Changeset 1513

Timestamp:

Jan 19, 2012, 1:56:41 PM (11 years ago)

Author:

Nicklas Nordborg

Message:

References #348: Consent form registration wizard should allow 'Yes' in all cases

This should more or less be working now... I hope I havn't missed some exotic case. Need to add more things when the blood registration wizard (#350) has been implemented so I'll keep this ticket open.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/consentform.jsp (modified) (3 diffs)
• resources/persinfo.jsp (modified) (6 diffs)
• resources/specimentube.jsp (modified) (1 diff)
• src/net/sf/basedb/reggie/Reggie.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/PersonalRegistrationServlet.java (modified) (8 diffs)
• src/net/sf/basedb/reggie/servlet/SpecimenTubeServlet.java (modified) (2 diffs)

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

@@ -135 +135 @@
     enableConsentOption('consent.yes', true);
     setInputStatus('consent', 'This case already exists.', 'valid');
-    Main.showInline('morehelp.yes');
+    Main.showInline('morehelp.yesonly');
     Main.show('gocancel');
     Main.show('goregister');
@@ -142 +142 @@
   {
     // There is no existing case but there are specimen related to it
-    // This wizard can't be used until the "Personal registration wizard"
-    // has been completed for this case
-    setInputStatus('consent', 'Specimen tubes for this case already exists.', 'invalid');
-    Main.showInline('morehelp.specimen');
-    Main.show('gorestart');
-    frm.consentDate.disabled = true;
+    // This wizard will only allow 'Yes' option on the consent form
+    enableConsentOption('consent.yes', true);
+    setInputStatus('consent', 'Specimen tubes for this case already exists.', 'valid');
+    Main.showInline('morehelp.yesonly');
+    Main.show('gocancel');
+    Main.show('goregister');
   }
   else
   {
-    // We have no information about this case
-    // The wizard will only allow 'No' and 'Not asked' option on the consent form
+    // We have no information about this case -- but allow a consent to be registered in any case
     enableConsentOption('consent.no', true);
     enableConsentOption('consent.notAsked');
-    Main.showInline('morehelp.no');
+    enableConsentOption('consent.yes');
+    Main.showInline('morehelp.any');
     Main.show('gocancel');
     Main.show('goregister');
@@ -377 +377 @@
         <td class="help" rowspan="2">
           <span id="consent.message" class="message" style="display: none;"></span>
-          <span id="morehelp.yes" style="display: none;">
+          <span id="morehelp.yesonly" style="display: none;">
             <b>Yes</b> is the only option supported by this wizard. The other alternatives 
             may require manual deletion of already registered information.
           </span>
-          <span id="morehelp.specimen" style="display: none;">
-            The <b>Personal information registration</b> wizard must be completed before a 
-            <b>Yes</b> can be registered. The other alternatives may require manual 
-            deletion of already registered information.
-          </span>
-          <span id="morehelp.no" style="display: none;">
-            The <b>Personal information registration</b> wizard must be completed for 
-            this case before a <b>Yes</b> can be registered.
+          <span id="morehelp.any" style="display: none;">
+            There is currently no information about this case.
           </span>
         </td>

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

@@ -473 +473 @@
   currentStep = 3;
   
-  var updateMode = caseInfo.id;
+  var updateMode = caseInfo.id && caseInfo.patient;
   
