880 lines
38 KiB
Python
880 lines
38 KiB
Python
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#!/usr/bin/env python3
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"""Prepare and optionally run tri-chain extension-stage evidence experiments.
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This script strengthens the extension-stage template evidence base with cases
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selected from three bbav5 chains:
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1. subfamily/reference classification
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2. gene structure and promoter/cis-element post-processing
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3. RNA-seq table post-processing with bounded input subsets
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RNA-seq cases use bounded table subsets and are promoted only as lightweight
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post-processing stages. A complete RNA-seq workflow remains outside the
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extension-stage boundary.
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"""
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from __future__ import annotations
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import argparse
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import csv
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import hashlib
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import html
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import json
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import os
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import shutil
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import subprocess
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import sys
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import traceback
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from dataclasses import dataclass
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from datetime import datetime
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from pathlib import Path
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from typing import Any
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PROJECT_ROOT = Path(__file__).resolve().parents[1]
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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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DEFAULT_EVIDENCE_JOB = PROJECT_ROOT / "workspace" / "job_1781949576460_93f63d"
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DEFAULT_VALIDATION_JOB = PROJECT_ROOT / "workspace" / "job_1780581757475_be7fd4"
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DEFAULT_PROMOTER_JOB = PROJECT_ROOT / "workspace" / "job_1782045849720_9a6952"
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DEFAULT_RNASEQ_JOB = PROJECT_ROOT / "workspace" / "job_1780313949486_3f3732"
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DEFAULT_OUTPUT_ROOT = PROJECT_ROOT / "项目记录" / "拓展分析阶段_三链路模板证据实验_20260622"
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@dataclass(frozen=True)
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class SourceFile:
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rel_path: str
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dest_name: str
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row_limit: int = 0
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required: bool = True
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@dataclass(frozen=True)
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class TriCase:
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index: int
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case_id: str
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group: str
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archetype_id: str
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stage: str
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split: str
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job_root: Path
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script_name: str
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script_content: str
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source_files: tuple[SourceFile, ...]
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required_outputs: tuple[str, ...]
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description: str
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candidate_only: bool = False
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validation_gap: str = ""
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@property
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def dir_name(self) -> str:
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suffix = "candidate" if self.candidate_only else self.split
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return f"{self.index:02d}_{self.case_id}_{suffix}"
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def _sh(script: str) -> str:
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return "#!/usr/bin/env bash\nset -euo pipefail\npython3 - <<'PY'\n" + script.strip() + "\nPY\n"
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SCRIPT_REFCLS = _sh(
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"""
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from pathlib import Path
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for src, dst in [
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('assignment.tsv', 'output.assignment.tsv'),
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('subfamily.tsv', 'output.subfamily.tsv'),
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('confidence.tsv', 'output.confidence.tsv'),
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('tree.nwk', 'output.tree.nwk'),
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]:
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p = Path(src)
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if p.exists():
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Path(dst).write_text(p.read_text(encoding='utf-8', errors='ignore'), encoding='utf-8')
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rows = [line for line in Path('assignment.tsv').read_text(encoding='utf-8', errors='ignore').splitlines() if line.strip()]
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subfamilies = set()
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for line in Path('subfamily.tsv').read_text(encoding='utf-8', errors='ignore').splitlines()[1:]:
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parts = line.split('\\t')
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if len(parts) > 1 and parts[1]:
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subfamilies.add(parts[1])
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Path('reference_classification_summary.tsv').write_text(
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'metric\\tvalue\\nassignment_rows\\t{}\\nsubfamily_count\\t{}\\n'.format(max(len(rows) - 1, 0), len(subfamilies)),
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encoding='utf-8',
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)
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"""
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)
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SCRIPT_STRUCTURE = _sh(
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"""
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from pathlib import Path
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gff = Path('structure.filtered.gff3').read_text(encoding='utf-8', errors='ignore')
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table = Path('structure.tsv').read_text(encoding='utf-8', errors='ignore')
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Path('output.structure.filtered.gff3').write_text(gff, encoding='utf-8')
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Path('output.structure.tsv').write_text(table, encoding='utf-8')
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features = 0
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genes = set()
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for line in gff.splitlines():
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if not line or line.startswith('#'):
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continue
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features += 1
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attrs = line.split('\\t')[-1] if '\\t' in line else ''
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for token in attrs.replace(';', '\\t').split('\\t'):
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if token.startswith('ID=') or token.startswith('Parent='):
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genes.add(token.split('=', 1)[1].split('.')[0])
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Path('structure_summary.tsv').write_text(
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'metric\\tvalue\\ngff_feature_rows\\t{}\\ngene_like_ids\\t{}\\nstructure_table_rows\\t{}\\n'.format(
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features, len(genes), max(len([x for x in table.splitlines() if x.strip()]) - 1, 0)
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),
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encoding='utf-8',
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)
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"""
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)
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SCRIPT_PROMOTER = _sh(
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"""
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from pathlib import Path
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rows = [line for line in Path('plantcare_filtered.tab').read_text(encoding='utf-8', errors='ignore').splitlines() if line.strip()]
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Path('output.cis_elements.tsv').write_text('\\n'.join(rows) + '\\n', encoding='utf-8')
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counts = Path('element_counts.txt')
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if counts.exists():
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Path('output.element_counts.tsv').write_text(counts.read_text(encoding='utf-8', errors='ignore'), encoding='utf-8')
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else:
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seen = {}
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for line in rows[1:]:
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parts = line.split('\\t')
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if len(parts) > 1:
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seen[parts[1]] = seen.get(parts[1], 0) + 1
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Path('output.element_counts.tsv').write_text('element\\tcount\\n' + ''.join(f'{k}\\t{v}\\n' for k, v in sorted(seen.items())), encoding='utf-8')
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bed = Path('PlantCARE.bed')
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if bed.exists():
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Path('output.promoter.bed').write_text(bed.read_text(encoding='utf-8', errors='ignore'), encoding='utf-8')
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Path('output.promoter_summary.tsv').write_text(
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'metric\\tvalue\\ncis_element_rows\\t{}\\nelement_count_rows\\t{}\\nbed_rows\\t{}\\n'.format(
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max(len(rows) - 1, 0),
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len([x for x in Path('output.element_counts.tsv').read_text(encoding='utf-8', errors='ignore').splitlines() if x.strip()]),
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len([x for x in bed.read_text(encoding='utf-8', errors='ignore').splitlines() if x.strip()]) if bed.exists() else 0,
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),
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encoding='utf-8',
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)
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"""
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)
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SCRIPT_RNASEQ_QUANT = _sh(
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"""
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from pathlib import Path
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for src, dst in [('count_matrix.txt', 'output.count_matrix.tsv'), ('tpm_matrix.txt', 'output.tpm_matrix.tsv')]:
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Path(dst).write_text(Path(src).read_text(encoding='utf-8', errors='ignore'), encoding='utf-8')
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counts = Path('count_matrix.txt').read_text(encoding='utf-8', errors='ignore').splitlines()
