2026-08-03 18:42:47 +08:00
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"""Semantic artifact resolver for bbav5 planning and diagnosis.
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The resolver maps a stage capability need such as ``target_proteome`` or
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``family_members_pep`` to concrete files from ProjectContextIndex. It is
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read-only and returns a decision trace so callers can explain why a file was
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selected or what alternatives were available.
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"""
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from __future__ import annotations
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from dataclasses import dataclass, field, asdict
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from pathlib import Path
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from typing import Any, Dict, Iterable, List, Optional
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import re
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from gfa_core.mas.context_index import ContextArtifact, ContextFile, ProjectContextIndex, build_project_context
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from gfa_core.mas.stage_capabilities import ArtifactNeed, get_stage_capability
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@dataclass
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class ResolveCandidate:
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path: str
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kind: str
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source: str
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role: str = ""
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species: str = ""
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family: str = ""
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exists: bool = True
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score: int = 0
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reason: str = ""
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def to_dict(self) -> Dict[str, Any]:
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return asdict(self)
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@dataclass
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class ResolveDecision:
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stage: str
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role: str
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kind: str
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resolved: bool
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selected: Optional[ResolveCandidate] = None
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candidates: List[ResolveCandidate] = field(default_factory=list)
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messages: List[str] = field(default_factory=list)
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def to_dict(self) -> Dict[str, Any]:
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data = asdict(self)
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data["selected"] = self.selected.to_dict() if self.selected else None
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data["candidates"] = [item.to_dict() for item in self.candidates]
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return data
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class ArtifactResolver:
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def __init__(self, context: ProjectContextIndex):
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self.context = context
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def resolve_stage(self, stage: str, species: str = "", family: str = "") -> Dict[str, ResolveDecision]:
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capability = get_stage_capability(stage)
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if not capability:
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return {}
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return {
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need.role: self.resolve_need(stage, need, species=species, family=family)
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for need in capability.consumes
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}
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def resolve_need(
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self,
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stage: str,
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need: ArtifactNeed,
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species: str = "",
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family: str = "",
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explicit_path: str = "",
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) -> ResolveDecision:
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decision = ResolveDecision(stage=stage, role=need.role, kind=need.kind, resolved=False)
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species = species or self._default_species(need)
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family = family or self.context.family
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if explicit_path:
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path = Path(explicit_path).expanduser()
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decision.candidates.append(ResolveCandidate(
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path=str(path),
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kind=need.kind,
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source="explicit",
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role=need.role,
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species=species,
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family=family,
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exists=path.exists(),
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score=1000 if path.exists() else 0,
