Merge oncokb-curation feature branch into master - #119

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calvinlu3 wants to merge 749 commits into

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Commits on Aug 13, 2024

Update pom version
oncokb-bot
committed
1aecfe2
Update docker-release.yml
zhx828
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ba29ccc
Update docker-release.yml
zhx828
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341934a
Update pom version
oncokb-bot
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eea2ce2
Update docker-release.yml
zhx828
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640d1c7
Update pom version
oncokb-bot
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7f7aed5
Update after-branch-commit.yml
zhx828
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77721c0
Update after-branch-commit.yml
zhx828
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a394639
Update pom version
oncokb-bot
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41a0340
Tagging release on sentry
zhx828
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dc18229

Commits on Aug 14, 2024

Allow excluded CT to be review (#415)
calvinlu3
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63d9572
Update pom version
oncokb-bot
committed
dd108ab

Commits on Aug 15, 2024

Commits on Aug 16, 2024

Commits on Aug 21, 2024

Use treatment valuePath when generating review for excludedRCTs
zhx828
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64b7e2c
Merge pull request #423 from zhx828/fix-ecluded-rcts
zhx828
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7950e4f
Update pom version
oncokb-bot
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3663def

Commits on Aug 22, 2024

Handle when Instant json element is a json object
zhx828
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ce5ea2e
Merge pull request #424 from zhx828/hot-fix
zhx828
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c3ce224

Commits on Aug 23, 2024

Textarea in review mode should fit text content (#427)
calvinlu3
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462c4c4
Update pom version
oncokb-bot
committed
565bc5b
Fix reject cancer type name review (#428)
calvinlu3
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f661d40

Commits on Aug 30, 2024

Add reference to oncokb sop alteration nomenclature in add mutation modal helper (#432)
calvinlu3
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2d1016a
Update pom version
oncokb-bot
committed
d831031

Commits on Sep 9, 2024

Avoid fetching management info repeatedly
zhx828
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7f64f9b
Do not rerender the side bar when loading session
zhx828
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6575c8c

Commits on Sep 10, 2024

Fix drug code not selectable (#435)
calvinlu3
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fee10a2
Merge pull request #434 from zhx828/fix-user-page
zhx828
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e0d7e91

Commits on Sep 13, 2024

Bump actions to latest version (#438)
calvinlu3
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860dbab

Commits on Sep 19, 2024

resize text area when input changes (#440)
bprize15
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5cc5a79

Commits on Sep 20, 2024

add sorting by firebase index (#443)
bprize15
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8f0b194

Commits on Sep 23, 2024

Delete mutation/tumor/treatment as last step to avoid stale index (#444)
calvinlu3
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f269cf8

Commits on Sep 24, 2024

Commits on Sep 25, 2024

Fixed data validation tool (#447)
jfkonecn
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f3e0d76
Allow curating mutation summary (#433)
zhx828
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0d93628

Commits on Sep 26, 2024

Parse protein change case insensitive (#441)
zhx828
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8200d24

Commits on Sep 30, 2024

Fix adding CDx biomarker association (#450)
calvinlu3
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88e15ca
use firebase properties directly in backend (#451)
bprize15
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cc47b5a

Commits on Oct 1, 2024

Commits on Oct 4, 2024

Add tests for stale indices check (#455)
calvinlu3
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df84037

Commits on Oct 9, 2024

Update setup-java action
zhx828
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3280ed7
Merge pull request #457 from oncokb/zhx828-patch-1
zhx828
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5ac76a1
Update pom version
oncokb-bot
committed
f4e870b

Commits on Oct 14, 2024

Re-support AsyncTable sorting (#459)
calvinlu3
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6c7b3af

Commits on Oct 15, 2024

Support uploading mutation in somatic and germline (#458)
zhx828
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7f20f2f

Commits on Oct 22, 2024

Update CDx curation panel to allow combination drugs (#461)
calvinlu3
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41ad5ad
Update pom version
oncokb-bot
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6824ffb
set cdx and type to undefined when fdaSubmissionEntity not found (#460)
bprize15
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1e73e6e

