fix handles not as default entry

add action handles

unilabos/devices/liquid_handling/biomek.py

@@ -32,46 +32,63 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
         self.py32_path = "/opt/py32"  # Biomek的Python 3.2路径
         self.aspirate_techniques = {
             'MC P300 high':{       
-                "Solvent": "Water",
+                            'Position': 'P1', 
-            }
+                            'Height': -2.0, 
+                            'Volume': '50', 
+                            'liquidtype': 'Well Contents', 
+                            'WellsX': 12, 
+                            'LabwareClass': 'Matrix96_750uL', 
+                            'AutoSelectPrototype': True, 
+                            'ColsFirst': True, 
+                            'CustomHeight': False, 
+                            'DataSetPattern': False, 
+                            'HeightFrom': 0, 
+                            'LocalPattern': True, 
+                            'Operation': 'Aspirate', 
+                            'OverrideHeight': False, 
+                            'Pattern': (True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True),
+                            'Prototype': 'MC P300 High', 
+                            'ReferencedPattern': '', 
+                            'RowsFirst': False, 
+                            'SectionExpression': '', 
+                            'SelectionInfo': (1,), 
+                            'SetMark': True, 
+                            'Source': True, 
+                            'StartAtMark': False, 
+                            'StartAtSelection': True, 
+                            'UseExpression': False},
             }
+      
         self.dispense_techniques = {
             'MC P300 high':{       
-            "Span8": False,
+                          'Position': 'P11', 
-            "Pod": "Pod1",
+                          'Height': -2.0, 
-            "Wash": False,
+                          'Volume': '50', 
-            "Dynamic?": True,
+                          'liquidtype': 'Tip Contents', 
-            "AutoSelectActiveWashTechnique": False,
+                          'WellsX': 12, 
-            "ActiveWashTechnique": "",
+                          'LabwareClass': 'Matrix96_750uL', 
-            "ChangeTipsBetweenDests": True,
+                          'AutoSelectPrototype': True, 
-            "ChangeTipsBetweenSources": False,
+                          'ColsFirst': True, 
-            "DefaultCaption": "",             
+                          'CustomHeight': False, 
-            "UseExpression": False,
+                          'DataSetPattern': False, 
-            "LeaveTipsOn": False,
+                          'HeightFrom': 0, 
-            "MandrelExpression": "",
+                          'LocalPattern': True, 
-            "Repeats": "1",
+                          'Operation': 'Dispense', 
-            "RepeatsByVolume": False,
+                          'OverrideHeight': False, 
-            "Replicates": "1",
+                          'Pattern': (True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True), 
-            "ShowTipHandlingDetails": False,
+                          'Prototype': 'MC P300 High', 
-            "ShowTransferDetails": True,
+                          'ReferencedPattern': '', 
-            "Span8Wash": False,
+                          'RowsFirst': False, 
-            "Span8WashVolume": "2",
+                          'SectionExpression': '', 
-            "Span8WasteVolume": "1",
+                          'SelectionInfo': (1,), 
-            "SplitVolume": False,
+                          'SetMark': True, 
-            "SplitVolumeCleaning": False,
+                          'Source': False, 
-            "Stop": "Destinations",
+                          'StartAtMark': False, 
-            "UseCurrentTips": False,    
+                          'StartAtSelection': True, 
-            "UseDisposableTips": False,
+                          'UseExpression': False}
-            "UseFixedTips": False,
-            "UseJIT": True,
-            "UseMandrelSelection": True,
-            "UseProbes": [True, True, True, True, True, True, True, True],
-            "WashCycles": "3",
-            "WashVolume": "110%",
-            "Wizard": False
-            }
         }
 
+
     @classmethod
     def deserialize(cls, data: dict, allow_marshal: bool = False) -> LiquidHandler:
         return LiquidHandler.deserialize(data, allow_marshal)
@@ -347,9 +364,63 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
 
         return 
 
+    def move_biomek(
+        self,
+        source: str,
+        target: str,
+    ):
+        """
+        处理Biomek移动板子的操作。
+
+        """
+
+        move_params = {
+            "Pod": "Pod1",
+            "GripSide": "A1 near",
+            "Source": source,
+            "Target": target,
+            "LeaveBottomLabware": False,
+        }
+        self.temp_protocol["steps"].append(move_params)
+
+        return
+    
+    def incubation_biomek(
+        self,
+        time: int,
+    ):
+        """
+        处理Biomek的孵育操作。
+        """
+        incubation_params = {
+            "Message": "Paused",
+            "Location": "the whole system",
+            "Time": time,
+            "Mode": "TimedResource"
+        }
+        self.temp_protocol["steps"].append(incubation_params)
+
+        return
+    
+    def oscillation_biomek(
+        self,
+        rpm: int,
+        time: int,
+    ):
+        """
+        处理Biomek的振荡操作。
+        """   
+        oscillation_params = {
+            'Device': 'OrbitalShaker0',
+            'Parameters': (str(rpm), '2', str(time), 'CounterClockwise'), 
+            'Command': 'Timed Shake'
+        }
+        self.temp_protocol["steps"].append(oscillation_params)
+
+        return
+
 
