fix: preserve confirmed species roles in agent planning
This commit is contained in:
potaser
+325
-51
@@ -711,6 +711,211 @@ def _confirmed_config_species_scope(job_id: str) -> Dict[str, list[str]]:
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return _configured_species_scope(job_id)
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def _reconcile_confirmed_gene_family_species(
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job_id: str,
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message: str,
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intent: Optional[Dict[str, Any]] = None,
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) -> Dict[str, Any]:
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"""Keep confirmed config roles separate from the current run selection."""
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config_scope = _confirmed_config_species_scope(job_id)
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if not config_scope:
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return {"applicable": False, "conflicts": []}
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from gfa_core.mas.utils.intent_parser import parse_explicit_species_role_mentions
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role_keys = {
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"targetSpecies": "target",
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"referenceSpecies": "reference",
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"comparativeSpecies": "comparative",
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}
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canonical_config = {
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key: _canonicalize_species_codes_for_job(job_id, config_scope.get(key) or [])
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for key in role_keys
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}
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config_role_by_species: Dict[str, str] = {}
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conflicts: list[Dict[str, str]] = []
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for key, role in role_keys.items():
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for species in canonical_config[key]:
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existing = config_role_by_species.get(species)
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if existing and existing != role:
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conflicts.append({
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"code": "config_species_role_conflict",
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"species": species,
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"config_role": f"{existing}/{role}",
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"requested_role": "",
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})
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else:
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config_role_by_species[species] = role
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explicit_raw = parse_explicit_species_role_mentions(message or "")
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explicit = {
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key: _canonicalize_species_codes_for_job(job_id, explicit_raw.get(key) or [])
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for key in (*role_keys, "unassigned")
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}
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for key, requested_role in role_keys.items():
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for species in explicit[key]:
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config_role = config_role_by_species.get(species)
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if config_role != requested_role:
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conflicts.append({
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"code": "user_config_species_role_conflict",
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"species": species,
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"config_role": config_role or "not_configured",
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"requested_role": requested_role,
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})
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routed_intent = intent or {}
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routed_params = routed_intent.get("params") or {}
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structured_targets = _canonicalize_species_codes_for_job(
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job_id,
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_param_list(routed_params.get("targetSpecies") or routed_intent.get("target_species")),
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)
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structured_refs = _canonicalize_species_codes_for_job(
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job_id,
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_param_list(routed_params.get("referenceSpecies") or routed_intent.get("reference_species")),
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)
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structured_comps = _canonicalize_species_codes_for_job(
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job_id,
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_param_list(routed_params.get("comparativeSpecies") or routed_intent.get("comparative_species")),
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)
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explicit_reference_set = set(explicit["referenceSpecies"])
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explicit_assigned_set = set(
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explicit["targetSpecies"]
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+ explicit["referenceSpecies"]
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+ explicit["comparativeSpecies"]
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)
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for species in structured_targets:
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config_role = config_role_by_species.get(species)
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if (
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config_role in {None, "reference"}
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and species not in explicit_reference_set
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and species not in explicit_assigned_set
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):
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conflicts.append({
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"code": "analysis_target_config_role_conflict",
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"species": species,
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"config_role": config_role or "not_configured",
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"requested_role": "analysis_target",
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})
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mentioned = list(dict.fromkeys(
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species
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for key in (*role_keys, "unassigned")
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for species in explicit[key]
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))
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target_candidates = list(dict.fromkeys([
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*structured_targets,
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*explicit["targetSpecies"],
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*explicit["unassigned"],
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]))
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comparative_candidates = list(dict.fromkeys([
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*structured_comps,
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*structured_targets,
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*explicit["comparativeSpecies"],
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*explicit["unassigned"],
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]))
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targets = [
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species for species in canonical_config["targetSpecies"]
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if species in target_candidates
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] or list(canonical_config["targetSpecies"])
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comparatives = [
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species for species in canonical_config["comparativeSpecies"]
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if species in comparative_candidates
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]
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references = [
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species for species in canonical_config["referenceSpecies"]
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if not structured_refs or species in structured_refs or species in mentioned
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] or list(canonical_config["referenceSpecies"])
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classification_species = list(dict.fromkeys([*targets, *comparatives]))
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unique_conflicts: list[Dict[str, str]] = []
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seen_conflicts: set[tuple[str, str, str, str]] = set()
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for conflict in conflicts:
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identity = (
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conflict["code"],
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conflict["species"],
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conflict["config_role"],
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conflict["requested_role"],
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)
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if identity not in seen_conflicts:
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seen_conflicts.add(identity)
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unique_conflicts.append(conflict)
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return {
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"applicable": True,
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"config_scope": canonical_config,
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"target_species": targets,
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"reference_species": references,
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"comparative_species": comparatives,
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"classification_species": classification_species,
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"conflicts": unique_conflicts,
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}
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def _species_role_conflict_message(conflicts: list[Dict[str, str]]) -> str:
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role_labels = {
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"target": "目标物种",
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"reference": "参考物种",
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"comparative": "比较物种",
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"analysis_target": "本轮分析对象",
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"not_configured": "未登记",
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}
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details = []
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for conflict in conflicts:
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species = conflict.get("species") or "未知物种"
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config_role = role_labels.get(conflict.get("config_role") or "", conflict.get("config_role") or "未知")
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requested_role = role_labels.get(conflict.get("requested_role") or "", conflict.get("requested_role") or "配置内部重复角色")
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details.append(f"{species}：config.xlsx 为{config_role}，本轮为{requested_role}")
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return (
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"检测到物种角色不一致："
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+ "；".join(details)
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+ "。为避免按错误范围执行，请发送“打开 config.xlsx”，核对并重新确认物种角色后再继续。"
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)
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def _apply_reconciled_species_to_intent(intent: Dict[str, Any], resolution: Dict[str, Any]) -> None:
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if not resolution.get("applicable") or resolution.get("conflicts"):
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return
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targets = list(resolution.get("target_species") or [])
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references = list(resolution.get("reference_species") or [])
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comparatives = list(resolution.get("comparative_species") or [])
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params = intent.setdefault("params", {})
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params.update({
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"targetSpecies": targets,
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"referenceSpecies": references,
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"comparativeSpecies": comparatives,
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})
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intent["target_species"] = targets
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intent["reference_species"] = references
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intent["comparative_species"] = comparatives
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scope_mode = (
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"target_plus_reference_plus_comparative"
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if references and comparatives
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else "target_plus_reference"
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if references
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else "target_plus_comparative"
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if comparatives
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else "target_only"
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)
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params["scopeMode"] = scope_mode
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intent["scopeMode"] = scope_mode
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def _is_gene_family_analysis_intent(intent: Optional[Dict[str, Any]]) -> bool:
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candidate = intent or {}
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stages = [str(stage or "").strip() for stage in candidate.get("stages") or []]
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if stages and all(stage.startswith("rnaseq_") or stage.startswith("wgs_") for stage in stages):
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return False
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params = candidate.get("params") or {}
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family = str(candidate.get("gene_family") or params.get("geneFamily") or "").strip()
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gene_family_stages = {
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"genome_prepare", "identify", "phylogeny", "motif", "domain",
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"structure", "combo", "reference_classification", "subfamily_confirm",
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"promoter", "tfbs", "synteny", "interspecies_synteny", "karyotype",
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"pep", "ortholog", "kaks", "ppi", "expression",
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}
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return bool(family or set(stages) & gene_family_stages)
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def _normalize_main_agent_analysis_intent(
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intent: Dict[str, Any],
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*,
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@@ -1356,6 +1561,14 @@ def _resolve_subfamily_request_species_roles(
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intent: Optional[Dict[str, Any]] = None,
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) -> Dict[str, list[str]]:
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"""Preserve config roles while resolving species mentioned in a subfamily request."""
