Changeset 1326

Timestamp:

Mar 29, 2011, 2:55:33 PM (13 years ago)

Author:

Nicklas Nordborg

Message:

References #302: Update functionality in the Personal information registration

Restructured the code which should make it easier to keep track of related reggie items (patient/case/specimen tube). It is also easier to make sure that JSON representations are consistent if more functions are needed in the future.

The wizard now recognises 3 variants of existing cases:

1. Match by exact name
2. Match by name of specimen tubes that have been merged with a different case
3. Match by [prefix] of ResonIfNoSpecimen? comment for a merged case without specimen tubes.

If an existing case is found, the wizard loads patient information, etc. and proceeds immediately to step 3 in "Update mode". Currently, only the laterality value can be updated. PAD, the various timestamps, comments, etc. are not yet supported.

Hopefully this has been done without breaking any of the functions for registering a new case...

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/persinfo.jsp (modified) (23 diffs)
• src/net/sf/basedb/reggie/JsonUtil.java (added)
• src/net/sf/basedb/reggie/Reggie.java (modified) (2 diffs)
• src/net/sf/basedb/reggie/dao (added)
• src/net/sf/basedb/reggie/dao/Case.java (added)
• src/net/sf/basedb/reggie/dao/Patient.java (added)
• src/net/sf/basedb/reggie/dao/ReggieItem.java (added)
• src/net/sf/basedb/reggie/dao/SpecimenTube.java (added)
• src/net/sf/basedb/reggie/servlet/PersonalRegistrationServlet.java (modified) (8 diffs)

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

@@ -139 +139 @@
   setInputStatus('case', '', 'valid');
   caseIsValid = true;
+  
+  getCaseInfo();
 }
 
@@ -208 +210 @@
 {
   lateralityIsValid = false;
+  var updateMode = caseInfo.id;
   
   // Check selected laterality against specimen tubes
@@ -219 +222 @@
     return;
   }
-  setInputStatus('laterality', '', 'valid');
+  
+  var numCases = patientInfo.cases ? patientInfo.cases.length : 0;
+  setInputStatus('laterality', updateMode && numCases > 1 ? 'NOTE! Some alternatives may be missing if there is another case for the patient.' : '', 'valid');
   lateralityIsValid = true;
   
@@ -249 +254 @@
     if (specimen.laterality != laterality)
     {
-      if (specimen.laterality == null)
+      if (specimen.laterality == null || updateMode)
       {
         setInputStatus('laterality', 'Specimen tubes are updated to: ' + laterality, 'valid')
@@ -260 +265 @@
     }
   }
+  
 }
 
@@ -292 +298 @@
   if (event.keyCode == 13) setTimeout("document.forms['reggie']."+inputField+".focus()", 200);
   return true;
+}
+
+function getCaseInfo()
+{
+  // Check entered case and pnr with AJAX
+  var frm = document.forms['reggie'];
+  var caseName = frm.caseName.value;
+  var request = Ajax.getXmlHttpRequest();
+  var url = 'PersonalRegistration.servlet?ID=<%=ID%>&cmd=GetCaseInfo';
+  url += '&caseName=' + caseName;
+  request.open("GET", url, false); 
+  request.send(null);
+  
+  setInnerHTML('debug', request.responseText);
+  var response = JSON.parse(request.responseText);
+  if (response.status != 'ok')
+  {
+    setFatalError(response.message);
+    return false;
+  }
+  
+  // Get biosource information from the AJAX response
+  caseInfo = response.caseInfo;
+  
+  if (caseInfo && caseInfo.patient)
+  {
+    frm.personalNumber.value = caseInfo.patient.personalNumber;
+    gotoStep2();
+  }
+  
 }
 
@@ -303 +339 @@
   
   var pnr = frm.personalNumber.value;
-  var caseName = frm.caseName.value;
   var request = Ajax.getXmlHttpRequest();
-  var url = 'PersonalRegistration.servlet?ID=<%=ID%>&cmd=CheckPersonalNumberAndCaseName';
+  var url = 'PersonalRegistration.servlet?ID=<%=ID%>&cmd=GetPatientInfo';
   url += '&personalNumber=' + pnr;
   url += '&pnrIsValid=' + pnrIsValid;
-  url += '&caseName=' + caseName;
   request.open("GET", url, false); 
   request.send(null);
   
