Changeset 1425 for extensions/net.sf.basedb.reggie

Timestamp:

Oct 28, 2011, 2:35:36 PM (12 years ago)

Author:

Martin Svensson

Message:

References #330 The partition wizard is now fully functional. Some testings are left to do.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/partitionform.jsp (modified) (6 diffs)
• src/net/sf/basedb/reggie/dao/SpecimenTube.java (modified) (6 diffs)
• src/net/sf/basedb/reggie/servlet/PartitionRegistrationServlet.java (modified) (4 diffs)

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

@@ -151 +151 @@
     var bloodyTitle = 'Bloody<br>';
     
-    var appearanceOptions = '<option selected></option>';  
-    appearanceOptions += '<option value=homogenus>Homogenus</option>';
-    appearanceOptions += '<option value=heterogenus>Heterogenus</option>';
-    
-    var necrosisOptions = '<option selected value=0>0</option>';
-    necrosisOptions += '<option value=20>20</option>';
-    necrosisOptions += '<option value=40>40</option>';
-    necrosisOptions += '<option value=60>60</option>';
-    necrosisOptions += '<option value=80>80</option>';
-    necrosisOptions += '<option value=100>100</option>';
+    var appearanceOptions = '<option selected ></option>';  
+    appearanceOptions += '<option value="HOMOGENUS">Homogenus</option>';
+    appearanceOptions += '<option value="HETEROGENUS">Heterogenus</option>';
+    
+    var necrosisOptions = '<option selected value="0">0</option>';
+    necrosisOptions += '<option value="20">20</option>';
+    necrosisOptions += '<option value="40">40</option>';
+    necrosisOptions += '<option value="60">60</option>';
+    necrosisOptions += '<option value="80">80</option>';
+    necrosisOptions += '<option value="100">100</option>';
     
     var fatOptions = '<option selected value=0>0</option>';
@@ -202 +202 @@
       inputWeightHtml += '<tr>';
       inputWeightHtml += '<td style="width:400px;" class="help"><span class="message" id="'+i+'.message"></span><span id="'+i+'.help"></span></td>';      
-      inputWeightHtml += '</tr>';
-      
+      inputWeightHtml += '</tr>';     
       inputWeightHtml += '<tr><td>&nbsp;</td></tr>';
     }
@@ -439 +438 @@
 function goCreate()
 {
-  alert('goCreate');
   if (!step3IsValid()) return;
   
   Main.hide('gocancel');
   Main.hide('gocreate');
-  var frm = document.forms['reggie'];
-  
-  var specimens = caseInfo.specimen;
+  
+  var frm = document.forms['reggie'];
+  var tubeInfo = new Object();
+  
+  var specimens = selectedTubes;
   var nofTubes = specimens.length;
   var partitionDateValue = frm.elements['partitionDate'].value;
-  //var partitionCommentValue = frm.elements['partitionComment'].value;
-  caseInfo.partitionDate = partitionDateValue;
-//  if (partitionCommentValue != null) caseInfo.otherPartitionComment = partitionCommentValue;
-  
+  tubeInfo.partitionDate = partitionDateValue;
   for (var i=0; i<nofTubes; i++)
   {
@@ -459 +456 @@
     frm.elements['hisWeight'+i].disabled = true;
     frm.elements['nofPieces'+i].disabled = true;
-    
+    frm.elements['bloody'+i].disabled = true;
+    frm.elements['appearance'+i].disabled = true;
+    frm.elements['necrosis'+i].disabled = true;
+    frm.elements['fat'+i].disabled = true;
+    frm.elements['coloured'+i].disabled = true;
+        
     var specimenTube = specimens[i];
     
@@ -471 +473 @@
     if (nofPiecesValue != '') specimenTube.nofPieces = nofPiecesValue;
     
-    caseInfo.specimen[i] = specimenTube;    
-  } 
+    var partitionComment = '';  
+    var appearanceElement = frm.elements['appearance'+i];
+    var necrosisElement = frm.elements['necrosis'+i];
+    var fatElement = frm.elements['fat'+i];
+    var appearanceValue = appearanceElement.options[appearanceElement.selectedIndex].value;   
+    var necrosisValue = necrosisElement.options[necrosisElement.selectedIndex].value;
+    var fatValue = fatElement.options[fatElement.selectedIndex].value;
+    
+    // Generate partition comment string
+    if (frm.elements['bloody'+i].checked == true) partitionComment += 'BLOODY';
+    if (appearanceValue != '') partitionComment += (partitionComment.length>0 ? ':' : '') + appearanceValue;
+    if (necrosisValue != '0') partitionComment += (partitionComment.length>0 ? ':' : '') + 'NECROSIS'+necrosisValue+'%';
+    if (fatValue != '0') partitionComment += (partitionComment.length>0 ? ':' : '') + 'FAT'+fatValue+'%';
+    if (frm.elements['coloured'+i].checked == true) partitionComment += partitionComment.length>0 ? ':COLOURED' : 'COLOURED';
+    
+    specimenTube.otherPartitionComment = partitionComment.length > 0 ? partitionComment : null;
+    
+    specimens[i] = specimenTube;    
+  } 
+  tubeInfo.specimens = specimens;
   var submitInfo = new Object();
-  submitInfo.caseInfo = caseInfo;
+  submitInfo.tubeInfo = tubeInfo;
   