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tpm = Path('tpm_matrix.txt').read_text(encoding='utf-8', errors='ignore').splitlines()
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Path('quant_summary.tsv').write_text(
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'metric\\tvalue\\ncount_matrix_rows\\t{}\\ntpm_matrix_rows\\t{}\\n'.format(max(len(counts) - 1, 0), max(len(tpm) - 1, 0)),
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encoding='utf-8',
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)
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"""
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)
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SCRIPT_RNASEQ_DE = _sh(
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"""
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from pathlib import Path
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text = Path('de_results.txt').read_text(encoding='utf-8', errors='ignore')
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Path('output.de_results.tsv').write_text(text, encoding='utf-8')
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lines = [line for line in text.splitlines() if line.strip()]
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Path('de_summary.tsv').write_text('metric\\tvalue\\nde_result_rows\\t{}\\n'.format(max(len(lines) - 1, 0)), encoding='utf-8')
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Path('top_de_preview.tsv').write_text('\\n'.join(lines[:51]) + ('\\n' if lines else ''), encoding='utf-8')
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"""
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)
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def tri_cases(evidence_job: Path, validation_job: Path, promoter_job: Path, rnaseq_job: Path) -> tuple[TriCase, ...]:
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return (
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TriCase(
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1,
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"reference_classification_hdzip_prediction",
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"subfamily_reference",
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"reference_classification",
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"reference_classification",
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"evidence",
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evidence_job,
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"run_reference_classification_tables.sh",
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SCRIPT_REFCLS,
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(
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SourceFile("final/Target.HDZIP.target-Si.ref-At.subfamily_prediction.reference_classification.assignment.tsv", "assignment.tsv"),
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SourceFile("final/Target.HDZIP.target-Si.ref-At.subfamily_prediction.reference_classification.subfamily.tsv", "subfamily.tsv"),
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SourceFile("final/Target.HDZIP.target-Si.ref-At.subfamily_prediction.reference_classification.confidence.tsv", "confidence.tsv"),
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SourceFile("final/Target.HDZIP.target-Si.ref-At.subfamily_prediction.reference_classification.tree.nwk", "tree.nwk"),
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),
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("output.assignment.tsv", "output.subfamily.tsv", "reference_classification_summary.tsv"),
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"Use Si HDZIP target plus At reference subfamily prediction outputs from job_1781949576460_93f63d.",
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),
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TriCase(
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2,
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"reference_classification_hdzip_target_plus_reference",
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"subfamily_reference",
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"reference_classification",
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"reference_classification",
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"validation",
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evidence_job,
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"run_reference_classification_tables.sh",
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SCRIPT_REFCLS,
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(
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SourceFile("final/Si.HDZIP.target_plus_reference.reference_classification.assignment.tsv", "assignment.tsv"),
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SourceFile("final/Si.HDZIP.target_plus_reference.reference_classification.subfamily.tsv", "subfamily.tsv"),
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SourceFile("final/Si.HDZIP.target_plus_reference.reference_classification.confidence.tsv", "confidence.tsv"),
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SourceFile("final/Si.HDZIP.target_plus_reference.reference_classification.tree.nwk", "tree.nwk", required=False),
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),
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("output.assignment.tsv", "output.subfamily.tsv", "reference_classification_summary.tsv"),
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"Use Si HDZIP target_plus_reference classification tables from the same completed job as an alternate split.",
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),
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TriCase(
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3,
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"gene_structure_hdzip",
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"gene_family_structure_promoter",
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"gene_structure_gff",
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"structure",
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"evidence",
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evidence_job,
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"run_gene_structure_gff.sh",
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SCRIPT_STRUCTURE,
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(
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SourceFile("structure/analysis/Target.HDZIP.target-Si.ref-At.subfamily_evidence.structure.filtered.gff3", "structure.filtered.gff3"),
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SourceFile("structure/analysis/Target.HDZIP.target-Si.ref-At.subfamily_evidence.structure.tsv", "structure.tsv"),
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),
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("output.structure.filtered.gff3", "output.structure.tsv", "structure_summary.tsv"),
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"Use Si HDZIP subfamily-evidence structure GFF/table from job_1781949576460_93f63d.",
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),
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TriCase(
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4,
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"gene_structure_ls",
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"gene_family_structure_promoter",
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"gene_structure_gff",
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"structure",
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"validation",
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validation_job,
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"run_gene_structure_gff.sh",
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SCRIPT_STRUCTURE,
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(
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SourceFile("structure/analysis/Ls.SPL.structure.filtered.gff3", "structure.filtered.gff3"),
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SourceFile("structure/analysis/Ls.SPL.structure.tsv", "structure.tsv"),
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),
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("output.structure.filtered.gff3", "output.structure.tsv", "structure_summary.tsv"),
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"Use Ls gene structure GFF/table as a held-out validation split.",
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),
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TriCase(
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5,
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"promoter_spl",
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"gene_family_structure_promoter",
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"promoter_cis_element",
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"promoter",
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"evidence",
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promoter_job,
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"run_promoter_cis_element.sh",
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SCRIPT_PROMOTER,
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(
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SourceFile("promoter/analysis/plantCARE_output_filtered.tab", "plantcare_filtered.tab"),
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SourceFile("promoter/analysis/element_counts.txt", "element_counts.txt"),
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SourceFile("promoter/analysis/PlantCARE.bed", "PlantCARE.bed"),
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),
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("output.cis_elements.tsv", "output.element_counts.tsv", "output.promoter_summary.tsv"),
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"Use existing SPL promoter PlantCARE/BED/count artifacts because job_1781949576460_93f63d has no promoter stage outputs.",
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),
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TriCase(
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6,
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"rnaseq_quant_subset",
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"rnaseq_table_extensions",
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"rnaseq_quant_matrix",
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"rnaseq_quant",
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"subset",
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rnaseq_job,
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"run_rnaseq_quant_subset.sh",
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SCRIPT_RNASEQ_QUANT,
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(
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SourceFile("final/Os.count_matrix.txt", "count_matrix.txt", row_limit=200),
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SourceFile("final/Os.tpm_matrix.txt", "tpm_matrix.txt", row_limit=200),
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),
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("output.count_matrix.tsv", "output.tpm_matrix.tsv", "quant_summary.tsv"),
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"Bounded RNA-seq quantification matrix subset for publishable table post-processing validation.",
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),
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TriCase(
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7,
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"rnaseq_de_subset",
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"rnaseq_table_extensions",
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"rnaseq_de_table",
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"rnaseq_de",
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"subset",
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rnaseq_job,
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"run_rnaseq_de_subset.sh",
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SCRIPT_RNASEQ_DE,
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(SourceFile("final/Os.rnaseq_de.H1_vs_Con.DE_results.txt", "de_results.txt", row_limit=200),),
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("output.de_results.tsv", "de_summary.tsv", "top_de_preview.tsv"),
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"Bounded RNA-seq DE result table subset for publishable table post-processing validation.",
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),
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)
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def main() -> int:
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parser = argparse.ArgumentParser(description=__doc__)
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parser.add_argument("--prepare", action="store_true", help="Create raw_code/raw_test_data/expected_outputs packages.")
