Stream: IG creation
Topic: Puzzed by jira spec issue
John Rhoads (Aug 13 2021 at 13:30):
Up to the wire and on the brink of getting booted out the Ballot round on the one remaining issue on Point of Care Implementation Guide
https://github.com/HL7/uv-pocd
https://github.com/HL7/JIRA-Spec-Artifacts/blob/master/xml/FHIR-pocd.xml
message from:
https://build.fhir.org/ig/HL7/uv-pocd/qa.html
warning The jira specification file appears to be out of date with the versions, artifacts and pages currently defined in the IG. A proposed revised file to be reviewed and, if appropriate, submitted as a pull request against the XML folder in https://github.com/HL7/JIRA-Spec-Artifacts. To see the differences, perform a file compare on 'template/jira-current.xml' (a normalized view of what is in Github) and 'template/jira-new.xml' (reflects current IG content)
To me, what is in template/jira-current.xml based on current GitHub content appears to make more sense than template/jira-new.xml based on IG content, which appears to garble together bits of CodeSystem artifact data with ValueSet data.
147,148c147,148
< key="CodeSystem-kind-of-relation"
< name="Kind of relation codes (CodeSystem)"
---
> key="ValueSet-kind-of-relation"
> name="Kind of relation codes (ValueSet)"
182,183c182,183
< key="CodeSystem-metric-availability"
< name="Metric availability codes (CodeSystem)"
---
> key="ValueSet-metric-availability"
> name="Metric availability codes (ValueSet)"
226,230d225
< deprecated="true"
< key="Observation"
< name="Observation"
< />
< <artifact
252,253c247,248
< key="CodeSystem-operating-mode"
< name="Operating mode codes (CodeSystem)"
---
> key="ValueSet-operating-mode"
> name="Operating mode codes (ValueSet)"
307,308c302,303
< key="CodeSystem-safety"
< name="Safety classification codes (CodeSystem)"
---
> key="ValueSet-safety"
> name="Safety classification codes (ValueSet)"
Advice would be deeply appreciated!
@Lloyd McKenzie ?
John Moehrke (Aug 13 2021 at 13:36):
have you contacted @Lloyd McKenzie ?
John Rhoads (Aug 13 2021 at 13:40):
Right, John. Done. Thanks! John R
Lloyd McKenzie (Aug 13 2021 at 14:15):
The order of the artifacts can be whatever you like - though alphabetic is generally best unless you want to put something really important first. You do need to make sure that all artifacts are listed, you need to ensure that all keys match what was in the original file checked into Git, and you need to ensure that all ids and names match what's in your current IG.
Jean Duteau (Aug 13 2021 at 16:11):
Hey @John Rhoads Melva reached out to me and I'm going to take a look and see if I can help you get a valid JIRA specification file.
Jean Duteau (Aug 13 2021 at 16:23):
okay, I see no reason why you can't just check in the jira-new.xml. The changes are all in the names of your code systems and value sets. And those come directly from your IG resource.
