Stream: implementers
Topic: Publisher 1.1.40 QA None of the codes provided are in the VS
Shahim Essaid (Nov 11 2020 at 20:45):
I'm seeing an error that I can't explain. QA is here: http://phenopackets.org/core-ig/master-fixes/qa.html
shows this error:
None of the codes provided are in the value set http://github.com/phenopackets/core-ig/ValueSet/phenotypic-modifier (http://github.com/phenopackets/core-ig/ValueSet/phenotypic-modifier), and a code from this value set is required) (codes = http://github.com/phenopackets/core-ig/CodeSystem/hpo#HP:0410401)
The example resource file:
https://github.com/phenopackets/core-ig/blob/b89722d7210b752729f51a6c48f3b02f5b4ee196/ig-root/input/examples/Observation-phenotypic-abnormality-valid-1.json#L50
But the ValueSet has the code, and it's the only code in the VS right now:
http://phenopackets.org/core-ig/master-fixes/ValueSet-phenotypic-modifier.html
The VS is bound as shown here:
https://github.com/phenopackets/core-ig/blob/b89722d7210b752729f51a6c48f3b02f5b4ee196/ig-root/input/resources/StructureDefinition-observation-phenotypic-abnormality.xml#L106
I'm sure it's some operator error but I've given up on noticing what I might have done wrong and I'd appreciate another pair of eyes :) Or maybe it's a bug. It happens with 1.1.39 and 1.1.35 as well but I haven't tried other versions. Thanks in advance!
Edit: this is on Windows 10 and Java 11 in case it matters.
Lloyd McKenzie (Nov 11 2020 at 20:56):
Try calling an 'expand' on tx.fhir.org/r4 and see what the valueset expansion is.
Shahim Essaid (Nov 11 2020 at 20:58):
The CS and VS are all local in my IG, not real ones. would calling tx.fhir.org/r4 help in this case?
The other VS in the IG are working with the bindings and the simple example resource. Just this one is not.
Lloyd McKenzie (Nov 11 2020 at 21:00):
The value set definition I see is intentional. It looks for codes that match 'is-a' HP:0012823, but excludes HP:0012823 and HP:0012824. The terminology server would be running an expansion to determine whether HP:0410401 falls within that set
Shahim Essaid (Nov 11 2020 at 21:03):
right, the value set is expanded based on the CS that is also in the IG. maybe i'm not understanding how the terminology part works for the publisher. is the expansion done on the server even if the resources are all local to my IG?
The intentional definition is properly expanded by the publisher for the VS and the other ones in the IG. I'll try tx.fhir.org/r4 to see how that works. I haven't interacted with it directly before.
Shahim Essaid (Nov 11 2020 at 21:05):
Lloyd McKenzie said:
The terminology server would be running an expansion to determine whether HP:0410401 falls within that set
The expansion is done and that code is in the expanded VS as you can see here: http://phenopackets.org/core-ig/master-fixes/ValueSet-phenotypic-modifier.html#expansion
Shahim Essaid (Nov 11 2020 at 21:16):
Source is here: https://github.com/phenopackets/core-ig/tree/b89722d7210b752729f51a6c48f3b02f5b4ee196/ig-root
Lloyd McKenzie (Nov 11 2020 at 21:35):
Nothing is jumping out on me. @Grahame Grieve ?
Shahim Essaid (Nov 11 2020 at 21:43):
In case you clone that repo, look at the "master-fixes" branch. It also has a PR: https://github.com/phenopackets/core-ig/pull/9
Grahame Grieve (Nov 12 2020 at 10:07):
I've put it in my queue
Grahame Grieve (Nov 13 2020 at 02:35):
yes bug in the mini terminology server inside the validator/publisher. Fixed next release
Shahim Essaid (Nov 13 2020 at 20:43):
Confirming that 1.1.42 fixed this issue.
Last updated: Apr 12 2022 at 19:14 UTC
