Stream: IG creation
Topic: ValueSet: Include whole code system
Sarah Gaunt (Jul 29 2020 at 01:48):
So we are trying to include a whole code system in a value set (https://build.fhir.org/ig/HL7/dental-data-exchange/branches/master/ValueSet-dental-observation-codes.html).
<include>
<system value="http://loinc.org"/>
</include>
Getting the following error: Error from server: Access violation at address 00000000006BA5AD in module 'FHIRServer.exe'. Read of address 0000000000000009
Get no errors if I remove the include above.
Sarah Gaunt (Jul 29 2020 at 01:50):
Log here: http://build.fhir.org/ig/HL7/dental-data-exchange/branches/master/qa.html
File here: https://github.com/HL7/dental-data-exchange/blob/master/input/resources/valueset/dental-observation-codes.xml
Grahame Grieve (Jul 29 2020 at 02:33):
remove the loinc file from the txCache and try again
Sarah Gaunt (Jul 29 2020 at 02:36):
This is the CI build.
Grahame Grieve (Jul 29 2020 at 02:36):
do you get it locally?
Sarah Gaunt (Jul 29 2020 at 02:37):
Don't know. Don't run anything locally - don't like how it slows my machine down!
Jose Costa Teixeira (Jul 29 2020 at 08:37):
As a general rule for investigating anything , I would strongly recommend to always build locally before checking further. Your machine is a controlled environment and running locally is a pre-step that really helps the people that want to help. A local build takes 2 minutes on average.
Jose Costa Teixeira (Jul 29 2020 at 08:40):
It takes (much) more time than that for anyone to pick up your IG and start to understand the issue. And it also slows our machine down, but that does not prevent us from trying to help
Sarah Gaunt (Jul 29 2020 at 10:52):
@David deRoode I think you're going to have to run this locally to see what the issue is...
Sarah Gaunt (Jul 29 2020 at 10:57):
@Jose Costa Teixeira I think your machine must be much better than mine! I'd be over the moon if an IG only took 2 minutes to run! :smile:
This isn't my IG though - I was just helping out with the debugging of the last few thorny issues, so I'll pass back over to @David deRoode now...
Jose Costa Teixeira (Jul 29 2020 at 11:59):
I thought it was your IG @Sarah Gaunt - sorry I didn't skip the opportunity to ask everyone to please try to build locally.
Jose Costa Teixeira (Jul 29 2020 at 12:01):
BTW, indeed David's dental IG did not commit the input-cache to github so it is a bit slower the first time you run.
But a few minutes are usually enough to build an IG as long as it's not UTG.
David deRoode (Jul 29 2020 at 16:01):
Understood, agreed and thanks for helping with this @Jose Costa Teixeira and @Grahame Grieve I wiped .fhir cache and re-ran locally with the latest (now 1.1.6) and still get "Error from server: Access violation at address 00000000006BA5AD in module 'FHIRServer.exe'. Read of address 0000000000000009" on ValueSet containing
<compose>
<include>
<system value="http://loinc.org"/>
</include>
<include>
<system value="http://www.ada.org/snodent"/>
<filter>
<property value="concept"/>
<op value="descendent-of"/>
<value value="165877D"/>
</filter>
<filter>
<property value="concept"/>
<op value="descendent-of"/>
<value value="165733D"/>
</filter>
</include>
<include>
<system value="http://snomed.info/sct"/>
<filter>
<property value="concept"/>
<op value="descendent-of"/>
<value value="404684003"/>
</filter>
<filter>
<property value="concept"/>
<op value="descendent-of"/>
<value value="243796009"/>
</filter>
</include>
</compose>
David Hay (Jul 29 2020 at 18:10):
I think you're supposed to remove input-cache/txcache...
David deRoode (Jul 29 2020 at 19:18):
Thanks @David Hay The first time I ran it locally this input-cache did not exist. I deleted this (and all output) folders and re-ran. I also wiped the .fhir and input-cache/txcache and ran 'publisher -resetTx'...the error persists
Grahame Grieve (Jul 30 2020 at 01:37):
ok fixed, though you'll need to clear out your txCache
Grahame Grieve (Jul 30 2020 at 01:38):
fixed now - clear out your txCache
David deRoode (Jul 30 2020 at 17:57):
Using 1.1.6 and clearing txCache, the error persists when all codes from icd-10-cm and loinc are included. The error goes away when removing icd-10-cm. Including all Loinc codes is no problem.
QA: https://build.fhir.org/ig/HL7/dental-data-exchange/qa.html
Valueset file: https://github.com/HL7/dental-data-exchange/blob/master/input/resources/valueset/dental-observation-codes.xml
David deRoode (Jul 31 2020 at 19:25):
@Grahame Grieve
Grahame Grieve (Jul 31 2020 at 20:15):
Unable to find the source file for ServiceRequest/Dental-extraction-example: not specified, so tried ServiceRequest-Dental-extraction-example.xml, Dental-extraction-example.ServiceRequest.xml, ServiceRequest-Dental-extraction-example.json, ServiceRequest/Dental-extraction-example.xml, ServiceRequest/Dental-extraction-example.json, Dental-extraction-example.xml, and Dental-extraction-example.json (and lowercase resource name variants) in dirs [C:\work\org.hl7.fhir.igs\dental-data-exchange\input, C:\work\org.hl7.fhir.igs\dental-data-exchange\input\resources]
trying to reproduce this
David deRoode (Jul 31 2020 at 20:18):
Rebuilding now
David deRoode (Jul 31 2020 at 20:23):
Ok
Eric Haas (Jul 31 2020 at 20:34):
I still getting similar errors as well. delete caches, update publisher etc.
David deRoode (Aug 04 2020 at 15:36):
@Grahame Grieve you should be able to see & reproduce this now
Grahame Grieve (Aug 06 2020 at 03:45):
I'm not sure what to look at?
David deRoode (Aug 06 2020 at 14:45):
'Error from Server: Not implemented' which seems to be caused by <include> Loinc codes (all) in dental-observation valueset
Grahame Grieve (Aug 06 2020 at 20:08):
i'll look at that. but that value set is almost certainly not defined correctly. You've said that you only want snomed codes that are descendents of both 404684003 and 243796009, and Snodent codes that are descendents of both 165877D and 165733D
Grahame Grieve (Aug 06 2020 at 20:08):
where as I think you want to say 'either'
Grahame Grieve (Aug 06 2020 at 21:21):
there is a bug on the terminology server that will be fixed shortly
David deRoode (Jul 27 2021 at 15:42):
Was the Snodent bug resolved @Grahame Grieve ? The ValueSet definition was corrected, but still getting this error: "Error from server: The filter "concept descendent-of 165877D" was not understood in the context of http://www.ada.org/snodent" here's the QA: https://build.fhir.org/ig/HL7/dental-data-exchange/qa.html. Also- this ValueSet isn't pulling in '(Clinical Finding (finding))' from Snodent.org
Lloyd McKenzie (Jul 27 2021 at 18:44):
@Rob Hausam might be able to answer?
Last updated: Apr 12 2022 at 19:14 UTC
