Pydantic switchover for omni is largely complete. Will need some debugging.

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

@@ -333,6 +333,7 @@ class BaseClass(Base):
 
     def check_all_attributes(self, attributes: dict) -> bool:
         """
+        Checks this instance against a dictionary of attributes to determine if they are a match.
 
         Args:
             attributes (dict): A dictionary of attributes to be check for equivalence
@@ -345,9 +346,16 @@ class BaseClass(Base):
             # print(getattr(self.__class__, key).property)
             if value.lower() == "none":
                 value = None
+            logger.debug(f"Attempting to grab attribute: {key}")
             self_value = getattr(self, key)
             class_attr = getattr(self.__class__, key)
-            match class_attr.property:
+            logger.debug(f"Self value: {self_value}, class attr: {class_attr} of type: {type(class_attr)}")
+            if isinstance(class_attr, property):
+                filter = "property"
+            else:
+                filter = class_attr.property
+            match filter:
+            # match class_attr:
                 case ColumnProperty():
                     match class_attr.type:
                         case INTEGER():
@@ -359,13 +367,25 @@ class BaseClass(Base):
                                 value = int(value)
                         case FLOAT():
                             value = float(value)
+                case "property":
+                    pass
                 case _RelationshipDeclared():
+                    logger.debug(f"Checking {self_value}")
                     try:
                         self_value = self_value.name
                     except AttributeError:
                         pass
                     if class_attr.property.uselist:
                         self_value = self_value.__str__()
+            try:
+                logger.debug(f"Check if {self_value.__class__} is subclass of {self.__class__}")
+                check = issubclass(self_value.__class__, self.__class__)
+            except TypeError as e:
+                logger.error(f"Couldn't check if {self_value.__class__} is subclass of {self.__class__} due to {e}")
+                check = False
+            if check:
+                logger.debug(f"Checking for subclass name.")
+                self_value = self_value.name
             logger.debug(f"Checking self_value {self_value} of type {type(self_value)} against attribute {value} of type {type(value)}")
             if self_value != value:
                 output = False
@@ -393,13 +413,15 @@ class BaseClass(Base):
                     logger.debug(f"Setting _RelationshipDeclared to {value}")
                     if field_type.property.uselist:
                         logger.debug(f"Setting with uselist")
-                        if self.__getattribute__(key) is not None:
+                        existing = self.__getattribute__(key)
+                        if existing is not None:
                             if isinstance(value, list):
-                                value = self.__getattribute__(key) + value
+                                value = existing + value
                             else:
-                                value = self.__getattribute__(key) + [value]
+                                value = existing + [value]
                         else:
                             value = [value]
+                        value = list(set(value))
                         return super().__setattr__(key, value)
                     else:
                         if isinstance(value, list):

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

@@ -15,6 +15,7 @@ from pandas import ExcelFile
 from pathlib import Path
 from . import Base, BaseClass, Organization, LogMixin
 from io import BytesIO
+from inspect import getouterframes, currentframe
 
 logger = logging.getLogger(f'submissions.{__name__}')
 
@@ -227,6 +228,20 @@ class KitType(BaseClass):
         # logger.debug(f"Output: {output}")
         return output, new_kit
 
+    @classmethod
+    def query_or_create(cls, **kwargs) -> Tuple[KitType, bool]:
+        from backend.validators.pydant import PydKitType
+        new = False
+        disallowed = ['expiry']
+        sanitized_kwargs = {k: v for k, v in kwargs.items() if k not in disallowed}
+        instance = cls.query(**sanitized_kwargs)
+        if not instance or isinstance(instance, list):
+            instance = PydKitType(**kwargs)
+            new = True
+            instance = instance.to_sql()
+        logger.info(f"Instance from query or create: {instance}")
+        return instance, new
+
     @classmethod
     @setup_lookup
     def query(cls,
@@ -380,8 +395,27 @@ class KitType(BaseClass):
                 new_process.equipment_roles.append(new_role)
         return new_kit
 