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reason="explicit user parameter",
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))
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decision.candidates.extend(self._candidates_from_artifacts(need, species, family))
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decision.candidates.extend(self._candidates_from_manifests(need, species, family))
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decision.candidates.extend(self._candidates_from_files(need, species, family))
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decision.candidates.extend(self._canonical_candidates(need, species, family))
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# Prefer existing candidates and then higher scores. Keep missing
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# candidates in the trace so the UI can explain attempted names.
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decision.candidates = self._dedupe(decision.candidates)
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decision.candidates.sort(key=lambda c: (c.exists, c.score), reverse=True)
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if decision.candidates and decision.candidates[0].exists:
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decision.selected = decision.candidates[0]
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decision.resolved = True
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decision.messages.append(f"resolved {need.role} from {decision.selected.source}: {decision.selected.path}")
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elif need.required:
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decision.messages.append(f"required artifact not resolved: {need.role} ({need.kind})")
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else:
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decision.messages.append(f"optional artifact not resolved: {need.role} ({need.kind})")
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return decision
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def _default_species(self, need: ArtifactNeed) -> str:
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if "reference" in need.source_roles and self.context.reference_species:
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return self.context.reference_species[0]
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if "comparative" in need.source_roles and self.context.comparative_species:
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return self.context.comparative_species[0]
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if self.context.target_species and len(self.context.target_species) == 1:
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return self.context.target_species[0]
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return ""
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def _candidates_from_artifacts(self, need: ArtifactNeed, species: str, family: str) -> List[ResolveCandidate]:
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candidates: List[ResolveCandidate] = []
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for artifact in self.context.artifacts:
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if not self._kind_matches(need.kind, artifact.kind):
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continue
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if not self._role_accepts_path(need.role, artifact.key, artifact.path):
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continue
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if need.role == "gene_subfamily" and artifact.stage not in {"reference_classification", "subfamily_confirm"}:
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continue
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if need.role == "reference_subfamily" and not self._reference_subfamily_candidate_ok(artifact.path, artifact.key):
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continue
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if need.role == "target_gff" and not species and self.context.target_species:
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if not any(
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self._path_mentions_species(artifact.path, target) or self._path_mentions_species(artifact.key, target)
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for target in self.context.target_species
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):
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continue
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if need.role == "target_proteome" and not species and self.context.target_species:
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if not any(
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self._path_mentions_species(artifact.path, target) or self._path_mentions_species(artifact.key, target)
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for target in self.context.target_species
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):
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continue
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if species and need.role in {"family_members_pep", "target_proteome", "target_gff", "target_genome", "reference_family_pep", "family_members_id", "gene_subfamily", "reference_subfamily", "tree"}:
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if not self._path_mentions_species(artifact.path, species) and not self._path_mentions_species(artifact.key, species):
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continue
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score = 500
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if self._artifact_key_matches(need.role, artifact.key):
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score += 200
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if self._stage_preference(need.role, artifact.stage):
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score += self._stage_preference(need.role, artifact.stage)
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if family and family.lower() in artifact.path.lower():