-  //setInnerHTML('debug', request.responseText);
+  setInnerHTML('debug', request.responseText);
   
   var response = JSON.parse(request.responseText);
@@ -321 +355 @@
   }
   
+  // Get patient information from the AJAX response
+  patientInfo = response.patientInfo;
+
   Main.show('gocancel');
-  
-  // Get biosource information from the AJAX response
-  patientInfo = response.patientInfo;
-  caseInfo = response.caseInfo;
   
   if (!patientInfo.id)
@@ -366 +399 @@
   currentStep = 3;
   
+  var updateMode = caseInfo.id;
+  
   // Generate list of specimen tubes
   var hasLeftSpecimen = false;
   var hasRightSpecimen = false;
   var hasUnknownSpecimen = false;
-  var thisCaseLaterality = null;
+  var thisCaseLaterality = caseInfo.laterality;
+  var thisCasePAD = null;
   var hasPAD = false;
   if (caseInfo.specimen && caseInfo.specimen.length > 0)
@@ -380 +416 @@
       var specimen = caseInfo.specimen[i];
       specimenTubes += specimen.name;
-      if (specimen.pad) hasPAD = true;
+      if (specimen.pad) 
+      {
+        hasPAD = true;
+        thisCasePAD = specimen.pad;
+      }
       if (specimen.laterality) 
       {
@@ -410 +450 @@
   }
 
-  Main.showHide('padSection', !hasPAD);
+  frm.pad.value = thisCasePAD;
+  Main.showHide('padSection', !hasPAD || updateMode);
   
   Main.show('caseSection');
@@ -424 +465 @@
     {
       var cc = patientInfo.cases[i];
-      cases += '<input type="radio" name="laterality" value="' + cc.id + '"';
       if (cc.laterality == 'LEFT') 
       {
-        if (hasLeftCase) setInputStatus('laterality', 'Two cases with laterality=LEFT', 'warning');
+        if (hasLeftCase && !updateMode) setInputStatus('laterality', 'Two cases with laterality=LEFT', 'warning');
         hasLeftCase = true;
       }
       else if (cc.laterality == 'RIGHT') 
       {
-        if (hasRightCase) setInputStatus('laterality', 'Two cases with laterality=RIGHT', 'warning');
+        if (hasRightCase && !updateMode) setInputStatus('laterality', 'Two cases with laterality=RIGHT', 'warning');
         hasRightCase = true;
       }
@@ -439 +479 @@
         hasUnknownCase = true;  
       }
-      if (cc.laterality == thisCaseLaterality) cases += ' checked';
-      cases += ' onclick="lateralityOnChange()">' + cc.name;
-      if (cc.laterality) 
-      {
-        cases += ' (' + cc.laterality + ')<br>';
-      }
-      else
-      {
-        cases += ' (<i>unknown laterality</i>)<br>';
+      if (!updateMode || cc.id == caseInfo.id)
+      {
+        cases += '<input type="radio" name="laterality" value="' + cc.id + '"';
+        if (cc.laterality == thisCaseLaterality) cases += ' checked';
+        cases += ' onclick="lateralityOnChange()">';
+        if (cc.laterality) 
+        {
+          cases += cc.laterality;
+        }
+        else
+        {
+          cases += '<i>unknown laterality</i>';
+        }
+        if (!updateMode)
+        {
+          cases += ' [merge with ' + cc.name + ']';
+        }
+        cases += '<br>';
       }
     }
     
-    if (patientInfo.cases.length == 1)
+    if (patientInfo.cases.length == 1 || updateMode)
     {
       if (!hasLeftCase)
@@ -457 +506 @@
         cases += '<input type="radio" name="laterality" value="LEFT" ';
         if (thisCaseLaterality == 'LEFT') cases += ' checked';
-        cases += ' onclick="lateralityOnChange()"><i>new case</i> (LEFT)<br>';
+        cases += ' onclick="lateralityOnChange()">LEFT';
+        if (!updateMode) cases += ' [<i>new case</i>]';
+        cases += '<br>';
       }
       if (!hasRightCase)
@@ -463 +514 @@
         cases += '<input type="radio" name="laterality" value="RIGHT"';
         if (thisCaseLaterality == 'RIGHT') cases += ' checked';
-        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>';
+        cases += ' onclick="lateralityOnChange()">RIGHT';
+        if (!updateMode) cases += ' [<i>new case</i>]';
+        cases += '<br>';
+      }
+      if (!updateMode && !hasLeftCase && !hasRightCase)
+      {
+        cases += '<input type="radio" name="laterality" value=""';
+        if (thisCaseLaterality == null) cases += ' checked';
+        cases += ' onclick="lateralityOnChange()"><i>unknown laterality</i> [<i>new case</i>]<br>';
+      }
     }
     
