Changeset 1290

Timestamp:

Feb 21, 2011, 2:29:46 PM (13 years ago)

Author:

Nicklas Nordborg

Message:

References #291: Personal information registration

Should now handle the case with an existing patient properly. Depedning on the number of cases already registered the user may create a new case or merge with an existing case.

Display messages after the registration and added a button to restart the wizard for a second registration.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/persinfo.jsp (modified) (24 diffs)
• src/net/sf/basedb/reggie/servlet/PersonalRegistrationServlet.java (modified) (4 diffs)

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

@@ -51 +51 @@
   if (caseName == '')
   {
-    setInputStatus('case', 'Missing', false);
+    setInputStatus('case', 'Missing', 'invalid');
     return;
   }
-  setInputStatus('case', '', true);
+  setInputStatus('case', '', 'valid');
   caseIsValid = true;
 }
@@ -66 +66 @@
   if (pnr.length < 12)
   {
-    setInputStatus('pnr', 'Too short', false);
+    setInputStatus('pnr', 'Too short', 'invalid');
     return;
   }
@@ -72 +72 @@
   if (!Dates.isDate(pnr.substring(0, 8), 'yyyyMMdd'))
   {
-    setInputStatus('pnr', 'Not a valid date', false);
+    setInputStatus('pnr', 'Not a valid date', 'invalid');
     return;
   }
@@ -91 +91 @@
   if (control != parseInt(pnr.substr(11, 1)))
   {
-    setInputStatus('pnr', 'Invalid control digit', false);
+    setInputStatus('pnr', 'Invalid control digit', 'invalid');
     return;
   }
   
-  setInputStatus('pnr', '', true);
+  setInputStatus('pnr', '', 'valid');
   pnrIsValid = true;
   
-  if (caseIsValid) gotoStep2();
-}
-
-function allFirstNamesOnKeyPress(event)
+  //if (caseIsValid) gotoStep2();
+}
+
+function lateralityOnChange()
+{
+  // Check selected laterality against specimen tubes
+  var frm = document.forms['reggie'];
+  var selectedLaterality = Forms.getCheckedRadio(frm.laterality);
+  
+  // No laterality/case selected
+  if (selectedLaterality == null) return;
+  
+  var laterality = selectedLaterality.value;
+  if (laterality != 'LEFT' && laterality != 'RIGHT')
+  {
+    // It is the ID of an existing case
+    for (var i = 0; i < patientInfo.cases.length; i++)
+    {
+      var cse = patientInfo.cases[i];
+      if (cse.id == laterality)
+      {
+        laterality = cse.laterality;
+        break;
+      }
+    }
+  }
+  
+  if (!laterality) return;
+  
+  // 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');
+      return;
+    }
+  }
+  setInputStatus('laterality', '', 'valid');
+}
+
+function goNextOnTab(event)
 {
   if (event.keyCode == 9) setTimeout('goNext()', 200);
@@ -153 +194 @@
     setInnerHTML('existing.dateOfBirth', patientInfo.dateOfBirth);
     setInnerHTML('existing.gender', patientInfo.gender);
-    
+    gotoStep3();
   }
 }
@@ -161 +202 @@
   // Check entered case and pnr with AJAX
   var frm = document.forms['reggie'];
-  if (frm.patientCode)
+
+  if (!patientInfo.id)
   {
     var formOk = true;
@@ -167 +209 @@
     if (frm.allFirstNames.value == '')
     {
-      setInputStatus('allFirstNames', 'Missing', false);
+      setInputStatus('allFirstNames', 'Missing', 'invalid');
       frm.allFirstNames.focus();
       formOk = false;
@@ -173 +215 @@
     else
     {
-      setInputStatus('allFirstNames', '', true);
+      setInputStatus('allFirstNames', '', 'valid');
     }
     
     if (frm.familyName.value == '')
     {
-      setInputStatus('familyName', 'Missing', false);
+      setInputStatus('familyName', 'Missing', 'invalid');
       frm.familyName.focus();
       formOk = false;
@@ -184 +226 @@
     else
     {
-      setInputStatus('familyName', '', true);
+      setInputStatus('familyName', '', 'valid');
     }
 
