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Documentation: Add documentation for the staging and production instance #317

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merged 7 commits into from
Aug 26, 2022
Merged

Documentation: Add documentation for the staging and production instance #317

merged 7 commits into from
Aug 26, 2022

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@jennyziyi-xu jennyziyi-xu added the documentation Improvements or additions to documentation label Aug 18, 2022
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frewmack requested changes Aug 18, 2022
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Just some minor suggestions for grammatical and formatting fixes, and a small addition to the Mongo section of local-dev.md (with regards to GRCh38 gnomAD annotations).

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themisteryang
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LGTM!

@jennyziyi-xu jennyziyi-xu linked an issue Aug 25, 2022 that may be closed by this pull request
Documentation: Create detailed documentation for dev and prod environments #308
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# Production

OSMP is deployed via Compose at [https://osmp.genomics4rd.ca](https://osmp.genomics4rd.ca). The key differences between the staging and production are the removal of the test node and increased memory and CPU resource allocations for the `server` container. The OSMP production instance is connected to the [production instance of G4RD Phenotips](https://phenotips.genomics4rd.ca). Similar to the staging stack, to deploy the frontend, compiled static bundles are uploaded to a designated MinIO bucket. The routing between the frontend and backend is handled by the HAProxy reverse proxy.
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OSMP is deployed via Compose at [https://osmp.genomics4rd.ca](https://osmp.genomics4rd.ca). The key differences between the staging and production are the removal of the test node and increased memory and CPU resource allocations for the `server` container. The OSMP production instance is connected to the [production instance of G4RD Phenotips](https://phenotips.genomics4rd.ca). Similar to the staging stack, to deploy the frontend, compiled static bundles are uploaded to a designated MinIO bucket. The routing between the frontend and backend is handled by the HAProxy reverse proxy.
OSMP is deployed via Docker Compose at [https://osmp.genomics4rd.ca](https://osmp.genomics4rd.ca). The key differences between the staging and production are the removal of the test node and increased memory and CPU resource allocations for the `server` container. The OSMP production instance is connected to the [production instance of G4RD Phenotips](https://phenotips.genomics4rd.ca). Similar to the staging stack, to deploy the frontend, compiled static bundles are uploaded to a designated MinIO bucket. The routing between the frontend and backend is handled by the HAProxy reverse proxy. User accounts are managed in [Keycloak](https://keycloak.genomics4rd.ca).

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# Staging

OSMP is deployed via Compose at [https://osmp.ccmdev.ca/](https://osmp.ccmdev.ca/). For G4RD data source, the OSMP staging instance is connected to the [staging instance of G4RD Phenotips](https://osmp.ccmdev.ca/). To deploy the frontend, compiled static bundles are uploaded to a designated MinIO bucket. The routing between the frontend and backend is handled by the HAProxy reverse proxy.
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OSMP is deployed via Compose at [https://osmp.ccmdev.ca/](https://osmp.ccmdev.ca/). For G4RD data source, the OSMP staging instance is connected to the [staging instance of G4RD Phenotips](https://osmp.ccmdev.ca/). To deploy the frontend, compiled static bundles are uploaded to a designated MinIO bucket. The routing between the frontend and backend is handled by the HAProxy reverse proxy.
OSMP is deployed via Docker Compose at [https://osmp.ccmdev.ca/](https://osmp.ccmdev.ca/). For G4RD data source, the OSMP staging instance is connected to the [staging instance of G4RD Phenotips](https://staging.phenotips.genomics4rd.ca). To deploy the frontend, compiled static bundles are uploaded to a designated MinIO bucket. The routing between the frontend and backend is handled by the HAProxy reverse proxy. User accounts are managed in [Keycloak](https://keycloak.ccmdev.ca).