-    if (patientInfo.cases.length == 2)
-    {
-      setInnerHTML('laterality.prompt', 'Merge with case'); 
-    }
-    else
-    {
-      setInnerHTML('laterality.prompt', 'Merge/create new case'); 
+    if (updateMode)
+    {
+      if (caseInfo.merged)
+      {
+        setInnerHTML('step3.title', 'Update case \''+caseInfo.originalName+'\' (which is merged with case \'' + caseInfo.name + '\')');
+      }
+      else
+      {
+        setInnerHTML('step3.title', 'Update case \''+caseInfo.name+'\'');
+      }
+      
+    }
+    else if (patientInfo.cases.length == 2)
+    {
+      setInnerHTML('step3.title', 'Merge with existing case');  
+    }
+    else if (patientInfo.cases.length > 0)
+    {
+      setInnerHTML('step3.title', 'Create new case or merge with existing case'); 
     }
     
@@ -484 +552 @@
 
   Main.hide('gonext');
-  Main.show('gocreate');
+  if (updateMode)
+  {
+    Main.show('goupdate');
+  }
+  else
+  {
+    Main.show('gocreate');
+  }
   
   if (!hasPAD && lateralityIsValid) frm.pad.focus();
@@ -495 +570 @@
   Main.hide('gocreate');
   Main.hide('gocancel');
+  Main.hide('goupdate');
   var frm = document.forms['reggie'];
 
@@ -508 +584 @@
   frm.pad.disabled = true;
 
+  var updateMode = caseInfo.id;
   var submitInfo = new Object();
   submitInfo.patientInfo = patientInfo;
@@ -515 +592 @@
   
   var request = Ajax.getXmlHttpRequest();
-  var url = 'PersonalRegistration.servlet?ID=<%=ID%>&cmd=Create';
+  var url = 'PersonalRegistration.servlet?ID=<%=ID%>&cmd=';
+  url += updateMode ? 'UpdateCase' : 'CreateCase';
   request.open("POST", url, false);
   request.setRequestHeader("Content-Type", "application/json");
   request.send(JSON.stringify(submitInfo));
 
-  //setInnerHTML('debug', request.responseText);
+  setInnerHTML('debug', request.responseText);
   
   var response = JSON.parse(request.responseText);
@@ -572 +650 @@
   Main.hide('gocancel');
   Main.show('gorestart');
+  var frm = document.forms['reggie'];
+  for (var i = 0; i < frm.elements.length; i++)
+  {
+    frm.elements[i].disabled = true;  
+  }
+
 }
 
@@ -831 +915 @@
   <tr>
     <td rowspan="2" class="stepno">3</td>
-    <td class="steptitle">About this case</td>
+    <td class="steptitle" id="step3.title">Create new case</td>
   </tr>
   <tr>
@@ -859 +943 @@
           onblur="padOnChange()"></td>
         <td class="status" id="pad.status"></td>
-        <td class="help"><span id="pad.message" class="message" style="display: none;"></span>PAD should be entered when no specimen tubes have been registered</td>
+        <td class="help"><span id="pad.message" class="message" style="display: none;"></span>PAD should be entered when no specimen tubes have been registered.</td>
       </tr>
       <tr id="reasonIfNoSpecimenSection" valign="top">
@@ -882 +966 @@
     <td><base:button id="gonext" title="Next" image="gonext.gif" onclick="goNext(true)"/></td>
     <td><base:button id="gocreate" title="Create" image="gonext.gif" onclick="goCreate()" style="display: none;"/></td>
+    <td><base:button id="goupdate" title="Update" image="gonext.gif" onclick="goCreate()" style="display: none;"/></td>
     <td><base:button id="gorestart" title="Restart" image="goback.gif" onclick="goRestart(true)" style="display: none;"/></td>
     <td id="gonext.message" class="message"></td>

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

@@ -1 +1 @@
 package net.sf.basedb.reggie;
 
+import java.util.Collections;
 import java.util.List;
 
