Stream: implementers
Topic: IG Publisher ValueSet Error?
Sean McIlvenna (Sep 21 2016 at 23:36):
I'm getting this odd error from the IG publisher when I include a ValueSet in the resources directory (didn't even reference it in the ImplementationGuide or control file):
Sean McIlvenna (Sep 21 2016 at 23:36):
Exception in thread "main" java.lang.Error: fetching org.hl7.fhir.dstu3.model.ValueSet not done yet for URI urn:oid:2.16.840.1.113883.1.11.1
at org.hl7.fhir.dstu3.utils.SimpleWorkerContext.fetchResource(SimpleWorkerContext.java:343)
at org.hl7.fhir.igtools.publisher.IGKnowledgeProvider.resolveBinding(IGKnowledgeProvider.java:331)
at org.hl7.fhir.dstu3.utils.ProfileUtilities.generateDescription(ProfileUtilities.java:1869)
at org.hl7.fhir.dstu3.utils.ProfileUtilities.generateDescription(ProfileUtilities.java:1804)
at org.hl7.fhir.dstu3.utils.ProfileUtilities.genElement(ProfileUtilities.java:1676)
at org.hl7.fhir.dstu3.utils.ProfileUtilities.genElement(ProfileUtilities.java:1702)
at org.hl7.fhir.dstu3.utils.ProfileUtilities.generateTable(ProfileUtilities.java:1566)
at org.hl7.fhir.igtools.renderers.StructureDefinitionRenderer.diff(StructureDefinitionRenderer.java:314)
at org.hl7.fhir.igtools.publisher.Publisher.generateOutputsStructureDefinition(Publisher.java:2064)
at org.hl7.fhir.igtools.publisher.Publisher.generateOutputs(Publisher.java:1799)
at org.hl7.fhir.igtools.publisher.Publisher.generate(Publisher.java:1254)
at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:236)
at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:2194)
Sean McIlvenna (Sep 21 2016 at 23:36):
Has anyone seen this before?
Sean McIlvenna (Sep 21 2016 at 23:37):
I just confirmed... the ValueSet is valid against both schema and schematron
Sean McIlvenna (Sep 21 2016 at 23:49):
Seems to be something related to the binding of the value set in a structure definition
Sean McIlvenna (Sep 21 2016 at 23:49):
Anyone know the inner-workings of the ig publisher when it comes to value sets?
Sean McIlvenna (Sep 21 2016 at 23:49):
I see that it connects to grahame's terminology server as one of the starting processes of the publisher
Sean McIlvenna (Sep 21 2016 at 23:50):
is it trying to retrieve the value set from grahame's server even though I already have it defined (and expanded) in the ig?
Sean McIlvenna (Sep 21 2016 at 23:53):
Nope.. that can't be it, I just posted the value set to the server no prob... ig publisher still complains
Sean McIlvenna (Sep 21 2016 at 23:56):
Also, is there a way to change which fhir server the ig publisher uses to resolve value sets?
Grahame Grieve (Sep 22 2016 at 09:21):
that error - which I really should fix - means that you're referring to a value set that doesn't exist in your binding statement
Sean McIlvenna (Sep 22 2016 at 15:57):
what do you mean by "doesn't exist"?
Sean McIlvenna (Sep 22 2016 at 15:58):
I included it in the ImplementationGuide that I'm publishing, and there is a file that is in the resources directory
Sean McIlvenna (Sep 22 2016 at 15:58):
is there something more that should be done?
Lloyd McKenzie (Sep 22 2016 at 15:59):
Is it used by any of your models?