@@ -190 +232 @@
     if (frm.patientCode.value == '')
     {
-      setInputStatus('patientCode', 'Missing', false);
+      setInputStatus('patientCode', 'Missing', 'invalid');
       frm.patientCode.focus();
       formOk = false;
@@ -196 +238 @@
     else
     {
-      setInputStatus('patientCode', '', true);
+      setInputStatus('patientCode', '', 'valid');
     } 
     if (!formOk) return;
@@ -211 +253 @@
   }
   
-  if (!patientInfo.cases || patientInfo.cases.length == 0)
-  {
-    Main.show('newCaseSection');  
-  }
-  
+  // Generate list of specimen tubes
+  var thisCaseLaterality;
   if (caseInfo.specimen && caseInfo.specimen.length > 0)
   {
@@ -228 +267 @@
         specimenTubes += ' ('+specimen.laterality + ')';
         Forms.checkRadio(frm.laterality, specimen.laterality);
+        
+        if (thisCaseLaterality && thisCaseLaterality != specimen.laterality)
+        {
+          setInputStatus('specimenTubes', 'Specimen tubes with different laterality', 'warning');
+        }
+        thisCaseLaterality = specimen.laterality;
       }
       specimenTubes += '<br>';
@@ -233 +278 @@
     setInnerHTML('specimenTubes', specimenTubes);
   }
-  
+
+  
+  Main.show('caseSection');
+  
+  // Existing cases for this patient
+  var hasLeftCase = false;
+  var hasRightCase = false;
+  if (patientInfo.cases && patientInfo.cases.length > 0)
+  {
+    var cases = '';
+    for (var i = 0; i < patientInfo.cases.length; i++)
+    {
+      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 LEFT', 'warning');
+        hasLeftCase = true;
+      }
+      if (cc.laterality == 'RIGHT') 
+      {
+        if (hasRightCase) setInputStatus('laterality', 'Two cases with RIGHT', 'warning');
+        hasRightCase = true;
+      }
+      if (cc.laterality == thisCaseLaterality) cases += ' checked';
+      cases += ' onclick="lateralityOnChange()">';
+      cases += cc.name + ' (' + cc.laterality + ')<br>';
+    }
+    
+    if (!hasLeftCase)
+    {
+      cases += '<input type="radio" name="laterality" value="LEFT" ';
+      if (thisCaseLaterality == 'LEFT') cases += ' checked';
+      cases += ' onclick="lateralityOnChange()"><i>new case</i> (LEFT)<br>';
+    }
+    if (!hasRightCase)
+    {
+      cases += '<input type="radio" name="laterality" value="RIGHT"';
+      if (thisCaseLaterality == 'RIGHT') cases += ' checked';
+      cases += ' onclick="lateralityOnChange()"><i>new case</i> (RIGHT)<br>';
+    }
+    
+    if (hasLeftCase && hasRightCase)
+    {
+      setInnerHTML('laterality.prompt', 'Merge with case'); 
+    }
+    else
+    {
+      setInnerHTML('laterality.prompt', 'Merge/create new case'); 
+    }
+    
+    setInnerHTML('laterality.input', cases);
+  }
+  lateralityOnChange();
+
   Main.hide('gonext');
   Main.show('gocreate');
@@ -240 +339 @@
 function goCreate()
 {
+  Main.hide('gocreate');
   var frm = document.forms['reggie'];
 
@@ -248 +348 @@
   submitInfo.patientInfo = patientInfo;
   submitInfo.caseInfo = caseInfo;
-  //alert(JSON.stringify(submitInfo));
 
   var request = Ajax.getXmlHttpRequest();
@@ -257 +356 @@
 
   setInnerHTML('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('gorestart');
+
 }
 