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parser.add_argument("--run", action="store_true", help="Run publish/validate loop for non-candidate cases.")
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parser.add_argument("--report", action="store_true", help="Write metrics and HTML/Markdown reports.")
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parser.add_argument("--all", action="store_true", help="Run prepare, non-candidate extension loop, and report.")
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parser.add_argument("--output-root", type=Path, default=DEFAULT_OUTPUT_ROOT)
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|
|
parser.add_argument("--evidence-job", type=Path, default=DEFAULT_EVIDENCE_JOB)
|
||
|
|
parser.add_argument("--validation-job", type=Path, default=DEFAULT_VALIDATION_JOB)
|
||
|
|
parser.add_argument("--promoter-job", type=Path, default=DEFAULT_PROMOTER_JOB)
|
||
|
|
parser.add_argument("--rnaseq-job", type=Path, default=DEFAULT_RNASEQ_JOB)
|
||
|
|
parser.add_argument("--converter", default="archetype_spec", choices=["archetype_spec", "deepseek_agent", "deepseek_api", "local_rule", "rule"])
|
||
|
|
parser.add_argument("--runtime-env", default="test4py311")
|
||
|
|
parser.add_argument("--include-candidates", action="store_true", help="Also send candidate-only cases to the extension loop.")
|
||
|
|
parser.add_argument("--stop-on-failure", action="store_true")
|
||
|
|
args = parser.parse_args()
|
||
|
|
if not any((args.prepare, args.run, args.report, args.all)):
|
||
|
|
args.prepare = True
|
||
|
|
args.report = True
|
||
|
|
|
||
|
|
output_root = args.output_root.resolve()
|
||
|
|
output_root.mkdir(parents=True, exist_ok=True)
|
||
|
|
cases = tri_cases(args.evidence_job.resolve(), args.validation_job.resolve(), args.promoter_job.resolve(), args.rnaseq_job.resolve())
|
||
|
|
|
||
|
|
if args.prepare or args.all:
|
||
|
|
prepare(cases, output_root)
|
||
|
|
if args.run or args.all:
|
||
|
|
run_batch(cases, output_root, args.converter, args.runtime_env, args.include_candidates, args.stop_on_failure)
|
||
|
|
if args.report or args.all:
|
||
|
|
write_report(output_root, cases)
|
||
|
|
write_manifest(output_root)
|
||
|
|
return 0
|
||
|
|
|
||
|
|
|
||
|
|
def prepare(cases: tuple[TriCase, ...], output_root: Path) -> None:
|
||
|
|
packages = output_root / "packages"
|
||
|
|
logs = output_root / "logs"
|
||
|
|
packages.mkdir(parents=True, exist_ok=True)
|
||
|
|
logs.mkdir(parents=True, exist_ok=True)
|
||
|
|
rows = []
|
||
|
|
for case in cases:
|
||
|
|
root = packages / case.dir_name
|
||
|
|
raw_code = root / "raw_code"
|
||
|
|
raw_data = root / "raw_test_data"
|
||
|
|
expected = root / "expected_outputs"
|
||
|
|
for path in (raw_code, raw_data, expected, root / "_raw_run_work"):
|
||
|
|
clean_dir(path)
|
||
|
|
script = raw_code / case.script_name
|
||
|
|
script.write_text(case.script_content, encoding="utf-8")
|
||
|
|
script.chmod(0o755)
|
||
|
|
write_json(raw_code / "bbav5_extension_hint.json", extension_hint(case))
|
||
|
|
copied = copy_sources(case, raw_data)
|
||
|
|
raw = run_raw(root, case, logs / f"{case.dir_name}.raw.log")
|
||
|
|
expected_ok = raw["success"] and all((expected / name).is_file() and (expected / name).stat().st_size > 0 for name in case.required_outputs)
|
||
|
|
record = {
|
||
|
|
"case_id": case.case_id,
|
||
|
|
"group": case.group,
|
||
|
|
"archetype_id": case.archetype_id,
|
||
|
|
"stage": case.stage,
|
||
|
|
"split": case.split,
|
||
|
|
"candidate_only": case.candidate_only,
|
||
|
|
"validation_gap": case.validation_gap,
|
||
|
|
"case_dir": str(root),
|
||
|
|
"source_job": str(case.job_root),
|
||
|
|
"source_files": copied,
|
||
|
|
"raw_code_ok": raw["success"],
|
||
|
|
"expected_output_ok": expected_ok,
|
||
|
|
"required_outputs": list(case.required_outputs),
|
||
|
|
"raw_run": raw,
|
||
|
|
}
|
||
|
|
rows.append(record)
|
||
|
|
write_json(root / "prepare_record.json", record)
|
||
|
|
(root / "README.md").write_text(case_readme(case, copied), encoding="utf-8")
|
||
|
|
write_json(output_root / "prepare_manifest.json", {
|
||
|
|
"schema_version": "extension_tri_chain_prepare_v1",
|
||
|
|
"created_at": now(),
|
||
|
|
"case_count": len(rows),
|
||
|
|
"prepared": sum(1 for row in rows if row["expected_output_ok"]),
|
||
|
|
"candidate_only": sum(1 for row in rows if row["candidate_only"]),
|
||
|
|
"cases": rows,
|
||
|
|
})
|
||
|
|
|
||
|
|
|
||
|
|
def copy_sources(case: TriCase, raw_data: Path) -> list[dict[str, Any]]:
|
||
|
|
copied = []
|
||
|
|
for source in case.source_files:
|
||
|
|
src = case.job_root / source.rel_path
|
||
|
|
if not src.is_file():
|
||
|
|
