Changeset 5756

Timestamp:

Nov 26, 2019, 7:56:23 AM (3 years ago)

Author:

olle

Message:

Refs #1029. Registration of blood and FFPE blocks updated to set registered item as child item to the related case item, in an attempt to restore an item heritage structure, that will facilitate navigating the item tree in the BASE interface. The registered item will still have String annotation CASE_ID set to the case name, as currently much of the navigation functionality in MeLuDI for the new naming scheme is depending on this, but it might change in the future:

1. Java servlet class/file BaseLineRegistrationServlet.java in src/net/sf/basedb/meludi/servlet/ updated:
   a. Protected method void doPost(HttpServletRequest req, HttpServletResponse resp) updated for command "UpdateCase" to set a registered blood item as child item to the related case item.
   b. Protected method void doPost(HttpServletRequest req, HttpServletResponse resp) updated for command "RegisterBloodSamples" to set a registered blood item as child item to the related case item.
   c. Protected method void doPost(HttpServletRequest req, HttpServletResponse resp) updated for command "RegisterFFPEBlocks" to set a registered FFPE block item as child item to the related case item.

File:

• extensions/net.sf.basedb.meludi/trunk/src/net/sf/basedb/meludi/servlet/BaseLineRegistrationServlet.java (modified) (3 diffs)

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

@@ -1469 +1469 @@
             blood.setItemSubtype(Subtype.BLOOD.load(dc));
             blood.setName(itemName);
+            BioMaterialEvent creationEvent = blood.getCreationEvent();
+            if (theCase != null)
+            {
+              creationEvent.setSource(theCase);
+            }
+            // !IMPORTANT - The sampling date must be set here and as an 'SamplingDateTime' annotation
+            creationEvent.setEventDate(samplingDate);
             dc.saveItem(blood);
-            // !IMPORTANT - The sampling date must be set here and as an 'SamplingDateTime' annotation
-            BioMaterialEvent creationEvent = blood.getCreationEvent();
-            creationEvent.setEventDate(samplingDate);
 
             // Update blood item with consent for case
@@ -1663 +1667 @@
             blood.setName(itemName);
             blood.setDescription(comment);
+            BioMaterialEvent creationEvent = blood.getCreationEvent();
+            if (theCase != null)
+            {
+              creationEvent.setSource(theCase.getSample());
+            }
             dc.saveItem(blood);
             // !IMPORTANT - The sampling date must be set here and as an 'SamplingDateTime' annotation
@@ -1841 +1850 @@
             ffpeBlock.setName(itemName);
             //ffpeBlock.setDescription(comment);
+            BioMaterialEvent creationEvent = ffpeBlock.getCreationEvent();
+            Case theCase = Case.findByName(dc, caseName);
+            if (theCase != null)
+            {
+              creationEvent.setSource(theCase.getSample());
+            }
             dc.saveItem(ffpeBlock);
 
             // Update FFPE block item with consent for case
-            Case theCase = Case.findByName(dc, caseName);
             if (theCase != null)
             {