mirror of
https://github.com/deepmodeling/Uni-Lab-OS
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feat: RNA add guided manual unload end_experiment action
- Add end_experiment manual_confirm action mirroring start_experiment, with three boolean operator gates and twelve EXECUTOR sibling-array output handles for unloaded material manifests.
- Add helpers _build_unload_materials_by_type, _classify_labware_mode, _iter_reagent_liquids, and _clear_unloaded_materials.
- Clear unloaded slots and zero reagent liquid contents on confirmation while preserving trough labware; publish single resource tree update after mutations.
- Wrap action body in _debug_call_session("end_experiment") for opt-in raw call capture.
This commit is contained in:
yxz321
@@ -755,6 +755,157 @@ class BioyondSirnaStation(BioyondWorkstation):
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"confirmation_message": "调度器启动成功" if result == 1 else "调度器启动失败，请检查 LIMS 状态",
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})
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@action(
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always_free=True,
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node_type=NodeType.MANUAL_CONFIRM,
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placeholder_keys={"assignee_user_ids": "unilabos_manual_confirm"},
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goal_default={
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"order_id": "",
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"samples_unloaded": False,
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"consumables_unloaded": False,
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"reagents_unloaded": False,
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"timeout_seconds": 3600,
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"assignee_user_ids": [],
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},
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feedback_interval=300,
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description=(
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"请按当前 deck 状态卸载实验物料；勾选三类卸载确认后才会清空资源树。"
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" 若上游 reagent-as-liquid 同步未启用，试剂列可能为空，仅展示 labware。"
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),
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handles=[
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ActionOutputHandle(
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key="unload_samples_name", data_type="array",
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label="样本-物料名称", data_key="unload_tables.Sample.material_name",
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data_source=DataSource.EXECUTOR,
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),
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ActionOutputHandle(
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key="unload_samples_code", data_type="array",
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label="样本-物料编号", data_key="unload_tables.Sample.material_code",
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data_source=DataSource.EXECUTOR,
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),
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ActionOutputHandle(
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key="unload_samples_location", data_type="array",
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label="样本-库位", data_key="unload_tables.Sample.location",
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data_source=DataSource.EXECUTOR,
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),
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ActionOutputHandle(
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key="unload_samples_quantity", data_type="array",
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label="样本-数量", data_key="unload_tables.Sample.quantity",
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data_source=DataSource.EXECUTOR,
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),
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ActionOutputHandle(
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key="unload_consumables_name", data_type="array",
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label="耗材-物料名称", data_key="unload_tables.Consumables.material_name",
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data_source=DataSource.EXECUTOR,
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),
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ActionOutputHandle(
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key="unload_consumables_code", data_type="array",
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label="耗材-物料编号", data_key="unload_tables.Consumables.material_code",
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data_source=DataSource.EXECUTOR,
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),
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ActionOutputHandle(
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key="unload_consumables_location", data_type="array",
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label="耗材-库位", data_key="unload_tables.Consumables.location",
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data_source=DataSource.EXECUTOR,
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),
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ActionOutputHandle(
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key="unload_consumables_quantity", data_type="array",
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label="耗材-数量", data_key="unload_tables.Consumables.quantity",
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data_source=DataSource.EXECUTOR,
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),
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ActionOutputHandle(
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key="unload_reagents_name", data_type="array",
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label="试剂-物料名称", data_key="unload_tables.Reagent.material_name",
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data_source=DataSource.EXECUTOR,
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),
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ActionOutputHandle(
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key="unload_reagents_code", data_type="array",
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label="试剂-物料编号", data_key="unload_tables.Reagent.material_code",
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data_source=DataSource.EXECUTOR,
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),
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ActionOutputHandle(
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key="unload_reagents_location", data_type="array",
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label="试剂-库位", data_key="unload_tables.Reagent.location",
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data_source=DataSource.EXECUTOR,
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),
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ActionOutputHandle(
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key="unload_reagents_quantity", data_type="array",
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label="试剂-数量", data_key="unload_tables.Reagent.quantity",
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data_source=DataSource.EXECUTOR,
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),
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],
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)
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def end_experiment(
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self,
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order_id: str = "",
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samples_unloaded: bool = False,
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consumables_unloaded: bool = False,
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reagents_unloaded: bool = False,
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timeout_seconds: int = 3600,
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assignee_user_ids: Optional[List[str]] = None,
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**kwargs: Any,
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) -> Dict[str, Any]:
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"""Guided manual-unload checkpoint that clears the deck after confirmation.
