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Dev #3531

Merged
merged 95 commits into from
Aug 1, 2023
Merged

Dev #3531

merged 95 commits into from
Aug 1, 2023

Commits on Jul 11, 2023

  1. add hail search status endpoint

    @hanars
    hanars committed Jul 11, 2023
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  2. add unit tests

    @hanars
    hanars committed Jul 11, 2023
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  3. add hail to test

    @hanars
    hanars committed Jul 11, 2023
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  4. fix python name

    @hanars
    hanars committed Jul 11, 2023
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  5. actually fix python name

    @hanars
    hanars committed Jul 11, 2023
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  6. checkout code

    @hanars
    hanars committed Jul 11, 2023
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  7. add docker ignore

    @hanars
    hanars committed Jul 11, 2023
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  8. codacy fixes

    @hanars
    hanars committed Jul 11, 2023
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Commits on Jul 14, 2023

  1. Support per project family-table-filters.

    @ShifaSZ
    ShifaSZ committed Jul 14, 2023
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Commits on Jul 15, 2023

  1. Bump cryptography from 41.0.0 to 41.0.2 

    Bumps [cryptography](https://github.com/pyca/cryptography) from 41.0.0 to 41.0.2.
- [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst)
- [Commits](pyca/cryptography@41.0.0...41.0.2)

---
updated-dependencies:
- dependency-name: cryptography
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
    @dependabot
    dependabot[bot] authored Jul 15, 2023
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Commits on Jul 17, 2023

  1. Merge pull request #3493 from broadinstitute/dependabot/pip/cryptogra… 

    …phy-41.0.2

Bump cryptography from 41.0.0 to 41.0.2
    @hanars
    hanars authored Jul 17, 2023
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  2. display new dbnsfp scores

    @hanars
    hanars committed Jul 17, 2023
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  3. support filtering with mutiple possible predictors

    @hanars
    hanars committed Jul 17, 2023
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  4. update unit tests

    @hanars
    hanars committed Jul 17, 2023
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  5. handle multiple values for single predictor

    @hanars
    hanars committed Jul 17, 2023
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  6. add test

    @hanars
    hanars committed Jul 17, 2023
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  7. clean up

    @hanars
    hanars committed Jul 17, 2023
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Commits on Jul 18, 2023

  1. Add gene id validation.

    @ShifaSZ
    ShifaSZ committed Jul 18, 2023
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  2. Update per reviews.

    @ShifaSZ
    ShifaSZ committed Jul 18, 2023
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  3. Merge pull request #3496 from broadinstitute/validate-gene-id-rnaseq-… 

    …data

Add gene id validation during RNASeq data loading
    @ShifaSZ
    ShifaSZ authored Jul 18, 2023
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  4. auu ui for clinvar conflictingPathogenicities

    @hanars
    hanars committed Jul 18, 2023
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  5. Merge branch 'dev' of https://github.com/broadinstitute/seqr into fat… 

    …hmm-mkl
    @hanars
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  6. update threshholds;

    @hanars
    hanars committed Jul 18, 2023
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  7. Remove possible test flappiness.

    @ShifaSZ
    ShifaSZ committed Jul 18, 2023
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  8. Merge pull request #3492 from broadinstitute/per-project-family-filter 

    Support per project family-table-filters.
    @ShifaSZ
    ShifaSZ authored Jul 18, 2023
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  9. Merge pull request #3499 from broadinstitute/remove-indiv-test-flappi… 

    …ness

Remove test flapping for the Individual tests
    @ShifaSZ
    ShifaSZ authored Jul 18, 2023
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  10. Merge branch 'dev' of https://github.com/broadinstitute/seqr into con… 

    …flictingPathogenicities-ui
    @hanars
    hanars committed Jul 18, 2023
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Commits on Jul 19, 2023

  1. Bump word-wrap from 1.2.3 to 1.2.4 in /ui 

    Bumps [word-wrap](https://github.com/jonschlinkert/word-wrap) from 1.2.3 to 1.2.4.
- [Release notes](https://github.com/jonschlinkert/word-wrap/releases)
- [Commits](jonschlinkert/word-wrap@1.2.3...1.2.4)

---
updated-dependencies:
- dependency-name: word-wrap
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
    @dependabot
    dependabot[bot] authored Jul 19, 2023
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  2. Merge pull request #3480 from broadinstitute/add-hail-status-check 

    Add hail backend - intitial status check
    @hanars
    hanars authored Jul 19, 2023
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  3. Merge pull request #3497 from broadinstitute/conflictingPathogeniciti… 

    …es-ui

add ui for clinvar conflictingPathogenicities
    @hanars
    hanars authored Jul 19, 2023
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  4. Merge pull request #3501 from broadinstitute/dependabot/npm_and_yarn/… 

    …ui/word-wrap-1.2.4

Bump word-wrap from 1.2.3 to 1.2.4 in /ui
    @hanars
    hanars authored Jul 19, 2023
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Commits on Jul 20, 2023

  1. Merge pull request #3498 from broadinstitute/fathmm-mkl 

    Fathmm mkl
    @hanars
    hanars authored Jul 20, 2023
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  2. Fix SV localtion interval filter bug.

