508 lines
20 KiB
Python
508 lines
20 KiB
Python
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"""Trusted request and result helpers for the canonical ``gwas_fmt`` stage."""
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from __future__ import annotations
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import gzip
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import json
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import os
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import shutil
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from pathlib import Path
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from typing import Any
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from gfa_core.genotype_context import genotype_scope_id_for_vcf, sha256_file
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_WGS_GWAS_INPUTS = (
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("wgs_maf_missing_filter", "final_snp_vcf"),
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("wgs_impute", "imputed_snp_vcf"),
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("wgs_variant_filter", "pass_snp_vcf"),
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)
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def _gwas_vcf(params: dict[str, Any]) -> str:
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return str(params.get("gwasVcf") or params.get("gwas_vcf") or "").strip()
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def _vcf_shape(path: Path) -> tuple[int, int]:
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opener = gzip.open if path.name.lower().endswith(".gz") else open
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samples = 0
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sites = 0
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header_found = False
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with opener(path, "rt", encoding="utf-8") as handle:
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for raw in handle:
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if raw.startswith("#CHROM\t"):
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header_found = True
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samples = max(0, len(raw.rstrip("\r\n").split("\t")) - 9)
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elif raw.strip() and not raw.startswith("#"):
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sites += 1
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if not header_found:
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raise ValueError("#CHROM header was not found")
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if samples <= 0 or sites <= 0:
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raise ValueError(f"VCF requires >0 samples and >0 sites; observed samples={samples}, sites={sites}")
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return samples, sites
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def _is_gwas_input_vcf(path: Path) -> bool:
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name = path.name.lower()
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if name.endswith((".g.vcf", ".g.vcf.gz", ".gvcf", ".gvcf.gz", ".tbi")):
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return False
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if ".gwas_fmt." in name:
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return False
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return name.endswith((".vcf", ".vcf.gz"))
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def _vcf_candidate(path: Path, source: str, *, root: Path | None = None, source_manifest: str = "") -> dict[str, Any] | None:
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try:
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resolved = path.resolve(strict=True)
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if root is not None:
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resolved.relative_to(root.resolve(strict=True))
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if not resolved.is_file() or not _is_gwas_input_vcf(resolved):
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return None
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samples, sites = _vcf_shape(resolved)
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digest = sha256_file(resolved)
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return {
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"path": str(resolved),
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"name": resolved.name,
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"source": source,
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"source_manifest": source_manifest,
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"size_bytes": resolved.stat().st_size,
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"sha256": digest,
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"genotype_scope_id": genotype_scope_id_for_vcf(resolved),
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"samples": samples,
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"sites": sites,
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}
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except (OSError, UnicodeError, ValueError, EOFError, gzip.BadGzipFile):
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return None
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def _manifest_artifact_entries(manifest: dict[str, Any]) -> list[dict[str, Any]]:
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artifacts = manifest.get("artifacts") or []
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if isinstance(artifacts, dict):
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return [value for value in artifacts.values() if isinstance(value, dict)]
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if isinstance(artifacts, list):
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return [value for value in artifacts if isinstance(value, dict)]
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return []
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def _manifest_artifact_for_role(manifest: dict[str, Any], role: str) -> dict[str, Any] | None:
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artifacts = manifest.get("artifacts") or {}
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if isinstance(artifacts, dict):
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direct = artifacts.get(role)
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if isinstance(direct, dict):
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return direct
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return next(
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(
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artifact
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for artifact in _manifest_artifact_entries(manifest)
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if str(artifact.get("role") or artifact.get("artifact") or "") == role
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),
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None,
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)
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def _manifest_artifact_path(artifact: dict[str, Any], workspace: Path, input_dir: Path) -> Path | None:
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for key in ("relpath_or_hint", "path", "full_path", "file"):
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text = str(artifact.get(key) or "").strip()
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if not text:
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continue
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raw = Path(text).expanduser()
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if raw.is_absolute():
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return raw
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candidates = (workspace / raw, workspace / "final" / raw, input_dir / raw)
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return next((candidate for candidate in candidates if candidate.exists()), candidates[0])
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return None
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def _gwas_resolution(candidates: list[dict[str, Any]], selected: str = "") -> dict[str, Any]:
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by_digest: dict[str, dict[str, Any]] = {}
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for candidate in sorted(candidates, key=lambda item: item["path"]):
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by_digest.setdefault(candidate["sha256"], candidate)
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unique = list(by_digest.values())
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selected_path = ""
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if selected:
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try:
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selected_path = str(Path(selected).expanduser().resolve(strict=True))
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except OSError:
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selected_path = ""
