Changeset 1762

Timestamp:

Dec 3, 2012, 12:27:11 PM (10 years ago)

Author:

Nicklas Nordborg

Message:

References #441: Register cDNA plate as completed

Added a simple for for registering a cDNA plate:

• Date
• Operator
• Protocol
• Comments

Location:

extensions/net.sf.basedb.reggie/branches/ticket-422

Files:

• resources/index.jsp (modified) (1 diff)
• resources/libprep/cdna_registration.jsp (added)
• resources/libprep/mrna_registration.jsp (modified) (1 diff)
• src/net/sf/basedb/reggie/dao/ReactionPlate.java (modified) (3 diffs)
• src/net/sf/basedb/reggie/servlet/MRnaServlet.java (modified) (3 diffs)

extensions/net.sf.basedb.reggie/branches/ticket-422/resources/index.jsp

@@ -290 +290 @@
             <ul>
             <li><a href="libprep/select_rna.jsp?ID=<%=ID%>">Create new mRNA plate</a>
-            <li><a href="libprep/mrna_protocol.jsp?ID=<%=ID%>">Lab protocol and files for mRNA and cDNA preparation</a>
-            <li><a href="libprep/mrna_registration.jsp?ID=<%=ID%>">Import mRNA quality control results</a>
-            <li><a href="?ID=<%=ID%>">cDNA registration</a>
+            <li><a href="libprep/mrna_protocol.jsp?ID=<%=ID%>">Lab protocols and files for mRNA and cDNA preparation</a>
+            <li><a href="libprep/mrna_registration.jsp?ID=<%=ID%>">mRNA registration and quality control results</a>
+            <li><a href="libprep/cdna_registration.jsp?ID=<%=ID%>">cDNA registration</a>
             </ul>
           </dd>

extensions/net.sf.basedb.reggie/branches/ticket-422/resources/libprep/mrna_registration.jsp

@@ -86 +86 @@
   {
     showLoadingAnimation('Loading histology work lists...');
-    var url = '../MRna.servlet?ID=<%=ID%>&cmd=GetUnprocessedMRnaPlates';    
+    var url = '../MRna.servlet?ID=<%=ID%>&cmd=GetUnprocessedPlates&plateType=MRNA';   
     request.open("GET", url, false);  
     request.send(null);

extensions/net.sf.basedb.reggie/branches/ticket-422/src/net/sf/basedb/reggie/dao/ReactionPlate.java

@@ -11 +11 @@
 import net.sf.basedb.core.BioPlate;
 import net.sf.basedb.core.BioPlateEvent;
+import net.sf.basedb.core.BioPlateEventType;
 import net.sf.basedb.core.BioPlateType;
 import net.sf.basedb.core.BioWell;
@@ -22 +23 @@
 import net.sf.basedb.core.MeasuredBioMaterial;
 import net.sf.basedb.core.PlateGeometry;
+import net.sf.basedb.core.SystemItems;
 import net.sf.basedb.core.Type;
 import net.sf.basedb.core.query.Expressions;
@@ -276 +278 @@
     @since 2.x
   */
-  public List<BioPlateEvent> findEvents(DbControl dc, String role)
+  public List<BioPlateEvent> findEvents(DbControl dc, String eventType, String role)
   {
     ItemQuery<BioPlateEvent> query = getItem().getEvents();
+    if (eventType != null)
+    {
+      int eventTypeId = SystemItems.getId(eventType);
+      if (eventTypeId != 0)
+      {
+        // Restrict on event type
+        query.restrict(Restrictions.eq(Hql.property("eventType"), Expressions.integer(eventTypeId)));
+      }
+      
+    }
     if (role != null)
     {

extensions/net.sf.basedb.reggie/branches/ticket-422/src/net/sf/basedb/reggie/servlet/MRnaServlet.java

@@ -89 +89 @@
         json.put("name", bioPlateType.generateNextName(dc, 1));
       }
-      else if ("GetUnprocessedMRnaPlates".equals(cmd))
-      {
-        dc = sc.newDbControl();
+      else if ("GetUnprocessedPlates".equals(cmd))
+      {
+        dc = sc.newDbControl();
+        BioplateType plateType = BioplateType.getByCName(req.getParameter("plateType"));
         
         ItemQuery<BioPlate> query = BioPlate.getQuery();
         query.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
         query.restrict(Restrictions.eq(Hql.property("eventDate"), null));
-        BioplateType.MRNA.addFilter(dc, query, true);
+        plateType.addFilter(dc, query, true);
         query.order(Orders.desc(Hql.property("id")));
         
@@ -366 +367 @@
         
         // Find the creation event for the mRNA plate
-        List<BioPlateEvent> events = mrnaReactionPlate.findEvents(dc, "destination");
+        List<BioPlateEvent> events = mrnaReactionPlate.findEvents(dc, BioPlateEventType.CREATE_BIOMATERIAL, "destination");
         if (events.size() > 1)
         {
@@ -447 +448 @@
         
         jsonMessages.add("Prepared child cDNA plate '" + cdnaPlateName + "' for future processing");
+        
+        dc.commit();
+      }
+      else if ("ImportCDnaResults".equals(cmd))
+      {
+        JSONObject jsonReq = (JSONObject)new JSONParser().parse(req.getReader());
+        
+        Number bioPlateId = (Number)jsonReq.get("bioplate");
+        Number cdnaProtocolId = (Number)jsonReq.get("cdnaProtocol");
+
+        dc = sc.newDbControl();
+        
+        // Load cDNA plate and the creation event
+        ReactionPlate cdnaReactionPlate = ReactionPlate.getById(dc, bioPlateId.intValue(), BioplateType.CDNA);
+        BioPlate cdnaPlate = cdnaReactionPlate.getBioPlate();
+        
+        // Find the creation event for the cDNA plate
+        List<BioPlateEvent> events = cdnaReactionPlate.findEvents(dc, BioPlateEventType.CREATE_BIOMATERIAL, "child");
+        if (events.size() > 1)
+        {
+          throw new InvalidDataException("Found > 1 creation event for cDNA plate: " + cdnaReactionPlate.getName());
+        }
+        // ...it may not exist if a plate has been created with a batch import...
+        BioPlateEvent cdnaPlateCreationEvent = events.size() == 0 ? null : events.get(0);
+        
+        // Set creation date and protocol
+        Date cdnaDate = Reggie.CONVERTER_STRING_TO_DATE.convert((String)jsonReq.get("cdnaDate"));
+        cdnaPlate.setEventDate(cdnaDate);
+        Protocol cdnaProtocol = cdnaProtocolId == null ? null : Protocol.getById(dc, cdnaProtocolId.intValue());
+        if (cdnaPlateCreationEvent != null)
+        {
+          // This automatically propagated to all mRNA items on the plate
+          cdnaPlateCreationEvent.setEventDate(cdnaDate);
+          cdnaPlateCreationEvent.setProtocol(cdnaProtocol);
+        }
+  
+        // Operator is an annotation
+        String operator = Values.getStringOrNull((String)jsonReq.get("cdnaOperator"));
+        Annotationtype.QC_OPERATOR.setAnnotationValue(dc, cdnaPlate, operator);
+        
+        
+        // Comment about the plate
+        cdnaPlate.setDescription((String)jsonReq.get("comment"));
+        
+        jsonMessages.add("cDNA plate registered: " + cdnaPlate.getName());
         
         dc.commit();