Broad 2025-02-27#4
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…h reference files for IGV panels #1
Adding user agent header when fetching resources from IGV (#1)
* add human-readable error for misconfigured PDO * user friendly error for malformed project URL * correctly format error responses * roperly handle single project PDO * codacy * correctly handle multi family multi data types comp het family filter * test case * Bump aiohttp from 3.10.2 to 3.10.11 in /hail_search Bumps [aiohttp](https://github.com/aio-libs/aiohttp) from 3.10.2 to 3.10.11. - [Release notes](https://github.com/aio-libs/aiohttp/releases) - [Changelog](https://github.com/aio-libs/aiohttp/blob/master/CHANGES.rst) - [Commits](aio-libs/aiohttp@v3.10.2...v3.10.11) --- updated-dependencies: - dependency-name: aiohttp dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * add errors for missing airtable gregor metadata * better error messages * fix tests * error for totally missing metadata * rename submit_to_clivar to report * update tests * update note ui * include note in reports * test report notes * fix kubectl helper script * limit internal family field updates to analysts * permission individual fields * local user columsn * explicitly set PDO status for sex/relatedness PDOs * add vlm route prefix * typo * update test * bump changelog * validated families have affected individuals * remove create from bulk family ui * disabe create empty family * check affected status before generating loading pedigree * fix locked dependency vulnerabilities * remove unused vulnerable dependency * bump webpack * correctly show conditional report pages in header * do jnot reset gencode from udpate_all_reference_data * parse query params * get stats * formatted results * raise vlm coverage needed * make vcf message for loading data shared (broadinstitute#4501) * make vcf message for loading data shared * fix * use read table instead of query table * local install download postgres init script * no default node * test vlm match endpoint * test vlm match endpoint * test macth format errors * test settings * clean up * codacy * codacy * additional check for invalid pdo configuration * hide gene search link on variant lookup page * change loading warning to "may" * update local install test * shared helper function * fix local install test * fix local install test * fix local install test * fix local install test * fix local install test * local install test setup * fix local install test * Updates for new reference data structure (broadinstitute#4509) * move reference data fixtures * Update mito table * Update tables * missed one * Update fixtures with emptry struct * update mito * Revert to existing fixtures :/ * Revert all fixture changes * fixtures * not correct * Correct 37 annotations table to account for missing dbnsfp * Fix issue with coalesced missing values * remove PATHOGENICTY_SORT_KEY reference * Fix incorrectly annotated type :/ * use liftover * fix liftover * fix liftover atomicity * run vlm tests when fixture data updates * update tests * test variant is requested on build missing froms eqr * do not use query_table for variant id queries * return seqr url for valid build * fix half counting of homs * fix chrom variant id format * dont double count homs in total * separate agg for variant lookup project data * actually filter to alleles * multi build abstraction * kwarg cleanup * clean up * clean up * actually query lift version * codacy fix * track build lifted guid buid * Bump django from 4.2.16 to 4.2.17 Bumps [django](https://github.com/django/django) from 4.2.16 to 4.2.17. - [Commits](django/django@4.2.16...4.2.17) --- updated-dependencies: - dependency-name: django dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * show lookup genome version in ui * fix: requirements-dev.txt to reduce vulnerabilities The following vulnerabilities are fixed by pinning transitive dependencies: - https://snyk.io/vuln/SNYK-PYTHON-DJANGO-8456315 - https://snyk.io/vuln/SNYK-PYTHON-DJANGO-8456316 * update readme (broadinstitute#4532) * update readme * Update README.md * Update language * Further tweak * Bump nanoid from 3.3.6 to 3.3.8 in /ui Bumps [nanoid](https://github.com/ai/nanoid) from 3.3.6 to 3.3.8. - [Release notes](https://github.com/ai/nanoid/releases) - [Changelog](https://github.com/ai/nanoid/blob/main/CHANGELOG.md) - [Commits](ai/nanoid@3.3.6...3.3.8) --- updated-dependencies: - dependency-name: nanoid dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * fix: requirements.txt to reduce vulnerabilities The following vulnerabilities are fixed by pinning transitive dependencies: - https://snyk.io/vuln/SNYK-PYTHON-DJANGO-8456315 - https://snyk.io/vuln/SNYK-PYTHON-DJANGO-8456316 * 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-DJANGO-8456315 - https://snyk.io/vuln/SNYK-PYTHON-DJANGO-8456316 - https://snyk.io/vuln/SNYK-PYTHON-REQUESTS-6928867 - https://snyk.io/vuln/SNYK-PYTHON-SQLPARSE-6615674 - https://snyk.io/vuln/SNYK-PYTHON-ZIPP-7430899 * fix: requirements.