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match = next((item for item in unique if item["path"] == selected_path), None)
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if match is None:
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return {
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"valid": False,
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"needs_confirmation": bool(len(unique) > 1),
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"issues": [{
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"severity": "error",
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"category": "input",
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"code": "invalid_external_vcf_selection",
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"message": "Selected VCF is not one of the current authoritative candidates",
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}],
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"decisions": {"external_vcf": {"resolved": False, "path": selected}},
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"candidates": unique,
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}
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unique = [match]
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if len(unique) == 1:
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selected_candidate = unique[0]
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return {
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"valid": True,
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"needs_confirmation": False,
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"issues": [],
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"decisions": {"external_vcf": {"resolved": True, **selected_candidate}},
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"candidates": unique,
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}
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if len(unique) > 1:
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return {
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"valid": False,
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"needs_confirmation": True,
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"issues": [{
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"severity": "warning",
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"category": "parameter_confirmation",
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"code": "ambiguous_external_vcf",
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"message": "Multiple valid VCF inputs were found; select one before execution",
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}],
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"decisions": {"external_vcf": {"resolved": False, "path": ""}},
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"candidates": unique,
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}
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return {
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"valid": False,
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"needs_confirmation": False,
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"issues": [{
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"severity": "error",
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"category": "input",
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"code": "missing_external_vcf",
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"message": "No valid VCF was found in the current job input or final directory",
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}],
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"decisions": {"external_vcf": {"resolved": False, "path": ""}},
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"candidates": [],
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}
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def resolve_gwas_fmt_input(
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*,
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job_id: str,
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prefix: str,
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params: dict[str, Any],
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project_root: Path,
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) -> dict[str, Any]:
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"""Resolve one authoritative GWAS VCF without filename or LLM guessing."""
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del prefix # Reserved for future registered lineage identity; never infer it from names.
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project_root = Path(project_root)
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input_dir = project_root / "input" / job_id
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workspace = project_root / "workspace" / job_id
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final_dir = workspace / "final"
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selected = _gwas_vcf(params)
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manifests_by_stage: dict[str, list[tuple[Path, dict[str, Any]]]] = {
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stage: [] for stage, _role in _WGS_GWAS_INPUTS
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}
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saw_wgs_manifest = False
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for manifest_path in sorted(final_dir.glob("*.manifest.json")) if final_dir.is_dir() else []:
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try:
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manifest = json.loads(manifest_path.read_text(encoding="utf-8"))
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except (OSError, UnicodeError, json.JSONDecodeError):
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continue
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stage = str(manifest.get("stage") or "")
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if stage not in manifests_by_stage:
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continue
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saw_wgs_manifest = True
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if str(manifest.get("status") or "") == "success":
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manifests_by_stage[stage].append((manifest_path, manifest))
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for stage, artifact_role in _WGS_GWAS_INPUTS:
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stage_manifests = manifests_by_stage[stage]
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if not stage_manifests:
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continue
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manifest_candidates: list[dict[str, Any]] = []
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manifest_errors: list[str] = []
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for manifest_path, manifest in stage_manifests:
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artifact = _manifest_artifact_for_role(manifest, artifact_role)
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if artifact is None:
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manifest_errors.append(
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f"Manifest is missing authoritative artifact {artifact_role}: {manifest_path}"
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)
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continue
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artifact_path = _manifest_artifact_path(artifact, workspace, input_dir)
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candidate = (
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_vcf_candidate(artifact_path, "manifest", source_manifest=str(manifest_path))
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if artifact_path is not None
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else None
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)
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expected_sha = str(artifact.get("sha256") or "").strip().lower()
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if candidate is None or len(expected_sha) != 64 or candidate["sha256"] != expected_sha:
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manifest_errors.append(f"Manifest VCF evidence is missing or invalid: {manifest_path}")
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continue
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manifest_candidates.append(candidate)
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if manifest_errors:
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return {
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"valid": False,
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"needs_confirmation": False,
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"issues": [{
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"severity": "error",
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"category": "input",
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"code": "invalid_manifest_input",
