Changeset 2125

Timestamp:

Nov 8, 2013, 2:28:14 PM (8 years ago)

Author:

Nicklas Nordborg

Message:

References #489: Histology scoring wizard

Implemented saving of scores. There are still some rough corners and error handling to take care of.

Location:

extensions/net.sf.basedb.reggie/branches/ticket-489

Files:

• resources/sampleproc/histology_score.jsp (modified) (24 diffs)
• src/net/sf/basedb/reggie/dao/HeGlass.java (modified) (3 diffs)
• src/net/sf/basedb/reggie/servlet/HistologyServlet.java (modified) (2 diffs)

extensions/net.sf.basedb.reggie/branches/ticket-489/resources/sampleproc/histology_score.jsp

@@ -35 +35 @@
 
 <script language="JavaScript">
-var debug = 1;
+var debug = 0;
 var currentStep = 1;
 var selectedSample;
 var heGlass;
+
+var SCORES = ['ScoreInvasiveCancer', 'ScoreInsituCancer', 'ScoreLymphocytes', 'ScoreNormal', 'ScoreStroma', 'ScoreFat'];
+var FIELDS = ['score_invasive_cancer', 'score_insitu_cancer', 'score_lymphocytes', 'score_normal', 'score_stroma', 'score_fat'];
 
 function init()
@@ -68 +71 @@
         var sample = glass.samples[sampleNo];
         
+        saveOriginalProperties(sample);
+        
         // Save ID of HE glass since we need that later
         sample.heGlassId = glass.id;
@@ -78 +83 @@
         
         // Calculate sum of scores
-        var total = calculateTotalScore(sample)
+        var total = calculateTotalScore(sample);
         
         // Generate text inside table cell
-        var html = sample.name.replace(/\.he\d+$/, '');
+        var html = '<div class="sample-name">'+sample.name.replace(/\.he\d+$/, '')+'</div>';
         html += '<div class="progress" id="'+sample.id+'.progress">' + total + '%</div>';
         
@@ -95 +100 @@
     if (firstGoodSample != null)
     {
+      Main.show('score-container');
       selectSample(firstGoodSample);
-      Main.show('score-container');
     }
     Main.show('gocreate');
+    window.addEventListener('beforeunload', confirmIfModified);
+
   }
   else
@@ -118 +125 @@
   // Wait a second until loading uncompleted HE glass
   setTimeout(loadUncompletedHeGlass, 1000);
-}
-
-function findHeGlass(glassName)
+  
+}
+
+/**
+  Remember the original properties so that we know if
+  a sample has been modified.
+*/
+function saveOriginalProperties(sample)
+{
+  var o = {};
+  for (var i = 0; i < SCORES.length; i++)
+  {
+    var p = SCORES[i];
+    o[p] = sample[p]; 
+  }
+  
+  o.GoodStain = sample.GoodStain;
+  o.ScoreComplete = sample.ScoreComplete;
+  sample.o = o;
+  sample.isModified = false;
+}
+
+/**
+  Check if a sample has been modified.
+*/
+function isModified(sample, useCache)
+{
+  if (useCache)
+  {
+    return sample.isModified;
+  }
+  var o = sample.o;
+  for (var p in o)
+  {
+    if (o[p] != sample[p]) return true;
+  }
+  return false;
+}
+
+function findHeGlass(glassName, autoFind)
 {
   var frm = document.forms['reggie'];
-  if (!glassName)
+  if (!glassName && autoFind != true)
   {
     glassName = frm.findGlassName.value;
@@ -135 +179 @@
     }
   }
-  location.href = '<%=home%>/sampleproc/histology_score.jsp?ID=<%=ID%>&name='+encodeURIComponent(glassName);
+  var url =  '<%=home%>/sampleproc/histology_score.jsp?ID=<%=ID%>';
+  if (glassName)
+  {
+    url += '&name='+encodeURIComponent(glassName);
+  }
+  
+  location.href = url;
 }
 
@@ -224 +274 @@
   }
   
-  if (sample.ScoreTotal == 0)
+  if (sample.ScoreTotal == null)
   {
     className += ' score-none';
@@ -235 +285 @@
   {
     className += ' score-complete';
+  }
+  
+  if (isModified(sample))
+  {
+    className += ' modified';
   }
   
