Update docs

unilabos/test/workflow/example_bio.json

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+{
+  "workflow": [
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "Liquid_1",
+        "targets": "Liquid_2",
+        "asp_vol": 66.0,
+        "dis_vol": 66.0,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 94.0
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "Liquid_2",
+        "targets": "Liquid_3",
+        "asp_vol": 58.0,
+        "dis_vol": 96.0,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 94.0
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "Liquid_4",
+        "targets": "Liquid_2",
+        "asp_vol": 85.0,
+        "dis_vol": 170.0,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 94.0
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "Liquid_4",
+        "targets": "Liquid_2",
+        "asp_vol": 63.333333333333336,
+        "dis_vol": 170.0,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 94.0
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "Liquid_2",
+        "targets": "Liquid_3",
+        "asp_vol": 72.0,
+        "dis_vol": 150.0,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 94.0
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "Liquid_4",
+        "targets": "Liquid_2",
+        "asp_vol": 85.0,
+        "dis_vol": 170.0,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 94.0
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "Liquid_4",
+        "targets": "Liquid_2",
+        "asp_vol": 63.333333333333336,
+        "dis_vol": 170.0,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 94.0
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "Liquid_2",
+        "targets": "Liquid_3",
+        "asp_vol": 72.0,
+        "dis_vol": 150.0,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 94.0
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "Liquid_2",
+        "targets": "Liquid_3",
+        "asp_vol": 20.0,
+        "dis_vol": 20.0,
+        "asp_flow_rate": 7.6,
+        "dis_flow_rate": 7.6
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "Liquid_5",
+        "targets": "Liquid_2",
+        "asp_vol": 6.0,
+        "dis_vol": 12.0,
+        "asp_flow_rate": 7.6,
+        "dis_flow_rate": 7.6
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "Liquid_5",
+        "targets": "Liquid_2",
+        "asp_vol": 10.666666666666666,
+        "dis_vol": 12.0,
+        "asp_flow_rate": 7.599999999999999,
+        "dis_flow_rate": 7.6
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "Liquid_2",
+        "targets": "Liquid_6",
+        "asp_vol": 12.0,
+        "dis_vol": 10.0,
+        "asp_flow_rate": 7.6,
+        "dis_flow_rate": 7.6
+      }
+    }
+  ],
+  "reagent": {
+    "Liquid_6": {
+      "slot": 1,
+      "well": [
+        "A2"
+      ],
+      "labware": "elution plate"
+    },
+    "Liquid_1": {
+      "slot": 2,
+      "well": [
+        "A1",
+        "A2",
+        "A4"
+      ],
+      "labware": "reagent reservoir"
+    },
+    "Liquid_4": {
+      "slot": 2,
+      "well": [
+        "A1",
+        "A2",
+        "A4"
+      ],
+      "labware": "reagent reservoir"
+    },
+    "Liquid_5": {
+      "slot": 2,
+      "well": [
+        "A1",
+        "A2",
+        "A4"
+      ],
+      "labware": "reagent reservoir"
+    },
+    "Liquid_2": {
+      "slot": 4,
+      "well": [
+        "A2"
+      ],
+      "labware": "TAG1 plate on Magnetic Module GEN2"
+    },
+    "Liquid_3": {
+      "slot": 12,
+      "well": [
+        "A1"
+      ],
+      "labware": "Opentrons Fixed Trash"
+    }
+  }
+}

unilabos/test/workflow/example_prcxi.json

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+{
+    "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}
+    ]
+}

unilabos/test/workflow/merge_workflow.py

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+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):
+    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)