Bump undici from 5.19.1 to 5.26.3 in /server #359
Merged
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
![dependabot[bot]](https://avatars.githubusercontent.com/in/29110?s=60&v=4){kind=small}
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] <[email protected]>
dependabot
bot
added
the
dependencies
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] <[email protected]> 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]>
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] <[email protected]>
….com:ccmbioinfo/osmp into dependabot/npm_and_yarn/server/undici-5.26.3
frewmack
approved these changes
Oct 17, 2023
frewmack
added a commit
that referenced
this pull request
Oct 17, 2023
* 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]>
frewmack
added a commit
that referenced
this pull request
Feb 12, 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> * Fix deprecation warning for strictQuery setting --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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/[email protected]/packages/apollo-server-core) --- updated-dependencies: - dependency-name: apollo-server-core dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> 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] <[email protected]> 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> * Update jest config for new axios version --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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 --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Jenny <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> * Fix deprecation warning for strictQuery setting --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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/[email protected]/packages/apollo-server-core) --- updated-dependencies: - dependency-name: apollo-server-core dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> 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] <[email protected]> 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> * Update jest config for new axios version --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> 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] <[email protected]> Co-authored-by: Jenny <[email protected]> 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> * Fix deprecation warning for strictQuery setting --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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/[email protected]/packages/apollo-server-core) --- updated-dependencies: - dependency-name: apollo-server-core dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> 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] <[email protected]> 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> * Update jest config for new axios version --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> 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] <[email protected]> Co-authored-by: Jenny <[email protected]> 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> * Fix deprecation warning for strictQuery setting --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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/[email protected]/packages/apollo-server-core) --- updated-dependencies: - dependency-name: apollo-server-core dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> 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] <[email protected]> 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> * Update jest config for new axios version --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> 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] <[email protected]> Co-authored-by: Jenny <[email protected]> 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> * Fix deprecation warning for strictQuery setting --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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/[email protected]/packages/apollo-server-core) --- updated-dependencies: - dependency-name: apollo-server-core dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> 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] <[email protected]> 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> * Update jest config for new axios version --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> 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] <[email protected]> Co-authored-by: Jenny <[email protected]> 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> * Fix deprecation warning for strictQuery setting --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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/[email protected]/packages/apollo-server-core) --- updated-dependencies: - dependency-name: apollo-server-core dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> 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] <[email protected]> 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> * 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> * 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] <[email protected]> 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> * Update jest config for new axios version --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mackenzie Ian Frew <[email protected]> * 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.
Bumps undici from 5.19.1 to 5.26.3.
Release notes
Sourced from undici's releases.
... (truncated)
Commits
227b9be5.26.35351f1finclude esbuild script in files12a6218Bumped v5.26.2e041de3Merge pull request from GHSA-wqq4-5wpv-mx2gc8c80b15.26.17bcb80cFix node detection omfg (#2341)69ea7b9hopefully this fixes it for good (#2338)4006aafBumped v5.26.0df97958fix: 🐛 fix process http2 header (#2332)b9d8368fix: 🏷️ add allowH2 to BuildOptions (#2334)Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting
@dependabot rebase.Dependabot commands and options
You can trigger Dependabot actions by commenting on this PR:
@dependabot rebasewill rebase this PR@dependabot recreatewill recreate this PR, overwriting any edits that have been made to it@dependabot mergewill merge this PR after your CI passes on it@dependabot squash and mergewill squash and merge this PR after your CI passes on it@dependabot cancel mergewill cancel a previously requested merge and block automerging@dependabot reopenwill reopen this PR if it is closed@dependabot closewill close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually@dependabot show <dependency name> ignore conditionswill show all of the ignore conditions of the specified dependency@dependabot ignore this major versionwill close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)@dependabot ignore this minor versionwill close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)@dependabot ignore this dependencywill close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)You can disable automated security fix PRs for this repo from the Security Alerts page.