Changeset 2143

Timestamp:

Nov 19, 2013, 9:16:07 AM (10 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #524: Auto-select RNA wizard should be able to start from a specific date

Added a 'Start date' field to the 'auto select' dialog. If empty the RNA is selected as before, eg. by position in the storage boxes. If a date is specified, the QiaCubeDate is used as a filter so that only RNA items extracted at or after the specified date are selected. The order is still by storage box location.

Added display field for QiaCubeDate (off by default) to the main plate view.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/libprep/auto_select_rna.jsp (modified) (5 diffs)
• resources/libprep/select_rna.jsp (modified) (6 diffs)
• src/net/sf/basedb/reggie/dao/Rna.java (modified) (3 diffs)
• src/net/sf/basedb/reggie/servlet/MRnaServlet.java (modified) (5 diffs)

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

@@ -36 +36 @@
   var frm = document.forms['options'];
   
+  var startDate = frm.startDate.value;
+  if (startDate && !Dates.isDate(startDate, 'yyyyMMdd'))
+  {
+    frm.startDate.focus();
+    alert('Not a valid date: ' + startDate);
+    return;
+  }
+  
   var qRegular = parseFloat(frm.quantity_regular.value);
   if (!(qRegular > 0))
@@ -52 +60 @@
   }
   
+  if (startDate) options.startDate = startDate;
   if (frm.remainingQuantity.checked) options.remainingQuantity = qRegular;
   if (frm.qualityScore.checked) options.qualityScore = qualityScore;
@@ -59 +68 @@
   {
     showLoadingAnimation('Finding RNA. Please wait...');
-    window.opener.autoSelect(options);
+    var msg = window.opener.autoSelect(options);
+    if (msg) alert(msg);
     window.close();
   }
@@ -78 +88 @@
   }
 }
+
+function setStartDate(frmName, dateField, date)
+{
+  var frm = document.forms[frmName];
+  frm[dateField].value = date;
+  frm[dateField].focus();
+}
+
 </script>
 <style>
@@ -95 +113 @@
   
     <table class="fullform input100">
+    <tr>
+      <th>Start date</th>
+      <td>
+        <input type="text" name="startDate" value="" style="width: 12em;" maxlength="10"
+          title="Enter start date in YYYYMMDD format">
+          <base:icon 
+            onclick="Dates.selectDate('Start date', 'options', 'startDate', 'setStartDate', 'yyyyMMdd')"
+            image="calendar.png" 
+            tooltip="Select a date from a calendar" 
+            tabindex="-1"
+          /> (empty = start from oldest)
+      </td>
+    </tr>
     <tr valign="top">
       <th>Active filters</th>

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

@@ -251 +251 @@
           warningMsg[warningMsg.length] = 'No NDConc value';
         }
+        if (info.QiaCubeDate)
+        {
+          text += '<div class="qiacube-date">'+info.QiaCubeDate+'</div>';
+        }
+        else
+        {
+          warningMsg[warningMsg.length] = 'No QiaCubeDate value';
+        }
       }
       else if (!rna.id)
@@ -903 +911 @@
     if (response.rna.length == 0)
     {
-      alert('Could not find any unprocessed RNA at this time.');
+      return 'Could not find any unprocessed RNA at this time.';
     }
     
@@ -1549 +1557 @@
 }
 .plate.hide-quality-score .quality-score
+{
+  display: none;
+}
+.plate.hide-qiacube-date .qiacube-date
 {
   display: none;
@@ -1808 +1820 @@
             <td>
               <input type="checkbox" name="volumes" id="volumes" onclick="toggleInfo('volumes')"><label for="volumes">Used volume+water</label><br>
+              <input type="checkbox" name="qiacube-date" id="qiacube-date" onclick="toggleInfo('qiacube-date')"><label for="qiacube-date">QiaCube date</label><br>
             </td>
           </tr>
@@ -1911 +1924 @@
         </div>
 
