Changeset 2049

Timestamp:

Oct 7, 2013, 3:38:52 PM (10 years ago)

Author:

Nicklas Nordborg

Message:

References #481: Register prepared flow cells

The wizard now creates a SequencingRunNNNN (derived bioassay) item and link the flow cells to it. The SequencingStartDate and SequencingOperator are added as annotation to the derived bioassay.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/index.jsp (modified) (2 diffs)
• resources/libprep/flowcell_registration.jsp (modified) (6 diffs)
• src/net/sf/basedb/reggie/dao/Annotationtype.java (modified) (1 diff)
• src/net/sf/basedb/reggie/dao/SequencingRun.java (added)
• src/net/sf/basedb/reggie/dao/Subtype.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/FlowCellServlet.java (modified) (5 diffs)
• src/net/sf/basedb/reggie/servlet/InstallServlet.java (modified) (3 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/index.jsp

@@ -295 +295 @@
       var msg = error || 'Number of flow cells waiting for registration';
       var count = error ? -1 : response.count;
-      setCount('count.flow-cells.0', count, 'flow cells', msg);
-      setCount('count.flow-cells', count, 'flow cells', msg);
+      setCount('count.flow-cells.1', count, 'flow cells', msg);
+      setCount('count.flow-cells.2', count, 'flow cells', msg);
     }
     
@@ -505 +505 @@
             <li><a href="libprep/pool_registration.jsp?ID=<%=ID%>">Register pooled libraries</a> <span class="counter" id="count.pools.2" title="Counting..."><img src="images/loading-small.gif"></span>
             <li><a href="libprep/create_flowcells.jsp?ID=<%=ID%>">Create flow cells</a> <span class="counter" id="count.pools.3" title="Counting..."><img src="images/loading-small.gif"></span>
-            <li><a href="libprep/flowcell_protocol.jsp?ID=<%=ID%>">Lab protocols for clustering</a> <span class="counter" id="count.flow-cells.0" title="Counting..."><img src="images/loading-small.gif"></span>
-            <li><a href="libprep/flowcell_registration.jsp?ID=<%=ID%>">Register flow cells</a> <span class="counter" id="count.flow-cells" title="Counting..."><img src="images/loading-small.gif"></span>
+            <li><a href="libprep/flowcell_protocol.jsp?ID=<%=ID%>">Lab protocols for clustering &amp; sequence start</a> <span class="counter" id="count.flow-cells.1" title="Counting..."><img src="images/loading-small.gif"></span>
+            <li><a href="libprep/flowcell_registration.jsp?ID=<%=ID%>">Register sequence start of flow cells</a> <span class="counter" id="count.flow-cells.2" title="Counting..."><img src="images/loading-small.gif"></span>
             </ul>
           </dd>

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

@@ -226 +226 @@
   if (date == '')
   {
-    setInputStatus(dateField, 'Missing date', 'warning');
+    var required = frm[dateField].className.indexOf('required') != -1;
+    setInputStatus(dateField, 'Missing date', required ? 'invalid' : 'warning');
+    if (required) dateIsValid[dateField] = false;
     return;
   }
@@ -320 +322 @@
   
   if (dateIsValid['clusterDate'] == false) return false;
-  if (dateIsValid['sequenceStartDate'] == false) return false;
+  if (dateIsValid['sequencingStartDate'] != true) 
+  {
+    dateOnChange('sequencingStartDate');
+    return false;
+  }
   
   var frm = document.forms['reggie'];
@@ -348 +354 @@
   frm.clusterDate.disabled = true;
   frm.clusterOperator.disabled = true;
-  frm.sequenceStartDate.disabled = true;
-  frm.sequenceOperator.disabled = true;
+  frm.sequencingStartDate.disabled = true;
+  frm.sequencingOperator.disabled = true;
   frm.clusterProtocol.disabled = true;
   frm.comments.disabled = true;
@@ -370 +376 @@
   submitInfo.clusterDate = frm.clusterDate.value;
   submitInfo.clusterOperator = frm.clusterOperator.value;
-  submitInfo.sequenceStartDate = frm.sequenceStartDate.value;
-  submitInfo.sequenceOperator = frm.sequenceOperator.value;
+  submitInfo.sequencingStartDate = frm.sequencingStartDate.value;
+  submitInfo.sequencingOperator = frm.sequencingOperator.value;
   submitInfo.comments = frm.comments.value;
   
