| |
| """ |
| Run the standard pathway agent eval manifest (fixed policy baseline). |
| |
| Scores via ``env.episode_outcome`` (orchestrator mode). Writes JSON summary. |
| """ |
|
|
| from __future__ import annotations |
|
|
| import argparse |
| import json |
| from pathlib import Path |
| from typing import Any, Dict, List |
|
|
| from pathway_analysis_env.models import PathwayAction |
| from pathway_analysis_env.server.analysis import gseapy_available, pydeseq2_available |
| from pathway_analysis_env.server.pathway_environment import ( |
| DATA_DIR, |
| PathwayEnvironment, |
| ) |
|
|
|
|
| def _run_episode(spec: Dict[str, Any], *, strict: bool) -> Dict[str, Any]: |
| case_file = spec["case_file"] |
| if spec.get("requires_pydeseq2") and not pydeseq2_available(): |
| return { |
| "id": spec["id"], |
| "skipped": True, |
| "reason": "pydeseq2_unavailable", |
| } |
| if spec.get("requires_gseapy") and not gseapy_available(): |
| return { |
| "id": spec["id"], |
| "skipped": True, |
| "reason": "gseapy_unavailable", |
| } |
|
|
| from pathway_analysis_env.server.pathway_environment import load_case |
|
|
| case = load_case(case_file) |
| ref = (case.get("default_contrast") or {}).get("reference") |
| alt = (case.get("default_contrast") or {}).get("alternate") |
|
|
| env = PathwayEnvironment(case_file=case_file) |
| env.reset(strict=strict, orchestrator_mode=True) |
|
|
| actions: List[str] = [] |
|
|
| def go(kind: str, **kw: Any): |
| actions.append(kind) |
| return env.step(PathwayAction(action_type=kind, **kw)) |
|
|
| go("understand_experiment_design") |
| go("inspect_dataset") |
| o_de = go( |
| "run_differential_expression", |
| condition_a=ref, |
| condition_b=alt, |
| ) |
| if o_de.metadata and o_de.metadata.get("failure_code"): |
| return { |
| "id": spec["id"], |
| "case_file": case_file, |
| "passed": False, |
| "stage": "de", |
| "failure_code": o_de.metadata.get("failure_code"), |
| "actions": actions, |
| } |
| o_ora = go("run_pathway_enrichment") |
| if o_ora.metadata and o_ora.metadata.get("failure_code"): |
| return { |
| "id": spec["id"], |
| "case_file": case_file, |
| "passed": False, |
| "stage": "ora", |
| "failure_code": o_ora.metadata.get("failure_code"), |
| "actions": actions, |
| } |
| hyp = spec.get("hypothesis", "") |
| go("submit_answer", hypothesis=hyp) |
| outcome = env.episode_outcome or {} |
| return { |
| "id": spec["id"], |
| "case_file": case_file, |
| "passed": bool(outcome.get("correct")), |
| "episode_outcome": outcome, |
| "actions": actions, |
| "steps": env.state.step_count, |
| } |
|
|
|
|
| def main() -> None: |
| parser = argparse.ArgumentParser() |
| parser.add_argument( |
| "--manifest", |
| type=Path, |
| default=DATA_DIR / "eval_manifest.json", |
| ) |
| parser.add_argument("--strict", action="store_true") |
| parser.add_argument("--json-out", type=Path, default=None) |
| args = parser.parse_args() |
|
|
| manifest = json.loads(args.manifest.read_text(encoding="utf-8")) |
| results = [_run_episode(ep, strict=args.strict) for ep in manifest.get("episodes", [])] |
| n_pass = sum(1 for r in results if r.get("passed")) |
| n_run = sum(1 for r in results if not r.get("skipped")) |
| summary = { |
| "manifest": str(args.manifest), |
| "passed": n_pass, |
| "run": n_run, |
| "total": len(results), |
| "pass_rate": (n_pass / n_run) if n_run else 0.0, |
| "results": results, |
| } |
| text = json.dumps(summary, indent=2) |
| if args.json_out: |
| args.json_out.parent.mkdir(parents=True, exist_ok=True) |
| args.json_out.write_text(text + "\n", encoding="utf-8") |
| print(text) |
|
|
|
|
| if __name__ == "__main__": |
| main() |
|
|
