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Dev #4446

Merged
merged 47 commits into from
Oct 22, 2024
Merged

Dev #4446

merged 47 commits into from
Oct 22, 2024

Commits on Oct 10, 2024

  1. note locations to update

    @hanars
    hanars committed Oct 10, 2024
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  2. clean up

    @hanars
    hanars committed Oct 10, 2024
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  3. Merge branch 'dev' of https://github.com/broadinstitute/seqr into sex… 

    …-aneuploidy
    @hanars
    hanars committed Oct 10, 2024
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  4. update sex options

    @hanars
    hanars committed Oct 10, 2024
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  5. add test case

    @hanars
    hanars committed Oct 10, 2024
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  6. Merge branch 'hail-search-sex-meatdata' of https://github.com/broadin… 

    …stitute/seqr into sex-aneuploidy
    @hanars
    hanars committed Oct 10, 2024
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  7. add aneuploidy data to loading pedigrees

    @hanars
    hanars committed Oct 10, 2024
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  8. report sex aneuploidy

    @hanars
    hanars committed Oct 10, 2024
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  9. fix sex search determination

    @hanars
    hanars committed Oct 10, 2024
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  10. better test updates

    @hanars
    hanars committed Oct 10, 2024
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Commits on Oct 11, 2024

  1. fix test fixture

    @hanars
    hanars committed Oct 11, 2024
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  2. handle sex detail in summary data

    @hanars
    hanars committed Oct 11, 2024
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  3. clean up

    @hanars
    hanars committed Oct 11, 2024
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  4. support aneuploidy in pedigree upload

    @hanars
    hanars committed Oct 11, 2024
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  5. fix sex options ui display

    @hanars
    hanars committed Oct 11, 2024
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  6. show sex onn individual row

    @hanars
    hanars committed Oct 11, 2024
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  7. fix aneuploidy pedigree display

    @hanars
    hanars committed Oct 11, 2024
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  8. fix parent lookup

    @hanars
    hanars committed Oct 11, 2024
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  9. fix parent lookup

    @hanars
    hanars committed Oct 11, 2024
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  10. show warning for sex chromosome variant aneuploidy

    @hanars
    hanars committed Oct 11, 2024
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  11. fix matchmaersex

    @hanars
    hanars committed Oct 11, 2024
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Commits on Oct 15, 2024

  1. remove unneeded comp het filter

    @hanars
    hanars committed Oct 15, 2024
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  2. Merge branch 'dev' of https://github.com/broadinstitute/seqr into sex… 

    …-aneuploidy
    @hanars
    hanars committed Oct 15, 2024
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  3. undo failed logic negation

    @hanars
    hanars committed Oct 15, 2024
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  4. Merge branch 'dev' of https://github.com/broadinstitute/seqr into com… 

    …p-het-min-affected
    @hanars
    hanars committed Oct 15, 2024
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  5. Bump cookie and express in /ui 

    Bumps [cookie](https://github.com/jshttp/cookie) and [express](https://github.com/expressjs/express). These dependencies needed to be updated together.

Updates `cookie` from 0.6.0 to 0.7.1
- [Release notes](https://github.com/jshttp/cookie/releases)
- [Commits](jshttp/cookie@v0.6.0...v0.7.1)

Updates `express` from 4.20.0 to 4.21.1
- [Release notes](https://github.com/expressjs/express/releases)
- [Changelog](https://github.com/expressjs/express/blob/4.21.1/History.md)
- [Commits](expressjs/express@4.20.0...4.21.1)

---
updated-dependencies:
- dependency-name: cookie
  dependency-type: indirect
- dependency-name: express
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
    @dependabot
    dependabot[bot] authored Oct 15, 2024
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Commits on Oct 16, 2024

  1. Merge pull request #4432 from broadinstitute/dependabot/npm_and_yarn/… 

    …ui/multi-9f37c16f8f

Bump cookie and express in /ui
    @hanars
    hanars authored Oct 16, 2024
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  2. fix: requirements-dev.txt to reduce vulnerabilities 