Commits on Oct 24, 2024

Added core submission logic (#370)

authored
a4a7ca4
Update pom version
oncokb-bot
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ec9801b

Commits on Oct 25, 2024

Update .version-level
jfkonecn
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2464ef6
Update action files to align the version level to minor
oncokb-bot
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45aafd2
Update pom version
oncokb-bot
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d5dc7b0
Update .version-level
jfkonecn
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ebc17a4
Update action files to align the version level to patch
oncokb-bot
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19d16a2
Update pom version
oncokb-bot
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93e8a6d

Commits on Oct 28, 2024

add genomic indicators to processDeletion (#464)
bprize15
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4160079

Commits on Oct 31, 2024

Commits on Nov 4, 2024

Give option to create gene when importing data
zhx828
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a8ad70b

Commits on Nov 6, 2024

Merge pull request #468 from zhx828/allow-create-gene
zhx828
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8708e25

Commits on Nov 7, 2024

Create gene on gene link click if does not exist (#469)
bprize15
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8b4edf6

Commits on Nov 8, 2024

move gene creation logic to gene page (#471)
bprize15
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25b0b77
Update pom version
oncokb-bot
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dbeec0c

Commits on Nov 12, 2024

Gene header redesign (#470)
calvinlu3
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a346824

Commits on Nov 13, 2024

Parse slash in mutation name (#473)
calvinlu3
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2008722

Commits on Nov 14, 2024

Align germline color scheme with public website
zhx828
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6d54e66
Meta review should be created by default (#474)
calvinlu3
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e6051f8
Update pom version
oncokb-bot
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296292f
Added synonyms to Drugs Endpoint (#476)
jfkonecn
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a493407
Merge pull request #475 from zhx828/update-germline-schem
zhx828
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ad18556

Commits on Nov 19, 2024

Allow user to unlock review mode (#478)
calvinlu3
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84a4d28

Commits on Nov 20, 2024

Fix transcript edit page (#477)
calvinlu3
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8768f5a
Check against undefined array items for core submissions (#479)
jfkonecn
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c6cb0c9

Commits on Nov 21, 2024

Add keycloak idp mapper for picture attribute (#480)
calvinlu3
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288ad33
Update pom version
oncokb-bot
committed
77ead36

Commits on Dec 13, 2024

Remove duplicate processDeletion call (#483)
calvinlu3
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8f60f5e

Commits on Dec 26, 2024

Create script to backfill all oncokb canonical transcripts (#485)
calvinlu3
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2b82b44
Update pom version
oncokb-bot
committed
0ac3ae7

Commits on Jan 10, 2025

Add readOnly in curation page (#481)
gebbing12
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73006f5
Fix exon annotation not showing (#484)
calvinlu3
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63bbd18

Commits on Jan 16, 2025

Fix germline page crash (#487)
jfkonecn
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6546ba1

Commits on Jan 23, 2025

Let some component lazy load (#489)
calvinlu3
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24d5da8
Update pom version
oncokb-bot
committed
58a387e

Commits on Jan 24, 2025

Mark transcript as canonical in TranscriptTable (#490)
calvinlu3
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bc94019

Commits on Jan 28, 2025

Fix review when associated variants is undefined
calvinlu3
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52438b5
Temporarily disable heap
calvinlu3
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91a650e
Merge pull request #491 from calvinlu3/fix/fh-germline-save
calvinlu3
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fbb45aa
Update pom version
oncokb-bot
committed
f0642cb

Commits on Jan 29, 2025

Handle empty snapshot value in DiffViewer (#492)
calvinlu3
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61e99ff
Update pom version
oncokb-bot
committed
5da279e
Add Google Tag Manager Back (#493)
jfkonecn
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c6787d4
Update pom version
oncokb-bot
committed
0582e20

Commits on Jan 30, 2025

Fix germline GI name review (#494)
calvinlu3
authored
90a67f0

Commits on Feb 18, 2025

fix bug where empty treatment caused empty collapsible (#499)
bprize15
authored
daa9e9c
Update pom version
oncokb-bot
committed
4ccc3b3
Fixed global search (#498)
jfkonecn
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61b8ed6
Update pom version
oncokb-bot
committed
dc44a1c
Add custom column filtering for synchronous react-table (#486)
gebbing12
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2786256

