test: Add API endpoint tests

[NishaSharma14]

No description provided.

[Copilot]

Pull request overview

This PR adds comprehensive API endpoint tests across multiple controllers, improving test coverage for authentication, data access, search, file system operations, and ELN integration. The changes also include necessary test infrastructure updates like disabling API throttling in the testing environment and updating factories for better test data generation.

Key Changes

• Added 10 new test files covering API endpoints for user authentication, data retrieval, search, and ELN workflows
• Disabled API throttling in the testing environment to allow full test suite execution
• Updated factory defaults for better test data consistency (Molecule identifier, FileSystemObject type)
• Commented out an unprotected DOI update route with security concerns

Reviewed changes

Copilot reviewed 14 out of 14 changed files in this pull request and generated 22 comments.

Show a summary per file

File	Description
tests/API/UserControllerTest.php	Tests for authenticated user info endpoint with various scenarios
tests/API/SearchControllerTest.php	Comprehensive search endpoint tests covering multiple query types and validation
tests/API/RegisterControllerTest.php	User registration tests with validation checks (has HTTP status code issues)
tests/API/LoginControllerTest.php	Login/logout functionality tests (has HTTP status code issues)
tests/API/FileSystemControllerTest.php	File system object retrieval tests (contains performance issue with sleep)
tests/API/ELNControllerTest.php	ELN upload and status tests with complex workflows (has hardcoded year issue)
tests/API/DataControllerTest.php	Public data listing, filtering, sorting, and retrieval tests
tests/API/DataCiteControllerTest.php	DataCite schema endpoint tests
tests/API/DataCatalogControllerTest.php	DataCatalog/Bioschemas endpoint tests
tests/API/BioschemasControllerTest.php	Bioschemas endpoint access control tests
routes/api.php	Commented out DOI update route due to security concerns (has typo)
database/factories/MoleculeFactory.php	Added unique identifier generation for test molecules
database/factories/FileSystemObjectFactory.php	Clarified 'directory' type usage in comment
bootstrap/app.php	Disabled API throttling during testing to allow test execution

[codecov]

Codecov Report

❌ Patch coverage is 85.71429% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 63.10%. Comparing base (6637646) to head (9bb30d1).

Files with missing lines	Patch %	Lines
...tp/Controllers/API/Auth/VerificationController.php	50.00%	1 Missing ⚠️

Additional details and impacted files

@@                Coverage Diff                @@
##             development    #1313      +/-   ##
=================================================
+ Coverage          56.63%   63.10%   +6.46%     
- Complexity          2268     2269       +1     
=================================================
  Files                207      207              
  Lines               8733     8738       +5     
=================================================
+ Hits                4946     5514     +568     
+ Misses              3787     3224     -563     

Flag	Coverage Δ
unittests	63.10% <85.71%> (+6.46%)	⬆️

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[NishaSharma14]

@vcnainala The update method of DOIController is not being used anywhere. The artisan command - nmrxiv:update-projects-dois make the direct model method calls: $model->updateDOIMetadata().