Fixed Tips not being written during export.

src/submissions/backend/db/models/procedures.py

@@ -995,6 +995,7 @@ class Procedure(BaseClass):
     def to_pydantic(self, **kwargs):
         from backend.validators.pydant import PydReagent
         output = super().to_pydantic()
+        print(f"Super to_pydantic: {output.equipment}")
         output.sample = [item.to_pydantic() for item in output.proceduresampleassociation]
         reagents = []
         for reagent in output.reagent:
@@ -1009,7 +1010,6 @@ class Procedure(BaseClass):
         output.result = [item.to_pydantic() for item in self.results]
         output.sample_results = flatten_list(
             [[result.to_pydantic() for result in item.results] for item in self.proceduresampleassociation])
-
         return output
 
     def create_proceduresampleassociations(self, sample):
@@ -2148,7 +2148,7 @@ class ProcedureEquipmentAssociation(BaseClass):
     @property
     def tips(self):
         try:
-            return Tips.query(id=self.tips_id, limit=1)
+            return TipsLot.query(id=self.tipslot_id, limit=1)
         except AttributeError:
             return None
 
@@ -2175,7 +2175,9 @@ class ProcedureEquipmentAssociation(BaseClass):
             PydEquipment: pydantic equipment model
         """
         from backend.validators import PydEquipment
-        return PydEquipment(**self.details_dict())
+        output = PydEquipment(**self.details_dict())
+        output.tips = self.tips.to_pydantic(pyd_model_name="PydTips")
+        return output
 
     @classmethod
     @setup_lookup
@@ -2232,7 +2234,7 @@ class ProcedureEquipmentAssociation(BaseClass):
             output['processversion'] = None
         try:
             output['tips'] = self.tipslot.details_dict()
-        except AttributeError:
+        except AttributeError as e:
             output['tips'] = None
         return output
 

src/submissions/backend/excel/writers/procedure_writers/__init__.py

@@ -15,7 +15,7 @@ class ProcedureInfoWriter(DefaultKEYVALUEWriter):
     header_order = []
     exclude = ['control', 'equipment', 'excluded', 'id', 'misc_info', 'plate_map', 'possible_kits',
                'procedureequipmentassociation', 'procedurereagentassociation', 'proceduresampleassociation', 'proceduretipsassociation', 'reagent',
-               'reagentrole', 'results', 'sample', 'tips', 'reagentlot']
+               'reagentrole', 'results', 'sample', 'tips', 'reagentlot', 'platemap']
 
     def __init__(self, pydant_obj, *args, **kwargs):
         super().__init__(pydant_obj=pydant_obj, *args, **kwargs)
@@ -45,7 +45,7 @@ class ProcedureReagentWriter(DefaultTABLEWriter):
 
 class ProcedureEquipmentWriter(DefaultTABLEWriter):
 
-    exclude = ['id']
+    exclude = ['id', "equipment_role"]
     header_order = ['equipmentrole', 'name', 'asset_number', 'process', 'tips']
 
     def __init__(self, pydant_obj, range_dict: dict | None = None, *args, **kwargs):

src/submissions/backend/managers/runs.py

@@ -14,10 +14,12 @@ class DefaultRunManager(DefaultManager):
     def write(self) -> Workbook:
         from backend.managers import DefaultClientSubmissionManager, DefaultProcedureManager
         logger.info(f"Initializing write")
-        clientsubmission = DefaultClientSubmissionManager(parent=self.parent, input_object=self.pyd.clientsubmission, submissiontype=self.pyd.clientsubmission.submissiontype)
+        self.clientsubmission = DefaultClientSubmissionManager(parent=self.parent, input_object=self.pyd.clientsubmission, submissiontype=self.pyd.clientsubmission.submissiontype)
         workbook = Workbook()
-        workbook = clientsubmission.write(workbook=workbook)
+        workbook = self.clientsubmission.write(workbook=workbook)
+        self.procedures = []
         for procedure in self.pyd.procedure:
             procedure = DefaultProcedureManager(proceduretype=procedure.proceduretype, parent=self.parent, input_object=procedure)
             workbook: Workbook = procedure.write(workbook=workbook)
+            self.procedures.append(procedure)
         return workbook

src/submissions/backend/validators/pydant.py

@@ -143,6 +143,7 @@ class PydReagentLot(PydBaseClass):
     missing: bool = Field(default=True)
     comment: str | None = Field(default="", validate_default=True)
 
+
 class PydReagent(PydBaseClass):
     lot: str | None
     reagentrole: str | None
@@ -388,23 +389,29 @@ class PydEquipment(PydBaseClass):
     @field_validator('tips', mode='before')
     @classmethod
     def tips_to_pydantic(cls, value, values):
+        print(f"Value coming into tips: {value}")
         if isinstance(value, GeneratorType):
             value = [item for item in value]
         value = convert_nans_to_nones(value)
         if not value:
             value = []
-        if isinstance(value, TipsLot):
-            value = value.to_pydantic(pyd_model_name="PydTips")
-        else:
-            try:
-                d: Tips = next(
-                    (tips for tips in value if values.data['name'] in [item.name for item in tips.equipment]),
-                    None)
-                if d:
-                    value = d.to_pydantic()
-            except AttributeError as e:
-                logger.error(f"Process Validation error due to {e}")
-                value = []
+        match value:
+            case TipsLot():
+                value = value.to_pydantic(pyd_model_name="PydTips")
+            case dict():
+                value = PydTips(**value)
+            case _:
+                pass
+        # else:
+        #     try:
+        #         d: Tips = next(
+        #             (tips for tips in value if values.data['name'] in [item.name for item in tips.equipment]),
+        #             None)
+        #         if d:
+        #             value = d.to_pydantic()
+        #     except AttributeError as e:
+        #         logger.error(f"Process Validation error due to {e}")
+        #         value = []
         return value
 
     @report_result
@@ -471,7 +478,6 @@ class PydEquipment(PydBaseClass):
         return {k: getattr(self, k) for k in fields}
 
 
-
 class PydContact(BaseModel):
     name: str
     phone: str | None