mirror of
https://github.com/deepmodeling/Uni-Lab-OS
synced 2026-05-25 09:35:58 +00:00
370 lines
14 KiB
Python
370 lines
14 KiB
Python
"""P2 v2 跨 slot transfer_liquid 合并 —— Stage 3 (`workflow/common.py`) 集成测试。
|
||
|
||
对应 ``product_designs/protocol_convert/02-cross-slot-merge.md`` §9.5 step 6.2。
|
||
|
||
v2 设计要点（与本测试用例的映射）
|
||
-----------------------------------
|
||
当 transfer_liquid 节点 ``params.targets`` 是 ``list[str]`` 时，``build_protocol_graph``
|
||
在该 transfer_liquid 之前**插入一个 merged ``set_liquid_from_plate`` 节点**：
|
||
|
||
- merged 节点的 ``param.wells`` 是按 ``params.targets`` 顺序通过 cursor 拼出来的有序跨板
|
||
well refs（每个元素是 ``{id, name, parent: reagent_key, type: "well"}``）。
|
||
- merged 节点接收来自每个涉及 plate 的 ``create_resource`` 节点的多入边
|
||
(``labware`` → ``wells_identifier``)。
|
||
- merged 节点的 ``output_wells`` 通过**单条边**连到 transfer_liquid 的 ``targets_identifier``。
|
||
- transfer_liquid 节点的 ``params.targets`` 被改写为 synthetic key
|
||
``_merged_targets_<idx>``（runtime 不消费 list 形态），保证 INPUT_PORT_MAPPING 走单边路径。
|
||
|
||
用例
|
||
----
|
||
- ``test_emit_merged_set_liquid_basic`` — 4 个 distinct reagent_key（51b9a5 主场景）。
|
||
- ``test_emit_merged_set_liquid_repeat_key`` — 同 reagent_key 重复（同板多孔）。
|
||
- ``test_emit_merged_set_liquid_mixed`` — 跨板混合 + 同板重复（cursor 推进）。
|
||
- ``test_emit_merged_set_liquid_8ch`` — 与 P1 multi-channel 复合（8 通道 cross-slot）。
|
||
- ``test_transfer_liquid_targets_rewrite`` — transfer_liquid 节点改写后只剩 1 条
|
||
``targets_identifier`` 入边；params.targets 不再是 list。
|
||
"""
|
||
from __future__ import annotations
|
||
|
||
import sys
|
||
import types
|
||
from pathlib import Path
|
||
from typing import Any, Dict, List
|
||
|
||
|
||
ROOT_DIR = Path(__file__).resolve().parents[2]
|
||
if str(ROOT_DIR) not in sys.path:
|
||
sys.path.insert(0, str(ROOT_DIR))
|
||
|
||
|
||
def _install_fake_optional_deps() -> None:
|
||
"""与 test_build_protocol_graph_target_device.py 一致的可选依赖 stub。"""
|
||
if "matplotlib" not in sys.modules:
|
||
sys.modules["matplotlib"] = types.ModuleType("matplotlib")
|
||
if "matplotlib.pyplot" not in sys.modules:
|
||
sys.modules["matplotlib.pyplot"] = types.ModuleType("matplotlib.pyplot")
|
||
try:
|
||
from networkx.drawing import nx_agraph # noqa: F401
|
||
except Exception:
|
||
nx_drawing = types.ModuleType("networkx.drawing")
|
||
nx_agraph_mod = types.ModuleType("networkx.drawing.nx_agraph")
|
||
nx_agraph_mod.to_agraph = lambda _g: None # type: ignore[attr-defined]
|
||
nx_drawing.nx_agraph = nx_agraph_mod # type: ignore[attr-defined]
|
||
sys.modules["networkx.drawing"] = nx_drawing
|
||
sys.modules["networkx.drawing.nx_agraph"] = nx_agraph_mod
|
||
|
||
|
||
_install_fake_optional_deps()
|
||
|