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"message": manifest_errors[0],
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}],
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"decisions": {"external_vcf": {"resolved": False, "path": ""}},
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"candidates": [],
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}
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input_candidates: list[dict[str, Any]] = []
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if input_dir.is_dir():
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for path in sorted(input_dir.rglob("*")):
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if not path.is_file() or not _is_gwas_input_vcf(path):
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continue
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candidate = _vcf_candidate(path, "input", root=input_dir)
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if candidate is not None:
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input_candidates.append(candidate)
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manifest_digests = {candidate["sha256"] for candidate in manifest_candidates}
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input_candidates = [
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candidate for candidate in input_candidates if candidate["sha256"] not in manifest_digests
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]
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return _gwas_resolution(manifest_candidates + input_candidates, selected)
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if saw_wgs_manifest:
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scanned_input: list[dict[str, Any]] = []
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if input_dir.is_dir():
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for path in sorted(input_dir.rglob("*")):
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if not path.is_file() or not _is_gwas_input_vcf(path):
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continue
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candidate = _vcf_candidate(path, "input", root=input_dir)
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if candidate is not None:
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scanned_input.append(candidate)
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return _gwas_resolution(scanned_input, selected)
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scanned: list[dict[str, Any]] = []
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for source, root in (("input", input_dir), ("final", final_dir)):
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if not root.is_dir():
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continue
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for path in sorted(root.rglob("*")):
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if not path.is_file() or not _is_gwas_input_vcf(path):
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continue
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candidate = _vcf_candidate(path, source, root=root)
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if candidate is not None:
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scanned.append(candidate)
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return _gwas_resolution(scanned, selected)
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def semantic_external_vcf_preflight(params: dict[str, Any]) -> dict[str, Any]:
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"""Validate an explicitly supplied VCF without sending it to artifact discovery."""
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raw = _gwas_vcf(params)
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path = Path(raw).expanduser() if raw else None
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if path is None or not path.is_absolute():
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return {
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"valid": False,
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"issues": [{
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"severity": "error",
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"category": "input",
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"code": "missing_external_vcf",
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"message": "gwas_fmt requires params.gwasVcf as an absolute path",
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}],
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"decisions": {"external_vcf": {"resolved": False, "path": raw}},
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}
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resolved = path.resolve()
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issues: list[dict[str, str]] = []
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if not resolved.is_file():
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issues.append({
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"severity": "error",
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"category": "input",
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"code": "missing_external_vcf",
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"message": f"External VCF does not exist: {resolved}",
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})
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samples = 0
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sites = 0
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if resolved.is_file():
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try:
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samples, sites = _vcf_shape(resolved)
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except Exception as exc:
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issues.append({
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"severity": "error", "category": "input", "code": "invalid_external_vcf",
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"message": f"External VCF is not a readable semantic VCF: {exc}",
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})
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tassel_text = str(params.get("tasselPipeline") or params.get("tassel_pipeline") or "run_pipeline.pl").strip()
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tassel_lookup = tassel_text
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if tassel_text == "run_pipeline.pl":
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tassel_lookup = str(os.environ.get("TASSEL_PIPELINE") or tassel_text).strip()
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tassel_candidate = Path(tassel_lookup).expanduser()
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tassel_resolved = (
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str(tassel_candidate.resolve()) if (tassel_candidate.is_absolute() or "/" in tassel_lookup)
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else str(shutil.which(tassel_lookup) or "")
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)
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tassel_executable = bool(tassel_resolved and Path(tassel_resolved).is_file() and os.access(tassel_resolved, os.X_OK))
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if not tassel_executable:
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issues.append({
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"severity": "error", "category": "tool", "code": "missing_tassel_executable",
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"message": f"TASSEL pipeline executable was not found or is not executable: {tassel_text}",
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})
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return {
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"valid": not issues,
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"needs_confirmation": False,
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"issues": issues,
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"decisions": {
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"external_vcf": {
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"resolved": resolved.is_file() and not any(item["code"] in {"missing_external_vcf", "invalid_external_vcf"} for item in issues),
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"path": str(resolved),
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"reason": "explicit params.gwasVcf",
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"samples": samples,
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"sites": sites,
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},
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"tassel": {"requested": tassel_text, "path": tassel_resolved, "executable": tassel_executable},
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},
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}
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|
||
|
|
|
||
|
|
def trusted_genotype_scope_id(stage: str, params: dict[str, Any]) -> str:
|
||
|
|
"""Derive genotype identity from the selected VCF; never trust a client hash."""
