Stream: committers
Topic: Making changes to R5 build
Sean McIlvenna (Oct 15 2021 at 19:56):
SD needs to make some changes to Composition in R5.
Is this the correct page describing the build process? https://confluence.hl7.org/display/FHIR/FHIR+Build+Process
Also, do I need to use PR for changes, or is it just good faith that I make sure the build isn't broken before committing to the main branch?
Sean McIlvenna (Oct 15 2021 at 19:56):
@Lloyd McKenzie and @Grahame Grieve
John Moehrke (Oct 15 2021 at 19:59):
you must do a PR and express the jira tickets it is addressing, and it must pass (long wait)... then you yourself accept the PR, delete the PR, update the jira tickets.
John Moehrke (Oct 15 2021 at 19:59):
seems all that is said on some confluence page, and I didn't see it on the page you found
Sean McIlvenna (Oct 26 2021 at 22:00):
@John Moehrke I meant to follow up sooner... Thanks for the clarification.
Sean McIlvenna (Oct 26 2021 at 22:01):
I found a confluence page (linked previously)
Sean McIlvenna (Oct 26 2021 at 22:01):
but, it didn't describe anything about a PR
Sean McIlvenna (Oct 26 2021 at 22:01):
PR seemed right to me, so that's why I asked
Sean McIlvenna (Oct 26 2021 at 22:01):
but, now I have a question about the PR... Should it include the vscache files?
Sean McIlvenna (Oct 26 2021 at 22:01):
For example:
image.png
Sean McIlvenna (Oct 26 2021 at 22:02):
I would think the PR should only include the changes I made, not the automatically generated files such as vscache
Vassil Peytchev (Oct 26 2021 at 22:57):
vscache are special files. Right now, it seems to be beneficial to merge them.
Grahame Grieve (Oct 26 2021 at 23:11):
yes you need to commit them. They are in response to changes you made (or someone else did, who didn't commit them)
Sean McIlvenna (Oct 27 2021 at 14:08):
huh! OK! Will do. thx
Sean McIlvenna (Oct 28 2021 at 15:20):
Ok. So, I used to be able to commit to the repo. Looks like my committer privileges were removed. Can someone re-add me as a committer to the FHIR repo? Username seanmcilvenna @Grahame Grieve @Lloyd McKenzie ?
Lloyd McKenzie (Oct 28 2021 at 15:21):
Hmm. Last time we pruned was probably 1.5 years ago or more when we yanked everyone who was evidently not monitoring #committers/announce. Are you now actively monitoring #committers/announce ? :)
Sean McIlvenna (Oct 28 2021 at 15:52):
if "actively monitoring" is looking at it once a week, yes
Sean McIlvenna (Oct 28 2021 at 16:01):
I just need to get some changes done to Composition for SDWG
Sean McIlvenna (Oct 28 2021 at 16:01):
if easier, I can do a PR on my personal github account
Sean McIlvenna (Oct 28 2021 at 16:01):
and you can merge it for me :)
Sean McIlvenna (Oct 28 2021 at 16:31):
@Lloyd McKenzie
Lloyd McKenzie (Oct 28 2021 at 16:42):
So long as you look at it before making commits, that's ok.
Lloyd McKenzie (Oct 28 2021 at 16:42):
Granted
Sean McIlvenna (Oct 28 2021 at 16:46):
is there something specific I should be on the lookout for? for exmaple "don't commit anything right now?"
Lloyd McKenzie (Oct 28 2021 at 16:56):
That's one of the key ones, yup. More common are things like "Tx server is going down for a few minutes".
Lloyd McKenzie (Oct 28 2021 at 16:57):
Committers/announce is super-low-traffic, so whatever messages are there are likely to be relevant - at least if they've been posted recently.
Sean McIlvenna (Oct 28 2021 at 18:03):
So, I just tried out a PR... Azure Pipelines failed at the Gradle task:
Error: The process '/home/markiantorno/azure-pipelines/_work/2/s/gradlew' failed with exit code 1
I have no idea what this implies... Can you help @Lloyd McKenzie ?
