427 lines
20 KiB
Python
Executable File
427 lines
20 KiB
Python
Executable File
#!/usr/bin/env python3
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"""Scope-aware whole-job summary and DeepSeek report stage.
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The deterministic layer first builds a traceable manifest/artifact index. By
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default that evidence is then passed to DeepSeek to produce the human-readable
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Chinese report. The evidence index remains a separate artifact so generated
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prose can always be audited against local results.
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"""
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import argparse
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import json
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import os
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import sys
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from datetime import datetime
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from pathlib import Path
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from typing import Any, Dict, Iterable, List, Optional, Tuple
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PROJECT_ROOT = Path(__file__).resolve().parents[2]
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if str(PROJECT_ROOT) not in sys.path:
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sys.path.insert(0, str(PROJECT_ROOT))
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CONDA_PREFIX = Path(sys.executable).resolve().parent.parent
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CONDA_BIN = str(CONDA_PREFIX / "bin")
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if CONDA_BIN not in os.environ.get("PATH", "").split(os.pathsep):
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os.environ["PATH"] = CONDA_BIN + os.pathsep + os.environ.get("PATH", "")
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def read_json(path: Path) -> Optional[Dict[str, Any]]:
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try:
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return json.loads(path.read_text(encoding="utf-8"))
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except Exception:
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return None
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def sanitize_token(value: str) -> str:
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safe = []
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for char in str(value):
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safe.append(char if char.isalnum() or char in "._-" else "-")
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return "".join(safe).strip(".-") or "default"
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def infer_workspace(manifest_path: Optional[Path], workspace_arg: str = "") -> Path:
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if workspace_arg:
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return Path(workspace_arg).expanduser().resolve()
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if not manifest_path:
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raise ValueError("--workspace is required when --manifest is not provided")
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data = read_json(manifest_path) or {}
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for key in ("workspace_root", "workspace"):
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value = data.get(key)
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if not value:
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continue
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p = Path(value).expanduser()
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if p.name == "final":
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p = p.parent
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if p.exists():
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return p.resolve()
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return manifest_path.resolve().parent.parent if manifest_path.parent.name == "final" else manifest_path.resolve().parent
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def artifact_iter(artifacts: Any) -> Iterable[Tuple[str, Dict[str, Any]]]:
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if isinstance(artifacts, dict):
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for key, value in artifacts.items():
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if isinstance(value, dict):
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yield key, value
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else:
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yield key, {"path": str(value)}
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elif isinstance(artifacts, list):
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for i, value in enumerate(artifacts):
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if isinstance(value, dict):
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yield str(value.get("artifact") or value.get("name") or i), value
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else:
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yield str(i), {"path": str(value)}
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def resolve_artifact_path(workspace: Path, manifest_file: Path, artifact: Dict[str, Any]) -> Optional[Path]:
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path_text = str(artifact.get("full_path") or artifact.get("path") or artifact.get("relpath_or_hint") or "").strip()
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if not path_text:
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return None
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path = Path(path_text)
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if path.is_absolute():
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return path
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candidates = [
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workspace / path,
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workspace / "final" / path.name,
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manifest_file.parent / path.name,
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Path(path_text),
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]
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return next((p for p in candidates if p.exists()), candidates[0])
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def manifest_scope(data: Dict[str, Any]) -> str:
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return str(data.get("scope_id") or data.get("parameters", {}).get("scope_id") or "unscoped")
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def manifest_family(data: Dict[str, Any], prefix: str) -> str:
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return str(data.get("family") or data.get("parameters", {}).get("family") or (prefix.split(".", 1)[1] if "." in prefix else ""))
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def is_scoped_filename(path: Path, scope_id: str) -> bool:
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return scope_id != "unscoped" and sanitize_token(scope_id) in path.name
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def collect_manifests(workspace: Path, prefix: str = "", scope_id: str = "") -> List[Dict[str, Any]]:
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final_dir = workspace / "final"
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paths = sorted(final_dir.glob("*.manifest.json"), key=lambda p: p.stat().st_mtime)
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records: List[Dict[str, Any]] = []
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for path in paths:
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data = read_json(path)
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if not data:
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continue
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stage = str(data.get("stage") or "")
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if not stage or stage in {"minimal", "summary"}:
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continue
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rec_prefix = str(data.get("prefix") or prefix)
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if prefix and rec_prefix and rec_prefix != prefix:
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# Per-target child manifests such as Multi.SPL.Lc_to_At.kaks.manifest.json
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# are indexed through the aggregate scoped manifest instead of treated as
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# independent top-level stages.