   // Generate list of specimen tubes
@@ -614 +614 @@
       if (!updateMode || cc.id == caseInfo.id)
       {
-        cases += '<input type="radio" name="laterality" value="' + cc.id + '"';
+        cases += '<input type="radio" name="laterality" value="' + cc.id + '" id="laterality'+cc.id+'"';
         if (cc.laterality == thisCaseLaterality) cases += ' checked';
-        cases += ' onclick="lateralityOnChange()">';
+        cases += ' onclick="lateralityOnChange()"><label for="laterality' + cc.id + '">';
         if (cc.laterality) 
         {
@@ -629 +629 @@
           cases += ' [merge with ' + cc.name + ']';
         }
-        cases += '<br>';
+        cases += '</label><br>';
       }
     }
@@ -637 +637 @@
       if (!hasLeftCase)
       {
-        cases += '<input type="radio" name="laterality" value="LEFT" ';
+        cases += '<input type="radio" name="laterality" value="LEFT" id="lateralityLeft"';
         if (thisCaseLaterality == 'LEFT') cases += ' checked';
-        cases += ' onclick="lateralityOnChange()">LEFT';
-        if (!updateMode) cases += ' [<i>new case</i>]';
+        cases += ' onclick="lateralityOnChange()"><label for="lateralityLeft">LEFT';
+        if (!updateMode) cases += ' [<i>new case</i>]</label>';
         cases += '<br>';
       }
       if (!hasRightCase)
       {
-        cases += '<input type="radio" name="laterality" value="RIGHT"';
+        cases += '<input type="radio" name="laterality" value="RIGHT" id="lateralityRight"';
         if (thisCaseLaterality == 'RIGHT') cases += ' checked';
-        cases += ' onclick="lateralityOnChange()">RIGHT';
-        if (!updateMode) cases += ' [<i>new case</i>]';
+        cases += ' onclick="lateralityOnChange()"><label for="lateralityRight">RIGHT';
+        if (!updateMode) cases += ' [<i>new case</i>]</label>';
         cases += '<br>';
       }
       if (!updateMode && !hasLeftCase && !hasRightCase)
       {
-        cases += '<input type="radio" name="laterality" value=""';
+        cases += '<input type="radio" name="laterality" value="" id="lateralityUnknown"';
         if (thisCaseLaterality == null) cases += ' checked';
-        cases += ' onclick="lateralityOnChange()"><i>unknown laterality</i> [<i>new case</i>]<br>';
+        cases += ' onclick="lateralityOnChange()"><label for="lateralityUnknown"><i>unknown laterality</i> [<i>new case</i>]</label><br>';
       }
     }
@@ -723 +723 @@
   frm.rnaLaterTime.disabled = true;
 
-  var updateMode = caseInfo.id;
+  var updateMode = caseInfo.id && caseInfo.patient;
   var submitInfo = new Object();
   submitInfo.patientInfo = patientInfo;
@@ -921 +921 @@
         <td class="prompt" id="laterality.prompt">Laterality</td>
         <td class="input" id="laterality.input">
-          <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>
+          <input type="radio" name="laterality" value="LEFT" id="lateralityLeft" onclick="lateralityOnChange()"><label for="lateralityLeft">LEFT</label><br>
+          <input type="radio" name="laterality" value="RIGHT" id="lateralityRight" onclick="lateralityOnChange()"><label for="lateralityRight">RIGHT</label><br>
+          <input type="radio" name="laterality" value="" checked id="lateralityUnknown" onclick="lateralityOnChange()"><i><label for="lateralityUnknown">unknown</label></i>
         </td>
         <td class="status" id="laterality.status"></td>

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

@@ -948 +948 @@
       <td class="prompt" id="laterality.prompt">Laterality</td>
       <td class="input" id="laterality.input">
-        <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>
+        <input type="radio" name="laterality" value="LEFT" id="lateralityLeft" onclick="lateralityOnChange()"><label for="lateralityLeft">LEFT</label><br>
+        <input type="radio" name="laterality" value="RIGHT" id="lateralityRight" onclick="lateralityOnChange()"><label for="lateralityRight">RIGHT</label><br>
+        <input type="radio" name="laterality" value="" id="lateralityUnknown" checked onclick="lateralityOnChange()"><i><label for="lateralityUnknown">unknown</label></i>
       </td>
       <td class="status" id="laterality.status"></td>

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

@@ -387 +387 @@
   }
 
+  /**
+    Copy annotation values between two items.
+    
+    @param from The item to copy from. If this item is not annotated with 
+      the given annotation type, nothing is copied
+    @param to The item to copy to. If this item already has been annotated with 
+      the given annotation type, the 'force' paremter decides if the annotation is
+      overwritten or not
+    @param at The annotation type to copy
+    @param force TRUE to overwrite existing annotations, FALSE to not
+    @return TRUE if this method copied annotations, FALSE if not
+    @since 2.2
+  */
+  public static boolean copyAnnotationValues(Annotatable from, Annotatable to, AnnotationType at, boolean force)
+  {
+    List<?> annotations = getAnnotationValues(from, at);
+    if (annotations == null || annotations.size() == 0) return false;
+    
+    if (!force)
+    {
+      // We need to check if the 'to' item already has the annotation
+      if (to.isAnnotated() && to.getAnnotationSet().hasAnnotation(at)) return false;
+    }
+    
+    // Copy the values
+    to.getAnnotationSet().getAnnotation(at).setValues(annotations);
+    return true;
+  }
   