@jennyziyi-xu jennyziyi-xu requested a review from frewmack August 25, 2022 14:39
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LGTM! 🚀

@jennyziyi-xu jennyziyi-xu merged commit 00f2abe into develop Aug 26, 2022
@jennyziyi-xu jennyziyi-xu deleted the jenny/documentation branch August 26, 2022 20:21
frewmack added a commit that referenced this pull request Feb 12, 2024
@frewmack @jennyziyi-xu @dependabot
Production update (#374)
c0630ed 
* Documentation: Add documentation for the staging and production instance (#317)

* Add documentation for staging and prod

* Modify README.md

* code formatting

* Grammatical fixes

* Add Keycloak related info

* Merge outstanding dependency updates (#331)

* Bump mongoose from 6.2.11 to 6.4.6 in /server

Bumps [mongoose](https://github.com/Automattic/mongoose) from 6.2.11 to 6.4.6.
- [Release notes](https://github.com/Automattic/mongoose/releases)
- [Changelog](https://github.com/Automattic/mongoose/blob/master/CHANGELOG.md)
- [Commits](Automattic/mongoose@6.2.11...6.4.6)

---
updated-dependencies:
- dependency-name: mongoose
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump jose from 2.0.5 to 2.0.6 in /test-node

Bumps [jose](https://github.com/panva/jose) from 2.0.5 to 2.0.6.
- [Release notes](https://github.com/panva/jose/releases)
- [Changelog](https://github.com/panva/jose/blob/v2.0.6/CHANGELOG.md)
- [Commits](panva/jose@v2.0.5...v2.0.6)

---
updated-dependencies:
- dependency-name: jose
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump loader-utils from 1.4.0 to 1.4.2 in /react

Bumps [loader-utils](https://github.com/webpack/loader-utils) from 1.4.0 to 1.4.2.
- [Release notes](https://github.com/webpack/loader-utils/releases)
- [Changelog](https://github.com/webpack/loader-utils/blob/v1.4.2/CHANGELOG.md)
- [Commits](webpack/loader-utils@v1.4.0...v1.4.2)

---
updated-dependencies:
- dependency-name: loader-utils
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump deep-object-diff from 1.1.7 to 1.1.9 in /react

Bumps [deep-object-diff](https://github.com/mattphillips/deep-object-diff) from 1.1.7 to 1.1.9.
- [Release notes](https://github.com/mattphillips/deep-object-diff/releases)
- [Commits](https://github.com/mattphillips/deep-object-diff/commits)

---
updated-dependencies:
- dependency-name: deep-object-diff
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump decode-uri-component from 0.2.0 to 0.2.2 in /react

Bumps [decode-uri-component](https://github.com/SamVerschueren/decode-uri-component) from 0.2.0 to 0.2.2.
- [Release notes](https://github.com/SamVerschueren/decode-uri-component/releases)
- [Commits](SamVerschueren/decode-uri-component@v0.2.0...v0.2.2)

---
updated-dependencies:
- dependency-name: decode-uri-component
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump json5 from 1.0.1 to 1.0.2 in /server

Bumps [json5](https://github.com/json5/json5) from 1.0.1 to 1.0.2.
- [Release notes](https://github.com/json5/json5/releases)
- [Changelog](https://github.com/json5/json5/blob/main/CHANGELOG.md)
- [Commits](json5/json5@v1.0.1...v1.0.2)

---
updated-dependencies:
- dependency-name: json5
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump json5 from 1.0.1 to 1.0.2 in /test-node

Bumps [json5](https://github.com/json5/json5) from 1.0.1 to 1.0.2.
- [Release notes](https://github.com/json5/json5/releases)
- [Changelog](https://github.com/json5/json5/blob/main/CHANGELOG.md)
- [Commits](json5/json5@v1.0.1...v1.0.2)

---
updated-dependencies:
- dependency-name: json5
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump json5 from 1.0.1 to 1.0.2 in /react

Bumps [json5](https://github.com/json5/json5) from 1.0.1 to 1.0.2.
- [Release notes](https://github.com/json5/json5/releases)
- [Changelog](https://github.com/json5/json5/blob/main/CHANGELOG.md)
- [Commits](json5/json5@v1.0.1...v1.0.2)

---
updated-dependencies:
- dependency-name: json5
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Add gnomadHet column w/ number of heterozygotes (#334)

* Add gnomadHet calculation
- Add comments

* Change gnomadHet to use PrimaryAF
- Kept AF displayed as max between primary and secondary AF

* Update tests

* Add maleCount field to table rows (#335)

* Fix male count (#337)

* Add allele count column, remove gnomadHet and male count (#338)

* Replace gnomadHet with AC count

* Add AC column to frontend
- update tests

* Update typedefs

* Fix graphQL query, frontend query preparing

* Hide male count by default

* Comment out male count; redundant info

* React: Bump timeout from 90 sec to 900 sec (#339)

* Bump timeout from 90 sec to 900 sec
- Suggested by Matt, Magda (2023-03-13)

* Reduce to 5 minutes

* Revert "Reduce to 5 minutes"

This reverts commit 758f9b9.