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continue
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rec_scope = manifest_scope(data)
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if scope_id and rec_scope != scope_id:
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continue
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records.append({"path": path, "data": data, "stage": stage, "prefix": rec_prefix, "scope_id": rec_scope})
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dedup: Dict[Tuple[str, str, str], Dict[str, Any]] = {}
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for rec in records:
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key = (rec["stage"], rec["scope_id"], rec["prefix"])
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prev = dedup.get(key)
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if not prev:
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dedup[key] = rec
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continue
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prev_scoped = is_scoped_filename(prev["path"], rec["scope_id"])
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rec_scoped = is_scoped_filename(rec["path"], rec["scope_id"])
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if (rec_scoped and not prev_scoped) or rec["path"].stat().st_mtime >= prev["path"].stat().st_mtime:
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dedup[key] = rec
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return sorted(dedup.values(), key=lambda r: (r["scope_id"], r["stage"]))
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def summarize_record(workspace: Path, rec: Dict[str, Any]) -> Dict[str, Any]:
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data = rec["data"]
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metrics = data.get("metrics") if isinstance(data.get("metrics"), dict) else {}
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artifacts = data.get("artifacts")
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artifact_rows = []
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missing = []
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for name, artifact in artifact_iter(artifacts):
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resolved = resolve_artifact_path(workspace, rec["path"], artifact)
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exists = bool(resolved and resolved.exists())
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if not exists:
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missing.append(name)
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artifact_rows.append({
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"stage": rec["stage"],
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"scope_id": rec["scope_id"],
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"artifact": name,
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"path": str(resolved or artifact.get("path") or ""),
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"exists": exists,
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"size": resolved.stat().st_size if exists else "",
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"type": artifact.get("type") or artifact.get("format") or "",
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})
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return {
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"stage": rec["stage"],
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"prefix": rec["prefix"],
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"scope_id": rec["scope_id"],
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"status": data.get("status", "unknown"),
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"family": manifest_family(data, rec["prefix"]),
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"target_species": data.get("target_species") or data.get("parameters", {}).get("target_species") or [],
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"reference_species": data.get("reference_species") or data.get("parameters", {}).get("reference_species") or [],
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"comparative_species": data.get("comparative_species") or data.get("parameters", {}).get("comparative_species") or [],
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"metrics": metrics,
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"artifact_count": len(artifact_rows),
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"missing_artifacts": missing,
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"manifest": str(rec["path"]),
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"artifact_rows": artifact_rows,
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}
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def compact_metrics(stage: str, metrics: Dict[str, Any]) -> str:
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priority = [
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"member_count", "total_members", "protein_count", "sequence_count", "num_sequences",
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"genes_analyzed", "gene_count", "ortholog_pairs", "species_runs", "input_pairs",
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"successful_pairs", "mean_ka_ks", "mean_ks", "total_interactions", "genes_in_network",
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"total_samples", "de_genes", "go_term_count", "module_count", "status",
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]
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parts = []
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for key in priority:
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if key in metrics:
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parts.append(f"{key}={metrics[key]}")
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if not parts:
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for key, value in list(metrics.items())[:5]:
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if isinstance(value, (str, int, float, bool)):
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parts.append(f"{key}={value}")
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return "; ".join(parts)
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def build_checks(summaries: List[Dict[str, Any]]) -> List[Dict[str, str]]:
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checks = []
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by_scope: Dict[str, List[Dict[str, Any]]] = {}
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for item in summaries:
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by_scope.setdefault(item["scope_id"], []).append(item)
