Stream: IG creation
Topic: IG publisher 1.1.97 - issue processing contained resources
Rob Eastwood (Jan 21 2022 at 04:04):
Hi, working with the HL7 Australia Base IG and am getting a failure to build (ie not completing) with IG Publisher v1.1.97 but not so using v1.1.96 or earlier.
The problem is with one of the example instances - the only one that has contained resources - and when this is commented out from the ig.xml, v1.1.97 runs successfully.
Error messages indicate that the contained resources are being sought as individual instances rather than as being included in the example.
The example: https://github.com/hl7au/au-fhir-base/blob/master/examples/list-0ebc46a8-4ea8-11e9-8647-d663bd873d93.xml
Failure build log: http://build.fhir.org/ig/hl7au/au-fhir-base/branches/master/failure/build.log, indicating:
Could not locate the included file 'Encounter-28060b9a-4ffb-11e9-8647-d663bd873d93-html.xhtml' in any of ...
Also note that the build log reports
Error Generating Narrative for MedicationUsage/7e6620b8-4ea9-11e9-8647-d663bd873d93: Cannot find definition for MedicationUsage
- this is a R4 IG
- the
idreported is one of the contained MedicationStatements in the same example - there are 5 errors like this for the 5 contained MedicationStatements
I have modified the example numerous ways with no impact to the build failure. And looking at the release notes for the v1.1.97 publisher there has been some recent attention to "Renderer: Create index for contained files" - so posting here to seek guidance whether this is a publisher issue.
Rob Eastwood (Jan 21 2022 at 04:10):
fyi @Brett Esler @Brian Postlethwaite
Brian Postlethwaite (Jan 21 2022 at 04:11):
@Lloyd McKenzie does this look like the same issue that you were dealing with in the SDC IG?
(or possibly related to the fix that was being done for it?)
Lloyd McKenzie (Jan 21 2022 at 05:09):
The SDC IG wasn't and still isn't failing. There was a recent fix. But it shouldn't have done anything that would trigger a failure.
@Rob Eastwood, can you provide a full stack trace?
Rob Eastwood (Jan 21 2022 at 06:16):
Lloyd McKenzie said:
Rob Eastwood, can you provide a full stack trace?
Note that on my local machine running the IG Publisher, it just hangs at "Jekyll: Generating..." and progresses no further; I have to kill the process. The following stack trace was generated using jstack at the point of 5 mins or so into the hang. Others in my team get the error as demonstrated in the build.log link above.
GitHub gist: https://gist.github.com/robeastwood-agency/94c65fe37e7e41267fe7d5ba9aca5513
(caveat - my first attempt getting stack trace & happy to be poked in another direction as needed)
Many thanks for looking into this @Lloyd McKenzie
Brian Postlethwaite (Jan 24 2022 at 05:29):
@Rob Eastwood still an issue I expect?
I might get a chance to look later in the week.
Rob Eastwood (Jan 24 2022 at 05:58):
Brian Postlethwaite said:
Rob Eastwood still an issue I expect?
Yes, still an issue for me
Lloyd McKenzie (Jan 24 2022 at 17:14):
I grabbed the IG from Git and ran it. Jekyll failed with the following:
Jekyll: Source: C:/Users/lloyd/Documents/SVN/_IGs/_other/au-fhir-base/temp (06:38.0772)
Jekyll: Generating... (06:38.0774)
Jekyll has failed. Complete output from running Jekyll: ←[31m Liquid Exception: Could not locate the included file 'Encounter-28060b9a-4ffb-11e9-8647-d663bd873d93-html.xhtml' in any of ["C:/Users/lloyd/Documents/SVN/_IGs/_other/au-fhir-base/temp/_includes"]. Ensure it exists in one of those directories and, if (06:56.0544)
Note: Check that Jekyll is installed correctly (06:56.0549)
Publishing Content Failed: Process exited with an error: 1 (Exit value: 1) (06:56.0558)
Grahame Grieve (Jan 27 2022 at 03:00):
is this fixed then?
Lloyd McKenzie (Jan 27 2022 at 03:31):
I don't know - but the issue seemed to be a problem with the IG.
Rob Eastwood (Feb 01 2022 at 01:47):
Grahame Grieve said:
is this fixed then?