if source.required:
|
||
|
|
raise FileNotFoundError(f"missing source for {case.case_id}: {src}")
|
||
|
|
copied.append({
|
||
|
|
"source": str(src),
|
||
|
|
"dest": source.dest_name,
|
||
|
|
"source_size": 0,
|
||
|
|
"dest_size": 0,
|
||
|
|
"sha256": "",
|
||
|
|
"row_limit": source.row_limit,
|
||
|
|
"copied_rows": 0,
|
||
|
|
"required": False,
|
||
|
|
"missing_optional": True,
|
||
|
|
})
|
||
|
|
continue
|
||
|
|
dest = raw_data / source.dest_name
|
||
|
|
dest.parent.mkdir(parents=True, exist_ok=True)
|
||
|
|
if source.row_limit and _looks_tabular(src):
|
||
|
|
copied_rows = copy_tabular_subset(src, dest, source.row_limit)
|
||
|
|
else:
|
||
|
|
shutil.copy2(src, dest)
|
||
|
|
copied_rows = 0
|
||
|
|
copied.append({
|
||
|
|
"source": str(src),
|
||
|
|
"dest": source.dest_name,
|
||
|
|
"source_size": src.stat().st_size,
|
||
|
|
"dest_size": dest.stat().st_size,
|
||
|
|
"sha256": sha256(dest),
|
||
|
|
"row_limit": source.row_limit,
|
||
|
|
"copied_rows": copied_rows,
|
||
|
|
"required": source.required,
|
||
|
|
})
|
||
|
|
return copied
|
||
|
|
|
||
|
|
|
||
|
|
def copy_tabular_subset(src: Path, dest: Path, row_limit: int) -> int:
|
||
|
|
rows = []
|
||
|
|
with src.open("r", encoding="utf-8", errors="ignore") as handle:
|
||
|
|
for index, line in enumerate(handle):
|
||
|
|
if index == 0 or index <= row_limit:
|
||
|
|
rows.append(line)
|
||
|
|
else:
|
||
|
|
break
|
||
|
|
dest.write_text("".join(rows), encoding="utf-8")
|
||
|
|
return max(len(rows) - 1, 0)
|
||
|
|
|
||
|
|
|
||
|
|
def run_raw(root: Path, case: TriCase, log_path: Path) -> dict[str, Any]:
|
||
|
|
work = root / "_raw_run_work"
|
||
|
|
expected = root / "expected_outputs"
|
||
|
|
copy_tree(root / "raw_test_data", work)
|
||
|
|
copy_tree(root / "raw_code", work)
|
||
|
|
before = file_set(work)
|
||
|
|
proc = subprocess.run(["bash", case.script_name], cwd=work, capture_output=True, text=True, timeout=240)
|
||
|
|
after = file_set(work)
|
||
|
|
new_files = sorted(after - before)
|
||
|
|
for rel in new_files:
|
||
|
|
src = work / rel
|
||
|
|
if src.is_file():
|
||
|
|
(expected / rel).parent.mkdir(parents=True, exist_ok=True)
|
||
|
|
shutil.copy2(src, expected / rel)
|
||
|
|
log_path.write_text(f"$ bash {case.script_name}\n\n[stdout]\n{proc.stdout}\n\n[stderr]\n{proc.stderr}\n", encoding="utf-8")
|
||
|
|
return {"success": proc.returncode == 0, "returncode": proc.returncode, "new_files": new_files, "stderr_tail": proc.stderr[-2000:]}
|
||
|
|
|
||
|
|
|
||
|
|
def run_batch(cases: tuple[TriCase, ...], output_root: Path, converter: str, runtime_env: str, include_candidates: bool, stop_on_failure: bool) -> None:
|
||
|
|
sys.path.insert(0, str(PROJECT_ROOT))
|
||
|
|
from gfa_core.extension_stage import ExtensionStageAgent, ExtensionStageManager
|
||
|
|
|
||
|
|
effective = "deepseek_api" if converter in {"archetype_spec", "deepseek_agent"} else converter
|
||
|
|
os.environ["BBAV5_EXTENSION_CONVERTER"] = effective
|
||
|
|
runnable = tuple(case for case in cases if include_candidates or not case.candidate_only)
|
||
|
|
if converter == "archetype_spec":
|
||
|
|
import gfa_core.extension_stage.agent as agent_module
|
||
|
|
|
||
|
|
def _convert_with_archetype_spec(**kwargs: Any) -> dict[str, Any]:
|
||
|
|
return local_conversion_spec(runnable, str(kwargs.get("display_name") or ""), str(kwargs.get("runtime_env") or runtime_env))
|
||
|
|
|
||
|
|
agent_module.convert_with_deepseek_api = _convert_with_archetype_spec
|
||
|
|
agent_module.repair_build_with_deepseek_api = _convert_with_archetype_spec
|
||
|
|
|
||
|
|
run_root = output_root / "runtime" / converter
|
||
|
|
for path in (run_root / "extension_stages", run_root / "workspace", run_root / "input", output_root / "results" / converter):
|
||
|
|
clean_dir(path)
|
||
|
|
manager = ExtensionStageManager(PROJECT_ROOT, store_root=run_root / "extension_stages", workspace_root=run_root / "workspace", input_root=run_root / "input")
|
||
|
|
agent = ExtensionStageAgent(manager)
|
||
|
|
rows = []
|
||
|
|
for case in runnable:
|
||
|
|
row = run_one(agent, output_root, case, converter, runtime_env)
|
||
|
|
rows.append(row)
|
||
|
|
if stop_on_failure and not row_success(row):
|
||
|
|
break
|
||
|
|
summary = {
|
||
|
|
"schema_version": "extension_tri_chain_batch_result_v1",
|
||
|
|
"created_at": now(),
|
||
|
|
"converter": converter,
|
||
|
|
"runtime_env": runtime_env,
|
||
|
|
"include_candidates": include_candidates,
|
||
|
|
"case_count": len(rows),
|
||
|
|
"passed": sum(1 for row in rows if row_success(row)),
|
||
|
|
"failed": sum(1 for row in rows if not row_success(row)),
|
||
|
|
"rows": rows,
|
||
|
|
}
|
||
|
|
