Stream: genomics/committers
Topic: Other ValueSets
Jamie Jones (Aug 20 2019 at 16:15):
Any ideas on these 2?
/scratch/ig-build-temp-SRV684/repo/src/resources/valueset-hgnc.xml
Path Severity Message
hgnc error Error from server: Unable to provide support for code system http://www.genenames.org (see Tx log)
/scratch/ig-build-temp-SRV684/repo/src/resources/valueset-hgvs.xml
Path Severity Message
hgvs error Error from server: Unable to provide support for code system http://varnomen.hgvs.org (see Tx log)
may just have to suppress them
Kevin Power (Aug 20 2019 at 16:36):
I do remember having this specific conversation with Grahame - Things like this would not prevent publication, because it is (effectively) a problem with the tooling right now that it doesn't support HGVS and HGNC. Maybe we shouldn't suppress them just yet - I think it is OK that we call out additional things that the tooling needs to support (even if it means CG group might need to do some work to get the tooling to support it).
Jamie Jones (Aug 20 2019 at 16:36):
another one: Grahame's server doesn't seem to include latest LOINC update - coord set and level of evidence don't resolve
Kevin Power (Aug 20 2019 at 16:38):
Correct, another 'not our problem' (for now :slight_smile:). There are also a number of warnings that shouldn't be happening that Grahame is aware of:
ValueSet http://loinc.org/vs/LL3856-3 not found
Jamie Jones (Aug 20 2019 at 16:42):
That basically just leaves the ~10 TBD codes for errors (and any new ones we introduce) :sunglasses:
Jamie Jones (Aug 20 2019 at 16:42):
once we get the TBD codes up, fixing the examples will be quick work
Jamie Jones (Aug 20 2019 at 16:43):
also finishing up the other placeholder examples I have locally
Patrick Werner (Aug 20 2019 at 19:55):
another one: Grahame's server doesn't seem to include latest LOINC update - coord set and level of evidence don't resolve
it does, you just have to delete the local tx cache (usability of this thing is a nightmare)
Patrick Werner (Aug 20 2019 at 19:56):
https://chat.fhir.org/#narrow/stream/179166-implementers/topic/java.20validator.20.26.20LOINC.20Answerlists/near/173661791
i did this locally and the new concepts are ok now. I just pushed the version after deleting the cache, hoping it will be fixed in the CI build as well
Kevin Power (Aug 20 2019 at 19:57):
But the LOINC ValueSets still generate a warning?
Patrick Werner (Aug 20 2019 at 19:58):
yes. Hope this will get fixed soon, i mentioned this issues several times...
Patrick Werner (Aug 20 2019 at 19:58):
For now we should ignore these warnings/errors
Bret H (Oct 09 2019 at 00:26):
@Patrick Werner know you are unwell. but http://build.fhir.org/ig/HL7/genomics-reporting/valueset-variant-inheritance.html is not showing the value set from SO. can it be fixed?
Kevin Power (Oct 09 2019 at 13:34):
That is because the SO CodeSystem isn't supported (I think).
Patrick Werner (Oct 09 2019 at 15:31):
The publisher doesn't support VS expansion. I tried several things today. Including the SO CodeSystem into the build didn't help.
Patrick Werner (Oct 09 2019 at 15:31):
If we include the expanded VS it would be rendered with all concept values.
Patrick Werner (Oct 09 2019 at 15:33):
unfortunately hapi also doesn't support subsumes at the moment.
Patrick Werner (Oct 09 2019 at 15:33):
just saw, the valueSets are incorrect. Will push an update in a sec.
Kevin Power (Oct 09 2019 at 15:42):
What is up?
Patrick Werner (Oct 09 2019 at 15:57):
Pushed a correction to the ValueSets. Thought i already fixed them. Now the filter is configured in a proper way.
Kevin Power (Oct 09 2019 at 16:13):
@Patrick Werner - conflicts on your commit? Since they are all in src-generated it is no big deal, but FYI in case it is:
Conflicts:
src-generated/resources/ig-expansion-parameters.json
src-generated/resources/ig-new.json
src-generated/resources/ig-validation-parameters.json
Patrick Werner (Oct 09 2019 at 16:23):
yes there were some conflicts. I guess because i pushed the version of the IG to 0.4
Patrick Werner (Oct 09 2019 at 16:26):
But even with corrections to the VSets they are not expanded during build. HL7 normally (in core) doesn't include expansions in their ValueSets. So i don't think this is a showstopper.
Patrick Werner (Oct 09 2019 at 16:28):
It would be nice to include this in the future. To be able to we (or somebody) has to either:
- include expansion into the IG publisher
- include descendent-of functionality into hapi
Last updated: Apr 12 2022 at 19:14 UTC
