FHIR Chat · firely-terminal-pipeline@v0.2.0 Failing

Stream: IG creation

Topic: firely-terminal-pipeline@v0.2.0 Failing

Kevin Mayfield (Jun 26 2021 at 04:43):

Our github integration with firely-terminal-pipeline started failing last week. We were using the alpha version of this pipeline ok.
New version also fails but with this error.

Screenshot-2021-06-26-at-05.42.47.png

@Ward Weistra

Kevin Mayfield (Jun 26 2021 at 04:52):

That is with dotnet validation enabled.
Java validation returns a different error code

Screenshot-2021-06-26-at-05.52.06.png

Lloyd McKenzie (Jun 26 2021 at 21:06):

@Ward Weistra

Ward Weistra (Jun 28 2021 at 09:57):

@Alexander Zautke also encountered and overcame this. Can you share?

Alexander Zautke (Jun 28 2021 at 12:41):

@Kevin Mayfield Starting with version 0.2.0 you will need to provide Simplifier login credentials. If you enable the .NET validation part, Firely.Terminal will also execute a set of quality control rules. By default only the minimal checks, but you can configure it to run your own set of rules specified in your repo. For quality control it's mandatory to run fhir login first. You can provide these credentials as repository secrets or organization secrets in GitHub (configured in the Settings part of the repository):

- name: Firely.Terminal (GitHub Actions)
  uses: FirelyTeam/firely-terminal-pipeline@v0.2.0
  with:
  [...]
  SIMPLIFIER_USERNAME: ${{ secrets.SIMPLIFIER_USERNAME }}
  SIMPLIFIER_PASSWORD: ${{ secrets.SIMPLIFIER_PASSWORD }}

I will add an error message if no credentials are configured before attempting to execute a login. Sorry for the inconvenience.

Alexander Zautke (Jun 28 2021 at 12:44):

@Kevin Mayfield Can you share the error that you get when the Java validation part is enabled? I have it running in a different project, happy to debug the issue.

Kevin Mayfield (Jun 28 2021 at 12:56):

first test looking good

Kevin Mayfield (Jun 28 2021 at 13:04):

Many thanks. Up and running again on the latest version.

Kevin Mayfield (Jun 28 2021 at 13:05):

That dot net validation

Kevin Mayfield (Jun 28 2021 at 13:10):

Java error is

image.png

I think that's because of the way we have our conformance resources structured. We have split the conformance resources into sub directories https://github.com/NHSDigital/NHSDigitial-FHIR-Clinical-ImplementationGuide

Grahame Grieve (Jun 28 2021 at 19:58):

then you have to nominate each subdirectory

Kevin Mayfield (Jun 29 2021 at 07:02):

@Alexander Zautke we are nominating each subdirectory (including examples) in our workflow file (e.g. https://github.com/NHSDigital/NHSDigitial-FHIR-ImplementationGuide/actions/runs/979052361/workflow). Does the pipeline take this into account when using java validation?

Kevin Mayfield (Jun 29 2021 at 07:03):

This would be ideal for us. Currently we are using java validation after IG publication, would like this also at an earlier stage.

Alexander Zautke (Jun 29 2021 at 07:42):

Yes, the pipeline should add all subfolders using the -ig parameter. The path to the CodeSystem folder looks off. Instead of $workspace/CodeSystem, there is another „ NHSDigitial-FHIR-ImplementationGuide“ in the path. Do you have a link directly to the action run? I can’t find it if I look through your history on GitHub.

Kevin Mayfield (Jun 29 2021 at 07:44):

https://github.com/NHSDigital/NHSDigitial-FHIR-Clinical-ImplementationGuide/actions/runs/979072265

Kevin Mayfield (Jun 29 2021 at 07:46):

That folder doesn't exist (the workflow file was copied from another project). I'll amend and re-run

Kevin Mayfield (Jun 29 2021 at 07:52):

Rerun was better
https://github.com/NHSDigital/NHSDigitial-FHIR-Clinical-ImplementationGuide/runs/2939761125

Failing with Error: Process completed with exit code 1.

Alexander Zautke (Jun 29 2021 at 08:06):

Could you set the EXPECTED_FAILS input to "VALIDATION_CONFORMANCE_JAVA VALIDATION_EXAMPLES_JAVA" to see if some part of the Java validation failing that doesn't get logged?

Kevin Mayfield (Jun 29 2021 at 09:06):

Passed https://github.com/NHSDigital/NHSDigitial-FHIR-Clinical-ImplementationGuide/runs/2940389129

It's the examples failing (mostly on UK SNOMED)

Alexander Zautke (Jun 29 2021 at 09:25):

Great to hear! With JAVA_VALIDATION_OPTIONS you can directly pass a string with arguments to the java validator. You could specify your own terminology server here.

Kevin Mayfield (Jun 29 2021 at 09:56):

Others worked.... terminology server will be a another battle - for some reason UK terminology has OAuth enabled.

Last updated: Apr 12 2022 at 19:14 UTC

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FHIR Chat · firely-terminal-pipeline@v0.2.0 Failing · IG creation