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score += 30
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if species and self._path_mentions_species(artifact.path, species):
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score += 50
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if need.role == "target_gff" and self.context.target_species:
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score += self._species_set_score(artifact.path, artifact.key, self.context.target_species, preferred_first=True)
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if need.role == "reference_subfamily":
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score += self._reference_subfamily_score(artifact.path, artifact.key, species, family)
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if need.role == "tree":
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score += self._artifact_scope_score(artifact.path, artifact.source_manifest)
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candidates.append(ResolveCandidate(
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path=artifact.path,
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kind=artifact.kind,
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source=f"artifact:{artifact.stage}:{artifact.key}",
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role=need.role,
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species=species,
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family=family,
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exists=artifact.exists,
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score=score,
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reason="manifest artifact",
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))
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return candidates
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def _candidates_from_manifests(self, need: ArtifactNeed, species: str = "", family: str = "") -> List[ResolveCandidate]:
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if need.role == "family_members_pep":
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candidates: List[ResolveCandidate] = []
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for manifest in self.context.manifests:
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if str(manifest.get("stage") or "") != "phylogeny":
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continue
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params = manifest.get("parameters") or {}
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if not isinstance(params, dict):
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continue
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fasta_text = str(params.get("scope_input_fasta") or "")
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if not fasta_text:
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continue
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path = Path(fasta_text)
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if not path.is_absolute():
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path = Path(self.context.workspace) / path
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scope_data = manifest.get("scope") or manifest.get("stage_context") or {}
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if not isinstance(scope_data, dict):
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scope_data = {}
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scope_targets = [str(x) for x in scope_data.get("target_species") or [] if str(x).strip()]
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scope_selected = [str(x) for x in scope_data.get("selected_species") or [] if str(x).strip()]
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manifest_species = scope_targets or scope_selected
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if species:
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if manifest_species and species not in manifest_species:
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continue
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if not manifest_species and not self._path_mentions_species(str(path), species):
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continue
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elif self.context.target_species:
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if manifest_species and not any(target in manifest_species for target in self.context.target_species):
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continue
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if not manifest_species and not any(
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self._path_mentions_species(str(path), target) for target in self.context.target_species
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):
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continue
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score = 760
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if str(manifest.get("scope_id") or ""):
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score += 260
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if str(manifest.get("status") or "") in {"success", "partial_success"}:
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score += 120
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scope_mode = str(scope_data.get("scope_mode") or manifest.get("scope_mode") or "")
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if species and manifest_species == [species]:
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score += 140
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elif species and species in manifest_species:
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score += 40
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if scope_mode == "target_only":
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score += 80
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if species and self._path_mentions_species(str(path), species):
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score += 80