Jean Duteau (Aug 13 2021 at 16:24):
Here is the diff I get when I run your current checked-in source:
31,32c31,32
< <artifact id="CodeSystem/kind-of-relation" key="CodeSystem-kind-of-relation" name="Kind of relation codes (CodeSystem)"/>
< <artifact id="ValueSet/kind-of-relation" key="ValueSet-kind-of-relation" name="Kind of relation codes (ValueSet)"/>
---
> <artifact id="CodeSystem/kind-of-relation" key="CodeSystem-kind-of-relation" name="Kind of relation code system"/>
> <artifact id="ValueSet/kind-of-relation" key="ValueSet-kind-of-relation" name="Kind of relation value set"/>
38,39c38
< <artifact id="CodeSystem/metric-availability" key="CodeSystem-metric-availability" name="Metric availability codes (CodeSystem)"/>
< <artifact id="ValueSet/metric-availability" key="ValueSet-metric-availability" name="Metric availability codes (ValueSet)"/>
---
> <artifact id="CodeSystem/metric-availability" key="CodeSystem-metric-availability" name="Metric availability code system"/>
40a40
> <artifact id="ValueSet/metric-availability" key="ValueSet-metric-availability" name="Metric availability value set"/>
47d46
< <artifact deprecated="true" key="Observation" name="Observation"/>
52,53c51
< <artifact id="CodeSystem/operating-mode" key="CodeSystem-operating-mode" name="Operating mode codes (CodeSystem)"/>
< <artifact id="ValueSet/operating-mode" key="ValueSet-operating-mode" name="Operating mode codes (ValueSet)"/>
---
> <artifact id="CodeSystem/operating-mode" key="CodeSystem-operating-mode" name="Operating mode code system"/>
54a53
> <artifact id="ValueSet/operating-mode" key="ValueSet-operating-mode" name="Operating mode value set"/>
63,64c62,63
< <artifact id="CodeSystem/safety" key="CodeSystem-safety" name="Safety classification codes (CodeSystem)"/>
< <artifact id="ValueSet/safety" key="ValueSet-safety" name="Safety classification codes (ValueSet)"/>
---
> <artifact id="CodeSystem/safety" key="CodeSystem-safety" name="Safety classification code system"/>
> <artifact id="ValueSet/safety" key="ValueSet-safety" name="Safety classification value set"/>
Jean Duteau (Aug 13 2021 at 16:32):
those are all changes because you must have changed the names of your code systems and value sets (to get rid if the '()').
John Rhoads (Aug 13 2021 at 16:34):
Bless your heart!
Lynn Laakso (Aug 13 2021 at 16:44):
@John Rhoads holler when you're ready for me to rebuild
John Rhoads (Aug 13 2021 at 19:00):
Pardon my unfamiliarity with the jira spec file (I am pinch hitting for an absent author). I cloned https://github.com/HL7/JIRA-Spec-Artifacts locally and brought in template/jira-new.xml from my local build,
renamed as xml/FHIR-pocd.xml and ran java -jar tools/ant/ant-launcher.jar.
Got a number of build errors
Buildfile: /Users/jrhoads/Projects/ProjectsFHIRDev/JIRA-Spec-Artifacts/build.xml
validate:
[xslt] Processing /Users/jrhoads/Projects/ProjectsFHIRDev/JIRA-Spec-Artifacts/xml/_workgroups.xml to /Users/jrhoads/Projects/ProjectsFHIRDev/JIRA-Spec-Artifacts/schemas/workgroups.xsd
[xslt] Loading stylesheet /Users/jrhoads/Projects/ProjectsFHIRDev/JIRA-Spec-Artifacts/tools/buildWGschema.xslt
[schemavalidate] /Users/jrhoads/Projects/ProjectsFHIRDev/JIRA-Spec-Artifacts/xml/FHIR-pocd.xml:32:116: Duplicate unique value [ValueSet-kind-of-relation] declared for identity constraint of element "specification".
[schemavalidate] /Users/jrhoads/Projects/ProjectsFHIRDev/JIRA-Spec-Artifacts/xml/FHIR-pocd.xml:32:116: Duplicate unique value [Kind of relation codes (ValueSet)] declared for identity constraint of element "specification".
[schemavalidate] /Users/jrhoads/Projects/ProjectsFHIRDev/JIRA-Spec-Artifacts/xml/FHIR-pocd.xml:39:125: Duplicate unique value [ValueSet-metric-availability] declared for identity constraint of element "specification".
[schemavalidate] /Users/jrhoads/Projects/ProjectsFHIRDev/JIRA-Spec-Artifacts/xml/FHIR-pocd.xml:39:125: Duplicate unique value [Metric availability codes (ValueSet)] declared for identity constraint of element "specification".