||
import pytest # noqa: E402
|
||
|
||
from unilabos.workflow.common import build_protocol_graph # noqa: E402
|
||
|
||
|
||
# ==================== 测试辅助：从工作流图中提取节点/边 ====================
|
||
|
||
|
||
def _nodes_by_template(graph, template_name: str) -> List[Dict[str, Any]]:
|
||
return [
|
||
{"id": nid, **node}
|
||
for nid, node in graph.nodes.items()
|
||
if node.get("template_name") == template_name
|
||
]
|
||
|
||
|
||
def _create_resource_by_slot(graph) -> Dict[str, str]:
|
||
"""slot_on_deck (str) -> create_resource 节点 ID。"""
|
||
out: Dict[str, str] = {}
|
||
for nid, node in graph.nodes.items():
|
||
if node.get("template_name") == "create_resource":
|
||
slot = str(node.get("param", {}).get("slot_on_deck") or "")
|
||
if slot:
|
||
out[slot] = nid
|
||
return out
|
||
|
||
|
||
def _edges_to(graph, target_id: str) -> List[Dict[str, Any]]:
|
||
return [e for e in graph.edges if e["target"] == target_id]
|
||
|
||
|
||
def _edges_from(graph, source_id: str) -> List[Dict[str, Any]]:
|
||
return [e for e in graph.edges if e["source"] == source_id]
|
||
|
||
|
||
# ==================== fixture：构造跨板 labware + steps ====================
|
||
|
||
|
||
def _cross_slot_labware_info() -> Dict[str, Dict[str, Any]]:
|
||
"""51b9a5 简化：slot1 source + slot2/3/5/6 target plates + slot12 tip。"""
|
||
return {
|
||
"l1": {
|
||
"slot": 1,
|
||
"well": ["A1"],
|
||
"labware": "nest_12_reservoir_15ml",
|
||
"object": "source",
|
||
},
|
||
"plate_slot2": {
|
||
"slot": 2,
|
||
"well": ["A1"],
|
||
"labware": "nest_96_wellplate_2ml_deep",
|
||
"object": "target",
|
||
},
|
||
"plate_slot3": {
|
||
"slot": 3,
|
||
"well": ["A1"],
|
||
"labware": "nest_96_wellplate_2ml_deep",
|
||
"object": "target",
|
||
},
|
||
"plate_slot5": {
|
||
"slot": 5,
|
||
"well": ["A1"],
|
||
"labware": "nest_96_wellplate_2ml_deep",
|
||
"object": "target",
|
||
},
|
||
"plate_slot6": {
|
||
"slot": 6,
|
||
"well": ["A1"],
|
||
"labware": "nest_96_wellplate_2ml_deep",
|
||
"object": "target",
|
||
},
|
||
"tiprack_12": {
|
||
"slot": 12,
|
||
"well": [],
|
||
"labware": "opentrons_96_tiprack_300ul",
|
||
"object": "tiprack",
|
||
},
|
||
}
|
||
|
||
|
||
def _cross_slot_protocol_steps(targets: List[str], dis_vols: List[float]) -> List[Dict[str, Any]]:
|
||
return [
|
||
{
|
||
"action": "transfer_liquid",
|
||
"parameters": {
|
||
"sources": "l1",
|
||
"targets": targets,
|
||
"tip_racks": "tiprack_12",
|
||
"asp_vols": dis_vols.copy(),
|
||
"dis_vols": dis_vols.copy(),
|
||
},
|
||
"step_number": 1,
|
||
}
|
||
]
|
||
|
||
|
||
# ==================== 用例 ====================
|
||
|
||
|
||
def test_emit_merged_set_liquid_basic():
|
||
