Changeset 1608

Timestamp:

Apr 20, 2012, 9:57:46 AM (11 years ago)

Author:

Nicklas Nordborg

Message:

References #379: Create "virtual" samples for cases when no specimen is received

I think this should work now, though I have probably not tested every possible scenario with respect to which order the various forms are registered.

In any case, when updating to this version it is important to complete this procedure before registering new cases or specimen tubes:

1. Update to Reggie 2.5
2. Create 'NoSpecimen?' items for all relevant cases. This step is best done with batch importer, but some exotic cases may need to be done manually (for example, if there are multiple no-specimen for a case). The following annotations should be copied from the 'Case' to the new 'NoSpecimen?' items:
   • ReasonIfNoSpecimen (without the [nnnnn] prefix)
   • PAD (copied from PADCase)
   • SamplingDateTime (copied from SamplingDate)
3. Remove the unused annotations from the 'Case' item. The last two are no longer needed and can then be completely deleted.
   • ReasonIfNoSpecimen
   • PADCase
   • SamplingDate
4. Done. It should now be possible to register new cases and specimen tubes again.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/persinfo.jsp (modified) (2 diffs)
• src/net/sf/basedb/reggie/Reggie.java (modified) (3 diffs)
• src/net/sf/basedb/reggie/dao/Case.java (modified) (5 diffs)
• src/net/sf/basedb/reggie/dao/NoSpecimen.java (added)
• src/net/sf/basedb/reggie/dao/Subtype.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/InstallServlet.java (modified) (5 diffs)
• src/net/sf/basedb/reggie/servlet/PersonalRegistrationServlet.java (modified) (12 diffs)

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

@@ -609 +609 @@
   else
   {
-    // No specimen tubes... if there is only one PAD on the case... use that
-    if (caseInfo.pad && caseInfo.pad.length == 1)
-    {
-      hasPAD = true;
-      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');
-      }
+    if (caseInfo.noSpecimen)
+    {
+      // This case is registered with 'NoSpecimen'
+      thisCasePAD = caseInfo.noSpecimen.pad;
+      thisCaseSamplingDate = caseInfo.noSpecimen.samplingDate;
+      frm.reasonIfNoSpecimen.value = caseInfo.noSpecimen.reasonIfNoSpecimen;
     }
     
@@ -653 +641 @@
     rnaLaterDateTimeOnChange();
   }
-
   
   frm.pad.value = thisCasePAD;
-  caseInfo.oldPad = thisCasePAD;
-  caseInfo.oldSamplingDate = thisCaseSamplingDate;
-  
-  if (updateMode && !hasSpecimen)
-  {
-    // Try to find 'reasonIfNoSpecimen' annotation on the case
-    for (var i = 0; i < caseInfo.reasonIfNoSpecimen.length; i++)
-    {
-      var rns = caseInfo.reasonIfNoSpecimen[i];
-      if (rns.indexOf('['+caseInfo.originalName+']') == 0)
-      {
-        caseInfo.oldReasonIfNoSpecimen = rns;
-        frm.reasonIfNoSpecimen.value = rns.substring(rns.indexOf(']')+2);
-        i = 999;
-      }
-    }
-  }
   
   Main.show('caseSection');

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

@@ -85 +85 @@
   /**
     The name of the "ReasonIfNoSpecimen" annotation type, used
-    for samples (Case). It is a multi-valued string annotation.
+    for samples (NoSpecimen). It is a string annotation.
   */
   public static final String ANNOTATION_REASON_IF_NO_SPECIMEN = "ReasonIfNoSpecimen";
-
+  
   /**
     The name of the "PAD" annotation type, used
@@ -96 +96 @@
 
   /**
-    The name of the "PADcase" annotation type, used
-    for samples (Case). It is a multi-valued string annotation.
-  */
-  public static final String ANNOTATION_PAD_CASE = "PADcase";
-  
-  /**
     The name of the "PathNote" annotation type, 
     used for samples (Case). It is a string annotation type.
@@ -114 +108 @@
 