 if __name__ == "__main__":
-
     steps_info = ''' 
     {
       "steps": [
@@ -612,11 +683,8 @@ if __name__ == "__main__":
       ]
     }
     '''
-
+    labware_with_liquid = '''
-
+    [    {
-
-labware_with_liquid = '''
-[    {
             "id": "stock plate on P1",
             "parent": "deck",
             "slot_on_deck": "P1",
@@ -825,31 +893,37 @@ labware_with_liquid = '''
         ]
         
         '''
+    handler = LiquidHandlerBiomek()
 
-
+    handler.temp_protocol = {
-
-handler = LiquidHandlerBiomek()
-
-handler.temp_protocol = {
         "meta": {},
         "labwares": [],
         "steps": []
-}
+    }
 
-input_steps = json.loads(steps_info)
+    input_steps = json.loads(steps_info)
-labwares = json.loads(labware_with_liquid)
+    labwares = json.loads(labware_with_liquid)
 
-for step in input_steps['steps']:
+    for step in input_steps['steps']:
-    if step['operation'] != 'transfer':
+        operation = step['operation']
-        continue
         parameters = step['parameters']
 
+        if operation == 'transfer':
             handler.transfer_biomek(source=parameters['source'],
                                     target=parameters['target'],
                                     volume=parameters['volume'],
                                     tip_rack=parameters['tip_rack'],
                                     aspirate_techniques='MC P300 high',
-                            dispense_techniques='MC P300 high'
+                                    dispense_techniques='MC P300 high')
-                            )
+        elif operation == 'move_labware':
+            handler.move_biomek(source=parameters['source'],
+                                  target=parameters['target'])
+        elif operation == 'oscillation':
+            handler.oscillation_biomek(rpm=parameters['rpm'],
+                                        time=parameters['time'])
+        elif operation == 'incubation':
+            handler.incubation_biomek(time=parameters['time'])
+
+    print(json.dumps(handler.temp_protocol, indent=4))
 
 

unilabos/devices/liquid_handling/biomek_test.py

@@ -1,14 +1,14 @@
-import requests
+# import requests
 from typing import List, Sequence, Optional, Union, Literal
 # from geometry_msgs.msg import Point
 # from unilabos_msgs.msg import Resource
-from pylabrobot.resources import (
+# from pylabrobot.resources import (
-    Resource,
+#     Resource,
-    TipRack,
+#     TipRack,
-    Container,
+#     Container,
-    Coordinate,
+#     Coordinate,
-    Well
+#     Well
-)
+# )
 # from unilabos.ros.nodes.resource_tracker import DeviceNodeResourceTracker  # type: ignore
 # from .liquid_handler_abstract import LiquidHandlerAbstract
 
@@ -270,6 +270,62 @@ class LiquidHandlerBiomek:
 
         return
 
+    def move_biomek(
+        self,
+        source: str,
+        target: str,
+    ):
+        """
+        处理Biomek移动板子的操作。
+
+        """
+
+        move_params = {
+            "Pod": "Pod1",
+            "GripSide": "A1 near",
+            "Source": source,
+            "Target": target,
+            "LeaveBottomLabware": False,
+        }
+        self.temp_protocol["steps"].append(move_params)
+
+        return
+    
+    def incubation_biomek(
+        self,
+        time: int,
+    ):
+        """
+        处理Biomek的孵育操作。
+        """
+        incubation_params = {
+            "Message": "Paused",
+            "Location": "the whole system",
+            "Time": time,
+            "Mode": "TimedResource"
+        }
+        self.temp_protocol["steps"].append(incubation_params)
+
+        return
+    
+    def oscillation_biomek(
+        self,
+        rpm: int,
+        time: int,
+    ):
+        """
+        处理Biomek的振荡操作。
+        """   
+        oscillation_params = {
+            'Device': 'OrbitalShaker0',
+            'Parameters': (str(rpm), '2', str(time), 'CounterClockwise'), 
+            'Command': 'Timed Shake'
+        }
+        self.temp_protocol["steps"].append(oscillation_params)
+
+        return
+                      
+
 
 if __name__ == "__main__":
 