@@ -198 +199 @@
   }
 
-  
+  /**
+    Get an array annotation value from an item. Returns an empty list if
+    there are no annotations of the given type.
+    @since 1.2
+  */
+  public static List<?> getAnnotationValues(Annotatable item, AnnotationType at)
+  {
+    if (!item.isAnnotated()) return Collections.emptyList();
+    AnnotationSet as = item.getAnnotationSet();
+    if (!as.hasAnnotation(at)) return Collections.emptyList();
+    return as.getAnnotation(at).getValues();
+  }
+    
+
+
 }

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

@@ -4 +4 @@
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
-import java.util.Date;
 import java.util.List;
 
@@ -28 +27 @@
 import net.sf.basedb.core.Sample;
 import net.sf.basedb.core.SessionControl;
-import net.sf.basedb.core.Type;
-import net.sf.basedb.core.query.Annotations;
 import net.sf.basedb.core.query.Expressions;
 import net.sf.basedb.core.query.Hql;
@@ -35 +32 @@
 import net.sf.basedb.core.query.Restrictions;
 import net.sf.basedb.reggie.Reggie;
+import net.sf.basedb.reggie.dao.Case;
+import net.sf.basedb.reggie.dao.Patient;
+import net.sf.basedb.reggie.dao.SpecimenTube;
 import net.sf.basedb.util.MD5;
 import net.sf.basedb.util.Values;
@@ -67 +67 @@
     try
     {
-      if ("CheckPersonalNumberAndCaseName".equals(cmd))
+      if ("GetCaseInfo".equals(cmd))
       {
+        /*
+          Load information about a single case when given the case name/barcode
+          If a case is found we will load annotations, the patient it is associated with
+          and specimen tubes for the case. If no case is found we check to see
+          if there are any specimen tubes that have the case name as prefix and
+          load information about them.
+        */
         dc = sc.newDbControl();
-        AnnotationType pnrType = Reggie.findAnnotationType(dc, Item.BIOSOURCE, Reggie.ANNOTATION_PERSONAL_NUMBER, true);
-        AnnotationType lateralityType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_LATERALITY, true);
-        AnnotationType padType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_PAD, true);
-        
+        
+        // Find a case by name
+        String caseName = req.getParameter("caseName");
+        Case theCase = Case.findByName(dc, caseName);
+        List<SpecimenTube> specimenTubes = null;
+        JSONObject jsonCase = null;
+        
+        if (theCase != null)
+        {
+          // Load the patient associated with the case
+          Patient patient = Patient.findByCase(dc, theCase);
+          if (patient == null)
+          {
+            throw new InvalidDataException("The case (" + caseName + ") was found but it is not associated " +
+                "with any patient. This wizard can't be used until that is corrected.");
+          }
+          
+          // Load specimen tubes for the case
+          specimenTubes = SpecimenTube.findByCase(dc, theCase, true);
+
+          // Continue to load some more info (annotations, etc...)
+          // ... case annotations
+          theCase.loadAnnotations(dc, "laterality", Reggie.ANNOTATION_LATERALITY);
+          theCase.loadAnnotations(dc, "pad", Reggie.ANNOTATION_PAD_CASE);
+          theCase.loadAnnotations(dc, "reasonIfNoSpecimen", Reggie.ANNOTATION_REASON_IF_NO_SPECIMEN);
+          
+          // ... patient annotations
+          patient.loadDefaultAnnotations(dc);
+          
+          // Wrap what we have so far up into JSON objects
+          jsonCase = theCase.asJSONObject();
+          jsonCase.put("patient", patient.asJSONObject());
+        }
+        else
+        {
+          // Could not find the registered case -- see if we can find any specimen tubes
+          specimenTubes = SpecimenTube.findByCaseName(dc, caseName);
+          jsonCase = new JSONObject();
+          jsonCase.put("name", caseName);
+        }
+
+        // Load specimen tube annotations
+        JSONArray jsonTubes = new JSONArray();
+        if (specimenTubes.size() > 0)
+        {
+          AnnotationType padType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_PAD, true);
+          AnnotationType lateralityType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_LATERALITY, true);
+          for (SpecimenTube tube : specimenTubes)
+          {
+            tube.loadAnnotations("pad", padType);
+            tube.loadAnnotations("laterality", lateralityType);
+            jsonTubes.add(tube.asJSONObject());
+          }
+        }
+        jsonCase.put("specimen", jsonTubes);
+        
+        // This is what we send back to the browser
+        json.put("caseInfo", jsonCase);
+
+      }
+      
+      else if ("GetPatientInfo".equals(cmd))
+      {
+        /*
+          Load information about a single patient when given a personal number
+          If a patient is found we will load annotations and the cases associated 
+          with it. If no patient is found, we populate a new object with some
+          information (eg. birth date and gender) from the information we have.
+        */
+        dc = sc.newDbControl();
+        
+        // Request parameters
         String pnr = req.getParameter("personalNumber");
-        String caseName = req.getParameter("caseName");
         boolean pnrIsValid = Values.getBoolean(req.getParameter("pnrIsValid"));
-        
-        // Find patient information given the personal number
-        ItemQuery<BioSource> patientQuery = BioSource.getQuery();
-        patientQuery.restrict(Annotations.eq(null, pnrType, pnr, false));
-        List<BioSource> patients = patientQuery.list(dc);
-        JSONObject jsonPat = new JSONObject();
-        jsonPat.put("personalNumber", pnr);
-        
-        if (patients.size() > 1)
-        {
-          throw new InvalidDataException(
-            "More than one patient with the given personal number was found. " +
-            "This wizard can't be used for registration until that is corrected.");
