bihealth / varfish-server

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LAST BUILD ON BRANCH fix-stuff

branch: fix-stuff

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• fix-stuff
• 102-word-templates
• 104-remove-vendored-assets
• 110-public-docker-deployment
• 115-fix-large-query
• 116-117-fix-search-sentry-integrations
• 123-129-docker-container-problems
• 125-undefined-variable-bug
• 127-result-rows-not-colored-any-more-in-v0.23.4
• 130-mismatch-of-root-and-admin-user
• 136-sodar-core-hotfix-remote-sync
• 150-adjust-usage-of-base-template-depending-on-block-extended
• 156-inconsistent-ensembl-info-display​
• 158-gender-cannot-be-edited-by-clinvar-submission-editor
• 158-gender-cannot-be-edited-by-clinvar-submission-editor-backport
• 161-fix-unlogged-tables
• 170-upgrade-sodar-core
• 177-document-how-to-update-disease-omim-and-hpo-databases
• 207-fix-importer-perms
• 208-complete-migrations-to-iconify
• 215-fix-varfish-kiosk
• 219-genomebuild-field
• 223-beacon-icon-broken-in-current-varfish-kiosk
• 234-too-large-data-sets-case-import-step-to-fail
• 237-varfish-irresponsive-after-deleting-a-sample-uploaded-to-category
• 238-bug-in-search-box
• 239-bug-in-flagging-commeting-cnv
• 240-fix-mutation-taster
• 241-split-union-queries
• 259-select-multiple-rows-in-results-to-create-same-annotation
• 267-extend-documentation-for-developers
• 275-skip-codacy
• 283-clinvar-submission-fixes
• 284-replace-wrongly-migrated-icons
• 289-phenotype-shortcut-buttons
• 296-ensure-that-filter-by-presence-in-clinvar-works-as-expected-backport
• 297-make-flags-and-color-codes-consistent
• 297-make-flags-and-color-codes-consistent-backport
• 302-clinvar-export-lazy-annotations
• 304-improve-project-list-performance
• 304-speedup-project-overview
• 319-properly-call-cadd-rest-api
• 32-build-background-database-for-structural-variants
• 323-action-check-trailers
• 323-patch-trailer-annotation
• 325-add-mitochondrial-inheritance
• 328-fix-variant-annotation-export
• 328-fix-variant-annotation-export-2
• 332-finalizing-rest-api
• 332-small-variant-query-rest-api
• 333-api-versioning
• 337-postgres-ci
• 338-postgres-14-support
• 344-easy-variant-annotation-update
• 348-complete-case-detail-variant-annotation
• 359-acmg-classification-fix
• 363-remove-display-hgmd-public-membership
• 367-functional-query-rest-api
• 367-query-settings-rest-api
• 371-load-prefetched-results-performance
• 371-optimize-rest
• 374-cap-project-cohort-queries
• 379-fix-closing-wrapper
• 386-fix-cnv-import
• 402-fixing-rest-query-presets-problems
• 404-fix-case-crash
• 406-prepare-varfish-athenea-release-candidate-v
• 409-remove-small-ui-glitches
• 410-prepare-initial-data-release-for-v
• 412-fix-multi-variant-annotation-bug
• 417-attributeerror-caseexporterxlsx-object-has-no-attribute-_get_genomebuild
• 419-typeerror-_closingwrapper-object-is-not-iterable
• 424-release-rc-v
• 428-document-casesmall-variant-qc-json-format
• 430-add-support-for-creating-database-dumps-easily
• 431-only-superusers-can-access-the-globa-import-info
• 432-ge-panelapp-gene-symbols-not-found
• 437-release-rc-v
• 450-extra-annotations-for-grch37-use-wrong-coordinates
