Changeset 1597

Timestamp:

Mar 30, 2012, 11:23:23 AM (11 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #374: Store operation date on case items

Added SamplingDateTimeCase annotation type that can hold multiple values.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/persinfo.jsp (modified) (3 diffs)
• src/net/sf/basedb/reggie/Reggie.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/InstallServlet.java (modified) (2 diffs)
• src/net/sf/basedb/reggie/servlet/PersonalRegistrationServlet.java (modified) (4 diffs)

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

@@ -596 +596 @@
       thisCaseLaterality = null;
     }
-
-    // Show and populate 'Sampling date' and 'RNA Later date' fields
+    
     Main.show('samplingDateSection');
     Main.show('rnaLaterDateSection');
-    if (thisCaseSamplingDate != null)
-    {
-      frm.samplingDate.value = thisCaseSamplingDate.substring(0, 8);
-      frm.samplingTime.value = thisCaseSamplingDate.substring(9, 13);
-      samplingDateTimeOnChange();
-    }
-    if (thisCaseRNALaterDate != null)
-    {
-      frm.rnaLaterDate.value = thisCaseRNALaterDate.substring(0, 8);
-      frm.rnaLaterTime.value = thisCaseRNALaterDate.substring(9, 13);
-      rnaLaterDateTimeOnChange();
-    }
+
   }
   else
@@ -621 +609 @@
       thisCasePAD = caseInfo.pad[0];
     }
+    if (caseInfo.samplingDate)
+    {
+      if (caseInfo.samplingDate.length == 1)
+      {
+        thisCaseSamplingDate = caseInfo.samplingDate[0];
+      }
+      else
+      {
+        frm.samplingDate.disabled = true;
+        frm.samplingTime.disabled = true;
+        setInputStatus('samplingDate', 'Multiple dates have already been registered for this case.', 'warning');
+      }
+    }
+    
     
     // Hide 'RNA Later date' field
@@ -626 +628 @@
   }
 
+  // Populate 'Sampling date' and 'RNA Later date' fields
+  if (thisCaseSamplingDate != null)
+  {
+    frm.samplingDate.value = thisCaseSamplingDate.substring(0, 8);
+    frm.samplingTime.value = thisCaseSamplingDate.substring(9, 13);
+    samplingDateTimeOnChange();
+  }
+  if (thisCaseRNALaterDate != null)
+  {
+    frm.rnaLaterDate.value = thisCaseRNALaterDate.substring(0, 8);
+    frm.rnaLaterTime.value = thisCaseRNALaterDate.substring(9, 13);
+    rnaLaterDateTimeOnChange();
+  }
+
+  
   frm.pad.value = thisCasePAD;
   caseInfo.oldPad = thisCasePAD;
+  caseInfo.oldSamplingDate = thisCaseSamplingDate;
   
   if (updateMode && !hasSpecimen)

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

@@ -114 +114 @@
 
   /**
+    The name of the "SamplingDateTimeCase" annotation type, used
+    for samples (Case). It is a multi-valued timestamp annotation.
+    @since 2.4
+  */
+  public static final String ANNOTATION_SAMPLING_DATETIME_CASE = "SamplingDateTimeCase";
+  
+  
+  /**
     The name of the "RNALaterDateTime" annotation type, used
     for samples (Specimen tube). It is a timestamp annotation.