@@ -524 +530 @@
         <td>
           <input type="text" name="clusterOperator" value="<%=HTML.encodeTags(user.getName()) %>" 
-            style="width: 95%;" maxlength="255" onkeypress="focusOnEnter(event, 'sequenceStartDate')">
+            style="width: 95%;" maxlength="255" onkeypress="focusOnEnter(event, 'sequencingStartDate')">
         </td>
         <td class="status" id="clusterDate.status"></td>
       </tr>
       <tr>
-        <td class="subprompt">Sequence start</td>
+        <td class="subprompt">Sequencing start</td>
         <td>
-          <input type="text" name="sequenceStartDate" maxlength="10" style="width: 8em;"
-            onblur="dateOnChange('sequenceStartDate')" onkeypress="focusOnEnter(event, 'sequenceOperator')">
+          <input type="text" class="required" name="sequencingStartDate" maxlength="10" style="width: 8em;"
+            onblur="dateOnChange('sequencingStartDate')" onkeypress="focusOnEnter(event, 'sequencingOperator')">
             <base:icon 
-              onclick="Dates.selectDate('Sequence start date', 'reggie', 'sequenceStartDate', 'setDate', 'yyyyMMdd')"
+              onclick="Dates.selectDate('Sequence start date', 'reggie', 'sequencingStartDate', 'setDate', 'yyyyMMdd')"
               image="calendar.png" 
               tooltip="Select a date from a calendar" 
@@ -541 +547 @@
         </td>
         <td>
-          <input type="text" name="sequenceOperator" value="<%=HTML.encodeTags(user.getName()) %>" 
+          <input type="text" name="sequencingOperator" value="<%=HTML.encodeTags(user.getName()) %>" 
             style="width: 95%;" maxlength="255" onkeypress="focusOnEnter(event, 'clusterProtocol')">
         </td>
-        <td class="status" id="sequenceStartDate.status"></td>
+        <td class="status" id="sequencingStartDate.status"></td>
       </tr>
       <tr valign="top">

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Annotationtype.java

@@ -563 +563 @@
     
   /**
+    The "SequencingStart" annotation, used for derived bioassays (SequencingRun).
+    @since 2.13
+  */
+  public static final Annotationtype SEQUENCING_START =
+    new Annotationtype("SequencingStart", Type.DATE, Item.DERIVEDBIOASSAY);
+
+  /**
+    The "SequencingOperator" annotation, used for derived bioassays (SequencingRun).
+    @since 2.13
+  */
+  public static final Annotationtype SEQUENCING_OPERATOR =
+    new Annotationtype("SequencingOperator", Type.STRING, Item.DERIVEDBIOASSAY);
+
+  
+  /**
     Get the annotation type by name of the static constant defined in this class.
     

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Subtype.java

@@ -182 +182 @@
   public static final Subtype FLOW_CELL = new Subtype("FlowCell", Item.PHYSICALBIOASSAY, false);
   
+  
+  /**
+    The definition of the "SequencingRun" derived bioassay subtype.
+    @since 2.12
+  */
+  public static final Subtype SEQUENCING_RUN = new Subtype("SequencingRun", Item.DERIVEDBIOASSAY, false);
+  
   /**
     The definition of the "mRNA preparation" protocol subtype.

