Changeset 1307

Timestamp:

Mar 4, 2011, 11:33:52 AM (11 years ago)

Author:

Nicklas Nordborg

Message:

References #291: Personal information registration

Allow laterality=unknown option since that is not always known at the time of registration. On the other hand, if a laterality has been selected but the associated specimen tubes doesn't have that information the specimen tubes will be updated with the selected laterality.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/persinfo.jsp (modified) (9 diffs)
• src/net/sf/basedb/reggie/Reggie.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/PersonalRegistrationServlet.java (modified) (3 diffs)

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

@@ -179 +179 @@
   
   var laterality = selectedLaterality.value;
-  if (laterality != 'LEFT' && laterality != 'RIGHT')
+  if (laterality.match(/\d+/))
   {
     // It is the ID of an existing case
@@ -192 +192 @@
     }
   }
-  
-  if (!laterality) return;
-  
-  // No specimen tubes
+  else  if (laterality == '') 
+  {
+    laterality = null;
+  }
+    
+  // No specimen tubes?
   if (!caseInfo.specimen || caseInfo.specimen.length == 0) return;
+  
   for (var i = 0; i < caseInfo.specimen.length; i++)
   {
     var specimen = caseInfo.specimen[i];
-    if (specimen.laterality && specimen.laterality != laterality)
-    {
-      setInputStatus('laterality', 'Not same laterality as specimen tubes', 'warning');
+    if (specimen.laterality != laterality)
+    {
+      if (specimen.laterality == null)
+      {
+        setInputStatus('laterality', 'Specimen tubes are updated to: ' + laterality, 'valid')
+      }
+      else
+      {
+        setInputStatus('laterality', 'Not same laterality as specimen tubes', 'warning');
+      }
       return;
     }
@@ -294 +304 @@
   
   // Generate list of specimen tubes
-  var thisCaseLaterality;
+  var hasLeftSpecimen = false;
+  var hasRightSpecimen = false;
+  var hasUnknownSpecimen = false;
+  var thisCaseLaterality = null;
   if (caseInfo.specimen && caseInfo.specimen.length > 0)
   {
@@ -302 +315 @@
     {
       var specimen = caseInfo.specimen[i];
-      specimenTubes += specimen.name ;
+      specimenTubes += specimen.name;
       if (specimen.laterality) 
       {
         specimenTubes += ' ('+specimen.laterality + ')';
         Forms.checkRadio(frm.laterality, specimen.laterality);
-        
-        if (thisCaseLaterality && thisCaseLaterality != specimen.laterality)
-        {
-          setInputStatus('specimenTubes', 'Specimen tubes with different laterality', 'warning');
-        }
+        if (specimen.laterality == 'LEFT') hasLeftSpecimen = true;
+        if (specimen.laterality == 'RIGHT') hasRightSpecimen = true;
         thisCaseLaterality = specimen.laterality;
       }
       else
       {
+        hasUnknownSpecimen = true;
         specimenTubes += ' (<i>unknown laterality</i>)';
       }
@@ -321 +332 @@
     }
     setInnerHTML('specimenTubes', specimenTubes);
-  }
-
-  
+    
+    // Check that all specimen tubes have the same laterality
+    var numLateralities = 0;
+    if (hasLeftSpecimen) numLateralities++;
+    if (hasRightSpecimen) numLateralities++;
+    if (hasUnknownSpecimen) numLateralities++;
+    if (numLateralities > 1)
+    {
+      setInputStatus('specimenTubes', 'Specimen tubes with different laterality', 'warning');
+      thisCaseLaterality = null;
+    }
+  }
+
   Main.show('caseSection');
   
@@ -329 +350 @@
   var hasLeftCase = false;
   var hasRightCase = false;
+  var hasUnknownCase = false;
   if (patientInfo.cases && patientInfo.cases.length > 0)
   {
@@ -338 +360 @@
       if (cc.laterality == 'LEFT') 
       {
-        if (hasLeftCase) setInputStatus('laterality', 'Two cases with LEFT', 'warning');
+        if (hasLeftCase) setInputStatus('laterality', 'Two cases with laterality=LEFT', 'warning');
         hasLeftCase = true;
       }
-      if (cc.laterality == 'RIGHT') 
-      {
-        if (hasRightCase) setInputStatus('laterality', 'Two cases with RIGHT', 'warning');
+      else if (cc.laterality == 'RIGHT') 
+      {
+        if (hasRightCase) setInputStatus('laterality', 'Two cases with laterality=RIGHT', 'warning');
         hasRightCase = true;
+      }
+      else
+      {
+        hasUnknownCase = true;  
       }
       if (cc.laterality == thisCaseLaterality) cases += ' checked';
@@ -372 +398 @@
         cases += ' onclick="lateralityOnChange()"><i>new case</i> (RIGHT)<br>';
       }
+      cases += '<input type="radio" name="laterality" value=""';
+      if (thisCaseLaterality == null) cases += ' checked';
+      cases += ' onclick="lateralityOnChange()"><i>new case</i> (<i>unknown laterality</i>)<br>';
     }
     