https://github.com/HL7/fhir/pull/1478
Jean Duteau (Oct 28 2021 at 18:09):
you need to look at the azure pipeline detail. in this case, it points to an error in the resource validator:
Error: null
java.lang.NullPointerException
at java.util.ResourceBundle.containsKey(ResourceBundle.java:1821)
at org.hl7.fhir.utilities.i18n.I18nBase.messageExistsForLocale(I18nBase.java:50)
at org.hl7.fhir.utilities.i18n.I18nBase.formatMessage(I18nBase.java:67)
at org.hl7.fhir.validation.BaseValidator.ruleHtml(BaseValidator.java:425)
at org.hl7.fhir.definitions.validation.ResourceValidator.rule(ResourceValidator.java:124)
at org.hl7.fhir.definitions.validation.ResourceValidator.checkSearchParams(ResourceValidator.java:383)
at org.hl7.fhir.definitions.validation.ResourceValidator.check(ResourceValidator.java:217)
at org.hl7.fhir.definitions.validation.ResourceValidator.check(ResourceValidator.java:594)
at org.hl7.fhir.tools.publisher.Publisher.validate(Publisher.java:1791)
at org.hl7.fhir.tools.publisher.Publisher.execute(Publisher.java:613)
at org.hl7.fhir.tools.publisher.Publisher.main(Publisher.java:478)
@Grahame Grieve @Mark Iantorno
Sean McIlvenna (Oct 28 2021 at 18:47):
huh... not sure I know what to do with that, either. :P
I ran publish on my local machine and it finished successfully. Where's the discrepency?
Jean Duteau (Oct 28 2021 at 18:52):
there's nothing you can do we need grahame or mark to chime in.
Vassil Peytchev (Oct 28 2021 at 20:01):
Just to double check, can you run clean and then publish again locally? I am assuming you've checked for any missed files via
git ls-files -o --exclude-standard
Sean McIlvenna (Oct 28 2021 at 21:22):
there were no missed files.
running clean and publish again locally
Grahame Grieve (Oct 29 2021 at 03:49):
so is this sorted?
Sean McIlvenna (Oct 29 2021 at 14:38):
no... trying to figure out why it's failing still
Sean McIlvenna (Oct 29 2021 at 14:38):
I ran clean and publish, and sure enough, found errors that didn't show up previously
Sean McIlvenna (Oct 29 2021 at 14:38):
Candidate for CodeableReference: [ClinicalImpression.prognosis]
This was a Full Build 1.524 35sec 1940MB
FHIR build failure @ Thu, Oct 28, 2021 14:22-0700 1.514 37sec 1940MB
Error: null
java.lang.NullPointerException
at java.base/java.util.ResourceBundle.containsKey(ResourceBundle.java:2302)
at org.hl7.fhir.utilities.i18n.I18nBase.messageExistsForLocale(I18nBase.java:50)
at org.hl7.fhir.utilities.i18n.I18nBase.formatMessage(I18nBase.java:67)
at org.hl7.fhir.validation.BaseValidator.ruleHtml(BaseValidator.java:425)
at org.hl7.fhir.definitions.validation.ResourceValidator.rule(ResourceValidator.java:124)
at org.hl7.fhir.definitions.validation.ResourceValidator.checkSearchParams(ResourceValidator.java:383)
at org.hl7.fhir.definitions.validation.ResourceValidator.check(ResourceValidator.java:217)
at org.hl7.fhir.definitions.validation.ResourceValidator.check(ResourceValidator.java:594)
at org.hl7.fhir.tools.publisher.Publisher.validate(Publisher.java:1791)
at org.hl7.fhir.tools.publisher.Publisher.execute(Publisher.java:613)
at org.hl7.fhir.tools.publisher.Publisher.main(Publisher.java:478)
Sean McIlvenna (Oct 29 2021 at 14:38):
My changes were entirely related to Composition, though... so I'm not sure why I'm getting errors on ClinicalImpression
Sean McIlvenna (Oct 29 2021 at 14:38):
ClinicalImpression doesn't appear to relate to Composition...
David Pyke (Oct 29 2021 at 14:52):
I get those from time to time. The only way I've found to fix it is a full delete and reclone of the git.
Sean McIlvenna (Oct 29 2021 at 15:36):
ugh
Sean McIlvenna (Oct 29 2021 at 15:36):
really?
David Pyke (Oct 29 2021 at 15:38):
Nothing else has worked for me. OTher people may have better ideas
Sean McIlvenna (Oct 29 2021 at 15:38):
maybe someone can help me understand why the Azure checks on the GitHub PR failed? The error seems to be different? I'd like to restart the pipeline run to see if it solves itself and was just glitch. But, I can't seem to find an option to do that, either
Sean McIlvenna (Oct 29 2021 at 15:38):
https://github.com/HL7/fhir/pull/1478
Vassil Peytchev (Oct 29 2021 at 16:25):
Looking at the PR, I see this:
Things I don't know:
- is this file supposed to be committed?
- why are there XML entities in the file instead of a single quote?
