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fix: preserve species roles through confirmation

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This commit is contained in:
potaser
2026-08-07 08:57:22 +08:00
parent 8c3d601072
commit 822baab367
4 changed files with 201 additions and 21 deletions
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gfa_core/mas/agents/intent_v2.py
+66 -10
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@@ -12,7 +12,13 @@ from gfa_core.mas.stage_catalog import (
STAGE_INFO as CATALOG_STAGE_INFO,
complete_dependencies as catalog_complete_dependencies,
)
from gfa_core.mas.utils.intent_parser import is_gwas_fmt_intent, parse_gene_family, resolve_gwas_intent, resolve_population_intent
from gfa_core.mas.utils.intent_parser import (
is_gwas_fmt_intent,
parse_gene_family,
parse_gene_family_scope_selection,
resolve_gwas_intent,
resolve_population_intent,
)
class IntentAgentV2(BaseAgent):
@@ -696,18 +702,68 @@ class IntentAgentV2(BaseAgent):
print(f"[IntentAgentV2] Stages expanded: {original_stages} -> {intent_data['stages']}")
query_lower = query.lower()
species_codes = re.findall(r"(?<![A-Za-z0-9])(?:Ft|At|Os|Sl|Zm|Gm|Br|Vv|Pt|Sb|Lc|Dl|Py|Cp|Lg)(?![A-Za-z0-9])", query, flags=re.IGNORECASE)
species_map = {code.lower(): code for code in ["Ft", "At", "Os", "Sl", "Zm", "Gm", "Br", "Vv", "Pt", "Sb", "Lc", "Dl", "Py", "Cp", "Lg"]}
target_species = []
for item in species_codes:
sp = species_map.get(item.lower())
if sp and sp not in target_species:
target_species.append(sp)
selection = parse_gene_family_scope_selection(query)
params = intent_data.setdefault("params", {})
def as_species_list(value: Any) -> List[str]:
if isinstance(value, str):
values = [item.strip() for item in value.split(",")]
elif isinstance(value, (list, tuple, set)):
values = [str(item).strip() for item in value]
else:
values = []
return list(dict.fromkeys(item for item in values if item))
target_species = as_species_list(selection.get("targetSpecies"))
reference_species = as_species_list(selection.get("referenceSpecies"))
comparative_species = as_species_list(selection.get("comparativeSpecies"))
has_query_scope = bool(target_species or reference_species or comparative_species)
prefix_species = provided_prefix.split(".", 1)[0].strip() if provided_prefix and "." in provided_prefix else ""
if not target_species and prefix_species:
target_species = [prefix_species]
if not target_species:
target_species = as_species_list(params.get("targetSpecies") or intent_data.get("target_species"))
if not reference_species:
reference_species = as_species_list(params.get("referenceSpecies") or intent_data.get("reference_species"))
if not comparative_species:
comparative_species = as_species_list(params.get("comparativeSpecies") or intent_data.get("comparative_species"))
if not target_species and not has_query_scope:
llm_species = str(intent_data.get("species") or "").strip()
if llm_species and llm_species != "Multi":
target_species = [llm_species]
reference_species = [sp for sp in reference_species if sp not in target_species]
comparative_species = [
sp for sp in comparative_species
if sp not in target_species and sp not in reference_species
]
scope_mode = (
"target_plus_reference_plus_comparative"
if reference_species and comparative_species
else "target_plus_reference"
if reference_species
else "target_plus_comparative"
if comparative_species
else "target_only"
)
intent_data["target_species"] = target_species
intent_data["reference_species"] = reference_species
intent_data["comparative_species"] = comparative_species
intent_data["scopeMode"] = scope_mode
params.update({
"targetSpecies": target_species,
"referenceSpecies": reference_species,
"comparativeSpecies": comparative_species,
"scopeMode": scope_mode,
"target_species": target_species,
})
explicit_species = bool(target_species)
if target_species:
intent_data["target_species"] = target_species
intent_data.setdefault("params", {})["target_species"] = target_species
intent_data["species"] = target_species[0] if len(target_species) == 1 else "Multi"
elif has_query_scope:
intent_data["species"] = ""
generic_identify = (
"identify" in intent_data.get("stages", [])
and not provided_prefix