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

Timestamp:

Apr 27, 2012, 11:37:17 AM (12 years ago)

Author:

Nicklas Nordborg

Comment:

--

net.sf.basedb.reggie.notes25

@@ -1 +1 @@
 = 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. The procedure is outlined in the description and comments of ticket:379.
+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 `SamplingDate`)
+
+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`
+  * `SamplingDate`
+
+Use 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.
+
+
+
+It should now be possible to register new cases and specimen tubes again.