@@ -254 +309 @@
   
   // Scores
-  frm.score_invasive_cancer.value = sample.ScoreInvasiveCancer;
-  frm.score_insitu_cancer.value = sample.ScoreInsituCancer;
-  frm.score_lymphocytes.value = sample.ScoreLymphocytes;
-  frm.score_normal.value = sample.ScoreNormal;
-  frm.score_stroma.value = sample.ScoreStroma;
-  frm.score_fat.value = sample.ScoreFat;
+  for (var i = 0; i < SCORES.length; i++)
+  {
+    frm[FIELDS[i]].value = sample[SCORES[i]];
+  }
   
   // Total score + score complete
@@ -266 +319 @@
   if (total == 100)
   {
-    frm.score_complete.disabled = false;
-    frm.score_complete.checked = sample.ScoreComplete;
-    setInputStatus('score_total', '', 'valid');
+    if (sample.numNullScores == 0)
+    {
+      frm.score_complete.disabled = false;
+      frm.score_complete.checked = sample.ScoreComplete;
+      setInputStatus('score_total', '', 'valid');
+    }
+    else
+    {
+      frm.score_complete.disabled = true;
+      frm.score_complete.checked = false;
+      setInputStatus('score_total', 'Enter 0 in empty fields to complete scoring', 'warning');
+    }
   }
   else
@@ -315 +377 @@
   var frm = document.forms['reggie'];
 
-  selectedSample.ScoreInvasiveCancer = toScore(frm.score_invasive_cancer.value);
-  selectedSample.ScoreInsituCancer = toScore(frm.score_insitu_cancer.value);
-  selectedSample.ScoreLymphocytes = toScore(frm.score_lymphocytes.value);
-  selectedSample.ScoreNormal = toScore(frm.score_normal.value);
-  selectedSample.ScoreStroma = toScore(frm.score_stroma.value);
-  selectedSample.ScoreFat = toScore(frm.score_fat.value);
+  for (var i = 0; i < SCORES.length; i++)
+  {
+    selectedSample[SCORES[i]] = toScore(frm[FIELDS[i]].value);
+  }
   
   var oldTotal = selectedSample.ScoreTotal;
+  var oldNumNull = selectedSample.numNullScores;
+  
   var total = calculateTotalScore(selectedSample);
   
@@ -330 +392 @@
   if (total == 100)
   {
-    frm.score_complete.disabled = false;
-    if (oldTotal != total)
-    {
-      // Only check the 'Score complete' if value has changed
-      frm.score_complete.checked = true;
-      selectedSample.ScoreComplete = true;
-    }
-    setInputStatus('score_total', '', 'valid');
+    if (selectedSample.numNullScores == 0)
+    {
+      // All scores have been entered
+      frm.score_complete.disabled = false;
+      if (oldTotal != total || oldNumNull != selectedSample.numNullScores)
+      {
+        // Only check the 'Score complete' if value has changed
+        frm.score_complete.checked = true;
+        selectedSample.ScoreComplete = true;
+      }
+      setInputStatus('score_total', '', 'valid');
+    }
+    else
+    {
+      frm.score_complete.disabled = true;
+      frm.score_complete.checked = false;
+      selectedSample.ScoreComplete = false;
+      setInputStatus('score_total', 'Enter 0 in empty fields to complete scoring', 'warning');
+    }
   }
   else
@@ -343 +416 @@
     frm.score_complete.disabled = true;
     frm.score_complete.checked = false;
-    selectedSample.ScoreComplete = false;
-    setInputStatus('score_total', 'Not 100%', 'warning');
+    
+    if (selectedSample.ScoreTotal != null)
+    {
+      selectedSample.ScoreComplete = false;
+      setInputStatus('score_total', 'Not 100%', 'warning');
+    }
+    else
+    {
+      selectedSample.ScoreComplete = null;
+      setInputStatus('score_total', '', '');
+    }
   }
 
@@ -352 +434 @@
 function calculateTotalScore(sample)
 {
-  var total = sumScore(sample.ScoreInvasiveCancer);
-  total += sumScore(sample.ScoreInsituCancer);
-  total += sumScore(sample.ScoreLymphocytes);
-  total += sumScore(sample.ScoreNormal);
-  total += sumScore(sample.ScoreStroma);
-  total += sumScore(sample.ScoreFat);
-  sample.ScoreTotal = total;
+  var total = 0;
+  var numNull = 0;
+  for (var i = 0; i < SCORES.length; i++)
+  {
+    var score = sample[SCORES[i]];
+    total += sumScore(score);
+    if (score == null) numNull++;
+  }
+  // Set summed total, null only if all values are null
+  sample.ScoreTotal = total == 0 && numNull == SCORES.length ? null : total;
+  sample.numNullScores = numNull;
   return total;
 }
@@ -394 +480 @@
       if (sample.well.location == selectedSample.well.location)
       {
-        sample.GoodStain = false;
-        var td = document.getElementById(glass.id+'-'+sample.well.location);
-        Main.removeClass(td, 'good-stain');
+        sample.GoodStain = null;
+        setSampleClassName(sample);
       }
     }
   }
   
