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Deploy 7.1.0 to production.#1313

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Merged

oblodgett merged 117 commits intomainalliance-genome/agr_ui:mainfrom testalliance-genome/agr_ui:testCopy head branch name to clipboardMay 2, 2024

+589-219

Commits

Commits on Feb 9, 2024

• first shot at linking to JB2 instead of JB1

  scottcain

  committed
  d091a9c

Commits on Feb 27, 2024

• Merge pull request #1263 from alliance-genome/stage

  Show description for 589cbc7
  scottcain

  authored
  589cbc7

Commits on Feb 28, 2024

• making generated JB2 links use only trackIds for tracks that actually exist

  Show description for a915be2
  scottcain

  committed
  a915be2

• Merge pull request #1266 from alliance-genome/main

  Show description for 25b448c
  oblodgett

  authored
  25b448c

• Merge pull request #1269 from alliance-genome/test

  Show description for 4de8954
  oblodgett

  authored
  4de8954

• fair chance I got the proxy settings for jbrowse2 right

  scottcain

  committed
  cb8b72e

• Merge pull request #1270 from alliance-genome/add_jbrowse2_cdk_to_stage

  Show description for d34bee4
  oblodgett

  authored
  d34bee4

• making the variant jbrowse link generation point at jbrowse2

  Show description for 0609c8a
  scottcain

  committed
  0609c8a

• removing species as an arg since taxonid is required.

  scottcain

  committed
  12e820e

Commits on Feb 29, 2024

• Merge pull request #1271 from alliance-genome/switch_to_jb2

  Show description for aae4711
  scottcain

  authored
  aae4711

• adding jbrowse orthology track templates to constants

  scottcain

  committed
  10df6b4

• Update package.json

  dustine32

  authored
  99c0c79

• Merge pull request #1274 from alliance-genome/wc-gocam-viz-34

  Show description for 55b116b
  dustine32

  authored
  55b116b

• added error checking for unlocalized genes and cleaned up presentation a little bit

  scottcain

  committed
  a7327d4

• forgot the '2' on the jbrowse2 link

  scottcain

  committed
  9a93049

• Merge pull request #1275 from alliance-genome/add_orthology_jbrowse2

  Show description for 03dfdde
  scottcain

  authored
  03dfdde

Commits on Mar 1, 2024

• Added the default styles for gocam-viz

  tmushayahama

  committed
  cc35c8b

• updated the gocam-viz to display current legend

  tmushayahama

  authored
  5af3172

• SCRUM-2025 update DiseaseToGeneTable for PG DAs

  adamgibs

  committed
  5c9203a

• Added dockerfile for ui build

  

  oblodgett

  authored and

  adamgibs

  committed
  47991a3

• Reverted deleted files

  

  oblodgett

  authored and

  adamgibs

  committed
  b2c2bb4

• Reverted deleted files

  

  oblodgett

  authored and

  adamgibs

  committed
  a785af1

• update package.json and Dockerfile

  adamgibs

  committed
  6266287

• Added back nginx conf file

  