"""51b9a5 主场景：targets=[A,B,C,D] → 1 merged set_liquid 节点
|
||
+ 4 条入边（来自 4 个 distinct create_resource）+ 1 条出边（去 transfer_liquid）。
|
||
"""
|
||
targets = ["plate_slot2", "plate_slot3", "plate_slot5", "plate_slot6"]
|
||
dis_vols = [8.3, 8.3, 8.3, 8.3]
|
||
g = build_protocol_graph(
|
||
labware_info=_cross_slot_labware_info(),
|
||
protocol_steps=_cross_slot_protocol_steps(targets, dis_vols),
|
||
workstation_name="PRCXI",
|
||
)
|
||
|
||
set_liquid_nodes = _nodes_by_template(g, "set_liquid_from_plate")
|
||
merged_nodes = [n for n in set_liquid_nodes if str(n.get("name", "")).startswith("_merged_targets_")]
|
||
assert len(merged_nodes) == 1, (
|
||
f"应有且仅有 1 个 merged set_liquid_from_plate 节点（v2 跨板聚合器）;"
|
||
f" 实际找到 {len(merged_nodes)}: {[n.get('name') for n in merged_nodes]}"
|
||
)
|
||
merged = merged_nodes[0]
|
||
merged_id = merged["id"]
|
||
|
||
# param.wells：长度 4，每元素的 parent 是对应 reagent_key
|
||
wells = merged.get("param", {}).get("wells") or []
|
||
assert len(wells) == 4
|
||
assert [w["parent"] for w in wells] == targets, "merged.wells 顺序必须严格按 targets 列表"
|
||
# well 字段映射到 reagent.well[0]（都是 "A1"）
|
||
for w, key in zip(wells, targets):
|
||
assert w["id"].endswith("/A1"), f"well id 应包含 well 名: {w}"
|
||
assert w["parent"] == key
|
||
|
||
# 入边：4 条来自 distinct create_resource 节点（slot 2/3/5/6），target_port=wells_identifier
|
||
cr_by_slot = _create_resource_by_slot(g)
|
||
in_edges = _edges_to(g, merged_id)
|
||
in_sources = {e["source"] for e in in_edges if e.get("target_handle_key") == "wells_identifier"}
|
||
expected_sources = {cr_by_slot[s] for s in ("2", "3", "5", "6")}
|
||
assert in_sources == expected_sources, (
|
||
f"merged 节点应接收 4 个 distinct create_resource 的 wells_identifier 边;"
|
||
f" 实际 {in_sources} vs 期望 {expected_sources}"
|
||
)
|
||
|
||
# 出边：1 条到 transfer_liquid（targets_identifier）
|
||
transfer_nodes = _nodes_by_template(g, "transfer_liquid")
|
||
assert len(transfer_nodes) == 1
|
||
transfer_id = transfer_nodes[0]["id"]
|
||
out_to_transfer = [
|
||
e for e in _edges_from(g, merged_id)
|
||
if e["target"] == transfer_id and e.get("target_handle_key") == "targets_identifier"
|
||
]
|
||
assert len(out_to_transfer) == 1, (
|
||
f"merged 节点应向 transfer_liquid.targets_identifier 发出唯一 1 条边;"
|
||
f" 实际 {len(out_to_transfer)}"
|
||
)
|
||
|
||
|
||
def test_emit_merged_set_liquid_repeat_key():
|
||
"""同 reagent_key 重复（同板多孔）：targets=[A,A,A] + reagent.A.well=[A1,A2,A3]
|
||
→ merged.wells 顺序 = [A/A1, A/A2, A/A3]（cursor 推进取每个 well）。
|
||
"""
|
||
labware = _cross_slot_labware_info()
|
||
labware["plate_slot2"]["well"] = ["A1", "A2", "A3"]
|
||
|
||
targets = ["plate_slot2", "plate_slot2", "plate_slot2"]
|
||
dis_vols = [10.0, 20.0, 30.0]