    @ShifaSZ
    ShifaSZ committed Jul 20, 2023
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Commits on Jul 21, 2023

  1. Update seqr/utils/search/elasticsearch/es_search.py 

    Update same chrom check

Co-authored-by: hanars <[email protected]>
    @ShifaSZ @hanars
    ShifaSZ and hanars authored Jul 21, 2023
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  2. fix tests.

    @ShifaSZ
    ShifaSZ committed Jul 21, 2023
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  3. Merge pull request #3503 from broadinstitute/fix-sv-location-filter-bug 

    Fix SV localtion interval filter bug.
    @ShifaSZ
    ShifaSZ authored Jul 21, 2023
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  4. fix minor issues with hail backend

    @hanars
    hanars committed Jul 21, 2023
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Commits on Jul 24, 2023

  1. Merge pull request #3508 from broadinstitute/hail-backend-twaeks 

    fix minor issues with hail backend
    @hanars
    hanars authored Jul 24, 2023
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  2. Update search params for outlier and gene searches.

    @ShifaSZ
    ShifaSZ committed Jul 24, 2023
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  3. do not return irrelevent family TPM genes

    @hanars
    hanars committed Jul 24, 2023
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  4. do not fetch tpm data for discovery tag families

    @hanars
    hanars committed Jul 24, 2023
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  5. update tests

    @hanars
    hanars committed Jul 24, 2023
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Commits on Jul 25, 2023

  1. fix unit tests

    @hanars
    hanars committed Jul 25, 2023
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  2. add filtering when no family genes

    @hanars
    hanars committed Jul 25, 2023
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  3. Merge pull request #3510 from broadinstitute/saved-variant-timeout 

    Saved variant timeout
    @hanars
    hanars authored Jul 25, 2023
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  4. Break the EMM/Outliner/Lirical links into mutiple lines.

    @ShifaSZ
    ShifaSZ committed Jul 25, 2023
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  5. initial variant sarch

    @hanars
    hanars committed Jul 25, 2023
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  6. Update default freqs and remove RareGeneSearchLink.

    @ShifaSZ
    ShifaSZ committed Jul 25, 2023
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  7. shared search test behavior

    @hanars
    hanars committed Jul 25, 2023
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  8. cleanup

    @hanars
    hanars committed Jul 25, 2023
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  9. test response

    @hanars
    hanars committed Jul 25, 2023
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  10. fix variantId

    @hanars
    hanars committed Jul 25, 2023
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  11. shared utilities for hailbackend tests

    @hanars
    hanars committed Jul 25, 2023
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  12. Merge branch 'hail-search-shared-tests' of https://github.com/broadin… 

    …stitute/seqr into hail-backend-variant-response
    @hanars
    hanars committed Jul 25, 2023
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  13. fix coverage

    @hanars
    hanars committed Jul 25, 2023
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  14. fix file structure

    @hanars
    hanars committed Jul 25, 2023
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  15. codacy fix

    @hanars
    hanars committed Jul 25, 2023
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Commits on Jul 26, 2023

  1. Merge branch 'hail-search-shared-tests' of https://github.com/broadin… 

    …stitute/seqr into hail-backend-variant-response
    @hanars
    hanars committed Jul 26, 2023
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  2. imporve tests

    @hanars
    hanars committed Jul 26, 2023
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  3. debug test failure

    @hanars
    hanars committed Jul 26, 2023
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  4. debug test failure

    @hanars
    hanars committed Jul 26, 2023
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  5. debug test failure

    @hanars
    hanars committed Jul 26, 2023
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  6. actually commit test family table

    @hanars
    hanars committed Jul 26, 2023
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  7. codacy fixes

    @hanars
    hanars committed Jul 26, 2023
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  8. Merge pull request #3512 from broadinstitute/hail-search-shared-tests 

    shared utilities for hail backend tests
    @hanars
    hanars authored Jul 26, 2023
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  9. Set all freq filter other than topmed to 0.03

    @ShifaSZ
    ShifaSZ committed Jul 26, 2023
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  10. cdacy fix

    @hanars
    hanars committed Jul 26, 2023
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  11. add additional test data

    @hanars
    hanars committed Jul 26, 2023
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  12. Merge branch 'dev' of https://github.com/broadinstitute/seqr into hai… 

    …l-backend-variant-response
    @hanars
    hanars committed Jul 26, 2023
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  13. remove test data

    @hanars
    hanars committed Jul 26, 2023
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  14. clean up transcript formatting

    @hanars
    hanars committed Jul 26, 2023
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  15. Change to use div.

