Changeset 2504

Timestamp:

Jun 13, 2014, 8:12:34 AM (9 years ago)

Author:

Nicklas Nordborg

Message:

References #604: New wizard "RNA dilution registration"

The lab protocol wizard now display dilution date and operator if it exists.

The mRNA registration wizard now only list plates that has a dilution date set and the dilution date/operator has been removed from that wizard.

Added link to the new wizard on the index page. The counters have been updated to count only plates with/without dilution date.

Location:

extensions/net.sf.basedb.reggie/branches/2.15-stable

Files:

• resources/index.jsp (modified) (5 diffs)
• resources/libprep/mrna_protocol.jsp (modified) (2 diffs)
• resources/libprep/mrna_protocol2.jsp (modified) (6 diffs)
• resources/libprep/mrna_registration.jsp (modified) (7 diffs)
• src/net/sf/basedb/reggie/servlet/MRnaServlet.java (modified) (6 diffs)

extensions/net.sf.basedb.reggie/branches/2.15-stable/resources/index.jsp

@@ -67 +67 @@
   var debug = false;
   var myPermissions = {};
+  var allCounts = {};
   
   function init()
@@ -187 +188 @@
       url = 'MRna.servlet?ID=<%=ID%>&cmd=CountRnaWithoutMRna';
     }
-    else if (what == 'mrna-plates')
-    {
-      url = 'MRna.servlet?ID=<%=ID%>&cmd=CountUnprocessedPlates&plateType=MRNA';
+    else if (what == 'undiluted-mrna-plates')
+    {
+      url = 'MRna.servlet?ID=<%=ID%>&cmd=CountUndilutedMRNAPlates';
+    }
+    else if (what == 'diluted-mrna-plates')
+    {
+      url = 'MRna.servlet?ID=<%=ID%>&cmd=CountDilutedMRNAPlates';
     }
     else if (what == 'cdna-plates')
@@ -322 +327 @@
       var count = error ? -1 : response.count;
       setCount('count.rna-without-mrna', count, 'RNA', msg);
-      startCounting('mrna-plates');
-    }
-    else if (currentCount == 'mrna-plates')
+      startCounting('undiluted-mrna-plates');
+    }
+    else if (currentCount == 'undiluted-mrna-plates')
+    {
+      var msg = error || 'Number of mRNA plates waiting for dilution';
+      var count = error ? -1 : response.count;
+      setCount('count.undiluted-mrna-plates', count, 'mRNA plates', msg);
+      startCounting('diluted-mrna-plates');
+    }
+    else if (currentCount == 'diluted-mrna-plates')
     {
       var msg = error || 'Number of mRNA plates waiting for registration';
       var count = error ? -1 : response.count;
-      setCount('count.mrna-plates.1', count, 'mRNA plates', msg);
-      setCount('count.mrna-plates.2', count, 'mRNA plates', msg);
+      setCount('count.diluted-mrna-plates', count, 'mRNA plates', msg);
+      setCount('count.mrna-plates', count + allCounts['count.undiluted-mrna-plates'], 'mRNA plates', 'Number of mRNA plates waiting for processing');
       startCounting('cdna-plates');
     }
@@ -410 +422 @@
   function setCount(id, count, unit, msg)
   {
+    allCounts[id] = count;
     var div = document.getElementById(id);
     div.title = msg;
@@ -618 +631 @@
           
           <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/mrna_protocol.jsp?ID=<%=ID%>"
-            >Lab protocols for mRNA and cDNA preparation</span> <span class="counter" id="count.mrna-plates.1" title="Counting..."><img src="images/loading-small.gif"></span>
-          
+            >Lab protocols for mRNA and cDNA preparation</span> <span class="counter" id="count.mrna-plates" title="Counting..."><img src="images/loading-small.gif"></span>
+          
+          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/rna_dilution_registration.jsp?ID=<%=ID%>"
+            >RNA dilution registration</span> <span class="counter" id="count.undiluted-mrna-plates" title="Counting..."><img src="images/loading-small.gif"></span>
+
           <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/mrna_registration.jsp?ID=<%=ID%>"
-            >mRNA registration and quality control results</span> <span class="counter" id="count.mrna-plates.2" title="Counting..."><img src="images/loading-small.gif"></span>
+            >mRNA registration and quality control results</span> <span class="counter" id="count.diluted-mrna-plates" title="Counting..."><img src="images/loading-small.gif"></span>
           
