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Bump mongoose from 6.4.6 to 6.11.3 in /server #349

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merged 2 commits into from
Aug 18, 2023

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Bumps mongoose from 6.4.6 to 6.11.3.

Release notes

Sourced from mongoose's releases.

6.10.1 / 2023-03-03

  • fix: avoid removing empty query filters in $and and $or #13086 #12898
  • fix(schematype): fixed validation for required UUID field #13018 lpizzinidev
  • fix(types): add missing Paths generic param to Model.populate() #13070
  • docs(migrating_to_6): added info about removal of reconnectTries and reconnectInterval options #13083 lpizzinidev
  • docs: fix code in headers for migrating_to_5 #13077 hasezoey
  • docs: backport misc documentation changes into 6.x #13091 hasezoey

6.10.0 / 2023-02-22

6.9.3 / 2023-02-22

  • fix(connection): delay calculating autoCreate and autoIndex until after initial connection established #13007 #12940 lpizzinidev
  • fix(discriminator): allows update doc with discriminatorKey #13056 #13055 abarriel
  • fix(query): avoid sending unnecessary empty projection to MongoDB server #13059 #13050
  • fix(model): avoid sending null session option with document operations #13053 #13052 lpizzinidev
  • fix(types): use MergeTypes for type overrides in HydratedDocument #13066 #13040
  • docs(middleware): list validate as a potential query middleware #13057 #12680
  • docs(getters-setters): explain that getters do not run by default on toJSON() #13058 #13049
  • docs: refactor docs generation scripts #13044 hasezoey

6.9.2 / 2023-02-16

6.9.1 / 2023-02-06

  • fix(document): isModified should not be triggered when setting a nested boolean to the same value as previously #12994 lpizzinidev
  • fix(document): save newly set defaults underneath single nested subdocuments #13002 #12905
  • fix(update): handle custom discriminator model name when casting update #12947 wassil
  • fix(connection): handles unique autoincrement ID for connections #12990 lpizzinidev
  • fix(types): fix type of options of Model.aggregate #12933 ghost91-
  • fix(types): fix "near" aggregation operator input type #12954 Jokero
  • fix(types): add missing Top operator to AccumulatorOperator type declaration #12952 lpizzinidev
  • docs(transactions): added example for Connection.transaction() method #12943 #12934 lpizzinidev
  • docs(populate): fix out of date comment referencing onModel property #13000
  • docs(transactions): fix typo in transactions.md #12995 Parth86

... (truncated)

Changelog

Sourced from mongoose's changelog.

6.11.3 / 2023-07-11

  • fix: avoid prototype pollution on init
  • fix(schema): correctly handle uuids with populate() #13317 #13595

7.3.3 / 2023-07-10

  • fix: avoid prototype pollution on init
  • fix(document): clean up all array subdocument modified paths on save() #13589 #13582
  • types: avoid unnecessary MergeType<> if TOverrides not set, clean up statics and insertMany() type issues #13577 #13529

7.3.2 / 2023-07-06

  • fix(model): avoid TypeError if insertMany() fails with error that does not have writeErrors property #13579 #13531
  • fix(query): convert findOneAndUpdate to findOneAndReplace when overwrite set for backwards compat with Mongoose 6 #13572 #13550
  • fix(query): throw readable error when executing a Query instance without an associated model #13571 #13570
  • types: support mongoose.Schema.ObjectId as alias for mongoose.Schema.Types.ObjectId #13543 #13534
  • docs(connections): clarify that socketTimeoutMS now defaults to 0 #13576 #13537
  • docs(migrating_to_7): add mapReduce() removal to migration guide #13568 #13548
  • docs(schemas): fix typo in schemas.md #13540 Metehan-Altuntekin

7.3.1 / 2023-06-21

  • fix(query): respect query-level strict option on findOneAndReplace() #13516 #13507
  • docs(connections): expand docs on serverSelectionTimeoutMS #13533 #12967
  • docs: add example of accessing save options in pre save #13498
  • docs(connections+faq): add info on localhost vs 127.0.0.1
  • docs(SchemaType): validate members are validator & message (not msg) #13521 lorand-horvath

7.3.0 / 2023-06-14

  • feat: upgrade mongodb -> 5.6.0 #13455 lorand-horvath
  • feat(aggregate): add Aggregate.prototype.finally() to be consistent with Promise API for TypeScript #13509
  • feat(schema): support selecting subset of fields to apply optimistic concurrency to #13506 #10591
  • feat(model): add ordered option to Model.create() #13472 #4038
  • feat(schema): consistently add .get() function to all SchemaType classes
  • feat(populate): pass virtual to match function to allow merging match options #13477 #12443
  • types: allow overwriting Paths in select() to tell TypeScript which fields are projected #13478 #13224
  • types(schema): add validateModifiedOnly as schema option #13503 #10153
  • docs: add note about validateModifiedOnly as a schema option #13503 #10153
  • docs(migrating_to_7): update migrating_to_7.md to include Model.countDocuments #13508 Climax777
  • docs(further_reading): remove style for "img" hasezoey

7.2.4 / 2023-06-12

  • fix(query): handle non-string discriminator key values in query #13496 #13492

7.2.3 / 2023-06-09

... (truncated)