• 450-extra-annotations-for-grch37-use-wrong-coordinates-backport
• 459-login-does-not-work-when-character-is-part-of-user-name
• 459-login-does-not-work-when-character-is-part-of-user-name-backport
• 464-clinvar-pathogenic-filter-apparently-does-not-work
• 464-clinvar-pathogenic-filter-apparently-does-not-work-backport
• 470-provide-easy-access-to-find-other-carriers-of-a-variant
• 470-provide-easy-access-to-find-other-carriers-of-a-variant-backport
• 472-fix-varfish-annotator-documentation
• 478-cannot-submit-to-cadd-from-project-based-filtration
• 478-cannot-submit-to-cadd-from-project-based-filtration-backport
• 479-v1-release-should-be-anthenea-but-is-athenea
• 479-v1-release-should-be-anthenea-but-is-athenea-backport
• 502-logic-error-in-query-generation-for-flags
• 502-logic-error-in-query-generation-for-flags-backport
• 508-filter-display-button-broken-in-microsoft-edge-and-chrome
• 508-filter-display-button-broken-in-microsoft-edge-and-chrome-backport
• 509-backport-prioritization-with-mutationtaster-is-broken
• 509-prioritization-with-mutationtaster-is-broken
• 516-backport-igv-dropdown-menu-broken
• 516-igv-dropdown-menu-broken
• 523-variantvalidator-query-broken
• 523-variantvalidator-query-broken-backport
• 53-55-refurbish-annotation-overview
• 531-updates-scripts-in-utility
• 533-improve-developer-setup-documentation
• 537-do-not-check-trailers-for-dependabot-commits
• 543-anthenea-stable-release-v1-2-1
• 546-gnomad-frequencies-only-present-for-chr1-in-varfish-annotator-db-20210728-grch378dbh2
• 551-update-manual-for-v1-2-1-anthenea-release
• 562-distinct-de-novo-inheritance-preset-setting
• 563-implement-filter-page-in-vue-js
• 565-clinvar-based-filtration-leads-to-duplicate-lines
• 565-clinvar-based-filtration-leads-to-duplicate-lines-backport
• 570-problem-in-taskssodar_sync_remote-without-a-remote
• 570-problem-in-taskssodar_sync_remote-without-a-remote-backport
• 573-implement-lookup-second-hit-for-small-variants
• 576-linkout-to-hgmd-professional
• 576-linkout-to-hgmd-professional-backport
• 579-allow-to-mark-cases-for-exclusion-in-background-database
• 597-exac-and-thousand-genomes-settings-not-shown-in-frequency-tab-for-grch37
• 597-exac-and-thousand-genomes-settings-not-shown-in-frequency-tab-for-grch37-backport
• 602-anthenea-stable-release-v1.2.2
• 607-report-error-in-the-form-template-if-genomebuild-variable-is-not-set
• 607-report-error-in-the-form-template-if-genomebuild-variable-is-not-set-backport
• 613-make-keyvalue-template-filter-not-crash-applications
• 616-add-simple-sv-filtration-filter-presets-and-adjust-defaults
• 620-display-disease-gene-flag-in-sv-results
• 622-pli-score-displayed-incorrectly
• 635-clinvar-query-is-very-slow-backport
• 639-switch-linting-from-codacy-to-default-python-tools
• 640-improve-clinvar-display-for-various-issues
• 641-adjust-setting-maximal-variants-to-display-to-1000-backport
• 646-hemizygous-count-not-displayed-in-fold-out
• 646-hemizygous-count-not-displayed-in-fold-out-backport
• 660-docker-builds-broken-because-of-conda-dependency
• 660-docker-builds-broken-because-of-conda-dependency-backport