* Fix comment

* CMH Integration  (#341)

* Fix typo in g4rdAdapter

* Add CMH adapter

* Add source prefixes; fix error messages

* Update docs

* Update staging server deploy with CMH vars

* Remove cmh env vars from docker prod (for now)

* Bump keycloak-connect from 17.0.0 to 21.0.1 in /server (#336)

Bumps [keycloak-connect](https://github.com/keycloak/keycloak-nodejs-connect) from 17.0.0 to 21.0.1.
- [Release notes](https://github.com/keycloak/keycloak-nodejs-connect/releases)
- [Commits](keycloak/keycloak-nodejs-connect@17.0.0...21.0.1)

---
updated-dependencies:
- dependency-name: keycloak-connect
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump undici from 5.9.1 to 5.19.1 in /server (#333)

Bumps [undici](https://github.com/nodejs/undici) from 5.9.1 to 5.19.1.
- [Release notes](https://github.com/nodejs/undici/releases)
- [Commits](nodejs/undici@v5.9.1...v5.19.1)

---
updated-dependencies:
- dependency-name: undici
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Rearrange columns, add tooltips  (#342)

* Add source to duplicate variant check

* Move some columns to Case Details

* Add tooltips for all the columns

* Fix CMH assembly (#343)

* Change CMH adapter to GRCh38

* Fix liftOver if no dataForAnnotation

* Perform LiftOver for CMH query results (GRCh38 -> h37) (#353)

* Add CMHVariantIndelCoordinate type

* More comments

* Update mongo query to accomodate CMH format

* Fix "chrchr" mapping in liftOver

* Remove logger debugs

* Fix gnomad query to exclude CMH if none found
- Fix getCoordinates to not do "chrchr"

* Remove ref[0] == alt[0] query check

* Bump word-wrap from 1.2.3 to 1.2.4 in /server (#350)

Bumps [word-wrap](https://github.com/jonschlinkert/word-wrap) from 1.2.3 to 1.2.4.
- [Release notes](https://github.com/jonschlinkert/word-wrap/releases)
- [Commits](jonschlinkert/word-wrap@1.2.3...1.2.4)

---
updated-dependencies:
- dependency-name: word-wrap
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump word-wrap from 1.2.3 to 1.2.4 in /test-node (#351)

Bumps [word-wrap](https://github.com/jonschlinkert/word-wrap) from 1.2.3 to 1.2.4.
- [Release notes](https://github.com/jonschlinkert/word-wrap/releases)
- [Commits](jonschlinkert/word-wrap@1.2.3...1.2.4)

---
updated-dependencies:
- dependency-name: word-wrap
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump word-wrap from 1.2.3 to 1.2.4 in /react (#352)

Bumps [word-wrap](https://github.com/jonschlinkert/word-wrap) from 1.2.3 to 1.2.4.
- [Release notes](https://github.com/jonschlinkert/word-wrap/releases)
- [Commits](jonschlinkert/word-wrap@1.2.3...1.2.4)

---
updated-dependencies:
- dependency-name: word-wrap
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump semver from 5.7.1 to 5.7.2 in /test-node (#348)

Bumps [semver](https://github.com/npm/node-semver) from 5.7.1 to 5.7.2.
- [Release notes](https://github.com/npm/node-semver/releases)
- [Changelog](https://github.com/npm/node-semver/blob/v5.7.2/CHANGELOG.md)
- [Commits](npm/node-semver@v5.7.1...v5.7.2)

---
updated-dependencies:
- dependency-name: semver
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump semver from 6.3.0 to 6.3.1 in /server (#347)

Bumps [semver](https://github.com/npm/node-semver) from 6.3.0 to 6.3.1.
- [Release notes](https://github.com/npm/node-semver/releases)
- [Changelog](https://github.com/npm/node-semver/blob/v6.3.1/CHANGELOG.md)
- [Commits](npm/node-semver@v6.3.0...v6.3.1)