 }

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

@@ -20 +20 @@
 import net.sf.basedb.core.BioSource;
 import net.sf.basedb.core.DbControl;
-import net.sf.basedb.core.InvalidDataException;
 import net.sf.basedb.core.Item;
 import net.sf.basedb.core.Sample;
@@ -82 +81 @@
         if (theCase != null)
         {
+          // Check that the registration is not prohibited
           theCase.verifyConsent(dc, 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);
+          if (specimenTubes.size() == 0)
+          {
+            // No specimen tubes are linked with the case -- see if we can find some unlinked
+            specimenTubes = SpecimenTube.findByCaseName(dc, caseName);
+          }
 
           // Continue to load some more info (annotations, etc...)
@@ -100 +97 @@
           theCase.loadAnnotations(dc, "pad", Reggie.ANNOTATION_PAD_CASE, null);
           theCase.loadAnnotations(dc, "reasonIfNoSpecimen", Reggie.ANNOTATION_REASON_IF_NO_SPECIMEN, null);
-          
-          // ... patient annotations
-          patient.loadDefaultAnnotations(dc);
-          
+
           // Wrap what we have so far up into JSON objects
           jsonCase = theCase.asJSONObject();
-          jsonCase.put("patient", patient.asJSONObject());
+
+          // Load the patient associated with the case
+          Patient patient = Patient.findByCase(dc, theCase);
+          // The patient can be null if (for example) we have only registered consent=yes so far
+          if (patient != null) 
+          {
+            patient.loadDefaultAnnotations(dc);
+            jsonCase.put("patient", patient.asJSONObject());
+          }
         }
         else
@@ -245 +247 @@
         
         dc = sc.newDbControl();
-        Number patientId = (Number)jsonPat.get("id");
-        BioSource patient = null;
-        
-        if (patientId != null)
-        {
-          patient = BioSource.getById(dc, patientId.intValue());
-        }
-        else
-        {
-          // Create new patient
-          patient = BioSource.getNew(dc);
-          patient.setItemSubtype(Subtype.PATIENT.load(dc));
-          patient.setName((String)jsonPat.get("name"));
-          String pnr = (String)jsonPat.get("personalNumber");
-          String dateOfBirth = (String)jsonPat.get("dateOfBirth");
-          String gender = (String)jsonPat.get("gender");
-          
-          AnnotationType personalNumberType = Reggie.findAnnotationType(dc, Item.BIOSOURCE, Reggie.ANNOTATION_PERSONAL_NUMBER, true);
-          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);
-          
-          AnnotationSet as = patient.getAnnotationSet();
-          as.getAnnotation(personalNumberType).setValue(pnr);
-          as.getAnnotation(familyNameType).setValue((String)jsonPat.get("familyName"));
-          as.getAnnotation(allFirstNamesType).setValue((String)jsonPat.get("allFirstNames"));
-          if (gender != null) as.getAnnotation(genderType).setValue(gender);
-          if (dateOfBirth != null)
-          {
-            SimpleDateFormat df = new SimpleDateFormat("yyyy-MM-dd");
-            df.setLenient(false);
-            as.getAnnotation(dateOfBirthType).setValue(df.parse(dateOfBirth));
-          }
-          if (gender == null || dateOfBirth == null)
-          {
-            patient.setDescription("This patient was recorded with a non-standard PersonalNumber. " +
-                "DateOfBirth and Gender annotations could not be automatically generated.");
-          }
-          dc.saveItem(patient);
-          
-          jsonMessages.add("Patient '" + patient.getName() + "' created successfully.");
-        }
+        BioSource patient = getOrCreatePatient(dc, jsonPat, jsonMessages);
+        
+        // If we already have a case with id it is probably due to an already registered consent=yes
+        Number preCaseId = (Number)jsonCase.get("id");
         