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confirmed_resolution = _reconcile_confirmed_gene_family_species(job_id, message, intent)
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if confirmed_resolution.get("applicable") and not confirmed_resolution.get("conflicts"):
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return {
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"target_species": list(confirmed_resolution.get("target_species") or []),
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"reference_species": list(confirmed_resolution.get("reference_species") or []),
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"comparative_species": list(confirmed_resolution.get("comparative_species") or []),
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"classification_species": list(confirmed_resolution.get("classification_species") or []),
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}
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routed_intent = intent or {}
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params = routed_intent.get("params") or {}
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structured_targets = _canonicalize_species_codes_for_job(
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@@ -1826,8 +2039,19 @@ def _resolve_contextual_gene_family_request(
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or contextual_stage_request
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):
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return {}
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role_resolution = _reconcile_confirmed_gene_family_species(
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job_id,
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text,
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routed_intent,
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)
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selection = _load_identify_species_selection(job_id)
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config_targets, config_refs, config_comps = _species_groups_from_selection(selection)
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if role_resolution.get("applicable") and not role_resolution.get("conflicts"):
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confirmed_scope = role_resolution.get("config_scope") or {}
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config_targets = list(confirmed_scope.get("targetSpecies") or [])
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config_refs = list(confirmed_scope.get("referenceSpecies") or [])
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config_comps = list(confirmed_scope.get("comparativeSpecies") or [])
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else:
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config_targets, config_refs, config_comps = _species_groups_from_selection(selection)
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family = _nonempty_prefix(_gene_family_from_config(INPUT_ROOT / job_id / "config.xlsx")) if job_id else ""
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if not family and request_prefix and "." in request_prefix:
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family = request_prefix.split(".", 1)[1]
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@@ -1839,37 +2063,38 @@ def _resolve_contextual_gene_family_request(
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prefix_species = request_prefix.split(".", 1)[0].strip()
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if prefix_species in {"Target", "Multi", "Ref", "Reference"}:
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prefix_species = ""
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mentioned_targets = [sp for sp in mentioned if sp in config_targets or sp == prefix_species or sp in confirmed_species]
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mentioned_refs = [sp for sp in mentioned if sp in config_refs]
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mentioned_comps = [sp for sp in mentioned if sp in config_comps]
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unassigned_mentions = [sp for sp in mentioned if sp not in mentioned_targets and sp not in mentioned_refs and sp not in mentioned_comps]
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if unassigned_mentions:
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is_all_species_request = _looks_like_all_species_query(text) or _looks_like_all_subfamily_species_query(text)
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is_intraspecies_synteny_request = _looks_like_intraspecies_synteny_query(text)
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if role_resolution.get("applicable") and not role_resolution.get("conflicts"):
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targets = list(role_resolution.get("target_species") or [])
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refs = list(role_resolution.get("reference_species") or [])
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comps = list(role_resolution.get("comparative_species") or [])
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else:
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mentioned_targets = [sp for sp in mentioned if sp in config_targets or sp == prefix_species or sp in confirmed_species]
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mentioned_refs = [sp for sp in mentioned if sp in config_refs]
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mentioned_comps = [sp for sp in mentioned if sp in config_comps]
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unassigned_mentions = [sp for sp in mentioned if sp not in mentioned_targets and sp not in mentioned_refs and sp not in mentioned_comps]
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for sp in unassigned_mentions:
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if sp not in mentioned_targets:
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mentioned_targets.append(sp)
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has_explicit_scope = bool(mentioned or structured_targets or structured_refs or structured_comps)
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is_all_species_request = _looks_like_all_species_query(text) or _looks_like_all_subfamily_species_query(text)
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is_intraspecies_synteny_request = _looks_like_intraspecies_synteny_query(text)
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if mentioned:
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targets = mentioned_targets or [sp for sp in mentioned if sp not in mentioned_refs and sp not in mentioned_comps]
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elif structured_targets:
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targets = list(structured_targets)
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elif is_all_species_request and config_targets:
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targets = list(config_targets)
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elif is_intraspecies_synteny_request and config_targets:
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targets = list(config_targets)
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elif prefix_species:
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targets = [prefix_species]
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elif config_targets:
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targets = [config_targets[0]] if len(config_targets) == 1 else list(config_targets)
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elif confirmed_species:
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targets = [confirmed_species[0]]
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else:
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targets = []
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refs = mentioned_refs or list(structured_refs) or (list(config_refs) if is_all_species_request else [])
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comps = mentioned_comps or list(structured_comps) or (list(config_comps) if is_all_species_request else [])
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if mentioned:
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targets = mentioned_targets or [sp for sp in mentioned if sp not in mentioned_refs and sp not in mentioned_comps]
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elif structured_targets:
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targets = list(structured_targets)
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elif is_all_species_request and config_targets:
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targets = list(config_targets)
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elif is_intraspecies_synteny_request and config_targets:
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targets = list(config_targets)
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elif prefix_species:
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targets = [prefix_species]
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elif config_targets:
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targets = [config_targets[0]] if len(config_targets) == 1 else list(config_targets)
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elif confirmed_species:
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targets = [confirmed_species[0]]
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else:
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targets = []
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refs = mentioned_refs or list(structured_refs) or (list(config_refs) if is_all_species_request else [])
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comps = mentioned_comps or list(structured_comps) or (list(config_comps) if is_all_species_request else [])
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if refs and comps:
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scope_mode = "target_plus_reference_plus_comparative"
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elif refs:
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@@ -1895,7 +2120,14 @@ def _resolve_contextual_gene_family_request(
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for sp, data in (subfamily_state.get("by_species") or {}).items()
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}
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all_targets_confirmed = bool(classifiable_species_for_labels) and bool(subfamily_state.get("all_confirmed"))
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explicit_custom_scope = bool(refs or comps or len(targets) > 1)
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if role_resolution.get("applicable") and not role_resolution.get("conflicts"):
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explicit_custom_scope = (
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targets != config_targets
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or refs != config_refs
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or comps != config_comps
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)
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else:
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explicit_custom_scope = bool(refs or comps or len(targets) > 1)
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skip_subfamily_labels = _skip_subfamily_label_query(text)
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if skip_subfamily_labels:
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context_route = "plain_phylogeny" if _looks_like_phylogeny_query(text) else "gene_family_without_subfamily"
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@@ -3959,9 +4191,6 @@ def _attach_agent_manifest_status(task: Dict) -> None:
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print(f"[API DEBUG] Failed to attach agent manifest status: {e}")
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app = FastAPI(title="BotanicalBaseAgent API")
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from gfa_core.extension_stage_lightweight.api import create_lightweight_extension_router
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app.include_router(create_lightweight_extension_router())
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# MainAgent runtime state. Analysis planning and execution remain owned by
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# the original IntentAgent/PlanningAgent/frontend flow below.
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llm_manager = None
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@@ -12701,7 +12930,7 @@ def _get_celery_overview() -> Dict[str, Any]:
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resource = snapshot(include_terminal=False)
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overview["resource_usage"] = resource.get("usage")
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overview["resource_tasks"] = resource.get("tasks", [])
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overview["resource_tasks"] = resource.get("tasks", [])[:20]
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except Exception as exc:
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overview["errors"].append(f"Resource governor snapshot failed: {exc}")
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overview["thresholds"] = {
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@@ -14302,8 +14531,9 @@ async def get_results(
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except Exception:
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pass
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# Results are a persisted job view. Apply manifests by execution time so
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# the latest attempt determines the visible stage status.
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# Result browsing is a persisted job view, so apply manifests in execution
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# order. The newest attempt for a stage becomes its visible status instead
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# of depending on filesystem iteration order.