   if (debug) Main.debug(JSON.stringify(caseInfo));
@@ -481 +501 @@
   var url = 'PartitionRegistration.servlet?ID=<%=ID%>&cmd=CreatePartitions';
   request.open("POST", url, false);
-  request.setRequestHeader("Content-Type", "application/json");
+  request.setRequestHeader("Content-Type", "application/json"); 
   request.send(JSON.stringify(submitInfo));
 

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

@@ -105 +105 @@
     
     ItemQuery<Sample> tubeQuery = Sample.getQuery();
-    tubeQuery.restrict(Restrictions.rlike(Hql.property("name"), Expressions.parameter("name", "^.+\\.[0-9]+$", Type.STRING)));
+    tubeQuery.restrict(Restrictions.and(Restrictions.eq(Hql.property("originalQuantity"), null),
+        Restrictions.rlike(Hql.property("name"), Expressions.parameter("name", "^.+\\.[0-9]+$", Type.STRING))));
     tubeQuery.order(Orders.desc(Hql.property("name")));
     tubeQuery.include(Include.ALL);
@@ -120 +121 @@
   private final String row;
   private final String column;
-  private final Float originalQuantity;
+//  private final Float originalQuantity;
   
   private SpecimenTube(Sample sample)
@@ -133 +134 @@
       row = wcfRow.format(well.getRow());     
       column = wcfColumn.format(well.getColumn());
-      originalQuantity = sample.getOriginalQuantity();
+//      originalQuantity = sample.getOriginalQuantity();
     }
     else
@@ -140 +141 @@
       row = null;
       column = null;
-      originalQuantity = null;
+//      originalQuantity = null;
     }
   } 
@@ -176 +177 @@
     return column;
   }
-  
-  public Float getOriginalQuantity()
-  {
-    return originalQuantity;
-  }
+//  
+//  public Float getOriginalQuantity()
+//  {
+//    return originalQuantity;
+//  }
   
   @SuppressWarnings("unchecked")
@@ -189 +190 @@
     json.put("row", row);
     json.put("column", column);
-    json.put("originalQuantity", originalQuantity);
+//    json.put("originalQuantity", originalQuantity);
   }
 }

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

@@ -28 +28 @@
 import net.sf.basedb.reggie.Reggie;
 import net.sf.basedb.reggie.converter.StringToDateConverter;
-import net.sf.basedb.reggie.dao.Case;
 import net.sf.basedb.reggie.dao.SpecimenTube;
 import net.sf.basedb.util.Values;
@@ -115 +114 @@
         dc = sc.newDbControl();
         JSONObject jsonReq = (JSONObject)new JSONParser().parse(req.getReader());       
-        JSONObject jsonCase = (JSONObject)jsonReq.get("caseInfo");        
-        JSONArray jsonSpecimens = (JSONArray)jsonCase.get("specimen");
+        JSONObject jsonInfo = (JSONObject)jsonReq.get("tubeInfo");        
+        JSONArray jsonSpecimens = (JSONArray)jsonInfo.get("specimens");
         
         AnnotationType partitionDateType = Reggie.findAnnotationType(dc, new Item[]{Item.EXTRACT, Item.SAMPLE}, Reggie.ANNOTATION_PARTITION_DATE, true);
@@ -122 +121 @@
         AnnotationType nofPiecesType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_NOF_PIECES, true);
         
-        StringToDateConverter dateConverter = new StringToDateConverter(new SimpleDateFormat("yyyyMMdd"));
-        String otherPartitionComment = Values.getStringOrNull((String)jsonCase.get("otherPartitionComment"));
-        Date partitionDate = dateConverter.convert((String)jsonCase.get("partitionDate"));
+        StringToDateConverter dateConverter = new StringToDateConverter(new SimpleDateFormat("yyyyMMdd"));        
+        Date partitionDate = dateConverter.convert((String)jsonInfo.get("partitionDate"));
         
         if (jsonSpecimens != null && jsonSpecimens.size()>0)
@@ -143 +141 @@
             Float apWeight = Values.getFloat((String)jsonSpecimen.get("apWeight"), null);
             Float hisWeight = Values.getFloat((String)jsonSpecimen.get("hisWeight"), null);           
-            Integer nofPieces = Values.getInteger((String)jsonSpecimen.get("nofPieces"), null); 
+            Integer nofPieces = Values.getInteger((String)jsonSpecimen.get("nofPieces"), null);
+            String otherPartitionComment = Values.getStringOrNull((String)jsonSpecimen.get("otherPartitionComment"));
             
             if (spWeight != null) spWeight = spWeight *1000;