    @ShifaSZ
    ShifaSZ committed Jul 26, 2023
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  16. aiohttp custom json serializer

    @hanars
    hanars committed Jul 26, 2023
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  17. Merge pull request #3511 from broadinstitute/rnaseq-link-new-line 

    Break the RNASeq links into new lines
    @ShifaSZ
    ShifaSZ authored Jul 26, 2023
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  18. clean up classmethods

    @hanars
    hanars committed Jul 26, 2023
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Commits on Jul 27, 2023

  1. Use constants.

    @ShifaSZ
    ShifaSZ committed Jul 27, 2023
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  2. whole project query

    @hanars
    hanars committed Jul 27, 2023
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  3. Merge branch 'dev' into harmonize-outlier-and-gene-search

    @ShifaSZ
    ShifaSZ committed Jul 27, 2023
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  4. add multi project search support

    @hanars
    hanars committed Jul 27, 2023
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  5. Update constants.

    @ShifaSZ
    ShifaSZ committed Jul 27, 2023
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  6. test multi project error

    @hanars
    hanars committed Jul 27, 2023
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  7. Merge pull request #3509 from broadinstitute/harmonize-outlier-and-ge… 

    …ne-search

Update search params for outlier and gene searches.
    @ShifaSZ
    ShifaSZ authored Jul 27, 2023
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Commits on Jul 28, 2023

  1. pr feedback

    @hanars
    hanars committed Jul 28, 2023
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  2. update tests with shared variant data

    @hanars
    hanars committed Jul 28, 2023
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  3. Merge branch 'hail-backend-variant-response' of https://github.com/br… 

    …oadinstitute/seqr into hail-backend-projects-response
    @hanars
    hanars committed Jul 28, 2023
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Commits on Jul 31, 2023

  1. fix: requirements-dev.txt to reduce vulnerabilities 

    The following vulnerabilities are fixed by pinning transitive dependencies:
- https://snyk.io/vuln/SNYK-PYTHON-CERTIFI-5805047
    @snyk-bot
    snyk-bot committed Jul 31, 2023
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  2. fix: requirements.txt to reduce vulnerabilities 

    The following vulnerabilities are fixed by pinning transitive dependencies:
- https://snyk.io/vuln/SNYK-PYTHON-CERTIFI-5805047
- https://snyk.io/vuln/SNYK-PYTHON-CRYPTOGRAPHY-5777683
    @snyk-bot
    snyk-bot committed Jul 31, 2023
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  3. pr feedback

    @hanars
    hanars committed Jul 31, 2023
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  4. Merge pull request #3513 from broadinstitute/hail-backend-variant-res… 

    …ponse

Hail backend: variant response
    @hanars
    hanars authored Jul 31, 2023
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  5. Merge branch 'dev' of https://github.com/broadinstitute/seqr into hai… 

    …l-backend-projects-response
    @hanars
    hanars committed Jul 31, 2023
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  6. fix on success function order

    @hanars
    hanars committed Jul 31, 2023
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Commits on Aug 1, 2023

  1. Merge pull request #3518 from broadinstitute/hail-backend-projects-re… 

    …sponse

Hail backend - multiple projects
    @hanars
    hanars authored Aug 1, 2023
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  2. Merge pull request #3525 from broadinstitute/snyk-fix-ab623dfb3689a22… 

    …cd854d7d8f28df4e2

[Snyk] Security upgrade certifi from 2022.12.7 to 2023.7.22
    @hanars
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  3. Merge pull request #3526 from broadinstitute/snyk-fix-8ddef8f24993a53… 

    …6148b8233c37f3571

[Snyk] Fix for 2 vulnerabilities
    @hanars
    hanars authored Aug 1, 2023
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  4. Merge pull request #3529 from broadinstitute/anvil-loading-e-not-a-fu… 

    …cntion

fix on success function order
    @hanars
    hanars authored Aug 1, 2023
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