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May 2024 update to production (#398)
* Documentation: Add documentation for the staging and production instance (#317) * Add documentation for staging and prod * Modify README.md * code formatting * Grammatical fixes * Add Keycloak related info * Merge outstanding dependency updates (#331) * Bump mongoose from 6.2.11 to 6.4.6 in /server Bumps [mongoose](https://github.com/Automattic/mongoose) from 6.2.11 to 6.4.6. - [Release notes](https://github.com/Automattic/mongoose/releases) - [Changelog](https://github.com/Automattic/mongoose/blob/master/CHANGELOG.md) - [Commits](Automattic/mongoose@6.2.11...6.4.6) --- updated-dependencies: - dependency-name: mongoose dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Bump jose from 2.0.5 to 2.0.6 in /test-node Bumps [jose](https://github.com/panva/jose) from 2.0.5 to 2.0.6. - [Release notes](https://github.com/panva/jose/releases) - [Changelog](https://github.com/panva/jose/blob/v2.0.6/CHANGELOG.md) - [Commits](panva/jose@v2.0.5...v2.0.6) --- updated-dependencies: - dependency-name: jose dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump loader-utils from 1.4.0 to 1.4.2 in /react Bumps [loader-utils](https://github.com/webpack/loader-utils) from 1.4.0 to 1.4.2. - [Release notes](https://github.com/webpack/loader-utils/releases) - [Changelog](https://github.com/webpack/loader-utils/blob/v1.4.2/CHANGELOG.md) - [Commits](webpack/loader-utils@v1.4.0...v1.4.2) --- updated-dependencies: - dependency-name: loader-utils dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump deep-object-diff from 1.1.7 to 1.1.9 in /react Bumps [deep-object-diff](https://github.com/mattphillips/deep-object-diff) from 1.1.7 to 1.1.9. - [Release notes](https://github.com/mattphillips/deep-object-diff/releases) - [Commits](https://github.com/mattphillips/deep-object-diff/commits) --- updated-dependencies: - dependency-name: deep-object-diff dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump decode-uri-component from 0.2.0 to 0.2.2 in /react Bumps [decode-uri-component](https://github.com/SamVerschueren/decode-uri-component) from 0.2.0 to 0.2.2. - [Release notes](https://github.com/SamVerschueren/decode-uri-component/releases) - [Commits](SamVerschueren/decode-uri-component@v0.2.0...v0.2.2) --- updated-dependencies: - dependency-name: decode-uri-component dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump json5 from 1.0.1 to 1.0.2 in /server Bumps [json5](https://github.com/json5/json5) from 1.0.1 to 1.0.2. - [Release notes](https://github.com/json5/json5/releases) - [Changelog](https://github.com/json5/json5/blob/main/CHANGELOG.md) - [Commits](json5/json5@v1.0.1...v1.0.2) --- updated-dependencies: - dependency-name: json5 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump json5 from 1.0.1 to 1.0.2 in /test-node Bumps [json5](https://github.com/json5/json5) from 1.0.1 to 1.0.2. - [Release notes](https://github.com/json5/json5/releases) - [Changelog](https://github.com/json5/json5/blob/main/CHANGELOG.md) - [Commits](json5/json5@v1.0.1...v1.0.2) --- updated-dependencies: - dependency-name: json5 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump json5 from 1.0.1 to 1.0.2 in /react Bumps [json5](https://github.com/json5/json5) from 1.0.1 to 1.0.2. - [Release notes](https://github.com/json5/json5/releases) - [Changelog](https://github.com/json5/json5/blob/main/CHANGELOG.md) - [Commits](json5/json5@v1.0.1...v1.0.2) --- updated-dependencies: - dependency-name: json5 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Add gnomadHet column w/ number of heterozygotes (#334) * Add gnomadHet calculation - Add comments * Change gnomadHet to use PrimaryAF - Kept AF displayed as max between primary and secondary AF * Update tests * Add maleCount field to table rows (#335) * Fix male count (#337) * Add allele count column, remove gnomadHet and male count (#338) * Replace gnomadHet with AC count * Add AC column to frontend - update tests * Update typedefs * Fix graphQL query, frontend query preparing * Hide male count by default * Comment out male count; redundant info * React: Bump timeout from 90 sec to 900 sec (#339) * Bump timeout from 90 sec to 900 sec - Suggested by Matt, Magda (2023-03-13) * Reduce to 5 minutes * Revert "Reduce to 5 minutes" This reverts commit 758f9b9. * Fix comment * CMH Integration (#341) * Fix typo in g4rdAdapter * Add CMH adapter * Add source prefixes; fix error messages * Update docs * Update staging server deploy with CMH vars * Remove cmh env vars from docker prod (for now) * Bump keycloak-connect from 17.0.0 to 21.0.1 in /server (#336) Bumps [keycloak-connect](https://github.com/keycloak/keycloak-nodejs-connect) from 17.0.0 to 21.0.1. - [Release notes](https://github.com/keycloak/keycloak-nodejs-connect/releases) - [Commits](keycloak/keycloak-nodejs-connect@17.0.0...21.0.1) --- updated-dependencies: - dependency-name: keycloak-connect dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump undici from 5.9.1 to 5.19.1 in /server (#333) Bumps [undici](https://github.com/nodejs/undici) from 5.9.1 to 5.19.1. - [Release notes](https://github.com/nodejs/undici/releases) - [Commits](nodejs/undici@v5.9.1...v5.19.1) --- updated-dependencies: - dependency-name: undici dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Rearrange columns, add tooltips (#342) * Add source to duplicate variant check * Move some columns to Case Details * Add tooltips for all the columns * Fix CMH assembly (#343) * Change CMH adapter to GRCh38 * Fix liftOver if no dataForAnnotation * Perform LiftOver for CMH query results (GRCh38 -> h37) (#353) * Add CMHVariantIndelCoordinate type * More comments * Update mongo query to accomodate CMH format * Fix "chrchr" mapping in liftOver * Remove logger debugs * Fix gnomad query to exclude CMH if none found - Fix getCoordinates to not do "chrchr" * Remove ref[0] == alt[0] query check * Bump word-wrap from 1.2.3 to 1.2.4 in /server (#350) 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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump word-wrap from 1.2.3 to 1.2.4 in /test-node (#351) 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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump word-wrap from 1.2.3 to 1.2.4 in /react (#352) 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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump semver from 5.7.1 to 5.7.2 in /test-node (#348) Bumps [semver](https://github.com/npm/node-semver) from 5.7.1 to 5.7.2. - [Release notes](https://github.com/npm/node-semver/releases) - [Changelog](https://github.com/npm/node-semver/blob/v5.7.2/CHANGELOG.md) - [Commits](npm/node-semver@v5.7.1...v5.7.2) --- updated-dependencies: - dependency-name: semver dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump semver from 6.3.0 to 6.3.1 in /server (#347) Bumps [semver](https://github.com/npm/node-semver) from 6.3.0 to 6.3.1. - [Release notes](https://github.com/npm/node-semver/releases) - [Changelog](https://github.com/npm/node-semver/blob/v6.3.1/CHANGELOG.md) - [Commits](npm/node-semver@v6.3.0...v6.3.1) --- updated-dependencies: - dependency-name: semver dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump semver from 5.7.1 to 5.7.2 in /react (#346) Bumps [semver](https://github.com/npm/node-semver) from 5.7.1 to 5.7.2. - [Release notes](https://github.com/npm/node-semver/releases) - [Changelog](https://github.com/npm/node-semver/blob/v5.7.2/CHANGELOG.md) - [Commits](npm/node-semver@v5.7.1...v5.7.2) --- updated-dependencies: - dependency-name: semver dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump tough-cookie from 4.0.0 to 4.1.3 in /react (#345) Bumps [tough-cookie](https://github.com/salesforce/tough-cookie) from 4.0.0 to 4.1.3. - [Release notes](https://github.com/salesforce/tough-cookie/releases) - [Changelog](https://github.com/salesforce/tough-cookie/blob/master/CHANGELOG.md) - [Commits](salesforce/tough-cookie@v4.0.0...v4.1.3) --- updated-dependencies: - dependency-name: tough-cookie dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump tough-cookie from 