           <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/cdna_registration.jsp?ID=<%=ID%>"

extensions/net.sf.basedb.reggie/branches/2.15-stable/resources/libprep/mrna_protocol.jsp

@@ -42 +42 @@
     {
       var bioplate = bioplates[i];
-      var option = new Option(bioplate.name, bioplate.id);
+      var name = bioplate.name;
+      if (bioplate.DilutionDate)
+      {
+        name += ' (diluted ' + formatDate(bioplate.DilutionDate) + ')';
+      }
+      var option = new Option(name, bioplate.id);
       option.bioplate = bioplate;
       plates.options[plates.length] = option;
@@ -56 +61 @@
     setFatalError(msg);
   }
+}
+
+function formatDate(value)
+{
+  if (!value) return '';
+  if (value.length == 8)
+  {
+    // YYYYMMDD
+    value = value.substr(0, 4) + '-' + value.substr(4, 2) + '-' + value.substr(6, 2);
+  }
+  else if (value.length == 13)
+  {
+    // YYYYMMDD HHMM
+    value = value.substr(0, 4) + '-' + value.substr(4, 2) + '-' + value.substr(6, 2) + ' ' + value.substr(9, 2) + ':' + value.substr(11, 2);
+  }
+  return value;
 }
 

extensions/net.sf.basedb.reggie/branches/2.15-stable/resources/libprep/mrna_protocol2.jsp

@@ -91 +91 @@
     }
     
+    var plate = response.plate;
+    if (plate.DilutionDate)
+    {
+      setInnerHTML('dilution-date', formatDate(plate.DilutionDate));
+      setInnerHTML('dilution-operator', plate.DilutionOperator);
+    }
+    
     var list = response.mrna;
     // Find QUANTITY_REGULAR = lowest used value
@@ -115 +122 @@
     }
     %>
+    Main.show('protocol');
+  }
+  
+  function formatDate(value)
+  {
+    if (!value) return '';
+    if (value.length == 8)
+    {
+      // YYYYMMDD
+      value = value.substr(0, 4) + '-' + value.substr(4, 2) + '-' + value.substr(6, 2);
+    }
+    else if (value.length == 13)
+    {
+      // YYYYMMDD HHMM
+      value = value.substr(0, 4) + '-' + value.substr(4, 2) + '-' + value.substr(6, 2) + ' ' + value.substr(9, 2) + ':' + value.substr(11, 2);
+    }
+    return value;
   }
   
@@ -534 +558 @@
   <h1>Lab protocol for mRNA and cDNA preparation <span class="reggie">Reggie <%=reggie.getAbout().getVersion() %></span></h1>
 
+  <div class="loading" id="loading" style="display: none;"><table><tr><td><img src="../images/loading.gif"></td><td id="loading.msg">Please wait...</td></tr></table></div>
+  <div class="messagecontainer error" id="errorMessage" style="display: none;"></div>
+
+  <div id="protocol" style="display: none;">
   <table style="width: 100%;" class="protocolheader">
   <tr style="border-bottom: 1px solid #000000;">
@@ -545 +573 @@
     <td rowspan="5" colspan="2" style="width: 50%; border-right: 1px solid #000000;"><%=HTML.niceFormat(plate.getDescription()) %></td>
     <td style="border-right: 1px solid #000000;">Dilution</td>
-    <td style="border-right: 1px solid #000000;"></td>
-    <td></td>
+    <td style="border-right: 1px solid #000000;" id="dilution-date"></td>
+    <td id="dilution-operator"></td>
   </tr>
   <tr style="border-top: 1px solid #CCCCCC;">
@@ -570 +598 @@
   </table>
 
-  <div class="loading" id="loading" style="display: none;"><table><tr><td><img src="../images/loading.gif"></td><td id="loading.msg">Please wait...</td></tr></table></div>
-  <div class="messagecontainer error" id="errorMessage" style="display: none;"></div>
   <%
   if (view.equals("list"))
@@ -690 +716 @@
   <i>Low quantity = The remaining quantity is too low for the RNA to be re-processed one more time</i>
   </div>
+  </div>
 </body>
 </html>

extensions/net.sf.basedb.reggie/branches/2.15-stable/resources/libprep/mrna_registration.jsp