-    def to_pydantic(self):
-        pass
+    def to_omni(self, expand: bool = False) -> "OmniKitType":
+        from backend.validators.omni_gui_objects import OmniKitType
+        # logger.debug(f"self.name: {self.name}")
+        # level = len(getouterframes(currentframe()))
+        # logger.warning(f"Function level is {level}")
+        if expand:
+            processes = [item.to_omni() for item in self.processes]
+            kit_reagentrole_associations = [item.to_omni() for item in self.kit_reagentrole_associations]
+            kit_submissiontype_associations = [item.to_omni() for item in self.kit_submissiontype_associations]
+        else:
+            processes = [item.name for item in self.processes]
+            kit_reagentrole_associations = [item.name for item in self.kit_reagentrole_associations]
+            kit_submissiontype_associations = [item.name for item in self.kit_submissiontype_associations]
+        data = dict(
+            name=self.name,
+            processes=processes,
+            kit_reagentrole_associations=kit_reagentrole_associations,
+            kit_submissiontype_associations=kit_submissiontype_associations
+        )
+        logger.debug(f"Creating omni for {pformat(data)}")
+        return OmniKitType(instance_object=self, **data)
 
 
 class ReagentRole(BaseClass):
@@ -413,6 +447,20 @@ class ReagentRole(BaseClass):
         """
         return f"<ReagentRole({self.name})>"
 
+    @classmethod
+    def query_or_create(cls, **kwargs) -> Tuple[ReagentRole, bool]:
+        new = False
+        disallowed = ['expiry']
+        sanitized_kwargs = {k: v for k, v in kwargs.items() if k not in disallowed}
+        instance = cls.query(**sanitized_kwargs)
+        if not instance or isinstance(instance, list):
+            instance = cls()
+            new = True
+        for k, v in sanitized_kwargs.items():
+            setattr(instance, k, v)
+        logger.info(f"Instance from query or create: {instance}")
+        return instance, new
+
     @classmethod
     @setup_lookup
     def query(cls,
@@ -496,6 +544,11 @@ class ReagentRole(BaseClass):
     def save(self):
         super().save()
 
+    def to_omni(self, expand: bool=False):
+        from backend.validators.omni_gui_objects import OmniReagentRole
+        logger.debug(f"Constructing OmniReagentRole with name {self.name}")
+        return OmniReagentRole(instance_object=self, name=self.name, eol_ext=self.eol_ext)
+
 
 class Reagent(BaseClass, LogMixin):
     """
@@ -1010,6 +1063,20 @@ class SubmissionType(BaseClass):
         from .submissions import BasicSubmission
         return BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.name)
 
+    @classmethod
+    def query_or_create(cls, **kwargs) -> Tuple[SubmissionType, bool]:
+        new = False
+        disallowed = ['expiry']
+        sanitized_kwargs = {k: v for k, v in kwargs.items() if k not in disallowed}
+        instance = cls.query(**sanitized_kwargs)
+        if not instance or isinstance(instance, list):
+            instance = cls()
+            new = True
+        for k, v in sanitized_kwargs.items():
+            setattr(instance, k, v)
+        logger.info(f"Instance from query or create: {instance}")
+        return instance, new
+
     @classmethod
     @setup_lookup
     def query(cls,
@@ -1112,6 +1179,43 @@ class SubmissionType(BaseClass):
             Organization.import_from_yml(filepath=filepath)
         return submission_type
 
+    def to_omni(self, expand: bool = False):
+        from backend.validators.omni_gui_objects import OmniSubmissionType
+        # level = len(getouterframes(currentframe()))
+        # logger.warning(f"Function level is {level}")
+        # try:
+        #     info_map = self.submission_type.info_map
+        # except AttributeError:
+        #     info_map = {}
+        # try:
+        #     defaults = self.submission_type.defaults
+        # except AttributeError:
+        #     defaults = {}
+        # try:
+        #     sample_map = self.submission_type.sample_map
+        # except AttributeError:
+        #     sample_map = {}
+        try:
+            template_file = self.template_file
+        except AttributeError:
+            template_file = bytes()
+        if expand:
+            try:
+                processes = [item.to_omni() for item in self.processes]
+            except AttributeError:
+                processes = []
+        else:
+            processes = [item.name for item in self.processes]
+        return OmniSubmissionType(
+            instance_object=self,
+            name=self.name,
+            info_map=self.info_map,
+            defaults=self.defaults,
+            template_file=template_file,
+            processes=processes,
+            sample_map=self.sample_map
+        )
+
 