result_dir = output_root / "results" / converter
|
||
|
|
write_json(result_dir / "summary.json", summary)
|
||
|
|
write_csv(result_dir / "summary.csv", rows)
|
||
|
|
(result_dir / "summary.md").write_text(summary_markdown(summary), encoding="utf-8")
|
||
|
|
|
||
|
|
|
||
|
|
def run_one(agent: Any, output_root: Path, case: TriCase, converter: str, runtime_env: str) -> dict[str, Any]:
|
||
|
|
case_root = output_root / "packages" / case.dir_name
|
||
|
|
result_dir = output_root / "results" / converter / "per_case" / case.dir_name
|
||
|
|
clean_dir(result_dir)
|
||
|
|
row = {
|
||
|
|
"case_id": case.case_id,
|
||
|
|
"group": case.group,
|
||
|
|
"archetype_id": case.archetype_id,
|
||
|
|
"stage": case.stage,
|
||
|
|
"split": case.split,
|
||
|
|
"converter": converter,
|
||
|
|
"candidate_only": case.candidate_only,
|
||
|
|
"raw_code_ok": (case_root / "prepare_record.json").exists(),
|
||
|
|
"expected_output_ok": expected_ok(case_root, case),
|
||
|
|
"build_success": False,
|
||
|
|
"extension_id": "",
|
||
|
|
"trial_success": False,
|
||
|
|
"confirm_success": False,
|
||
|
|
"validate_success": False,
|
||
|
|
"golden_status": "",
|
||
|
|
"template_gate_status": "",
|
||
|
|
"publish_success": False,
|
||
|
|
"output_count": 0,
|
||
|
|
"error": "",
|
||
|
|
}
|
||
|
|
try:
|
||
|
|
build = agent.create_from_uploads(
|
||
|
|
display_name=f"tri_chain_{case.case_id}",
|
||
|
|
command=f"bash {case.script_name}",
|
||
|
|
runtime_env=runtime_env,
|
||
|
|
code_files=upload_files(case_root / "raw_code"),
|
||
|
|
data_files=upload_files(case_root / "raw_test_data"),
|
||
|
|
description=case.description,
|
||
|
|
)
|
||
|
|
write_json(result_dir / "build_response.json", build)
|
||
|
|
extension = build.get("extension") or {}
|
||
|
|
extension_id = str(extension.get("extension_id") or "")
|
||
|
|
row.update({"build_success": bool(build.get("success") and extension_id), "extension_id": extension_id})
|
||
|
|
trial = agent.trial_run(extension_id)
|
||
|
|
write_json(result_dir / "trial_run.json", trial)
|
||
|
|
row["trial_success"] = bool(trial.get("success"))
|
||
|
|
row["output_count"] = len((trial.get("run") or {}).get("outputs") or [])
|
||
|
|
outputs = (trial.get("extension") or {}).get("outputs_detected") or (trial.get("run") or {}).get("outputs") or []
|
||
|
|
confirm = agent.confirm(extension_id, outputs=outputs, nl_triggers=[case.case_id, case.stage, case.archetype_id])
|
||
|
|
write_json(result_dir / "confirm_response.json", confirm)
|
||
|
|
row["confirm_success"] = bool(confirm.get("success"))
|
||
|
|
validation = agent.validate(extension_id)
|
||
|
|
write_json(result_dir / "validate_response.json", validation)
|
||
|
|
run = validation.get("run") or {}
|
||
|
|
row["validate_success"] = bool(validation.get("success"))
|
||
|
|
row["golden_status"] = str((run.get("golden_comparison") or {}).get("status") or "")
|
||
|
|
row["template_gate_status"] = str((run.get("template_gate") or {}).get("status") or "")
|
||
|
|
publish = agent.publish(extension_id)
|
||
|
|
write_json(result_dir / "publish_response.json", publish)
|
||
|
|
row["publish_success"] = bool(publish.get("success"))
|
||
|
|
except Exception as exc:
|
||
|
|
row["error"] = str(exc)
|
||
|
|
write_json(result_dir / "error.json", {"error": str(exc), "traceback": traceback.format_exc(), "row": row})
|
||
|
|
write_json(result_dir / "result_row.json", row)
|
||
|
|
return row
|
||
|
|
|
||
|
|
|
||
|
|
def extension_hint(case: TriCase) -> dict[str, Any]:
|
||
|
|
if case.archetype_id:
|
||
|
|
from gfa_core.extension_stage.template_cases import ARCHETYPE_BY_ID
|
||
|
|
|
||
|
|
archetype = ARCHETYPE_BY_ID[case.archetype_id]
|
||
|
|
input_roles = {key: dict(value) for key, value in archetype.input_roles.items()}
|
||
|
|
output_contract = [dict(item) for item in archetype.output_contract]
|
||
|
|
comparator_plan = dict(archetype.comparator_plan)
|
||
|
|
analysis_type = archetype.analysis_type
|
||
|
|
tool_family = archetype.tool_family
|
||
|
|
else:
|
||
|
|
input_roles = {"input_file": {"role": "generic_input_file", "required": True}}
|
||
|
|
output_contract = [
|
||
|
|
{"name_pattern": name, "type": out_type(name), "primary": index == 0, "required": True, "allow_empty": False, "semantic_role": "rnaseq_table_candidate", "compare_mode": "table", "required_for_golden": True}
|
||
|
|
for index, name in enumerate(case.required_outputs)
|
||
|
|
]
|
||
|
|
comparator_plan = {"mode": "pipeline_golden_diff", "default_compare": "structured", "allowed_differences": []}
|
||
|
|
analysis_type = "table_filter"
|
||
|
|
tool_family = "python"
|
||
|
|
return {
|
||
|
|
"schema_version": "bbav5_tri_chain_extension_hint_v1",
|
||
|
|