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if item["status"] not in {"success", "partial_success"}:
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checks.append({"level": "error", "scope_id": item["scope_id"], "message": f"{item['stage']} status={item['status']}"})
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if item["missing_artifacts"]:
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checks.append({"level": "warning", "scope_id": item["scope_id"], "message": f"{item['stage']} missing artifacts: {', '.join(item['missing_artifacts'][:5])}"})
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for scope, items in by_scope.items():
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families = sorted({str(x.get("family") or "") for x in items if x.get("family")})
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if len(families) > 1:
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checks.append({"level": "warning", "scope_id": scope, "message": f"Multiple family labels in same scope: {', '.join(families)}"})
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stages = {x["stage"] for x in items}
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if "kaks" in stages and "ortholog" not in stages:
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checks.append({"level": "warning", "scope_id": scope, "message": "kaks present but ortholog manifest not found in same scope"})
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if "combo" in stages:
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missing = [s for s in ("phylogeny", "motif", "domain", "structure") if s not in stages]
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if missing:
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checks.append({"level": "warning", "scope_id": scope, "message": f"combo present but missing dependencies: {', '.join(missing)}"})
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if not checks:
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checks.append({"level": "ok", "scope_id": "all", "message": "No manifest-level consistency issues detected"})
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return checks
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def write_files_tsv(path: Path, rows: List[Dict[str, Any]]) -> None:
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headers = ["scope_id", "stage", "artifact", "type", "exists", "size", "path"]
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with path.open("w", encoding="utf-8") as handle:
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handle.write("\t".join(headers) + "\n")
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for row in rows:
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handle.write("\t".join(str(row.get(h, "")) for h in headers) + "\n")
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def write_report(path: Path, prefix: str, summaries: List[Dict[str, Any]], checks: List[Dict[str, str]], files_tsv: Path) -> None:
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by_scope: Dict[str, List[Dict[str, Any]]] = {}
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for item in summaries:
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by_scope.setdefault(item["scope_id"], []).append(item)
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with path.open("w", encoding="utf-8") as f:
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f.write(f"# Analysis Summary - {prefix}\n\n")
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f.write(f"Generated: {datetime.now().isoformat()}\n\n")
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f.write("This summary is an objective result index and QC report. Deep biological interpretation should be generated as a separate step.\n\n")
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f.write("## Scope Overview\n\n")
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for scope, items in sorted(by_scope.items()):
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stages = ", ".join(sorted({x["stage"] for x in items}))
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f.write(f"- **{scope}**: {len(items)} stage manifest(s); stages: {stages}\n")
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f.write("\n## Stage Metrics\n\n")
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f.write("| Scope | Stage | Status | Target | Reference | Key metrics |\n")
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f.write("|---|---|---|---|---|---|\n")
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for item in summaries:
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target = ",".join(map(str, item.get("target_species") or []))
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ref = ",".join(map(str, item.get("reference_species") or []))
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f.write(f"| {item['scope_id']} | {item['stage']} | {item['status']} | {target} | {ref} | {compact_metrics(item['stage'], item['metrics'])} |\n")
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f.write("\n## Consistency Checks\n\n")
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for check in checks:
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f.write(f"- **{check['level']}** `{check['scope_id']}`: {check['message']}\n")
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f.write("\n## Files\n\n")
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f.write(f"Artifact index: `{files_tsv.name}`\n")
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def main():
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parser = argparse.ArgumentParser(description="Summary stage - whole-job manifest summary")
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parser.add_argument("--manifest", help="Any manifest from the job; used to infer workspace/prefix")
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parser.add_argument("--workspace", help="workspace/<job_id> directory")
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parser.add_argument("--prefix", help="analysis prefix")
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parser.add_argument("--scope-file", help="optional scope JSON; when set, writes an additional scoped summary")
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parser.add_argument("--scope-id", help="optional explicit scope_id filter")
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parser.add_argument("--force", action="store_true", help="overwrite existing results")
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parser.add_argument("--log-file", help="log file path")
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parser.add_argument("--no-deepseek", action="store_true", help="write only the deterministic evidence index")