- is this related to the NPE?
Sean McIlvenna (Oct 29 2021 at 17:26):
I was told those files should be part of the commit... See earlier I asked with a screenshot if those extra tools and vscache files should be included, and Grahame indicated they shoudl be
Vassil Peytchev (Oct 29 2021 at 17:29):
I think we both meant vscache... But in this case the original file was wrong, so it should be corrected. I am running the publish locally on master, and will fix the single quote, and run again. Unfortunately I am running the build in a VM, so it takes a bit longer than usual.
Vassil Peytchev (Oct 29 2021 at 18:04):
The build is failing now due to examples with invalid NDC, LOINC and SNOMED codes. Something must have changed in the tx.fhir.org server to cause the amount of errors.
@Rob Hausam @Grahame Grieve
Rob Hausam (Oct 29 2021 at 18:18):
I think what has actually changed is more likely in the validator in that it is now caring about some things that were being overlooked before - @Grahame Grieve can comment on this. I'm pretty sure that both SNOMED (at least the International and US Editions, and probably all of them) and LOINC (except possibly for some LOINC answer lists and value sets?) are correct on tx.fhir.org. NDC has issues where the updated version drops codes that were included in earlier versions, since those products are no longer being marketed. We may have to do something about that. But if we do something it can't be based solely on what NDC provides as current - so the issue there is most likely not with the validator or tx.fhir.org, but with NDC itself.
Grahame Grieve (Oct 29 2021 at 18:37):
see thread in #Medication
Vassil Peytchev (Oct 29 2021 at 18:44):
It's not just NDC codes, there are LOINC and SNOMED codes as well:
Summary: Errors=47, Warnings=3786, Information messages=657
ERROR @ CapabilityStatement.url (line 0, col0): capabilitystatement-example:: CapabilityStatement.url: UUIDs must be valid (src = InstanceValidator)
ERROR @ CapabilityStatement2.url (line 0, col0): capabilitystatement2-example:: CapabilityStatement2.url: UUIDs must be valid (src = InstanceValidator)
ERROR @ Citation.url (line 0, col0): citation-example-systematic-meta-review:: Citation.url: Canonical URLs must be absolute URLs if they are not fragment references (Citation/citation-example-systematic-meta-review) (src = InstanceValidator)
ERROR @ Composition.category[0].coding[0] (line 0, col0): composition-example:: Composition.category[0].coding[0]: The code "LP173421-1" is not valid in the system http://loinc.org; The code provided (http://loinc.org#LP173421-1) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4) for 'http://loinc.org#LP173421-1' (src = TerminologyEngine)
ERROR @ Composition.category[0].coding[0] (line 0, col0): composition-example-mixed:: Composition.category[0].coding[0]: The code "LP173421-1" is not valid in the system http://loinc.org; The code provided (http://loinc.org#LP173421-1) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4) for 'http://loinc.org#LP173421-1' (src = TerminologyEngine)
[...]
and
[...]
ERROR @ MedicationDispense.quantity (line 0, col0): medicationdispense0314:: MedicationDispense.quantity: Unable to find code 415818005 in http://snomed.info/sct (version http://snomed.info/sct/900000000000207008/version/20190731); The code "415818005" is not valid in the system http://snomed.info/sct; The code provided (http://snomed.info/sct#415818005) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4) for 'http://snomed.info/sct#415818005' (src = TerminologyEngine)
ERROR @ MedicationDispense.quantity (line 0, col0): medicationdispense0317:: MedicationDispense.quantity: Unable to find code 415818005 in http://snomed.info/sct (version http://snomed.info/sct/900000000000207008/version/20190731); The code "415818005" is not valid in the system http://snomed.info/sct; The code provided (http://snomed.info/sct#415818005) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4) for 'http://snomed.info/sct#415818005' (src = TerminologyEngine)
ERROR @ MedicationDispense.contained[0].ofType(Medication).code.coding[0] (line 0, col0): medicationdispense0319:: MedicationDispense.contained[0].ofType(Medication).code.coding[0]: Code "33261-141-20" not found in NDC; The code "33261-141-20" is not valid in the system http://hl7.org/fhir/sid/ndc; The code provided (http://hl7.org/fhir/sid/ndc#33261-141-20) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4) for 'http://hl7.org/fhir/sid/ndc#33261-141-20' (src = TerminologyEngine)
Grahame Grieve (Oct 29 2021 at 19:23):
I don't get LOINC and Snomed errors - weird?
Last updated: Apr 12 2022 at 19:14 UTC