  oblodgett

  authored and

  adamgibs

  committed
  7d33185

• SCRUM-3647 add AnnotatedEntitiesPopupCuration to DiseaseToGeneTable

  adamgibs

  committed
  eb0bd62

• Merge pull request #1276 from alliance-genome/SCRUM-2016

  Show description for 9d0076c
  adamgibs

  authored
  9d0076c

Commits on Mar 4, 2024

• Merge pull request #1277 from alliance-genome/update-gocam-viz-1272

  Show description for 9104175
  oblodgett

  authored
  9104175

• SCRUM-3647 switched column order

  adamgibs

  committed
  78cc317

• SCRUM-3647 add additional details columns

  adamgibs

  committed
  a412920

• SCRUM-3647 suppress annotation details if via orthology

  adamgibs

  committed
  173bfea

• SCRUM-3647 add reference link for via-orthology annotations

  adamgibs

  committed
  a5087a2

• SCRUM-3647 add evidence code for via-orthology annotations

  adamgibs

  committed
  fef5637

• Merge pull request #1278 from alliance-genome/SCRUM-3647

  Show description for c9d5764
  adamgibs

  authored
  c9d5764

• SCRUM-3647 fix column error

  adamgibs

  committed
  0551bcb

• SCRUM-3647 make assertedGenes link internal

  adamgibs

  committed
  4b28407

Commits on Mar 5, 2024

• Merge pull request #1279 from alliance-genome/SCRUM-3647

  Show description for e006638
  adamgibs

  authored
  e006638

• SCRUM-3648 add filter code to columns

  adamgibs

  committed
  627c9e7

• SCRUM-3648 add sortOptions

  adamgibs

  committed
  31c0eed

Commits on Mar 6, 2024

• SCRUM-3648 remove hardcoding for evidence code

  adamgibs

  committed
  8a9af29

Commits on Mar 7, 2024

• adding a few proxy lines to allow fetching RGD and XenBase data

  scottcain

  committed
  594ad0e

• Merge pull request #1281 from alliance-genome/SCRUM-3648

  Show description for adb6f83
  adamgibs

  authored
  adb6f83

• SCRUM-3649 add back download button

  adamgibs

  committed
  fa58a7c

• Merge pull request #1283 from alliance-genome/SCRUM-3649

  Show description for a4f01a9
  adamgibs

  authored
  a4f01a9

• rename filter for disease column

  cmpich

  committed
  67bd1a2

• Merge pull request #1284 from alliance-genome/SCRUM-3648

  Show description for b56fda7
  cmpich

  authored
  b56fda7

• update disease filter

  adamgibs

  committed
  a04239d

• SCRUM-3648 update basedOn column help text

  adamgibs

  committed
  5a6705c

• SCRUM-3648 update gene filter name

  adamgibs

  committed
  2207047

• Merge pull request #1286 from alliance-genome/SCRUM-3648

  Show description for 3647e38
  adamgibs

  authored
  3647e38

• Merge pull request #1285 from alliance-genome/disease-filter-update

  oblodgett

  authored
  66b6b17

• Merge pull request #1282 from alliance-genome/update-jbrowse-proxy

  Show description for 991b13c
  scottcain

  authored
  991b13c

Commits on Mar 12, 2024

• update gene diseaseAnnotationTable reference column to use pumModIds

  adamgibs

  committed
  e8ebe6c

Commits on Mar 14, 2024

• upate diseasePage associated genes table to use pubmedPubModIDs

  adamgibs

  committed
  d4178b2

• update allelePage disease assocations table to use pubmedPubModIDs

  adamgibs

  committed
  bd45a70

• remove getRefStrings

  adamgibs

  committed
  220ae66

Commits on Mar 15, 2024

• update AnnotatedEntitiesPopupCuration to use pubModIds

  adamgibs

  committed
  5e6c0cc

• remove getRefString

  adamgibs

  committed
  e43fd77

• remove underscores in disease qualifiers

  adamgibs

  committed
  9332de4

• Merge pull request #1287 from alliance-genome/update-ref-string

  Show description for 108c3c9
  adamgibs

  authored
  108c3c9

Commits on Mar 26, 2024

• bumping seqpanel version to give explicit warning about inferred sequences

  scottcain

  committed
  d0b65f2

• Merge pull request #1288 from alliance-genome/KANBAN-522

  Show description for 689b681
  scottcain

  authored
  689b681

Commits on Mar 28, 2024

• Update README.md

  motenko

  authored
  4bb010c

• Merge pull request #1289 from alliance-genome/motenko-patch-1

  Show description for bdd06bf
  motenko

  authored
  bdd06bf

Commits on Apr 2, 2024

• adding region highlighting for variants linked out to JBrowse

  scottcain

  committed
  7bb6909

Commits on Apr 3, 2024

• updating jbrowse menu link to point at JB2

  scottcain

  committed
  0ebdcb1

• Merge pull request #1294 from alliance-genome/update_jbrowse_link

  Show description for e5f1628
  scottcain

  authored
  e5f1628

• Merge pull request #1293 from alliance-genome/jbrowse_add_var_hilite

  Show description for 22e8b2f
  scottcain

  authored
  22e8b2f

• improving the buffer around genes when highlighting a variant

  scottcain

  committed
  fea5a7d

• Merge pull request #1295 from alliance-genome/improve_jb2_buffer

  Show description for cff3508
  scottcain

  authored
  cff3508

Commits on Apr 4, 2024

• Made changes to columns according to new API Response

  VarunReddy1111

  committed
  6b5e93f

Commits on Apr 5, 2024

• Indentation

  VarunReddy1111

  committed
  8da7bb0

• Changed the disease link rendering component

  VarunReddy1111

  committed
  9d3fe07

• Added filter names

  VarunReddy1111

  committed
  c4c06f3

Commits on Apr 8, 2024

• Changes to Gene Table in Disease Page

  VarunReddy1111

  committed
  5228560

• Merge pull request #1296 from alliance-genome/SCRUM-3743

  Show description for 71d2a75
  VarunReddy1111

  authored
  71d2a75

• Revert "SCRUM-3743 UI work to display disease page associated alleles from persistent store"

