Changes between Version 1 and Version 2 of net.sf.basedb.reggie.notes25


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Timestamp:
Apr 27, 2012, 11:37:17 AM (8 years ago)
Author:
Nicklas Nordborg
Comment:

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  • net.sf.basedb.reggie.notes25

    v1 v2  
    11= Updating to Reggie 2.5 =
    22
    3 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. The procedure is outlined in the description and comments of ticket:379.
     3Updating 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:
     4
     5== 1. Update to Reggie 2.5 ==
     6
     7== 2. Create `NoSpecimen` items for all relevant cases ==
     8
     9Find 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:
     10
     11 * 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).
     12 * Parent: The parent item of the `NoSpecimen` item should be the `Case` item that holds the original `ReasonIfNoSpecimen` item.
     13
     14The following annotations should be copied from the parent `Case` to the `NoSpecimen` items:
     15  * `ReasonIfNoSpecimen` (without the [nnnnn] prefix)
     16  * `PAD` (copied from `PADCase`)
     17  * `SamplingDateTime` (copied from `SamplingDate`)
     18
     19This 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.
     20
     21Note 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.
     22
     23== 3. Remove the unused annotations from the 'Case' items ==
     24
     25After the update no `Case` item should have values for the following annotation types:
     26
     27  * `ReasonIfNoSpecimen`
     28  * `PADCase`
     29  * `SamplingDate`
     30
     31Use the annotation importer to remove those annotations. After this there should be no items that use the `PADCase` or `SamplingDate` annotations so they can be deleted from the system. The `ReasonIfNoSpecimen` annotation type should have the multiplicity setting changed to 1.
     32
     33
     34
     35It should now be possible to register new cases and specimen tubes again.