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if family and family.lower() in path.name.lower():
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score += 40
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candidates.append(ResolveCandidate(
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path=str(path),
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kind="protein_fasta",
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source=f"manifest:{manifest.get('stage', '')}:scope_input_fasta",
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role=need.role,
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species=species,
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family=self.context.family,
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exists=path.exists(),
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score=score,
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reason="phylogeny scoped input fasta",
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))
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if candidates:
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return candidates
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if need.kind != "manifest" and need.role != "stage_manifests":
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return []
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candidates: List[ResolveCandidate] = []
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for manifest in self.context.manifests:
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path = manifest.get("path", "")
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if not path:
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continue
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status = str(manifest.get("status") or "")
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score = 400 if status in {"success", "partial_success"} else 100
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candidates.append(ResolveCandidate(
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path=path,
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kind="manifest",
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source=f"manifest:{manifest.get('stage', '')}",
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role=need.role,
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exists=Path(path).exists(),
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score=score,
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reason="stage manifest index",
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))
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return candidates
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def _candidates_from_files(self, need: ArtifactNeed, species: str, family: str) -> List[ResolveCandidate]:
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candidates: List[ResolveCandidate] = []
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for file in self.context.files:
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if not self._kind_matches(need.kind, file.kind):
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continue
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if not self._role_accepts_path(need.role, "", file.path):
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continue
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if need.role == "reference_subfamily" and not self._reference_subfamily_candidate_ok(file.path, ""):
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continue
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if need.role == "target_gff" and not species and self.context.target_species:
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if file.species:
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if file.species not in self.context.target_species:
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continue
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elif not any(self._path_mentions_species(file.path, target) for target in self.context.target_species):
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continue
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if need.role == "target_proteome" and not species and self.context.target_species:
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if file.species:
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if file.species not in self.context.target_species:
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continue
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elif not any(self._path_mentions_species(file.path, target) for target in self.context.target_species):
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continue
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if species and need.role in {"family_members_pep", "target_proteome", "target_gff", "target_genome", "reference_family_pep", "family_members_id", "gene_subfamily", "reference_subfamily", "tree"}:
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if file.species and file.species != species:
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continue
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if not file.species and not self._path_mentions_species(file.path, species):
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continue
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score = 100
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if family and (file.family == family or family.lower() in Path(file.path).name.lower()):
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score += 40
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if species and (file.species == species or self._path_mentions_species(file.path, species)):
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score += 60
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if file.source == "final":
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score += 60
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elif file.source.startswith("manifest:"):
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score += 80
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elif file.source == "config":