   /**
-    The name of the "SamplingDateCase" annotation type, used
-    for samples (Case). The value is basically a copy of the 
-    date part of the {@link #ANNOTATION_SAMPLING_DATETIME}
-    annotation, but also allow registration of a date when
-    no specimen has been received. It is a multi-valued date annotation.
-    @since 2.4
-  */
-  public static final String ANNOTATION_SAMPLING_DATE_CASE = "SamplingDateCase";
-  
-  /**
     The name of the "RNALaterDateTime" annotation type, used
     for samples (Specimen tube). It is a timestamp annotation.
   */
   public static final String ANNOTATION_RNALATER_DATETIME = "RNALaterDateTime";
-
   
   /**

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Case.java

@@ -15 +15 @@
 import net.sf.basedb.core.Sample;
 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;
@@ -36 +35 @@
     on the name of a sample. If exactly one match is found this is the
     (primary) case. More than one match is an error condition. If no
-    match is found, we look harder by trying to find a case with 
-    specimen tubes that have names matching the case we are looking 
+    match is found, we look harder by trying to find a child sample with 
+    'Specimen' or 'NoSpecimen' that have names matching the case we are looking 
     for (eg. xxx.1, xxx.2, etc.). If exactly one match is found this is 
     the (merged) case. More than one match is an error condition. No match 
@@ -64 +63 @@
     {
       // Not found... see if we can find a different case 
-      // with specimen tubes belonging to this case (merged case)
+      // with 'Specimen'/'NoSpecimen' child items belonging to this case (merged case)
       merged = true;
       caseQuery = Sample.getQuery();
@@ -71 +70 @@
       caseQuery.join(Hql.innerJoin("cce", "event", "evt"));
       caseQuery.join(Hql.innerJoin("evt", "bioMaterial", "sp")); // 'sp' should now reference a specimen tube
-      Subtype.SPECIMEN.addFilter(dc, caseQuery, "sp");
+      
+      // Restrict to 'Specimen' or 'NoSpecimen' child items
+      caseQuery.restrict(Restrictions.or(Subtype.SPECIMEN.restriction(dc, "sp"), Subtype.NO_SPECIMEN.restriction(dc, "sp")));
       caseQuery.restrict(Restrictions.like(Hql.property("sp", "name"), Expressions.parameter("name", name + ".%", Type.STRING)));
       caseQuery.setDistinct(true);
@@ -86 +87 @@
       }
       
-      if (cases.size() == 0)
-      {
-        // Still not found... last chance is to find a (merged) case with ReasonIfNoSpecimen comment
-        // that has [caseName] as prefix...
-        AnnotationType reasonIfNoSpecimenType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_REASON_IF_NO_SPECIMEN, true);
-        caseQuery = Sample.getQuery();
-        Subtype.CASE.addFilter(dc, caseQuery);
-        caseQuery.restrict(Annotations.like(null, reasonIfNoSpecimenType, "[" + name + "]%", false));
-        cases = caseQuery.list(dc);
-        
-        
-        if (cases.size() > 1)
-        {
-          // ...something is very incorrectly registered... 
-          // we different cases with comments for this case
-          throw new InvalidDataException(
-            "Found " + cases.size() + " cases with ReasonIfNoSpecimen comments " +
-            "for this case (" + name + "). This wizard can't be used until that is corrected.");
-        }
-        
-      }
-      
     }
 

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Subtype.java

@@ -61 +61 @@
   */
   public static final Subtype SPECIMEN = new Subtype("Specimen", Item.SAMPLE);
+
+  /**
+    The definition of the "NoSpecimen" subtype (for cases when no specimen has been received).
+    @since 2.5
+  */
+  public static final Subtype NO_SPECIMEN = new Subtype("NoSpecimen", Item.SAMPLE);
+
   