-          
-        }
-        
-        if (patients.size() == 1)
-        {
-          AnnotationType familyNameType = Reggie.findAnnotationType(dc, Item.BIOSOURCE, Reggie.ANNOTATION_FAMILY_NAME, true);
-          AnnotationType allFirstNamesType = Reggie.findAnnotationType(dc, Item.BIOSOURCE, Reggie.ANNOTATION_ALL_FIRST_NAMES, true);
-          AnnotationType genderType = Reggie.findAnnotationType(dc, Item.BIOSOURCE, Reggie.ANNOTATION_GENDER, true);
-          AnnotationType dateOfBirthType = Reggie.findAnnotationType(dc, Item.BIOSOURCE, Reggie.ANNOTATION_DATE_OF_BIRTH, true);
-          SimpleDateFormat df = new SimpleDateFormat("yyyy-MM-dd");
-          BioSource bs = patients.get(0);
-          jsonPat.put("id", bs.getId());
-          jsonPat.put("name", bs.getName());
-          jsonPat.put("familyName", Reggie.getAnnotationValue(bs, familyNameType));
-          jsonPat.put("allFirstNames", Reggie.getAnnotationValue(bs, allFirstNamesType));
-          jsonPat.put("gender", Reggie.getAnnotationValue(bs, genderType));
-          jsonPat.put("dateOfBirth", df.format((Date)Reggie.getAnnotationValue(bs, dateOfBirthType)));
-          
-          // Find existing cases for the patient
-          ItemQuery<Sample> caseQuery = bs.getSamples();
-          caseQuery.include(Include.ALL);
+
+        // Find a patient by personalNumber
+        Patient patient = Patient.findByPersonalNumber(dc, pnr);
+        JSONObject jsonPat = null;
+        
+        if (patient != null)
+        {
+          // Load patient annotations
+          patient.loadDefaultAnnotations(dc);
+
+          // Load cases associated with this patient
+          List<Case> cases = Case.findByPatient(dc, patient);
+          
+          // Load case annotations
           JSONArray jsonCases = new JSONArray();
-          for (Sample s : caseQuery.list(dc))
-          {
-            JSONObject jsonCase = new JSONObject();
-            jsonCase.put("id", s.getId());
-            jsonCase.put("name", s.getName());
-            jsonCase.put("laterality",  Reggie.getAnnotationValue(s, lateralityType));
-            jsonCases.add(jsonCase);
-          }
+          if (cases.size() > 0)
+          {
+            AnnotationType lateralityType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_LATERALITY, true);
+            for (Case c : cases)
+            {
+              c.loadAnnotations("laterality", lateralityType);
+              jsonCases.add(c.asJSONObject());
+            }
+          }
+          
+          jsonPat = patient.asJSONObject();
           jsonPat.put("cases", jsonCases);
+
         }
         else
         {
-          // Try to find the highest existing patient number
-          patientQuery = BioSource.getQuery();
+          // No patient was found -- try to find the highest existing patient number
+          ItemQuery<BioSource> patientQuery = BioSource.getQuery();
           patientQuery.restrict(Restrictions.like(Hql.property("name"), Expressions.string("PAT%")));
           patientQuery.order(Orders.desc(Hql.property("name")));
           patientQuery.setMaxResults(1);
           patientQuery.include(Include.ALL);
-          patients = patientQuery.list(dc);
-          
+          List<BioSource> patients = patientQuery.list(dc);
+          jsonPat = new JSONObject();
+          jsonPat.put("personalNumber", pnr);
           if (patients.size() == 0)
           {
@@ -150 +209 @@
             jsonPat.put("gender", Integer.parseInt(pnr.substring(10,11)) % 2 == 0 ? "F" : "M");
           }
-          
-        }
-        
-        // Check for existing case
-        ItemQuery<Sample> caseQuery = Sample.getQuery();
-        caseQuery.restrict(Restrictions.eq(Hql.property("name"), Expressions.parameter("name", caseName, Type.STRING)));
-        List<Sample> cases = caseQuery.list(dc);
-        JSONObject jsonCase = new JSONObject();
-        if (cases.size() >= 1)
-        {
-          throw new InvalidDataException(
-            "At least one case with the given case name already exists. " +
-            "This wizard can't be used for registration until that is corrected.");
-        }
-        jsonCase.put("name", caseName);
-        
-        // Find specimen information
-        ItemQuery<Sample> specimenQuery = Sample.getQuery();
-        specimenQuery.restrict(Restrictions.like(Hql.property("name"), Expressions.parameter("name", caseName + ".%", Type.STRING)));
-
-        JSONArray jsonSpecimens = new JSONArray();
-        for (Sample specimen : specimenQuery.list(dc))
-        {
-          JSONObject jsonSpecimen = new JSONObject();
-          jsonSpecimen.put("id", specimen.getId());
-          jsonSpecimen.put("name", specimen.getName());
-          jsonSpecimen.put("laterality", Reggie.getAnnotationValue(specimen, lateralityType));
-          jsonSpecimen.put("pad", Reggie.getAnnotationValue(specimen, padType));
-          jsonSpecimens.add(jsonSpecimen);
-        }
-        jsonCase.put("specimen", jsonSpecimens);
-        
+        }
+
         json.put("patientInfo", jsonPat);
-        json.put("caseInfo", jsonCase);
       }
     }
@@ -222 +250 @@
     try
     {
-      if ("Create".equals(cmd))
+      if ("CreateCase".equals(cmd))
       {
         JSONObject jsonReq = (JSONObject)new JSONParser().parse(req.getReader());
-        
         JSONObject jsonPat = (JSONObject)jsonReq.get("patientInfo");
         JSONObject jsonCase = (JSONObject)jsonReq.get("caseInfo");
@@ -322 +349 @@
           {
             JSONObject jsonSpec = (JSONObject)jsonSpecimen.get(i);
-            Sample specimen = Sample.getById(dc, ((Long)jsonSpec.get("id")).intValue());
+            Sample specimen = Sample.getById(dc, ((Number)jsonSpec.get("id")).intValue());
             // Set specimen to 'pooled' and link with case
             specimen.setPooled(true);
@@ -360 +387 @@
         