• 663-bump-pythondependencies
• 668-cannot-remove-hpo-terms-from-sample-in-clinvar-submission
• 668-cannot-remove-hpo-terms-from-sample-in-clinvar-submission-backport
• 673-pink-colored-wip-result-rows
• 673-pink-colored-wip-result-rows-backport
• 677-adjust-clinvar-xml-generation-to-latest-update
• 677-adjust-clinvar-xml-generation-to-latest-update-backport
• 686-bug-in-refresh_individual_sex_affected
• 686-bug-in-refresh_individual_sex_affected-backport
• 689-do-not-write-out-observedintraitsettraitname-in-clinvar-xml-export
• 689-do-not-write-out-observedintraitsettraitname-in-clinvar-xml-export-backport
• 692-add-javascript-unit-tests-for-clinvar_export-vuejs-app
• 693-clinvar-link-redirects-to-coordinate-and-not-vcv-entry
• 693-clinvar-link-redirects-to-coordinate-and-not-vcv-entry-backport
• 701-add-code-coverage-via-codecov
• 713-deleting-clinvar-export-submission-sets-does-not-work
• 716-remove-dependency-on-bootstrap-vue
• 720-migrate-from-vuex-to-pinia
• 748-linkout-to-genoox-franklin-anthenea
• 79-better-docs
• 80-copy-case-uuid
• 81-not-hom-alt-filter
• 86-celery-sv-cleanup
• 92-bump-dependencies
• 96-fix-disabled-site-wide-apps
• add-missing-migrations
• admin-install-minor-typo
• ahujameg-226-clinvar-xsd-update
• anthenea
• athenea
• bump-docker
• case-list-bug
• codacy-sarif
• coveralls-coverage
• dependabot/npm_and_yarn/varfish/vueapp/ansi-html-and-webpack-dev-server--removed
• dependabot/npm_and_yarn/varfish/vueapp/async-2.6.4
• dependabot/npm_and_yarn/varfish/vueapp/color-string-1.6.0
• dependabot/npm_and_yarn/varfish/vueapp/eventsource-1.1.1
• dependabot/npm_and_yarn/varfish/vueapp/eventsource-1.1.2
• dependabot/npm_and_yarn/varfish/vueapp/follow-redirects-1.14.7
• dependabot/npm_and_yarn/varfish/vueapp/follow-redirects-1.14.8
• dependabot/npm_and_yarn/varfish/vueapp/jsdom-and-vue/cli-plugin-unit-jest-16.7.0
• dependabot/npm_and_yarn/varfish/vueapp/minimist-1.2.6
• dependabot/npm_and_yarn/varfish/vueapp/node-fetch-2.6.7
• dependabot/npm_and_yarn/varfish/vueapp/postcss-7.0.39
• dependabot/npm_and_yarn/varfish/vueapp/shell-quote-1.7.3
• dependabot/npm_and_yarn/varfish/vueapp/ssri-6.0.2
• dependabot/npm_and_yarn/varfish/vueapp/terser-4.8.1
• dependabot/npm_and_yarn/varfish/vueapp/tmpl-1.0.5
• dependabot/npm_and_yarn/varfish/vueapp/url-parse-1.5.10
• dependabot/npm_and_yarn/varfish/vueapp/url-parse-1.5.3
• dependabot/npm_and_yarn/varfish/vueapp/url-parse-1.5.7
• dependabot/npm_and_yarn/varfish/vueapp/ws-5.2.3
• docs-beacon-site
• extending-developers-documentation
• fix-broken-structural-variant-details
• fix-dockerfile-icon-pulling
• fix-kiosk-bug
• fix-mt-and-igv-dropdown
• fix-svs-case-detail-page
• fix/docker-migrate
• fixing-broken-sv-annotation
• github-ci
• github-ci-bug
• head-include
• holtgrewe-patch-1
• main
• master
• postgres-12-docker
• python-3.10-in-ci
• release-v0.23
• release-v0.23.1
• release-v1-1-4
• release-v1-2-0
• revise-developer-manual
• test
• update-docker-entrypoint-with-numbers-of-gunicorn-workers
• v0.23.8
• v0.23.9
• v1.1.1
• v1.1.2
• v1.1.3
• v1.1.4
• v1.2.0
• v1.2.1
• v1.2.2
• varfish-course
• various-link-outs

Merge f2c45a9b7 into 3eb9a2673