Changeset 3481

Timestamp:

Sep 9, 2015, 8:19:27 AM (8 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #805: LinkedSpecimen? should set value for items with missing date

Added MissingDate as a new value to the LinkedSpecimen annotation. The report after running the wizard has been modified to include this option.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/batch/linked-specimen.js (modified) (2 diffs)
• resources/batch/linked-specimen.jsp (modified) (4 diffs)
• src/net/sf/basedb/reggie/servlet/InstallServlet.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/LinkedSpecimenServlet.java (modified) (3 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/batch/linked-specimen.js

@@ -32 +32 @@
   ls.linkedSpecimenDone = function(response)
   {
-    Doc.element('num-updated').innerHTML = response.numUpdated;
-    Doc.element('num-no-date').innerHTML = response.numNoDate;
-    
     for (var c = 0; c < response.counters.length; c++)
     {
@@ -42 +39 @@
       Doc.element(name + '-after').innerHTML = counter.after;
     }
+    
+    Wizard.showFinalMessage(['Number of updated annotations: ' + response.numUpdated]);
     
     Doc.show('update-results');

extensions/net.sf.basedb.reggie/trunk/resources/batch/linked-specimen.jsp

@@ -68 +68 @@
       creation date of the specimen.
       <ol>
-        <li>If the patient has any specimen without date: <b>No value</b>
+        <li>If the patient has any specimen without date: <b>MissingDate</b>
         <li>If the same case has a prior core biopsy: <b>IpsilateralCoreBiopsy</b>
         <li>If the other case (opposite laterality) has a prior core biopsy: <b>ContralateralCoreBiopsy</b>
@@ -79 +79 @@
   </div>
 
-  <table id="update-results" style="display: none;">
-    <tr>
-      <th class="bg-filled-100 rightborder">Number of updated annotations</th>
-      <td colspan="2" id="num-updated">?</td>
-    </tr>
-    <tr>
-      <th class="bg-filled-100 rightborder">Number without date</th>
-      <td colspan="2" id="num-no-date">?</td>
-    </tr>
-    <tr class="bg-filled-100 topborder bottomborder">
+
+  <div id="wizard-status"></div>
+
+  <table id="update-results" style="display: none; margin-top: 1em;">
+    <tr class="bg-filled-100 bottomborder">
       <th style="width: 20em;">LinkedSpecimen</th>
       <th style="width: 10em;">Before</th>
@@ -97 +92 @@
       <td id="novalue-before">?</td>
       <td id="novalue-after">?</td>
+    </tr>
+    <tr class="bottomborder" style="border-bottom-style: dotted;">
+      <th class="bg-filled-100 rightborder">MissingDate</th>
+      <td id="MissingDate-before">?</td>
+      <td id="MissingDate-after">?</td>
     </tr>
     <tr>
@@ -121 +121 @@
     
 
-    <div id="wizard-status"></div>
-
     <table class="navigation" id="navigation">
     <tr>

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

@@ -338 +338 @@
             effectivePermissionsUse, createIfMissing));
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.LINKED_SPECIMEN, 1,
-            new ValueOptions("IpsilateralCoreBiopsy", "ContralateralCoreBiopsy", "IpsilateralSample", "ContralateralSample"), 
+            new ValueOptions("IpsilateralCoreBiopsy", "ContralateralCoreBiopsy", "IpsilateralSample", "ContralateralSample", "MissingDate"), 
             effectivePermissionsUse, createIfMissing));
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.NOF_PIECES, 1, null, effectivePermissionsUse, createIfMissing));

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

@@ -112 +112 @@
         Map<String, Counter> counters = new HashMap<String, Counter>();
         counters.put(null, new Counter(null));
+        counters.put("MissingDate", new Counter("MissingDate"));
         counters.put("IpsilateralCoreBiopsy", new Counter("IpsilateralCoreBiopsy"));
         counters.put("ContralateralCoreBiopsy", new Counter("ContralateralCoreBiopsy"));
@@ -144 +145 @@
           
           String currentLinkedSpecimenValue = (String)Annotationtype.LINKED_SPECIMEN.getAnnotationValue(dc, snapshot, specimen);
-          String newLinkedSpecimenValue = null;
+          String newLinkedSpecimenValue = "MissingDate";
           
           // Update counter and the annotation if needed
@@ -200 +201 @@
           {
             // Clear annotations
+            newLinkedSpecimenValue = "MissingDate";
             numNoDate++;
           }