4.0.0 to 4.1.3 in /server (#344) Bumps [tough-cookie](https://github.com/salesforce/tough-cookie) from 4.0.0 to 4.1.3. - [Release notes](https://github.com/salesforce/tough-cookie/releases) - [Changelog](https://github.com/salesforce/tough-cookie/blob/master/CHANGELOG.md) - [Commits](salesforce/tough-cookie@v4.0.0...v4.1.3) --- updated-dependencies: - dependency-name: tough-cookie dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump mongoose from 6.4.6 to 6.11.3 in /server (#349) * Bump mongoose from 6.4.6 to 6.11.3 in /server Bumps [mongoose](https://github.com/Automattic/mongoose) from 6.4.6 to 6.11.3. - [Release notes](https://github.com/Automattic/mongoose/releases) - [Changelog](https://github.com/Automattic/mongoose/blob/master/CHANGELOG.md) - [Commits](Automattic/mongoose@6.4.6...6.11.3) --- updated-dependencies: - dependency-name: mongoose dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Fix deprecation warning for strictQuery setting --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <mackenzie.frew@sickkids.ca> * Set ApolloServer cache to bounded (#354) * Bump apollo-server-core from 3.10.1 to 3.12.1 in /server (#356) Bumps [apollo-server-core](https://github.com/apollographql/apollo-server/tree/HEAD/packages/apollo-server-core) from 3.10.1 to 3.12.1. - [Release notes](https://github.com/apollographql/apollo-server/releases) - [Commits](https://github.com/apollographql/apollo-server/commits/apollo-server-core@3.12.1/packages/apollo-server-core) --- updated-dependencies: - dependency-name: apollo-server-core dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Add check for hg38 before filtering gene hits (#357) * Bump @babel/traverse from 7.17.3 to 7.23.2 in /react (#360) Bumps [@babel/traverse](https://github.com/babel/babel/tree/HEAD/packages/babel-traverse) from 7.17.3 to 7.23.2. - [Release notes](https://github.com/babel/babel/releases) - [Changelog](https://github.com/babel/babel/blob/main/CHANGELOG.md) - [Commits](https://github.com/babel/babel/commits/v7.23.2/packages/babel-traverse) --- updated-dependencies: - dependency-name: "@babel/traverse" dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump graphql from 16.3.0 to 16.8.1 in /server (#358) * Bump graphql from 16.3.0 to 16.8.1 in /server Bumps [graphql](https://github.com/graphql/graphql-js) from 16.3.0 to 16.8.1. - [Release notes](https://github.com/graphql/graphql-js/releases) - [Commits](graphql/graphql-js@v16.3.0...v16.8.1) --- updated-dependencies: - dependency-name: graphql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Bump @babel/traverse from 7.17.3 to 7.23.2 in /react (#360) Bumps [@babel/traverse](https://github.com/babel/babel/tree/HEAD/packages/babel-traverse) from 7.17.3 to 7.23.2. - [Release notes](https://github.com/babel/babel/releases) - [Changelog](https://github.com/babel/babel/blob/main/CHANGELOG.md) - [Commits](https://github.com/babel/babel/commits/v7.23.2/packages/babel-traverse) --- updated-dependencies: - dependency-name: "@babel/traverse" dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump graphql from 16.3.0 to 16.8.1 in /server Bumps [graphql](https://github.com/graphql/graphql-js) from 16.3.0 to 16.8.1. - [Release notes](https://github.com/graphql/graphql-js/releases) - [Commits](graphql/graphql-js@v16.3.0...v16.8.1) --- updated-dependencies: - dependency-name: graphql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <mackenzie.frew@sickkids.ca> * Bump undici from 5.19.1 to 5.26.3 in /server (#359) * Bump undici from 5.19.1 to 5.26.3 in /server Bumps [undici](https://github.com/nodejs/undici) from 5.19.1 to 5.26.3. - [Release notes](https://github.com/nodejs/undici/releases) - [Commits](nodejs/undici@v5.19.1...v5.26.3) --- updated-dependencies: - dependency-name: undici dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump @babel/traverse from 7.17.3 to 7.23.2 in /react (#360) Bumps [@babel/traverse](https://github.com/babel/babel/tree/HEAD/packages/babel-traverse) from 7.17.3 to 7.23.2. - [Release