Commits
  • e9eb8ab chore: release 6.11.3
  • 688da8f test: fix flakey tests, remove test for #9597 because it affects global state...
  • 4f264a8 test: fix tests re: #13317
  • 9616af7 fix(schema): correctly handle uuids with populate()
  • 305ce4f fix: avoid prototype pollution on init
  • 35e59eb docs: link to migrating to 6 in 6.x docs
  • a28933e chore: release 6.11.2
  • 3a6b0dd chore: use deno v1.34 in test for MMS HTTP issues
  • f7c6d3e Merge pull request #13476 from Automattic/vkarpov15/gh-13453
  • 5552107 fix(cursor): allow find middleware to modify query cursor options
  • Additional commits viewable in compare view

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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)

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@dependabot dependabot bot added the dependencies Pull requests that update a dependency file label Jul 18, 2023
@frewmack frewmack merged commit e449998 into develop Aug 18, 2023
@frewmack frewmack deleted the dependabot/npm_and_yarn/server/mongoose-6.11.3 branch August 18, 2023 18:45
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)
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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* Fix deprecation warning for strictQuery setting

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* Set ApolloServer cache to bounded (#354)

* Bump apollo-server-core from 3.10.1 to 3.12.1 in /server (#356)

Bumps [apollo-server-core](https://github.com/apollographql/apollo-server/tree/HEAD/packages/apollo-server-core) from 3.10.1 to 3.12.1.
- [Release notes](https://github.com/apollographql/apollo-server/releases)
- [Commits](https://github.com/apollographql/apollo-server/commits/apollo-server-core@3.12.1/packages/apollo-server-core)

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* 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)

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* 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.
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* Bump @babel/traverse from 7.17.3 to 7.23.2 in /react (#360)

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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* Bump @babel/traverse from 7.17.3 to 7.23.2 in /react (#360)

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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* Update jest config for new axios version

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* 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

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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.
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* 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)
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* 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)
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* 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.
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* 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)
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* 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.
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* 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.
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* 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.
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* 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)
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* 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.
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* 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.
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* 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.
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* 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.
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* 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)
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* 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)
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* 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)
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* 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.
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* 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.
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* 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)
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* Fix deprecation warning for strictQuery setting

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* 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)
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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)
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* 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)
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* 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)
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* 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.
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* 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.
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* 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)
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* 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.
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* 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)
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* 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.
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* 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.
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* 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)
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* 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)
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* 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)
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* 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)
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* 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.
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* 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)

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* 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)
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* 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.
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* 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)
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* Update jest config for new axios version

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)
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* Add CMH environment to node prod workflow (#397)

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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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)
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* 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)

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* 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)
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* 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)
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* 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)
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* 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.
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* 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.
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* 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)
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* Fix deprecation warning for strictQuery setting

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* 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)
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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)
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* 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.
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* 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)
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* 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.
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* 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.
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* 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)
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* 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)
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* 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)
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* 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.
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* 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)
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* 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.
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* 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.
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* 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)
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* 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.
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* 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.
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* 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)
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* 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)
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* 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)

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* 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)
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* Update jest config for new axios version

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* Add CMH environment to node prod workflow (#397)

* Trim whitespace from sources in environment (#399)

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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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)
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* Fix deprecation warning for strictQuery setting

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* Set ApolloServer cache to bounded (#354)

* Bump apollo-server-core from 3.10.1 to 3.12.1 in /server (#356)

Bumps [apollo-server-core](https://github.com/apollographql/apollo-server/tree/HEAD/packages/apollo-server-core) from 3.10.1 to 3.12.1.
- [Release notes](https://github.com/apollographql/apollo-server/releases)
- [Commits](https://github.com/apollographql/apollo-server/commits/apollo-server-core@3.12.1/packages/apollo-server-core)

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* 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)
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* 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)

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* 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)

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* 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)
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* 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)
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* 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)

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* 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)
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* 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)

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* 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)
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* 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)
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* 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)

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* 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)

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* 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)

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* 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)
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* 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)

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* 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)

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* 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)

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* 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)

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* 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)
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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* Update jest config for new axios version

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* Add CMH environment to node prod workflow (#397)

* Trim whitespace from sources in environment (#399)

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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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* Fix deprecation warning for strictQuery setting

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* Set ApolloServer cache to bounded (#354)

* Bump apollo-server-core from 3.10.1 to 3.12.1 in /server (#356)

Bumps [apollo-server-core](https://github.com/apollographql/apollo-server/tree/HEAD/packages/apollo-server-core) from 3.10.1 to 3.12.1.
- [Release notes](https://github.com/apollographql/apollo-server/releases)
- [Commits](https://github.com/apollographql/apollo-server/commits/apollo-server-core@3.12.1/packages/apollo-server-core)

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* 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)

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* 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)

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* 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)
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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* Update jest config for new axios version

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* Add CMH environment to node prod workflow (#397)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* Fix deprecation warning for strictQuery setting

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* Set ApolloServer cache to bounded (#354)

* Bump apollo-server-core from 3.10.1 to 3.12.1 in /server (#356)

Bumps [apollo-server-core](https://github.com/apollographql/apollo-server/tree/HEAD/packages/apollo-server-core) from 3.10.1 to 3.12.1.
- [Release notes](https://github.com/apollographql/apollo-server/releases)
- [Commits](https://github.com/apollographql/apollo-server/commits/apollo-server-core@3.12.1/packages/apollo-server-core)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* 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)

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* Update jest config for new axios version

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* Add PT Pagination support for G4RD Staging (#366)

* Add fetchPhenotipsVariant for collecting paginated results…
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