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-DJANGO-8456315 - https://snyk.io/vuln/SNYK-PYTHON-DJANGO-8456316 - https://snyk.io/vuln/SNYK-PYTHON-REQUESTS-6928867 - https://snyk.io/vuln/SNYK-PYTHON-SQLPARSE-6615674 - https://snyk.io/vuln/SNYK-PYTHON-ZIPP-7430899 * Improve status designation for in progress DAG (broadinstitute#4539) * fix allowed filter values for sv search * fix tests * filter project genome build for data loading * prompt VLM users to add phenotype and extra questions (broadinstitute#4535) * send slack notification on failed airtabe record update * make relatedness check file downloadable (broadinstitute#4542) * upload relatedness check file to slack instead of adding the link * whitespace * add timeout s * use downloadable link * Update check_for_new_samples_from_pipeline.py * Update communication_utils.py * make gene order in search deterministic * only allow mee submission for valid seqr genes * fix iranome link * fix hail search tests * correctly checkin index file is updates * single loading error per project * handle missing lifted variant * fix super * testmutli build lookup * update action to increment seqr and hail-search chart versions (broadinstitute#4534) * update action to increment seqr and hail-search chart versions * more explicit steps * update hail-search chart * remove prerelease-tag * hail search * update lookup test * include analysed by in family metadata * update fixtures (broadinstitute#4563) * add loading failed analysis status * update failed analysis status for failed families * show family sort in search ui * add family sort * remove clinvar tag description * shared notification url formatting * better identity check for saved searches with gene list * add dropdown for loadable vcf * update docs * load availabel VCFS from loading dir * loading vcfs local only * add test * fix test * correctly set allow missing * move utility tests into usage test * clean up * pr feedback * fix prod-release chart name bug (broadinstitute#4579) * trigger DELETE_FAMILIES dag on transfer families command (broadinstitute#4565) * use selectedMOIs from saved search * do not include selectedMOIs in search locus rawItems * v1 * test * review * supers * review comments, tidier * test inheritance * pr comments wip * share as much as i can in airflowtestcase * private * self review * share even more code * fix codacy and test * tiny diff changes * tiny diff changes * tiny diff changes * oops * oops * pr comments * codacy? * some pr comments and variable path change * remove kwargs from setUp * add selectedMOIs to saved search (broadinstitute#4570) * add selectedMOIs to saved search * componentdidupdate * lockfile * it WORKS * single reduce method * update gcnv loading pedigree path * add error handling for reload annotations failure * use smaller batch size for updated annotations query * handle emaill error log * fix typo * update faq (broadinstitute#4543) * update faq for uploading new data * fix add data faq * additional faq * report pipeline validation errors from seqr (broadinstitute#4581) * first pass report errors * kwargs * make one ls call * write files * test cases cover most new code * mock file stuff * review comments * move up new sample logic * clean up email template * better logging for family reloading * only reload families with new samples * clearer error log * clearer error log * accurately sort variant ids * group varint id intervals * group lookup calls by chromosome * update tests * add local check samples test * correctly check airtable * update tests * standardize pipeline options in Load Data UI (broadinstitute#4603) * fix load data dag parameters * s * a few more * pr comments * oops * more * order on ui * only include passign samples in data loading * properly handle regex for directory name * am run success checks before validation failure checks * actually move validation call to end * report malformed validation error * increase lookup chunk size * codacy fix * tweak lookup chunk size * Remove trailing whitespace * Made changes to Dockerfile to push to our repo. Fixed one line to make a directory that appears to be required for now. --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: hanars <hsnow@broadinstitute.org> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Julia Klugherz <juliaklugherz@gmail.com> Co-authored-by: Benjamin Blankenmeister <b.p.blankenmeister@gmail.com> Co-authored-by: snyk-bot <snyk-bot@snyk.io> Co-authored-by: Benjamin Blankenmeister <bblanken@broadinstitute.org> Co-authored-by: Michael Li <7130126+mike8115@users.noreply.github.com>
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