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score += 70
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elif file.source == "input":
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score += 40
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if self._filename_matches_role(need.role, Path(file.path).name):
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score += 80
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if need.role == "target_gff" and self.context.target_species:
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score += self._species_set_score(file.path, "", self.context.target_species, preferred_first=True)
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if need.role == "reference_subfamily":
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score += self._reference_subfamily_score(file.path, "", species, family)
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if need.role == "tree":
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score += self._artifact_scope_score(file.path, "")
|
|
|
|
|
candidates.append(ResolveCandidate(
|
|
|
|
|
path=file.path,
|
|
|
|
|
kind=file.kind,
|
|
|
|
|
source=file.source,
|
|
|
|
|
role=need.role,
|
|
|
|
|
species=file.species or species,
|
|
|
|
|
family=file.family or family,
|
|
|
|
|
exists=file.exists,
|
|
|
|
|
score=score,
|
|
|
|
|
reason="context file scan",
|
|
|
|
|
))
|
|
|
|
|
return candidates
|
|
|
|
|
|
|
|
|
|
def _canonical_candidates(self, need: ArtifactNeed, species: str, family: str) -> List[ResolveCandidate]:
|
|
|
|
|
final_dir = Path(self.context.final_dir)
|
|
|
|
|
paths: List[Path] = []
|
|
|
|
|
prefix = f"{species}.{family}" if species and family else family or species
|
|
|
|
|
|
|
|
|
|
if need.role in {"family_members_pep", "target_proteome"} and prefix:
|
|
|
|
|
paths.extend([
|
|
|
|
|
final_dir / f"{prefix}.final_members.pep.fa",
|
|
|
|
|
final_dir / f"{prefix}.pep.fa",
|
|
|
|
|
final_dir / f"{prefix}.protein.fa",
|
|
|
|
|
])
|
|
|
|
|
if need.role == "reference_family_pep" and species and family:
|
|
|
|
|
paths.extend([
|
|
|
|
|
final_dir / f"{species}.{family}.pep.fa",
|
|
|
|
|
final_dir / f"{species}.{family}.pep.fasta",
|
|
|
|
|
final_dir / f"{species}.{family}.ncbi_fetch.protein.fa",
|
|
|
|
|
])
|
|
|
|
|
if need.role == "family_members_id" and prefix:
|
|
|
|
|
paths.append(final_dir / f"{prefix}.final_members.id")
|
|
|
|
|
if need.role == "tree" and prefix:
|
|
|
|
|
expected_prefix = str(getattr(self.context, "expected_output_prefix", "") or "")
|
|
|
|
|
tree_prefixes = [prefix]
|
|
|
|
|
if expected_prefix and expected_prefix not in tree_prefixes:
|
|
|
|
|
tree_prefixes.insert(0, expected_prefix)
|
|
|
|
|
for tree_prefix in tree_prefixes:
|
|
|
|
|
paths.extend([
|
|
|
|
|
final_dir / f"{tree_prefix}.tree.nwk",
|
|
|
|
|
final_dir / f"{tree_prefix}.phylogeny.treefile",
|
|
|
|
|
final_dir / f"{tree_prefix}.iqtree.treefile",
|
|
|
|
|
])
|
|
|
|
|
if need.role == "target_gff" and species:
|
|
|
|
|
paths.extend([
|
|
|
|
|
final_dir / f"{species}_final.gff3",
|
|
|
|
|
Path(self.context.input_dir) / f"{species}_final.gff3",
|
|
|
|
|
])
|
|
|
|
|
if need.role == "target_genome" and species:
|
|
|
|
|
paths.extend([
|
|
|
|
|
final_dir / f"{species}.genome.fasta",
|
|
|
|
|
final_dir / f"{species}.genome.fa",
|
|
|
|
|
Path(self.context.input_dir) / f"{species}.genome.fasta",
|
|
|
|
|
Path(self.context.input_dir) / f"{species}.genome.fa",
|
|
|
|
|
])
|
|
|
|
|
if need.role == "plant_tf_motif_database" or need.kind == "meme":
|
|
|
|
|
project_root = Path(__file__).resolve().parents[2]
|
|
|
|
|
paths.extend([
|
|
|
|
|
project_root / "data" / "tfbs" / "jaspar2026" / "combined" / "JASPAR2026_CORE_plants_non-redundant.meme",
|
|
|
|
|
])
|
|
|
|
|
if need.role == "gene_subfamily" and prefix:
|
|
|
|
|
expected_prefix = str(getattr(self.context, "expected_output_prefix", "") or "")
|
|
|
|
|
subfamily_prefixes = [prefix]
|
|
|
|
|
if expected_prefix and expected_prefix not in subfamily_prefixes:
|
|
|
|
|
subfamily_prefixes.insert(0, expected_prefix)
|
|
|
|
|
for subfamily_prefix in subfamily_prefixes:
|
|
|
|
|
paths.extend([
|
|
|
|
|
final_dir / f"{subfamily_prefix}.confirmed_subfamily.tsv",
|
|
|
|
|
final_dir / f"{subfamily_prefix}.geneID.subfamily",
|
|
|
|
|
final_dir / f"{subfamily_prefix}.reference_classification.subfamily.tsv",
|
|
|
|
|
Path(self.context.input_dir) / f"{subfamily_prefix}.confirmed_subfamily.tsv",
|
|
|
|
|
Path(self.context.input_dir) / f"{subfamily_prefix}.geneID.subfamily",
|
|
|
|
|
])
|
|
|
|
|
if need.role == "motif_result" and prefix:
|
|
|
|
|
paths.extend([
|
|
|
|
|
final_dir / f"{prefix}.motif.tsv",
|
|
|
|
|
final_dir / f"{prefix}.motif.txt",
|
|
|
|
|
final_dir / f"{prefix}.meme.tsv",
|
|
|
|
|
])
|
|
|
|
|
if need.role == "domain_result" and prefix:
|
|
|
|
|
paths.extend([
|
|
|
|
|
final_dir / f"{prefix}.domain.tsv",
|
|
|
|
|
final_dir / f"{prefix}.domain.txt",
|
|
|
|
|
])
|
|
|
|
|
if need.role == "structure_result" and prefix:
|
|
|
|
|
paths.extend([
|
|
|
|
|
final_dir / f"{prefix}.structure.gff.tsv",
|
|
|
|
|
final_dir / f"{prefix}.structure.tsv",
|
|
|
|
|
final_dir / f"{prefix}.gene_structure.tsv",
|
|
|
|
|
])
|
|
|
|
|
if need.role == "reference_subfamily":
|
|
|
|
|
ref_species = species or (self.context.reference_species[0] if self.context.reference_species else "")
|
|
|
|
|
if ref_species and family:
|
|
|
|
|
paths.extend([
|
|
|
|
|
Path(self.context.input_dir) / f"{ref_species}.{family}.subfamily",
|
|
|
|
|
Path(self.context.input_dir) / f"{ref_species}.{family}.geneID.subfamily",
|
|
|
|
|
final_dir / f"{ref_species}.{family}.subfamily",
|
|
|
|
|
final_dir / f"{ref_species}.{family}.geneID.subfamily",
|
|
|
|
|
])
|
|
|
|
|
if prefix:
|
|
|
|
|
paths.append(final_dir / f"{prefix}.geneID.subfamily")
|
|
|
|
|
if need.role == "pfam_database" or need.kind == "hmm_database":
|
|
|
|
|
paths.extend([
|
|
|
|
|
Path(__file__).resolve().parents[2] / "data" / "hmm" / "Pfam-A.hmm",
|
|
|
|
|
])
|
|
|
|
|
if need.role == "hmm_profile" or need.kind == "hmm":
|
|
|
|
|
paths.extend([
|
|
|
|
|
Path(self.context.input_dir) / f"{family}.hmm",
|
|
|
|
|
Path(self.context.input_dir) / f"{family}.hmmprofile",
|
|
|
|
|
])
|
|
|
|
