wiki:net.sf.basedb.reggie/notes410

Version 2 (modified by Nicklas Nordborg, 4 years ago) (diff)

Update notes for Reggie 4.10

Updating to Reggie 4.10

The following changes can be made after installing Reggie 4.10.

Update the MultPieces annotation for Lysate items

All Lysate items with a creation date after YYYY-MM-DD that has no value for the MultPieces annotation should be update to MultPieces=false. It should be fairly simple to filter out the lysates in the web interface and then export the "Name" column. Open the exported file in a spreadsheet and add a second column for the MultPieces annotation. Use the annotation importer to update the annotation.

Set ReferenceDate and ReferenceDateSource on all Case items

The ReferenceDate and ReferenceDateSource are new annotations that should be set on all existing Case item. There are four cases that depends on what information we already have about the case.

  1. All cases that has a value for the INCA_A030DiaDat annotation should be update to: ReferenceDate=INCA_A030DiaDat and ReferenceDateSource=IncaDiagnosisDate.
  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.
  4. All remaining cases should be updated to: ReferenceDate=Registered and ReferenceDateSource=RegistrationDate.

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.

Recipe for step 2

  1. Create a new item list with member type: Sample.
  2. 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')
  3. Sync the item list. This will create a list containing all Specimen/NoSpecimen items that has a parent Case without a ReferenceDate.
  4. Go to the Samples list page and make sure the following columns are displayed:
    • Parent items
    • Created
    • Item list
  5. Filter the samples with the item list created in step a.
  6. 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.
  7. Export the "Parent items" and "Created" column.
  8. In a spreadsheet, add third column for ReferenceDateSource and fill all rows with SamplingDate.
  9. 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".
  10. Verify that the import worked by re-syncing the item list created in step 1. It should should now be empty.