|
||
g = build_protocol_graph(
|
||
labware_info=labware,
|
||
protocol_steps=_cross_slot_protocol_steps(targets, dis_vols),
|
||
workstation_name="PRCXI",
|
||
)
|
||
|
||
merged_nodes = [
|
||
n for n in _nodes_by_template(g, "set_liquid_from_plate")
|
||
if str(n.get("name", "")).startswith("_merged_targets_")
|
||
]
|
||
assert len(merged_nodes) == 1
|
||
wells = merged_nodes[0]["param"]["wells"]
|
||
assert [w["id"].rsplit("/", 1)[-1] for w in wells] == ["A1", "A2", "A3"], (
|
||
"cursor 应依次取 reagent.A.well[0/1/2]"
|
||
)
|
||
assert all(w["parent"] == "plate_slot2" for w in wells)
|
||
|
||
|
||
def test_emit_merged_set_liquid_mixed():
|
||
"""跨板 + 同板重复：targets=[A,B,A,C] + reagent.A.well=[A1,A2]
|
||
→ merged.wells = [A/A1, B/A1, A/A2, C/A1]。
|
||
"""
|
||
labware = _cross_slot_labware_info()
|
||
labware["plate_slot2"]["well"] = ["A1", "A2"]
|
||
|
||
targets = ["plate_slot2", "plate_slot3", "plate_slot2", "plate_slot5"]
|
||
dis_vols = [10.0, 20.0, 30.0, 40.0]
|
||
g = build_protocol_graph(
|
||
labware_info=labware,
|
||
protocol_steps=_cross_slot_protocol_steps(targets, dis_vols),
|
||
workstation_name="PRCXI",
|
||
)
|
||
|
||
merged_nodes = [
|
||
n for n in _nodes_by_template(g, "set_liquid_from_plate")
|
||
if str(n.get("name", "")).startswith("_merged_targets_")
|
||
]
|
||
assert len(merged_nodes) == 1
|
||
wells = merged_nodes[0]["param"]["wells"]
|
||
ids = [(w["parent"], w["id"].rsplit("/", 1)[-1]) for w in wells]
|
||
assert ids == [
|
||
("plate_slot2", "A1"),
|
||
("plate_slot3", "A1"),
|
||
("plate_slot2", "A2"),
|
||
("plate_slot5", "A1"),
|
||
]
|
||
|
||
|
||
def test_emit_merged_set_liquid_8ch():
|
||
"""与 P1 multi-channel 复合：targets=[A]*8+[B]*8（每列 8 通道）。
|
||
|
||
merged.wells 长度 16，前 8 全 plate_slot2 的 8 个 well，后 8 全 plate_slot3 的 8 个 well。
|
||
"""
|
||
labware = _cross_slot_labware_info()
|
||
# 8 通道场景 reagent.well 已被 P1 multi 展开为长度 8
|
||
labware["plate_slot2"]["well"] = [f"{r}1" for r in "ABCDEFGH"]
|
||
labware["plate_slot3"]["well"] = [f"{r}1" for r in "ABCDEFGH"]
|
||
|
||
targets = ["plate_slot2"] * 8 + ["plate_slot3"] * 8
|
||
dis_vols = [5.0] * 16
|
||
g = build_protocol_graph(
|
||
labware_info=labware,
|
||
protocol_steps=_cross_slot_protocol_steps(targets, dis_vols),
|
||
workstation_name="PRCXI",
|
||
)
|
||
|
||
merged_nodes = [
|
||
n for n in _nodes_by_template(g, "set_liquid_from_plate")
|
||
if str(n.get("name", "")).startswith("_merged_targets_")
|
||
]
|
||
assert len(merged_nodes) == 1
|
||
wells = merged_nodes[0]["param"]["wells"]
|
||
assert len(wells) == 16
|
||
# 前 8 全 plate_slot2，后 8 全 plate_slot3（满足 cross-slot × 8ch 列对齐约束）
|
||
assert all(w["parent"] == "plate_slot2" for w in wells[:8])