  VarunReddy1111

  authored
  9efb2b6

• Merge pull request #1297 from alliance-genome/revert-1296-SCRUM-3743

  Show description for 4b6901b
  VarunReddy1111

  authored
  4b6901b

Commits on Apr 9, 2024

• Fixed gene table in disease page according to API fields

  VarunReddy1111

  committed
  82e4d03

• better spacing

  VarunReddy1111

  committed
  b70e725

• Removed the method getGeneObject

  VarunReddy1111

  committed
  3faee95

Commits on Apr 10, 2024

• Merge pull request #1298 from alliance-genome/fixing-disease-table-gene-page

  Show description for 13d0600
  VarunReddy1111

  authored
  13d0600

Commits on Apr 17, 2024

• Fixing gene hyperlink

  VarunReddy1111

  committed
  13f059a

• Disabling downloads for data tables larger than 90000 rows

  VarunReddy1111

  committed
  c19e141

• Added downloads page link

  VarunReddy1111

  committed
  f05e868

• indentation fix

  VarunReddy1111

  committed
  7950217

• Removed unsued useState import

  VarunReddy1111

  committed
  b924504

• Removed setDisabled function

  VarunReddy1111

  committed
  1152225

Commits on Apr 18, 2024

• Changed the constant name to DOWNLOAD_BUTTON_THRESHOLD

  VarunReddy1111

  committed
  803c50f

• Merge pull request #1300 from alliance-genome/SCRUM-3919

  Show description for e5f8b25
  VarunReddy1111

  authored
  e5f8b25

• Merge pull request #1301 from alliance-genome/SCRUM-3943

  Show description for e2ba550
  VarunReddy1111

  authored
  e2ba550

• Change to fix allele page disease associations table to not display Additional implicated genes and Strain Background

  VarunReddy1111

  committed
  ade3c70

• Merge pull request #1303 from alliance-genome/fixing-allele-page-disease-associations

  Show description for b6d1c4c
  VarunReddy1111

  authored
  b6d1c4c

Commits on Apr 19, 2024

• Change to display the additional implicated genes in annotation pop details

  VarunReddy1111

  committed
  48fcacc

• Merge pull request #1304 from alliance-genome/SCRUM-3943

  Show description for 3f14cd7
  VarunReddy1111

  authored
  3f14cd7

• adding proxy entries for JB2 for test and production

  scottcain

  committed
  690445a

• Change in annotation details pop

  VarunReddy1111

  committed
  4f99f6f

• Merge pull request #1306 from alliance-genome/fixing-allele-page-disease-associations

  Show description for 1e986f6
  VarunReddy1111

  authored
  1e986f6

Commits on Apr 26, 2024

• Update release to the snapshot date

  oblodgett

  committed
  66d03f7

• Merge pull request #1307 from alliance-genome/change_release_date

  Show description for 6b56143
  oblodgett

  authored
  6b56143

• SCRUM-3985 update basedOn and GeneticModifiersCellCuration identifiers

  adamgibs

  committed
  b0e24ec

• remove unused release data variable

  adamgibs

  committed
  f5966eb

• Merge pull request #1308 from alliance-genome/SCRUM-3985

  Show description for 36c279d
  adamgibs

  authored
  36c279d

Commits on Apr 29, 2024

• SCRUM-3986 update StrainBackground identifier

  adamgibs

  committed
  fbd317c

• Merge pull request #1309 from alliance-genome/SCRUM-3986

  Show description for b4f7df5
  adamgibs

  authored
  b4f7df5

Commits on May 1, 2024

• Updated test API server

  oblodgett

  committed
  96047c4

• Merge branch 'stage' into update_cdk_jbrowse

  oblodgett

  authored
  f632691

• Merge branch 'test' into stage

  oblodgett

  authored
  45caf96

• Merge branch 'stage' into update_cdk_jbrowse

  oblodgett

  authored
  c543694

• Updated test API server

  oblodgett

  committed
  bee3bcb

• Merge branch 'stage' into update_cdk_jbrowse

  oblodgett

  authored
  940f53d

• Merge pull request #1305 from alliance-genome/update_cdk_jbrowse

  Show description for be79cb9
  oblodgett

  authored
  be79cb9

• Merge pull request #1310 from alliance-genome/stage

  Show description for b05013c
  oblodgett

  authored
  b05013c

Commits on May 2, 2024

• fixes undefined problem, but not the ui problem (the jbrowse orthology panel shouldn't display for sars)

  scottcain

  committed
  8b46914

• removes the jbrowse orthology link panel for sars-cov-2

  scottcain

  committed
  5164a60

• Merge pull request #1311 from alliance-genome/fix_jbrowse_covid

  Show description for 2373ad2
  oblodgett

  authored
  2373ad2

• Added new make file targets for ui deployments

  oblodgett

  committed
  9c92040

• Merge pull request #1312 from alliance-genome/fix_redirects

  Show description for 94f6920
  oblodgett

  authored
  94f6920