Create "virtual" samples for cases when no specimen is received

[Nicklas Nordborg]

This use case has always been a bit awkward to handle. The information that goes with the non-existing specimen (eg. PAD, operation date, etc.) has been added to the "Case" item that is the parent item to the (non-existing) specimen. This was ok when only a single non-existing specimen was associated with a case, but new routines may increase the likelihood that a single "Case" may be merged with more than one no-specimen event. This is messy and one will have to go back to the physical referral forms to know which PAD is associated with which date, etc.

So, the idea is that we should create a "virtual" sample with the subtype "NoSpecimen" to represent events when no specimen is received. The annotations that are used for normal "Specimen" (eg. PAD, SamplingDate) should be used. This means that there is no longer any need for duplicating information on the parent "Case" item so the PADCase, SamplingDateCase, etc. are no longer needed.

A manual procedure is needed to fix already existing cases that has a no-specimen associated with them. Basically, one has to find all 'Case' items that has a value for ReasonIfNoSpecimen annotation. Then, a new child item with subtype 'NoSpecimen' should be created and the PAD, and other information copied to it. This should be relatively easy for the majority of the cases which are not merged with other cases. This can probably be handled by batch importers. There are a few cases that are merged. Further investigation is needed before we know how to handle those.

[Nicklas Nordborg]

(In [1608]) References #379: Create "virtual" samples for cases when no specimen is received

I think this should work now, though I have probably not tested every possible scenario with respect to which order the various forms are registered.

In any case, when updating to this version it is important to complete this procedure before registering new cases or specimen tubes:

1. Update to Reggie 2.5
2. Create 'NoSpecimen' items for all relevant cases. This step is best done with batch importer, but some exotic cases may need to be done manually (for example, if there are multiple no-specimen for a case). The following annotations should be copied from the 'Case' to the new 'NoSpecimen' items:
   • ReasonIfNoSpecimen (without the [nnnnn] prefix)
   • PAD (copied from PADCase)
   • SamplingDateTime (copied from SamplingDate)
3. Remove the unused annotations from the 'Case' item. The last two are no longer needed and can then be completely deleted.
   • ReasonIfNoSpecimen
   • PADCase
   • SamplingDate
4. Done. It should now be possible to register new cases and specimen tubes again.

[Nicklas Nordborg]

Seems to be working now.