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Mirrors :meth:`start_experiment` in shape: three boolean gates default
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to ``False``, three sibling-array display tables (Sample / Consumables
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/ Reagent × material_name / material_code / location / quantity)
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populated from current deck state, and a raise-on-missing-gate path.
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Args:
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order_id: 可选；只展示 ``unilabos_extra["order_id"]`` 等于该值的物料。
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未指定则覆盖整个 deck。
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samples_unloaded: 操作员勾选确认 ``Sample`` 类已卸载。
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consumables_unloaded: 操作员勾选确认 ``Consumables`` 类已卸载。
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reagents_unloaded: 操作员勾选确认 ``Reagent`` 类已卸载（含 trough 试剂内容）。
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timeout_seconds: 框架超时时间（秒）。
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assignee_user_ids: 框架分配用户列表。
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"""
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with self._debug_call_session("end_experiment"):
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del timeout_seconds, assignee_user_ids, kwargs
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order_filter = order_id.strip() if isinstance(order_id, str) else ""
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manifest = self._build_unload_materials_by_type(
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order_id_filter=order_filter or None,
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)
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unload_tables = self._build_manual_load_tables(manifest)
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category_specs = [
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("Sample", self._as_manual_gate(samples_unloaded), "样本", "samples_unloaded"),
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("Consumables", self._as_manual_gate(consumables_unloaded), "耗材", "consumables_unloaded"),
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("Reagent", self._as_manual_gate(reagents_unloaded), "试剂", "reagents_unloaded"),
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]
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gates: Dict[str, Dict[str, Any]] = {}
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missing_labels: List[str] = []
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for mode_key, ticked, label, gate_key in category_specs:
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required = bool(manifest.get(mode_key))
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gates[gate_key] = {"label": label, "required": required, "ticked": bool(ticked)}
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if required and not ticked:
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missing_labels.append(label)
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if missing_labels:
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raise RuntimeError(
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f"以下分类卸载尚未确认，无法清空资源树: {', '.join(missing_labels)}"
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)
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cleared = self._clear_unloaded_materials(manifest)
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# Refresh the table snapshot so consumers see the post-mutation state.
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post_manifest = self._build_unload_materials_by_type(
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order_id_filter=order_filter or None,
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)
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return {
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"success": True,
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"order_id": order_filter,
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"unloaded": cleared,
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"gates": gates,
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"unload_tables": unload_tables,
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"post_unload_tables": self._build_manual_load_tables(post_manifest),
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"confirmation_message": (
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"deck 已按操作员确认清空" if any(cleared.values()) else "deck 当前为空，无需卸载"
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),
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}
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@action(
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always_free=True,
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node_type=NodeType.MANUAL_CONFIRM,
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@@ -1747,6 +1898,261 @@ class BioyondSirnaStation(BioyondWorkstation):
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"machine_name": "",
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}
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def _classify_labware_mode(self, child: Any) -> str:
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"""Map a placed labware to ``Sample`` / ``Consumables`` / ``Reagent``.
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Resolution order:
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1. ``unilabos_extra["material_bioyond_type_mode"]`` if previously set
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by the load path (``_register_materials_to_tree``) — most reliable.
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2. PLR class identity: troughs map to ``Reagent``; tip racks map to
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``Consumables``; everything else (plates, tubes, etc.) defaults
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to ``Sample``.
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The classifier is intentionally permissive: an unrecognized class
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falls back to ``Sample`` so the operator still sees the row instead
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of the unload silently dropping it.
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"""
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extra = getattr(child, "unilabos_extra", None) or {}
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if isinstance(extra, dict):
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mode = str(extra.get("material_bioyond_type_mode") or "")
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if mode in {"Sample", "Consumables", "Reagent"}:
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return mode
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try:
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from unilabos.resources.bioyond.sirna_materials import (
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BioyondSirna_ReagentTrough,
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)
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except Exception: # pragma: no cover - lightweight env
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BioyondSirna_ReagentTrough = None # type: ignore[assignment]
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if BioyondSirna_ReagentTrough is not None and isinstance(child, BioyondSirna_ReagentTrough):
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return "Reagent"
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category_attr = getattr(child, "category", "") or ""
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category = str(category_attr).lower()
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if "tip" in category:
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return "Consumables"
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if "trough" in category or "reagent" in category:
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return "Reagent"
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# Class-name heuristic for environments without category metadata.
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cls_name = type(child).__name__.lower()
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if "tip" in cls_name:
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return "Consumables"
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if "trough" in cls_name or "reagent" in cls_name:
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return "Reagent"
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return "Sample"
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def _iter_reagent_liquids(self, parent: Any) -> Iterable[Dict[str, Any]]:
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"""Yield reagent-content rows attached to ``parent`` via ``_attach_liquid_to_parent``.