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manifest_payloads.sort(
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key=lambda item: (item[0].stat().st_mtime, item[0].name)
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)
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@@ -16754,11 +16984,27 @@ async def _run_agent_chat(
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verified_intent = outcome.get("intent")
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if action == "propose_analysis" and isinstance(verified_intent, dict):
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verified_intent = _normalize_main_agent_analysis_intent(
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verified_intent,
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job_id=request.job_id,
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context_terms=router_context_terms,
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role_resolution = (
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_reconcile_confirmed_gene_family_species(
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request.job_id,
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request.message,
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verified_intent,
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)
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if _is_gene_family_analysis_intent(verified_intent)
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else {"applicable": False, "conflicts": []}
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)
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if role_resolution.get("conflicts"):
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action = "clarify"
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outcome["message"] = _species_role_conflict_message(role_resolution["conflicts"])
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outcome["proposal"] = None
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verified_intent = None
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else:
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verified_intent = _normalize_main_agent_analysis_intent(
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verified_intent,
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job_id=request.job_id,
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context_terms=router_context_terms,
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)
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_apply_reconciled_species_to_intent(verified_intent, role_resolution)
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verified_stages = (
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verified_intent.get("stages")
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if isinstance(verified_intent, dict)
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@@ -19732,6 +19978,28 @@ async def agent_plan(request: AgentPlanRequest):
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extension_intent = _match_extension_stage_intent(request.message, request.job_id or "")
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if extension_intent:
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return _extension_stage_plan_response(extension_intent, session_id, request.job_id or "")
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plan_role_resolution = (
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||||
_reconcile_confirmed_gene_family_species(
|
||||
request.job_id,
|
||||
request.message,
|
||||
request.intent,
|
||||
)
|
||||
if _is_gene_family_analysis_intent(request.intent)
|
||||
else {"applicable": False, "conflicts": []}
|
||||
)
|
||||
if plan_role_resolution.get("conflicts"):
|
||||
return {
|
||||
"success": False,
|
||||
"status": "species_role_conflict",
|
||||
"message": _species_role_conflict_message(plan_role_resolution["conflicts"]),
|
||||
"issues": plan_role_resolution["conflicts"],
|
||||
"suggested_command": "打开 config.xlsx",
|
||||
"session_id": session_id,
|
||||
}
|
||||
if plan_role_resolution.get("applicable"):
|
||||
request.intent = dict(request.intent or {})
|
||||
request.intent["params"] = dict(request.intent.get("params") or {})
|
||||
_apply_reconciled_species_to_intent(request.intent, plan_role_resolution)
|
||||
query_lower_for_context = (request.message or "").lower()
|
||||
subfamily_confirm_query_for_context = any(
|
||||
kw in query_lower_for_context
|
||||
@@ -21042,18 +21310,24 @@ async def agent_plan(request: AgentPlanRequest):
|
||||
intent["prefix"] = request.prefix
|
||||
intent.setdefault("params", {})["prefix"] = request.prefix
|
||||
plan_params["prefix"] = request.prefix
|
||||
_apply_scope_selection_to_intent(intent, request.message)
|
||||
if plan_role_resolution.get("applicable"):
|
||||
_apply_reconciled_species_to_intent(intent, plan_role_resolution)
|
||||
else:
|
||||
_apply_scope_selection_to_intent(intent, request.message)
|
||||
if subfamily_prediction_query:
|
||||
explicit_species = _extract_species_codes_from_text_for_job(request.job_id, request.message or "")
|
||||
if explicit_species:
|
||||
intent["target_species"] = explicit_species
|
||||
intent.setdefault("params", {})["targetSpecies"] = explicit_species
|
||||
intent["species"] = explicit_species[0] if len(explicit_species) == 1 else "Multi"
|
||||
ref_defaults = [
|
||||
item.get("species")
|
||||
for item in ((_load_identify_species_selection(request.job_id).get("groups") or {}).get("reference") or [])
|
||||
if item.get("species")
|
||||
] if request.job_id else []
|
||||
if not plan_role_resolution.get("applicable"):
|
||||
explicit_species = _extract_species_codes_from_text_for_job(request.job_id, request.message or "")
|
||||
if explicit_species:
|
||||
intent["target_species"] = explicit_species
|
||||
intent.setdefault("params", {})["targetSpecies"] = explicit_species
|
||||
intent["species"] = explicit_species[0] if len(explicit_species) == 1 else "Multi"
|
||||
ref_defaults = list(plan_role_resolution.get("reference_species") or [])
|
||||
if not ref_defaults and request.job_id:
|
||||
ref_defaults = [
|
||||
item.get("species")
|
||||
for item in ((_load_identify_species_selection(request.job_id).get("groups") or {}).get("reference") or [])
|
||||
if item.get("species")
|
||||
]
|
||||
if ref_defaults:
|
||||
intent["reference_species"] = ref_defaults
|
||||
intent.setdefault("params", {})["referenceSpecies"] = ref_defaults
|
||||
|
||||
@@ -415,6 +415,50 @@ def parse_gene_family_scope_selection(query: str) -> Dict[str, object]:
|
||||
}
|
||||
|
||||
|
||||
def parse_explicit_species_role_mentions(query: str) -> Dict[str, List[str]]:
|
||||
"""Return explicit roles without promoting unassigned species to targets."""
|
||||
text = str(query or "")
|
||||
|
||||
def mentioned_species(value: str) -> List[str]:
|
||||
parsed = _species_mentions_with_roles(value)
|
||||
return _unique_keep_order([
|
||||
species
|
||||
for key in ("targetSpecies", "referenceSpecies", "comparativeSpecies", "unassigned")
|
||||
for species in parsed.get(key) or []
|
||||
])
|
||||
|