@@ -727 +756 @@
         <td class="prompt" id="laterality.prompt">Laterality</td>
         <td class="input" id="laterality.input">
-          <input type="radio" name="laterality" value="LEFT" onclick="lateralityOnChange()">LEFT
-          <input type="radio" name="laterality" value="RIGHT" onclick="lateralityOnChange()">RIGHT
+          <input type="radio" name="laterality" value="LEFT" onclick="lateralityOnChange()">LEFT<br>
+          <input type="radio" name="laterality" value="RIGHT" onclick="lateralityOnChange()">RIGHT<br>
+          <input type="radio" name="laterality" value="" checked onclick="lateralityOnChange()"><i>unknown</i>
         </td>
         <td class="status" id="laterality.status"></td>

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/Reggie.java

@@ -178 +178 @@
     return as.getAnnotation(at).getValues().get(0);
   }
+
+  /**
+    Set a (single) annotation value on an item.
+  */
+  public static void setAnnotationValue(Annotatable item, AnnotationType at, Object value)
+  {
+    item.getAnnotationSet().getAnnotation(at).setValue(value);
+  }
+
   
 }

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

@@ -252 +252 @@
         }
         
-        String laterality = (String)jsonCase.get("laterality");
-        
+        // Get laterality
+        String laterality = Values.getStringOrNull((String)jsonCase.get("laterality"));
+        AnnotationType lateralityType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_LATERALITY, true);
+        
+        // Load/create case
         String originalCaseName = (String)jsonCase.get("name");
+        // If merging with an existing case the 'laterality' value holds the id
+        int caseId = Values.getInt(laterality); 
         Sample theCase = null;
-        if ("LEFT".equals(laterality) || "RIGHT".equals(laterality))
+        if (caseId > 0)
+        {
+          // Merge with existing case
+          theCase = Sample.getById(dc, caseId);
+          laterality = (String)Reggie.getAnnotationValue(theCase, lateralityType);
+          jsonMessages.add("Case '" + originalCaseName + "' merged with case '" + theCase.getName() + "' successfully.");
+        }
+        else
         {
           // Register a new case
           theCase = Sample.getNew(dc);
           theCase.setName(originalCaseName);
-          AnnotationType lateralityType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_LATERALITY, true);
-          AnnotationSet as = theCase.getAnnotationSet();
-          as.getAnnotation(lateralityType).setValue((String)jsonCase.get("laterality"));
+          if (laterality != null)
+          {
+            Reggie.setAnnotationValue(theCase, lateralityType, laterality);
+          }
           theCase.setBioSource(patient);
           dc.saveItem(theCase);
           jsonMessages.add("Case '" + originalCaseName + "' created successfully.");
-        }
-        else
-        {
-          // Merge with existing case
-          theCase = Sample.getById(dc, Values.getInt(laterality));
-          jsonMessages.add("Case '" + originalCaseName + "' merged with case '" + theCase.getName() + "' successfully.");
         }
         
@@ -282 +289 @@
           AnnotationType padType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_PAD, true);
           AnnotationType padCaseType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_PAD_CASE, true);
-          List padCase = new ArrayList(caseAnnotations.getAnnotation(padCaseType).getValues());
+          List padCase = new ArrayList();
+          if (caseAnnotations.hasAnnotation(padCaseType))
+          {
+            padCase.addAll(caseAnnotations.getAnnotation(padCaseType).getValues());
+          }
           for (int i = 0; i < jsonSpecimen.size(); ++i)
           {
@@ -293 +304 @@
             String pad = (String)Reggie.getAnnotationValue(specimen, padType);
             if (pad != null && !padCase.contains(pad)) padCase.add(pad);
+            // Set laterality on the specimen tube if it is missing
+            if (laterality != null)
+            {
+              String specimenLaterality = (String)Reggie.getAnnotationValue(specimen, lateralityType);
+              if (specimenLaterality == null) 
+              {
+                Reggie.setAnnotationValue(specimen, lateralityType, laterality);
+                jsonMessages.add("Updated laterality on '" + specimen.getName() + "' to " + laterality + ".");
+              }
+            }
+            
           }
           if (padCase.size() > 0) caseAnnotations.getAnnotation(padCaseType).setValues(padCase);
-          jsonMessages.add(jsonSpecimen.size() + " specimen tubes linked with case '" + theCase.getName() + "' successfully.");
+          jsonMessages.add(jsonSpecimen.size() + " specimen tube(s) linked with case '" + theCase.getName() + "' successfully.");
         }
         else