@@ -267 +384 @@
 }
 
-function setInputStatus(prefix, message, isValid)
+function setInputStatus(prefix, message, clazz)
 {
   var tag = document.getElementById(prefix + '.status');
-  Main.addClass(tag, isValid ? 'isvalid' : 'invalid');
-  Main.removeClass(tag, isValid ? 'invalid' : 'isvalid');
+  tag.className = 'status ' + clazz;
   
   setInnerHTML(prefix + '.message', message);
@@ -381 +497 @@
   content: url('../../images/error.gif');
 }
-.status.isvalid:before
+.status.warning:before
+{
+  content: url('../../images/warning.gif');
+}
+.status.valid:before
 {
   content: url('../../images/ok.gif');
 }
-
+.success ul
+{
+  list-style-image: url('../../images/ok.gif');
+}
 </style>
 </base:head>
@@ -407 +530 @@
       <table border="0" cellspacing="0" cellpadding="0" width="100%">
       <tr valign="top">
-        <td class="prompt">Case Name</td>
+        <td class="prompt">Case name</td>
         <td class="input"><input type="text" name="caseName" 
           size="18" maxlength="12" onblur="caseNameOnChange()"></td>
@@ -414 +537 @@
       </tr>
       <tr>
-        <td class="prompt">Personal Number</td>
+        <td class="prompt">Personal number</td>
         <td class="input"><input type="text" name="personalNumber" 
-          size="18" maxlength="12" onkeyup="personalNumberOnChange()"></td>
+          size="18" maxlength="12" onkeyup="personalNumberOnChange()" onkeypress="goNextOnTab(event)"></td>
         <td class="status" id="pnr.status"></td>
         <td class="help"><span id="pnr.message" class="message" style="display: none;"></span>(YYYYMMDDZZZZ)</td>
@@ -452 +575 @@
         <td class="prompt">All first names</td>
         <td class="input"><input type="text" name="allFirstNames" 
-          size="35" maxlength="255" onkeypress="allFirstNamesOnKeyPress(event)"></td>
+          size="35" maxlength="255" onkeypress="goNextOnTab(event)"></td>
         <td class="status" id="allFirstNames.status"></td>
         <td class="help"><span id="allFirstNames.message" class="message" style="display: none;"></span>Type all names, see FamilyName comment on valid characters.</td>
@@ -522 +645 @@
 
 
-  <!-- 3. New case registration -->
-  <div id="newCaseSection" style="display: none;">
+  <!-- 3. Case registration -->
+  <div id="caseSection" style="display: none;">
   <p>
   <table border="0" cellspacing="0" cellpadding="0" class="stepform">
   <tr>
     <td rowspan="2" class="stepno">3</td>
-    <td class="steptitle">New case: Enter information</td>
+    <td class="steptitle">About this case</td>
   </tr>
   <tr>
     <td class="stepfields">
       <table border="0" cellspacing="0" cellpadding="0" width="100%">
-      <tr>
-        <td class="prompt">Laterality</td>
-        <td class="input">
-          <input type="radio" name="laterality" value="LEFT">LEFT
-          <input type="radio" name="laterality" value="RIGHT">RIGHT
+      <tr valign="top">
+        <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
         </td>
-        <td class="status"></td>
-        <td class="help"></td>
+        <td class="status" id="laterality.status"></td>
+        <td class="help"><span id="laterality.message" class="message" style="display: none;"></span></td>
       </tr>
       <tr valign="top">
         <td class="prompt">Specimen tubes</td>
-        <td class="input" id="specimenTubes">not found</td>
-        <td class="status"></td>
-        <td class="help">The specimen tube(s) associated with this case.</td>
-      </tr>
-        
+        <td class="input" id="specimenTubes"><i>not found</i></td>
+        <td class="status" id="specimenTubes.status"></td>
+        <td class="help"><span id="specimenTubes.message" class="message" style="display: none;"></span>The specimen tube(s) associated with this case.</td>
+      </tr>
       <tr id="reasonIfNoSpecimenSection" valign="top">
         <td class="prompt">Reason if no specimen</td>
@@ -562 +684 @@
 