[schemavalidate] /Users/jrhoads/Projects/ProjectsFHIRDev/JIRA-Spec-Artifacts/xml/FHIR-pocd.xml:52:110: Duplicate unique value [ValueSet-operating-mode] declared for identity constraint of element "specification".
[schemavalidate] /Users/jrhoads/Projects/ProjectsFHIRDev/JIRA-Spec-Artifacts/xml/FHIR-pocd.xml:52:110: Duplicate unique value [Operating mode codes (ValueSet)] declared for identity constraint of element "specification".
[schemavalidate] /Users/jrhoads/Projects/ProjectsFHIRDev/JIRA-Spec-Artifacts/xml/FHIR-pocd.xml:63:101: Duplicate unique value [ValueSet-safety] declared for identity constraint of element "specification".
[schemavalidate] /Users/jrhoads/Projects/ProjectsFHIRDev/JIRA-Spec-Artifacts/xml/FHIR-pocd.xml:63:101: Duplicate unique value [Safety classification codes (ValueSet)] declared for identity constraint of element "specification".
BUILD FAILED
/Users/jrhoads/Projects/ProjectsFHIRDev/JIRA-Spec-Artifacts/build.xml:19: /Users/jrhoads/Projects/ProjectsFHIRDev/JIRA-Spec-Artifacts/xml/FHIR-pocd.xml is not a valid XML document.
Here's the FHIR-pocd.xml (formerly jira-new.xml) that used:
@Jean Duteau ?
John Rhoads (Aug 13 2021 at 19:04):
@Lynn Laakso alas not hollering yet...
@Lloyd McKenzie
Jean Duteau (Aug 13 2021 at 19:06):
the jira-new that was created when I ran the build is different from what you just posted. The one that you posted does have errors:
<artifact id="CodeSystem/kind-of-relation" key="ValueSet-kind-of-relation" name="Kind of relation codes (ValueSet)"/>
<artifact id="ValueSet/kind-of-relation" key="ValueSet-kind-of-relation" name="Kind of relation codes (ValueSet)"/>
These two different artifacts have the same key and the same name. But that differs from what I'm seeing when I build locally:
<artifact id="CodeSystem/kind-of-relation" key="CodeSystem-kind-of-relation" name="Kind of relation code system"/>
<artifact id="ValueSet/kind-of-relation" key="ValueSet-kind-of-relation" name="Kind of relation value set"/>
Jean Duteau (Aug 13 2021 at 19:07):
Use this jira-new.xml which corresponds to what is in the CI build:
jira-new.xml
John Rhoads (Aug 13 2021 at 20:07):
Once again @Jean Duteau , many thanks. With one small change, it built without errors. I put up a pull request.
@Lynn Laakso @Todd Cooper
Lynn Laakso (Aug 13 2021 at 20:12):
so this was a change to the jira-spec-artifacats, not the pocd repo/build?
Todd Cooper (Aug 13 2021 at 20:14):
Woohoo!!!
John Rhoads (Aug 13 2021 at 20:25):
@Lynn Laakso Yes, that's correct. Only change was to the jira-spec-artifacts, as you say
Lynn Laakso (Aug 13 2021 at 20:26):
@John Rhoads https://build.fhir.org/ig/HL7/uv-pocd/qa.html still shows the warning
John Rhoads (Aug 13 2021 at 20:28):
Yes, looks like the pull request on https://github.com/HL7/JIRA-Spec-Artifacts has not yet been put in, so I guess that would be expected. Who does that, @Lloyd McKenzie ?
Jean Duteau (Aug 13 2021 at 20:32):
yes, we need lloyd to merge the pull request and then the uv-pocd can be rebuilt and should be fine.
Lloyd McKenzie (Aug 14 2021 at 02:49):
done
Lynn Laakso (Aug 14 2021 at 12:32):
still getting the jiraspec warning on https://build.fhir.org/ig/HL7/uv-pocd/qa.html. so the pull request didn't fix the issue?
