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

May 2, 2017, 9:01:06 AM (7 years ago)
Nicklas Nordborg

Update notes for Reggie 4.10


  • net.sf.basedb.reggie/notes410

    v1 v2  
    1818 1. All cases that has a value for the INCA_A030DiaDat annotation should be update to:
    1919    `ReferenceDate=INCA_A030DiaDat` and `ReferenceDateSource=IncaDiagnosisDate`.
    20  2. TODO
     20 2. All cases that has at least one Specimen or !NoSpecimen item with a creation date
     21    should be updated to `ReferenceDate=earliest created date` and `ReferenceDateSource=SamplingDate`.
     22    See below for a recipe.
    2123 3. Remaining cases that has a value for the !ConsentDate annotation should be updated to:
    2224    `ReferenceDate=ConsentDate` and `ReferenceDateSource=ConsentDate`.
    26281, 3 and 4 can be done with a simple export/import operation with the help of a spreadsheet to
    27 fill in the !ReferenceDateSource value.
     29fill in the !ReferenceDateSource value.
     31'''Recipe for step 2'''
     33 a. Create a new item list with member type: Sample.
     34 b. Add the following synchronization filters:
     35   * Parent Sample that matches filter must exist:
     36     `itemSubtype = 'Case' AND {ReferenceDateSource} = null`
     37   * Sample must match filter:  `creationEvent.eventDate !=  AND itemSubtype IN ('NoSpecimen', 'Specimen')`
     38 c. Sync the item list. This will create a list containing all Specimen/!NoSpecimen items that has
     39    a parent Case without a !ReferenceDate.
     40 d. Go to the Samples list page and make sure the following columns are displayed:
     41    * Parent items
     42    * Created
     43    * Item list
     44 e. Filter the samples with the item list created in step a.
     45 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.
     46 g. Export the "Parent items" and "Created" column.
     47 h. In a spreadsheet, add third column for `ReferenceDateSource`  and fill all rows with `SamplingDate`.
     48 i. Use the annotation importer to update the `ReferenceDate` and `ReferenceDateSource` annotations. The "Parent items" column maps to "Name".
     49    '''IMPORTANT!! ''' Make sure that the error handling option "Too many values" is set to "Crop".
     50 j. Verify that the import worked by re-syncing the item list created in step 1. It should should now be empty.