"case_id": case.case_id,
|
||
|
|
"archetype_id": case.archetype_id,
|
||
|
|
"group": case.group,
|
||
|
|
"representative_stage": case.stage,
|
||
|
|
"recommended_original_command": f"bash {case.script_name}",
|
||
|
|
"analysis_type": analysis_type,
|
||
|
|
"tool_family": tool_family,
|
||
|
|
"input_roles": input_roles,
|
||
|
|
"output_contract": output_contract,
|
||
|
|
"comparator_plan": comparator_plan,
|
||
|
|
"requires_user_confirmation": bool(case.candidate_only),
|
||
|
|
"candidate_only": case.candidate_only,
|
||
|
|
"validation_gap": case.validation_gap,
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
def local_conversion_spec(cases: tuple[TriCase, ...], display_name: str, runtime_env: str) -> dict[str, Any]:
|
||
|
|
case = case_from_display(cases, display_name)
|
||
|
|
hint = extension_hint(case)
|
||
|
|
return {
|
||
|
|
"template_type": "tri_chain_archetype_spec",
|
||
|
|
"archetype_id": case.archetype_id,
|
||
|
|
"original_command": f"bash {case.script_name}",
|
||
|
|
"command_template": f"bash {{code_dir}}/{case.script_name} --input-dir {{input_dir}} --output-dir {{output_dir}}",
|
||
|
|
"semantic_command_template": "",
|
||
|
|
"wrapper_command_template": f"bash {{code_dir}}/{case.script_name} --input-dir {{input_dir}} --output-dir {{output_dir}}",
|
||
|
|
"analysis_type": hint["analysis_type"],
|
||
|
|
"tool_family": hint["tool_family"],
|
||
|
|
"input_roles": hint["input_roles"],
|
||
|
|
"inputs": {key: {"required": value.get("required", True)} for key, value in hint["input_roles"].items()},
|
||
|
|
"parameters": {},
|
||
|
|
"outputs": {"directory": "outputs", "patterns": list(case.required_outputs)},
|
||
|
|
"output_contract": hint["output_contract"],
|
||
|
|
"comparator_plan": hint["comparator_plan"],
|
||
|
|
"requires_user_confirmation": bool(case.candidate_only),
|
||
|
|
"notes": "Tri-chain deterministic archetype spec; RNA-seq cases are bounded table post-processing subsets, not full RNA-seq workflows.",
|
||
|
|
"converter": {"type": "archetype_spec", "mode": "tri_chain_reproducible", "runtime_env": runtime_env},
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
def write_report(output_root: Path, cases: tuple[TriCase, ...]) -> None:
|
||
|
|
prepare_manifest = read_json(output_root / "prepare_manifest.json")
|
||
|
|
summaries = {}
|
||
|
|
for converter in ("archetype_spec", "deepseek_agent", "deepseek_api", "local_rule", "rule"):
|
||
|
|
path = output_root / "results" / converter / "summary.json"
|
||
|
|
if path.exists():
|
||
|
|
summaries[converter] = read_json(path)
|
||
|
|
metrics = {
|
||
|
|
"schema_version": "extension_tri_chain_metrics_v1",
|
||
|
|
"created_at": now(),
|
||
|
|
"case_count": len(cases),
|
||
|
|
"prepared": prepare_manifest.get("prepared", 0),
|
||
|
|
"candidate_only": sum(1 for case in cases if case.candidate_only),
|
||
|
|
"template_cases": sum(1 for case in cases if case.archetype_id),
|
||
|
|
"groups": group_metrics(cases, prepare_manifest, summaries),
|
||
|
|
"summaries": summaries,
|
||
|
|
"validation_gaps": [case.validation_gap for case in cases if case.validation_gap],
|
||
|
|
}
|
||
|
|
write_json(output_root / "tri_chain_metrics.json", metrics)
|
||
|
|
write_csv(output_root / "tri_chain_case_table.csv", case_rows(cases, prepare_manifest))
|
||
|
|
(output_root / "tri_chain_report.md").write_text(report_markdown(metrics), encoding="utf-8")
|
||
|
|
(output_root / "tri_chain_report.html").write_text(report_html(metrics), encoding="utf-8")
|
||
|
|
|
||
|
|
|
||
|
|
def group_metrics(cases: tuple[TriCase, ...], prepare_manifest: dict[str, Any], summaries: dict[str, Any]) -> list[dict[str, Any]]:
|
||
|
|
rows = []
|
||
|
|
prepared_by_case = {row.get("case_id"): row for row in prepare_manifest.get("cases") or []}
|
||
|
|
for group in sorted({case.group for case in cases}):
|
||
|
|
group_cases = [case for case in cases if case.group == group]
|
||
|
|
rows.append({
|
||
|
|
"group": group,
|
||
|
|
"case_count": len(group_cases),
|
||
|
|
"prepared": sum(1 for case in group_cases if (prepared_by_case.get(case.case_id) or {}).get("expected_output_ok")),
|
||
|
|
"candidate_only": sum(1 for case in group_cases if case.candidate_only),
|
||
|
|
"template_archetypes": sorted({case.archetype_id for case in group_cases if case.archetype_id}),
|
||
|
|
"run_passed": {
|
||
|
|
name: sum(1 for row in summary.get("rows") or [] if row.get("group") == group and row_success(row))
|
||
|
|
for name, summary in summaries.items()
|
||
|
|
},
|
||
|
|
})
|
||
|
|
return rows
|
||
|
|
|
||
|
|
|
||
|
|
def case_rows(cases: tuple[TriCase, ...], prepare_manifest: dict[str, Any]) -> list[dict[str, Any]]:
|
||
|
|