@@ -763,16 +819,23 @@ input_steps = json.loads(steps_info)
 labwares = json.loads(labware_with_liquid)
 
 for step in input_steps['steps']:
-    if step['operation'] != 'transfer':
+    operation = step['operation']
-        continue
     parameters = step['parameters']
 
+    if operation == 'transfer':
         handler.transfer_biomek(source=parameters['source'],
                                 target=parameters['target'],
                                 volume=parameters['volume'],
                                 tip_rack=parameters['tip_rack'],
                                 aspirate_techniques='MC P300 high',
-                            dispense_techniques='MC P300 high'
+                                dispense_techniques='MC P300 high')
-                            )
+    elif operation == 'move_labware':
+        handler.move_biomek(source=parameters['source'],
+                              target=parameters['target'])
+    elif operation == 'oscillation':
+        handler.oscillation_biomek(rpm=parameters['rpm'],
+                                    time=parameters['time'])
+    elif operation == 'incubation':
+        handler.incubation_biomek(time=parameters['time'])
 
 print(json.dumps(handler.temp_protocol, indent=4))

unilabos/registry/devices/liquid_handler.yaml

@@ -340,6 +340,21 @@ liquid_handler.biomek:
           none_keys: none_keys
         feedback: {}
         result: {}
+        handles:
+          input:
+            - handler_key: liquid-input
+              label: Liquid Input
+              data_type: resource
+              io_type: target
+              data_source: handle
+              data_key: liquid
+          output:
+            - handler_key: liquid-output
+              label: Liquid Output
+              data_type: resource
+              io_type: source
+              data_source: executor
+              data_key: liquid
       transfer_biomek:
         type: LiquidHandlerTransferBiomek
         goal:
@@ -351,6 +366,21 @@ liquid_handler.biomek:
           dispense_techniques: dispense_techniques
         feedback: {}
         result: {}
+        handles:
+          input:
+            - handler_key: liquid-input
+              label: Liquid Input
+              data_type: resource
+              io_type: target
+              data_source: handle
+              data_key: liquid
+          output:
+            - handler_key: liquid-output
+              label: Liquid Output
+              data_type: resource
+              io_type: source
+              data_source: executor
+              data_key: liquid
   schema:
     type: object
     properties: {}

unilabos/registry/registry.py

@@ -64,6 +64,7 @@ class Registry:
                                 "goal_default": yaml.safe_load(
                                     io.StringIO(get_yaml_from_goal_type(self.ResourceCreateFromOuter.Goal))
                                 ),
+                                "handles": {},
                             },
                             "create_resource": {
                                 "type": self.ResourceCreateFromOuterEasy,
@@ -84,6 +85,7 @@ class Registry:
                                 "goal_default": yaml.safe_load(
                                     io.StringIO(get_yaml_from_goal_type(self.ResourceCreateFromOuterEasy.Goal))
                                 ),
+                                "handles": {},
                             },
                             "test_latency": {
                                 "type": self.EmptyIn,
@@ -92,6 +94,7 @@ class Registry:
                                 "result": {"latency_ms": "latency_ms", "time_diff_ms": "time_diff_ms"},
                                 "schema": ros_action_to_json_schema(self.EmptyIn),
                                 "goal_default": {},
+                                "handles": {},
                             },
                         },
                     },
@@ -214,6 +217,8 @@ class Registry:
                         # 处理动作值映射
                         if "action_value_mappings" in device_config["class"]:
                             for action_name, action_config in device_config["class"]["action_value_mappings"].items():
+                                if "handles" not in action_config:
+                                    action_config["handles"] = []
                                 if "type" in action_config:
                                     action_config["type"] = self._replace_type_with_class(
                                         action_config["type"], device_id, f"动作 {action_name}"

unilabos_msgs/action/LiquidHandlerMoveBiomek.action

@@ -0,0 +1,6 @@
+string source
+string target
+
+---
+bool success
+---

unilabos_msgs/action/LiquidHandlerOscillationBiomek.action

@@ -0,0 +1,6 @@
+int32 rpm
+int32 time
+
+---
+bool success
+---

unilabos_msgs/action/LiquidHandlerPauseBiomek.action

@@ -0,0 +1,5 @@
+int32 time
+
+---
+bool success
+---

unilabos_msgs/action/LiquidHandlerTransferBiomek.action

@@ -6,5 +6,5 @@ string aspirate_technique
 string dispense_technique
 
 ---
-
+bool success
 ---