(sorry, I have been on leave for a few days)
No, not yet fixed:
Build details:
- HL7 Australia AU Base 2 IG, latest master commit #3111965a7
- using IG Publisher v1.1.97
- fresh build manually triggered for build.fhir.org (using instructions here), with the resultant failure build.log including this:
Jekyll has failed. Complete output from running Jekyll: [31m Liquid Exception: Could not locate the included file 'Encounter-28060b9a-4ffb-11e9-8647-d663bd873d93-html.xhtml' in any of ["/scratch/ig-build-temp-YZMUH0/repo/temp/_includes"]. Ensure it exists in one of those directories and, if it is a symlink, d (04:33.0448)
Note: Check that Jekyll is installed correctly (04:33.0448)
Publishing Content Failed: Process exited with an error: 1 (Exit value: 1) (04:33.0449)
(04:33.0449)
Use -? to get command line help (04:33.0449)
(04:33.0449)
Stack Dump (for debugging): (04:33.0449)
org.apache.commons.exec.ExecuteException: Process exited with an error: 1 (Exit value: 1)
at org.apache.commons.exec.DefaultExecutor.executeInternal(DefaultExecutor.java:404)
at org.apache.commons.exec.DefaultExecutor.execute(DefaultExecutor.java:166)
at org.apache.commons.exec.DefaultExecutor.execute(DefaultExecutor.java:153)
at org.hl7.fhir.igtools.publisher.Publisher.runJekyll(Publisher.java:6053)
at org.hl7.fhir.igtools.publisher.Publisher.runTool(Publisher.java:5974)
at org.hl7.fhir.igtools.publisher.Publisher.generate(Publisher.java:5335)
at org.hl7.fhir.igtools.publisher.Publisher.createIg(Publisher.java:960)
at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:798)
at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:9079)
The build.log also reports an inability to find MedicationUsage instances with ids that are only are included as references to contained MedicationStatements in a List example (see this and this). When the List example is excluded from being processed by the publisher, the build is successful using v1.1.97.
Note the same IG successfully runs using v1.1.96.
I'd be happy to provide more information, if that would help.
Rob Eastwood (Feb 01 2022 at 23:20):
Update re IG Publisher v1.1.98
HL7 AU build still fails, with identical error message reported above re "Could not locate the included file 'Encounter-28060b9a-4ffb-11e9-8647-d663bd873d93-html.xhtml'" (new build log). Note
- the ig.xml does not have a listing for an Encounter instance with this id - the id is only present in a List example as a reference for List.encounter to an internal contained Encounter resource
- when this List example is excluded from the build, it runs successfully
- maybe this List example is doing containment incorrectly, but I can't see it - please suggest variations if anyone has ideas
Also note that the earlier reported messages re "inability to find MedicationUsage instances" are no longer present in the 1.1.98 build.log (presumably related to the publisher release note "Renderer: Stop trying to use R5 version of contained resource for internal rendering")
Grahame Grieve (Feb 03 2022 at 22:49):
I can't reproduce this?
Rob Eastwood (Feb 04 2022 at 00:18):
Grahame Grieve said:
I can't reproduce this?
mmm, that's not good! Thanks for looking @Grahame Grieve
Even though it happens on local PCs for us, it also occurs (ie fails) in the cloud build.fhir environment; see the link above for the build.log indicating how the auto-builder fails to complete.
I confess to being at a total loss to know what else to do to problem solve this one - anyone have any suggestions?
Grahame Grieve (Feb 04 2022 at 01:39):
I think that this is a problem in the Australian template
Rob Eastwood (Feb 04 2022 at 01:57):
Grahame Grieve said:
I think that this is a problem in the Australian template
Actually, I have come to the same conclusion - I have just copied the problematic HL7AU List example into a fresh IG using the https://github.com/FHIR/sample-ig - and it doesn't fail to build.
Grahame Grieve (Feb 04 2022 at 02:13):
fixed.
Rob Eastwood (Feb 04 2022 at 02:31):
Grahame Grieve said:
fixed.
Many many thanks Graham for your decisive input here.
And apologies for casting doubt on the IG publisher; that was not intended.
Last updated: Apr 12 2022 at 19:14 UTC
