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Tests will pass after the release of VariantEffect/mavehgvs#40 and VariantEffect/mavehgvs#41. |
Refactors dataframe validation logic into 3 component files: column.py, dataframe.py, and variant.py. This simplifies the validation structure and logically separates validation function based on the part of the df they operate on.
Refactors most of the test suite to better identify dependency separation problems. Validation tests may now be run with only core (and dev) dependencies installed, and fixtures which operate on server dependencies are conditionally loaded based on the installed modules. With this change, it will be much more straightforward to identify dependency 'leaks', or server dependencies which mistakenly are leaked into validation type code.
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This allows the use of the vs-code pytest extension but still prevents the use of external connections. Enabling this socket makes it easier to test within the code editor.
The hgvs package is not able to parse allelic variation (multi-variants denoted by brackets), which are often a key variant string in base editor data. We work around this by: - Parsing the multi-variant into MaveHGVS without any target info to ascertain whether it is syntactically valid - Parsing each subvariant against the provided transcript to ascertain whether it is informationally valid
Adds tests for multi-variant validation for accession based variants. As part of this change, an additional transcript was added to tests genomic based protein variants in addition to just testing nucleotide based variants.
Prior to this, we weren't really using SeqRepo to do transcript resolution (unintentionally). Note that to use SeqRepo in this manner, a new environment variable `HGVS_SEQREPO_DIR` should be set.
This change will need to pull in the new MaveHGVS version.
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MaveHGVS 0.7.0 includes a fix to multi-variant validation.
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SA complains about unitialized names for models when some are not imported. This is usually done in the server_main file, but becomes an issue when testing on only core dependencies since not all models are loaded and that file is no longer imported by the test suite. Do this step up front in the top level conftest file instead to ensure we load all model objects into the SA namespace for testing.
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