e.getCreationEvent();
     
     cdna.loadBioPlateLocation();
     cdna.setAnnotation("registrationDate", Reggie.CONVERTER_DATE_TO_STRING.convert(e.getEntryDate()));
     cdna.setAnnotation("editable", e.hasPermission(Permission.WRITE));  
-    cdna.setAnnotation("extractionDate", Reggie.CONVERTER_DATE_TO_STRING.convert(created.getEventDate()));
+    // Get BioPlate SynthesisDate annotation
+    BioPlate plate = cdna.getItem().getBioWell().getPlate();
+    Date synthesisDate = (Date) Annotationtype.SYNTHESIS_DATE.getAnnotationValue(dc, plate);
+    cdna.setAnnotation("extractionDate", Reggie.CONVERTER_DATE_TO_STRING.convert(synthesisDate));
   }
 
@@ -533 +538 @@
   {
     Extract e = lib.getExtract();
-    BioMaterialEvent created = e.getCreationEvent();
     
     lib.loadBioPlateLocation();
     lib.setAnnotation("registrationDate", Reggie.CONVERTER_DATE_TO_STRING.convert(e.getEntryDate()));
     lib.setAnnotation("editable", e.hasPermission(Permission.WRITE)); 
-    lib.setAnnotation("extractionDate", Reggie.CONVERTER_DATE_TO_STRING.convert(created.getEventDate()));
+    // Get BioPlate CleanupDate annotation
+    BioPlate plate = lib.getItem().getBioWell().getPlate();
+    Date cleanupDate = (Date) Annotationtype.CLEANUP_DATE.getAnnotationValue(dc, plate);
+    lib.setAnnotation("extractionDate", Reggie.CONVERTER_DATE_TO_STRING.convert(cleanupDate));
     lib.setAnnotation("originalQuantity", e.getOriginalQuantity());
     lib.setAnnotation("remainingQuantity", e.getRemainingQuantity());