   <div class="error" id="errorMessage" style="display: none; width: 800px; margin-left: 20px; margin-bottom: 0px;"></div>
+
+  <div id="done" class="success" style="display: none; width: 800px; margin-left: 20px; margin-top: 20px;"></div>
 
   <table style="margin-left: 20px; margin-top: 10px;">

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

@@ -35 +35 @@
 import net.sf.basedb.reggie.Reggie;
 import net.sf.basedb.util.MD5;
+import net.sf.basedb.util.Values;
 import net.sf.basedb.util.error.ThrowableUtil;
 import net.sf.basedb.util.formatter.DateFormatter;
@@ -204 +205 @@
     JSONObject json = new JSONObject();
     json.put("status", "ok");
+    
+    JSONArray jsonMessages = new JSONArray();
   
     final SessionControl sc = Application.getSessionControl(ID, req.getRemoteAddr());
@@ -245 +248 @@
           as.getAnnotation(dateOfBirthType).setValue(df.parseString(pnr.substring(0, 8)));
           dc.saveItem(patient);
-        }
-        
-        // Create new case
-        Sample cse = Sample.getNew(dc);
-        cse.setName((String)jsonCase.get("name"));
-        AnnotationType lateralityType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_LATERALITY, true);
-        AnnotationSet as = cse.getAnnotationSet();
-        as.getAnnotation(lateralityType).setValue((String)jsonCase.get("laterality"));
-        cse.setBioSource(patient);
-        dc.saveItem(cse);
+          
+          jsonMessages.add("Patient '" + patient.getName() + "' created successfully.");
+        }
+        
+        String laterality = (String)jsonCase.get("laterality");
+        
+        String originalCaseName = (String)jsonCase.get("name");
+        Sample theCase = null;
+        if ("LEFT".equals(laterality) || "RIGHT".equals(laterality))
+        {
+          // 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"));
+          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.");
+        }
         
         // Link the case with specimen
+        AnnotationSet caseAnnotations = theCase.getAnnotationSet();
         JSONArray jsonSpecimen = (JSONArray)jsonCase.get("specimen");
         if (jsonSpecimen != null && jsonSpecimen.size() > 0)
@@ -262 +282 @@
           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(as.getAnnotation(padCaseType).getValues());
+          List padCase = new ArrayList(caseAnnotations.getAnnotation(padCaseType).getValues());
           for (int i = 0; i < jsonSpecimen.size(); ++i)
           {
             JSONObject jsonSpec = (JSONObject)jsonSpecimen.get(i);
             Sample specimen = Sample.getById(dc, ((Long)jsonSpec.get("id")).intValue());
+            // Set specimen to 'pooled' and link with case
             specimen.setPooled(true);
-            specimen.getCreationEvent().addSource(cse, null);
+            specimen.getCreationEvent().addSource(theCase, null);
+            // Copy PAD annotation on specimen to PADcase annotation on case
             String pad = (String)Reggie.getAnnotationValue(specimen, padType);
             if (pad != null && !padCase.contains(pad)) padCase.add(pad);
           }
-          as.getAnnotation(padCaseType).setValues(padCase);
+          if (padCase.size() > 0) caseAnnotations.getAnnotation(padCaseType).setValues(padCase);
+          jsonMessages.add(jsonSpecimen.size() + " specimen tubes linked with case '" + theCase.getName() + "' successfully.");
         }
         else
         {
           AnnotationType reasonIfNoSpecimenType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_REASON_IF_NO_SPECIMEN, true);
-          Annotation reasonIfNoSpecimen = as.getAnnotation(reasonIfNoSpecimenType);
+          Annotation reasonIfNoSpecimen = caseAnnotations.getAnnotation(reasonIfNoSpecimenType);
           List values = new ArrayList(reasonIfNoSpecimen.getValues());
-          values.add("[" + cse.getName() + "] " + jsonCase.get("reasonIfNoSpecimen"));
+          values.add("[" + originalCaseName + "] " + jsonCase.get("reasonIfNoSpecimen"));
           reasonIfNoSpecimen.setValues(values);
         }
         
         dc.commit();
+        json.put("messages", jsonMessages);
         
       }