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Clinical Trial Intelligence — Advanced Learning Guide

For engineers extending or operating this subject.

Source: core/agents/clinical-trial · 47 Python files · 23,396 LOC · 14 test files

Registered capabilities

Capability Type Status Endpoint
clinical-trial-intelligence-agent agent live localhost:8538

UI :8538 · API :8539 (platform convention: registry endpoint is the UI, API is UI + 1)

Principal modules

src/clinical_workflows.py

BaseTrialWorkflow, ProtocolDesignWorkflow, PatientMatchingWorkflow, SiteSelectionWorkflow, EligibilityOptimizationWorkflow, AdaptiveDesignWorkflow

  • BaseTrialWorkflow — Abstract base for all clinical trial workflows.
  • ProtocolDesignWorkflow — Protocol design workflow that generates evidence-based protocol
  • PatientMatchingWorkflow — Patient-trial matching workflow that evaluates a patient profile
  • SiteSelectionWorkflow — Site selection and ranking workflow based on weighted scoring

src/knowledge.py

no public symbols

src/agent.py

EvidenceLevel, TrialPhase, RegulatoryBody, SeverityLevel, TrialResponse, SearchPlan

  • EvidenceLevel — Clinical evidence hierarchy for trial recommendations.
  • TrialPhase — Clinical trial phases.
  • RegulatoryBody — Regulatory bodies referenced in trial intelligence.
  • SeverityLevel — Finding severity classification.

src/rag_engine.py

TrialSearchResult, get_all_collection_names, TrialRAGEngine

  • TrialSearchResult — A single search result from a Milvus collection.
  • get_all_collection_names — Return all collection names.
  • TrialRAGEngine — Multi-collection RAG engine for clinical trial intelligence.

src/query_expansion.py

QueryExpander

  • QueryExpander — Expand clinical trial queries with related domain terms.

Dependencies

anthropic==0.25.0, apscheduler==3.10.4, fastapi==0.111.0, httpx==0.27.0, loguru==0.7.2, lxml==5.2.1, numpy>=1.24.0, prometheus-client==0.20.0, pydantic-settings==2.2.1, pydantic==2.7.4, pymilvus==2.4.1, python-docx==1.1.0, python-dotenv>=1.0.0, python-multipart==0.0.9

Running the tests

.venv/bin/python scripts/run_all_tests.py clinical-trial

Two traps the shared harness handles, which a hand-rolled pytest invocation will not:

  1. Several subjects ship src/vector_collections.py, which shadows the Python standard library. Putting their src/ on PYTHONPATH kills the interpreter before collection.
  2. structural-biology/vendor_rfdiffusion/ is vendored third-party code needing gated GPU packages and is excluded.

Operational notes

Matching is informational. Eligibility is determined by the trial investigators, not by this agent.

Before changing a port, read ../../build/PORT_MAP.md. The convention is enforced by scripts/validate_registry.py, which also cross-checks health-monitor.sh — a port change in one place and not the other fails the build.

Extending it

  1. Add or change code under core/agents/clinical-trial.
  2. Keep the capability entry in lib/hcls_common/capabilities.json truthful — a live status must answer a health probe. Two capabilities were found registered live with nothing bound to their ports; do not add a third.
  3. Run the gate: ruff, pytest lib/hcls_common, validate_registry.py, run_all_tests.py.