Migrate "e2e" api tests to javascript

[alisman]

Migrate E2E tests from Java to JavaScript/TypeScript (Mocha)

Summary

This PR migrates all E2E tests from Java to JavaScript/TypeScript using Mocha, Chai, and Axios. The new test suite provides better developer experience with faster test execution and clearer test patterns.

Changes

New JavaScript/TypeScript E2E Tests

• ✅ Created src/e2e/js/ directory with complete test infrastructure
• ✅ Migrated 3 test suites to TypeScript/Mocha (11 total tests):
  • AlterationEnrichmentController (7 tests)
  • ColumnStoreMutationController (3 tests)
  • ColumnStoreStudyController (1 test)
• ✅ All tests passing against cgds_public_2025_06_24 database

Test Infrastructure

• Framework: Mocha + Chai for assertions
• Language: TypeScript with strict type checking
• HTTP Client: Axios for API requests
• Data Processing: Lodash for all array/object operations
• Test Organization: Each test suite in its own directory with co-located test data

Key Features

• ✨ TypeScript types derived from official Swagger API documentation
• ✨ Inline test logic with comprehensive comments (no hidden helper methods)
• ✨ Lodash used consistently for all data transformations
• ✨ Stack trace inspection for automatic test data discovery
• ✨ Clear test structure with descriptive assertions

Removed

• 🗑️ Deleted entire src/e2e/java/ directory and all Java E2E tests
• 🗑️ Removed Java E2E test references from documentation
• 🗑️ Removed e2e-test Maven profile

Documentation

• 📝 Updated README.md with JavaScript E2E test instructions
• 📝 Created CLAUDE.md with comprehensive test writing guidelines
• 📝 Updated environment variable documentation
• 📝 Clarified test layer tools and purpose

Testing

All 11 tests verified passing:

cd src/e2e/js
CBIOPORTAL_URL=http://localhost:8082 npm test

Results: ✅ 11 passing (15s)

Prerequisites for Running Tests

• Node.js v18 or higher
• Running cBioPortal instance with cgds_public_2025_06_24 database
• Server accessible at http://localhost:8080 (or set CBIOPORTAL_URL)

Example Test Structure

describe('AlterationEnrichmentController E2E Tests', () => {
  it('should handle combination comparison session', async () => {
    // Load test data containing 104 samples across two studies
    const testData = await TestUtils.loadTestData('all_alterations.json');

    // Call the enrichment endpoint to get gene statistics
    const enrichments = await TestUtils.callEnrichmentEndpoint(testData);

    // Find the TP53 gene enrichment from the results using Lodash
    const tp53Enrichment = _.find(enrichments, { hugoGeneSymbol: 'TP53' });
    expect(tp53Enrichment, 'TP53 should be present').to.not.be.undefined;

    // Calculate total profiled samples by summing profiledCount
    const totalProfiled = _.sumBy(tp53Enrichment!.counts, 'profiledCount');
    expect(totalProfiled).to.equal(103, 'TP53 should have 103 profiled samples');
  });
});

Benefits

1. Faster Execution: JavaScript tests run in ~15s vs Java Spring Boot context startup
2. Better DX: TypeScript provides excellent IDE support and type safety
3. Clear Test Logic: All data processing visible inline with comments
4. Easier Maintenance: Co-located test data and clear patterns
5. Modern Tooling: Leverages Node.js ecosystem (npm, TypeScript, Mocha)

Migration Notes

All Java E2E test functionality has been preserved:

• ✅ AlterationEnrichmentController: All 7 test scenarios migrated
• ✅ ColumnStoreMutationController: All 3 projection tests migrated
• ✅ ColumnStoreStudyController: Study fetch test migrated
• ❌ HealthCheckE2ETest: Not migrated (simple health check, can be added if needed)

Related Documentation

• Test writing guide: src/e2e/js/CLAUDE.md
• Running tests: See README.md "JavaScript/TypeScript E2E Tests" section

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Branch: alisman:js-e2e → cbioportal:master