Changeset 2062

Timestamp:

Oct 14, 2013, 8:54:18 AM (10 years ago)

Author:

Nicklas Nordborg

Message:

References #481 and #501. If 'Flow cell ID' is already known for a flow cell, print it on the lab protocol and pre-fill the registration form.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/libprep/flowcell_protocol2.jsp (modified) (2 diffs)
• resources/libprep/flowcell_registration.jsp (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/FlowCellServlet.java (modified) (3 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/libprep/flowcell_protocol2.jsp

@@ -134 +134 @@
       setInnerHTML('flowCellName.'+flowCellNo, flowCellName);       
       setInnerHTML('flowCellDescription.'+flowCellNo, flowCellDescription);       
-      setInnerHTML('readString.'+flowCellNo, readString);       
+      setInnerHTML('readString.'+flowCellNo, readString);
+      setInnerHTML('flowCellId.'+flowCellNo, flowCell.externalId);
       var flowCellLanes = flowCell['lanes'];
       for (laneKey in flowCellLanes)
@@ -339 +340 @@
     <tr valign="top" style="border-top: 1px solid #000000;">
       <th style="border-right: 1px solid #000000;">Flow cell ID</th>
-      <td colspan="2" style="border-right: 1px solid #000000;"></td>
+      <td colspan="2" style="border-right: 1px solid #000000;"><div id="flowCellId.<%=c%>" ></div></td>
     </tr>
     <tr valign="top" style="border-top: 1px solid #000000;">

extensions/net.sf.basedb.reggie/trunk/resources/libprep/flowcell_registration.jsp

@@ -232 +232 @@
       frm[prefix+'.comments'].value = fc.comments;
       commentsOnChange(prefix+'.comments');
+      frm[prefix+'.id'].value = fc.externalId;
+      flowCellIdOnBlur(prefix+'.id');
       index++;
     }

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

@@ -25 +25 @@
 import net.sf.basedb.core.Hardware;
 import net.sf.basedb.core.ItemQuery;
-import net.sf.basedb.core.ItemResultList;
 import net.sf.basedb.core.ItemSubtype;
 import net.sf.basedb.core.PhysicalBioAssay;
@@ -143 +142 @@
         {
           fc.loadAnnotations(dc, "ReadString", Annotationtype.READ_STRING, null);
+          fc.loadAnnotations(dc, "externalId", Annotationtype.FLOWCELL_ID, null);
           fc.setAnnotation("comments", fc.getPhysicalBioAssay().getDescription());
           jsonFlowCells.add(fc.asJSONObject());
@@ -170 +170 @@
         for (FlowCell fc: flowCellList)
         {
-          JSONObject jsonFlowCell = new JSONObject();
-          jsonFlowCell.put("name", fc.getName());
-          // Get ReadString annotation
           PhysicalBioAssay physBA = fc.getPhysicalBioAssay();
-          jsonFlowCell.put("description", physBA.getDescription());
-          int numLanes = physBA.getSize();
-          String readString = (String) Annotationtype.READ_STRING.getAnnotationValue(dc, manager, physBA);
-          jsonFlowCell.put("readString", readString);
+          fc.setAnnotation("description", physBA.getDescription());
+          fc.setAnnotation("numLanes", physBA.getSize());
+          fc.loadAnnotations(dc, "readString", Annotationtype.READ_STRING, null);
+          fc.loadAnnotations(dc, "externalId", Annotationtype.FLOWCELL_ID, null);
+          
           // Get flow cell lane info
           JSONObject jsonFlowCellLanes = new JSONObject();
-          // Note: Lane positions start with 1, not 0
-          for (int pos = 1; pos <= numLanes; pos++)
+          for (BioMaterialEventSource eventSource : physBA.getCreationEvent().getEventSources().list(dc))
           {
-            ItemResultList<Extract> fcExtractList = fc.getPhysicalBioAssay().getExtracts(pos).list(dc);
-            for (Extract extract: fcExtractList)
-            {
-              jsonFlowCellLanes.put(pos, extract.getName());
-            }
+            Extract pool = (Extract)eventSource.getBioMaterial();
+            jsonFlowCellLanes.put(eventSource.getPosition(), pool.getName());
           }
-          jsonFlowCell.put("numLanes", numLanes);
-          jsonFlowCell.put("lanes", jsonFlowCellLanes);
-          //
-          jsonFlowCellInfo.add(jsonFlowCell);
+          fc.setAnnotation("lanes", jsonFlowCellLanes);
+          jsonFlowCellInfo.add(fc.asJSONObject());
         }
         json.put("flowCellInfo", jsonFlowCellInfo);