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all-of-us/workbench 28

All of Us Researcher Workbench

broadinstitute/htslib 2

C library for high-throughput sequencing data formats. This is the repository for any necessary gamgee-specific changes.

broadinstitute/GitDescribe-Maven-Plugin 0

Sets the maven attribute 'describe' to the current git describe output. Currently directly executes git describe, no JGit implementation yet.

jmthibault79/dataproc-initialization-actions 0

Run in all nodes of your cluster before the cluster starts - lets you customize your cluster

jmthibault79/disq 0

A library for manipulating bioinformatics sequencing formats in Apache Spark

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Joel Thibault

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Joel Thibault

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import cleanup

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Joel Thibault

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CH Albach

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[RW-7151][risk=no] Add Spark console links to runtime panel (#6144)

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aweng98

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[no ticket][risk=no] e2e refactor export dataset to notebook test (#6135) * refactor export dataset to notebook test * undo unrelated

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aweng98

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[no ticket][risk=no] Fix code: missing keyword await in async func (#6159)

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aweng98

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[no ticket][risk=no] Fix cdr-version-upgrade.spec (#6160)

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aweng98

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[no ticket][risk=no] Fix modal getText xpath (#6161)

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jmthibault79

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[risk=low][no ticket] make moduleName mandatory and add a second signature for updateBypassTime() (#6157)

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Joel Thibault

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Access Tiers -> Data Access Tiers

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Joel Thibault

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allow othertext to push down modules table

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Joel Thibault

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format data access tier names

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Joel Thibault

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WIP AccessModuleTable

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Joel Thibault

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add non-functional bypass toggles and order modules add text to indicate bypass/not and changed/not

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Joel Thibault

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toggles work

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better save button behavior for bypass toggles

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[risk=low][no ticket] make moduleName mandatory and add a second signature for updateBypassTime() (#6157)

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[risk=low][no ticket] make moduleName mandatory for bypass requests

It's meaningless to specify this without a moduleName, and Typescript can enforce this.

Also a small improvement to nearby code

<!-- Replace this template with your PR description. Please remember to keep in mind the security levels outlined in CONTRIBUTING.md and to include a risk tag of the form [risk=no|low|moderate|severe] in the PR title

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Yonghao Yu

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[RW-7691][risk=low] enable workflow in non-prod env. (#6150) * enable workflow * enable workflow

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Yonghao Yu

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remove unsed flag (#6151)

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Brian Freeman

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fixing CDR build (#6153) [no ticket][risk=no] fixing CDR build

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[risk=low][no ticket] Bump engine.io from 6.1.0 to 6.1.1 in /ui (#6152) Bumps [engine.io](https://github.com/socketio/engine.io) from 6.1.0 to 6.1.1. - [Release notes](https://github.com/socketio/engine.io/releases) - [Changelog](https://github.com/socketio/engine.io/blob/master/CHANGELOG.md) - [Commits](https://github.com/socketio/engine.io/compare/6.1.0...6.1.1) --- updated-dependencies: - dependency-name: engine.io dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

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jmthibault79

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[risk=no][no ticket] rm unused node-gyp (#6148)

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Brian Freeman

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promoting cdr indices (#6155) [no ticket][risk=no] promoting cdr index in test

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chavanr2019

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[RW-7697] Chavanr/user admin UI update (#6139) * updated the xpath * updated the function names * lint-fixes * updated the getInitialCreditUsedValue function * updated the function names * yarn lint:fix * made the changes as per review-2 * correction made

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aweng98

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alternative xpath to find domain cards (#6156)

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Joel Thibault

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make moduleName mandatory and add a second signature for updateBypassTime()

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Joel Thibault

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Access Tiers -> Data Access Tiers

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Joel Thibault

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allow othertext to push down modules table

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Joel Thibault

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format data access tier names

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WIP AccessModuleTable

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add non-functional bypass toggles and order modules add text to indicate bypass/not and changed/not

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toggles work

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[risk=low][no ticket] make moduleName mandatory for bypass requests

Description: <!-- Replace this template with your PR description. Please remember to keep in mind the security levels outlined in CONTRIBUTING.md and to include a risk tag of the form [risk=no|low|moderate|severe] in the PR title

  • no: None
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  • [ ] If this includes a UI change, I have taken screen recordings or screenshots of the new behavior and notified the PO and UX designer
  • [ ] If this includes an API change, I have updated the appropriate Swagger definitions and notified API consumers
  • [ ] If this includes a new feature flag, I have created and linked new JIRA tickets to (a) turn on the feature flag and (b) remove it later
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jmthibault79

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[risk=no][no ticket] rm unused node-gyp (#6148)

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<!-- Replace this template with your PR description. Please remember to keep in mind the security levels outlined in CONTRIBUTING.md and to include a risk tag of the form [risk=no|low|moderate|severe] in the PR title

