365 vat python testing additions

[RoriCremer]

Docker image added---I think we'll want to implement whatever we are doing for the jars for the docker images in parallel

I'm planning to add an additional python test to this and then I want to dig into how to make sure they run during docker build

outside the scope for this specific round of python testing, but it will be worth reaching out the the coworker who spotted both previous clinvar issues to ask for additional spot testing cases

[codecov]

Codecov Report

❗ No coverage uploaded for pull request base (ah_var_store@75b5115). Click here to learn what that means.
The diff coverage is n/a.

@@               Coverage Diff                @@
##             ah_var_store     #7756   +/-   ##
================================================
  Coverage                ?   86.305%           
  Complexity              ?     35190           
================================================
  Files                   ?      2170           
  Lines                   ?    164837           
  Branches                ?     17775           
================================================
  Hits                    ?    142262           
  Misses                  ?     16253           
  Partials                ?      6322           

[rsasch]

I tried running ./build_docker.sh and it failed with the following error:

ImportError: Failed to import test module: create_variant_annotation_table_test
Traceback (most recent call last):
  File "/opt/miniconda3/envs/gvs/lib/python3.8/unittest/loader.py", line 154, in loadTestsFromName
    module = __import__(module_name)
  File "/Users/rasch/p/gatk/scripts/variantstore/wdl/extract/create_variant_annotation_table_test.py", line 13, in <module>
    from create_variant_annotation_table import make_annotated_json_row
  File "/Users/rasch/p/gatk/scripts/variantstore/wdl/extract/create_variant_annotation_table.py", line 8, in <module>
    import ijson
ModuleNotFoundError: No module named 'ijson'

[RoriCremer]

oooh, re: ijson, should I just add checking for and installing it into the ./build_docker.sh file?

I've had it forever since I need it to run the python script. It's in requirements.txt, where else should I put it?

[rsasch]

I think it would be good for there to be as little lift as possible required to run the tests, so adding it to ./build_docker.sh is probably best.

[mcovarr]

dumb question probably but I don't follow why this is needed

[RoriCremer]

Python dicts use None and json uses null and the testing doesn't seem to be able to reconcile.

[mcovarr]

a couple of Python nitpicks, otherwise looks good

[mcovarr]

This shouldn't be necessary, the Python json library should handle this automatically. The issue appears to be that the "expected" files have the values that are meant to be nulls wrapped in quotes so json (correctly) treats them as strings. e.g.

  "gnomad_nfr_ac": "null",

should be

  "gnomad_nfr_ac": null,

[RoriCremer]

Bec's change resolved!