---
updated-dependencies:
- dependency-name: semver
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump semver from 5.7.1 to 5.7.2 in /react (#346)

Bumps [semver](https://github.com/npm/node-semver) from 5.7.1 to 5.7.2.
- [Release notes](https://github.com/npm/node-semver/releases)
- [Changelog](https://github.com/npm/node-semver/blob/v5.7.2/CHANGELOG.md)
- [Commits](npm/node-semver@v5.7.1...v5.7.2)

---
updated-dependencies:
- dependency-name: semver
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump tough-cookie from 4.0.0 to 4.1.3 in /react (#345)

Bumps [tough-cookie](https://github.com/salesforce/tough-cookie) from 4.0.0 to 4.1.3.
- [Release notes](https://github.com/salesforce/tough-cookie/releases)
- [Changelog](https://github.com/salesforce/tough-cookie/blob/master/CHANGELOG.md)
- [Commits](salesforce/tough-cookie@v4.0.0...v4.1.3)

---
updated-dependencies:
- dependency-name: tough-cookie
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump tough-cookie from 4.0.0 to 4.1.3 in /server (#344)

Bumps [tough-cookie](https://github.com/salesforce/tough-cookie) from 4.0.0 to 4.1.3.
- [Release notes](https://github.com/salesforce/tough-cookie/releases)
- [Changelog](https://github.com/salesforce/tough-cookie/blob/master/CHANGELOG.md)
- [Commits](salesforce/tough-cookie@v4.0.0...v4.1.3)

---
updated-dependencies:
- dependency-name: tough-cookie
  dependency-type: indirect
...

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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump mongoose from 6.4.6 to 6.11.3 in /server (#349)

* Bump mongoose from 6.4.6 to 6.11.3 in /server

Bumps [mongoose](https://github.com/Automattic/mongoose) from 6.4.6 to 6.11.3.
- [Release notes](https://github.com/Automattic/mongoose/releases)
- [Changelog](https://github.com/Automattic/mongoose/blob/master/CHANGELOG.md)
- [Commits](Automattic/mongoose@6.4.6...6.11.3)

---
updated-dependencies:
- dependency-name: mongoose
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

* Fix deprecation warning for strictQuery setting

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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)

---
updated-dependencies:
- dependency-name: apollo-server-core
  dependency-type: indirect
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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)

---
updated-dependencies:
- dependency-name: "@babel/traverse"
  dependency-type: indirect
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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)

---
updated-dependencies:
- dependency-name: graphql
  dependency-type: direct:production
...

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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)

---
updated-dependencies:
- dependency-name: "@babel/traverse"
  dependency-type: indirect
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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](graphql/graphql-js@v16.3.0...v16.8.1)

---
updated-dependencies:
- dependency-name: graphql
  dependency-type: direct:production
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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)

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.
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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.
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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)
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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
@frewmack @jennyziyi-xu @dependabot
May 2024 update to production (#398)
e4c0ca2 
* 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)
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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)
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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)
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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.
- [Release notes](https://github.com/json5/json5/releases)
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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.
- [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 /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.
- [Release notes](https://github.com/salesforce/tough-cookie/releases)
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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.
- [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.
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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)
- [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.
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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)
- [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)
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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)
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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)
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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)
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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)
- [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)

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frewmack added a commit that referenced this pull request May 27, 2024
@frewmack @jennyziyi-xu @dependabot
Trim whitespace from source list in environment (#400)
61e2e86 
* 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)
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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)
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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)
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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.
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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)
- [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.
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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)
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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)

---
updated-dependencies:
- dependency-name: ip
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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
@frewmack @jennyziyi-xu @dependabot
Bring production up to date properly (#401)
33e4c23 
* 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)
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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)
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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)
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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)
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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 (#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)
- [Commits](graphql/graphql-js@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](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)
- [Commits](graphql/graphql-js@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](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)
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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)
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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)
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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.
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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
@frewmack @jennyziyi-xu @dependabot
Production to develop, to try and fix the Git history (#402)
03317d1 
* 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)
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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

* 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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  dependency-type: direct:production
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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)

---
updated-dependencies:
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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)
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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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@themisteryang themisteryang themisteryang approved these changes

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Documentation: Create detailed documentation for dev and prod environments
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