   /**

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

@@ -124 +124 @@
         jsonChecks.add(checkSubtype(dc, Subtype.BLOOD, createIfMissing, Subtype.PATIENT));
         jsonChecks.add(checkSubtype(dc, Subtype.SPECIMEN,createIfMissing, Subtype.CASE));
+        jsonChecks.add(checkSubtype(dc, Subtype.NO_SPECIMEN,createIfMissing, Subtype.CASE));
         jsonChecks.add(checkSubtype(dc, Subtype.HISTOLOGY, createIfMissing, Subtype.SPECIMEN));
         jsonChecks.add(checkSubtype(dc, Subtype.LYSATE, createIfMissing, Subtype.SPECIMEN));
@@ -169 +170 @@
         jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_LATERALITY, Item.SAMPLE, Type.STRING, 1,
             new EnumerationOptions("LEFT", "RIGHT"), effectiveOptions, createIfMissing));
-        jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_REASON_IF_NO_SPECIMEN, Item.SAMPLE, Type.STRING, 0,
+        jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_REASON_IF_NO_SPECIMEN, Item.SAMPLE, Type.STRING, 1,
             null, effectiveOptions, createIfMissing));
         jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_PAD, Item.SAMPLE, Type.STRING, 1, 
             null, effectiveOptions, createIfMissing));
+        /*
+        TODO - remove
         jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_PAD_CASE, Item.SAMPLE, Type.STRING, 0, 
             null, effectiveOptions, createIfMissing));
+        */
+        
         jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_BLOOD_SAMPLING_DATETIME, Item.SAMPLE, Type.TIMESTAMP, 1,
             null, effectiveOptions, createIfMissing));
@@ -183 +188 @@
         jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_SAMPLING_DATETIME, Item.SAMPLE, Type.TIMESTAMP, 1, 
             null, effectiveOptions, createIfMissing));
+        /*
+        TODO - remove
         jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_SAMPLING_DATE_CASE, Item.SAMPLE, Type.DATE, 0, 
             null, effectiveOptions, createIfMissing));
+        */
+        
         jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_RNALATER_DATETIME, Item.SAMPLE, Type.TIMESTAMP, 1, 
             null, effectiveOptions, createIfMissing));
@@ -231 +240 @@
         jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.CASE, createIfMissing, 
             Reggie.ANNOTATION_CONSENT, Reggie.ANNOTATION_CONSENT_DATE,
-            Reggie.ANNOTATION_LATERALITY, Reggie.ANNOTATION_SAMPLING_DATE_CASE,
-            Reggie.ANNOTATION_PAD_CASE, Reggie.ANNOTATION_REASON_IF_NO_SPECIMEN));
+            Reggie.ANNOTATION_LATERALITY));
         
         jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.BLOOD, createIfMissing, 
@@ -246 +254 @@
             Reggie.ANNOTATION_PAD, Reggie.ANNOTATION_RNALATER_DATETIME, 
             Reggie.ANNOTATION_SAMPLING_DATETIME, Reggie.ANNOTATION_SPECIMEN_TYPE));
+        
+        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.NO_SPECIMEN, createIfMissing, 
+            Reggie.ANNOTATION_PAD, Reggie.ANNOTATION_REASON_IF_NO_SPECIMEN,
+            Reggie.ANNOTATION_SAMPLING_DATETIME
+            ));
+        
         jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.LYSATE, createIfMissing, 
             Reggie.ANNOTATION_PARTITION_DATE));

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

@@ -21 +21 @@
 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;
@@ -28 +29 @@
 import net.sf.basedb.reggie.dao.Case;
 import net.sf.basedb.reggie.dao.Consent;
+import net.sf.basedb.reggie.dao.NoSpecimen;
 import net.sf.basedb.reggie.dao.Patient;
 import net.sf.basedb.reggie.dao.SpecimenTube;
@@ -80 +82 @@
         
         List<SpecimenTube> specimenTubes = null;
+        NoSpecimen noSpecimen = null;
         JSONObject jsonCase = null;
         JSONObject jsonBlood = null;
@@ -95 +98 @@
             specimenTubes = SpecimenTube.findByCaseName(dc, caseName);
           }
+          
+          if (specimenTubes.size() == 0)
+          {
+            // Still not found -- check if there are any 'NoSpecimen' items
+            List<NoSpecimen> nsList = NoSpecimen.findByCase(dc, theCase, true);
+            if (nsList.size() > 1)
+            {
+              // There should be at most one 'NoSpecimen' item
+              throw new InvalidDataException(
+                "Found " + nsList.size() + " 'NoSpecimen' samples for the case (" + caseName + 
+                "). This wizard can't be used until that is corrected.");
+            }
+            else if (nsList.size() == 1)
+            {
+              noSpecimen = nsList.get(0);
+            }
+          }
 