         // Get laterality
@@ -304 +267 @@
           // Load the real laterality from the case
           laterality = (String)Reggie.getAnnotationValue(theCase, lateralityType);
+          
+          if (preCaseId != null)
+          {
+            // Remove the pre-registered case but copy consent information first
+            AnnotationType consentType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_CONSENT, true);
+            AnnotationType consentDateType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_CONSENT_DATE, true);
+            
+            Sample preCase = Sample.getById(dc, preCaseId.intValue());
+            Reggie.copyAnnotationValues(preCase, theCase, consentType, false);
+            Reggie.copyAnnotationValues(preCase, theCase, consentDateType, false);
+            dc.deleteItem(preCase);
+          }
+          
           jsonMessages.add("Case '" + originalCaseName + "' merged with case '" + theCase.getName() + "' successfully.");
         }
         else
         {
-          // Register a new case
-          theCase = Sample.getNew(dc);
+          if (preCaseId != null)
+          {
+            // Load existing case
+            theCase = Sample.getById(dc, preCaseId.intValue());
+          }
+          else
+          {
+            // Register a new case
+            theCase = Sample.getNew(dc);
+            dc.saveItem(theCase);
+          }
           theCase.setItemSubtype(Subtype.CASE.load(dc));
           theCase.setName(originalCaseName);
@@ -317 +302 @@
           }
           theCase.getCreationEvent().setSource(patient);
-          dc.saveItem(theCase);
           jsonMessages.add("Case '" + originalCaseName + "' created successfully.");
         }
@@ -368 +352 @@
         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());
@@ -461 +445 @@
   }
   
+  @SuppressWarnings("unchecked")
+  private BioSource getOrCreatePatient(DbControl dc, JSONObject jsonPat, JSONArray jsonMessages)
+    throws Exception
+  {
+    Number patientId = (Number)jsonPat.get("id");
+    BioSource patient = null;
+    
+    if (patientId != null)
+    {
+      patient = BioSource.getById(dc, patientId.intValue());
+    }
+    else
+    {
+      // Create new patient
+      patient = BioSource.getNew(dc);
+      patient.setItemSubtype(Subtype.PATIENT.load(dc));
+      patient.setName((String)jsonPat.get("name"));
+      String pnr = (String)jsonPat.get("personalNumber");
+      String dateOfBirth = (String)jsonPat.get("dateOfBirth");
+      String gender = (String)jsonPat.get("gender");
+      
+      AnnotationType personalNumberType = Reggie.findAnnotationType(dc, Item.BIOSOURCE, Reggie.ANNOTATION_PERSONAL_NUMBER, true);
+      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);
+      
+      AnnotationSet as = patient.getAnnotationSet();
+      as.getAnnotation(personalNumberType).setValue(pnr);
+      as.getAnnotation(familyNameType).setValue((String)jsonPat.get("familyName"));
+      as.getAnnotation(allFirstNamesType).setValue((String)jsonPat.get("allFirstNames"));
+      if (gender != null) as.getAnnotation(genderType).setValue(gender);
+      if (dateOfBirth != null)
+      {
+        SimpleDateFormat df = new SimpleDateFormat("yyyy-MM-dd");
+        df.setLenient(false);
+        as.getAnnotation(dateOfBirthType).setValue(df.parse(dateOfBirth));
+      }
+      if (gender == null || dateOfBirth == null)
+      {
+        patient.setDescription("This patient was recorded with a non-standard PersonalNumber. " +
+            "DateOfBirth and Gender annotations could not be automatically generated.");
+      }
+      dc.saveItem(patient);
+      
+      jsonMessages.add("Patient '" + patient.getName() + "' created successfully.");
+    }
+    return patient;
+
+  }
   
   

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

@@ -69 +69 @@
         
         String caseName = req.getParameter("caseName");
-        Case theCase = Case.findByName(dc, caseName);       
+        Case theCase = Case.findByName(dc, caseName);
+
         if (theCase != null)
         {
-          throw new InvalidDataException("The case (" + caseName + ") already exists in BASE. " +
-              "This wizard cannot be used to update tubes that already been connected to a case.");
+          // Verify that consent has been given
+          theCase.verifyConsent(dc, null);
         }
         
@@ -79 +80 @@
         if (specimenTubes.size() > 0)
         {
-          throw new InvalidDataException("There are already specimen tubes in this case.");
-        }
-        
-        JSONObject jsonCase = null;
-        if (theCase == null)
-        {         
-          jsonCase = new JSONObject();
-          jsonCase.put("name", caseName);
-        }             
+          throw new InvalidDataException(specimenTubes.size() + 
+            " specimen tubes have already been registered for this case. This wizard can't be used for updating.");
+        }
+        
+        JSONObject jsonCase = new JSONObject();
+        jsonCase.put("name", caseName);
         json.put("caseInfo", jsonCase);
       }