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parser.add_argument("--framework", help="optional Markdown framework for the DeepSeek report")
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parser.add_argument("--deepseek-model", default="", help="optional DeepSeek model override")
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parser.add_argument("--deepseek-max-tokens", type=int, default=16000)
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args = parser.parse_args()
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manifest_path = Path(args.manifest).expanduser().resolve() if args.manifest else None
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if manifest_path and not manifest_path.exists():
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print(f"Error: manifest not found: {manifest_path}")
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sys.exit(1)
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workspace = infer_workspace(manifest_path, args.workspace)
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final_dir = workspace / "final"
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final_dir.mkdir(parents=True, exist_ok=True)
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seed_manifest = read_json(manifest_path) if manifest_path else {}
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prefix = args.prefix or str((seed_manifest or {}).get("prefix") or "")
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scope_id = args.scope_id or ""
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if args.scope_file:
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scope_data = read_json(Path(args.scope_file).expanduser())
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if scope_data:
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scope_id = scope_id or str(scope_data.get("scope_id") or "")
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prefix = prefix or str(scope_data.get("prefix") or "")
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if not prefix:
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candidates = collect_manifests(workspace)
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prefix = candidates[0]["prefix"] if candidates else workspace.name
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all_records = collect_manifests(workspace, prefix=prefix)
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summaries = [summarize_record(workspace, rec) for rec in all_records]
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artifact_rows = [row for item in summaries for row in item["artifact_rows"]]
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checks = build_checks(summaries)
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evidence_index = final_dir / f"{prefix}.summary_evidence_index.md"
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files_tsv = final_dir / f"{prefix}.summary.files.tsv"
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manifest_out = final_dir / f"{prefix}.summary.manifest.json"
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write_files_tsv(files_tsv, artifact_rows)
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write_report(evidence_index, prefix, summaries, checks, files_tsv)
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manifest_data = {
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"manifest_version": "1.0",
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"stage": "summary",
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"status": "success",
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"prefix": prefix,
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"timestamp": datetime.now().isoformat(),
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"workspace": str(workspace),
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"metrics": {
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"manifest_count": len(summaries),
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"scope_count": len({x["scope_id"] for x in summaries}),
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"artifact_count": len(artifact_rows),
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"check_count": len(checks),
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},
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"summaries": summaries,
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"checks": checks,
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"artifacts": {
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"summary_evidence_index": {"path": f"final/{evidence_index.name}", "type": "markdown", "size": evidence_index.stat().st_size},
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"files_tsv": {"path": f"final/{files_tsv.name}", "type": "tsv", "size": files_tsv.stat().st_size},
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},
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}
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manifest_out.write_text(json.dumps(manifest_data, indent=2, ensure_ascii=False), encoding="utf-8")
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scoped_manifest = None
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scoped_data = None
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if scope_id:
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scoped_items = [x for x in summaries if x["scope_id"] == scope_id]
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scoped_rows = [row for x in scoped_items for row in x["artifact_rows"]]
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scoped_checks = [x for x in checks if x["scope_id"] in {scope_id, "all"}]
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token = sanitize_token(scope_id)
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scoped_evidence_index = final_dir / f"{prefix}.{token}.summary_evidence_index.md"
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scoped_files = final_dir / f"{prefix}.{token}.summary.files.tsv"
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scoped_manifest = final_dir / f"{prefix}.{token}.summary.manifest.json"
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write_files_tsv(scoped_files, scoped_rows)
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write_report(scoped_evidence_index, prefix, scoped_items, scoped_checks, scoped_files)
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scoped_data = dict(manifest_data)
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scoped_data.update({
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"scope_id": scope_id,
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"metrics": {