Jean Duteau (Aug 14 2021 at 13:39):
i don't know what @John Rhoads checked in but it is not the proper JIRA spec.
Jean Duteau (Aug 14 2021 at 13:46):
i just checked in the proper JIRA spec, so if @Lloyd McKenzie can merge the new pull request, this guide should be ready to go.
Lloyd McKenzie (Aug 14 2021 at 18:50):
Merged
Lynn Laakso (Aug 14 2021 at 19:49):
OK, still getting jira spec warning. Now what?
Lloyd McKenzie (Aug 14 2021 at 20:35):
I think something is broken on my end. Will investigate
Jean Duteau (Aug 14 2021 at 21:25):
hmm, the JIRA spec file that is created doesn't have an entry for Observation. If you check in the JIRA file that is created, the build fails saying it is missing an entry for "Observation" which is true. Where do deprecated entries get made?
Lloyd McKenzie (Aug 15 2021 at 04:47):
The issue is that it's matching on a different resource and isn't propagating. I'm debugging
Nathan Davis (Aug 20 2021 at 16:01):
@Lloyd McKenzie it seems that I'm getting a similar error in regards to the Jira Spec file. I didn't get this error until the FHIR-us-covid19 Jira Spec file (the one I need for my IG) was merged. Here's the error I'm getting:
[xslt] : Warning! The source document is in no namespace, but the template rules all expect elements in a namespace
First "url" contact telecom must start with "http://hl7.org/Special/committees/"
[xslt] C:\Users\nrdavis1\HL7_covid-19_IG\fhir-COVID19Library-ig\template\scripts\onGenerate.jira.xslt:20: Fatal Error! Processing terminated by xsl:message at line 20 in onGenerate.jira.xslt
[xslt] Failed to process C:\Users\nrdavis1\HL7_covid-19_IG\fhir-COVID19Library-ig\template\jira.tmp.xml
Publishing Content Failed: Fatal error during transformation using C:\Users\nrdavis1\HL7_covid-19_IG\fhir-COVID19Library-ig\template\scripts\onGenerate.jira.xslt: Processing terminated by xsl:message at line 20 in onGenerate.jira.xslt; SystemID: file:/C:/Users/nrdavis1/HL7_covid-19_IG/fhir-COVID19Library-ig/template/scripts/onGenerate.jira.xslt; Line#: 20; Column#: -1 (01:56.0502)
Lloyd McKenzie (Aug 20 2021 at 17:01):
Actually, I think it may have been triggered by you adding the package-list.json. That's what allows the publisher to generate a 'proposed' Jira file. The part of the error to pay attention to is: First "url" contact telecom must start with "http://hl7.org/Special/committees/"
Nathan Davis (Aug 20 2021 at 19:33):
I was able to build after adding the package-list but not after the Jira spec
Lloyd McKenzie (Aug 20 2021 at 19:55):
If you fix the IG contact, that should address the problem.
Nathan Davis (Aug 20 2021 at 22:06):
I don't think that's the problem. This is what it looks like in the sushi-config.yaml:
publisher:
-
name: Logica
url: https://www.logicahealth.org/
-
name: HL7
url: https://www.hl7.org
and the resulting contact section in the IG Contact:
"contact": [
{
"name": "Logica",
"telecom": [
{
"system": "url",
"value": "https://www.logicahealth.org/"
}
]
},
{
"name": "HL7",
"telecom": [
{
"system": "url",
"value": "https://www.hl7.org"
}
]
}
Lloyd McKenzie (Aug 20 2021 at 22:23):
That is the problem. The first URL must be one that starts with "http://hl7.org/Special/committees/" - i.e. it must be the URL of the work group with overall responsible for the IG.
Lloyd McKenzie (Aug 20 2021 at 22:24):
(from the HL7 home page)
Last updated: Apr 12 2022 at 19:14 UTC
