update rdflib-jsonld for py3-10 🐍⬆

[shaikh-rashid]

This is a release of the candig/chord-metadata:v1.4.2 image built with python 3.10 and alpine 3.16. Please pull and test the image to verify that it works as expected. Testing can be done in candig-dev before being promoted to candig-prod.

[kcranston]

Looks like the tests are failing because the "rdflib-jsonld package has been integrated into rdflib as of rdflib==6.0.1. Please remove rdflib-jsonld from your project's dependencies."

The tests are running on python3.7, so it looks like dependency woes. Can we update the test python to 3.10 and see if we can get those passing?

[kcranston]

The test suite uses nose, which is currently incompatible with python 3.10 xlcnd/isbnlib#95

[codecov-commenter]

Codecov Report

Merging #42 (e6ba858) into develop (6d89420) will decrease coverage by 15.99%.
The diff coverage is n/a.

@@             Coverage Diff              @@
##           develop      #42       +/-   ##
============================================
- Coverage    84.21%   68.22%   -16.00%     
============================================
  Files           95       56       -39     
  Lines         3941     1605     -2336     
  Branches       518      143      -375     
============================================
- Hits          3319     1095     -2224     
- Misses         412      505       +93     
+ Partials       210        5      -205     

Impacted Files	Coverage Δ
chord_metadata_service/restapi/fhir_utils.py	8.02% <0.00%> (-77.60%)	⬇️
chord_metadata_service/restapi/argo_utils.py	13.79% <0.00%> (-70.69%)	⬇️
chord_metadata_service/patients/signals.py	73.33% <0.00%> (-26.67%)	⬇️
chord_metadata_service/phenopackets/serializers.py	67.93% <0.00%> (-20.62%)	⬇️
chord_metadata_service/resources/models.py	80.00% <0.00%> (-20.00%)	⬇️
chord_metadata_service/restapi/serializers.py	80.00% <0.00%> (-20.00%)	⬇️
chord_metadata_service/phenopackets/signals.py	57.44% <0.00%> (-15.53%)	⬇️
chord_metadata_service/restapi/validators.py	75.00% <0.00%> (-15.00%)	⬇️
chord_metadata_service/chord/models.py	83.69% <0.00%> (-14.04%)	⬇️
...hord_metadata_service/restapi/description_utils.py	88.23% <0.00%> (-11.77%)	⬇️
... and 45 more

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[daisieh]

This works fine on candig-dev.

[kcranston]

This works fine on candig-dev.

Can you humour me with a little more detail? i.e. what tests did you run? I feel a little squeamish about merging this with failing CI without knowing more about the assertion that it is fine.

[daisieh]

This works fine on candig-dev.

Can you humour me with a little more detail? i.e. what tests did you run? I feel a little squeamish about merging this with failing CI without knowing more about the assertion that it is fine.

I loaded this version on candig-dev and then checked the http://candig-dev.hpc4healthlocal:5080/katsu/api/datasets endpoint to see that it returned something. It was not a particularly rigorous test.

Of course, now that I've been (very reasonably) shamed about my lack of rigor in testing, I'm trying to ingest the synthetic dataset again on the server and noticed that I've missed an env var in docker-compose. I'll push that change to CanDIG/CanDIGv2#142.