wiki:net.sf.basedb.reggie.notes25

Updating to Reggie 2.5

Updating to Reggie 2.5 require some manual changes to the items that already exists. This is due to the decision to register no-specimen-received events as individual NoSpecimen sample items instead of putting that information on the parent Case item. See ticket:379 for more information. Follow this procedure:

1. Update to Reggie 2.5

2. Create NoSpecimen items for all relevant cases

Find all Case items that have a value for the ReasonIfNoSpecimen annotation. For each value of the ReasonIfNoSpecimen annotation a new item with NoSpecimen subtype should be created, with the following properties:

  • Name: The name of the new item should be the case number taken from the ReasonIfNoSpecimen value + '.1' as suffix (this can be different from the name of the Case item).
  • Parent: The parent item of the NoSpecimen item should be the Case item that holds the original ReasonIfNoSpecimen item.

The following annotations should be copied from the parent Case to the NoSpecimen items:

  • ReasonIfNoSpecimen (without the [nnnnn] prefix)
  • PAD (copied from PADCase)
  • SamplingDateTime (copied from SamplingDateCase). This value should also be set as the 'Created' date for the NoSpecimen.

This should not be too difficult to fix by first exporting a text file with the name and annotation values for the items that must be fixed. A macro or search-and-replace operation in a spreadsheet program can then probably be used to create a file that can be used by the sample and annotation batch importers.

Note that some Case items may have multiple ReasonIfNoSpecimen annotation values. Each annotation value should result in one new NoSpecimen item. The export will only create a single row which must be manually duplicated so that each row only contain a single set of values. In this case it may be impossible to know which PAD and SamplingDate that belong to a given ReasonIfNoSpecimen. If unsure, the original referral form should be consulted.

3. Remove the unused annotations from the 'Case' items

After the update no Case item should have values for the following annotation types:

  • ReasonIfNoSpecimen
  • PADCase
  • SamplingDateCase

Use the annotation importer to remove those annotations. After this there should be no items that use the PADCase or SamplingDateCase annotations so they can be deleted from the system. The ReasonIfNoSpecimen annotation type should have the multiplicity setting changed to 1.

It should now be possible to register new cases and specimen tubes again.

Last modified 5 years ago Last modified on May 4, 2012, 2:16:58 PM