       }
+      
+      else if ("UpdateCase".equals(cmd))
+      {
+        JSONObject jsonReq = (JSONObject)new JSONParser().parse(req.getReader());
+        JSONObject jsonCase = (JSONObject)jsonReq.get("caseInfo");
+        
+        dc = sc.newDbControl();
+        Number caseId = (Number)jsonCase.get("id");
+        
+        Sample theCase = Sample.getById(dc, caseId.intValue());
+        
+        // Get laterality
+        String laterality = Values.getStringOrNull((String)jsonCase.get("laterality"));
+        // If the 'laterality' value is a number, then it hasn't changed
+        if (Values.getInt(laterality) == 0)
+        {
+          AnnotationType lateralityType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_LATERALITY, true);
+          Reggie.setAnnotationValue(theCase, lateralityType, laterality);
+          int numSpecimen = 0;
+          for (Sample specimen : theCase.getChildSamples().list(dc))
+          {
+            Reggie.setAnnotationValue(specimen, lateralityType, laterality);
+            numSpecimen++;
+          }
+          jsonMessages.add("Updated case '" + theCase.getName() + "' and " +numSpecimen + 
+              " specimen tube(s) to laterality="+laterality);
+        }
+
+        dc.commit();
+        json.put("messages", jsonMessages);
+      }
+      
     }
     catch (Throwable t)