Changeset 5832

Timestamp:

Feb 21, 2020, 4:19:57 PM (3 years ago)

Author:

olle

Message:

Refs #1029. FFPE section (specimen) registration wizard updated by removing input fields for tumour cell percentage for H&E glass items, since these should be moved to a separate wizard. Also, created FFPE sections (specimens) now made children of the FFPE block instead of the case item:

1. Javascript file ffpe_section_registration_alt_rec.js in resources/personal/ updated by removing code related to input fields for tumour cell percentage for H&E glass items.
2. Java servlet class/file BaseLineRegistrationServlet.java in src/net/sf/basedb/meludi/servlet/ updated in protected method void doPost(HttpServletRequest req, HttpServletResponse resp) for command "RegisterFFPESections" to not set tumour cell percentage for H&E glass items. Also, created FFPE sections (specimens) now made children of the FFPE block instead of the case item.

Location:

extensions/net.sf.basedb.meludi/trunk

Files:

• resources/personal/ffpe_section_registration_alt_rec.js (modified) (7 diffs)
• src/net/sf/basedb/meludi/servlet/BaseLineRegistrationServlet.java (modified) (4 diffs)

extensions/net.sf.basedb.meludi/trunk/resources/personal/ffpe_section_registration_alt_rec.js

@@ -167 +167 @@
       var yellowLabelMsg = 'Assigned yellow label for '+ffpeSectionName+' (selected for processing).';
       var nofSectionsMsg = 'Number of sections for '+ffpeSectionName+'.';
-      var pctViabTumourCellsMsg = '% Viable tumour cells for '+ffpeSectionName+'.';
+      //var pctViabTumourCellsMsg = '% Viable tumour cells for '+ffpeSectionName+'.';
       var opDelCmtMsg = 'In this field, enter information specific for for '+ffpeSectionName+'.';
       var disabledAttribute = '';
@@ -209 +209 @@
       var heGlassEBoxMsg = 'Box-number and position where the H&E glass "E" will be placed.';
       var disabledAttribute = '';
-      var pctTumourCellsFMsg = '% Tumour cells for '+ffpeSectionName+'.F.'
-      var pctTumourCellsEMsg = '% Tumour cells for '+ffpeSectionName+'.E.'
+      //var pctTumourCellsFMsg = '% Tumour cells for '+ffpeSectionName+'.F.'
+      //var pctTumourCellsEMsg = '% Tumour cells for '+ffpeSectionName+'.E.'
 
 /*
@@ -282 +282 @@
       html += '</tr>';
 
+/*
       // H&E glass "Front" percentage of tumor cells 
       html += '<tr>';
@@ -291 +292 @@
       html += '<td class="help"><span id="pctTumourCellsF.'+i+'.message" class="message"></span>'+pctTumourCellsFMsg+'<span id="pctTumourCellsF.'+i+'.message" class="message"></span></td>';
       html += '</tr>';
+*/
 
       // H&E glass "End"
@@ -304 +306 @@
       html += '</tr>';
 
+/*
       // H&E glass "End" percentage of tumor cells 
       html += '<tr>';
@@ -313 +316 @@
       html += '<td class="help"><span id="pctTumourCellsE.'+i+'.message" class="message"></span>'+pctTumourCellsEMsg+'<span id="pctTumourCellsE.'+i+'.message" class="message"></span></td>';
       html += '</tr>';
+*/
     }
     Doc.element('ffpe-sections').innerHTML = html;
@@ -854 +858 @@
       ffpeSection.heGlassFBox = frm['heGlassFBox.'+i].value;
       ffpeSection.heGlassFPosition = frm['heGlassFPosition.'+i].value;
-      ffpeSection.pctTumourCellsF = frm['pctTumourCellsF.'+i].value;
+      //ffpeSection.pctTumourCellsF = frm['pctTumourCellsF.'+i].value;
 
       ffpeSection.heGlassEBox = frm['heGlassEBox.'+i].value;
       ffpeSection.heGlassEPosition = frm['heGlassEPosition.'+i].value;
-      ffpeSection.pctTumourCellsE = frm['pctTumourCellsE.'+i].value;
+      //ffpeSection.pctTumourCellsE = frm['pctTumourCellsE.'+i].value;
       //
       ffpeSectionInfo.ffpeSections[i] = ffpeSection;

extensions/net.sf.basedb.meludi/trunk/src/net/sf/basedb/meludi/servlet/BaseLineRegistrationServlet.java

@@ -1924 +1924 @@
             String heGlassFBox = (String)jsonFfpeSection.get("heGlassFBox");
             String heGlassFPosition = (String)jsonFfpeSection.get("heGlassFPosition");
-            int pctTumourCellsF = Integer.parseInt((String)jsonFfpeSection.get("pctTumourCellsF"));
+            //int pctTumourCellsF = Integer.parseInt((String)jsonFfpeSection.get("pctTumourCellsF"));
 
             String heGlassEBox = (String)jsonFfpeSection.get("heGlassEBox");
             String heGlassEPosition = (String)jsonFfpeSection.get("heGlassEPosition");
-            int pctTumourCellsE = Integer.parseInt((String)jsonFfpeSection.get("pctTumourCellsE"));
+            //int pctTumourCellsE = Integer.parseInt((String)jsonFfpeSection.get("pctTumourCellsE"));
 
             // Find case name from FFPE block
@@ -1958 +1958 @@
 
             BioMaterialEvent creationEvent = specimen.getCreationEvent();
+            /*
             // Link the specimen with the case
             if (theCase != null)
             {
               creationEvent.setSource(theCase.getSample());
+            }
+            creationEvent.setEventDate(createDate);
+            */
+
+            // Link the specimen with the FFPE block
+            if (ffpeBlock != null)
+            {
+              creationEvent.setSource(ffpeBlock.getSample());
             }
             creationEvent.setEventDate(createDate);
@@ -2066 +2075 @@
             dc.saveItem(stained);
 
-            Annotationtype.TUMOUR_CELLS_PERCENT.setAnnotationValue(dc, stained, pctTumourCellsF);
+            //Annotationtype.TUMOUR_CELLS_PERCENT.setAnnotationValue(dc, stained, pctTumourCellsF);
             // Get location for stain on glass plate
             BioWell stainedFWell = heGlassF.getBioWell(0, 0);
@@ -2112 +2121 @@
             dc.saveItem(stained);
 
-            Annotationtype.TUMOUR_CELLS_PERCENT.setAnnotationValue(dc, stained, pctTumourCellsE);
+            //Annotationtype.TUMOUR_CELLS_PERCENT.setAnnotationValue(dc, stained, pctTumourCellsE);
             // Get location for stain on glass plate
             BioWell stainedEWell = heGlassE.getBioWell(0, 0);