-  selectedSample.GoodStain = frm.good_stain.checked;
+  selectedSample.GoodStain = frm.good_stain.checked ? true : null;
   frm.good_stain.disabled = true;
   setSampleClassName(selectedSample);
@@ -423 +508 @@
   }
   finally
-  {
-    //hideLoadingAnimation();
-  }
+  {}
   
   if (debug) Main.debug(request.responseText);
@@ -443 +526 @@
       
         html += '<div class="menuitem enabled" id="glass-'+glass.id+'">';
-        html += Main.encodeTags(glass.name)+'</div>';
+        html += Main.encodeTags(glass.name)+' ('+glass.numUncompleteSamples +')</div>';
       }
       setInnerHTML('select-uncompleted-heglass-menu', html);
@@ -473 +556 @@
   findHeGlass(event.target.innerHTML);
 }
+
+/**
+  Confirm if leaving the page is ok. If no event is passed this method
+  is called manually and need to display dialog, otherwise the browser
+  is taking care of this automatically.
+*/
+function confirmIfModified(event)
+{
+  var numModified = 0;
+  for (var glassNo = 0; glassNo < heGlass.length; glassNo++)
+  {
+    var glass = heGlass[glassNo];
+    for (var sampleNo = 0; sampleNo < glass.samples.length; sampleNo++)
+    {
+      var sample = glass.samples[sampleNo];
+      if (isModified(sample))
+      {
+        numModified++;
+      }
+    }
+  }
+  
+  var okToContinue = true;
+  if (numModified > 0)
+  {
+    if (event) 
+    {
+      event.returnValue = 'There are unsaved modifications. Continue?';
+    }
+    else
+    {
+      if (!confirm('There are unsaved modifications. Continue?'))
+      {
+        okToContinue = false;
+      }
+    }
+  }
+  
+  return okToContinue;
+}
+
+function saveModified()
+{
+  var samples = [];
+  var glassInfo = [];
+  
+  for (var glassNo = 0; glassNo < heGlass.length; glassNo++)
+  {
+    var glass = heGlass[glassNo];
+    var scoreCompleteForGlass = true;
+    for (var sampleNo = 0; sampleNo < glass.samples.length; sampleNo++)
+    {
+      var sample = glass.samples[sampleNo];
+      if (isModified(sample))
+      {
+        samples[samples.length] = sample;
+      }
+      
+      if (sample.GoodStain && sample.ScoreComplete != true || sample.ScoreComplete == false)
+      {
+        scoreCompleteForGlass = false;
+      }
+    }
+    
+    var tmp = {};
+    tmp.id = glass.id;
+    tmp.ScoreComplete = scoreCompleteForGlass;
+    glassInfo[glassInfo.length] = tmp;
+  }
+  
+  if (samples.length == 0)
+  {
+    if (!confirm('Nothing has changed! Continue saving?'))
+    {
+      return;
+    }
+  }
+  
+  Main.hide('score-container');
+  Main.addClass(document.getElementById('he-glass-container'), 'disabled');
+    
+  var submitInfo = {};
+  submitInfo.samples = samples;
+  submitInfo.heGlass = glassInfo;
+  
+  if (debug) Main.debug(JSON.stringify(submitInfo));      
+  var request = Ajax.getXmlHttpRequest();
+  
+  try
+  {
+    showLoadingAnimation('Saving...');
+    var url = '../Histology.servlet?ID=<%=ID%>&cmd=SaveHeScore';
+    request.open("POST", url, false);
+    request.setRequestHeader("Content-Type", "application/json"); 
+    request.send(JSON.stringify(submitInfo));
+  }
+  finally
+  {
+    hideLoadingAnimation();
+  }
+
+  if (debug) Main.debug(request.responseText);
+
+
+  var response = JSON.parse(request.responseText);
+  if (response.status != 'ok')
+  {
+    setFatalError(response.message);
+    return false;
+  }
+  
+  var msg = '<ul>';
+  for (var i = 0; i < response.messages.length; i++)
+  {
+    msg += '<li>' + response.messages[i];
+  }
+  msg += '</ul>';
+  setInnerHTML('done', msg);
+  
+  Main.show('done');
+  Main.show('gonext');
+  Main.hide('gocreate');
+
+}
+
 </script>
 <style>
@@ -585 +793 @@
 {
   background-color: #D8FFFF;
-  border: 2px solid #2288AA;
-  border-radius: 4px;
-  padding: 1px;
 }
 