|
||
assert all(w["parent"] == "plate_slot3" for w in wells[8:])
|
||
# well 名顺序：A1..H1 重复两遍
|
||
assert [w["id"].rsplit("/", 1)[-1] for w in wells[:8]] == [f"{r}1" for r in "ABCDEFGH"]
|
||
assert [w["id"].rsplit("/", 1)[-1] for w in wells[8:]] == [f"{r}1" for r in "ABCDEFGH"]
|
||
|
||
|
||
def test_transfer_liquid_targets_rewrite():
|
||
"""transfer_liquid 节点改写后只剩 1 条 targets_identifier 入边；params.targets 不再是 list。"""
|
||
targets = ["plate_slot2", "plate_slot3", "plate_slot5", "plate_slot6"]
|
||
dis_vols = [8.3, 8.3, 8.3, 8.3]
|
||
g = build_protocol_graph(
|
||
labware_info=_cross_slot_labware_info(),
|
||
protocol_steps=_cross_slot_protocol_steps(targets, dis_vols),
|
||
workstation_name="PRCXI",
|
||
)
|
||
|
||
transfer_nodes = _nodes_by_template(g, "transfer_liquid")
|
||
assert len(transfer_nodes) == 1
|
||
tnode = transfer_nodes[0]
|
||
transfer_id = tnode["id"]
|
||
|
||
# params.targets：v2 中 list 形态在 INPUT_PORT_MAPPING 处理后被清空（[]）或为单字符串
|
||
# （不再是原始 list[str]——避免下游 runtime 对其再做无序聚合）
|
||
tparams = tnode.get("param", {}) or {}
|
||
assert not isinstance(tparams.get("targets"), list) or tparams.get("targets") == [], (
|
||
f"v2：params.targets 不再是非空 list；实际 {tparams.get('targets')!r}"
|
||
)
|
||
|
||
# targets_identifier 端口：只有 1 条入边
|
||
in_targets_edges = [
|
||
e for e in _edges_to(g, transfer_id)
|
||
if e.get("target_handle_key") == "targets_identifier"
|
||
]
|
||
assert len(in_targets_edges) == 1, (
|
||
f"v2：transfer_liquid.targets_identifier 必须是单入边（来自 merged set_liquid）;"
|
||
f" 实际 {len(in_targets_edges)}"
|
||
)
|
||
|
||
# 这条入边的源端口必须是 output_wells
|
||
edge = in_targets_edges[0]
|
||
assert edge.get("source_handle_key") == "output_wells"
|
||
|
||
|
||
def test_str_targets_no_merged_node_emitted():
|
||
"""对照组：targets 为 str（单 reagent） → 不插入 merged set_liquid_from_plate 节点。
|
||
|
||
保证 v2 改造**只**对 list 形态触发，单 reagent 走 P3 原有 per-plate set_liquid 路径。
|
||
"""
|
||
labware = _cross_slot_labware_info()
|
||
labware["plate_slot2"]["well"] = ["A1", "A2", "A3"]
|
||
|
||
steps = [
|
||
{
|
||
"action": "transfer_liquid",
|
||
"parameters": {
|
||
"sources": "l1",
|
||
"targets": "plate_slot2", # ← 单 str，非 list
|
||
"tip_racks": "tiprack_12",
|
||
"asp_vols": [8.3, 8.3, 8.3],
|
||
"dis_vols": [8.3, 8.3, 8.3],
|
||
},
|
||
"step_number": 1,
|
||
}
|
||
]
|
||
g = build_protocol_graph(
|
||
labware_info=labware,
|
||
protocol_steps=steps,
|
||
workstation_name="PRCXI",
|
||
)
|
||
merged_nodes = [
|
||
n for n in _nodes_by_template(g, "set_liquid_from_plate")
|
||
if str(n.get("name", "")).startswith("_merged_targets_")
|
||
]
|
||
assert merged_nodes == [], "str 形态 targets 不应触发 v2 merged 聚合节点"
|