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Deploy 7.1.0 to production.#1313

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

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Commits on Feb 9, 2024

• first shot at linking to JB2 instead of JB1

  scottcain

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Commits on Feb 27, 2024

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

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Commits on Feb 28, 2024

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

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

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  oblodgett

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

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  oblodgett

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• fair chance I got the proxy settings for jbrowse2 right

  scottcain

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

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  oblodgett

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• making the variant jbrowse link generation point at jbrowse2

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• removing species as an arg since taxonid is required.

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Commits on Feb 29, 2024

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

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• adding jbrowse orthology track templates to constants

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• Update package.json

  dustine32

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

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

  scottcain

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• forgot the '2' on the jbrowse2 link

  scottcain

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

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  scottcain

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Commits on Mar 1, 2024

• Added the default styles for gocam-viz

  tmushayahama

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• updated the gocam-viz to display current legend

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• SCRUM-2025 update DiseaseToGeneTable for PG DAs

  adamgibs

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• Added dockerfile for ui build

  

  oblodgett

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• Reverted deleted files

  

  oblodgett

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• Reverted deleted files

  

  oblodgett

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• update package.json and Dockerfile

  adamgibs

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• Added back nginx conf file

  

  oblodgett

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  adamgibs

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• SCRUM-3647 add AnnotatedEntitiesPopupCuration to DiseaseToGeneTable

  adamgibs

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

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Commits on Mar 4, 2024

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

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  oblodgett

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• SCRUM-3647 switched column order

  adamgibs

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• SCRUM-3647 add additional details columns

  adamgibs

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• SCRUM-3647 suppress annotation details if via orthology

  adamgibs

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

  adamgibs

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

  adamgibs

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

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  adamgibs

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• SCRUM-3647 fix column error

  adamgibs

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• SCRUM-3647 make assertedGenes link internal

  adamgibs

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Commits on Mar 5, 2024

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

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  adamgibs

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• SCRUM-3648 add filter code to columns

  adamgibs

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• SCRUM-3648 add sortOptions

  adamgibs

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Commits on Mar 6, 2024

• SCRUM-3648 remove hardcoding for evidence code

  adamgibs

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Commits on Mar 7, 2024

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

  scottcain

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

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  adamgibs

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• SCRUM-3649 add back download button

  adamgibs

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

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  adamgibs

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• rename filter for disease column

  cmpich

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

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  cmpich

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• update disease filter

  adamgibs

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• SCRUM-3648 update basedOn column help text

  adamgibs

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• SCRUM-3648 update gene filter name

  adamgibs

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

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  adamgibs

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

  oblodgett

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

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  scottcain

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Commits on Mar 12, 2024

• update gene diseaseAnnotationTable reference column to use pumModIds

  adamgibs

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Commits on Mar 14, 2024

• upate diseasePage associated genes table to use pubmedPubModIDs

  adamgibs

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• update allelePage disease assocations table to use pubmedPubModIDs

  adamgibs

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• remove getRefStrings

  adamgibs

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Commits on Mar 15, 2024

• update AnnotatedEntitiesPopupCuration to use pubModIds

  adamgibs

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• remove getRefString

  adamgibs

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• remove underscores in disease qualifiers

  adamgibs

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

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  adamgibs

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Commits on Mar 26, 2024

• bumping seqpanel version to give explicit warning about inferred sequences

  scottcain

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

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  scottcain

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Commits on Mar 28, 2024

• Update README.md

  motenko

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

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Commits on Apr 2, 2024

• adding region highlighting for variants linked out to JBrowse

  scottcain

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Commits on Apr 3, 2024

• updating jbrowse menu link to point at JB2

  scottcain

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

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

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  scottcain

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• improving the buffer around genes when highlighting a variant

  scottcain

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

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  scottcain

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Commits on Apr 4, 2024

• Made changes to columns according to new API Response

  VarunReddy1111

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Commits on Apr 5, 2024

• Indentation

  VarunReddy1111

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• Changed the disease link rendering component

  VarunReddy1111

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• Added filter names

  VarunReddy1111

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Commits on Apr 8, 2024

• Changes to Gene Table in Disease Page

  VarunReddy1111

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

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

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

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Commits on Apr 9, 2024

• Fixed gene table in disease page according to API fields

  VarunReddy1111

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• better spacing

  VarunReddy1111

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• Removed the method getGeneObject

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Commits on Apr 10, 2024

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

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  VarunReddy1111

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Commits on Apr 17, 2024

• Fixing gene hyperlink

  VarunReddy1111

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• Disabling downloads for data tables larger than 90000 rows

  VarunReddy1111

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• Added downloads page link

  VarunReddy1111

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• indentation fix

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• Removed unsued useState import

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• Removed setDisabled function

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Commits on Apr 18, 2024

• Changed the constant name to DOWNLOAD_BUTTON_THRESHOLD

  VarunReddy1111

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

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  VarunReddy1111

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

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  VarunReddy1111

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

  VarunReddy1111

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

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Commits on Apr 19, 2024

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

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

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• adding proxy entries for JB2 for test and production

  scottcain

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• Change in annotation details pop

  VarunReddy1111

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

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Commits on Apr 26, 2024

• Update release to the snapshot date

  oblodgett

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

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• SCRUM-3985 update basedOn and GeneticModifiersCellCuration identifiers

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• remove unused release data variable

  adamgibs

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

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Commits on Apr 29, 2024

• SCRUM-3986 update StrainBackground identifier

  adamgibs

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

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  adamgibs

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Commits on May 1, 2024

• Updated test API server

  oblodgett

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• Merge branch 'stage' into update_cdk_jbrowse

  oblodgett

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• Merge branch 'test' into stage

  oblodgett

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• Merge branch 'stage' into update_cdk_jbrowse

  oblodgett

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• Updated test API server

  oblodgett

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• Merge branch 'stage' into update_cdk_jbrowse

  oblodgett

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

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

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Commits on May 2, 2024

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

  scottcain

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

  scottcain

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

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• Added new make file targets for ui deployments

  oblodgett

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

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