@@ -609 +814 @@
 {
   background-image: url('../images/score-complete.png');
+}
+
+td.modified .sample-name:after
+{
+  content: ' *';
+  color: #2244FF;
 }
 
@@ -686 +897 @@
   %>
   
-  <div id="select-uncompleted-heglass" class="menu vertical" style="width: 150px; display: none;"
+  <div id="select-uncompleted-heglass" class="menu vertical" style="width: 150px; display: none; z-index: 999;"
     onclick="uncompletedGlassSelected(event)">
     <div id="select-uncompleted-heglass-menu"></div>
@@ -693 +904 @@
   <form name="reggie" onsubmit="return false;">
   
-  <table class="stepform">
+  <table class="stepform" id="step.1.section">
   <tr>
     <td rowspan="3" class="stepno">1</td>
@@ -827 +1038 @@
             title="Uncheck if scoring is not complete"></span></td>
           <td class="status" id="score_complete.status"></td>
-          <td class="help">Uncheck 
-            if scoring is not complete. Disabled if the total score is not 100%.
+          <td class="help">
+            Uncheck if scoring is not complete. Disabled if some scores 
+            are missing or the total score is not 100%.
           </td>
         </tr>
@@ -855 +1067 @@
     <tr>
       <td><base:button id="gocancel" title="Cancel" onclick="goRestart(false)" style="display: none;" /></td>
-      <td><base:button id="gonext" title="Next" image="<%=home+"/images/gonext.png"%>" onclick="goNext(true)" style="display: none;" /></td>
-      <td><base:button id="gocreate" title="Save" image="<%=home+"/images/gonext.png"%>" onclick="goCreate()" style="display: none;" /></td>
+      <td><base:button id="gonext" title="Next HE glass set" image="<%=home+"/images/gonext.png"%>" onclick="findHeGlass(null, true)" style="display: none;" /></td>
+      <td><base:button id="gocreate" title="Save" image="<%=home+"/images/gonext.png"%>" onclick="saveModified()" style="display: none;" /></td>
       <td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" onclick="goRestart(true)" style="display: none;"/></td>
       <td id="gonext.message" class="message"></td>

extensions/net.sf.basedb.reggie/branches/ticket-489/src/net/sf/basedb/reggie/dao/HeGlass.java

@@ -12 +12 @@
 import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.Sample;
+import net.sf.basedb.core.query.Annotations;
+import net.sf.basedb.core.query.Expressions;
 import net.sf.basedb.core.query.Hql;
+import net.sf.basedb.core.query.Orders;
 import net.sf.basedb.core.query.Restrictions;
 import net.sf.basedb.reggie.JsonUtil;
@@ -90 +93 @@
     query.join(Hql.innerJoin("bw", "bioPlate", "bp"));
     query.restrict(Restrictions.eq(Hql.alias("bp"), Hql.entity(heGlass)));
+    query.order(Orders.asc(Hql.property("bw", "row")));
+    query.order(Orders.asc(Hql.property("bw", "column")));
     
     for (Sample s : query.list(dc))
@@ -110 +115 @@
       jsonSamples.add(jsonSample);
     }
+  }
+  
+  public long countUncompletedSamples(DbControl dc)
+  {
+    BioPlate heGlass = getBioPlate();
+    ItemQuery<Sample> query = Sample.getQuery();
+    query.join(Hql.innerJoin("bioWell", "bw"));
+    query.join(Hql.innerJoin("bw", "bioPlate", "bp"));
+    query.restrict(Restrictions.eq(Hql.alias("bp"), Hql.entity(heGlass)));
+    query.join(Annotations.leftJoin(null, Annotationtype.SCORE_COMPLETE.load(dc), "sc"));
+    query.join(Annotations.leftJoin(null, Annotationtype.GOOD_STAIN.load(dc), "gs"));
+    query.restrict(
+      Restrictions.or(
+        Restrictions.eq(Hql.alias("sc"), Expressions.bool(false)),
+        Restrictions.and(
+            Restrictions.eq(Hql.alias("gs"), Expressions.bool(true)),
+            Restrictions.eq(Hql.alias("sc"), null)
+          )
+        ));
     