notes](https://github.com/babel/babel/releases) - [Changelog](https://github.com/babel/babel/blob/main/CHANGELOG.md) - [Commits](https://github.com/babel/babel/commits/v7.23.2/packages/babel-traverse) --- updated-dependencies: - dependency-name: "@babel/traverse" dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump graphql from 16.3.0 to 16.8.1 in /server (#358) * Bump graphql from 16.3.0 to 16.8.1 in /server Bumps [graphql](https://github.com/graphql/graphql-js) from 16.3.0 to 16.8.1. - [Release notes](https://github.com/graphql/graphql-js/releases) - [Commits](graphql/graphql-js@v16.3.0...v16.8.1) --- updated-dependencies: - dependency-name: graphql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Bump @babel/traverse from 7.17.3 to 7.23.2 in /react (#360) Bumps [@babel/traverse](https://github.com/babel/babel/tree/HEAD/packages/babel-traverse) from 7.17.3 to 7.23.2. - [Release notes](https://github.com/babel/babel/releases) - [Changelog](https://github.com/babel/babel/blob/main/CHANGELOG.md) - [Commits](https://github.com/babel/babel/commits/v7.23.2/packages/babel-traverse) --- updated-dependencies: - dependency-name: "@babel/traverse" dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump graphql from 16.3.0 to 16.8.1 in /server Bumps [graphql](https://github.com/graphql/graphql-js) from 16.3.0 to 16.8.1. - [Release notes](https://github.com/graphql/graphql-js/releases) - [Commits](graphql/graphql-js@v16.3.0...v16.8.1) --- updated-dependencies: - dependency-name: graphql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <mackenzie.frew@sickkids.ca> * Bump undici from 5.19.1 to 5.26.3 in /server Bumps [undici](https://github.com/nodejs/undici) from 5.19.1 to 5.26.3. - [Release notes](https://github.com/nodejs/undici/releases) - [Commits](nodejs/undici@v5.19.1...v5.26.3) --- updated-dependencies: - dependency-name: undici dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <mackenzie.frew@sickkids.ca> * Bump @babel/traverse from 7.17.9 to 7.23.2 in /server (#361) * Bump @babel/traverse from 7.17.9 to 7.23.2 in /server Bumps [@babel/traverse](https://github.com/babel/babel/tree/HEAD/packages/babel-traverse) from 7.17.9 to 7.23.2. - [Release notes](https://github.com/babel/babel/releases) - [Changelog](https://github.com/babel/babel/blob/main/CHANGELOG.md) - [Commits](https://github.com/babel/babel/commits/v7.23.2/packages/babel-traverse) --- updated-dependencies: - dependency-name: "@babel/traverse" dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump graphql from 16.3.0 to 16.8.1 in /server (#358) * Bump graphql from 16.3.0 to 16.8.1 in /server Bumps [graphql](https://github.com/graphql/graphql-js) from 16.3.0 to 16.8.1. - [Release notes](https://github.com/graphql/graphql-js/releases) - [Commits](graphql/graphql-js@v16.3.0...v16.8.1) --- updated-dependencies: - dependency-name: graphql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Bump @babel/traverse from 7.17.3 to 7.23.2 in /react (#360) Bumps [@babel/traverse](https://github.com/babel/babel/tree/HEAD/packages/babel-traverse) from 7.17.3 to 7.23.2. - [Release notes](https://github.com/babel/babel/releases) - [Changelog](https://github.com/babel/babel/blob/main/CHANGELOG.md) - [Commits](https://github.com/babel/babel/commits/v7.23.2/packages/babel-traverse) --- updated-dependencies: - dependency-name: "@babel/traverse" dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump graphql from 16.3.0 to 16.8.1 in /server Bumps [graphql](https://github.com/graphql/graphql-js) from 16.3.0 to 16.8.1. - [Release notes](https://github.com/graphql/graphql-js/releases) - [Commits](graphql/graphql-js@v16.3.0...v16.8.1) --- updated-dependencies: - dependency-name: graphql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <mackenzie.frew@sickkids.ca> * Bump undici from 5.19.1 to 5.26.3 in /server (#359) * Bump undici from 5.19.1 to 5.26.3 in /server Bumps [undici](https://github.com/nodejs/undici) from 5.19.1 to 5.26.3. - [Release notes](https://github.com/nodejs/undici/releases) - [Commits](nodejs/undici@v5.19.1...v5.26.3) --- updated-dependencies: - dependency-name: