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SCRUM-3511: deployment to production #1387

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b3ec6a7
Fixed tab issues
oblodgett Oct 25, 2023
2978fa0
Changed to amazon issued cert
oblodgett Oct 25, 2023
8b45e65
Attempt to fix test containers
oblodgett Oct 26, 2023
c5c6a4f
Merge pull request #1306 from alliance-genome/fix_tabs
oblodgett Oct 26, 2023
609f3db
Import cleanup
oblodgett Sep 21, 2023
ec97ee7
Removed JOINs
oblodgett Sep 21, 2023
29c250d
Remove json specific fields
oblodgett Sep 21, 2023
40d4ade
Refactored inject
oblodgett Sep 21, 2023
0271bbf
Updated imports and fixed classes
oblodgett Sep 21, 2023
f741632
Fix app file
oblodgett Sep 21, 2023
d51a9b0
Another import cleanup
oblodgett Oct 25, 2023
b5956f8
Added migration for missing stuff
oblodgett Oct 26, 2023
7a15795
Removed eager fetch of alliance member
oblodgett Oct 26, 2023
abc4c93
Replaced depricated variable
oblodgett Oct 26, 2023
bf0f688
Updated annotations
oblodgett Oct 26, 2023
36c48ca
Update seq's
oblodgett Oct 26, 2023
7a4a60c
Removed column type alias as it NPE's
oblodgett Oct 26, 2023
8cfd95d
Fixed timestamps in tests
oblodgett Oct 26, 2023
db24129
Merge branch 'alpha' into PRmerge/beta
mluypaert Oct 27, 2023
d37e720
Merge pull request #1308 from alliance-genome/PRmerge/beta
mluypaert Oct 27, 2023
061b8c0
Removed OneToOne unique constraints
oblodgett Oct 27, 2023
26b5930
Update SiteLayout.js
VarunReddy1111 Oct 30, 2023
567c3ab
Updated as per the comments by Olin
VarunReddy1111 Oct 30, 2023
37b3742
Merge branch 'alpha' into PRmerge/production
mluypaert Oct 31, 2023
354755c
Merge pull request #1311 from alliance-genome/PRmerge/production
mluypaert Oct 31, 2023
467a2bd
Removed exception suppression due to lambda
oblodgett Oct 31, 2023
4a14750
Change how lists are handled
oblodgett Oct 31, 2023
6870e64
Hopefully this works
oblodgett Nov 1, 2023
6370324
Updated test containers to run blue team ES
oblodgett Nov 1, 2023
d28aca9
Added new version of ES client
oblodgett Nov 1, 2023
0e0d28c
Updated teset containers
oblodgett Nov 1, 2023
1b55cd3
Merge branch 'alpha' into quarkus_3
oblodgett Nov 1, 2023
61d6026
Updated indexes and constraints
oblodgett Nov 2, 2023
cc78f1f
Merge pull request #1253 from alliance-genome/quarkus_3
oblodgett Nov 2, 2023
cd4cadc
Fix the default query to match all
oblodgett Nov 2, 2023
106d8ec
Merge branch 'alpha' into SCRUM-3385
oblodgett Nov 2, 2023
183e454
Merge pull request #1312 from alliance-genome/quarkus_3
oblodgett Nov 3, 2023
679b52e
Added condition for empty search filters
oblodgett Nov 3, 2023
76e5105
Merge pull request #1313 from alliance-genome/quarkus_3
oblodgett Nov 3, 2023
a445bf5
Merge branch 'alpha' into SCRUM-3385
oblodgett Nov 3, 2023
e9e2268
Fixed null query lists
oblodgett Nov 3, 2023
5867468
Merge branch 'alpha' into quarkus_3
oblodgett Nov 3, 2023
85d22f9
Merge pull request #1309 from alliance-genome/SCRUM-3385
oblodgett Nov 3, 2023
8e397dd
Merge branch 'alpha' into quarkus_3
oblodgett Nov 3, 2023
4f24b47
Merge pull request #1314 from alliance-genome/quarkus_3
oblodgett Nov 3, 2023
14baaa8
Fix for indexing on alpha
oblodgett Nov 9, 2023
e2b88f4
Merge pull request #1315 from alliance-genome/quarkus_3_fix
oblodgett Nov 9, 2023
54c89ea
Fixed issue with failing vocab query, however frontend needs to send …
oblodgett Nov 9, 2023
e728431
Merge pull request #1316 from alliance-genome/quarkus_3_fix
oblodgett Nov 10, 2023
9c8fad2
SCRUM-3439 update onChangeHandler for DatabaseStatusForm, FullNameForm,
adamgibs Oct 24, 2023
070681c
SCRUM-3439 update onValueChange functions
adamgibs Oct 24, 2023