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Cross-references ``parent.unilabos_extra["reagent_bioyond_ids"]`` (the
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structured Bioyond metadata source-of-truth) with ``parent.tracker.liquids``
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when present. Tolerates missing metadata so this helper is usable even
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on legacy decks that predate the reagent-as-liquid plan.
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"""
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extra = getattr(parent, "unilabos_extra", None) or {}
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reagent_ids: List[Any] = []
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if isinstance(extra, dict):
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reagent_ids = list(extra.get("reagent_bioyond_ids") or [])
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parent_name = getattr(parent, "name", "") or ""
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warehouse = getattr(parent, "parent", None)
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warehouse_name = getattr(warehouse, "name", "") or ""
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location_label = f"{warehouse_name}/{parent_name}" if warehouse_name else parent_name
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for entry in reagent_ids:
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if not isinstance(entry, dict):
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continue
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yield {
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"materialName": str(entry.get("material_bioyond_name") or ""),
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"materialCode": str(entry.get("material_bioyond_code") or ""),
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"materialTypeCode": str(entry.get("material_bioyond_type_code") or ""),
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"materialTypeMode": "Reagent",
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"locationCode": "",
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"locationShowName": location_label,
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"quantity": entry.get("quantity") or "",
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"trough": parent,
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"material_bioyond_id": str(entry.get("material_bioyond_id") or ""),
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}
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def _build_unload_materials_by_type(
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self,
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*,
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order_id_filter: Optional[str] = None,
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) -> Dict[str, List[Dict[str, Any]]]:
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"""Walk ``self.deck`` and emit a Bioyond-shaped material list grouped by mode.
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Output rows expose ``materialName / materialCode / locationCode /
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locationShowName / quantity / materialTypeMode`` keys, mirroring the
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fields :meth:`_build_manual_load_tables` consumes. No side effects.
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Args:
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order_id_filter: When provided, slot-bound labware whose
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``unilabos_extra["order_id"]`` does not equal this value is
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skipped. Reagent contents are not order-scoped.
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"""
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grouped: Dict[str, List[Dict[str, Any]]] = {
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"Sample": [],
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"Consumables": [],
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"Reagent": [],
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}
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deck = getattr(self, "deck", None)
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if deck is None:
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return grouped
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for warehouse in getattr(deck, "children", []) or []:
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ordering = getattr(warehouse, "_ordering", None)
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if not isinstance(ordering, dict):
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continue
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for slot_label in ordering.keys():
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try:
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child = warehouse[slot_label]
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except (KeyError, IndexError, TypeError):
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continue
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# Distinguish placed labware from unoccupied ResourceHolder
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# variants. Empty slots show as None on this carrier.
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if child is None:
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continue
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if not hasattr(child, "tracker") and not hasattr(child, "children"):
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continue
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# Plain ResourceHolder placeholders for empty sites are skipped.
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if type(child).__name__ == "ResourceHolder" and not list(getattr(child, "children", []) or []):
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continue
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extra = getattr(child, "unilabos_extra", None) or {}
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if not isinstance(extra, dict):
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extra = {}
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if order_id_filter and extra.get("order_id") and extra.get("order_id") != order_id_filter:
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continue
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mode = self._classify_labware_mode(child)
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row = {
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"materialName": str(extra.get("material_bioyond_name") or getattr(child, "name", "") or ""),
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"materialCode": str(extra.get("material_bioyond_code") or getattr(child, "name", "") or ""),
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"materialTypeCode": str(extra.get("material_bioyond_type_code") or ""),
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"materialTypeMode": mode,
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"locationCode": str(extra.get("location_code") or slot_label or ""),
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"locationShowName": f"{getattr(warehouse, 'name', '')}/{slot_label}",
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"quantity": getattr(child, "quantity", 1),
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"_warehouse": warehouse,
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"_slot_label": str(slot_label),
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"_child": child,
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}
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grouped.setdefault(mode, []).append(row)
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# Reagent contents on this trough/labware (from reagent_bioyond_ids).
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for liquid_row in self._iter_reagent_liquids(child):
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grouped["Reagent"].append(liquid_row)
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return grouped
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def _clear_unloaded_materials(
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self,
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manifest: Dict[str, List[Dict[str, Any]]],
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) -> Dict[str, List[Dict[str, Any]]]:
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"""Apply the unload mutation: clear slot-bound labware, zero reagent liquids.
