feat: add anyvlm database

[korikuzma]

close #23

• Started some docs work for Add ReadTheDocs #25
• I'll probably be making modifications (such as leveraging pydantic models for qcFilters, ancillaryResults, retrieval functions, etc in Write function to retrieve CAF data for VLM response #16)
  • UPDATE: I did make changes to Pydantic models in Write function to retrieve CAF data for VLM response #16

[jennifer-bowser]

I mostly have a question about how we're configuring our docker setup, but I found a couple of pylance errors/some other nitpicky suggestions as well.

[korikuzma]

TIL my pylance extension was not working (... but is now after some struggles of getting the configs right again)

[korikuzma]

I was having issues locally, so pinned to latest commit

[jennifer-bowser]

For some reason I'm getting failures in test_clients.py; though it looks like these are all passing when GitHub runs them so maybe I've got something whack going on in my local environment?

FAILED tests/unit/anyvar/test_clients.py::test_put_allele_expressions[anyvar_python_client] - AssertionError: assert ['ga4gh:VA.ru...G6bLwQesDU2g'] == ['ga4gh:VA.0y...0Nv8OMN359HC']
FAILED tests/unit/anyvar/test_clients.py::test_put_allele_expressions[anyvar_http_client] - AssertionError: assert ['ga4gh:VA.ru...G6bLwQesDU2g'] == ['ga4gh:VA.0y...0Nv8OMN359HC']
FAILED tests/unit/anyvar/test_clients.py::test_put_allele_expressions_handle_invalid[anyvar_http_client] - anyvlm.anyvar.base_client.AnyVarClientError
FAILED tests/unit/anyvar/test_clients.py::test_search_by_interval[anyvar_populated_python_client] - AssertionError: assert [Allele(id='g...g(root='C')))] == [Allele(id='g...nitLength=1))]
FAILED tests/unit/anyvar/test_clients.py::test_search_by_interval[anyvar_http_client] - AssertionError: assert [Allele(id='g...g(root='C')))] == [Allele(id='g...nitLength=1))]
FAILED tests/unit/anyvar/test_clients.py::test_search_by_interval_with_alias[anyvar_populated_python_client] - AssertionError: assert [Allele(id='g...g(root='C')))] == [Allele(id='g...nitLength=1))]
FAILED tests/unit/anyvar/test_clients.py::test_search_by_interval_with_alias[anyvar_http_client] - AssertionError: assert [Allele(id='g...g(root='C')))] == [Allele(id='g...nitLength=1))]

[korikuzma]

For some reason I'm getting failures in test_clients.py; though it looks like these are all passing when GitHub runs them so maybe I've got something whack going on in my local environment?

FAILED tests/unit/anyvar/test_clients.py::test_put_allele_expressions[anyvar_python_client] - AssertionError: assert ['ga4gh:VA.ru...G6bLwQesDU2g'] == ['ga4gh:VA.0y...0Nv8OMN359HC']
FAILED tests/unit/anyvar/test_clients.py::test_put_allele_expressions[anyvar_http_client] - AssertionError: assert ['ga4gh:VA.ru...G6bLwQesDU2g'] == ['ga4gh:VA.0y...0Nv8OMN359HC']
FAILED tests/unit/anyvar/test_clients.py::test_put_allele_expressions_handle_invalid[anyvar_http_client] - anyvlm.anyvar.base_client.AnyVarClientError
FAILED tests/unit/anyvar/test_clients.py::test_search_by_interval[anyvar_populated_python_client] - AssertionError: assert [Allele(id='g...g(root='C')))] == [Allele(id='g...nitLength=1))]
FAILED tests/unit/anyvar/test_clients.py::test_search_by_interval[anyvar_http_client] - AssertionError: assert [Allele(id='g...g(root='C')))] == [Allele(id='g...nitLength=1))]
FAILED tests/unit/anyvar/test_clients.py::test_search_by_interval_with_alias[anyvar_populated_python_client] - AssertionError: assert [Allele(id='g...g(root='C')))] == [Allele(id='g...nitLength=1))]
FAILED tests/unit/anyvar/test_clients.py::test_search_by_interval_with_alias[anyvar_http_client] - AssertionError: assert [Allele(id='g...g(root='C')))] == [Allele(id='g...nitLength=1))]

Can you nuke your dbs? @jennifer-bowser

[jennifer-bowser]

For some reason I'm getting failures in test_clients.py; though it looks like these are all passing when GitHub runs them so maybe I've got something whack going on in my local environment?

FAILED tests/unit/anyvar/test_clients.py::test_put_allele_expressions[anyvar_python_client] - AssertionError: assert ['ga4gh:VA.ru...G6bLwQesDU2g'] == ['ga4gh:VA.0y...0Nv8OMN359HC']
FAILED tests/unit/anyvar/test_clients.py::test_put_allele_expressions[anyvar_http_client] - AssertionError: assert ['ga4gh:VA.ru...G6bLwQesDU2g'] == ['ga4gh:VA.0y...0Nv8OMN359HC']
FAILED tests/unit/anyvar/test_clients.py::test_put_allele_expressions_handle_invalid[anyvar_http_client] - anyvlm.anyvar.base_client.AnyVarClientError
FAILED tests/unit/anyvar/test_clients.py::test_search_by_interval[anyvar_populated_python_client] - AssertionError: assert [Allele(id='g...g(root='C')))] == [Allele(id='g...nitLength=1))]
FAILED tests/unit/anyvar/test_clients.py::test_search_by_interval[anyvar_http_client] - AssertionError: assert [Allele(id='g...g(root='C')))] == [Allele(id='g...nitLength=1))]
FAILED tests/unit/anyvar/test_clients.py::test_search_by_interval_with_alias[anyvar_populated_python_client] - AssertionError: assert [Allele(id='g...g(root='C')))] == [Allele(id='g...nitLength=1))]
FAILED tests/unit/anyvar/test_clients.py::test_search_by_interval_with_alias[anyvar_http_client] - AssertionError: assert [Allele(id='g...g(root='C')))] == [Allele(id='g...nitLength=1))]

Can you nuke your dbs? @jennifer-bowser

Ok I nuked my DBs, but I'm still getting errors. When I check my AnyVar instance after running tests, I'm mostly seeing log output with this kind of error:

ga4gh.vrs.dataproxy.DataProxyValidationError: Reference mismatch at GRCh38:Y position 2781760-2781761 (input gave 'A' but correct ref is 'C')

Maybe this is just wonkyness on my end though, since I'm not sure why your changes would be causing these tests to fail and my AnyVar/AnyVLM environment has been challenging lately.

UPDATE: Never mind, I had the wrong version of vrs-python installed in my AnyVar instance.

[jennifer-bowser]

I got my tests to pass, thanks Kori!