Sean McIlvenna (Sep 22 2016 at 16:08):
yes.. one of my StructureDefinition's elements does use it
Sean McIlvenna (Sep 22 2016 at 16:09):
I think Grahame was indicating that the binding in the element of my StructureDefinition is what's causing the problem... says the value set doesn't actually exist. but I'm not sure how to resolve it
Lloyd McKenzie (Sep 22 2016 at 16:16):
Make sure your id and your fullUrl align in the ValueSet. Make sure the value set filename is "valueset-" + id + ".xml" and make sure the binding uses the fullUrl. If that's all right, I'm not sure what the issue might be
Sean McIlvenna (Sep 22 2016 at 16:16):
ok. I'll give those a shot
Sean McIlvenna (Sep 22 2016 at 16:16):
only thing I think I haven't done yet is the valueset-ID.xml format
Sean McIlvenna (Sep 22 2016 at 16:17):
I think mine right now is valueset/ID.xml
Sean McIlvenna (Sep 22 2016 at 16:17):
so I will try valueset/valueset-ID.xml
Grahame Grieve (Sep 22 2016 at 17:16):
I'll try and find time to get to this this afternoon - really hard to get to things while at the HL7 meeting. soryr
Grahame Grieve (Sep 22 2016 at 17:17):
but urn:oid:2.16.840.1.113883.1.11.1 is what's in the binding. So you must have a ValueSet with a url of urn:oid:2.16.840.1.113883.1.11.1, and the value set must be registered in the ig.xml
Sean McIlvenna (Sep 22 2016 at 18:06):
ok
Sean McIlvenna (Sep 22 2016 at 18:07):
I'll double check that I'm doing that right
Sean McIlvenna (Sep 22 2016 at 18:07):
if it's not working still after, I will send an example zip and see if either of you can help me figure out what's wrong
Sean McIlvenna (Sep 22 2016 at 19:06):
ok... so, this is what I have:
Sean McIlvenna (Sep 22 2016 at 19:06):
binding.valueSetReference = urn:oid.2.16.840.1.113883.1.11.1
Sean McIlvenna (Sep 22 2016 at 19:06):
ImplementationGuide has a resource with sourceReference.reference = ValueSet/2.16.840.1.113883.1.11.1
Sean McIlvenna (Sep 22 2016 at 19:07):
And I have a ValueSet XML file in resources/valueset/2.16.840.1.113883.1.11.1.xml that has a url of "urn:oid:2.16.840.1.113883.1.11.1"
Sean McIlvenna (Sep 22 2016 at 19:07):
still getting the same error
Sean McIlvenna (Sep 22 2016 at 19:08):
Exception in thread "main" java.lang.Error: fetching org.hl7.fhir.dstu3.model.ValueSet not done yet for URI urn:oid:2.16.840.1.113883.1.11.1
Sean McIlvenna (Sep 22 2016 at 19:11):
Found the .java file that this error is produced from.
Sean McIlvenna (Sep 22 2016 at 19:11):
as far as I can tell, fetchResource() does not seem to support uri's
Sean McIlvenna (Sep 22 2016 at 19:11):
it only seems to support http://
Sean McIlvenna (Sep 22 2016 at 19:11):
also, doesn't appear to support https://
Sean McIlvenna (Sep 22 2016 at 19:13):
...not much of a java guy, though. so maybe I'm missing something
Sean McIlvenna (Sep 22 2016 at 19:19):
ok. figured stuff out a bit
Sean McIlvenna (Sep 22 2016 at 19:19):
I should have figured this out sooner... @Rick Geimer mentioned this to me last week
Sean McIlvenna (Sep 22 2016 at 19:19):
but, basically, the ig publisher doesn't currently support non-http value set urls
Sean McIlvenna (Sep 22 2016 at 19:20):
once I changed the binding's "valueSetReference" to "http://test.com/2.16...." and changed the ValueSet resource's url to "http://test.com/2.16..." the publish worked
Sean McIlvenna (Sep 22 2016 at 19:21):
does anyone know if there is a gforge tracker issue already submitted for this?
