feat(orchestrator): Implement real API orchestration and production networking standards#10
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ravindraogg wants to merge 2 commits intoreactome:mainfrom
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feat(orchestrator): Implement real API orchestration and production networking standards#10ravindraogg wants to merge 2 commits intoreactome:mainfrom
ravindraogg wants to merge 2 commits intoreactome:mainfrom
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Replaces the simulated response layer with a functional adapter that interacts directly with the Reactome Content and Analysis REST APIs. Key improvements: - Implemented eal_adapter.py using Python's standard urllib.request. - Added production networking standards: User-Agent headers, 15s timeouts, and comprehensive error handling for API request failures. - Updated executor.py to wire the planning logic into live services. - Refined demo.py to provide a complete trace of real-world biological tasks (search, enrichment, and pathway lookup). - Maintained a zero-dependency architecture for low-friction setup. This change moves the orchestration layer from a conceptual prototype to a functional tool for multi-step biological query execution.
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This PR upgrades the experimental orchestration layer from a mock-based prototype to a functional system that executes multi-step biological queries against the live Reactome REST APIs. This enables the orchestration of real-world biological workflows (Search -> Analysis -> Detailed Lookup) using only the Python standard library.
Key Changes
real_adapter.py: Added a production-ready adapter that interfaces with the Reactome Content Service and Analysis Service.urllib.requestto ensure the orchestrator remains lightweight and has no external dependencies (likerequests), keeping the barrier to entry low for bioinformatics users.reactome-mcp-orchestrator/1.0) for server-side traffic monitoring.executor.pyto use the real adapter as the default, transforming thedemo.pyfrom a simulation into a live diagnostic tool.Verification
I have verified that the
orchestrator/demo.pysuccessfully plans and executes the following patterns against live data:Testing
Run the diagnostic demo to verify live connectivity: