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Release Dev to Test #238

Merged
merged 18 commits into from
Mar 19, 2024
Merged

Release Dev to Test #238

merged 18 commits into from
Mar 19, 2024

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NickPhura
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Links to Jira Tickets

https://apps.nrs.gov.bc.ca/int/jira/browse/SIMSBIOHUB-541

Description of Changes

Release latest changes from Dev to Test

Testing Notes

n/a

KjartanE and others added 18 commits June 26, 2023 11:38
* added button to apply security

* fix unique state updates around datagrid

* roll back

* remove extra button, remove disable
#204)

* SIMSBIOHUB-110: Added pluralize util

* SIMSBIOHUB-110: Added security rules to API response object

* SIMSBIOHUB-110: Refactor apply security

* SIMSBIOHUB-110: Added loading props to YesNoDialog

* SIMSBIOHUB-110: Show already applied security rules

* SIMSBIOHUB-110: Fixed tests

* SIMSBIOHUB-110: ignore-skip

* SIMSBIOHUB-110: Fix tests, lint + format fix

* SIMSBIOHUB-110: Fix test

* SIMSBIOHUB-110: Fix tests part 2

* Lint fix

* SIMSBIOHUB-110: Added error dialogs

* SIMSBIOHUB-110: PR refactor
Added delete functionality to artifacts
* Added supplementary data that reflects if the related dataset has documents pending review

* Front end changes to show pending review status when applicable
* Submission Feature Migrations and Test Seeding
Remove DB_SCHEMA usage in most places.
Remove DB Views
Add Mock test data seed (disabled by default)
* Created endpoint for dataset intake
* Created API methods to run validation on datasets
* Created API methods to insert submission and submission features into database
* Added features to review and secure dataset submissions: See New BioHub Submissions; See Completed BioHub Submissions; Complete Review and Publish Subissions; Admin Review Submission Page; Secure Submission; Unsecure Published Dataset.
* Added supplementary changes from SIMS: Ports header improvements from SIMS; Ports latest Keycloak changes from SIMS.
Fixing the sort menu interfaces for submissions.

---------

Co-authored-by: jeznorth <[email protected]>
Bump horizontal autoscaler version from v2beta2 to v2
- Create new tabs for submissions that have completed reviews, but are either unpublished or published.
- Tabs to differentiate between unpublished and published states of submissions.
* New static security rules
* Artifact download button + generating signed URL from API.
* Updated endpoints and service and repo methods to support applying security to selected features.

* Refactored the frontend to support selecting features, applying security rules, and to see already applied security rules.
SIMSBIOHUB-426: Added support for calculating regions for a submission
* Security UI Fixes

---------

Co-authored-by: Curtis Upshall <[email protected]>
Support artifact submission intake.
Make uuid a source submitted field for submission.
make source_id optional for submission_features.
Add required_value column to feature_type_property to mark feature properties as required vs optional.
Update validation logic to account for required vs optional properties.
Fix submission ingest not assigning parent submission feature id.
Adjust get unreviewed/completed/published submission SQL.
---------
Co-authored-by: Curtis Upshall <[email protected]>
Co-authored-by: Alfred Rosenthal <[email protected]>
taxon / taxon_alias / language_lookup / taxon_alias_origin tables
Design BioHub taxonomy endpoint + services/repositories.
- Taxon Search endpoint
  - Search by term to SOLR service from frontend
- Taxon ids lookup endpoint
  - Query DB for cached tsn's
  - Search SOLR for tsn's not found in DB, update accordingly
  - Return list of Taxons
* Fixed a race condition that occurs when two requests try to read/write from the taxon table.
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Quality Gate Failed Quality Gate failed

Failed conditions
6.0% Duplication on New Code (required ≤ 3%)

See analysis details on SonarCloud

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Codecov Report

Attention: Patch coverage is 81.28755% with 218 lines in your changes are missing coverage. Please review.

Project coverage is 63.52%. Comparing base (e7e77e2) to head (2f5cd0d).
Report is 2 commits behind head on test.

Files Patch % Lines
...ministrative/security/submission/{submissionId}.ts 0.00% 35 Missing ⚠️
api/src/repositories/security-repository.ts 55.81% 19 Missing ⚠️
api/src/paths/submission/search-idx.ts 0.00% 17 Missing ⚠️
...pi/src/paths/administrative/security/categories.ts 0.00% 16 Missing ⚠️
api/src/paths/administrative/security/rules.ts 0.00% 16 Missing ⚠️
...ministrative/submission/{submissionId}/messages.ts 66.66% 14 Missing ⚠️
api/src/services/security-service.ts 59.37% 12 Missing and 1 partial ⚠️
api/src/repositories/submission-repository.ts 91.22% 3 Missing and 7 partials ⚠️
api/src/services/search-index-service.ts 80.76% 4 Missing and 6 partials ⚠️
api/src/app.ts 0.00% 8 Missing ⚠️
... and 27 more
Additional details and impacted files
@@            Coverage Diff             @@
##             test     #238      +/-   ##
==========================================
- Coverage   69.21%   63.52%   -5.70%     
==========================================
  Files         211      267      +56     
  Lines        5960     7470    +1510     
  Branches      934     1039     +105     
==========================================
+ Hits         4125     4745     +620     
- Misses       1612     2470     +858     
- Partials      223      255      +32     

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@jeznorth jeznorth self-requested a review March 19, 2024 17:01
@NickPhura NickPhura merged commit d89012f into test Mar 19, 2024
23 of 24 checks passed
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8 participants