|
||
|
|
if str(stage or "") != "gwas_fmt":
|
||
|
|
return str(params.get("genotypeScopeId") or params.get("genotype_scope_id") or "").strip()
|
||
|
|
preflight = semantic_external_vcf_preflight(params)
|
||
|
|
decision = preflight["decisions"]["external_vcf"]
|
||
|
|
if not decision.get("resolved"):
|
||
|
|
return ""
|
||
|
|
return genotype_scope_id_for_vcf(Path(str(decision["path"])))
|
||
|
|
|
||
|
|
|
||
|
|
def _gwas_fmt_metrics_proven(manifest: dict[str, Any]) -> bool:
|
||
|
|
metrics = manifest.get("metrics") if isinstance(manifest.get("metrics"), dict) else {}
|
||
|
|
if metrics.get("sample_conservation") is not True or metrics.get("variant_conservation") is not True:
|
||
|
|
return False
|
||
|
|
params = manifest.get("parameters") if isinstance(manifest.get("parameters"), dict) else {}
|
||
|
|
lossy_mask = params.get("unsupported_marker_policy") == "mask" and metrics.get("lossy_conversion") is True
|
||
|
|
if lossy_mask:
|
||
|
|
try:
|
||
|
|
return (
|
||
|
|
metrics.get("strict_genotype_conservation") is True
|
||
|
|
and int(metrics.get("strict_marker_count") or 0) > 0
|
||
|
|
and int(metrics.get("genotypes_compared") or 0) > 0
|
||
|
|
and int(metrics.get("unsupported_marker_count") or 0) > 0
|
||
|
|
)
|
||
|
|
except (TypeError, ValueError):
|
||
|
|
return False
|
||
|
|
return metrics.get("genotype_conservation") is True
|
||
|
|
|
||
|
|
|
||
|
|
def _gwas_fmt_tassel_version_proven(manifest: dict[str, Any]) -> bool:
|
||
|
|
software = manifest.get("software") if isinstance(manifest.get("software"), dict) else {}
|
||
|
|
tassel = software.get("tassel") if isinstance(software.get("tassel"), dict) else {}
|
||
|
|
return str(tassel.get("version") or "unknown").strip().lower() != "unknown"
|
||
|
|
|
||
|
|
|
||
|
|
def _is_core_manifest_v1_shape(manifest: dict[str, Any]) -> bool:
|
||
|
|
string_fields = (
|
||
|
|
"manifest_version", "job_id", "stage", "run_id", "prefix", "timestamp",
|
||
|
|
"status", "start_time", "end_time", "workspace_root", "workspace", "input_dir",
|
||
|
|
)
|
||
|
|
if any(not isinstance(manifest.get(field), str) for field in string_fields):
|
||
|
|
return False
|
||
|
|
elapsed = manifest.get("elapsed_sec")
|
||
|
|
if isinstance(elapsed, bool) or not isinstance(elapsed, (int, float)) or elapsed < 0:
|
||
|
|
return False
|
||
|
|
cmd = manifest.get("cmd")
|
||
|
|
if not isinstance(cmd, list) or any(not isinstance(item, str) for item in cmd):
|
||
|
|
return False
|
||
|
|
if manifest.get("manifest_version") != "1.0" or manifest.get("status") not in {"success", "failed"}:
|
||
|
|
return False
|
||
|
|
return (
|
||
|
|
isinstance(manifest.get("artifacts"), dict)
|
||
|
|
and isinstance(manifest.get("parameters"), dict)
|
||
|
|
and isinstance(manifest.get("metrics"), dict)
|
||
|
|
)
|
||
|
|
|
||
|
|
|
||
|
|
def gwas_fmt_result_artifacts(
|
||
|
|
manifest: dict[str, Any], expected_scope: str = "", workspace_dir: Path | None = None,
|
||
|
|
) -> list[dict[str, Any]]:
|
||
|
|
"""Return only canonical successful result roles from the requested genotype scope."""
