Support mapper update for multi-target score sets#436
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bencap merged 6 commits intorelease-2025.2.0from Jun 11, 2025
Merged
Support mapper update for multi-target score sets#436bencap merged 6 commits intorelease-2025.2.0from
bencap merged 6 commits intorelease-2025.2.0from
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This all looks good to me. The tests will need to be edited to reflect the new mapping results style, and we should also add more tests for accession based and multi target mappings now that they are supported.
src/mavedb/worker/jobs.py
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| # TODO(VariantEffect/dcd-mapping2#3) after adding accession-based score set mapping support: | ||
| # this also assumes that the score set is based on a target sequence, not a target accession |
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This TODO is now addressed by these changes correct?
src/mavedb/worker/jobs.py
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| ANNOTATION_LAYERS = { | ||
| "g": "genomic", | ||
| "p": "protein", | ||
| "c": "cdna", | ||
| } |
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Could we move this to a new file src/mavedb/lib/mapping.py? Along with this layer dictionary, we can also move the VRSMap class from src/mavedb/data_providers/services.py to that file. That would better centralize these objects for use across the code base.
src/mavedb/worker/jobs.py
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| pre_mapped_metadata[ANNOTATION_LAYERS[annotation_layer]] = { | ||
| k: layer_premapped[k] | ||
| for k in set(list(layer_premapped.keys())) | ||
| - excluded_pre_mapped_keys # TODO does this work if no 'sequence' key? |
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.
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Jun 5, 2025
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