undici dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump @babel/traverse from 7.17.3 to 7.23.2 in /react (#360) Bumps [@babel/traverse](https://github.com/babel/babel/tree/HEAD/packages/babel-traverse) from 7.17.3 to 7.23.2. - [Release notes](https://github.com/babel/babel/releases) - [Changelog](https://github.com/babel/babel/blob/main/CHANGELOG.md) - [Commits](https://github.com/babel/babel/commits/v7.23.2/packages/babel-traverse) --- updated-dependencies: - dependency-name: "@babel/traverse" dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump graphql from 16.3.0 to 16.8.1 in /server (#358) * Bump graphql from 16.3.0 to 16.8.1 in /server Bumps [graphql](https://github.com/graphql/graphql-js) from 16.3.0 to 16.8.1. - [Release notes](https://github.com/graphql/graphql-js/releases) - [Commits](graphql/graphql-js@v16.3.0...v16.8.1) --- updated-dependencies: - dependency-name: graphql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Bump @babel/traverse from 7.17.3 to 7.23.2 in /react (#360) Bumps [@babel/traverse](https://github.com/babel/babel/tree/HEAD/packages/babel-traverse) from 7.17.3 to 7.23.2. - [Release notes](https://github.com/babel/babel/releases) - [Changelog](https://github.com/babel/babel/blob/main/CHANGELOG.md) - [Commits](https://github.com/babel/babel/commits/v7.23.2/packages/babel-traverse) --- updated-dependencies: - dependency-name: "@babel/traverse" dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump graphql from 16.3.0 to 16.8.1 in /server Bumps [graphql](https://github.com/graphql/graphql-js) from 16.3.0 to 16.8.1. - [Release notes](https://github.com/graphql/graphql-js/releases) - [Commits](graphql/graphql-js@v16.3.0...v16.8.1) --- updated-dependencies: - dependency-name: graphql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <mackenzie.frew@sickkids.ca> * Bump undici from 5.19.1 to 5.26.3 in /server Bumps [undici](https://github.com/nodejs/undici) from 5.19.1 to 5.26.3. - [Release notes](https://github.com/nodejs/undici/releases) - [Commits](nodejs/undici@v5.19.1...v5.26.3) --- updated-dependencies: - dependency-name: undici dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <mackenzie.frew@sickkids.ca> * Bump @babel/traverse from 7.17.9 to 7.23.2 in /server Bumps [@babel/traverse](https://github.com/babel/babel/tree/HEAD/packages/babel-traverse) from 7.17.9 to 7.23.2. - [Release notes](https://github.com/babel/babel/releases) - [Changelog](https://github.com/babel/babel/blob/main/CHANGELOG.md) - [Commits](https://github.com/babel/babel/commits/v7.23.2/packages/babel-traverse) --- updated-dependencies: - dependency-name: "@babel/traverse" dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <mackenzie.frew@sickkids.ca> * Bump browserify-sign from 4.2.1 to 4.2.2 in /react (#363) Bumps [browserify-sign](https://github.com/crypto-browserify/browserify-sign) from 4.2.1 to 4.2.2. - [Changelog](https://github.com/browserify/browserify-sign/blob/main/CHANGELOG.md) - [Commits](browserify/browserify-sign@v4.2.1...v4.2.2) --- updated-dependencies: - dependency-name: browserify-sign dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump chromedriver from 100.0.0 to 119.0.1 in /server (#364) Bumps [chromedriver](https://github.com/giggio/node-chromedriver) from 100.0.0 to 119.0.1. - [Commits](giggio/node-chromedriver@100.0.0...119.0.1) --- updated-dependencies: - dependency-name: chromedriver dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump axios from 0.26.1 to 1.6.0 in /server (#365) * Bump axios from 0.26.1 to 1.6.0 in /server Bumps [axios](https://github.com/axios/axios) from 0.26.1 to 1.6.0. - [Release notes](https://github.com/axios/axios/releases) - [Changelog](https://github.com/axios/axios/blob/v1.x/CHANGELOG.md) - [Commits](axios/axios@v0.26.1...v1.6.0) --- updated-dependencies: - dependency-name: axios dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Update jest config for new axios version --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <mackenzie.frew@sickkids.ca> * Add PT Pagination support for