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SIMSBIOHUB-400: BioHub Dataset & Security Feature Branch #212

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merged 193 commits into from
Jan 4, 2024

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NickPhura
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@NickPhura NickPhura commented Dec 6, 2023

Overview

Review and Secure Dataset Submissions.

Links to Jira tickets

Description of relevant changes

  • 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

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codecov bot commented Dec 6, 2023

Codecov Report

Attention: 507 lines in your changes are missing coverage. Please review.

Comparison is base (71c8882) 69.00% compared to head (8fe0002) 62.08%.
Report is 1 commits behind head on dev.

Files Patch % Lines
api/src/repositories/search-index-respository.ts 44.64% 31 Missing ⚠️
...issions/components/ManageSecurityReasonsDialog.tsx 0.00% 31 Missing ⚠️
app/src/components/security/SecurityRuleForm.tsx 0.00% 30 Missing ⚠️
app/src/components/security/SecuritiesDialog.tsx 0.00% 27 Missing ⚠️
app/src/contexts/submissionContext.tsx 6.89% 27 Missing ⚠️
api/src/paths/administrative/security/apply.ts 0.00% 17 Missing ⚠️
api/src/paths/submission/search-idx.ts 0.00% 17 Missing ⚠️
.../dashboard/components/ReviewedSubmissionsTable.tsx 5.55% 17 Missing ⚠️
...rc/paths/administrative/security/category/fetch.ts 0.00% 16 Missing ⚠️
...rc/paths/administrative/security/category/index.ts 0.00% 16 Missing ⚠️
... and 56 more
Additional details and impacted files
@@            Coverage Diff             @@
##              dev     #212      +/-   ##
==========================================
- Coverage   69.00%   62.08%   -6.93%     
==========================================
  Files         214      263      +49     
  Lines        6094     7152    +1058     
  Branches      938     1007      +69     
==========================================
+ Hits         4205     4440     +235     
- Misses       1665     2472     +807     
- Partials      224      240      +16     

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KjartanE and others added 26 commits December 6, 2023 15:29
Update dashboard page to load submission data.
Add tests for service/repo functions.
@NickPhura NickPhura marked this pull request as ready for review January 3, 2024 23:06
MacQSL and others added 7 commits January 3, 2024 16:17
Port Auth changes from SIMS (newer keycloak libraries, etc)

Refactor service client authentication

- No longer relies on any hard-coded keycloak service client values, everything is read in from the database.
- Added new db-constants.ts file, which is used to load constants from the database during API initialization (currently only loads service client information, but can be updated to support other constants as needed).

Populate submission source_system column from live submission data.

- Was hard coded before.

Update seed to mark a pseudo-random number of submissions as reviewed, and a subset of those as published.

UI change for Jer: Change default switch case for security review status to UNSECURED (rather than PENDING), so that the user only ever sees either UNSECURED, SECURED, or PARTIAL status.
Continuation of #219.

Ported over auth/keycloak changes from SIMS but missed some changes that impacted the pipeline (wouldn't be noticed when running locally).
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sonarqubecloud bot commented Jan 4, 2024

Quality Gate Failed Quality Gate failed

Failed conditions

7.1% Duplication on New Code (required ≤ 3%)
C Reliability Rating on New Code (required ≥ A)

See analysis details on SonarCloud

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@KjartanE KjartanE left a comment

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🐱 Ran locally, functioning properly

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@al-rosenthal al-rosenthal left a comment

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looks good

@curtisupshall curtisupshall changed the title BioHub Dataset & Security Feature Branch SIMSBIOHUB-400: BioHub Dataset & Security Feature Branch Jan 4, 2024
@curtisupshall curtisupshall merged commit c21daaf into dev Jan 4, 2024
18 of 21 checks passed
KjartanE pushed a commit that referenced this pull request Jan 4, 2024
* 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.
@NickPhura NickPhura deleted the dataset_security_feature branch September 24, 2024 16:10
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6 participants