7b9385f
SCRUM-3439 update datatable dataKeys
adamgibs Oct 25, 2023
26dc2ce
SCRUM-3439 upgrade to prime-react 10
adamgibs Nov 7, 2023
223288c
SCRUM-3439 updated DataTableHeaderFooterTemplate styling
adamgibs Nov 8, 2023
c5d3b17
SCRUM-3439 update ConditionRelationTable test
adamgibs Oct 23, 2023
1be86f2
SCRUM-3439 update Filter styles
adamgibs Nov 13, 2023
c304d31
SCRUM-3439 update DataTableHeaderFooterTemplate styles
adamgibs Nov 13, 2023
f2fbb66
Merge pull request #1323 from alliance-genome/SCRUM-3439
adamgibs Nov 13, 2023
6487447
Fix typo
markquintontulloch Nov 13, 2023
88de091
Merge branch 'alpha' into SCRUM-3501
oblodgett Nov 13, 2023
c317837
Merge pull request #1324 from alliance-genome/SCRUM-3501
markquintontulloch Nov 13, 2023
49b6c60
Merge branch 'alpha' into gh-actions-mergeback-v0.27.3-alpha
actions-user Nov 14, 2023
5a70c71
Merge pull request #1327 from alliance-genome/PRmerge/production
mluypaert Nov 14, 2023
9dacb8a
Reorged yet again the base sql query stuff
oblodgett Nov 10, 2023
2f34f04
Maybe fix for sets
oblodgett Nov 14, 2023
eb89175
Update set logic
oblodgett Nov 14, 2023
d730a1c
Merge pull request #1318 from alliance-genome/quarkus_3_fix
oblodgett Nov 14, 2023
228f728
Merge branch 'alpha' into gh-actions-mergeback-v0.27.3-alpha
mluypaert Nov 14, 2023
5ec1fc4
Merge pull request #1326 from alliance-genome/gh-actions-mergeback-v0…
mluypaert Nov 14, 2023
156a831
Fixed issue with child counts but calculating closure is slow
oblodgett Nov 9, 2023
657631a
Removed cors filter and added quarkus cors filter
oblodgett Nov 9, 2023
4bf30c5
Merge pull request #1328 from alliance-genome/fix_ontology_child_counts
oblodgett Nov 14, 2023
7a3edd2
Merge branch 'alpha' into fix_health_cors
oblodgett Nov 14, 2023
7ca7be3
Merge pull request #1329 from alliance-genome/fix_health_cors
oblodgett Nov 15, 2023
6de04b7
Limit reference list to 5 refs with link to detail page
markquintontulloch Nov 15, 2023
f1703c3
Use enum for file extensions
markquintontulloch Nov 15, 2023
d66ff7f
Merge branch 'alpha' into SCRUM-3499
markquintontulloch Nov 15, 2023
01af773
species model
VarunReddy1111 Nov 8, 2023
fc7877b
Revert "species model"
VarunReddy1111 Nov 8, 2023
59cec32
Revert "Revert "species model""
VarunReddy1111 Nov 8, 2023
2d772bc
adding migration file
VarunReddy1111 Nov 8, 2023
d56adf4
switched from javax to jakarta
VarunReddy1111 Nov 8, 2023
10ba139
Adding sequences
VarunReddy1111 Nov 8, 2023
74f3ffa
changes made as per linkml model
VarunReddy1111 Nov 10, 2023
53dade6
Changes in migration file
VarunReddy1111 Nov 14, 2023
0789f72
changes in db migration
VarunReddy1111 Nov 15, 2023
3167f40
Merge pull request #1330 from alliance-genome/set_file_extension
markquintontulloch Nov 15, 2023
ed0993b
Merge branch 'alpha' into SCRUM-3499
markquintontulloch Nov 15, 2023
6f0a5e1
Merge pull request #1331 from alliance-genome/SCRUM-3499
markquintontulloch Nov 15, 2023
e14c2dd
Fix link
markquintontulloch Nov 15, 2023
aaed1a7
Merge pull request #1333 from alliance-genome/SCRUM-3499_link_fix
markquintontulloch Nov 15, 2023
5ba5b87
Fix bug in gene ID lookup for RGD loads
markquintontulloch Nov 15, 2023
2f09ec3
Merge pull request #1335 from alliance-genome/SCRUM-3514
markquintontulloch Nov 15, 2023
09e5e6b
Changes in db migration to pass against validation tests
VarunReddy1111 Nov 15, 2023
849484d
Possible fix for 'failed to initialize collection...' error
markquintontulloch Nov 15, 2023
dc30e4c
Merge branch 'alpha' into SCRUM-3507
markquintontulloch Nov 15, 2023
39fb819
Use Hibernate.initialize instead of size to avoid NPE
markquintontulloch Nov 16, 2023
2c523a1
