PRCXI Update

修改prcxi连线

prcxi样例图

Create example_prcxi.json

scripts/workflow.py

@@ -92,7 +92,7 @@ def refactor_data(data: List[Dict[str, Any]]) -> List[Dict[str, Any]]:
     # 定义操作映射，包含生物实验和有机化学的所有操作
     OPERATION_MAPPING = {
         # 生物实验操作
-        "transfer_liquid": "SynBioFactory-liquid_handler.transfer_liquid",
+        "transfer_liquid": "SynBioFactory-liquid_handler.prcxi-transfer_liquid",
         "transfer": "SynBioFactory-liquid_handler.biomek-transfer",
         "incubation": "SynBioFactory-liquid_handler.biomek-incubation",
         "move_labware": "SynBioFactory-liquid_handler.biomek-move_labware",
@@ -159,7 +159,10 @@ def build_protocol_graph(
     protocol_steps = refactor_data(protocol_steps)
 
     # 检查协议步骤中的模板来判断协议类型
-    has_biomek_template = any("biomek" in step.get("template", "") for step in protocol_steps)
+    has_biomek_template = any(
+        ("biomek" in step.get("template", "")) or ("prcxi" in step.get("template", ""))
+        for step in protocol_steps
+    )
 
     if has_biomek_template:
         # 生物实验协议图构建
@@ -178,12 +181,14 @@ def build_protocol_graph(
             resource_last_writer[labware_id] = f"{node_id}:labware"
 
         # 处理协议步骤
+        prev_node = None
         for i, step in enumerate(protocol_steps):
             node_id = str(uuid.uuid4())
             G.add_node(node_id, **step)
 
             # 添加控制流边
-            G.add_edge(prev_node, node_id, source_port="ready", target_port="ready")
+            if prev_node is not None:
+                G.add_edge(prev_node, node_id, source_port="ready", target_port="ready")
             prev_node = node_id
 
             # 处理物料流
@@ -198,7 +203,8 @@ def build_protocol_graph(
         # 添加协议结束节点
         end_id = str(uuid.uuid4())
         G.add_node(end_id, template=f"{LAB_NAME}-liquid_handler.biomek-run_protocol")
-        G.add_edge(prev_node, end_id, source_port="ready", target_port="ready")
+        if prev_node is not None:
+            G.add_edge(prev_node, end_id, source_port="ready", target_port="ready")
 
     else:
         # 有机化学协议图构建

test/workflow/example_prcxi.json

@@ -0,0 +1,63 @@
+{
+    "steps_info": [
+        {
+            "step_number": 1,
+            "action": "transfer_liquid",
+            "parameters": {
+                "source": "sample supernatant",
+                "target": "antibody-coated well",
+                "volume": 100
+            }
+        },
+        {
+            "step_number": 2,
+            "action": "transfer_liquid",
+            "parameters": {
+                "source": "washing buffer",
+                "target": "antibody-coated well",
+                "volume": 200
+            }
+        },
+        {
+            "step_number": 3,
+            "action": "transfer_liquid",
+            "parameters": {
+                "source": "washing buffer",
+                "target": "antibody-coated well",
+                "volume": 200
+            }
+        },
+        {
+            "step_number": 4,
+            "action": "transfer_liquid",
+            "parameters": {
+                "source": "washing buffer",
+                "target": "antibody-coated well",
+                "volume": 200
+            }
+        },
+        {
+            "step_number": 5,
+            "action": "transfer_liquid",
+            "parameters": {
+                "source": "TMB substrate",
+                "target": "antibody-coated well",
+                "volume": 100
+            }
+        }
+    ],
+    "labware_info": [
+        {"reagent_name": "sample supernatant", "material_name": "96深孔板", "positions": 1},
+        {"reagent_name": "washing buffer", "material_name": "储液槽", "positions": 2},
+        {"reagent_name": "TMB substrate", "material_name": "储液槽", "positions": 3},
+        {"reagent_name": "antibody-coated well", "material_name": "96 细胞培养皿", "positions": 4},
+        {"reagent_name": "", "material_name": "300μL Tip头", "positions": 5},
+        {"reagent_name": "", "material_name": "300μL Tip头", "positions": 6},
+        {"reagent_name": "", "material_name": "300μL Tip头", "positions": 7},
+        {"reagent_name": "", "material_name": "300μL Tip头", "positions": 8},
+        {"reagent_name": "", "material_name": "300μL Tip头", "positions": 9},
+        {"reagent_name": "", "material_name": "300μL Tip头", "positions": 10},
+        {"reagent_name": "", "material_name": "300μL Tip头", "positions": 11},
+        {"reagent_name": "", "material_name": "300μL Tip头", "positions": 13}
+    ]
+}

