Switching to pydantic as primary object for Omni-manager

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

@@ -53,6 +53,7 @@ class BaseClass(Base):
     singles = ['id']
     omni_removes = ["id", 'submissions', "omnigui_class_dict", "omnigui_instance_dict"]
     omni_sort = ["name"]
+    omni_inheritable = []
 
     @classproperty
     def skip_on_edit(cls):
@@ -330,7 +331,15 @@ class BaseClass(Base):
         query_kwargs = {relationship_instance.query_alias: relationship_instance}
         return cls.query(**query_kwargs)
 
-    def check_all_attributes(self, attributes: dict):
+    def check_all_attributes(self, attributes: dict) -> bool:
+        """
+
+        Args:
+            attributes (dict): A dictionary of attributes to be check for equivalence
+
+        Returns:
+            bool: If a single unequivocal value is found will be false, else true.
+        """
         logger.debug(f"Incoming attributes: {attributes}")
         for key, value in attributes.items():
             # print(getattr(self.__class__, key).property)
@@ -365,7 +374,11 @@ class BaseClass(Base):
         return True
 
     def __setattr__(self, key, value):
-        logger.debug(f"Attempting to set {key} to {pformat(value)}")
+        """
+        Custom dunder method to handle potential list relationship issues.
+        """
+        if key != "_sa_instance_state":
+            logger.debug(f"Attempting to set {key} to {pformat(value)}")
         try:
             field_type = getattr(self.__class__, key)
         except AttributeError:
@@ -395,8 +408,10 @@ class BaseClass(Base):
                             else:
                                 raise ValueError("Object is too long to parse a single value.")
                         return super().__setattr__(key, value)
+                case _:
+                    return super().__setattr__(key, value)
         else:
-            super().__setattr__(key, value)
+            return super().__setattr__(key, value)
 
 
 class ConfigItem(BaseClass):

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

@@ -380,6 +380,9 @@ class KitType(BaseClass):
                 new_process.equipment_roles.append(new_role)
         return new_kit
 
+    def to_pydantic(self):
+        pass
+
 
 class ReagentRole(BaseClass):
     """
@@ -1232,6 +1235,7 @@ class KitTypeReagentRoleAssociation(BaseClass):
 
     omni_removes = BaseClass.omni_removes + ["submission_type_id", "kits_id", "reagent_roles_id", "last_used"]
     omni_sort = ["submission_type", "kit_type", "reagent_role", "required", "uses"]
+    omni_inheritable = ["submission_type", "kit_type"]
 
     reagent_roles_id = Column(INTEGER, ForeignKey("_reagentrole.id"),
                               primary_key=True)  #: id of associated reagent type

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

@@ -417,9 +417,11 @@ class BasicSubmission(BaseClass, LogMixin):
         except Exception as e:
             logger.error(f"Column count error: {e}")
         # NOTE: Get kit associated with this submission
+        logger.debug(f"Checking associations with submission type: {self.submission_type_name}")
         assoc = next((item for item in self.extraction_kit.kit_submissiontype_associations if
                       item.submission_type == self.submission_type),
                      None)
+        logger.debug(f"Got association: {assoc}")
         # NOTE: If every individual cost is 0 this is probably an old plate.
         if all(item == 0.0 for item in [assoc.constant_cost, assoc.mutable_cost_column, assoc.mutable_cost_sample]):
             try:
@@ -1325,7 +1327,10 @@ class BasicSubmission(BaseClass, LogMixin):
         if dlg.exec():
             equipment = dlg.parse_form()
             for equip in equipment:
+                logger.debug(f"Parsed equipment: {equip}")
                 _, assoc = equip.to_sql(submission=self)
+                logger.debug(f"Got equipment association: {assoc.__dict__}")
+
                 try:
                     assoc.save()
                 except AttributeError as e:

src/submissions/backend/validators/pydant.py

@@ -355,12 +355,14 @@ class PydEquipment(BaseModel, extra='ignore'):
                 # TODO: This seems precarious. What if there is more than one process?
                 # NOTE: It looks like the way fetching the processes is done in the SQL model, this shouldn't be a problem, but I'll include a failsafe.
                 # NOTE: I need to find a way to filter this by the kit involved.
+
                 if len(self.processes) > 1:
                     process = Process.query(submissiontype=submission.get_submission_type(), kittype=extraction_kit, equipmentrole=self.role)
                 else:
                     process = Process.query(name=self.processes[0])
                 if process is None:
                     logger.error(f"Found unknown process: {process}.")
+                logger.debug(f"Using process: {process}")
                 assoc.process = process
                 assoc.role = self.role
             else:
@@ -779,8 +781,10 @@ class PydSubmission(BaseModel, extra='allow'):
         """
         report = Report()
         dicto = self.improved_dict()
+        logger.debug(f"Pydantic submission type: {self.submission_type['value']}")
         instance, result = BasicSubmission.query_or_create(submission_type=self.submission_type['value'],
                                                            rsl_plate_num=self.rsl_plate_num['value'])
+        logger.debug(f"Created or queried instance: {instance}")
         report.add_result(result)
         self.handle_duplicate_samples()
         for key, value in dicto.items():
@@ -864,6 +868,7 @@ class PydSubmission(BaseModel, extra='allow'):
                             continue
                     else:
                         logger.warning(f"{key} already == {value} so no updating.")
+        logger.debug(f"Entering cost calculation for {instance}")
         try:
             instance.calculate_base_cost()
         except (TypeError, AttributeError) as e: