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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.
…ssing from targets list
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.
…ontributor Modified add_contributor function and add two more related tests.
…s-path-to-score-range-data-model Add OddsPath Property to ScoreRange Data Model
variant_mapper_manager previously failed because of an incorrectly placed 'where' function and because we did two related db queries, one for a score set and one for target gene(s) within that score set, which resulted in an error when adding the score set changes to the db. Instead, query to select the score set, and then loop through the score set's target genes rather than querying the target genes table in the db.
…SetsAndExperiments Bugfix/estelle/61/num score sets and experiments
Support mapper update for multi-target score sets
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This release adds support for ClinGen Allele ID (CAID) linkages in MaveDB, the storing of Base Editor data, the ability to link ClinVar controls to mapped variants (via CAID) and the ability to support multi-target and accession based score sets via our mapping process.
Features
Closes #311, Closes #314 and Closes #381: #388
Closes #317: #395
VariantEffect/dcd_mapping2#2 and VariantEffect/dcd_mapping2#3: #436
Enhancements
Closes #350: #420
Bug Fixes
Fixes #432: #433
Fixes #441: #442
Fixes #61: #447