71 lines
2.5 KiB
Python
71 lines
2.5 KiB
Python
#!/usr/bin/env python3
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"""CLI for the plan-scoped formal gene-family result report."""
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from __future__ import annotations
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import argparse
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import json
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from pathlib import Path
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import sys
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from typing import Sequence
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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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from gfa_core.gene_family_report import GeneFamilyReportResult, generate_gene_family_report
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def _parser() -> argparse.ArgumentParser:
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parser = argparse.ArgumentParser(description="Generate or open a gene-family result report")
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parser.add_argument("--workspace", type=Path, required=True)
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parser.add_argument("--prefix", required=True)
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parser.add_argument("--job-id", default="")
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parser.add_argument("--expected-stages", default="")
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parser.add_argument("--stage-statuses-json", default="{}")
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parser.add_argument("--scope-id", default="")
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parser.add_argument("--analysis-route", default="")
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parser.add_argument("--member-set-id", default="")
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parser.add_argument("--rnaseq-scope-id", default="")
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parser.add_argument("--action", choices=("generate", "open"), default="generate")
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parser.add_argument("--no-model", action="store_true")
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return parser
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def main(argv: Sequence[str] | None = None) -> GeneFamilyReportResult:
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args = _parser().parse_args(argv)
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statuses = json.loads(args.stage_statuses_json)
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if not isinstance(statuses, dict):
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raise ValueError("--stage-statuses-json must contain a JSON object")
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result = generate_gene_family_report(
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args.workspace,
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args.prefix,
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expected_stages=[value.strip() for value in args.expected_stages.split(",") if value.strip()],
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stage_statuses={str(key): str(value) for key, value in statuses.items()},
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scope_id=args.scope_id,
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analysis_route=args.analysis_route,
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member_set_id=args.member_set_id,
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rnaseq_scope_id=args.rnaseq_scope_id,
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use_model=not args.no_model,
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action=args.action,
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job_id=args.job_id,
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)
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print(
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json.dumps(
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{
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"status": "success",
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"report_path": str(result.report_path),
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"manifest_path": str(result.manifest_path),
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"report_status": result.report_status,
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"generation_mode": result.generation_mode,
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"reused": result.reused,
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},
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ensure_ascii=False,
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)
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)
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return result
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if __name__ == "__main__":
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main()
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