|
||
|
|
if not _is_core_manifest_v1_shape(manifest):
|
||
|
|
return []
|
||
|
|
if str(manifest.get("stage") or "") != "gwas_fmt" or str(manifest.get("status") or "") != "success":
|
||
|
|
return []
|
||
|
|
manifest_scope = str(
|
||
|
|
manifest.get("genotype_scope_id")
|
||
|
|
or (manifest.get("parameters") or {}).get("genotype_scope_id")
|
||
|
|
or (manifest.get("stage_context") or {}).get("genotype_scope_id")
|
||
|
|
or ""
|
||
|
|
).strip()
|
||
|
|
if not manifest_scope:
|
||
|
|
return []
|
||
|
|
if expected_scope and manifest_scope != expected_scope:
|
||
|
|
return []
|
||
|
|
if workspace_dir is not None and (
|
||
|
|
not _gwas_fmt_metrics_proven(manifest) or not _gwas_fmt_tassel_version_proven(manifest)
|
||
|
|
):
|
||
|
|
return []
|
||
|
|
artifacts = manifest.get("artifacts")
|
||
|
|
if (
|
||
|
|
not isinstance(artifacts, dict)
|
||
|
|
or not artifacts
|
||
|
|
or any(not isinstance(value, dict) for value in artifacts.values())
|
||
|
|
):
|
||
|
|
return []
|
||
|
|
canonical_roles = {"sorted_vcf", "tassel_hapmap", "environment", "report"}
|
||
|
|
if set(artifacts) != canonical_roles:
|
||
|
|
return []
|
||
|
|
records = []
|
||
|
|
for key, value in artifacts.items():
|
||
|
|
if value.get("role") != key or value.get("artifact") != key:
|
||
|
|
return []
|
||
|
|
if any(not isinstance(value.get(field), str) or not value.get(field) for field in ("path", "full_path", "type", "sha256")):
|
||
|
|
return []
|
||
|
|
declared_size = value.get("size")
|
||
|
|
declared_size_bytes = value.get("size_bytes")
|
||
|
|
if (
|
||
|
|
isinstance(declared_size, bool)
|
||
|
|
or not isinstance(declared_size, int)
|
||
|
|
or declared_size < 0
|
||
|
|
or isinstance(declared_size_bytes, bool)
|
||
|
|
or not isinstance(declared_size_bytes, int)
|
||
|
|
or declared_size_bytes != declared_size
|
||
|
|
):
|
||
|
|
return []
|
||
|
|
declared_sha = str(value["sha256"]).strip().lower()
|
||
|
|
if len(declared_sha) != 64 or any(c not in "0123456789abcdef" for c in declared_sha):
|
||
|
|
return []
|
||
|
|
records.append(dict(value))
|
||
|
|
if workspace_dir is not None:
|
||
|
|
base = Path(workspace_dir).resolve()
|
||
|
|
if (
|
||
|
|
Path(manifest["workspace_root"]).resolve() != base
|
||
|
|
or Path(manifest["workspace"]).resolve() != (base / "final").resolve()
|
||
|
|
):
|
||
|
|
return []
|
||
|
|
for record in records:
|
||
|
|
raw_path = Path(str(record["path"]))
|
||
|
|
if raw_path.is_absolute():
|
||
|
|
return []
|
||
|
|
try:
|
||
|
|
artifact_path = (raw_path if raw_path.is_absolute() else base / raw_path).resolve(strict=True)
|
||
|
|
artifact_path.relative_to(base)
|
||
|
|
except (OSError, ValueError):
|
||
|
|
return []
|
||
|
|
try:
|
||
|
|
if Path(str(record["full_path"])).resolve(strict=True) != artifact_path:
|
||
|
|
return []
|
||
|
|
except OSError:
|
||
|
|
return []
|
||
|
|
declared_sha = str(record["sha256"]).strip().lower()
|
||
|
|
if not artifact_path.is_file():
|
||
|
|
return []
|
||
|
|
if sha256_file(artifact_path) != declared_sha:
|
||
|
|
return []
|
||
|
|
if record["size"] != artifact_path.stat().st_size:
|
||
|
|
return []
|
||
|
|
return records
|
||
|
|
|
||
|
|
|
||
|
|
def canonicalize_gwas_task_results(
|
||
|
|
stage_files: dict[str, dict[str, list]], all_images: list[str], all_files: list[dict],
|
||
|
|
canonical_files: list[dict],
|
||
|
|
) -> tuple[list[str], list[dict]]:
|
||
|
|
"""Replace filename-discovered GWAS task output with manifest-authoritative files."""
|
||
|
|
previous = stage_files.setdefault("gwas_fmt", {"images": [], "files": []})
|
||
|
|
stale_images = set(previous.get("images") or [])
|
||
|
|
stale_file_paths = {item.get("path") for item in previous.get("files") or []}
|
||
|
|
previous["images"] = []
|
||
|
|
previous["files"] = list(canonical_files)
|
||
|
|
filtered_images = [item for item in all_images if item not in stale_images]
|
||
|
|
filtered_files = [item for item in all_files if item.get("path") not in stale_file_paths]
|
||
|
|
filtered_files.extend(canonical_files)
|
||
|
|
return filtered_images, filtered_files
|