||||
explicit_patterns = {
|
||||
"targetSpecies": r"目标物种|目标基因组|作为目标|是目标|\btarget(?:\s+species|\s+genome)?\b",
|
||||
"referenceSpecies": r"参考物种|参考基因组|作为参考|是参考|\breference(?:\s+species|\s+genome)?\b|\bseed_reference\b|\bknown_family_reference\b",
|
||||
"comparativeSpecies": r"比较物种|比较基因组|作为比较|是比较|作为外群|是外群|\bcomparative(?:\s+species|\s+genome)?\b|\boutgroup\b",
|
||||
}
|
||||
roles: Dict[str, List[str]] = {
|
||||
"targetSpecies": [],
|
||||
"referenceSpecies": [],
|
||||
"comparativeSpecies": [],
|
||||
"unassigned": [],
|
||||
}
|
||||
for clause in re.split(r"[,，;；。\n]+", text):
|
||||
clause_species = mentioned_species(clause)
|
||||
matched_roles = [
|
||||
key
|
||||
for key, pattern in explicit_patterns.items()
|
||||
if re.search(pattern, clause, flags=re.IGNORECASE)
|
||||
]
|
||||
if len(matched_roles) == 1:
|
||||
roles[matched_roles[0]].extend(clause_species)
|
||||
|
||||
assigned = set(
|
||||
roles["targetSpecies"]
|
||||
+ roles["referenceSpecies"]
|
||||
+ roles["comparativeSpecies"]
|
||||
)
|
||||
roles["unassigned"] = [
|
||||
species for species in mentioned_species(text) if species not in assigned
|
||||
]
|
||||
return {key: _unique_keep_order(value) for key, value in roles.items()}
|
||||
|
||||
|
||||
def parse_promoter_plot_revise_request(query: str) -> Dict:
|
||||
"""Extract parameters for custom promoter cis-element plotting."""
|
||||
text = str(query or "").strip()
|
||||
|
||||
@@ -0,0 +1,888 @@
|
||||
from __future__ import annotations
|
||||
|
||||
import importlib
|
||||
import json
|
||||
|
||||
import pytest
|
||||
|
||||
from apps.web.vue3 import main as WEB_MAIN
|
||||
from gfa_core.mas.agent_state_repository import SQLiteAgentStateRepository
|
||||
from gfa_core.mas.persistent_conversation import PersistentConversationStore
|
||||
|
||||
|
||||
@pytest.fixture
|
||||
def web_main(monkeypatch):
|
||||
monkeypatch.setattr(WEB_MAIN, "llm_manager", object())
|
||||
return WEB_MAIN
|
||||
|
||||
|
||||
def _install_router(monkeypatch, outcome, captured):
|
||||
router_module = importlib.import_module("gfa_core.mas.agents.router")
|
||||
|
||||
async def fake_execute(_self, state, message):
|
||||
captured.append(message.payload)
|
||||
state.results["router_outcome"] = outcome
|
||||
return state
|
||||
|
||||
monkeypatch.setattr(router_module.RouterAgent, "execute", fake_execute)
|
||||
|
||||
|
||||
def test_agent_conversation_store_initializes_from_env(
|
||||
monkeypatch,
|
||||
web_main,
|
||||
tmp_path,
|
||||
):
|
||||
database_path = tmp_path / "state" / "agent-state.sqlite3"
|
||||
monkeypatch.setenv("PLANTAI_AGENT_STATE_DB", str(database_path))
|
||||
monkeypatch.setattr(web_main, "agent_conversation_store", None, raising=False)
|
||||
|
||||
web_main.initialize_agent_conversation_store()
|
||||
|
||||
assert database_path.is_file()
|
||||
assert isinstance(web_main.agent_conversation_store, PersistentConversationStore)
|
||||
|
||||
|
||||
@pytest.mark.asyncio
|
||||
@pytest.mark.parametrize(
|
||||
("action", "task_type", "expected_intent"),
|
||||
[
|
||||
("reply", "faq", None),
|
||||
("clarify", "clarification", None),
|
||||
("show_result", "result_view", None),
|
||||
("propose_analysis", "analysis", {"stages": ["motif"], "stage": "motif"}),
|
||||
(
|
||||
"propose_utility",
|
||||
"utility",
|
||||
{
|
||||
"taskType": "utility",
|
||||
"utility_tool": "fasta_header_clean",
|
||||
"stages": ["sequence_extract_by_id"],
|
||||
"params": {"sequenceExtractFasta": "test.fa"},
|
||||
},
|
||||
),
|
||||
],
|
||||
)
|
||||
async def test_agent_chat_maps_router_actions_and_passes_context(
|
||||
monkeypatch, web_main, action, task_type, expected_intent
|
||||
):
|
||||
captured = []
|
||||
outcome = {
|
||||
"status": "ok",
|
||||
"action": action,
|
||||
"message": f"message for {action}",
|
||||
"intent": expected_intent,
|
||||
"sources": [{"path": "final/result.tsv"}],
|
||||
"tool_trace": [{"name": "inspect_analysis_results", "result": "large"}] * 12,
|
||||
}
|
||||
_install_router(monkeypatch, outcome, captured)
|
||||
history = [{"role": "user", "content": "上一轮"}]
|
||||
|
||||
result = await web_main.agent_chat(
|
||||
web_main.AgentChatRequest(
|
||||
message="请接着处理",
|
||||
session_id="session-7",
|
||||
job_id="job-7",
|
||||
history=history,
|
||||
)
|
||||
)
|
||||
|
||||
assert captured == [
|
||||
{
|
||||
"query": "请接着处理",
|
||||
"history": history,
|
||||
"session_id": "session-7",
|
||||
"job_id": "job-7",
|
||||
}
|
||||
]
|
||||
assert result["success"] is True
|
||||
assert result["status"] == "ok"
|
||||
assert result["action"] == action
|
||||
assert result["intent"]["taskType"] == task_type
|
||||
assert result["intent"]["message"] == f"message for {action}"
|
||||
assert result["sources"] == [{"path": "final/result.tsv"}]
|
||||
assert len(result["tool_trace"]) <= 5
|
||||
assert all(len(item["result"]) <= 1000 for item in result["tool_trace"])
|
||||
if action in {"propose_analysis", "propose_utility"}:
|
||||
assert result["intent"]["stages"] == expected_intent["stages"]
|
||||
else:
|
||||
assert result["intent"]["stages"] == []
|
||||
|
||||
|
||||
@pytest.mark.asyncio
|
||||
async def test_agent_chat_persists_router_proposal_without_analysis_intent(
|
||||
monkeypatch,
|
||||
web_main,
|
||||
tmp_path,
|
||||
):
|
||||
repository = SQLiteAgentStateRepository(tmp_path / "agent-state.sqlite3")
|
||||
repository.initialize()
|
||||
store = PersistentConversationStore(repository)
|
||||
monkeypatch.setattr(web_main, "agent_conversation_store", store)
|
||||
captured = []
|
||||
proposal = {
|
||||
"proposal_id": "proposal-123",
|
||||
"request": "执行 Ft 的数据准备",
|
||||
"subject": "执行 Ft 的数据准备",
|
||||
}
|
||||
_install_router(
|
||||
monkeypatch,
|
||||
{
|
||||
"status": "ok",
|
||||
"action": "clarify",
|
||||
"message": "我理解为只执行 Ft 数据准备，是否确认？",
|
||||
"intent": None,
|
||||
"proposal": proposal,
|
||||
"sources": [],
|
||||
"tool_trace": [],
|
||||
},
|
||||
captured,
|
||||
)
|
||||
|
||||
result = await web_main.agent_chat(
|
||||
web_main.AgentChatRequest(
|
||||
message="执行 Ft 的数据准备",
|
||||
session_id="proposal-session",
|
||||
job_id="job-ft",
|
||||
history=[],
|
||||
)
|
||||
)
|
||||
|
||||
assert result["action"] == "clarify"
|
||||
assert result["intent"]["stages"] == []
|
||||
ledger = repository.get_goal_ledger(result["session_id"])
|
||||
assert ledger is not None
|
||||
assert ledger.user_terms["pending_proposal"] == {
|
||||
**proposal,
|
||||
"job_id": "job-ft",
|
||||
}
|
||||
|
||||
|
||||
@pytest.mark.asyncio
|
||||
async def test_agent_chat_exposes_confirmed_request_for_original_planner(
|
||||
monkeypatch,
|
||||
web_main,
|
||||
):
|
||||
captured = []
|
||||
proposal = {
|
||||
"proposal_id": "proposal-next",
|
||||
"request": "我已确认 config.xlsx，接下来应该做什么分析",
|
||||
"subject": "启动苦荞SPL基因家族分析",
|
||||
}
|
||||
_install_router(
|
||||
monkeypatch,
|
||||
{
|
||||
"status": "ok",
|
||||
"action": "propose_analysis",
|
||||
"message": "已交给现有分析系统识别。",
|
||||
"intent": {"stages": ["genome_prepare"]},
|
||||
"proposal": proposal,
|
||||
"sources": [],
|
||||
"tool_trace": [],
|
||||
},
|
||||
captured,
|
||||
)
|
||||
|
||||