           // Continue to load some more info (annotations, etc...)
           // ... case annotations
           theCase.loadAnnotations(dc, "laterality", Reggie.ANNOTATION_LATERALITY, null);
+          /*
+          TODO - remove
           theCase.loadAnnotations(dc, "pad", Reggie.ANNOTATION_PAD_CASE, null);
           theCase.loadAnnotations(dc, "samplingDate", Reggie.ANNOTATION_SAMPLING_DATE_CASE, Reggie.CONVERTER_DATE_TO_STRING);
           theCase.loadAnnotations(dc, "reasonIfNoSpecimen", Reggie.ANNOTATION_REASON_IF_NO_SPECIMEN, null);
+          */
 
           // Wrap what we have so far up into JSON objects
@@ -142 +165 @@
         }
         
-        // Load specimen tube annotations
+        // Load 'Specimen'/'NoSpecimen' annotations
         JSONArray jsonTubes = new JSONArray();
+        AnnotationType padType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_PAD, true);
+        AnnotationType samplingDateType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_SAMPLING_DATETIME, true);
         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);
-          AnnotationType samplingDateType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_SAMPLING_DATETIME, true);
           AnnotationType rnaLaterDateType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_RNALATER_DATETIME, true);
           for (SpecimenTube tube : specimenTubes)
@@ -160 +183 @@
         }
         jsonCase.put("specimen", jsonTubes);
+        
+        if (noSpecimen != null)
+        {
+          noSpecimen.loadAnnotations("pad", padType, null);
+          noSpecimen.loadAnnotations("samplingDate", samplingDateType, Reggie.CONVERTER_DATE_TO_STRING);
+          noSpecimen.loadAnnotations(dc, "reasonIfNoSpecimen", Reggie.ANNOTATION_REASON_IF_NO_SPECIMEN, null);
+          jsonCase.put("noSpecimen", noSpecimen.asJSONObject());
+        }
         
         // This is what we send back to the browser
@@ -337 +368 @@
         AnnotationSet caseAnnotations = theCase.getAnnotationSet();
         JSONArray jsonSpecimen = (JSONArray)jsonCase.get("specimen");
-        // PAD value
-        AnnotationType padCaseType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_PAD_CASE, true);
+        
+        // Annotations that are always used
+        AnnotationType padType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_PAD, true);
+        AnnotationType samplingDateTimeType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_SAMPLING_DATETIME, true);
+        
         String pad = Values.getStringOrNull((String)jsonCase.get("pad"));
-        if (pad != null) Reggie.appendAnnotationValueIfUnique(theCase, padCaseType, pad);
-        
-        // Sampling date on Case
-        AnnotationType samplingDateCaseType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_SAMPLING_DATE_CASE, true);
-        Date samplingDate = Reggie.CONVERTER_STRING_TO_DATE.convert((String)jsonCase.get("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 samplingDateTimeType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_SAMPLING_DATETIME, true);
           AnnotationType rnaLaterType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_RNALATER_DATETIME, true);
+          Date rnaLaterDateTime = Reggie.CONVERTER_STRING_TO_DATETIME.convert((String)jsonCase.get("rnaLaterDate"));
           Date samplingDateTime = Reggie.CONVERTER_STRING_TO_DATETIME.convert((String)jsonCase.get("samplingDate"));
-          Date rnaLaterDateTime = Reggie.CONVERTER_STRING_TO_DATETIME.convert((String)jsonCase.get("rnaLaterDate"));
 
           for (int i = 0; i < jsonSpecimen.size(); ++i)
@@ -366 +389 @@
             creationEvent.setSource(theCase);
             // !IMPORTANT - The sampling date must be set here and as an 'SamplingDateTime' annotation
-            creationEvent.setEventDate(samplingDate);
+            creationEvent.setEventDate(samplingDateTime);
             