|
|
|
|
|
|
return [
|
|
|
|
|
ResolveCandidate(
|
|
|
|
|
path=str(path),
|
|
|
|
|
kind=need.kind,
|
|
|
|
|
source="canonical",
|
|
|
|
|
role=need.role,
|
|
|
|
|
species=species,
|
|
|
|
|
family=family,
|
|
|
|
|
exists=path.exists(),
|
|
|
|
|
score=300 if path.exists() else 10,
|
|
|
|
|
reason="canonical filename",
|
|
|
|
|
)
|
|
|
|
|
for path in paths
|
|
|
|
|
]
|
|
|
|
|
|
|
|
|
|
@staticmethod
|
|
|
|
|
def _kind_matches(required: str, actual: str) -> bool:
|
|
|
|
|
if required == actual:
|
|
|
|
|
return True
|
|
|
|
|
aliases = {
|
|
|
|
|
"fasta": {"protein_fasta", "cds_fasta", "genome_fasta", "alignment_fasta"},
|
|
|
|
|
"protein_fasta": {"fasta"},
|
|
|
|
|
"table": {"id_list", "expression_matrix"},
|
|
|
|
|
"manifest": {"metadata"},
|
2026-08-05 09:40:45 +08:00
|
|
|
"tree": {"newick"},
|
2026-08-03 18:42:47 +08:00
|
|
|
}
|
|
|
|
|
return actual in aliases.get(required, set())
|
|
|
|
|
|
|
|
|
|
@staticmethod
|
|
|
|
|
def _artifact_key_matches(role: str, key: str) -> bool:
|
|
|
|
|
key = key.lower()
|
|
|
|
|
role = role.lower()
|
|
|
|
|
patterns = {
|
|
|
|
|
"family_members_pep": ["final_members", "final_proteins", "proteins"],
|
|
|
|
|
"target_proteome": ["prepared_protein", "protein", "pep"],
|
|
|
|
|
"target_genome": ["genome", "fasta", "fa"],
|
|
|
|
|
"reference_family_pep": ["reference", "protein", "pep"],
|
|
|
|
|
"family_members_id": ["final_members_id", "gene_ids", "ids"],
|
|
|
|
|
"tree": ["tree"],
|
|
|
|
|
"target_gff": ["gff", "gff3"],
|
|
|
|
|
"plant_tf_motif_database": ["jaspar", "planttfdb", "motif", "meme"],
|
|
|
|
|
"gene_subfamily": ["subfamily"],
|
|
|
|
|
"reference_subfamily": ["subfamily"],
|
|
|
|
|
"motif_result": ["motif", "meme"],
|
|
|
|
|
"domain_result": ["domain", "pfam"],
|
|
|
|
|
"structure_result": ["structure", "gff"],
|
|
|
|
|
}
|
|
|
|
|
return any(token in key for token in patterns.get(role, [role]))
|
|
|
|
|
|
|
|
|
|
@staticmethod
|
|
|
|
|
def _stage_preference(role: str, stage: str) -> int:
|
|
|
|
|
prefs = {
|
|
|
|
|
"target_proteome": {"genome_prepare": 160, "genome_prepare_v2": 160, "identify": 60},
|
|
|
|
|
"target_genome": {"genome_prepare": 160, "genome_prepare_v2": 160},
|
|
|
|
|
"family_members_pep": {"identify": 180, "phylogeny": 120},
|
|
|
|
|
"family_members_id": {"identify": 180},
|
|
|
|
|
"tree": {"phylogeny": 180},
|
|
|
|
|
"gene_subfamily": {"subfamily_confirm": 240, "reference_classification": 180},
|
|
|
|
|
"reference_subfamily": {"reference_classification": 80},
|
|
|
|
|
"target_gff": {"genome_prepare": 160, "genome_prepare_v2": 160},
|
|
|
|
|
"motif_result": {"motif": 180},
|
|
|
|
|
"domain_result": {"domain": 180},
|
|
|
|
|
"structure_result": {"structure": 180},
|
|
|
|
|
}
|
|
|
|
|
return prefs.get(role, {}).get(stage, 0)
|
|
|
|
|
|
|
|
|
|
@staticmethod
|
|
|
|
|
def _filename_matches_role(role: str, name: str) -> bool:
|
|
|
|
|
lowered = name.lower()
|
|
|
|
|
patterns = {
|
|
|
|
|
"target_proteome": ["pep", "protein", "proteome"],
|
|
|
|
|
"target_genome": ["genome", ".fna", ".fa", ".fasta"],
|
|
|
|
|
"family_members_pep": ["final_members.pep", "final_gfmembers.pep"],
|
|
|
|
|
"reference_family_pep": ["ncbi_fetch.protein", ".pep.fa", ".pep.fasta"],
|
|
|
|
|
"family_members_id": ["final_members.id", "final_gfmembers.id"],
|
|
|
|
|
"tree": [".tree.nwk"],
|
|
|
|
|
"target_gff": ["_final.gff3", ".gff3", ".gff"],
|
|
|
|
|
"plant_tf_motif_database": ["jaspar", "planttfdb", ".meme"],
|
|
|
|
|
"gene_subfamily": ["subfamily"],
|
|
|
|
|
"reference_subfamily": [".subfamily", "geneid.subfamily", "confirmed_subfamily"],
|
|
|
|
|
"motif_result": ["motif.tsv", "motif.txt", "meme.tsv"],
|
|
|
|
|
"domain_result": ["domain.tsv", "domain.txt"],
|
|
|
|
|
"structure_result": ["structure.gff.tsv", "structure.tsv", "gene_structure.tsv"],
|
|
|
|
|
}
|
|
|
|
|
return any(token in lowered for token in patterns.get(role, [role.lower()]))
|
|
|
|
|
|
|
|
|
|
@staticmethod
|
|
|
|
|
def _role_accepts_path(role: str, key: str, path: str) -> bool:
|
|
|
|
|
text = f"{key} {Path(path).name}".lower()
|
|
|
|
|
if role == "wgs_sample_config":
|
|
|
|
|
return Path(path).name.lower() == "wgs_samples.yaml"
|
|
|
|
|
if role == "family_members_pep":
|
|
|
|
|
return any(token in text for token in ["final_members", "final_gfmembers", "scope_input", "input.pep.clean"])
|
|
|
|
|
if role == "family_members_id":
|
|
|
|
|
if any(token in text for token in ["interproscan", "domain_review", "domain_check", ".tsv", ".csv"]):
|
|
|
|
|
return False
|
|
|
|
|
return any(token in text for token in ["final_members.id", "final_gfmembers.id", "members.id", "curated_members.id"])
|
|
|
|
|
if role == "target_proteome":
|
|
|
|
|
return not any(token in text for token in ["final_members", "final_gfmembers", "ref_family", "ref_combined", "_ref_", "ref_pep", "ncbi_fetch.protein", "known_family"])
|
|
|
|
|
if role == "reference_family_pep":
|
|
|
|
|
if any(token in text for token in ["final_members", "final_gfmembers", ".msa.", "alignment", "tree"]):
|
|
|
|
|
return False
|
|
|
|
|
return any(token in text for token in ["ref_family", "known_family", "ncbi_fetch.protein", ".pep.fa", ".pep.fasta", ".protein.fa", ".faa"])
|
|
|
|
|
if role == "tree":
|
|
|
|
|
return any(token in text for token in [".tree.nwk", ".treefile", ".newick", ".nwk"])
|
|
|
|
|
if role == "motif_result":
|
|
|
|
|
return any(token in text for token in ["motif.tsv", "motif.txt", "meme.tsv"])
|
|
|
|
|
if role == "domain_result":
|
|
|
|
|
return any(token in text for token in ["domain.tsv", "domain.txt", "pfam.tsv"]) and "domain_review" not in text
|
|
|
|
|
if role == "structure_result":
|
|
|
|
|
return any(token in text for token in ["structure.gff.tsv", "structure.tsv", "gene_structure.tsv"])
|
|
|
|
|
if role == "gene_subfamily":
|
|
|
|
|
return ArtifactResolver._gene_subfamily_candidate_ok(path, key)
|
|
|
|
|
if role == "reference_subfamily":
|
|
|
|
|
return ArtifactResolver._reference_subfamily_candidate_ok(path, key)
|
|
|
|
|
return True
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
def _artifact_scope_score(self, path: str, source_manifest: str = "") -> int:
|
|
|
|
|
"""Score candidates against the request scope carried on ProjectContextIndex."""