Commits on Feb 28, 2025

Allow user to get a list of newly released genes (#501)
calvinlu3
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d6c4c46

Commits on Mar 12, 2025

Sync history between react-router-dom and mobx router store (#504)
calvinlu3
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0beadc9
Update pom version
oncokb-bot
committed
34566bd

Commits on Mar 20, 2025

All curators can access save button (#505)
jfkonecn
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c8f1109

Commits on Apr 11, 2025

Added null checks on validation table (#508)
jfkonecn
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3f6c715
Update pom version
oncokb-bot
committed
c204467

Commits on Apr 16, 2025

Decode Hugo Symbol in Curation Page (#510)
jfkonecn
authored
9e9906a

Commits on Apr 18, 2025

Removed quotes from value on data upload (#509)
jfkonecn
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90bf1e3
Update pom version
oncokb-bot
committed
62e4e85

Commits on Apr 21, 2025

Update arrays to objects in firebase (#507)
calvinlu3
authored
9e18561
Update action files to align the version level to minor
oncokb-bot
committed
60fc6f1
Update pom version
oncokb-bot
committed
99d446b

Commits on Apr 22, 2025

Cache drug list into Redis (#512)
calvinlu3
authored
7abb39f
Update pom version
oncokb-bot
committed
0bc7557
do not append null to inframe string (#511)
bprize15
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8c67c5f
Update .version-level
calvinlu3
authored
4a493ab
Update action files to align the version level to patch
oncokb-bot
committed
abb4116
Update pom version
oncokb-bot
committed
8298486
Wait for drug list before rendering curation page (#513)
calvinlu3
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1cead81

Commits on Apr 23, 2025

Other Biomarkers Now Works for Review Page (#514)
jfkonecn
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20a0189
Update pom version
oncokb-bot
committed
9794df7

Commits on Apr 24, 2025

fix duplicate authors in history tab (#515)
bprize15
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25958e4
Update pom version
oncokb-bot
committed
5d5fca1
allow download callback for oncokb table (#517)
bprize15
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c4c5a62

Commits on Apr 25, 2025

Improve import data UX and allow imports to override existing data (#516)
calvinlu3
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df5f5d4

Commits on Apr 28, 2025

Added back missing json fields in CompanionDiagnosticDevice (#518)
jfkonecn
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3dd1710

Commits on Apr 29, 2025

Added back missing json fields in CompanionDiagnosticDevice (#518)
jfkonecn
authored
0ee1a14
Update pom version
oncokb-bot
committed
07f1f99

Commits on May 5, 2025

Convert FdaSubmission decisionDate and dateReceived from Instant to LocalDate (#520)
calvinlu3
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af5be5a
Update pom version
oncokb-bot
committed
48ca1fb

Commits on May 7, 2025

Fix FDASubmission fetch and show FDASubmission form in popover (#521)
calvinlu3
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4bf940e

Commits on May 19, 2025

Add excel like column filtering and fix CDx table searching (#522)
calvinlu3
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aec2479

Commits on May 20, 2025

Feature/data download (#523)
calvinlu3
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c8e296f
Update pom version
oncokb-bot
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dc06030
automatically end review mode if no active reviewer for 5 minutes (#524)
bprize15
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90c1b81
Update pom version
oncokb-bot
committed
3a9ae04

Commits on Jun 2, 2025

only set needs review if non name uuids (#525)
bprize15
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e93cdf3

Commits on Jun 10, 2025

Curation page no longer freezing (#527)
jfkonecn
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be684df

Commits on Jun 30, 2025

Unauthorized page is no longer blank (#528)

ReshmaRamaiah10
and
Ramaiah
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8e8e058
Update pom version
oncokb-bot
committed
8610b04

Commits on Jul 3, 2025

allow selecting neither and unknown as gene types (#526)
bprize15
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325567f