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Returns a dict shaped like the manifest but with each row reduced to
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the minimal fields downstream consumers need (material code/name, the
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warehouse name, and the slot label or trough name).
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"""
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cleared: Dict[str, List[Dict[str, Any]]] = {
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"Sample": [],
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"Consumables": [],
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"Reagent": [],
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}
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affected_warehouses: List[Any] = []
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def _remember(warehouse: Any) -> None:
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if warehouse is None:
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return
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if any(warehouse is existing for existing in affected_warehouses):
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return
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affected_warehouses.append(warehouse)
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# 1) Slot-bound labware (Sample / Consumables).
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for mode in ("Sample", "Consumables"):
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for row in manifest.get(mode, []):
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warehouse = row.get("_warehouse")
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slot_label = row.get("_slot_label") or row.get("locationCode") or ""
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if warehouse is None and slot_label:
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try:
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warehouse, _idx = self._resolve_location_to_warehouse(slot_label)
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except (ValueError, RuntimeError) as exc:
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logger.warning(
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"卸载物料 %s 时无法解析库位 %s: %s",
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row.get("materialCode"), slot_label, exc,
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)
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continue
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if warehouse is None or not slot_label:
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continue
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try:
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if warehouse[slot_label] is not None:
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warehouse[slot_label] = None
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cleared[mode].append({
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"material_code": str(row.get("materialCode") or ""),
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"material_name": str(row.get("materialName") or ""),
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"location": slot_label,
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"warehouse": getattr(warehouse, "name", ""),
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})
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_remember(warehouse)
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except (IndexError, KeyError, TypeError) as exc:
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logger.warning(
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"卸载物料 %s 时清空库位 %s[%s] 失败: %s",
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row.get("materialCode"), getattr(warehouse, "name", "?"),
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slot_label, exc,
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)
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# 2) Reagent rows: contents on a parent trough vs slot-bound trough labware.
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for row in manifest.get("Reagent", []):
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trough = row.get("trough")
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if trough is not None:
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tracker = getattr(trough, "tracker", None)
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if tracker is not None and hasattr(tracker, "set_liquids"):
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try:
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tracker.set_liquids([])
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except Exception as exc: # pragma: no cover - tracker variants
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logger.debug("tracker.set_liquids 失败（非阻塞）: %s", exc)
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extra = getattr(trough, "unilabos_extra", None)
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if isinstance(extra, dict):
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extra["reagent_bioyond_ids"] = []
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try:
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setattr(trough, "unilabos_extra", extra)
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except Exception: # pragma: no cover - read-only proxy
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pass
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cleared["Reagent"].append({
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"material_name": str(row.get("materialName") or ""),
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"material_code": str(row.get("materialCode") or ""),
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"trough": getattr(trough, "name", ""),
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"warehouse": getattr(getattr(trough, "parent", None), "name", ""),
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})
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_remember(getattr(trough, "parent", None))
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continue
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# Slot-bound Reagent labware (e.g. trough labware). Preserve the
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# labware on the deck — only its contents (liquids + reagent ids)
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# are zeroed. ``reset`` is the LIMS-side path for full removal.
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child = row.get("_child")
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if child is not None:
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tracker = getattr(child, "tracker", None)
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if tracker is not None and hasattr(tracker, "set_liquids"):
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try:
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tracker.set_liquids([])
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except Exception as exc: # pragma: no cover - tracker variants
|
||||
logger.debug("tracker.set_liquids 失败（非阻塞）: %s", exc)
|
||||
extra = getattr(child, "unilabos_extra", None)
|
||||
if isinstance(extra, dict) and extra.get("reagent_bioyond_ids"):
|
||||
extra["reagent_bioyond_ids"] = []
|
||||
try:
|
||||
setattr(child, "unilabos_extra", extra)
|
||||
except Exception: # pragma: no cover - read-only proxy
|
||||
pass
|
||||
_remember(row.get("_warehouse") or getattr(child, "parent", None))
|
||||
continue
|
||||
|
||||
# 3) Publish the deck after mutations. ``_publish_resource_tree_update``
|
||||
# publishes the whole deck, so a single call covers all warehouses we
|
||||
# touched. ``affected_warehouses`` is kept for telemetry / tests.
|
||||
if affected_warehouses:
|
||||
self._publish_resource_tree_update()
|
||||
return cleared
|
||||
|
||||
def _build_manual_load_probe(
|
||||
self,
|
||||
materials_by_type: Dict[str, List[Dict[str, Any]]],
|
||||
|
||||
Reference in New Issue
Block a user