Grahame Grieve (Sep 22 2016 at 19:53):
I don't think there is. but it sounds trivial to fix, actually. In fact, I feel bad that I didn't think of that
Sean McIlvenna (Sep 22 2016 at 20:29):
np
Sean McIlvenna (Sep 22 2016 at 20:29):
I wouldn't complain about a quick fix :)
Grahame Grieve (Sep 22 2016 at 20:30):
version 9871 should fix it
Sean McIlvenna (Sep 22 2016 at 21:16):
holy cow
Sean McIlvenna (Sep 22 2016 at 21:16):
that was less than a minute!
Sean McIlvenna (Sep 22 2016 at 21:16):
lol
Sean McIlvenna (Sep 22 2016 at 21:39):
Is am I correct in thinking that http://hl7-fhir.github.io/org.hl7.fhir.igpublisher.jar is up-to-date with the latest build (including the fix you made)?
Sean McIlvenna (Sep 22 2016 at 21:39):
looked at travis ci's build logs, and it seems to publish to hl7-fhir.github.io...
Grahame Grieve (Sep 22 2016 at 21:40):
yes that's the one. You need to hang out until that one hits #9871
Sean McIlvenna (Sep 22 2016 at 21:46):
I think it did... https://travis-ci.org/hl7-fhir/fhir-svn shows git-svn-id: http://gforge.hl7.org/svn/fhir/trunk/build@9871
Sean McIlvenna (Sep 22 2016 at 21:46):
and it shows completed
Grahame Grieve (Sep 22 2016 at 21:50):
yeah but it takes a little time to post to the current build
Sean McIlvenna (Sep 22 2016 at 21:50):
oh ok
Sean McIlvenna (Sep 22 2016 at 21:50):
any way to know when it's done?
Grahame Grieve (Sep 22 2016 at 21:51):
wait till the build number at the foot of the downloads page updates
Sean McIlvenna (Sep 22 2016 at 21:51):
oh heh yah! duh! thanks
Sean McIlvenna (Sep 24 2016 at 00:12):
hey grahame... so, not sure that the fix solved the problem. now I get this:
Sean McIlvenna (Sep 24 2016 at 00:12):
java.lang.NullPointerException
at org.hl7.fhir.dstu3.context.SimpleWorkerContext.fetchResource(SimpleWorkerContext.java:361)
at org.hl7.fhir.igtools.publisher.ValidationServices.fetch(ValidationServices.java:38)
at org.hl7.fhir.dstu3.validation.InstanceValidator.resolve(InstanceValidator.java:1739)
at org.hl7.fhir.dstu3.validation.InstanceValidator.checkReference(InstanceValidator.java:1148)
at org.hl7.fhir.dstu3.validation.InstanceValidator.validateElement(InstanceValidator.java:2752)
Sean McIlvenna (Sep 24 2016 at 00:12):
prior to updating the ig publisher to the latest version you were mentioning, I was getting the error about not having retrieved the value set yet
Sean McIlvenna (Sep 24 2016 at 00:15):
I'll send an example of the package I'm building with the ig publisher in a PM
Sean McIlvenna (Sep 26 2016 at 17:32):
any ideas?
Sean McIlvenna (Sep 28 2016 at 15:44):
any update?
Lloyd McKenzie (Sep 28 2016 at 20:33):
Yes, I got that. It relates to external resolution that wasn't previously happening and it's not handling resource references that are by URI - where the type can't be extracted. I've got a candidate fix for that, but I'm running into other issues that I want to figure out before I can commit.
Sean McIlvenna (Sep 28 2016 at 20:58):
ok. great, thanks @Lloyd McKenzie If you don't mind, please let me know when that fix is committed. I am anxious to get the fix and see it work. Thanks
Grahame Grieve (Sep 29 2016 at 03:26):
how do I reproduce this?
Sean McIlvenna (Sep 29 2016 at 21:11):
I sent a zip package to you that demonstrates this issue.
Sean McIlvenna (Sep 29 2016 at 21:12):
It is in a private message
Last updated: Apr 12 2022 at 19:14 UTC
