Changeset 5121

Timestamp:

Nov 21, 2018, 9:08:15 AM (4 years ago)

Author:

olle

Message:

Refs #1029. FFPE section (specimen) registration wizard updated with bug fix when finding H%E glass box position, when no box exists. Also marking registered items as used, so as not to appear in selections list for FFPE section registration wizard again:

1. Java servlet class/file BaseLineRegistrationServlet.java in src/net/sf/basedb/meludi/servlet/ updated:
   a. Protected method void doGet(HttpServletRequest req, HttpServletResponse resp) updated for command "FindStoragePositions" with bug fix when finding H%E glass box position, when no box exists.
   b. Protected method void doPost(HttpServletRequest req, HttpServletResponse resp) updated for command "RegisterFFPESections" by marking registered items as used, so as not to appear in selections list for FFPE section registration wizard again.

File:

• extensions/net.sf.basedb.meludi/trunk/src/net/sf/basedb/meludi/servlet/BaseLineRegistrationServlet.java (modified) (9 diffs)

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

@@ -506 +506 @@
           // Store H&E glass box name as "Tray" parameter instead of as "Name"
           heGlass.setTray(heGlass.getName());
-          heGlass.setPosition("1");
+          heGlass.setPosition("0");
         }
 
@@ -1850 +1850 @@
               nofSections = Integer.parseInt(nofSectionsString);
             }
-/*
-            Integer viableTumourCellsPercent = null;
-            String viableTumourCellsPercentString = (String)jsonFfpeSection.get("viableTumourCellsPercent");
-            if (viableTumourCellsPercentString != null && !viableTumourCellsPercentString.equals(""))
-            {
-              viableTumourCellsPercent = Integer.parseInt(viableTumourCellsPercentString);
-            }
-*/
             String comment = (String)jsonFfpeSection.get("comment");
             //String operator = (String)jsonFfpeSection.get("operator");
@@ -1865 +1857 @@
             //Date samplingDate = Meludi.CONVERTER_STRING_TO_DATE.convert(samplingDateString);
             //Date arrivalDate = Meludi.CONVERTER_STRING_TO_DATE.convert(arrivalDateString);
-
-/*
-            String dnaBox = (String)jsonFfpeSection.get("dnaBox");
-            String dnaRow = (String)jsonFfpeSection.get("dnaRow");
-            int dnaColumn = Integer.parseInt((String)jsonFfpeSection.get("dnaColumn"));
-
-            String rnaBox = (String)jsonFfpeSection.get("rnaBox");
-            String rnaRow = (String)jsonFfpeSection.get("rnaRow");
-            int rnaColumn = Integer.parseInt((String)jsonFfpeSection.get("rnaColumn"));
-*/
 
             String heGlassFBox = (String)jsonFfpeSection.get("heGlassFBox");
@@ -1931 +1913 @@
             Annotationtype.YELLOW_LABEL.setAnnotationValue(dc, specimen, yellowLabel);
             Annotationtype.NOF_SECTIONS.setAnnotationValue(dc, specimen, nofSections);
-            //Annotationtype.VIABLE_TUMOUR_CELLS_PERCENT.setAnnotationValue(dc, specimen, viableTumourCellsPercent);
             //if (samplingDate != null) Annotationtype.SAMPLING_DATE.setAnnotationValue(dc, specimen, samplingDate);
             //if (arrivalDate != null) Annotationtype.ARRIVAL_DATE.setAnnotationValue(dc, specimen, arrivalDate);
@@ -2007 +1988 @@
 
             BioPlateEventParticipant stainEventParticipant = stainEvent.addParticipant(heGlassF, "glass", stainNo);
-            //numNewHEGlass++;
           
-            //heGlassF.setTray(storageBox);
             heGlassF.setTray(heGlassFBox);
             heGlassF.setPosition(heGlassFPosition);
@@ -2020 +1999 @@
             stained.setItemSubtype(Subtype.STAINED.load(dc));
             stained.setName(stainedName); // Safe, since this is a new stain
-            //stained.setBioWell(heGlass.getBioWell(heCoordinate));
             stained.setDescription(histology.getDescription());
             dc.saveItem(stained);
@@ -2056 +2034 @@
 
             stainEventParticipant = stainEvent.addParticipant(heGlassE, "glass", stainNo);
-            //numNewHEGlass++;
           
-            //heGlassE.setTray(storageBox);
             heGlassE.setTray(heGlassEBox);
             heGlassE.setPosition(heGlassEPosition);
@@ -2069 +2045 @@
             stained.setItemSubtype(Subtype.STAINED.load(dc));
             stained.setName(stainedName); // Safe, since this is a new stain
-            //stained.setBioWell(heGlass.getBioWell(heCoordinate));
             stained.setDescription(histology.getDescription());
             dc.saveItem(stained);
@@ -2086 +2061 @@
             jsonMessages.add("HE stain '" + stained.getName() + "' created successfully.");
 
-/*
             // Update the FFPE block annotations
             Annotationtype.USED_FOR_FFPE_SECTION.setAnnotationValue(dc, ffpeBlock.getSample(), Boolean.TRUE);
-*/
           }
           jsonMessages.add(numUpdatedFfpeSections + " Specimen(s) updated.");