G4RD Staging (#366) * Add fetchPhenotipsVariant for collecting paginated results * Don't infinite loop * Finish pagination support for G4RD * Fix linting issues * Formatting * Fix test suite * Server: fix pagination bugs with G4RD (#369) * Fix searching for X, Y chromosomes by position * Add "pagination" for patient queries * Linting and formatting * Use function to get auth token to prevent token expiry mid-query * Better debug messages * format * Add retries to fetchPhenotipsVariants (#370) - Add check for failed patient query to prevent uncaught exception * Server: formatting * Handle null params passed to transform func (#371) * TEMPORARY: trace GC in staging/prod server (#372) * TEMPORARY: Add heap profiler for staging/prod (#373) * TEMPORARY: inspect-brk * TEMPORARY: inspect-brk to localhost * TEMPORARY: put inspect back to global * TEMPORARY: revert to inspect, not inspect-brk * TEMPORARY: make smaller heap to debug * TEMPORARY: smaller heap limit * Remove node debugging flags * All: Merge outstanding dependency updates (#378) * Bump follow-redirects from 1.14.9 to 1.15.4 in /react Bumps [follow-redirects](https://github.com/follow-redirects/follow-redirects) from 1.14.9 to 1.15.4. - [Release notes](https://github.com/follow-redirects/follow-redirects/releases) - [Commits](follow-redirects/follow-redirects@v1.14.9...v1.15.4) --- updated-dependencies: - dependency-name: follow-redirects dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump follow-redirects from 1.15.3 to 1.15.4 in /server Bumps [follow-redirects](https://github.com/follow-redirects/follow-redirects) from 1.15.3 to 1.15.4. - [Release notes](https://github.com/follow-redirects/follow-redirects/releases) - [Commits](follow-redirects/follow-redirects@v1.15.3...v1.15.4) --- updated-dependencies: - dependency-name: follow-redirects dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump undici from 5.26.3 to 5.28.3 in /server Bumps [undici](https://github.com/nodejs/undici) from 5.26.3 to 5.28.3. - [Release notes](https://github.com/nodejs/undici/releases) - [Commits](nodejs/undici@v5.26.3...v5.28.3) --- updated-dependencies: - dependency-name: undici dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump ip from 2.0.0 to 2.0.1 in /server Bumps [ip](https://github.com/indutny/node-ip) from 2.0.0 to 2.0.1. - [Commits](indutny/node-ip@v2.0.0...v2.0.1) --- updated-dependencies: - dependency-name: ip dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump ip from 1.1.5 to 1.1.9 in /react Bumps [ip](https://github.com/indutny/node-ip) from 1.1.5 to 1.1.9. - [Commits](indutny/node-ip@v1.1.5...v1.1.9) --- updated-dependencies: - dependency-name: ip dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Frontend: Update search bar to allow search by position only (#382) * Rename from GeneSearch to GeneNameSearch * Move search component to separate folder * Create GenePositionSearch component * Update validator to fail on first rule break * Create combined search bar * Fix no variants found error * Use combobox instead of select element * WIP making new dropdown for search bar styling * Fix styling * Adjust spacing * Formatting + linting * Server formatting * React: Remove errant console.log * React/Server: Add Gene Name to results table (#383) * Add Gene Name to results table * Formatting * Server: implement support for Pagination API on CMH (#390) * Update /rest/variants/match request * Do the pagination * Update to support CMH * Fix 2nd page fetch fail * Add liftover for positions * Fix requests * CI/CD: Fix deprecated workflow commands in GitHub Actions workflows (#391) * Replace deprecated set-output with GITHUB_OUTPUT env file append * Update actions versions * Undo SSH configure workflow change (#392) * Server: Fix Gnomad annotation bug with GRCh38 + CMH (#395) * Fix form to clear gene when switching assemblies * Update Gnomad model handling to use factory functions * format * All: merge outstanding dependencies (#396) * Bump jose from 2.0.6 to 2.0.7 in /test-node Bumps [jose](https://github.com/panva/jose) from 