Frontend: Update search bar to allow search by position only #382
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
frewmack
added a commit
that referenced
this pull request
May 21, 2024
* 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>
frewmack
added a commit
that referenced
this pull request
May 27, 2024
* 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) * Trim whitespace from sources in environment (#399) --------- 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>
frewmack
added a commit
that referenced
this pull request
May 28, 2024
* 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) * Trim whitespace from sources in environment (#399) --------- 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>
frewmack
added a commit
that referenced
this pull request
May 28, 2024
* 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](https://github.com/Automattic/mongoose/compare/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](https://github.com/panva/jose/compare/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](https://github.com/webpack/loader-utils/compare/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](https://github.com/SamVerschueren/decode-uri-component/compare/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](https://github.com/json5/json5/compare/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](https://github.com/json5/json5/compare/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](https://github.com/json5/json5/compare/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 758f9b951a284c76a7a0fb8072b09f4a8c767744. * 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](https://github.com/keycloak/keycloak-nodejs-connect/compare/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](https://github.com/nodejs/undici/compare/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](https://github.com/jonschlinkert/word-wrap/compare/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](https://github.com/jonschlinkert/word-wrap/compare/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](https://github.com/jonschlinkert/word-wrap/compare/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](https://github.com/npm/node-semver/compare/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](https://github.com/npm/node-semver/compare/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](https://github.com/npm/node-semver/compare/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](https://github.com/salesforce/tough-cookie/compare/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](https://github.com/salesforce/tough-cookie/compare/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](https://github.com/Automattic/mongoose/compare/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](https://github.com/graphql/graphql-js/compare/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](https://github.com/graphql/graphql-js/compare/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](https://github.com/nodejs/undici/compare/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](https://github.com/graphql/graphql-js/compare/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](https://github.com/graphql/graphql-js/compare/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](https://github.com/nodejs/undici/compare/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](https://github.com/graphql/graphql-js/compare/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](https://github.com/graphql/graphql-js/compare/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](https://github.com/nodejs/undici/compare/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](https://github.com/graphql/graphql-js/compare/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](https://github.com/graphql/graphql-js/compare/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](https://github.com/nodejs/undici/compare/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](https://github.com/crypto-browserify/browserify-sign/compare/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](https://github.com/giggio/node-chromedriver/compare/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](https://github.com/axios/axios/compare/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](https://github.com/follow-redirects/follow-redirects/compare/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](https://github.com/follow-redirects/follow-redirects/compare/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](https://github.com/nodejs/undici/compare/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](https://github.com/indutny/node-ip/compare/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](https://github.com/indutny/node-ip/compare/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](https://github.com/panva/jose/compare/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](https://github.com/follow-redirects/follow-redirects/compare/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](https://github.com/follow-redirects/follow-redirects/compare/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](https://github.com/expressjs/express/compare/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](https://github.com/expressjs/express/compare/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](https://github.com/expressjs/express/compare/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](https://github.com/nodejs/undici/compare/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](https://github.com/isaacs/node-tar/compare/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](https://github.com/sidorares/node-mysql2/compare/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](https://github.com/mde/ejs/compare/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> * Trim whitespace from source list in environment (#400) * 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](https://github.com/Automattic/mongoose/compare/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](https://github.com/panva/jose/compare/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](https://github.com/webpack/loader-utils/compare/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](https://github.com/SamVerschueren/decode-uri-component/compare/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](https://github.com/json5/json5/compare/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](https://github.com/json5/json5/compare/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](https://github.com/json5/json5/compare/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 758f9b951a284c76a7a0fb8072b09f4a8c767744. * 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](https://github.com/keycloak/keycloak-nodejs-connect/compare/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](https://github.com/nodejs/undici/compare/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](https://github.com/jonschlinkert/word-wrap/compare/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](https://github.com/jonschlinkert/word-wrap/compare/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](https://github.com/jonschlinkert/word-wrap/compare/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](https://github.com/npm/node-semver/compare/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](https://github.com/npm/node-semver/compare/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](https://github.com/npm/node-semver/compare/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](https://github.com/salesforce/tough-cookie/compare/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](https://github.com/salesforce/tough-cookie/compare/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](https://github.com/Automattic/mongoose/compare/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](https://github.com/graphql/graphql-js/compare/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](https://github.com/graphql/graphql-js/compare/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](https://github.com/nodejs/undici/compare/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](https://github.com/graphql/graphql-js/compare/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](https://github.com/graphql/graphql-js/compare/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](https://github.com/nodejs/undici/compare/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](https://github.com/graphql/graphql-js/compare/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](https://github.com/graphql/graphql-js/compare/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](https://github.com/nodejs/undici/compare/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](https://github.com/graphql/graphql-js/compare/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](https://github.com/graphql/graphql-js/compare/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](https://github.com/nodejs/undici/compare/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](https://github.com/crypto-browserify/browserify-sign/compare/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](https://github.com/giggio/node-chromedriver/compare/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](https://github.com/axios/axios/compare/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…
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Closes #362