Commits on Jul 14, 2025

Handle case when name_review does not exist (#529)
calvinlu3
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d61d5c0
Update pom version
oncokb-bot
committed
3be268e

Commits on Jul 21, 2025

Don't check lastActiveReview when determine if there is unreviewed content (#531)
calvinlu3
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99fd6ac
Update pom version
oncokb-bot
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0ba33c6

Commits on Jul 22, 2025

Feat/support hgvsg (#530)
bprize15
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79f019b
Update pom version
oncokb-bot
committed
53a5896

Commits on Aug 1, 2025

Fixed infinite re-rendering when you delete a cancer type (#533)
ReshmaRamaiah10
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952e6ce

Commits on Aug 18, 2025

review uuid doesn't have 'false' value any more (#534)
ReshmaRamaiah10
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c009293

Commits on Aug 20, 2025

Added request/response status logging (#537)
jfkonecn
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4462bb0

Commits on Aug 21, 2025

use somatic gene type and background for both somatic and germline (#536)
bprize15
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367da90

Commits on Sep 4, 2025

Feat/support p14 (#541)
bprize15
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c4e681b

Commits on Sep 22, 2025

Update docker-release.yml (#548)
jfkonecn
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8ee753a
Update pom version
oncokb-bot
committed
3147ffb

Commits on Sep 30, 2025

Fix collapsible incorrectly showing no entry (#549)
jfkonecn
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8c5dbb9

Commits on Oct 2, 2025

Prevent duplicate VUS from being added (#550)
jfkonecn
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7cdaf66

Commits on Oct 9, 2025

Removed need to change version controlled files configurations for local development (#551)
jfkonecn
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46e265b

Commits on Oct 10, 2025

Fixed Failed to promote VUS to mutation (#552)
jfkonecn
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471ac4b

Commits on Oct 15, 2025

Allow mutation effect curation in germline (#553)
calvinlu3
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360b519

Commits on Oct 31, 2025

Map allele state to mechanism of inheritance in GI
calvinlu3
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2f56336
Merge pull request #558 from calvinlu3/replace-allele-state-with-moi
calvinlu3
authored
9a82e84
Update pom version
oncokb-bot
committed
a4dfe91

Commits on Nov 5, 2025

Update firebase-gene-service.ts (#559)
calvinlu3
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8a981a4
Update pom version
oncokb-bot
committed
d7f26bf

Commits on Nov 11, 2025

Trigger a gene save when exiting review or button click (#560)
calvinlu3
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1828e73
Update pom version
oncokb-bot
committed
74026cf

Commits on Nov 14, 2025

Allow Cdx biomarker association to be edited (#561)
calvinlu3
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ef46345

Commits on Nov 20, 2025

Trim off comment in string mutation (#562)
calvinlu3
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b49d07e
Update pom version
oncokb-bot
committed
546e314

Commits on Nov 25, 2025

Update as firebase list when updating association variants (#563)
calvinlu3
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13b60db
Update pom version
oncokb-bot
committed
3c75f55

Commits on Dec 2, 2025

Fix gene type evidence download (#564)
calvinlu3
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cf84e81
Update pom version
oncokb-bot
committed
27a2821

Commits on Dec 3, 2025

Add alteration object when generating pathogenic variants (#565)
calvinlu3
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91c202c
Update pom version
oncokb-bot
committed
22a2fc3

Commits on Dec 12, 2025

Show save gene button on germline pages (#566)
calvinlu3
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38331f3
Update pom version
oncokb-bot
committed
7e1c9fe
Fix failing webdriver tests (#568)
calvinlu3
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c1625fe
Add name uuid to vus (#569)
calvinlu3
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7f18ae1

Commits on Dec 17, 2025

Return gemrline and somatic gene releases (#570)
calvinlu3
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848ee00
Update pom version
oncokb-bot
committed
cc9c0bb

Commits on Jan 6, 2026

do not allow vus to be added if it is a hotspot (#571)
bprize15
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8c21047

Commits on Jan 15, 2026

Restrict protein start and end to numbers only (#575)
calvinlu3
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b1d7298