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  • [ ] If this includes a UI change, I have taken screen recordings or screenshots of the new behavior and notified the PO and UX designer
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[risk=low][no ticket] Bump engine.io from 6.1.0 to 6.1.1 in /ui (#6152) Bumps [engine.io](https://github.com/socketio/engine.io) from 6.1.0 to 6.1.1. - [Release notes](https://github.com/socketio/engine.io/releases) - [Changelog](https://github.com/socketio/engine.io/blob/master/CHANGELOG.md) - [Commits](https://github.com/socketio/engine.io/compare/6.1.0...6.1.1) --- updated-dependencies: - dependency-name: engine.io dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

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Bump engine.io from 6.1.0 to 6.1.1 in /ui dependencies javascript

Bumps engine.io from 6.1.0 to 6.1.1. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/socketio/engine.io/releases">engine.io's releases</a>.</em></p> <blockquote> <h2>6.1.1</h2> <p>:warning: This release contains an important security fix :warning:</p> <p>A malicious client could send a specially crafted HTTP request, triggering an uncaught exception and killing the Node.js process:</p> <blockquote> <p>RangeError: Invalid WebSocket frame: RSV2 and RSV3 must be clear at Receiver.getInfo (/.../node_modules/ws/lib/receiver.js:176:14) at Receiver.startLoop (/.../node_modules/ws/lib/receiver.js:136:22) at Receiver._write (/.../node_modules/ws/lib/receiver.js:83:10) at writeOrBuffer (internal/streams/writable.js:358:12)</p> </blockquote> <p>This bug was introduced by <a href="https://github.com/socketio/engine.io/commit/f3c291fa613a9d50c924d74293035737fdace4f2">this commit</a>, included in <code>engine.io@4.0.0</code>, so previous releases are not impacted.</p> <p>Thanks to Marcus Wejderot from Mevisio for the responsible disclosure.</p> <h3>Bug Fixes</h3> <ul> <li>properly handle invalid data sent by a malicious websocket client (<a href="https://github.com/socketio/engine.io/commit/c0e194d44933bd83bf9a4b126fca68ba7bf5098c">c0e194d</a>)</li> </ul> <h4>Links</h4> <ul> <li>Diff: <a href="https://github.com/socketio/engine.io/compare/6.1.0...6.1.1">https://github.com/socketio/engine.io/compare/6.1.0...6.1.1</a></li> <li>Client release: -</li> <li>ws version: <a href="https://github.com/websockets/ws/releases/tag/8.2.3">~8.2.3</a></li> </ul> </blockquote> </details> <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/socketio/engine.io/blob/master/CHANGELOG.md">engine.io's changelog</a>.</em></p> <blockquote> <h2><a href="https://github.com/socketio/engine.io/compare/6.1.0...6.1.1">6.1.1</a> (2022-01-11)</h2> <p>:warning: This release contains an important security fix :warning:</p> <p>A malicious client could send a specially crafted HTTP request, triggering an uncaught exception and killing the Node.js process:</p> <blockquote> <p>RangeError: Invalid WebSocket frame: RSV2 and RSV3 must be clear at Receiver.getInfo (/.../node_modules/ws/lib/receiver.js:176:14) at Receiver.startLoop (/.../node_modules/ws/lib/receiver.js:136:22) at Receiver._write (/.../node_modules/ws/lib/receiver.js:83:10) at writeOrBuffer (internal/streams/writable.js:358:12)</p> </blockquote> <p>This bug was introduced by <a href="https://github.com/socketio/engine.io/commit/f3c291fa613a9d50c924d74293035737fdace4f2">this commit</a>, included in <code>engine.io@4.0.0</code>, so previous releases are not impacted.</p> <p>Thanks to Marcus Wejderot from Mevisio for the responsible disclosure.</p> <h3>Bug Fixes</h3> <ul> <li>properly handle invalid data sent by a malicious websocket client (<a href="https://github.com/socketio/engine.io/commit/c0e194d44933bd83bf9a4b126fca68ba7bf5098c">c0e194d</a>)</li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/socketio/engine.io/commit/f3b761dc560e6cd045ef42939dc28d7138f245e9"><code>f3b761d</code></a> chore(release): 6.1.1</li> <li><a href="https://github.com/socketio/engine.io/commit/c0e194d44933bd83bf9a4b126fca68ba7bf5098c"><code>c0e194d</code></a> fix: properly handle invalid data sent by a malicious websocket client</li> <li><a href="https://github.com/socketio/engine.io/commit/b04967b52eb1574cfaa6e24bdf164096322be96a"><code>b04967b</code></a> refactor: import Node's setTimeout & clearTimeout to prevent ambiguity (<a href="https://github-redirect.dependabot.com/socketio/engine.io/issues/632">#632</a>)</li> <li>See full diff in <a href="https://github.com/socketio/engine.io/compare/6.1.0...6.1.1">compare view</a></li> </ul> </details> <br />

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CH Albach

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[RW-7652][risk=no] Mitigate egress suspension test timeouts (#6129)