+    query.order(Orders.asc(Hql.property("bw", "row")));
+    query.order(Orders.asc(Hql.property("bw", "column")));
+    return query.count(dc);
   }
 

extensions/net.sf.basedb.reggie/branches/ticket-489/src/net/sf/basedb/reggie/servlet/HistologyServlet.java

@@ -427 +427 @@
         for (HeGlass heGlass : plates)
         {
+          heGlass.setAnnotation("numUncompleteSamples", heGlass.countUncompletedSamples(dc));
           jsonHeGlasses.add(heGlass.asJSONObject());
         }
@@ -769 +770 @@
         {
           dc.saveItem(stainEvent);
+        }
+        
+        dc.commit();
+      }
+      else if ("SaveHeScore".equals(cmd))
+      {
+        JSONObject jsonReq = (JSONObject)new JSONParser().parse(req.getReader());
+        JSONArray jsonSamples = (JSONArray)jsonReq.get("samples");
+        JSONArray jsonHeGlass = (JSONArray)jsonReq.get("heGlass");
+        dc = sc.newDbControl();
+
+        // Update scores on samples
+        for (int sampleNo = 0; sampleNo < jsonSamples.size(); ++sampleNo)
+        {
+          JSONObject jsonSample = (JSONObject)jsonSamples.get(sampleNo);
+          Number sampleId = (Number)jsonSample.get("id");
+          Boolean goodStain = (Boolean)jsonSample.get("GoodStain");
+          Boolean scoreComplete = (Boolean)jsonSample.get("ScoreComplete");
+          
+          Sample he = Sample.getById(dc, sampleId.intValue());
+          
+          Annotationtype.GOOD_STAIN.setAnnotationValue(dc, he, goodStain);
+          Annotationtype.SCORE_INVASIVE_CANCER.setAnnotationValue(dc, he, jsonSample.get("ScoreInvasiveCancer"));
+          Annotationtype.SCORE_INSITU_CANCER.setAnnotationValue(dc, he, jsonSample.get("ScoreInsituCancer"));
+          Annotationtype.SCORE_LYMPHOCYTES.setAnnotationValue(dc, he, jsonSample.get("ScoreLymphocytes"));
+          Annotationtype.SCORE_NORMAL.setAnnotationValue(dc, he, jsonSample.get("ScoreNormal"));
+          Annotationtype.SCORE_STROMA.setAnnotationValue(dc, he, jsonSample.get("ScoreStroma"));
+          Annotationtype.SCORE_FAT.setAnnotationValue(dc, he, jsonSample.get("ScoreFat"));
+          Annotationtype.SCORE_COMPLETE.setAnnotationValue(dc, he, scoreComplete);
+          he.setDescription(Values.getStringOrNull((String)jsonSample.get("comments")));
+          
+          if (Boolean.TRUE.equals(scoreComplete))
+          {
+            jsonMessages.add("Scoring complete for sample: " + he.getName() + (Boolean.TRUE.equals(goodStain) ? " (GoodStain)" : ""));
+          }
+          else if (Boolean.FALSE.equals(scoreComplete))
+          {
+            jsonMessages.add("Score updated for sample: " + he.getName() + " (Not complete)");
+          }
+          else
+          {
+            jsonMessages.add("Scores removed from sample: " + he.getName());
+          }
+        }
+        
+        // ScoreComplete on HE glass
+        for (int glassNo = 0; glassNo < jsonHeGlass.size(); ++glassNo)
+        {
+          JSONObject jsonGlass = (JSONObject)jsonHeGlass.get(glassNo);
+          Number glassId = (Number)jsonGlass.get("id");
+          Boolean scoreComplete = (Boolean)jsonGlass.get("ScoreComplete");
+          
+          BioPlate heGlass = BioPlate.getById(dc, glassId.intValue());
+          
+          Annotationtype.SCORE_COMPLETE.setAnnotationValue(dc, heGlass, scoreComplete);
+          
+          if (Boolean.TRUE.equals(scoreComplete))
+          {
+            jsonMessages.add("Scoring complete for HE glass: " + heGlass.getName());
+          }
+          else
+          {
+            jsonMessages.add("Score updated for HE glass: " + heGlass.getName() + " (Not complete)");
+            
+          }
         }