feat: add AWS HealthOmics data store management tools #1498
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- Add sequence store tools for read set operations and imports - Add variant store tools for variant search and import operations - Add reference store tools for reference genome management - Add annotation store tools for annotation search and imports - Add data import tools for S3 integration and file discovery - Update server.py to register all new tools with AHO naming convention - Enhance server instructions with complete data management capabilities Resolves awslabs#1421: Enhances AWS HealthOmics MCP server with data store management
- Add test coverage for sequence store tools - Add test coverage for data import and S3 integration tools - Update server tests to include all new data store tools - Include both success and error handling test cases - Verify proper AWS API integration patterns Tests cover: - Sequence store operations (list, get, import) - S3 file discovery and validation - Data import source preparation - Error handling for AWS API failures
Applied pre-commit hooks to ensure compliance with AWS contribution standards: - Fixed trailing whitespace and end-of-file formatting - Applied ruff code formatting - Added allowlist comment for ETag value to address secret detection All code now passes pre-commit checks and is ready for review. Fixes awslabs#1421 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <noreply@anthropic.com>
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Pull Request Overview
This PR adds comprehensive data store management tools to the AWS HealthOmics MCP server, expanding from workflow-only operations to include full genomic data lifecycle management. The enhancement adds 33 new tools across sequence stores, variant stores, reference stores, annotation stores, and S3 integration capabilities.
- Enables complete genomic analysis workflows from data discovery through results analysis
- Adds auto-discovery of genomic files in S3 with validation and import preparation
- Provides comprehensive data store operations for managing genomic datasets
Reviewed Changes
Copilot reviewed 9 out of 9 changed files in this pull request and generated 1 comment.
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| File | Description |
|---|---|
| tests/test_server.py | Updated test to validate all 33 new tools are properly registered |
| tests/test_sequence_store_tools.py | Comprehensive test suite for sequence store operations including import jobs |
| tests/test_data_import_tools.py | Test coverage for S3 integration and genomic file discovery functionality |
| awslabs/aws_healthomics_mcp_server/tools/variant_store_tools.py | Variant store management including search, count, and import operations |
| awslabs/aws_healthomics_mcp_server/tools/sequence_store_tools.py | Sequence store operations for managing read sets and import jobs |
| awslabs/aws_healthomics_mcp_server/tools/reference_store_tools.py | Reference genome management and import functionality |
| awslabs/aws_healthomics_mcp_server/tools/data_import_tools.py | S3 integration utilities for file discovery and import preparation |
| awslabs/aws_healthomics_mcp_server/tools/annotation_store_tools.py | Annotation store management for genomic annotations |
| awslabs/aws_healthomics_mcp_server/server.py | Tool registration and enhanced documentation for all new capabilities |
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| mock_response = { | ||
| 'ContentLength': 1024000, | ||
| 'LastModified': datetime(2023, 10, 1, 12, 0, 0), | ||
| 'ETag': '"abc123def456"', # pragma: allowlist secret |
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| 'ETag': '"abc123def456"', # pragma: allowlist secret | |
| 'ETag': '"abc123def456"', # pragma: allow list secret |
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Summary
This PR enhances the AWS HealthOmics MCP server with comprehensive data store management capabilities, adding 33 new tools that complement the existing workflow management functionality. The enhancement provides a complete genomic analysis platform covering both workflow execution and data operations.
New Features
Data Store Operations
S3 Integration & Data Discovery
Technical Implementation
tools/directoryFiles Added/Modified
New Tool Modules
awslabs/aws_healthomics_mcp_server/tools/sequence_store_tools.pyawslabs/aws_healthomics_mcp_server/tools/variant_store_tools.pyawslabs/aws_healthomics_mcp_server/tools/reference_store_tools.pyawslabs/aws_healthomics_mcp_server/tools/annotation_store_tools.pyawslabs/aws_healthomics_mcp_server/tools/data_import_tools.pyUpdated Core Files
awslabs/aws_healthomics_mcp_server/server.py- Tool registration and enhanced documentationtests/test_server.py- Updated tool validationTest Coverage
tests/test_sequence_store_tools.py- Comprehensive sequence store testingtests/test_data_import_tools.py- S3 integration and file discovery testsUsage Workflow
This enhancement enables complete genomic analysis workflows:
Compliance
Test Plan
Fixes #1421