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[risk=low][no ticket] Bump follow-redirects from 1.14.6 to 1.14.7 in /ui (#6145) Bumps [follow-redirects](https://github.com/follow-redirects/follow-redirects) from 1.14.6 to 1.14.7. - [Release notes](https://github.com/follow-redirects/follow-redirects/releases) - [Commits](https://github.com/follow-redirects/follow-redirects/compare/v1.14.6...v1.14.7) --- updated-dependencies: - dependency-name: follow-redirects dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

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bumping RT CDR (#6146) [no ticket][risk=no] bumping test RT CDR

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commit sha 02828aaa3a0d0069707804f327a78b3658c19f45

[risk=low][no ticket] Bump follow-redirects from 1.14.4 to 1.14.7 in /e2e (#6147) Bumps [follow-redirects](https://github.com/follow-redirects/follow-redirects) from 1.14.4 to 1.14.7. - [Release notes](https://github.com/follow-redirects/follow-redirects/releases) - [Commits](https://github.com/follow-redirects/follow-redirects/compare/v1.14.4...v1.14.7) --- updated-dependencies: - dependency-name: follow-redirects dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

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revert test RT CDR (#6149) [no ticket][risk=no] revert test RT CDR

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Access Tiers -> Data Access Tiers

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allow othertext to push down modules table

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format data access tier names

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WIP AccessModuleTable

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bumping RT CDR (#6146) [no ticket][risk=no] bumping test RT CDR

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commit sha 02828aaa3a0d0069707804f327a78b3658c19f45

[risk=low][no ticket] Bump follow-redirects from 1.14.4 to 1.14.7 in /e2e (#6147) Bumps [follow-redirects](https://github.com/follow-redirects/follow-redirects) from 1.14.4 to 1.14.7. - [Release notes](https://github.com/follow-redirects/follow-redirects/releases) - [Commits](https://github.com/follow-redirects/follow-redirects/compare/v1.14.4...v1.14.7) --- updated-dependencies: - dependency-name: follow-redirects dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

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[risk=low][no ticket] Bump follow-redirects from 1.14.4 to 1.14.7 in /e2e (#6147) Bumps [follow-redirects](https://github.com/follow-redirects/follow-redirects) from 1.14.4 to 1.14.7. - [Release notes](https://github.com/follow-redirects/follow-redirects/releases) - [Commits](https://github.com/follow-redirects/follow-redirects/compare/v1.14.4...v1.14.7) --- updated-dependencies: - dependency-name: follow-redirects dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

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PR merged all-of-us/workbench

Bump follow-redirects from 1.14.4 to 1.14.7 in /e2e dependencies javascript

Bumps follow-redirects from 1.14.4 to 1.14.7. <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/follow-redirects/follow-redirects/commit/2ede36d7c60d3acdcd324dcd99a9dbd52e4fb3a6"><code>2ede36d</code></a> Release version 1.14.7 of the npm package.</li> <li><a href="https://github.com/follow-redirects/follow-redirects/commit/8b347cbcef7c7b72a6e9be20f5710c17d6163c22"><code>8b347cb</code></a> Drop Cookie header across domains.</li> <li><a href="https://github.com/follow-redirects/follow-redirects/commit/6f5029ae1a0fdab4dc25f6379a5ee303c2319070"><code>6f5029a</code></a> Release version 1.14.6 of the npm package.</li> <li><a href="https://github.com/follow-redirects/follow-redirects/commit/af706bee57de954414c0bde0a9f33e62beea3e52"><code>af706be</code></a> Ignore null headers.</li> <li><a href="https://github.com/follow-redirects/follow-redirects/commit/d01ab7a5c5df3617c7a40a03de7af6427fdfac55"><code>d01ab7a</code></a> Release version 1.14.5 of the npm package.</li> <li><a href="https://github.com/follow-redirects/follow-redirects/commit/40052ea8aa13559becee5795715c1d45b1f0eb76"><code>40052ea</code></a> Make compatible with Node 17.</li> <li><a href="https://github.com/follow-redirects/follow-redirects/commit/86f7572f9365dadc39f85916259b58973819617f"><code>86f7572</code></a> Fix: clear internal timer on request abort to avoid leakage</li> <li><a href="https://github.com/follow-redirects/follow-redirects/commit/2e1eaf0218c5315a2ab27f53964d0535d4dafb51"><code>2e1eaf0</code></a> Keep Authorization header on subdomain redirects.</li> <li><a href="https://github.com/follow-redirects/follow-redirects/commit/2ad9e82b6277ae2104f7770e9ff1186cc6da29d4"><code>2ad9e82</code></a> Carry over Host header on relative redirects (<a href="https://github-redirect.dependabot.com/follow-redirects/follow-redirects/issues/172">#172</a>)</li> <li>See full diff in <a href="https://github.com/follow-redirects/follow-redirects/compare/v1.14.4...v1.14.7">compare view</a></li> </ul> </details> <br />

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pull request commentall-of-us/workbench

Bump follow-redirects from 1.14.4 to 1.14.7 in /e2e

e2e version of #6145

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PR opened all-of-us/workbench

[risk=no][no ticket] rm unused node-gyp

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PR checklist

  • [ ] This PR meets the Acceptance Criteria in the JIRA story
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