2.0.6 to 2.0.7. - [Release notes](https://github.com/panva/jose/releases) - [Changelog](https://github.com/panva/jose/blob/v2.0.7/CHANGELOG.md) - [Commits](panva/jose@v2.0.6...v2.0.7) --- updated-dependencies: - dependency-name: jose dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump follow-redirects from 1.15.4 to 1.15.6 in /server Bumps [follow-redirects](https://github.com/follow-redirects/follow-redirects) from 1.15.4 to 1.15.6. - [Release notes](https://github.com/follow-redirects/follow-redirects/releases) - [Commits](follow-redirects/follow-redirects@v1.15.4...v1.15.6) --- updated-dependencies: - dependency-name: follow-redirects dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump follow-redirects from 1.15.4 to 1.15.6 in /react Bumps [follow-redirects](https://github.com/follow-redirects/follow-redirects) from 1.15.4 to 1.15.6. - [Release notes](https://github.com/follow-redirects/follow-redirects/releases) - [Commits](follow-redirects/follow-redirects@v1.15.4...v1.15.6) --- updated-dependencies: - dependency-name: follow-redirects dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump express from 4.17.3 to 4.19.2 in /server Bumps [express](https://github.com/expressjs/express) from 4.17.3 to 4.19.2. - [Release notes](https://github.com/expressjs/express/releases) - [Changelog](https://github.com/expressjs/express/blob/master/History.md) - [Commits](expressjs/express@4.17.3...4.19.2) --- updated-dependencies: - dependency-name: express dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Bump express from 4.17.3 to 4.19.2 in /react Bumps [express](https://github.com/expressjs/express) from 4.17.3 to 4.19.2. - [Release notes](https://github.com/expressjs/express/releases) - [Changelog](https://github.com/expressjs/express/blob/master/History.md) - [Commits](expressjs/express@4.17.3...4.19.2) --- updated-dependencies: - dependency-name: express dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump express from 4.17.3 to 4.19.2 in /test-node Bumps [express](https://github.com/expressjs/express) from 4.17.3 to 4.19.2. - [Release notes](https://github.com/expressjs/express/releases) - [Changelog](https://github.com/expressjs/express/blob/master/History.md) - [Commits](expressjs/express@4.17.3...4.19.2) --- updated-dependencies: - dependency-name: express dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Bump undici from 5.28.3 to 5.28.4 in /server Bumps [undici](https://github.com/nodejs/undici) from 5.28.3 to 5.28.4. - [Release notes](https://github.com/nodejs/undici/releases) - [Commits](nodejs/undici@v5.28.3...v5.28.4) --- updated-dependencies: - dependency-name: undici dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump tar from 6.1.11 to 6.2.1 in /react Bumps [tar](https://github.com/isaacs/node-tar) from 6.1.11 to 6.2.1. - [Release notes](https://github.com/isaacs/node-tar/releases) - [Changelog](https://github.com/isaacs/node-tar/blob/main/CHANGELOG.md) - [Commits](isaacs/node-tar@v6.1.11...v6.2.1) --- updated-dependencies: - dependency-name: tar dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump mysql2 from 2.3.3 to 3.9.7 in /test-node Bumps [mysql2](https://github.com/sidorares/node-mysql2) from 2.3.3 to 3.9.7. - [Release notes](https://github.com/sidorares/node-mysql2/releases) - [Changelog](https://github.com/sidorares/node-mysql2/blob/master/Changelog.md) - [Commits](sidorares/node-mysql2@v2.3.3...v3.9.7) --- updated-dependencies: - dependency-name: mysql2 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Bump ejs from 3.1.7 to 3.1.10 in /react Bumps [ejs](https://github.com/mde/ejs) from 3.1.7 to 3.1.10. - [Release notes](https://github.com/mde/ejs/releases) - [Commits](mde/ejs@v3.1.7...v3.1.10) --- updated-dependencies: - dependency-name: ejs dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Add CMH environment to node prod workflow (#397) --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Jenny <ziyixu686@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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