@@ -100 +100 @@
   {
     showLoadingAnimation('Loading histology work lists...');
-    var url = '../MRna.servlet?ID=<%=ID%>&cmd=GetUnprocessedPlates&plateType=MRNA';   
+    var url = '../MRna.servlet?ID=<%=ID%>&cmd=GetUnprocessedPlates&plateType=MRNA&onlyDiluted=1';   
     request.open("GET", url, false);  
     request.send(null);
@@ -153 +153 @@
   }
   
-  frm.dilutionDate.focus();
+  frm.purificationDate.focus();
 }
 
@@ -308 +308 @@
   if (!pdfIsValid || !commentsIsValid) return false;
   
-  if (dateIsValid['dilutionDate'] == false) return false;
   if (dateIsValid['purificationDate'] == false) return false;
   if (dateIsValid['fragmentationDate'] == false) return false;
@@ -339 +338 @@
   frm['pdf.path'].disabled = true;
   Main.addClass(document.getElementById('btnPdf'), 'disabled');
-  frm.dilutionDate.disabled = true;
-  frm.dilutionOperator.disabled = true;
   frm.purificationDate.disabled = true;
   frm.purificationOperator.disabled = true;
@@ -355 +352 @@
   submitInfo.failed = document.getElementById('outcomeSuccess').checked ? false : true;
   submitInfo.pdf = pdfId;
-  submitInfo.dilutionDate = frm.dilutionDate.value;
-  submitInfo.dilutionOperator = frm.dilutionOperator.value;
   submitInfo.purificationDate = frm.purificationDate.value;
   submitInfo.purificationOperator = frm.purificationOperator.value;
@@ -457 +452 @@
         <td class="help"><span id="bioplate.message" class="message" style="display: none;"></span>
           Select an existing mRNA bioplate. The list contain all mRNA bioplates that
-          has not yet been processed (determined by the absence of a 'creation' date).
+          has been diluted, but not yet registered as completed (determined by the absence of a 
+          'creation' date).
         </td>
       </tr>
@@ -495 +491 @@
         <td><b>Operator</b></td>
         <td class="status"></td>
-        <td class="help" rowspan="5">
+        <td class="help" rowspan="4">
           <span id="mrnaDate.message" class="message" style="display: none;"></span>
           Enter date and operator for each step in the mRNA preparation.
           (YYYYMMDD or MMDD)
         </td>
-      </tr>
-      <tr>
-        <td class="subprompt">Dilution</td>
-        <td>
-          <input type="text" name="dilutionDate" maxlength="10" style="width: 8em;"
-            onblur="dateOnChange('dilutionDate')" onkeypress="focusOnEnter(event, 'dilutionOperator')">
-            <base:icon 
-              onclick="Dates.selectDate('Dilution date', 'reggie', 'dilutionDate', 'setDate', 'yyyyMMdd')"
-              image="calendar.png" 
-              tooltip="Select a date from a calendar" 
-              tabindex="-1"
-            />
-        </td>
-        <td>
-          <input type="text" name="dilutionOperator" value="<%=HTML.encodeTags(user.getName()) %>" 
-            style="width: 95%;" maxlength="255" onkeypress="focusOnEnter(event, 'purificationDate')">
-        </td>
-        <td class="status" id="dilutionDate.status"></td>
       </tr>
       <tr>

extensions/net.sf.basedb.reggie/branches/2.15-stable/src/net/sf/basedb/reggie/servlet/MRnaServlet.java