 class SubmissionTypeKitTypeAssociation(BaseClass):
     """
@@ -1164,10 +1268,18 @@ class SubmissionTypeKitTypeAssociation(BaseClass):
     def kittype(self):
         return self.kit_type
 
+    @kittype.setter
+    def kittype(self, value):
+        self.kit_type = value
+
     @hybrid_property
     def submissiontype(self):
         return self.submission_type
 
+    @submissiontype.setter
+    def submissiontype(self, value):
+        self.submission_type = value
+
     @property
     def name(self):
         try:
@@ -1175,6 +1287,20 @@ class SubmissionTypeKitTypeAssociation(BaseClass):
         except AttributeError:
             return "Blank SubmissionTypeKitTypeAssociation"
 
+    @classmethod
+    def query_or_create(cls, **kwargs) -> Tuple[SubmissionTypeKitTypeAssociation, bool]:
+        new = False
+        disallowed = ['expiry']
+        sanitized_kwargs = {k: v for k, v in kwargs.items() if k not in disallowed}
+        instance = cls.query(**sanitized_kwargs)
+        if not instance or isinstance(instance, list):
+            instance = cls()
+            new = True
+        for k, v in sanitized_kwargs.items():
+            setattr(instance, k, v)
+        logger.info(f"Instance from query or create: {instance}")
+        return instance, new
+
     @classmethod
     @setup_lookup
     def query(cls,
@@ -1226,6 +1352,36 @@ class SubmissionTypeKitTypeAssociation(BaseClass):
         base_dict['kit_type'] = self.kit_type.to_export_dict(submission_type=self.submission_type)
         return base_dict
 
+    def to_omni(self, expand: bool = False):
+        from backend.validators.omni_gui_objects import OmniSubmissionTypeKitTypeAssociation
+        # level = len(getouterframes(currentframe()))
+        # logger.warning(f"Function level is {level}")
+        if expand:
+            try:
+                submissiontype = self.submission_type.to_omni()
+            except AttributeError:
+                submissiontype = ""
+            try:
+                kittype = self.kit_type.to_omni()
+            except AttributeError:
+                kittype = ""
+        else:
+            submissiontype = self.submission_type.name
+            kittype = self.kit_type.name
+        # try:
+        #     processes = [item.to_omni() for item in self.submission_type.processes]
+        # except AttributeError:
+        #     processes = []
+        return OmniSubmissionTypeKitTypeAssociation(
+            instance_object=self,
+            submissiontype=submissiontype,
+            kittype=kittype,
+            mutable_cost_column=self.mutable_cost_column,
+            mutable_cost_sample=self.mutable_cost_sample,
+            constant_cost=self.constant_cost
+            # processes=processes,
+        )
+
 
 class KitTypeReagentRoleAssociation(BaseClass):
     """
@@ -1312,11 +1468,26 @@ class KitTypeReagentRoleAssociation(BaseClass):
             raise ValueError(f'{value} is not a reagentrole')
         return value
 