result = await web_main.agent_chat(
|
||||
web_main.AgentChatRequest(
|
||||
message="确认",
|
||||
session_id="session-next",
|
||||
job_id="job-next",
|
||||
history=[],
|
||||
)
|
||||
)
|
||||
|
||||
assert result["action"] == "propose_analysis"
|
||||
assert result["handoff_request"] == proposal["request"]
|
||||
assert "尚未执行" in result["intent"]["message"]
|
||||
|
||||
|
||||
@pytest.mark.asyncio
|
||||
async def test_agent_chat_rejects_job_change_before_analysis_handoff(
|
||||
monkeypatch,
|
||||
web_main,
|
||||
tmp_path,
|
||||
):
|
||||
from fastapi import HTTPException
|
||||
|
||||
repository = SQLiteAgentStateRepository(tmp_path / "agent-state.sqlite3")
|
||||
repository.initialize()
|
||||
store = PersistentConversationStore(repository)
|
||||
monkeypatch.setattr(web_main, "agent_conversation_store", store)
|
||||
turn = store.begin_turn(
|
||||
session_id="bound-session",
|
||||
job_id="job-ft",
|
||||
query="分析 Ft.SPL",
|
||||
client_history=[],
|
||||
)
|
||||
|
||||
with pytest.raises(HTTPException) as exc_info:
|
||||
await web_main.agent_chat(
|
||||
web_main.AgentChatRequest(
|
||||
message="分析 Os.SPL",
|
||||
session_id=turn.conversation_id,
|
||||
job_id="job-os",
|
||||
history=[],
|
||||
)
|
||||
)
|
||||
|
||||
assert exc_info.value.status_code == 409
|
||||
assert exc_info.value.detail == "conversation job binding conflict"
|
||||
|
||||
|
||||
def test_main_agent_normalization_uses_confirmed_config_family_as_authority(
|
||||
monkeypatch,
|
||||
web_main,
|
||||
):
|
||||
monkeypatch.setattr(
|
||||
web_main,
|
||||
"_confirmed_config_species_scope",
|
||||
lambda _job_id: {
|
||||
"targetSpecies": ["Ft"],
|
||||
"referenceSpecies": ["At"],
|
||||
"comparativeSpecies": [],
|
||||
},
|
||||
)
|
||||
monkeypatch.setattr(
|
||||
web_main,
|
||||
"_infer_family_from_config_or_final",
|
||||
lambda _job_id: "SPL",
|
||||
)
|
||||
|
||||
normalized = web_main._normalize_main_agent_analysis_intent(
|
||||
{
|
||||
"stages": ["genome_prepare"],
|
||||
"gene_family": "xlsx，接下来应该做什么分析",
|
||||
"prefix": "Ft.xlsx，接下来应该做什么分析",
|
||||
},
|
||||
job_id="job-ft",
|
||||
)
|
||||
|
||||
assert normalized["gene_family"] == "SPL"
|
||||
assert normalized["prefix"] == "Ft.SPL"
|
||||
assert normalized["params"]["geneFamily"] == "SPL"
|
||||
|
||||
|
||||
def test_main_agent_normalization_uses_hydrated_job_identity_without_config(
|
||||
monkeypatch,
|
||||
web_main,
|
||||
):
|
||||
monkeypatch.setattr(web_main, "_confirmed_config_species_scope", lambda _job: {})
|
||||
|
||||
normalized = web_main._normalize_main_agent_analysis_intent(
|
||||
{"stages": ["identify"], "params": {}},
|
||||
job_id="job-hkl",
|
||||
context_terms={
|
||||
"gene_family": "HKL",
|
||||
"target_species": ["Sv"],
|
||||
"reference_species": ["At"],
|
||||
},
|
||||
)
|
||||
|
||||
assert normalized["gene_family"] == "HKL"
|
||||
assert normalized["prefix"] == "Sv.HKL"
|
||||
assert normalized["target_species"] == ["Sv"]
|
||||
assert normalized["reference_species"] == ["At"]
|
||||
assert normalized["stages"] == ["identify"]
|
||||
|
||||
|
||||
def test_rnaseq_family_member_normalization_keeps_species_prefix(
|
||||
monkeypatch,
|
||||
web_main,
|
||||
):
|
||||
monkeypatch.setattr(web_main, "_confirmed_config_species_scope", lambda _job: {})
|
||||
|
||||
normalized = web_main._normalize_main_agent_analysis_intent(
|
||||
{
|
||||
"gene_family": "HKL",
|
||||
"rna_route": "family_member",
|
||||
"stages": ["rnaseq_de"],
|
||||
"params": {"analysisRoute": "family_member"},
|
||||
},
|
||||
job_id="job-os",
|
||||
context_terms={"target_species": ["Os"]},
|
||||
)
|
||||
|
||||
assert normalized["prefix"] == "Os"
|
||||
assert normalized["params"]["prefix"] == "Os"
|
||||
assert normalized["params"]["geneFamily"] == "HKL"
|
||||
|
||||
|
||||
def test_current_job_hydration_fills_identity_without_planning_stages(
|
||||
monkeypatch,
|
||||
web_main,
|
||||
tmp_path,
|
||||
):
|
||||
final_dir = tmp_path / "workspace" / "job-hkl" / "final"
|
||||
final_dir.mkdir(parents=True)
|
||||
(final_dir / "Sv.HKL.subfamily_confirm.manifest.json").write_text(
|
||||
json.dumps(
|
||||
{
|
||||
"stage": "subfamily_confirm",
|
||||
"status": "success",
|
||||
"prefix": "Sv.HKL",
|
||||
"target_species": ["Sv"],
|
||||
"reference_species": ["At"],
|
||||
"analysis_route": "confirmed_subfamily",
|
||||
}
|
||||
),
|
||||
encoding="utf-8",
|
||||
)
|
||||
(final_dir / "Sv.HKL.ppi.manifest.json").write_text(
|
||||
json.dumps(
|
||||
{
|
||||
"stage": "ppi",
|
||||
"status": "success",
|
||||
"prefix": "Sv.HKL",
|
||||
"target_species": ["Sv"],
|
||||
"reference_species": ["string_taxon_4555"],
|
||||
}
|
||||
),
|
||||
encoding="utf-8",
|
||||
)
|
||||
monkeypatch.setattr(web_main, "WORKSPACE_ROOT", tmp_path / "workspace")
|
||||
monkeypatch.setattr(web_main, "_confirmed_config_species_scope", lambda _job: {})
|
||||
monkeypatch.setattr(web_main, "_infer_family_from_config_or_final", lambda _job: "HKL")
|
||||
|
||||
hydrated = web_main._hydrate_goal_terms_from_current_job(
|
||||
{"reference_species": ["ExplicitRef"]},
|
||||
"job-hkl",
|
||||
)
|
||||
|
||||
assert hydrated["gene_family"] == "HKL"
|
||||
assert hydrated["target_species"] == ["Sv"]
|
||||
assert hydrated["reference_species"] == ["ExplicitRef"]
|
||||
assert "stages" not in hydrated
|
||||
assert "requested_stages" not in hydrated
|
||||
|
||||
canonical = web_main._hydrate_goal_terms_from_current_job({}, "job-hkl")
|
||||
assert canonical["reference_species"] == ["At"]
|
||||
|
||||
|
||||
def test_whole_genome_rna_job_does_not_inherit_later_gene_family_context(
|
||||
monkeypatch,
|
||||
web_main,
|
||||
tmp_path,
|
||||
):
|
||||
final_dir = tmp_path / "workspace" / "job-rna" / "final"
|
||||
final_dir.mkdir(parents=True)
|
||||
for name, payload in {
|
||||
"Os.HKL.subfamily_confirm.manifest.json": {
|
||||
"stage": "subfamily_confirm",
|
||||
"status": "success",
|
||||
"prefix": "Os.HKL",
|
||||
"target_species": ["Os"],
|
||||
"reference_species": ["At"],
|
||||
},
|
||||
"Os.rnaseq_de.manifest.json": {
|
||||
"stage": "rnaseq_de",
|
||||
"status": "success",
|
||||
"prefix": "Os",
|
||||
"foreground_mode": "global",
|
||||
},
|
||||
}.items():
|
||||
(final_dir / name).write_text(json.dumps(payload), encoding="utf-8")
|
||||
monkeypatch.setattr(web_main, "WORKSPACE_ROOT", tmp_path / "workspace")
|
||||
monkeypatch.setattr(web_main, "_confirmed_config_species_scope", lambda _job: {})
|
||||
monkeypatch.setattr(web_main, "_infer_family_from_config_or_final", lambda _job: "HKL")
|
||||
|
||||
hydrated = web_main._hydrate_goal_terms_from_current_job({}, "job-rna")
|
||||
|
||||
assert hydrated["rna_route"] == "whole_genome"
|
||||
assert hydrated["target_species"] == ["Os"]
|
||||
assert "gene_family" not in hydrated
|
||||
assert "reference_species" not in hydrated
|
||||
|
||||
|
||||
@pytest.mark.asyncio
|
||||
async def test_agent_chat_provider_failure_has_no_faq_fallback(monkeypatch, web_main):
|
||||
captured = []
|
||||
_install_router(
|
||||
monkeypatch,
|
||||
{
|
||||
"status": "agent_unavailable",
|
||||
"action": None,
|
||||
"message": "The Router model is currently unavailable.",
|
||||