prepared = {row.get("case_id"): row for row in prepare_manifest.get("cases") or []}
|
||
|
|
rows = []
|
||
|
|
for case in cases:
|
||
|
|
prep = prepared.get(case.case_id) or {}
|
||
|
|
rows.append({
|
||
|
|
"case_id": case.case_id,
|
||
|
|
"group": case.group,
|
||
|
|
"archetype_id": case.archetype_id,
|
||
|
|
"stage": case.stage,
|
||
|
|
"split": case.split,
|
||
|
|
"candidate_only": case.candidate_only,
|
||
|
|
"source_job": str(case.job_root),
|
||
|
|
"expected_output_ok": prep.get("expected_output_ok", False),
|
||
|
|
"validation_gap": case.validation_gap,
|
||
|
|
})
|
||
|
|
return rows
|
||
|
|
|
||
|
|
|
||
|
|
def report_markdown(metrics: dict[str, Any]) -> str:
|
||
|
|
lines = [
|
||
|
|
"# 拓展分析阶段三链路模板证据实验",
|
||
|
|
"",
|
||
|
|
f"- Cases: {metrics.get('case_count')}",
|
||
|
|
f"- Prepared: {metrics.get('prepared')}",
|
||
|
|
f"- Template cases: {metrics.get('template_cases')}",
|
||
|
|
f"- Candidate-only cases: {metrics.get('candidate_only')}",
|
||
|
|
"",
|
||
|
|
"## Coverage",
|
||
|
|
"",
|
||
|
|
"| Group | Cases | Prepared | Candidate-only | Template archetypes |",
|
||
|
|
"|---|---:|---:|---:|---|",
|
||
|
|
]
|
||
|
|
for row in metrics.get("groups") or []:
|
||
|
|
lines.append(f"| `{row.get('group')}` | {row.get('case_count')} | {row.get('prepared')} | {row.get('candidate_only')} | {', '.join(row.get('template_archetypes') or [])} |")
|
||
|
|
lines.extend(["", "## Validation Gaps", ""])
|
||
|
|
for gap in metrics.get("validation_gaps") or []:
|
||
|
|
lines.append(f"- {gap}")
|
||
|
|
if not metrics.get("validation_gaps"):
|
||
|
|
lines.append("- None recorded.")
|
||
|
|
lines.append("")
|
||
|
|
return "\n".join(lines)
|
||
|
|
|
||
|
|
|
||
|
|
def report_html(metrics: dict[str, Any]) -> str:
|
||
|
|
rows = "".join(
|
||
|
|
"<tr><td>{}</td><td>{}</td><td>{}</td><td>{}</td><td>{}</td></tr>".format(
|
||
|
|
html.escape(str(row.get("group"))),
|
||
|
|
row.get("case_count"),
|
||
|
|
row.get("prepared"),
|
||
|
|
row.get("candidate_only"),
|
||
|
|
html.escape(", ".join(row.get("template_archetypes") or [])),
|
||
|
|
)
|
||
|
|
for row in metrics.get("groups") or []
|
||
|
|
)
|
||
|
|
gaps = "".join(f"<li>{html.escape(str(gap))}</li>" for gap in metrics.get("validation_gaps") or [])
|
||
|
|
return f"""<!doctype html><html lang="zh-CN"><head><meta charset="utf-8"><title>拓展分析阶段三链路模板证据实验</title><style>body{{font:14px/1.65 Arial,'Microsoft YaHei',sans-serif;margin:0;color:#172033}}main{{max-width:1120px;margin:auto;padding:28px}}h1{{font-size:26px}}table{{border-collapse:collapse;width:100%;margin:14px 0}}td,th{{border:1px solid #d8dee9;padding:8px;text-align:left}}th{{background:#edf3f7}}.metric{{display:inline-block;margin:6px 12px 6px 0;padding:10px 14px;border:1px solid #d8dee9;background:#f8fafc;border-radius:6px}}.metric b{{display:block;font-size:22px;color:#255f85}}</style></head><body><main><h1>拓展分析阶段三链路模板证据实验</h1><div class="metric"><b>{metrics.get('prepared')}</b>prepared</div><div class="metric"><b>{metrics.get('template_cases')}</b>template cases</div><div class="metric"><b>{metrics.get('candidate_only')}</b>candidate-only cases</div><h2>Coverage</h2><table><tr><th>Group</th><th>Cases</th><th>Prepared</th><th>Candidate-only</th><th>Template archetypes</th></tr>{rows}</table><h2>Validation Gaps</h2><ul>{gaps or '<li>None recorded.</li>'}</ul></main></body></html>"""
|
||
|
|
|
||
|
|
|
||
|
|
def case_from_display(cases: tuple[TriCase, ...], text: str) -> TriCase:
|
||
|
|
for case in cases:
|
||
|
|
if case.case_id in text or (case.archetype_id and case.archetype_id in text):
|
||
|
|
return case
|
||
|
|
raise ValueError(f"cannot infer tri-chain case from display_name: {text}")
|
||
|
|
|
||
|
|
|
||
|
|
def upload_files(root: Path) -> list[tuple[str, bytes]]:
|
||
|
|
return [(path.name, path.read_bytes()) for path in sorted(root.iterdir()) if path.is_file()]
|
||
|
|
|
||
|
|
|
||
|
|
def expected_ok(root: Path, case: TriCase) -> bool:
|
||
|
|
return all((root / "expected_outputs" / name).is_file() and (root / "expected_outputs" / name).stat().st_size > 0 for name in case.required_outputs)
|
||
|
|
|
||
|
|
|
||
|
|
def row_success(row: dict[str, Any]) -> bool:
|
||
|
|
return all(bool(row.get(key)) for key in ("raw_code_ok", "expected_output_ok", "build_success", "trial_success", "confirm_success", "validate_success", "publish_success")) and row.get("golden_status") == "passed" and row.get("template_gate_status") == "passed"
|
||
|
|
|
||
|
|
|
||
|
|
def clean_dir(path: Path) -> None:
|
||
|
|
if path.exists():
|
||
|
|
shutil.rmtree(path)
|
||
|
|
path.mkdir(parents=True, exist_ok=True)
|
||
|
|
|
||
|
|
|
||
|
|
def copy_tree(src: Path, dst: Path) -> None:
