Merge origin/master before analysis handoff push

apps/cli/run_subfamily_confirm.py

@@ -118,7 +118,7 @@ def _atomic_promote_pair(curated_id: Path, curated_pep: Path, final_id: Path, fi
     tmp_pep.write_text(curated_pep.read_text(encoding="utf-8", errors="ignore"), encoding="utf-8")
     tmp_ids = _read_id_list(tmp_id)
     tmp_fasta_ids = _read_fasta_ids(tmp_pep)
-    if tmp_ids != tmp_fasta_ids:
+    if sorted(tmp_ids) != sorted(tmp_fasta_ids):
         tmp_id.unlink(missing_ok=True)
         tmp_pep.unlink(missing_ok=True)
         raise RuntimeError(f"Temporary final member validation failed for {final_id.stem}")
@@ -160,7 +160,7 @@ def _promote_curated_members_to_final(final_dir: Path, prefixes: Iterable[str],
         if not curated_ids:
             raise ValueError(f"Curated member ID file is empty: {curated_id}")
         fasta_ids = _read_fasta_ids(curated_pep)
-        if curated_ids != fasta_ids:
+        if sorted(curated_ids) != sorted(fasta_ids):
             raise ValueError(
                 f"Curated member ID/FASTA mismatch for {member_prefix}: "
                 f"{len(curated_ids)} IDs vs {len(fasta_ids)} FASTA records"
@@ -179,7 +179,7 @@ def _promote_curated_members_to_final(final_dir: Path, prefixes: Iterable[str],
 
         promoted_ids = _read_id_list(final_id)
         promoted_fasta_ids = _read_fasta_ids(final_pep)
-        if promoted_ids != curated_ids or promoted_fasta_ids != curated_ids:
+        if sorted(promoted_ids) != sorted(curated_ids) or sorted(promoted_fasta_ids) != sorted(curated_ids):
             raise RuntimeError(f"Post-promotion final member validation failed for {member_prefix}")
         promotions.append({
             "prefix": member_prefix,

apps/web/vue3/main.py

@@ -777,18 +777,12 @@ def _reconcile_confirmed_gene_family_species(
         job_id,
         _param_list(routed_params.get("comparativeSpecies") or routed_intent.get("comparative_species")),
     )
-    explicit_reference_set = set(explicit["referenceSpecies"])
-    explicit_assigned_set = set(
-        explicit["targetSpecies"]
-        + explicit["referenceSpecies"]
-        + explicit["comparativeSpecies"]
-    )
+    explicit_unassigned_set = set(explicit["unassigned"])
     for species in structured_targets:
         config_role = config_role_by_species.get(species)
         if (
             config_role in {None, "reference"}
-            and species not in explicit_reference_set
-            and species not in explicit_assigned_set
+            and species in explicit_unassigned_set
         ):
             conflicts.append({
                 "code": "analysis_target_config_role_conflict",
@@ -865,10 +859,24 @@ def _species_role_conflict_message(conflicts: list[Dict[str, str]]) -> str:
         config_role = role_labels.get(conflict.get("config_role") or "", conflict.get("config_role") or "未知")
         requested_role = role_labels.get(conflict.get("requested_role") or "", conflict.get("requested_role") or "配置内部重复角色")
         details.append(f"{species}：config.xlsx 为{config_role}，本轮为{requested_role}")
+    conflict_codes = {str(conflict.get("code") or "") for conflict in conflicts}
+    detail_text = "；".join(details)
+    if "config_species_role_conflict" in conflict_codes:
+        return (
+            "检测到 config.xlsx 内部物种角色冲突："
+            + detail_text
+            + "。请发送“打开 config.xlsx”，修正并重新确认物种角色后再继续。"
+        )
+    if "analysis_target_config_role_conflict" in conflict_codes:
+        return (
+            "检测到系统意图解析发生角色漂移："
+            + detail_text
+            + "。config.xlsx 未被修改，系统已阻止按错误范围执行，请重新提交当前分析请求。"
+        )
     return (
-        "检测到物种角色不一致："
-        + "；".join(details)
-        + "。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。"
+        "检测到本轮请求与项目物种角色不一致："
+        + detail_text
+        + "。系统已阻止执行，请按 config.xlsx 中已确认的角色重新描述分析范围。"
     )