"intent": None,
|
||||
"sources": [],
|
||||
"tool_trace": [],
|
||||
},
|
||||
captured,
|
||||
)
|
||||
|
||||
result = await web_main.agent_chat(
|
||||
web_main.AgentChatRequest(message="请做 motif 分析", job_id="job-7")
|
||||
)
|
||||
|
||||
assert result["success"] is False
|
||||
assert result["status"] == "agent_unavailable"
|
||||
assert result["action"] is None
|
||||
assert result["intent"] is None
|
||||
assert "知识库" not in result["message"]
|
||||
|
||||
|
||||
@pytest.mark.asyncio
|
||||
async def test_agent_chat_manager_initialization_failure_is_agent_unavailable(
|
||||
monkeypatch, web_main
|
||||
):
|
||||
from gfa_core.mas.config import config as mas_config
|
||||
|
||||
monkeypatch.setattr(web_main, "llm_manager", None)
|
||||
monkeypatch.setattr(
|
||||
mas_config,
|
||||
"load_llm_config",
|
||||
lambda: (_ for _ in ()).throw(RuntimeError("missing provider config")),
|
||||
)
|
||||
|
||||
result = await web_main.agent_chat(
|
||||
web_main.AgentChatRequest(message="请做 motif 分析", job_id="job-7")
|
||||
)
|
||||
|
||||
assert result["success"] is False
|
||||
assert result["status"] == "agent_unavailable"
|
||||
assert result["action"] is None
|
||||
assert result["intent"] is None
|
||||
|
||||
|
||||
@pytest.mark.asyncio
|
||||
async def test_only_propose_analysis_can_return_plannable_intent(monkeypatch, web_main):
|
||||
captured = []
|
||||
_install_router(
|
||||
monkeypatch,
|
||||
{
|
||||
"status": "ok",
|
||||
"action": "reply",
|
||||
"message": "这是解释，不是分析请求。",
|
||||
"intent": {"stages": ["phylogeny"], "stage": "phylogeny"},
|
||||
"sources": [],
|
||||
"tool_trace": [],
|
||||
},
|
||||
captured,
|
||||
)
|
||||
|
||||
result = await web_main.agent_chat(
|
||||
web_main.AgentChatRequest(message="这个树为什么这样", job_id="job-7")
|
||||
)
|
||||
|
||||
assert result["action"] == "reply"
|
||||
assert result["intent"]["taskType"] == "faq"
|
||||
assert result["intent"]["stages"] == []
|
||||
|
||||
|
||||
@pytest.mark.asyncio
|
||||
async def test_proposed_analysis_normalizes_scope_from_the_current_user_action(
|
||||
monkeypatch,
|
||||
web_main,
|
||||
):
|
||||
captured = []
|
||||
_install_router(
|
||||
monkeypatch,
|
||||
{
|
||||
"status": "ok",
|
||||
"action": "propose_analysis",
|
||||
"message": "已识别当前数据准备操作。",
|
||||
"intent": {
|
||||
"gene_family": "SPL",
|
||||
"target_species": ["At"],
|
||||
"reference_species": [],
|
||||
"stages": ["genome_prepare"],
|
||||
"primary_stage": "genome_prepare",
|
||||
"params": {
|
||||
"targetSpecies": ["Ft"],
|
||||
"referenceSpecies": [],
|
||||
"comparativeSpecies": [],
|
||||
"scopeMode": "target_only",
|
||||
},
|
||||
},
|
||||
"sources": [],
|
||||
"tool_trace": [],
|
||||
},
|
||||
captured,
|
||||
)
|
||||
|
||||
result = await web_main.agent_chat(
|
||||
web_main.AgentChatRequest(
|
||||
message="执行Ft的数据准备",
|
||||
job_id="job-ft",
|
||||
)
|
||||
)
|
||||
|
||||
assert result["intent"]["target_species"] == ["Ft"]
|
||||
assert result["intent"]["reference_species"] == []
|
||||
assert result["intent"]["params"]["targetSpecies"] == ["Ft"]
|
||||
assert result["intent"]["prefix"] == "Ft.SPL"
|
||||
|
||||
|
||||
@pytest.mark.asyncio
|
||||
async def test_proposed_analysis_uses_intent_params_as_the_scope_authority(
|
||||
monkeypatch,
|
||||
web_main,
|
||||
):
|
||||
captured = []
|
||||
_install_router(
|
||||
monkeypatch,
|
||||
{
|
||||
"status": "ok",
|
||||
"action": "propose_analysis",
|
||||
"message": "已识别目标与参考物种。",
|
||||
"intent": {
|
||||
"gene_family": "SPL",
|
||||
"species": "At",
|
||||
"target_species": ["At"],
|
||||
"reference_species": [],
|
||||
"stages": ["identify"],
|
||||
"primary_stage": "identify",
|
||||
"params": {
|
||||
"targetSpecies": ["Ft"],
|
||||
"referenceSpecies": ["At"],
|
||||
"comparativeSpecies": [],
|
||||
"scopeMode": "target_plus_reference",
|
||||
},
|
||||
},
|
||||
"sources": [],
|
||||
"tool_trace": [],
|
||||
},
|
||||
captured,
|
||||
)
|
||||
|
||||
result = await web_main.agent_chat(
|
||||
web_main.AgentChatRequest(
|
||||
message=(
|
||||
"我想开展苦荞的SPL基因家族分析，"
|
||||
"Ft是目标物种，At是参考物种"
|
||||
),
|
||||
job_id="job-ft",
|
||||
)
|
||||
)
|
||||
|
||||
assert result["intent"]["target_species"] == ["Ft"]
|
||||
assert result["intent"]["reference_species"] == ["At"]
|
||||
assert result["intent"]["params"]["targetSpecies"] == ["Ft"]
|
||||
assert result["intent"]["params"]["referenceSpecies"] == ["At"]
|
||||
assert result["intent"]["prefix"] == "Ft.SPL"
|
||||
|
||||
|
||||
@pytest.mark.asyncio
|
||||
async def test_confirmed_config_species_roles_override_polluted_intent(
|
||||
monkeypatch,
|
||||
web_main,
|
||||
tmp_path,
|
||||
):
|
||||
import pandas as pd
|
||||
from gfa_core.mas import confirmation_snapshot
|
||||
|
||||
input_root = tmp_path / "input"
|
||||
job_dir = input_root / "job-ft"
|
||||
job_dir.mkdir(parents=True)
|
||||
pd.DataFrame(
|
||||
[
|
||||
{"Species_Code": "Ft", "Species_Role": "target", "Ref": False},
|
||||
{"Species_Code": "At", "Species_Role": "reference", "Ref": True},
|
||||
]
|
||||
).to_excel(job_dir / "config.xlsx", index=False)
|
||||
monkeypatch.setattr(web_main, "INPUT_ROOT", input_root)
|
||||
monkeypatch.setattr(
|
||||
confirmation_snapshot,
|
||||
"build_confirmation_snapshot",
|
||||
lambda *_args, **_kwargs: {
|
||||
"config_confirmed": True,
|
||||
"samples_confirmed": False,
|
||||
"subfamily_confirmed": False,
|
||||
"config": {"artifact_path": str(job_dir / "config.xlsx")},
|
||||
"samples": None,
|
||||
"subfamily": None,
|
||||
"errors": (),
|
||||
},
|
||||
)
|
||||
captured = []
|
||||
_install_router(
|
||||
monkeypatch,
|
||||
{
|
||||
"status": "ok",
|
||||
"action": "propose_analysis",
|
||||
"message": "已识别目标与参考物种。",
|
||||
"intent": {
|
||||
"gene_family": "SPL",
|
||||
"species": "unknown",
|
||||
"target_species": [],
|
||||
"reference_species": ["Ft", "At"],
|
||||
"stages": ["identify"],
|
||||
"primary_stage": "identify",
|
||||
"params": {
|
||||
"targetSpecies": [],
|
||||
"referenceSpecies": ["Ft", "At"],
|
||||
"scopeMode": "target_plus_reference",
|
||||
},
|
||||
},
|
||||
"sources": [],
|
||||
"tool_trace": [],
|
||||
},
|
||||
captured,
|
||||
)
|
||||
|
||||
result = await web_main.agent_chat(
|
||||
web_main.AgentChatRequest(
|
||||
message=(
|
||||
"苦荞数据在 /data/ref_data/Tartary_genome，"
|
||||
"拟南芥数据在 /data/ref_data/ath"
|
||||
),
|
||||
job_id="job-ft",
|
||||
)
|
||||
)
|
||||
|
||||
assert result["intent"]["target_species"] == ["Ft"]
|
||||
assert result["intent"]["reference_species"] == ["At"]
|
||||
assert result["intent"]["params"]["targetSpecies"] == ["Ft"]
|
||||
assert result["intent"]["params"]["referenceSpecies"] == ["At"]
|
||||
assert result["intent"]["prefix"] == "Ft.SPL"
|
||||
|
||||
|
||||
@pytest.mark.asyncio
|
||||
async def test_explicit_species_role_conflict_returns_actionable_clarification(
|
||||
monkeypatch,
|
||||
web_main,
|
||||
tmp_path,
|
||||
):
|
||||
import pandas as pd
|
||||
from gfa_core.mas import confirmation_snapshot
|
||||
|
||||
input_root = tmp_path / "input"
|
||||
job_dir = input_root / "job-os"
|
||||
job_dir.mkdir(parents=True)
|
||||
pd.DataFrame(
|
||||
[
|
||||