    The following vulnerabilities are fixed by pinning transitive dependencies:
- https://snyk.io/vuln/SNYK-PYTHON-DJANGO-7435780
- https://snyk.io/vuln/SNYK-PYTHON-DJANGO-7436273
- https://snyk.io/vuln/SNYK-PYTHON-DJANGO-7436514
- https://snyk.io/vuln/SNYK-PYTHON-DJANGO-7436646
- https://snyk.io/vuln/SNYK-PYTHON-DJANGO-7642790
- https://snyk.io/vuln/SNYK-PYTHON-DJANGO-7642791
- https://snyk.io/vuln/SNYK-PYTHON-DJANGO-7642813
- https://snyk.io/vuln/SNYK-PYTHON-DJANGO-7642814
- https://snyk.io/vuln/SNYK-PYTHON-DJANGO-7886958
- https://snyk.io/vuln/SNYK-PYTHON-DJANGO-7886959
- https://snyk.io/vuln/SNYK-PYTHON-REQUESTS-6928867
- https://snyk.io/vuln/SNYK-PYTHON-SQLPARSE-6615674
- https://snyk.io/vuln/SNYK-PYTHON-ZIPP-7430899
    @snyk-bot
    snyk-bot committed Oct 16, 2024
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  3. conditionally show dataset type selector for local installs

    @hanars
    hanars committed Oct 16, 2024
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  4. Merge pull request #4434 from broadinstitute/snyk-fix-b03e0aca476f710… 

    …6266887098d0c056f

[Snyk] Fix for 13 vulnerabilities
    @hanars
    hanars authored Oct 16, 2024
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  5. add skip validatioon option

    @hanars
    hanars committed Oct 16, 2024
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  6. support updated load data fields

    @hanars
    hanars committed Oct 16, 2024
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  7. do not allow triggering non-snv indel pipeline

    @hanars
    hanars committed Oct 16, 2024
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  8. Revert "do not allow triggering non-snv indel pipeline" 

    This reverts commit ebc3ab2.
    @hanars
    hanars committed Oct 16, 2024
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  9. update unit tests

    @hanars
    hanars committed Oct 16, 2024
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  10. Merge branch 'dev' of https://github.com/broadinstitute/seqr into loc… 

    …al-load-data-ui-update
    @hanars
    hanars committed Oct 16, 2024
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  11. include vairant type in metadata report

    @hanars
    hanars committed Oct 16, 2024
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  12. update varian type logic

    @hanars
    hanars committed Oct 16, 2024
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  13. Merge pull request #4435 from broadinstitute/local-load-data-ui-update 

    Local load data UI update
    @hanars
    hanars authored Oct 16, 2024
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  14. update tests

    @hanars
    hanars committed Oct 16, 2024
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  15. test SNV

    @hanars
    hanars committed Oct 16, 2024
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  16. update gregor import

    @hanars
    hanars committed Oct 16, 2024
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  17. Merge pull request #4436 from broadinstitute/gregor-variant-type 

    Gregor report variant type update
    @hanars
    hanars authored Oct 16, 2024
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  18. Merge pull request #4430 from broadinstitute/comp-het-min-affected 

    Remove extra comp het filtering
    @hanars
    hanars authored Oct 16, 2024
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Commits on Oct 21, 2024

  1. get cached gene counts for comp hets

    @hanars
    hanars committed Oct 21, 2024
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  2. Merge pull request #4442 from broadinstitute/cached-comp-hets-gene-agg 

    get cached gene counts for comp hets
    @hanars
    hanars authored Oct 21, 2024
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Commits on Oct 22, 2024

  1. Merge pull request #4418 from broadinstitute/sex-aneuploidy 

    Sex aneuploidy
    @hanars
    hanars authored Oct 22, 2024
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