test/workflow/merge_workflow.py

@@ -1,14 +1,94 @@
-import pytest
 import json
+import sys
+from datetime import datetime
+from pathlib import Path
+
+ROOT_DIR = Path(__file__).resolve().parents[2]
+if str(ROOT_DIR) not in sys.path:
+    sys.path.insert(0, str(ROOT_DIR))
+
+import pytest
+
 from scripts.workflow import build_protocol_graph, draw_protocol_graph, draw_protocol_graph_with_ports
 
 
+ROOT_DIR = Path(__file__).resolve().parents[2]
+if str(ROOT_DIR) not in sys.path:
+    sys.path.insert(0, str(ROOT_DIR))
+
+
+def _normalize_steps(data):
+    normalized = []
+    for step in data:
+        action = step.get("action") or step.get("operation")
+        if not action:
+            continue
+        raw_params = step.get("parameters") or step.get("action_args") or {}
+        params = dict(raw_params)
+
+        if "source" in raw_params and "sources" not in raw_params:
+            params["sources"] = raw_params["source"]
+        if "target" in raw_params and "targets" not in raw_params:
+            params["targets"] = raw_params["target"]
+
+        description = step.get("description") or step.get("purpose")
+        step_dict = {"action": action, "parameters": params}
+        if description:
+            step_dict["description"] = description
+        normalized.append(step_dict)
+    return normalized
+
+
+def _normalize_labware(data):
+    labware = {}
+    for item in data:
+        reagent_name = item.get("reagent_name")
+        key = reagent_name or item.get("material_name") or item.get("name")
+        if not key:
+            continue
+        key = str(key)
+        idx = 1
+        original_key = key
+        while key in labware:
+            idx += 1
+            key = f"{original_key}_{idx}"
+
+        labware[key] = {
+            "slot": item.get("positions") or item.get("slot"),
+            "labware": item.get("material_name") or item.get("labware"),
+            "well": item.get("well", []),
+            "type": item.get("type", "reagent"),
+            "role": item.get("role", ""),
+            "name": key,
+        }
+    return labware
+
+
 @pytest.mark.parametrize("protocol_name", [
     "example_bio",
     # "bioyond_materials_liquidhandling_1",
+    "example_prcxi",
 ])
 def test_build_protocol_graph(protocol_name):
-    d = json.load(open(f"{protocol_name}.json"))
-    graph = build_protocol_graph(labware_info=d["reagent"], protocol_steps=d["workflow"], workstation_name="PRCXi")
-    draw_protocol_graph_with_ports(graph, "graph.png")
+    data_path = Path(__file__).with_name(f"{protocol_name}.json")
+    with data_path.open("r", encoding="utf-8") as fp:
+        d = json.load(fp)
+
+    if "workflow" in d and "reagent" in d:
+        protocol_steps = d["workflow"]
+        labware_info = d["reagent"]
+    elif "steps_info" in d and "labware_info" in d:
+        protocol_steps = _normalize_steps(d["steps_info"])
+        labware_info = _normalize_labware(d["labware_info"])
+    else:
+        raise ValueError("Unsupported protocol format")
+
+    graph = build_protocol_graph(
+        labware_info=labware_info,
+        protocol_steps=protocol_steps,
+        workstation_name="PRCXi",
+    )
+    timestamp = datetime.now().strftime("%Y%m%d_%H%M")
+    output_path = data_path.with_name(f"{protocol_name}_graph_{timestamp}.png")
+    draw_protocol_graph_with_ports(graph, str(output_path))
     print(graph)