Merge branch 'SCRUM-3507' of https://github.com/alliance-genome/agr_c…
markquintontulloch Nov 16, 2023
c833060
Merge pull request #1336 from alliance-genome/SCRUM-3507
markquintontulloch Nov 16, 2023
2332ae7
Added data loads events vs bus
oblodgett Nov 9, 2023
3fe4ac4
Updated loading to use DTO specific classes
oblodgett Nov 15, 2023
17adeab
Updated scedulers
oblodgett Nov 15, 2023
8ffddbe
Merge branch 'alpha' into implement_species_model
oblodgett Nov 16, 2023
be9f1e3
Merge pull request #1334 from alliance-genome/data_loads
oblodgett Nov 16, 2023
8501160
Update views
markquintontulloch Nov 16, 2023
edaf3f8
Merge pull request #1338 from alliance-genome/SCRUM-3507_view_update
markquintontulloch Nov 16, 2023
7be8387
Merge branch 'alpha' into implement_species_model
oblodgett Nov 16, 2023
371b123
Changed the file name of db migration
VarunReddy1111 Nov 16, 2023
8ee174e
Removed unused import
VarunReddy1111 Nov 16, 2023
ecce2aa
Merge pull request #1332 from alliance-genome/implement_species_model
VarunReddy1111 Nov 17, 2023
88d699b
Initial commit for supplemental data in APIResponse
markquintontulloch Nov 17, 2023
f97d83d
Remove tooltip for references on allele page
markquintontulloch Nov 17, 2023
c657a6d
Merge branch 'alpha' into SCRUM-3499_remove_tooltip
markquintontulloch Nov 17, 2023
8f925e6
Merge pull request #1339 from alliance-genome/SCRUM-3499_remove_tooltip
markquintontulloch Nov 17, 2023
e5f13de
changes made in UI SCRUM-3517
VarunReddy1111 Nov 17, 2023
149c459
Merge pull request #1340 from alliance-genome/implement_species_model
VarunReddy1111 Nov 17, 2023
dd9eaec
Fix consolidated error message and supplemental map
markquintontulloch Nov 19, 2023
7000089
Rename map
markquintontulloch Nov 20, 2023
cc7aff5
Add single-value slot annotations to supplemental data error map
markquintontulloch Nov 20, 2023
ef82da2
Move counts to Entity Counts page
markquintontulloch Nov 20, 2023
1368700
UI test fixes
markquintontulloch Nov 20, 2023
f4c4624
Merge pull request #1341 from alliance-genome/SCRUM-3438
markquintontulloch Nov 20, 2023
3783da1
SCRUM-3350 sticky header and move save button to top
adamgibs Nov 17, 2023
7a98e71
SCRUM-3350 adjust header styling
adamgibs Nov 20, 2023
a44a1ba
Merge pull request #1342 from alliance-genome/SCRUM-3350
adamgibs Nov 20, 2023
9583a82
SCRUM-3524 refactor isEnabled
adamgibs Nov 20, 2023
f1a6ca1
SCRUM-3524 update column definition arrays
adamgibs Nov 20, 2023
2947bc5
Additional error logic
markquintontulloch Nov 20, 2023
be6db58
Merge branch 'alpha' into SCRUM-3473
markquintontulloch Nov 20, 2023
352f2ba
SCRUM-3524 update initial value of isInEditMode
adamgibs Nov 20, 2023
e53776c
removed sorting for common names column
VarunReddy1111 Nov 20, 2023
730b5ca
Merge pull request #1343 from alliance-genome/SCRUM-3524
adamgibs Nov 20, 2023
5200cdd
Small fixes
markquintontulloch Nov 20, 2023
c80eec3
Rename method
markquintontulloch Nov 20, 2023
b8eb5f7
Merge branch 'alpha' into SCRUM-3473
markquintontulloch Nov 20, 2023
0c66741
remove save button from AlleleDetailPage
adamgibs Nov 20, 2023
c433a8e
Merge pull request #1345 from alliance-genome/remove-save
adamgibs Nov 21, 2023
6c3930b
added species to dashboard SCRUM-3517
VarunReddy1111 Nov 21, 2023
ee40819
Merge pull request #1346 from alliance-genome/implement_species_model
VarunReddy1111 Nov 21, 2023
aa31424
Refactored map logic into one place
oblodgett Nov 21, 2023
ea815c5
Merge pull request #1347 from alliance-genome/SCRUM-3473_refactor
markquintontulloch Nov 21, 2023
5bf6b6b
Merge branch 'alpha' into SCRUM-3473
markquintontulloch Nov 21, 2023
4ae9a33
Merge branch 'alpha' into SCRUM-3473