{"Species_Code": "Os", "Species_Role": "target", "Ref": False},
|
||||
{"Species_Code": "At", "Species_Role": "reference", "Ref": True},
|
||||
]
|
||||
).to_excel(job_dir / "config.xlsx", index=False)
|
||||
monkeypatch.setattr(web_main, "INPUT_ROOT", input_root)
|
||||
monkeypatch.setattr(
|
||||
confirmation_snapshot,
|
||||
"build_confirmation_snapshot",
|
||||
lambda *_args, **_kwargs: {
|
||||
"config_confirmed": True,
|
||||
"samples_confirmed": False,
|
||||
"subfamily_confirmed": False,
|
||||
"config": {"artifact_path": str(job_dir / "config.xlsx")},
|
||||
"samples": None,
|
||||
"subfamily": None,
|
||||
"errors": (),
|
||||
},
|
||||
)
|
||||
captured = []
|
||||
_install_router(
|
||||
monkeypatch,
|
||||
{
|
||||
"status": "ok",
|
||||
"action": "propose_analysis",
|
||||
"message": "已识别分析需求。",
|
||||
"intent": {
|
||||
"gene_family": "PEBP",
|
||||
"target_species": ["At"],
|
||||
"reference_species": ["Os"],
|
||||
"stages": ["identify"],
|
||||
"primary_stage": "identify",
|
||||
"params": {
|
||||
"targetSpecies": ["At"],
|
||||
"referenceSpecies": ["Os"],
|
||||
},
|
||||
},
|
||||
"sources": [],
|
||||
"tool_trace": [],
|
||||
},
|
||||
captured,
|
||||
)
|
||||
|
||||
result = await web_main.agent_chat(
|
||||
web_main.AgentChatRequest(
|
||||
message="At是目标物种，Os是参考物种，请执行PEBP基因家族分析",
|
||||
job_id="job-os",
|
||||
)
|
||||
)
|
||||
|
||||
assert result["action"] == "clarify"
|
||||
assert result["intent"]["taskType"] == "clarification"
|
||||
assert "At" in result["intent"]["message"]
|
||||
assert "Os" in result["intent"]["message"]
|
||||
assert "打开 config.xlsx" in result["intent"]["message"]
|
||||
assert result["intent"]["stages"] == []
|
||||
|
||||
|
||||
@pytest.mark.asyncio
|
||||
@pytest.mark.parametrize(
|
||||
"candidate",
|
||||
[
|
||||
None,
|
||||
{},
|
||||
[],
|
||||
"not-an-intent",
|
||||
{"foo": "bar"},
|
||||
{"stages": []},
|
||||
{"stages": [""]},
|
||||
{"stages": "motif"},
|
||||
],
|
||||
)
|
||||
async def test_propose_analysis_without_verified_intent_fails_closed(
|
||||
monkeypatch, web_main, candidate
|
||||
):
|
||||
captured = []
|
||||
_install_router(
|
||||
monkeypatch,
|
||||
{
|
||||
"status": "ok",
|
||||
"action": "propose_analysis",
|
||||
"message": "分析建议",
|
||||
"intent": candidate,
|
||||
"sources": [],
|
||||
"tool_trace": [],
|
||||
},
|
||||
captured,
|
||||
)
|
||||
|
||||
result = await web_main.agent_chat(
|
||||
web_main.AgentChatRequest(message="继续分析", job_id="job-7")
|
||||
)
|
||||
|
||||
assert result["success"] is False
|
||||
assert result["status"] == "invalid_response"
|
||||
assert result["action"] is None
|
||||
assert result["intent"] is None
|
||||
|
||||
|
||||
@pytest.mark.asyncio
|
||||
@pytest.mark.parametrize("query", ["那两个", "继续后面的", "刚才的结果"])
|
||||
async def test_coreference_journeys_reach_router_with_prior_history(
|
||||
monkeypatch, web_main, query
|
||||
):
|
||||
captured = []
|
||||
_install_router(
|
||||
monkeypatch,
|
||||
{
|
||||
"status": "ok",
|
||||
"action": "clarify",
|
||||
"message": "请确认你指的是哪一项。",
|
||||
"intent": None,
|
||||
"sources": [],
|
||||
"tool_trace": [],
|
||||
},
|
||||
captured,
|
||||
)
|
||||
history = [
|
||||
{"role": "user", "content": "比较 motif 和 domain"},
|
||||
{"role": "assistant", "content": "我找到了两个结果。"},
|
||||
]
|
||||
|
||||
result = await web_main.agent_chat(
|
||||
web_main.AgentChatRequest(message=query, history=history, job_id="job-7")
|
||||
)
|
||||
|
||||
assert captured[0]["query"] == query
|
||||
assert captured[0]["history"] == history
|
||||
assert result["action"] == "clarify"
|
||||
|
||||
|
||||
@pytest.mark.asyncio
|
||||
async def test_agent_chat_uses_persisted_history_and_goal_ledger(
|
||||
monkeypatch,
|
||||
web_main,
|
||||
tmp_path,
|
||||
):
|
||||
repository = SQLiteAgentStateRepository(tmp_path / "agent-state.sqlite3")
|
||||
repository.initialize()
|
||||
store = PersistentConversationStore(repository)
|
||||
monkeypatch.setattr(web_main, "agent_conversation_store", store, raising=False)
|
||||
captured = []
|
||||
_install_router(
|
||||
monkeypatch,
|
||||
{
|
||||
"status": "ok",
|
||||
"action": "propose_analysis",
|
||||
"message": "已记录初始目标。",
|
||||
"intent": {"stages": ["motif"], "stage": "motif"},
|
||||
"sources": [],
|
||||
"tool_trace": [],
|
||||
"interaction_kind": "independent",
|
||||
},
|
||||
captured,
|
||||
)
|
||||
first = await web_main.agent_chat(
|
||||
web_main.AgentChatRequest(
|
||||
message="进行 motif 分析",
|
||||
session_id="legacy-session",
|
||||
job_id="job-ft",
|
||||
)
|
||||
)
|
||||
_install_router(
|
||||
monkeypatch,
|
||||
{
|
||||
"status": "ok",
|
||||
"action": "propose_analysis",
|
||||
"message": "已按修正后的目标处理。",
|
||||
"intent": {"stages": ["domain"], "stage": "domain"},
|
||||
"sources": [],
|
||||
"tool_trace": [],
|
||||
"interaction_kind": "correction",
|
||||
},
|
||||
captured,
|
||||
)
|
||||
|
||||
second = await web_main.agent_chat(
|
||||
web_main.AgentChatRequest(
|
||||
message="不是 motif，改成 domain",
|
||||
session_id=first["session_id"],
|
||||
job_id="",
|
||||
history=[{"role": "user", "content": "客户端伪造历史"}],
|
||||
)
|
||||
)
|
||||
|
||||
assert captured[1]["job_id"] == "job-ft"
|
||||
assert captured[1]["history"] == [
|
||||
{"role": "user", "content": "进行 motif 分析"},
|
||||
{"role": "assistant", "content": "已记录初始目标。"},
|
||||
]
|
||||
assert captured[1]["goal_ledger"].active_goal == "进行 motif 分析"
|
||||
ledger = repository.get_goal_ledger(second["session_id"])
|
||||
assert ledger is not None
|
||||
assert ledger.active_goal == "不是 motif，改成 domain"
|
||||
assert ledger.corrections == ("不是 motif，改成 domain",)
|
||||
assert [item.content for item in repository.list_messages(second["session_id"])] == [
|
||||
"进行 motif 分析",
|
||||
"已记录初始目标。",
|
||||
"不是 motif，改成 domain",
|
||||
"已按修正后的目标处理。",
|
||||
]
|
||||
|
||||
|
||||
@pytest.mark.asyncio
|
||||
async def test_deterministic_utility_turn_uses_same_persistent_conversation(
|
||||
monkeypatch,
|
||||
web_main,
|
||||
tmp_path,
|
||||
):
|
||||
repository = SQLiteAgentStateRepository(tmp_path / "agent-state.sqlite3")
|
||||
repository.initialize()
|
||||
store = PersistentConversationStore(repository)
|
||||
monkeypatch.setattr(web_main, "agent_conversation_store", store, raising=False)
|
||||
monkeypatch.setattr(
|
||||
web_main.extension_stage_agent,
|
||||
"list_extensions",
|
||||
lambda include_drafts=False: [],
|
||||
)
|
||||
message = "请从 proteins.fa 按 ids.txt 提取蛋白序列"
|
||||
|
||||
result = await web_main.agent_chat(
|
||||
web_main.AgentChatRequest(
|
||||
message=message,
|
||||
session_id="browser-session",
|
||||
job_id="job-ft",
|
||||
)
|
||||
)
|
||||
|
||||
assert result["action"] == "propose_utility"
|
||||
assert result["status"] == "ok"
|
||||
assert [item.content for item in repository.list_messages(result["session_id"])] == [
|
||||
message,
|
||||
result["intent"]["message"],
|
||||
]
|
||||
ledger = repository.get_goal_ledger(result["session_id"])
|
||||
assert ledger is not None
|
||||
assert ledger.active_goal == message
|
||||
@@ -0,0 +1,32 @@
|
||||
from gfa_core.mas.utils.intent_parser import (
|
||||
parse_explicit_species_role_mentions,
|
||||