|
|
|
|
|
expected_mode = str(getattr(self.context, "expected_scope_mode", "") or "").strip()
|
|
|
|
|
expected_route = str(getattr(self.context, "expected_analysis_route", "") or "").strip()
|
|
|
|
|
if not expected_mode and not expected_route:
|
|
|
|
|
return 0
|
|
|
|
|
score = 0
|
|
|
|
|
text = Path(path).name.lower()
|
|
|
|
|
manifest = {}
|
|
|
|
|
if source_manifest:
|
|
|
|
|
try:
|
|
|
|
|
import json
|
|
|
|
|
manifest = json.loads(Path(source_manifest).read_text(encoding="utf-8"))
|
|
|
|
|
except Exception:
|
|
|
|
|
manifest = {}
|
|
|
|
|
manifest_mode = str(manifest.get("scope_mode") or (manifest.get("parameters") or {}).get("scope_mode") or "").strip()
|
|
|
|
|
manifest_route = str(manifest.get("analysis_route") or (manifest.get("parameters") or {}).get("analysis_route") or "").strip()
|
|
|
|
|
if expected_mode:
|
|
|
|
|
if manifest_mode == expected_mode:
|
|
|
|
|
score += 260
|
|
|
|
|
elif manifest_mode:
|
|
|
|
|
score -= 220
|
|
|
|
|
if expected_mode == "target_only":
|
|
|
|
|
if "target_only" in text:
|
|
|
|
|
score += 220
|
|
|
|
|
if "target_plus_reference" in text or "ref-" in text:
|
|
|
|
|
score -= 240
|
|
|
|
|
elif expected_mode and expected_mode in text:
|
|
|
|
|
score += 180
|
|
|
|
|
targets = [str(item).strip().lower() for item in getattr(self.context, "target_species", []) if str(item).strip()]
|
|
|
|
|
if len(targets) == 1 and "target-" in text:
|
|
|
|
|
match = re.search(r"target-([a-z0-9_-]+)", text)
|
|
|
|
|
if match:
|
|
|
|
|
encoded = [item for item in match.group(1).split("-") if item]
|
|
|
|
|
if targets[0] in encoded and len(encoded) == 1:
|
|
|
|
|
score += 220
|
|
|
|
|
elif targets[0] in encoded:
|
|
|
|
|
score -= 120
|
|
|
|
|
else:
|
|
|
|
|
score -= 260
|
|
|
|
|
if expected_route:
|
|
|
|
|
if manifest_route == expected_route:
|
|
|
|
|
score += 180
|
|
|
|
|
elif manifest_route:
|
|
|
|
|
score -= 160
|
|
|
|
|
return score
|
|
|
|
|
|
|
|
|
|
@staticmethod
|
|
|
|
|
def _species_set_score(path: str, key: str, species_list: List[str], preferred_first: bool = False) -> int:
|
|
|
|
|
text_path = path
|
|
|
|
|
text_key = key or ""
|
|
|
|
|
for idx, species in enumerate(species_list):
|
|
|
|
|
if ArtifactResolver._path_mentions_species(text_path, species) or ArtifactResolver._path_mentions_species(text_key, species):
|
|
|
|
|
return 140 + (20 if preferred_first and idx == 0 else 0)
|
|
|
|
|
return 0
|
|
|
|
|
|
|
|
|
|
@staticmethod
|
|
|
|
|
def _reference_subfamily_candidate_ok(path: str, key: str = "") -> bool:
|
|
|
|
|
text = f"{key} {Path(path).name}".lower()
|
|
|
|
|
bad_tokens = [
|
|
|
|
|
"domain_review",
|
|
|
|
|
"interproscan",
|
|
|
|
|
"domain_check",
|
|
|
|
|
"hmmer",
|
|
|
|
|
"blast",
|
|
|
|
|
"combined.ids",
|
|
|
|
|
"gene_mrna_cds.ids",
|
|
|
|
|
"final_members.id",
|
|
|
|
|
"members.id",
|
|
|
|
|
]
|
|
|
|
|
if any(token in text for token in bad_tokens):
|
|
|
|
|
return False
|
|
|
|
|
if "reference_classification" in text or "target-" in text or ".ref-" in text:
|
|
|
|
|
return False
|
|
|
|
|
good_tokens = [
|
|
|
|
|
".subfamily",
|
|
|
|
|
"geneid.subfamily",
|
|
|
|
|
"confirmed_subfamily",
|
|
|
|
|
]
|
|
|
|
|
return any(token in text for token in good_tokens)
|
|
|
|
|
|
|
|
|
|
@staticmethod
|
|
|
|
|
def _gene_subfamily_candidate_ok(path: str, key: str = "") -> bool:
|
|
|
|
|
text = f"{key} {Path(path).name}".lower()
|
|
|
|
|
name = Path(path).name.lower()
|
|
|
|
|
bad_tokens = [
|
|
|
|
|
"candidate_members",
|
|
|
|
|
"curated_members",
|
|
|
|
|
"final_members",
|
|
|
|
|
"final_gfmembers",
|
|
|
|
|
"members.id",
|
|
|
|
|
"subfamily_evidence",
|
|
|
|
|
"_evidence",
|
|
|
|
|
"domain_review",