@@ -123 +123 @@
         json.put("count", count);
       }
+      else if ("CountUndilutedMRNAPlates".equals(cmd))
+      {
+        dc = sc.newDbControl();
+        BioplateType plateType = BioplateType.MRNA;
+        
+        // Find plates of the given 'plate type' without 'dilution date' and no 'destroyed' flag set
+        ItemQuery<BioPlate> query = BioPlate.getQuery();
+        query.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+        // Must not have a DILUTION_DATE annotation
+        query.join(Annotations.leftJoin(null, Annotationtype.DILUTION_DATE.load(dc), "dd"));
+        query.restrict(Restrictions.eq(Hql.alias("dd"), null));
+        plateType.addFilter(dc, query, true);
+        query.setCacheResult(true);
+        long count = query.count(dc);
+        json.put("count", count);
+      }
+      else if ("CountDilutedMRNAPlates".equals(cmd))
+      {
+        dc = sc.newDbControl();
+        BioplateType plateType = BioplateType.MRNA;
+        
+        // Find plates of the given 'plate type' with 'dilution date', but no 'create date' and no 'destroyed' flag set
+        ItemQuery<BioPlate> query = BioPlate.getQuery();
+        query.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+        // Must have a DILUTION_DATE annotation
+        query.join(Annotations.leftJoin(null, Annotationtype.DILUTION_DATE.load(dc), "dd"));
+        query.restrict(Restrictions.neq(Hql.alias("dd"), null));
+        query.restrict(Restrictions.eq(Hql.property("eventDate"), null));
+        plateType.addFilter(dc, query, true);
+        query.setCacheResult(true);
+        long count = query.count(dc);
+        json.put("count", count);
+      }
       else if ("GetUnprocessedPlates".equals(cmd))
       {
@@ -133 +166 @@
         query.restrict(Restrictions.eq(Hql.property("eventDate"), null));
         plateType.addFilter(dc, query, true);
+        
+        if (req.getParameter("onlyDiluted") != null)
+        {
+          // Must have a DILUTION_DATE annotation
+          query.join(Annotations.leftJoin(null, Annotationtype.DILUTION_DATE.load(dc), "dd"));
+          query.restrict(Restrictions.neq(Hql.alias("dd"), null));
+        }
+        
         query.order(Orders.desc(Hql.property("id")));
         
@@ -143 +184 @@
           jsonPlate.put("name", plate.getName());
           jsonPlate.put("comments", plate.getDescription());
+          if (plateType == BioplateType.MRNA)
+          {
+            jsonPlate.put("DilutionDate", Reggie.CONVERTER_DATE_TO_STRING.convert((Date)Annotationtype.DILUTION_DATE.getAnnotationValue(dc, plate)));
+            jsonPlate.put("DilutionOperator", Annotationtype.DILUTION_OPERATOR.getAnnotationValue(dc, plate));
+          }
           jsonPlate.put("poolSchema", Annotationtype.POOL_SCHEMA.getAnnotationValue(dc, plate));
           jsonPlates.add(jsonPlate);
@@ -199 +245 @@
         BioPlate mRnaPlate = BioPlate.getById(dc, mRnaPlateId);
 
+        JSONObject jsonPlate = new JSONObject();
+        jsonPlate.put("id", mRnaPlate.getId());
+        jsonPlate.put("name", mRnaPlate.getName());
+        jsonPlate.put("comments", mRnaPlate.getDescription());
+        jsonPlate.put("DilutionDate", Reggie.CONVERTER_DATE_TO_STRING.convert((Date)Annotationtype.DILUTION_DATE.getAnnotationValue(dc, mRnaPlate)));
+        jsonPlate.put("DilutionOperator", Annotationtype.DILUTION_OPERATOR.getAnnotationValue(dc, mRnaPlate));
+        jsonPlate.put("poolSchema", Annotationtype.POOL_SCHEMA.getAnnotationValue(dc, mRnaPlate));
+        
         ItemQuery<Extract> query = Extract.getQuery();
         query.join(Hql.innerJoin(null, "bioWell", "bw", true));
@@ -241 +295 @@
                 
         json.put("mrna", jsonMRna);
+        json.put("plate", jsonPlate);
       }
 
@@ -606 +661 @@
         
         // Dates and operators 
-        Annotationtype.DILUTION_DATE.setAnnotationValue(dc, mrnaPlate, Reggie.CONVERTER_STRING_TO_DATE.convert((String)jsonReq.get("dilutionDate")));
-        Annotationtype.DILUTION_OPERATOR.setAnnotationValue(dc, mrnaPlate, Values.getStringOrNull((String)jsonReq.get("dilutionOperator")));
         Annotationtype.PURIFICATION_DATE.setAnnotationValue(dc, mrnaPlate, Reggie.CONVERTER_STRING_TO_DATE.convert((String)jsonReq.get("purificationDate")));
         Annotationtype.PURIFICATION_OPERATOR.setAnnotationValue(dc, mrnaPlate, Values.getStringOrNull((String)jsonReq.get("purificationOperator")));