feat: add gene family result reports

2026-08-09 04:32:28 +08:00
parent 65f79207f0
commit cb122fd088
20 changed files with 3676 additions and 20 deletions
@@ -0,0 +1,70 @@
+#!/usr/bin/env python3
+"""CLI for the plan-scoped formal gene-family result report."""
+
+from __future__ import annotations
+
+import argparse
+import json
+from pathlib import Path
+import sys
+from typing import Sequence
+
+PROJECT_ROOT = Path(__file__).resolve().parents[2]
+if str(PROJECT_ROOT) not in sys.path:
+    sys.path.insert(0, str(PROJECT_ROOT))
+
+from gfa_core.gene_family_report import GeneFamilyReportResult, generate_gene_family_report
+
+
+def _parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(description="Generate or open a gene-family result report")
+    parser.add_argument("--workspace", type=Path, required=True)
+    parser.add_argument("--prefix", required=True)
+    parser.add_argument("--job-id", default="")
+    parser.add_argument("--expected-stages", default="")
+    parser.add_argument("--stage-statuses-json", default="{}")
+    parser.add_argument("--scope-id", default="")
+    parser.add_argument("--analysis-route", default="")
+    parser.add_argument("--member-set-id", default="")
+    parser.add_argument("--rnaseq-scope-id", default="")
+    parser.add_argument("--action", choices=("generate", "open"), default="generate")
+    parser.add_argument("--no-model", action="store_true")
+    return parser
+
+
+def main(argv: Sequence[str] | None = None) -> GeneFamilyReportResult:
+    args = _parser().parse_args(argv)
+    statuses = json.loads(args.stage_statuses_json)
+    if not isinstance(statuses, dict):
+        raise ValueError("--stage-statuses-json must contain a JSON object")
+    result = generate_gene_family_report(
+        args.workspace,
+        args.prefix,
+        expected_stages=[value.strip() for value in args.expected_stages.split(",") if value.strip()],
+        stage_statuses={str(key): str(value) for key, value in statuses.items()},
+        scope_id=args.scope_id,
+        analysis_route=args.analysis_route,
+        member_set_id=args.member_set_id,
+        rnaseq_scope_id=args.rnaseq_scope_id,
+        use_model=not args.no_model,
+        action=args.action,
+        job_id=args.job_id,
+    )
+    print(
+        json.dumps(
+            {
+                "status": "success",
+                "report_path": str(result.report_path),
+                "manifest_path": str(result.manifest_path),
+                "report_status": result.report_status,
+                "generation_mode": result.generation_mode,
+                "reused": result.reused,
+            },
+            ensure_ascii=False,
+        )
+    )
+    return result
+
+
+if __name__ == "__main__":
+    main()