|
|
|
|
|
"interproscan",
|
|
|
|
|
"domain_check",
|
|
|
|
|
"motif.tsv",
|
|
|
|
|
"motif.txt",
|
|
|
|
|
"domain.tsv",
|
|
|
|
|
"domain.txt",
|
|
|
|
|
"structure.tsv",
|
|
|
|
|
"structure.gff.tsv",
|
|
|
|
|
"gene_structure.tsv",
|
|
|
|
|
"combined.ids",
|
|
|
|
|
"gene_mrna_cds.ids",
|
|
|
|
|
"conservation_profile",
|
|
|
|
|
"msa_conserved",
|
|
|
|
|
"results",
|
|
|
|
|
".msa.",
|
|
|
|
|
".tree.",
|
|
|
|
|
]
|
|
|
|
|
if any(token in text for token in bad_tokens):
|
|
|
|
|
return False
|
|
|
|
|
if "reference_classification.subfamily" in name:
|
|
|
|
|
return True
|
|
|
|
|
if "geneid.subfamily" in name:
|
|
|
|
|
return True
|
|
|
|
|
if "confirmed_subfamily" in name:
|
|
|
|
|
return True
|
|
|
|
|
return False
|
|
|
|
|
|
|
|
|
|
@staticmethod
|
|
|
|
|
def _reference_subfamily_score(path: str, key: str, species: str, family: str) -> int:
|
|
|
|
|
name = Path(path).name.lower()
|
|
|
|
|
score = 0
|
|
|
|
|
if name.endswith(".subfamily"):
|
|
|
|
|
score += 260
|
|
|
|
|
if "geneid.subfamily" in name:
|
|
|
|
|
score += 220
|
|
|
|
|
if "confirmed_subfamily" in name:
|
|
|
|
|
score += 240
|
|
|
|
|
if "reference_classification.subfamily" in name:
|
|
|
|
|
score += 200
|
|
|
|
|
if species and ArtifactResolver._path_mentions_species(path, species):
|
|
|
|
|
score += 120
|
|
|
|
|
if family and family.lower() in name:
|
|
|
|
|
score += 60
|
|
|
|
|
if key and "reference" in key.lower():
|
|
|
|
|
score += 80
|
|
|
|
|
return score
|
|
|
|
|
|
|
|
|
|
@staticmethod
|
|
|
|
|
def _path_mentions_species(path: str, species: str) -> bool:
|
|
|
|
|
if not species:
|
|
|
|
|
return False
|
|
|
|
|
name = Path(path).name.lower()
|
|
|
|
|
species_lower = species.lower()
|
|
|
|
|
return bool(re.search(rf"(^|[._-]){re.escape(species_lower)}([._-]|$)", name))
|
|
|
|
|
|
|
|
|
|
@staticmethod
|
|
|
|
|
def _dedupe(candidates: Iterable[ResolveCandidate]) -> List[ResolveCandidate]:
|
|
|
|
|
best: Dict[str, ResolveCandidate] = {}
|
|
|
|
|
for candidate in candidates:
|
|
|
|
|
old = best.get(candidate.path)
|
|
|
|
|
if old is None or candidate.score > old.score:
|
|
|
|
|
best[candidate.path] = candidate
|
|
|
|
|
return list(best.values())
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
def resolve_stage_artifacts(job_id: str, stage: str, prefix: str = "", species: str = "", family: str = "") -> Dict[str, Dict[str, Any]]:
|
|
|
|
|
context = build_project_context(job_id=job_id, prefix=prefix)
|
|
|
|
|
resolver = ArtifactResolver(context)
|
|
|
|
|
return {role: decision.to_dict() for role, decision in resolver.resolve_stage(stage, species=species, family=family).items()}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
def main() -> int:
|
|
|
|
|
import argparse
|
|
|
|
|
import json
|
|
|
|
|
|
|
|
|
|
parser = argparse.ArgumentParser(description="Resolve bbav5 semantic stage artifacts")
|
|
|
|
|
parser.add_argument("job_id")
|
|
|
|
|
parser.add_argument("stage")
|
|
|
|
|
parser.add_argument("--prefix", default="")
|
|
|
|
|
parser.add_argument("--species", default="")
|
|
|
|
|
parser.add_argument("--family", default="")
|
|
|
|
|
parser.add_argument("--output", default="")
|
|
|
|
|
args = parser.parse_args()
|
|
|
|
|
|
|
|
|
|
result = resolve_stage_artifacts(args.job_id, args.stage, prefix=args.prefix, species=args.species, family=args.family)
|
|
|
|
|
text = json.dumps(result, indent=2, ensure_ascii=False)
|
|
|
|
|
if args.output:
|
|
|
|
|
Path(args.output).write_text(text + "\n", encoding="utf-8")
|
|
|
|
|
else:
|
|
|
|
|
print(text)
|
|
|
|
|
return 0
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
if __name__ == "__main__":
|
|
|
|
|
raise SystemExit(main())
|