|
||
|
|
dst.mkdir(parents=True, exist_ok=True)
|
||
|
|
if not src.exists():
|
||
|
|
return
|
||
|
|
for item in src.iterdir():
|
||
|
|
target = dst / item.name
|
||
|
|
if item.is_dir():
|
||
|
|
shutil.copytree(item, target, dirs_exist_ok=True)
|
||
|
|
else:
|
||
|
|
shutil.copy2(item, target)
|
||
|
|
|
||
|
|
|
||
|
|
def file_set(root: Path) -> set[str]:
|
||
|
|
return {path.relative_to(root).as_posix() for path in root.rglob("*") if path.is_file()}
|
||
|
|
|
||
|
|
|
||
|
|
def write_json(path: Path, data: Any) -> None:
|
||
|
|
path.parent.mkdir(parents=True, exist_ok=True)
|
||
|
|
path.write_text(json.dumps(data, indent=2, ensure_ascii=False) + "\n", encoding="utf-8")
|
||
|
|
|
||
|
|
|
||
|
|
def read_json(path: Path) -> dict[str, Any]:
|
||
|
|
if not path.exists():
|
||
|
|
return {}
|
||
|
|
return json.loads(path.read_text(encoding="utf-8"))
|
||
|
|
|
||
|
|
|
||
|
|
def write_csv(path: Path, rows: list[dict[str, Any]]) -> None:
|
||
|
|
path.parent.mkdir(parents=True, exist_ok=True)
|
||
|
|
fields = sorted({key for row in rows for key in row}) if rows else ["empty"]
|
||
|
|
with path.open("w", encoding="utf-8", newline="") as handle:
|
||
|
|
writer = csv.DictWriter(handle, fieldnames=fields)
|
||
|
|
writer.writeheader()
|
||
|
|
for row in rows:
|
||
|
|
writer.writerow({field: row.get(field, "") for field in fields})
|
||
|
|
|
||
|
|
|
||
|
|
def summary_markdown(summary: dict[str, Any]) -> str:
|
||
|
|
lines = [
|
||
|
|
"# Tri-chain Extension Batch",
|
||
|
|
"",
|
||
|
|
f"Converter: `{summary.get('converter')}`",
|
||
|
|
f"Cases: {summary.get('case_count')} passed={summary.get('passed')} failed={summary.get('failed')}",
|
||
|
|
"",
|
||
|
|
"| Case | Build | Trial | Validate | Golden | Gate | Publish | Error |",
|
||
|
|
"|---|---:|---:|---:|---|---|---:|---|",
|
||
|
|
]
|
||
|
|
for row in summary.get("rows") or []:
|
||
|
|
error = str(row.get("error") or "")[:120].replace("|", "/")
|
||
|
|
lines.append(f"| `{row.get('case_id')}` | {row.get('build_success')} | {row.get('trial_success')} | {row.get('validate_success')} | `{row.get('golden_status')}` | `{row.get('template_gate_status')}` | {row.get('publish_success')} | {error} |")
|
||
|
|
return "\n".join(lines) + "\n"
|
||
|
|
|
||
|
|
|
||
|
|
def case_readme(case: TriCase, copied: list[dict[str, Any]]) -> str:
|
||
|
|
lines = [
|
||
|
|
f"# {case.case_id}",
|
||
|
|
"",
|
||
|
|
f"- Group: `{case.group}`",
|
||
|
|
f"- Stage: `{case.stage}`",
|
||
|
|
f"- Archetype: `{case.archetype_id or 'candidate_only'}`",
|
||
|
|
f"- Split: `{case.split}`",
|
||
|
|
f"- Candidate only: `{case.candidate_only}`",
|
||
|
|
"",
|
||
|
|
case.description,
|
||
|
|
"",
|
||
|
|
"## Source Files",
|
||
|
|
"",
|
||
|
|
]
|
||
|
|
for item in copied:
|
||
|
|
rows = f", subset rows={item['copied_rows']}" if item.get("row_limit") else ""
|
||
|
|
lines.append(f"- `{item['source']}` -> `raw_test_data/{item['dest']}` ({item['dest_size']} bytes{rows})")
|
||
|
|
if case.validation_gap:
|
||
|
|
lines.extend(["", "## Validation Gap", "", case.validation_gap])
|
||
|
|
lines.append("")
|
||
|
|
return "\n".join(lines)
|
||
|
|
|
||
|
|
|
||
|
|
def _looks_tabular(path: Path) -> bool:
|
||
|
|
return path.suffix.lower() in {".txt", ".tsv", ".csv", ".tab"}
|
||
|
|
|
||
|
|
|
||
|
|
def out_type(name: str) -> str:
|
||
|
|
lower = name.lower()
|
||
|
|
if lower.endswith((".tsv", ".csv", ".txt", ".tab")):
|
||
|
|
return "table"
|
||
|
|
if lower.endswith((".gff", ".gff3", ".bed")):
|
||
|
|
return "annotation"
|
||
|
|
if lower.endswith(".nwk"):
|
||
|
|
return "tree"
|
||
|
|
return "file"
|
||
|
|
|
||
|
|
|
||
|
|
def write_manifest(output_root: Path) -> None:
|
||
|
|
files = []
|
||
|
|
for path in sorted(item for item in output_root.rglob("*") if item.is_file() and item.name != "MANIFEST.json"):
|
||
|
|
files.append({"path": path.relative_to(output_root).as_posix(), "size": path.stat().st_size, "sha256": sha256(path)})
|
||
|
|
write_json(output_root / "MANIFEST.json", {
|
||
|
|
"schema_version": "extension_tri_chain_experiment_manifest_v1",
|
||
|
|
"created_at": now(),
|
||
|
|
"root": str(output_root),
|
||
|
|
"file_count": len(files),
|
||
|
|
"files": files,
|
||
|
|
})
|
||
|
|
|
||
|
|
|
||
|
|
def sha256(path: Path) -> str:
|
||
|
|
digest = hashlib.sha256()
|
||
|
|
with path.open("rb") as handle:
|
||
|
|
for chunk in iter(lambda: handle.read(1024 * 1024), b""):
|
||
|
|
digest.update(chunk)
|
||
|
|
return digest.hexdigest()
|
||
|
|
|
||
|
|
|
||
|
|
def now() -> str:
|
||
|
|
return datetime.now().isoformat(timespec="seconds")
|
||
|
|
|
||
|
|
|
||
|
|
if __name__ == "__main__":
|
||
|
|
raise SystemExit(main())
|