             // Update the specimen annotations
@@ -379 +402 @@
         else
         {
+          Date samplingDate = Reggie.CONVERTER_STRING_TO_DATE.convert((String)jsonCase.get("samplingDate"));
+
+          // Create new 'NoSpecimen' item
+          Sample noSpecimen = Sample.getNew(dc);
+          dc.saveItem(noSpecimen);
+          noSpecimen.setItemSubtype(Subtype.NO_SPECIMEN.load(dc));
+          noSpecimen.setName(originalCaseName+".1");
+          BioMaterialEvent creationEvent = noSpecimen.getCreationEvent();
+          creationEvent.setSource(theCase);
+          creationEvent.setEventDate(samplingDate);
+          
           AnnotationType reasonIfNoSpecimenType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_REASON_IF_NO_SPECIMEN, true);
-          Reggie.appendAnnotationValueIfUnique(theCase, reasonIfNoSpecimenType, "[" + originalCaseName + "] " + jsonCase.get("reasonIfNoSpecimen"));
+          Reggie.setAnnotationValue(noSpecimen, padType, pad);
+          Reggie.setAnnotationValue(noSpecimen, reasonIfNoSpecimenType, jsonCase.get("reasonIfNoSpecimen"));
+          if (samplingDate != null) Reggie.setAnnotationValue(noSpecimen, samplingDateTimeType, samplingDate);
+          
+          jsonMessages.add("Virtual specimen '" + noSpecimen.getName() + "' created successfully.");
         }
         
@@ -406 +444 @@
         boolean updateLaterality = Values.getInt(laterality, -1) == -1;
         String pad = Values.getStringOrNull((String)jsonCase.get("pad"));
-        String oldPad = Values.getStringOrNull((String)jsonCase.get("oldPad"));
         JSONArray jsonSpecimen = (JSONArray)jsonCase.get("specimen");
+        JSONObject jsonNoSpecimen = (JSONObject)jsonCase.get("noSpecimen");
       
         // Update laterality and PAD for the case
         AnnotationType lateralityType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_LATERALITY, true);
-        AnnotationType padCaseType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_PAD_CASE, true);
         if (updateLaterality)
         {
           Reggie.setAnnotationValue(theCase, lateralityType, laterality);
         }
-
-        if (oldPad != null) Reggie.removeAnnotationValue(theCase, padCaseType, oldPad);
-        if (pad != null) Reggie.appendAnnotationValueIfUnique(theCase, padCaseType, pad);
-
-        // Sampling date on Case
-        AnnotationType samplingDateCaseType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_SAMPLING_DATE_CASE, true);
-        Date samplingDate = Reggie.CONVERTER_STRING_TO_DATE.convert((String)jsonCase.get("samplingDate"));
-        Date oldSamplingDate = Reggie.CONVERTER_STRING_TO_DATE.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.");
         
@@ -450 +471 @@
             Sample specimen = Sample.getById(dc, ((Number)jsonSpec.get("id")).intValue());
             // !IMPORTANT - The sampling date must be set here and as an 'SamplingDateTime' annotation
-            specimen.getCreationEvent().setEventDate(samplingDate);
+            specimen.getCreationEvent().setEventDate(samplingDateTime);
             
             // Update the specimen annotations
@@ -462 +483 @@
 
         }
-        else
-        {
-          // No specimen tubes...update the 'reasonIfNoSpecimen' annotation
+        else if (jsonNoSpecimen != null)
+        {
+          // Update the 'NoSpecimen' item
+          AnnotationType padType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_PAD, true);
+          AnnotationType samplingDateType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_SAMPLING_DATETIME, true);
           AnnotationType reasonIfNoSpecimenType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_REASON_IF_NO_SPECIMEN, true);
-          
-          String rns = Values.getString((String)jsonCase.get("reasonIfNoSpecimen"));
-          String oldRns = Values.getString((String)jsonCase.get("oldReasonIfNoSpecimen"));
-          if (oldRns != null)
-          {
-            Reggie.removeAnnotationValue(theCase, reasonIfNoSpecimenType, oldRns);
-          }
-          if (rns != null)
-          {
-            Reggie.appendAnnotationValueIfUnique(theCase, reasonIfNoSpecimenType, "[" + originalCaseName + "] " + rns);
-          }
-          
+
+          Date samplingDate = Reggie.CONVERTER_STRING_TO_DATE.convert((String)jsonCase.get("samplingDate"));
+
+          Sample noSpecimen = Sample.getById(dc, ((Number)jsonNoSpecimen.get("id")).intValue());
+          noSpecimen.getCreationEvent().setEventDate(samplingDate);
+
+          Reggie.setAnnotationValue(noSpecimen, padType, pad);
+          Reggie.setAnnotationValue(noSpecimen, samplingDateType, samplingDate);
+          Reggie.setAnnotationValue(noSpecimen, reasonIfNoSpecimenType, Values.getString((String)jsonCase.get("reasonIfNoSpecimen")));
         }