markquintontulloch Nov 21, 2023
48fda11
SCRUM-3350 update AlleleDetailPage header styling
adamgibs Nov 21, 2023
f876172
Rename helper
markquintontulloch Nov 21, 2023
f5e652b
Merge pull request #1344 from alliance-genome/SCRUM-3473
markquintontulloch Nov 21, 2023
a4f0142
Merge branch 'alpha' into SCRUM-3350
oblodgett Nov 21, 2023
fa71cd5
Merge pull request #1348 from alliance-genome/SCRUM-3350
adamgibs Nov 21, 2023
e35385c
Rename construct association subject
markquintontulloch Nov 22, 2023
b3a9b83
Fixed NPE on failed load after a server restart
oblodgett Nov 22, 2023
c0585ab
Rename association fields
markquintontulloch Nov 22, 2023
49b58de
Merge pull request #1349 from alliance-genome/fix_failed_loads
oblodgett Nov 22, 2023
81dcfc1
Update UI for field name changes
markquintontulloch Nov 22, 2023
0a21d9e
Update sort field
markquintontulloch Nov 22, 2023
dad1b38
Refactor slot annotation validation
markquintontulloch Nov 23, 2023
47ef9ae
Clean up orphaned slot annotations
markquintontulloch Nov 23, 2023
d93953d
Refactor note cleanup and validation
markquintontulloch Nov 24, 2023
1e6ae12
Remove unused injection
markquintontulloch Nov 24, 2023
ac588f3
Cleanup
markquintontulloch Nov 24, 2023
8c1e396
More refactoring
markquintontulloch Nov 24, 2023
09ca9b1
Space and import cleanup
markquintontulloch Nov 24, 2023
c49872d
Merge pull request #1350 from alliance-genome/SCRUM-3519
markquintontulloch Nov 27, 2023
8c6654b
Update migration version
markquintontulloch Nov 27, 2023
5aff160
Merge branch 'alpha' into rename_construct_association_subject
markquintontulloch Nov 27, 2023
ced9102
SCRUM-3388 modify UI code to for new errorMap
adamgibs Nov 22, 2023
8833fca
SCRUM-3388 update field errorMessages
adamgibs Nov 27, 2023
e348d04
Merge pull request #1351 from alliance-genome/SCRUM-3388
adamgibs Nov 27, 2023
6a79c1b
Fix NPE with jobs
oblodgett Nov 28, 2023
9d1238a
Merge pull request #1352 from alliance-genome/fix_jobs
oblodgett Nov 28, 2023
0fd8c24
Merge branch 'alpha' into SCRUM-3529
markquintontulloch Nov 28, 2023
840b378
Fix mock data
markquintontulloch Nov 28, 2023
0509f96
Merge pull request #1353 from alliance-genome/SCRUM-3529
markquintontulloch Nov 28, 2023
9851565
Update ALB timeout
oblodgett Nov 30, 2023
267e9e5
Merge pull request #1354 from alliance-genome/update_timeout
oblodgett Nov 30, 2023
531e9d2
Merge branch 'beta' into release/v0.28.0-rc1
mluypaert Dec 1, 2023
8b5b27c
Merge pull request #1356 from alliance-genome/release/v0.28.0-rc1
abecerra Dec 1, 2023
893b671
Merge branch 'beta' into release/v0.28.0-rc2
oblodgett Jan 8, 2024
467b38c
Fixed fetches
oblodgett Jan 8, 2024
681368a
Merge pull request #1385 from alliance-genome/release/v0.28.0-rc2
oblodgett Jan 8, 2024
c5cbe7c
SCRUM-3511: release notes
abecerra Jan 8, 2024
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1 change: 1 addition & 0 deletions .ebextensions/loadbalancer.config
Original file line number Diff line number Diff line change
Expand Up @@ -33,3 +33,4 @@ option_settings:
Protocol: HTTP
aws:elbv2:loadbalancer:
SecurityGroups: sg-21ac675b
IdleTimeout: 600
3 changes: 3 additions & 0 deletions .github/workflows/github-actions-PR-validation.yml
Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,9 @@ jobs:
- name: Package API
run: |
mvn clean package -Dquarkus.package.type=uber-jar -ntp
- name: Create test containers properties file
run: |
touch ~/.testcontainers.properties
- name: Run Integration tests
run: |
make integration-test
Expand Down
4 changes: 4 additions & 0 deletions RELEASE-NOTES.md
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,10 @@

