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computed identifiers using pydantic model serializers #342

Merged
merged 22 commits into from
Feb 21, 2024
Merged

computed identifiers using pydantic model serializers #342

merged 22 commits into from
Feb 21, 2024

Commits on Feb 7, 2024

  1. move digest from VO to GA4GH identifiable

    @ahwagner
    ahwagner committed Feb 7, 2024
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  2. add ga4gh serialize to models

    @ahwagner
    ahwagner committed Feb 7, 2024
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  3. remove computed field and add get_or_create

    @ahwagner
    ahwagner committed Feb 7, 2024
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Commits on Feb 10, 2024

  1. attribute ordering fixes

    @ahwagner
    ahwagner committed Feb 10, 2024
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  2. add tests for schema to pydantic matching

    @ahwagner
    ahwagner committed Feb 10, 2024
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  3. update is_identifiable

    @ahwagner
    ahwagner committed Feb 10, 2024
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  4. update model validations

    @ahwagner
    ahwagner committed Feb 10, 2024
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  5. refactor identifier code

    @ahwagner
    ahwagner committed Feb 10, 2024
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  6. fix IRI behavior when serialized alone

    @ahwagner
    ahwagner committed Feb 10, 2024
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  7. restore haplotype as unordered List with Serializer override

    @ahwagner
    ahwagner committed Feb 10, 2024
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  8. add context control support for in-place edits

    @ahwagner
    ahwagner committed Feb 10, 2024
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Commits on Feb 15, 2024

  1. Use LiteralSequenceExpression for ambiguous insertions that cannot be… 

    … derived from the reference sequence
    @ehclark
    ehclark committed Feb 15, 2024
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  2. Update VCF unit tests to match new digest logic

    @ehclark
    ehclark committed Feb 15, 2024
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Commits on Feb 16, 2024

  1. update digests and message structure for trx test

    @ahwagner
    ahwagner committed Feb 16, 2024
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Commits on Feb 19, 2024

  1. Revert "Use LiteralSequenceExpression for ambiguous insertions that c… 

    …annot be derived from the reference sequence"

This reverts commit f407fd0.
    @ahwagner
    ahwagner committed Feb 19, 2024
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  2. remove unnecessary try/except

    @ahwagner
    ahwagner committed Feb 19, 2024
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  3. check insertions for ambiguous novel sequence

    @ahwagner
    ahwagner committed Feb 19, 2024
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  4. update test cassettes

    @ahwagner
    ahwagner committed Feb 19, 2024
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  5. Merge branch 'main' into issue-341

    @korikuzma
    korikuzma committed Feb 19, 2024
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  6. restore use of VOCA seed for RSL

    @ahwagner
    ahwagner committed Feb 19, 2024
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  7. add TODO

    @ahwagner
    ahwagner committed Feb 19, 2024
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Commits on Feb 21, 2024

  1. test: fix vcf annotation test 

    chr19-54220999-A-A had that `C` was the actual ref seq, but it should
have been `T`
    @korikuzma
    korikuzma committed Feb 21, 2024
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