parse_gene_family_scope_selection,
|
||||
)
|
||||
|
||||
|
||||
def test_ref_data_path_does_not_assign_species_roles() -> None:
|
||||
query = (
|
||||
"苦荞基因组数据在 "
|
||||
"/home/xia-lab/wutx_old/wutx/plantAnalysisAgent/ref_data/Tartary_genome，"
|
||||
"拟南芥基因组数据在 "
|
||||
"/home/xia-lab/wutx_old/wutx/plantAnalysisAgent/ref_data/ath，"
|
||||
"Ft是目标物种，At是参考物种"
|
||||
)
|
||||
|
||||
scope = parse_gene_family_scope_selection(query)
|
||||
|
||||
assert scope["targetSpecies"] == ["Ft"]
|
||||
assert scope["referenceSpecies"] == ["At"]
|
||||
|
||||
|
||||
def test_explicit_role_parser_keeps_unassigned_mentions_separate() -> None:
|
||||
roles = parse_explicit_species_role_mentions(
|
||||
"Os和At的数据已经准备好；Os是目标物种，At是参考物种，Ppy稍后再分析"
|
||||
)
|
||||
|
||||
assert roles == {
|
||||
"targetSpecies": ["Os"],
|
||||
"referenceSpecies": ["At"],
|
||||
"comparativeSpecies": [],
|
||||
"unassigned": ["Ppy"],
|
||||
}
|
||||
@@ -3,6 +3,8 @@ import json
|
||||
from pathlib import Path
|
||||
from types import SimpleNamespace
|
||||
|
||||
import pytest
|
||||
|
||||
from gfa_core.gene_family_stage_context import (
|
||||
enrich_stage_params_with_context,
|
||||
infer_analysis_route,
|
||||
@@ -330,3 +332,177 @@ def test_direct_stage_preserves_species_roles_from_intent_when_selector_is_empty
|
||||
assert details["phylogeny"]["params"]["analysisRoute"] == "subfamily_evidence"
|
||||
assert details["motif"]["params"]["analysisRoute"] == "subfamily_evidence"
|
||||
assert details["phylogeny"]["params"]["memberSetId"] == details["motif"]["params"]["memberSetId"]
|
||||
|
||||
|
||||
def test_contextual_handoff_uses_confirmed_config_roles_when_selector_is_empty(monkeypatch):
|
||||
main = _load_vue3_main()
|
||||
monkeypatch.setattr(main, "_load_identify_species_selection", lambda _job_id: {})
|
||||
monkeypatch.setattr(
|
||||
main,
|
||||
"_confirmed_config_species_scope",
|
||||
lambda _job_id: {
|
||||
"targetSpecies": ["Os"],
|
||||
"referenceSpecies": ["At"],
|
||||
"comparativeSpecies": [],
|
||||
},
|
||||
)
|
||||
monkeypatch.setattr(main, "_gene_family_from_config", lambda _path: "PEBP")
|
||||
monkeypatch.setattr(main, "_confirmed_subfamily_species", lambda _job_id, _family: [])
|
||||
monkeypatch.setattr(
|
||||
main,
|
||||
"_extract_species_codes_from_text_for_job",
|
||||
lambda _job_id, _text: ["Os", "At"],
|
||||
)
|
||||
monkeypatch.setattr(
|
||||
main,
|
||||
"_subfamily_state_for_targets",
|
||||
lambda _job_id, species, _family: {
|
||||
"all_confirmed": species == ["Os"],
|
||||
"by_species": {"Os": {"status": "confirmed"}},
|
||||
"issues": [],
|
||||
},
|
||||
)
|
||||
monkeypatch.setattr(
|
||||
main,
|
||||
"_validate_gene_family_stage_context",
|
||||
lambda **_kwargs: {"valid": True, "issues": [], "evidence": {}},
|
||||
)
|
||||
|
||||
contextual = main._resolve_contextual_gene_family_request(
|
||||
"job-real",
|
||||
(
|
||||
"执行水稻PEBP基因家族分析。基因家族 PEBP；"
|
||||
"目标物种 Os；参考物种 At；亚家族分类已经确认。"
|
||||
),
|
||||
"Os.PEBP",
|
||||
requested_stages=["phylogeny", "motif", "domain", "structure", "combo"],
|
||||
request_intent={
|
||||
"gene_family": "PEBP",
|
||||
"target_species": ["Os"],
|
||||
"reference_species": ["At"],
|
||||
"params": {
|
||||
"targetSpecies": ["Os"],
|
||||
"referenceSpecies": ["At"],
|
||||
},
|
||||
},
|
||||
)
|
||||
|
||||
assert contextual["targetSpecies"] == ["Os"]
|
||||
assert contextual["referenceSpecies"] == ["At"]
|
||||
assert contextual["prefix"] == "Os.PEBP"
|
||||
assert contextual["context_route"] == "post_subfamily_gene_family_analysis"
|
||||
|
||||
|
||||
def test_confirmed_multi_species_roles_remain_separate(monkeypatch):
|
||||
main = _load_vue3_main()
|
||||
monkeypatch.setattr(
|
||||
main,
|
||||
"_confirmed_config_species_scope",
|
||||
lambda _job_id: {
|
||||
"targetSpecies": ["Ft"],
|
||||
"referenceSpecies": ["At"],
|
||||
"comparativeSpecies": ["Ppy"],
|
||||
},
|
||||
)
|
||||
|
||||
resolved = main._reconcile_confirmed_gene_family_species(
|
||||
"job-multi",
|
||||
"Ft是目标物种，Ppy是比较物种，At是参考物种，执行联合亚家族分类",
|
||||
{
|
||||
"gene_family": "SPL",
|
||||
"target_species": ["Ft", "Ppy"],
|
||||
"reference_species": ["At"],
|
||||
"params": {
|
||||
"targetSpecies": ["Ft", "Ppy"],
|
||||
"referenceSpecies": ["At"],
|
||||
},
|
||||
},
|
||||
)
|
||||
|
||||
assert resolved["conflicts"] == []
|
||||
assert resolved["target_species"] == ["Ft"]
|
||||
assert resolved["comparative_species"] == ["Ppy"]
|
||||
assert resolved["reference_species"] == ["At"]
|
||||
assert resolved["classification_species"] == ["Ft", "Ppy"]
|
||||
|
||||
|
||||
def test_confirmed_config_duplicate_roles_are_blocked(monkeypatch):
|
||||
main = _load_vue3_main()
|
||||
monkeypatch.setattr(
|
||||
main,
|
||||
"_confirmed_config_species_scope",
|
||||
lambda _job_id: {
|
||||
"targetSpecies": ["Ft"],
|
||||
"referenceSpecies": ["Ft", "At"],
|
||||
"comparativeSpecies": [],
|
||||
},
|
||||
)
|
||||
|
||||
resolved = main._reconcile_confirmed_gene_family_species(
|
||||
"job-invalid-config",
|
||||
"执行SPL基因家族分析",
|
||||
{"gene_family": "SPL", "stages": ["identify"]},
|
||||
)
|
||||
|
||||
assert any(
|
||||
conflict["code"] == "config_species_role_conflict"
|
||||
and conflict["species"] == "Ft"
|
||||
for conflict in resolved["conflicts"]
|
||||
)
|
||||
assert "打开 config.xlsx" in main._species_role_conflict_message(resolved["conflicts"])
|
||||
|
||||
|
||||
@pytest.mark.asyncio
|
||||
async def test_plan_api_blocks_confirmed_config_role_conflict(monkeypatch, tmp_path):
|
||||
import pandas as pd
|
||||
from gfa_core.mas import confirmation_snapshot
|
||||
|
||||
main = _load_vue3_main()
|
||||
input_root = tmp_path / "input"
|
||||
job_dir = input_root / "job-os"
|
||||
job_dir.mkdir(parents=True)
|
||||
pd.DataFrame(
|
||||
[
|
||||
{"Species_Code": "Os", "Species_Role": "target", "Ref": False},
|
||||
{"Species_Code": "At", "Species_Role": "reference", "Ref": True},
|
||||
]
|
||||
).to_excel(job_dir / "config.xlsx", index=False)
|
||||
monkeypatch.setattr(main, "INPUT_ROOT", input_root)
|
||||
monkeypatch.setattr(
|
||||
confirmation_snapshot,
|
||||
"build_confirmation_snapshot",
|
||||
lambda *_args, **_kwargs: {
|
||||
"config_confirmed": True,
|
||||
"samples_confirmed": False,
|
||||
"subfamily_confirmed": False,
|
||||
"config": {"artifact_path": str(job_dir / "config.xlsx")},
|
||||
"samples": None,
|
||||
"subfamily": None,
|
||||
"errors": (),
|
||||
},
|
||||
)
|
||||
|
||||
result = await main.agent_plan(
|
||||
main.AgentPlanRequest(
|
||||
message="At是目标物种，Os是参考物种，请执行PEBP基因家族分析",
|
||||
session_id="role-conflict",
|
||||
job_id="job-os",
|
||||
prefix="Os.PEBP",
|
||||
intent={
|
||||
"gene_family": "PEBP",
|
||||
"stages": ["identify"],
|
||||
"target_species": ["At"],
|
||||
"reference_species": ["Os"],
|
||||
"params": {
|
||||
"geneFamily": "PEBP",
|
||||
"targetSpecies": ["At"],
|
||||
"referenceSpecies": ["Os"],
|
||||
},
|
||||
},
|
||||
)
|
||||
)
|
||||
|
||||
assert result["success"] is False
|
||||
assert result["status"] == "species_role_conflict"
|
||||
assert "打开 config.xlsx" in result["message"]
|
||||
assert "plan" not in result
|
||||
|
||||
Reference in New Issue
Block a user