Stream: IG creation
Topic: error: None of the codes provided are in the value set
Patrick Werner (Dec 09 2020 at 09:01):
In the CG IG we are getting qa errors for ValueSets wich can't be validated, e.g.:
None of the codes provided are in the value set http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs (http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs), and a code from this value set is required) (codes = http://example.org/HGVS.g#NC_000003.11:g.128625063C>T)
Patrick Werner (Dec 09 2020 at 09:02):
As HGVS is a grammar, there won't be a CS which can be added.
Patrick Werner (Dec 09 2020 at 09:03):
The WG thinks, that the IG Creator (and Java Validator) shouldn't throw errors for something which can't be validated. This should throw a warning about not be able to Validate the Coding, but not an error.
Grahame Grieve (Dec 09 2020 at 10:24):
HGVS can be valdiated
Patrick Werner (Dec 09 2020 at 13:38):
Yes but the IG Publisher can't.
Patrick Werner (Dec 09 2020 at 13:40):
This is a more generic question: If the IG Publisher/Java Validator can't validate a code, it should throw a warning, not an error.
Patrick Werner (Dec 09 2020 at 14:39):
Probably special-url ist the solution to this problem, will try it out and report back.
Patrick Werner (Dec 09 2020 at 15:04):
And multiple examples on our side were wrong :crying_cat:
Grahame Grieve (Dec 09 2020 at 19:09):
it should be validating HGVS codes.
Jamie Jones (Apr 10 2021 at 00:11):
HGVS validation on tx.fhir.org is throwing errors on wildtype calls (e.g. NC_000010.10:g.96521657C=) it is expecting a '>' but '=' should also be valid
Grahame Grieve (Apr 16 2021 at 08:00):
that's a pass thrugh error from the underlying HGVS server
Grahame Grieve (Apr 16 2021 at 08:01):
I have a to do to upgrade it
Last updated: Apr 12 2022 at 19:14 UTC