Commits on Jan 22, 2026

Commits on Jan 27, 2026

implement add range modal (#573)
bprize15
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1fd1741

Commits on Feb 3, 2026

Fix trailing whitespace not displayed in diff viewer
calvinlu3
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62fe8ce
Feature/germline evidence download (#579)
calvinlu3
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4bd5502

Commits on Feb 4, 2026

Commits on Feb 11, 2026

Add column indicating if imported germline variant is curated in somatic
calvinlu3
committed
abd4ddd

Commits on Feb 16, 2026

Add PR label validation workflow (#584)
jfkonecn
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e31d107

Commits on Feb 18, 2026

Merge pull request #582 from calvinlu3/germline-somatic-overlap
calvinlu3
authored
9ccd957

Commits on Feb 19, 2026

Update check-pr-label.yml
jfkonecn
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f5c20ec
Update pom version
oncokb-bot
committed
2f4aa18

Commits on Feb 20, 2026

Debug websocket issue
calvinlu3
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1b4031f
Get rid of debugging stuff
calvinlu3
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2c7a228
Merge pull request #586 from oncokb/fix/websocket
calvinlu3
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1c56c1b
Update pom version
oncokb-bot
committed
73ffcb1

Commits on Feb 25, 2026

Fix/drug review (#587)
calvinlu3
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1c5d7d4

Commits on Mar 3, 2026

Revert "Revert "implement add range modal"" (#585)
bprize15
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c1df3d6
allow curators to add description to range (#578)
bprize15
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b7c1b37
Update pom version
oncokb-bot
committed
b8b1576

Commits on Mar 16, 2026

fix curation references tab (#588)
bprize15
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32c84f5
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oncokb-bot
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e384fa7
return undefined instead of NaN when protein position is undefined (#589)
bprize15
authored
de4653b
Update pom version
oncokb-bot
committed
7e4cfaf

Commits on Mar 30, 2026

Remove prop/fda level fields for germline
calvinlu3
committed
307f3a4
Merge pull request #592 from oncokb/disable-fields-germline
calvinlu3
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7792b51
Update pom version
oncokb-bot
committed
40974ca

Commits on Apr 23, 2026

Commits on May 1, 2026

Support gemrline tx data download (#596)
calvinlu3
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e83fc2b

Commits on May 4, 2026

Fix stale entity writes when accepting create reviews (#593)
jfkonecn
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d848600
Update pom version
oncokb-bot
committed
a0d751b
Feature/tt specific desc (#591)
calvinlu3
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431cc41

Commits on May 12, 2026

Feature for rich text editor using TipTap library so we can more structured texts
calvinlu3
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7476e0e
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oncokb-bot
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1b37488

Commits on May 13, 2026

Updates to tiptap feature (#598)
calvinlu3
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0b9382b
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oncokb-bot
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bd19603

Commits on May 18, 2026

Fix/editor bugs (#599)
calvinlu3
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a298626
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oncokb-bot
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afd7c18

Commits on May 22, 2026

Fix stale drugs fetch (#600)
calvinlu3
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af43d9d
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oncokb-bot
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4a9557e

Commits on Jun 1, 2026

Investigate/create existing gene (#601)
calvinlu3
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2404c7c
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oncokb-bot
committed
8ff8eea
Make sure tooltip does not close when user is actively editing (#602)
calvinlu3
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827e204

Commits on Jun 4, 2026

Fix placement of ref in editor (#603)
calvinlu3
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916b81b
Update pom version
oncokb-bot
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b823f7a

Commits on Jul 2, 2026

Fix missing references on copy (#605)
calvinlu3
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0d0e497
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oncokb-bot
committed
2c2ba3d

Commits on Jul 6, 2026

Fix needsReview for empty sections (#606)
calvinlu3
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3f8d7dd

Commits on Jul 15, 2026

Add new save to preview environment button (#608)
calvinlu3
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c064fb5
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oncokb-bot
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65b95c2

Commits on Aug 5, 2026

Update import tool to normalize germline variants (#609)
calvinlu3
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7455e33
Update pom version
oncokb-bot
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6a320b0