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3a955ad
feat: add core data models for genomics file search
markjschreiber Oct 7, 2025
918e521
feat(search): implement pattern matching and scoring engine
markjschreiber Oct 7, 2025
2945749
feat: implement file association detection system
markjschreiber Oct 7, 2025
27b3e36
feat: implement S3 search engine with configuration management
markjschreiber Oct 7, 2025
a62f7a1
feat:(search) adds a search interface to the healthomics sequence and…
markjschreiber Oct 7, 2025
5e6623b
feat(genomics-search): implement search orchestrator and MCP tool han…
markjschreiber Oct 7, 2025
52e0261
feat(search): adds result ranking and response assembly
markjschreiber Oct 7, 2025
30254d0
docs: add genomics file search capabilities to README and CHANGELOG
markjschreiber Oct 7, 2025
5eca2a7
Fix SearchGenomicsFiles tool: regex patterns, S3 client calls, and fi…
markjschreiber Oct 8, 2025
aa4dd8a
perf(s3-search): optimize S3 API calls with lazy loading, caching, an…
markjschreiber Oct 8, 2025
ddd784f
Fix genomics file search for HealthOmics reference stores
markjschreiber Oct 8, 2025
7ba4bbe
feat(search): enhance HealthOmics sequence and reference store search…
markjschreiber Oct 8, 2025
5f6407e
feat: performance improvements and minor fixes
markjschreiber Oct 9, 2025
1d1484c
feat: implement efficient storage-level pagination for genomics file …
markjschreiber Oct 9, 2025
bc9dfb6
fix: correct the associate of bwa files and fix pyright type errors
markjschreiber Oct 9, 2025
65c6826
feat(tests): implement comprehensive testing framework with MCP Field…
markjschreiber Oct 10, 2025
0f93475
fix(tests): repair healthomics search engine tests
markjschreiber Oct 10, 2025
a64c8d5
test(s3): add comprehensive tests for S3SearchEngine
markjschreiber Oct 10, 2025
119c998
fix(tests): fix failing healthomics search engine tests
markjschreiber Oct 10, 2025
317e389
test(result-ranker): achieve 100% test coverage for ResultRanker
markjschreiber Oct 10, 2025
49cd8b9
test(json-response-builder): achieve 100% test coverage for JsonRespo…
markjschreiber Oct 10, 2025
2b94eee
test(config-utils): achieve 100% test coverage for config utilities
markjschreiber Oct 10, 2025
194fbca
feat(s3-utils): optimize bucket validation and achieve 99% coverage
markjschreiber Oct 10, 2025
0364e5c
feat(genomics-search-orchestrator): achieve 49% test coverage with co…
markjschreiber Oct 10, 2025
c0b91d4
perf(genomics-search-orchestrator): optimize test performance by 94%
markjschreiber Oct 10, 2025
205883a
feat(healthomics-search-engine): improve test coverage from 61% to 69%
markjschreiber Oct 10, 2025
2c8d7d1
fix: clean up files and reformats some files failing lints
markjschreiber Oct 10, 2025
a80a1e0
Merge remote-tracking branch 'upstream/main' into feature/genomics-fi…
markjschreiber Oct 10, 2025
3a93788
security: fix bandit security issues
markjschreiber Oct 10, 2025
2843406
fix(tests): mock AWS account/region methods to prevent credential access
markjschreiber Oct 10, 2025
0a8c6a1
fix: fix pyright issues
markjschreiber Oct 10, 2025
5010d5e
feat: improve test coverage
markjschreiber Oct 10, 2025
298acc4
feat: increases coverage of pagination logic, filtering, fallbacks an…
markjschreiber Oct 10, 2025
23f8a51
fix: mock aws credentials
markjschreiber Oct 10, 2025
afa8b02
feat: improve test coverage of exception handling, continuation token…
markjschreiber Oct 10, 2025
9cd825b
fix: pyright type error fixed
markjschreiber Oct 10, 2025
7c48aca
feat: more test coverage to stop codecov nagging me
markjschreiber Oct 10, 2025
8049bea
feat: improvements to branch coverage
markjschreiber Oct 10, 2025
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6 changes: 6 additions & 0 deletions package-lock.json

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9 changes: 9 additions & 0 deletions src/aws-healthomics-mcp-server/CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Added

- **Genomics File Search Tool** - Comprehensive file discovery across multiple storage systems
- Added `SearchGenomicsFiles` tool for intelligent file discovery across S3 buckets, HealthOmics sequence stores, and reference stores
- Pattern matching with fuzzy search capabilities for file paths and object tags
- Automatic file association detection (BAM/BAI indexes, FASTQ R1/R2 pairs, FASTA indexes, BWA index collections)
- Relevance scoring and ranking system based on pattern match quality, file type relevance, and associated files
- Support for standard genomics file formats: FASTQ, FASTA, BAM, CRAM, SAM, VCF, GVCF, BCF, BED, GFF, and their indexes
- Configurable S3 bucket paths via environment variables
- Structured JSON responses with comprehensive file metadata including storage class, size, and access paths
- Performance optimizations with parallel searches and result streaming
- S3 URI support for workflow definitions in `CreateAHOWorkflow` and `CreateAHOWorkflowVersion` tools
- Added `definition_uri` parameter as alternative to `definition_zip_base64`
- Supports direct reference to workflow definition ZIP files stored in S3
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