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"manifest_count": len(scoped_items),
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"scope_count": 1 if scoped_items else 0,
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"artifact_count": len(scoped_rows),
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"check_count": len(scoped_checks),
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},
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"summaries": scoped_items,
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"checks": scoped_checks,
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"artifacts": {
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"summary_evidence_index": {"path": f"final/{scoped_evidence_index.name}", "type": "markdown", "size": scoped_evidence_index.stat().st_size},
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"files_tsv": {"path": f"final/{scoped_files.name}", "type": "tsv", "size": scoped_files.stat().st_size},
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},
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})
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scoped_manifest.write_text(json.dumps(scoped_data, indent=2, ensure_ascii=False), encoding="utf-8")
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if args.no_deepseek:
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fallback_report = final_dir / (
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f"{prefix}.{sanitize_token(scope_id)}.summary_report.md" if scope_id else f"{prefix}.summary_report.md"
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)
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source_index = scoped_evidence_index if scope_id else evidence_index
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fallback_report.write_text(source_index.read_text(encoding="utf-8"), encoding="utf-8")
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target_manifest = scoped_manifest if scope_id and scoped_manifest else manifest_out
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target_data = read_json(target_manifest) or manifest_data
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target_data.setdefault("artifacts", {})["summary_report"] = {
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"path": f"final/{fallback_report.name}",
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"type": "markdown",
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"size": fallback_report.stat().st_size,
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"generation": "deterministic_no_deepseek",
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}
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target_data["deepseek_generation"] = {"status": "skipped", "reason": "--no-deepseek"}
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target_manifest.write_text(json.dumps(target_data, indent=2, ensure_ascii=False), encoding="utf-8")
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else:
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try:
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from gfa_core.mas.agents.deepseek_summary import generate_deepseek_summary
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result = generate_deepseek_summary(
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final_dir=final_dir,
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prefix=prefix,
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job_id=workspace.name,
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summaries=summaries,
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scope_id=scope_id,
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framework_path=Path(args.framework).expanduser() if args.framework else None,
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model=args.deepseek_model,
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max_tokens=max(4096, int(args.deepseek_max_tokens)),
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)
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effective_scope = str(result.get("scope_id") or "")
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target_manifest = scoped_manifest if scope_id and scoped_manifest else manifest_out
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target_data = read_json(target_manifest) or manifest_data
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report_path = Path(result["report_path"])
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evidence_path = Path(result["evidence_path"])
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metadata_path = Path(result["metadata_path"])
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target_data.setdefault("artifacts", {}).update({
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"summary_report": {
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"path": f"final/{report_path.name}", "type": "markdown", "size": report_path.stat().st_size,
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"generation": "deepseek_api",
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},
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"summary_evidence": {
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"path": f"final/{evidence_path.name}", "type": "json", "size": evidence_path.stat().st_size,
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},
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"deepseek_metadata": {
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"path": f"final/{metadata_path.name}", "type": "json", "size": metadata_path.stat().st_size,
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},
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})
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target_data["deepseek_generation"] = {
|
|
"status": "success",
|
|
"scope_id": effective_scope,
|
|
"provider": result["metadata"].get("provider"),
|
|
"model": result["metadata"].get("model"),
|
|
"validation": result["metadata"].get("validation"),
|
|
}
|
|
target_manifest.write_text(json.dumps(target_data, indent=2, ensure_ascii=False), encoding="utf-8")
|
|
except Exception as exc:
|
|
target_manifest = scoped_manifest if scope_id and scoped_manifest else manifest_out
|
|
target_data = read_json(target_manifest) or manifest_data
|
|
target_data["status"] = "failed"
|
|
target_data["deepseek_generation"] = {"status": "failed", "error": str(exc)[:2000]}
|
|
target_manifest.write_text(json.dumps(target_data, indent=2, ensure_ascii=False), encoding="utf-8")
|
|
print(f"Error: DeepSeek summary generation failed: {exc}", file=sys.stderr)
|
|
sys.exit(2)
|
|
|
|
print("Summary complete")
|
|
print(f" - {evidence_index}")
|
|
print(f" - {files_tsv}")
|
|
print(f" - {manifest_out}")
|
|
|
|
|
|
if __name__ == "__main__":
|
|
main()
|