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

@@ -173 +173 @@
         jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_SAMPLING_DATETIME, Item.SAMPLE, Type.TIMESTAMP, 1, 
             null, effectiveOptions, createIfMissing));
+        jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_SAMPLING_DATETIME_CASE, Item.SAMPLE, Type.TIMESTAMP, 0, 
+            null, effectiveOptions, createIfMissing));
         jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_RNALATER_DATETIME, Item.SAMPLE, Type.TIMESTAMP, 1, 
             null, effectiveOptions, createIfMissing));
@@ -219 +221 @@
         jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.CASE, createIfMissing, 
             Reggie.ANNOTATION_CONSENT, Reggie.ANNOTATION_CONSENT_DATE,
-            Reggie.ANNOTATION_LATERALITY, Reggie.ANNOTATION_SAMPLING_DATETIME,
+            Reggie.ANNOTATION_LATERALITY, Reggie.ANNOTATION_SAMPLING_DATETIME_CASE,
             Reggie.ANNOTATION_PAD_CASE, Reggie.ANNOTATION_REASON_IF_NO_SPECIMEN));
         

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

@@ -100 +100 @@
           theCase.loadAnnotations(dc, "laterality", Reggie.ANNOTATION_LATERALITY, null);
           theCase.loadAnnotations(dc, "pad", Reggie.ANNOTATION_PAD_CASE, null);
+          theCase.loadAnnotations(dc, "samplingDate", Reggie.ANNOTATION_SAMPLING_DATETIME_CASE, Reggie.CONVERTER_DATETIME_TO_STRING);
           theCase.loadAnnotations(dc, "reasonIfNoSpecimen", Reggie.ANNOTATION_REASON_IF_NO_SPECIMEN, null);
 
@@ -340 +341 @@
         String pad = Values.getStringOrNull((String)jsonCase.get("pad"));
         if (pad != null) Reggie.appendAnnotationValueIfUnique(theCase, padCaseType, pad);
-        // Sampling date
-        AnnotationType samplingDateType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_SAMPLING_DATETIME, true);
+        
+        // Sampling date on Case
+        AnnotationType samplingDateCaseType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_SAMPLING_DATETIME_CASE, true);
         Date samplingDate = Reggie.CONVERTER_STRING_TO_DATETIME.convert((String)jsonCase.get("samplingDate"));
-        if (samplingDate != null) Reggie.setAnnotationValue(theCase, samplingDateType, samplingDate);
+        if (samplingDate != null) 
+        {
+          Reggie.appendAnnotationValueIfUnique(theCase, samplingDateCaseType, samplingDate);
+        }
         
         if (jsonSpecimen != null && jsonSpecimen.size() > 0)
         {
           AnnotationType padType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_PAD, true);
+          AnnotationType samplingDateType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_SAMPLING_DATETIME, true);
           AnnotationType rnaLaterType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_RNALATER_DATETIME, true);
           Date rnaLaterDate = Reggie.CONVERTER_STRING_TO_DATETIME.convert((String)jsonCase.get("rnaLaterDate"));
@@ -413 +419 @@
         if (pad != null) Reggie.appendAnnotationValueIfUnique(theCase, padCaseType, pad);
 
-        // Sampling date
-        AnnotationType samplingDateType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_SAMPLING_DATETIME, true);
+        // Sampling date on Case
+        AnnotationType samplingDateCaseType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_SAMPLING_DATETIME_CASE, true);
         Date samplingDate = Reggie.CONVERTER_STRING_TO_DATETIME.convert((String)jsonCase.get("samplingDate"));
-        if (samplingDate != null) Reggie.setAnnotationValue(theCase, samplingDateType, samplingDate);
+        Date oldSamplingDate = Reggie.CONVERTER_STRING_TO_DATETIME.convert((String)jsonCase.get("oldSamplingDate"));
+        if (oldSamplingDate != null)
+        {
+          Reggie.removeAnnotationValue(theCase, samplingDateCaseType, oldSamplingDate);
+        }
+        if (samplingDate != null) 
+        {
+          Reggie.appendAnnotationValueIfUnique(theCase, samplingDateCaseType, samplingDate);
+        }
         
         jsonMessages.add("Case '" + originalCaseName + "' updated successfully.");
@@ -424 +438 @@
         {
           AnnotationType padType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_PAD, true);
+          AnnotationType samplingDateType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_SAMPLING_DATETIME, true);
           AnnotationType rnaLaterType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_RNALATER_DATETIME, true);