https://agr-jira.atlassian.net/wiki/spaces/ATEAM/overview

## v0.28.0-rc2
* Updates quarkus to version 3
* Fixes and

## v0.27.2 & v0.27.3
* Fixes and maintenance
* Fixes for permissions and dependent workflow triggering on automated release creation (SCRUM-3444)
Expand Down
33 changes: 17 additions & 16 deletions pom.xml
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@
<okta.version>3.0.1</okta.version>
<okta.authn.version>2.0.0</okta.authn.version>
<okta-jwt.version>0.5.1</okta-jwt.version>
<quarkus.platform.version>2.16.11.Final</quarkus.platform.version>
<quarkus.platform.version>3.5.0</quarkus.platform.version>
<surefire-plugin.version>3.0.0-M7</surefire-plugin.version>
</properties>

Expand Down Expand Up @@ -134,10 +134,6 @@
<groupId>io.quarkus</groupId>
<artifactId>quarkus-hibernate-search-orm-elasticsearch</artifactId>
</dependency>
<dependency>
<groupId>io.quarkus</groupId>
<artifactId>quarkus-elasticsearch-rest-high-level-client</artifactId>
</dependency>
<dependency>
<groupId>io.quarkus</groupId>
<artifactId>quarkus-resteasy</artifactId>
Expand Down Expand Up @@ -183,7 +179,12 @@
<groupId>io.quarkus</groupId>
<artifactId>quarkus-vertx</artifactId>
</dependency>


<dependency>
<groupId>io.quarkus</groupId>
<artifactId>quarkus-elasticsearch-rest-high-level-client</artifactId>
<version>3.2.7.Final</version>
</dependency>
<dependency>
<groupId>io.quarkus</groupId>
<artifactId>quarkus-smallrye-openapi</artifactId>
Expand All @@ -210,11 +211,6 @@
<artifactId>quarkus-junit5-mockito</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>io.quarkiverse.hibernatetypes</groupId>
<artifactId>quarkus-hibernate-types</artifactId>
<version>0.2.0</version>
</dependency>

<dependency>
<groupId>io.rest-assured</groupId>
Expand Down Expand Up @@ -287,7 +283,7 @@
<dependency>
<groupId>com.github.mmazi</groupId>
<artifactId>rescu</artifactId>
<version>2.1.0</version>
<version>3.0</version>
</dependency>

<dependency>
Expand Down Expand Up @@ -352,17 +348,22 @@
<artifactId>postgresql</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>elasticsearch</artifactId>
<scope>test</scope>
</dependency>

<dependency>
<groupId>org.reflections</groupId>
<artifactId>reflections</artifactId>
<version>0.10.2</version>
</dependency>

<dependency>
<groupId>org.jsoup</groupId>
<artifactId>jsoup</artifactId>
<version>1.13.1</version>
<groupId>org.jsoup</groupId>
<artifactId>jsoup</artifactId>
<version>1.13.1</version>
</dependency>
</dependencies>

Expand Down
9 changes: 4 additions & 5 deletions src/main/cliapp/package-lock.json

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

4 changes: 2 additions & 2 deletions src/main/cliapp/package.json
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@
"moment": "^2.29.1",
"primeflex": "3.1.0",
"primeicons": "^5.0.0",
"primereact": "^8.7.3",
"primereact": "^10.0.9",
"prismjs": "1.9.0",
"react": "^17.0.1",
"react-app-polyfill": "^1.0.6",
Expand All @@ -48,7 +48,7 @@
"scripts": {
"start": "react-scripts start",
"build": "react-scripts build",
"test": "react-scripts test",
"test": "react-scripts test --maxWorkers=1",
"eject": "react-scripts eject"
},
"eslintConfig": {
Expand Down
11 changes: 0 additions & 11 deletions src/main/cliapp/src/__mocks__temp/BaseAuthService.js

This file was deleted.

8 changes: 0 additions & 8 deletions src/main/cliapp/src/__mocks__temp/PersonSettingsService.js

This file was deleted.

11 changes: 0 additions & 11 deletions src/main/cliapp/src/__mocks__temp/SearchService.js

This file was deleted.

8 changes: 0 additions & 8 deletions src/main/cliapp/src/__mocks__temp/SystemService.js

This file was deleted.

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