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

@@ -21 +21 @@
 import net.sf.basedb.core.BioMaterialEventSource;
 import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.DerivedBioAssay;
 import net.sf.basedb.core.Extract;
 import net.sf.basedb.core.ItemQuery;
@@ -38 +39 @@
 import net.sf.basedb.reggie.dao.PooledLibrary;
 import net.sf.basedb.reggie.dao.ReactionPlate;
+import net.sf.basedb.reggie.dao.SequencingRun;
 import net.sf.basedb.reggie.dao.Subtype;
 import net.sf.basedb.util.Values;
@@ -326 +328 @@
         JSONArray jsonFlowCells = (JSONArray)jsonReq.get("flowCells");
         
+        DerivedBioAssay sequenceRun = null;
+        if (!failed)
+        {
+          sequenceRun = DerivedBioAssay.getNew(dc, true, null);
+          sequenceRun.setName(SequencingRun.generateNamesForBatch(dc, 1, 1).get(0));
+          sequenceRun.setDescription(comment);
+          dc.saveItem(sequenceRun);
+
+          Date seqStartDate = Reggie.CONVERTER_STRING_TO_DATE.convert((String)jsonReq.get("sequencingStartDate"));
+          
+          Annotationtype.SEQUENCING_START.setAnnotationValue(dc, sequenceRun, seqStartDate);
+          Annotationtype.SEQUENCING_OPERATOR.setAnnotationValue(dc, sequenceRun, Values.getStringOrNull((String)jsonReq.get("sequencingOperator")));
+          
+          jsonMessages.add("Created '" + sequenceRun.getName()+"'.");
+        }
+        
         for (int fcNo = 0; fcNo < jsonFlowCells.size(); ++fcNo)
         {
@@ -332 +350 @@
           
           PhysicalBioAssay flowCell = PhysicalBioAssay.getById(dc, fcId.intValue());
-          
           BioMaterialEvent createEvent = flowCell.getCreationEvent();
           createEvent.setEventDate(clusterDate);
           createEvent.setProtocol(clusterProtocol);
           createEvent.setComment(comment);
-          
-          flowCell.setDescription(comment);
+
+          if (sequenceRun != null)
+          {
+            sequenceRun.addPhysicalBioAssay(flowCell);
+          }
+          
+          //flowCell.setDescription(comment);
           Annotationtype.OPERATOR.setAnnotationValue(dc, flowCell, operator);
           Annotationtype.READ_STRING.setAnnotationValue(dc, flowCell, jsonFlowCell.get("ReadString"));
@@ -354 +376 @@
           {
             Annotationtype.PLATE_PROCESS_RESULT.setAnnotationValue(dc, flowCell, ReactionPlate.PROCESS_SUCCESSFUL);
-            jsonMessages.add("Flow cell '" + flowCell.getName() + "' registered as completed.");
-            
-            // TODO - Create DerivedBioAssay SequenceRun000N and add selected flow cells to it??
-            // Should the SEQUENCE_START_DATE be added to this instead of the flow cells??
+            jsonMessages.add("Sequencing started for flow cell '" + flowCell.getName() + "'.");
             
           }

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

@@ -167 +167 @@
         jsonChecks.add(checkSubtype(dc, Subtype.CALIPER_WELL_TABLE, createIfMissing));
         jsonChecks.add(checkSubtype(dc, Subtype.QUBIT_CSV, createIfMissing));
+        jsonChecks.add(checkSubtype(dc, Subtype.SEQUENCING_RUN, createIfMissing, Subtype.FLOW_CELL));
 
         // Plate geometries
@@ -284 +285 @@
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.READ_STRING, 1, null, effectiveOptions, createIfMissing));
         
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.SEQUENCING_START, 1, null, effectiveOptions, createIfMissing));
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.SEQUENCING_OPERATOR, 1, null, effectiveOptions, createIfMissing));
+        
         // Annotation type categories
         jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.PATIENT, createIfMissing, 
@@ -361 +365 @@
             Annotationtype.FLOWCELL_ID, Annotationtype.READ_STRING, Annotationtype.OPERATOR, 
             Annotationtype.PLATE_PROCESS_RESULT));
+        
+        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.SEQUENCING_RUN, createIfMissing, 
+            Annotationtype.SEQUENCING_START, Annotationtype.SEQUENCING_OPERATOR
+          ));
         
         // Plugin definitions and configurations