Changes between Version 1 and Version 2 of net.sf.basedb.reggie/notes410

Timestamp:

May 2, 2017, 9:01:06 AM (8 years ago)

Author:

Nicklas Nordborg

Comment:

Update notes for Reggie 4.10

net.sf.basedb.reggie/notes410

@@ -18 +18 @@
  1. All cases that has a value for the INCA_A030DiaDat annotation should be update to:
     `ReferenceDate=INCA_A030DiaDat` and `ReferenceDateSource=IncaDiagnosisDate`.
- 2. TODO
+ 2. All cases that has at least one Specimen or !NoSpecimen item with a creation date 
+    should be updated to `ReferenceDate=earliest created date` and `ReferenceDateSource=SamplingDate`.
+    See below for a recipe.
  3. Remaining cases that has a value for the !ConsentDate annotation should be updated to:
     `ReferenceDate=ConsentDate` and `ReferenceDateSource=ConsentDate`.
@@ -25 +27 @@
 
 1, 3 and 4 can be done with a simple export/import operation with the help of a spreadsheet to
-fill in the !ReferenceDateSource value.
- 
+fill in the !ReferenceDateSource value. 
+
+'''Recipe for step 2'''
+
+ a. Create a new item list with member type: Sample.
+ b. Add the following synchronization filters:
+   * Parent Sample that matches filter must exist:
+     `itemSubtype = 'Case' AND {ReferenceDateSource} = null`
+   * Sample must match filter:  `creationEvent.eventDate !=  AND itemSubtype IN ('NoSpecimen', 'Specimen')`
+ c. Sync the item list. This will create a list containing all Specimen/!NoSpecimen items that has 
+    a parent Case without a !ReferenceDate.
+ d. Go to the Samples list page and make sure the following columns are displayed:
+    * Parent items
+    * Created
+    * Item list
+ e. Filter the samples with the item list created in step a.
+ f. '''IMPORTANT!! ''' Sort the samples by "Created" date in ascending order. This allows the annotation import in step i to select the earliest date for each item.
+ g. Export the "Parent items" and "Created" column.
+ h. In a spreadsheet, add third column for `ReferenceDateSource`  and fill all rows with `SamplingDate`.
+ i. Use the annotation importer to update the `ReferenceDate` and `ReferenceDateSource` annotations. The "Parent items" column maps to "Name".
+    '''IMPORTANT!! ''' Make sure that the error handling option "Too many values" is set to "Crop".
+ j. Verify that the import worked by re-syncing the item list created in step 1. It should should now be empty.