-        <table class="plate hide-volumes hide-ndconc hide-quality-score" style="margin: 1em 1em 0 1em;" id="plate"
+        <table class="plate hide-volumes hide-ndconc hide-quality-score hide-qiacube-date" style="margin: 1em 1em 0 1em;" id="plate"
           onmouseup="contextEvent(event)"
           oncontextmenu="contextEvent(event)"
@@ -1958 +1971 @@
             {
               %>
-              <td id="well.<%=r%>.<%=c%>" 
+              <td id="well.<%=r%>.<%=c%>" class="well empty primary"
                 onclick="toggleWell(<%=r%>,<%=c%>)"
                 onmouseenter="highlightReplicated(<%=r%>, <%=c%>, true)" 
                 onmouseleave="highlightReplicated(<%=r%>, <%=c%>, false)"
-                title="Select/deselect this well"></td>
+                title="Select/deselect this well">empty</td>
               <%
             }

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

@@ -305 +305 @@
     if (rnaqc.size() > 0)
     {
-      lastQc = rnaqc.get(0);
       Date lastQcDate = null;
       // Try to find the last QC run on either Caliper or BioAnalyzer
@@ -323 +322 @@
         BioWell well = qc.getBioWell();
         Date qcDate = null;
+        // Try to get QC date from RNAQC reaction plate
         if (well != null)
         {
@@ -328 +328 @@
           qcDate = (Date)Annotationtype.QC_RUN_DATE.getAnnotationValue(dc, plate);
         }
+        // If not found, get creation date from extract
         if (qcDate == null)
         {
           qcDate = qc.getCreationEvent().getEventDate();
         }
-        if ((lastQcDate == null && qcDate != null) || (qcDate != null && qcDate.after(lastQcDate)))
+        
+        // Use the current RNAQC if this is the first found or if the date is after
+        if (lastQc == null || lastQcDate != null && qcDate != null && qcDate.after(lastQcDate))
         {
           lastQcDate = qcDate;

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

@@ -301 +301 @@
           r.setAnnotation("remainingQuantity", r.getExtract().getRemainingQuantity());
           r.loadAnnotations(dc, "NDConc", Annotationtype.ND_CONC, null);
+          r.loadAnnotations(dc, "QiaCubeDate", Annotationtype.QIACUBE_DATE, Reggie.CONVERTER_DATE_TO_STRING);
           r.setAnnotation("comment", r.getExtract().getDescription());
           jsonRna.add(r.asJSONObject());
@@ -316 +317 @@
         JSONArray jsonIgnore = (JSONArray)jsonReq.get("ignore");
         
+        Date startDate = Reggie.CONVERTER_STRING_TO_DATE.convert((String)jsonReq.get("startDate"));
         Float remainingQuantityLimit = JsonUtil.getAsFloat(jsonReq, "remainingQuantity");
         Float qualityScoreLimit = JsonUtil.getAsFloat(jsonReq, "qualityScore");
@@ -331 +333 @@
         }
         
-        // Filter for non-empty creation date
+        // Filter for non-empty creation date or creation date after startdate
         query.join(Hql.innerJoin("creationEvent", "ce"));
-        query.restrict(Restrictions.neq(Hql.property("ce", "eventDate"), null));
+        if (startDate == null)
+        {
+          query.restrict(Restrictions.neq(Hql.property("ce", "eventDate"), null));
+        }
+        else
+        {
+          query.restrict(Restrictions.gteq(Hql.property("ce", "eventDate"), Expressions.parameter("startDate", startDate, Type.DATE)));
+        }
+        
         // Filter on parent != null (to get rid of 'Stratagene'
         query.restrict(Restrictions.neq(Hql.property("parent"), null));
@@ -390 +400 @@
             r.loadBioPlateLocation();
             Float qualityScore = r.loadRnaQc(dc);
+            if (qualityScore == null) continue; // QC has not been measuered; ignore
+            
             r.setAnnotation("remainingQuantity", remainingQuantity);
             r.loadAnnotations(dc, "NDConc", Annotationtype.ND_CONC, null);
+            r.loadAnnotations(dc, "QiaCubeDate", Annotationtype.QIACUBE_DATE, Reggie.CONVERTER_DATE_TO_STRING);
             
             if (reProcess)
@@ -410 +423 @@
               if (okToProcess && qualityScoreLimit != null)
               {
-                if (qualityScore == null || qualityScore < qualityScoreLimit)
+                if (qualityScore < qualityScoreLimit)
                 {
                   okToProcess = false;