+    @classmethod
+    def query_or_create(cls, **kwargs) -> Tuple[KitTypeReagentRoleAssociation, bool]:
+        new = False
+        disallowed = ['expiry']
+        sanitized_kwargs = {k: v for k, v in kwargs.items() if k not in disallowed}
+        instance = cls.query(**sanitized_kwargs)
+        if not instance or isinstance(instance, list):
+            instance = cls()
+            new = True
+        for k, v in sanitized_kwargs.items():
+            setattr(instance, k, v)
+        logger.info(f"Instance from query or create: {instance}")
+        return instance, new
+
     @classmethod
     @setup_lookup
     def query(cls,
               kittype: KitType | str | None = None,
               reagentrole: ReagentRole | str | None = None,
+              submissiontype: SubmissionType | str | None = None,
               limit: int = 0,
               **kwargs
               ) -> KitTypeReagentRoleAssociation | List[KitTypeReagentRoleAssociation]:
@@ -1346,6 +1517,14 @@ class KitTypeReagentRoleAssociation(BaseClass):
                 query = query.join(ReagentRole).filter(ReagentRole.name == reagentrole)
             case _:
                 pass
+        match submissiontype:
+            case SubmissionType():
+                query = query.filter(cls.submission_type == submissiontype)
+            case str():
+                query = query.join(SubmissionType).filter(SubmissionType.name == submissiontype)
+            case _:
+                pass
+        pass
         if kittype is not None and reagentrole is not None:
             limit = 1
         return cls.execute_query(query=query, limit=limit)
@@ -1388,13 +1567,46 @@ class KitTypeReagentRoleAssociation(BaseClass):
     @classproperty
     def json_edit_fields(cls) -> dict:
         dicto = dict(
-                    sheet="str",
-                    expiry=dict(column="int", row="int"),
-                    lot=dict(column="int", row="int"),
-                    name=dict(column="int", row="int")
-            )
+            sheet="str",
+            expiry=dict(column="int", row="int"),
+            lot=dict(column="int", row="int"),
+            name=dict(column="int", row="int")
+        )
         return dicto
 
+    def to_omni(self, expand: bool = False) -> "OmniReagentRole":
+        from backend.validators.omni_gui_objects import OmniKitTypeReagentRoleAssociation
+        try:
+            eol_ext = self.reagent_role.eol_ext
+        except AttributeError:
+            eol_ext = timedelta(days=0)
+        if expand:
+            try:
+                submission_type = self.submission_type.to_omni()
+            except AttributeError:
+                submission_type = ""
+            try:
+                kit_type = self.kit_type.to_omni()
+            except AttributeError:
+                kit_type = ""
+            try:
+                reagent_role = self.reagent_role.to_omni()
+            except AttributeError:
+                reagent_role = ""
+        else:
+            submission_type = self.submission_type.name
+            kit_type = self.kit_type.name
+            reagent_role = self.reagent_role.name
+        return OmniKitTypeReagentRoleAssociation(
+            instance_object=self,
+            reagent_role=reagent_role,
+            eol_ext=eol_ext,
+            required=self.required,
+            submission_type=submission_type,
+            kit_type=kit_type,
+            uses=self.uses
+        )
+
 
 class SubmissionReagentAssociation(BaseClass):
     """
@@ -1716,9 +1928,28 @@ class EquipmentRole(BaseClass):
         pyd_dict['processes'] = self.get_processes(submission_type=submission_type, extraction_kit=extraction_kit)
         return PydEquipmentRole(equipment=equipment, **pyd_dict)
 
+    @classmethod
+    def query_or_create(cls, **kwargs) -> Tuple[EquipmentRole, bool]:
+        new = False
+        disallowed = ['expiry']
+        sanitized_kwargs = {k: v for k, v in kwargs.items() if k not in disallowed}
+        instance = cls.query(**sanitized_kwargs)
+        if not instance or isinstance(instance, list):
+            instance = cls()
+            new = True
+        for k, v in sanitized_kwargs.items():
+            setattr(instance, k, v)
+        logger.info(f"Instance from query or create: {instance}")
+        return instance, new
+
     @classmethod
     @setup_lookup
-    def query(cls, name: str | None = None, id: int | None = None, limit: int = 0) -> EquipmentRole | List[
+    def query(cls,
+              name: str | None = None,
+              id: int | None = None,
+              limit: int = 0,
+              **kwargs
+              ) -> EquipmentRole | List[
         EquipmentRole]:
         """
         Lookup Equipment roles.
@@ -1779,6 +2010,10 @@ class EquipmentRole(BaseClass):
         processes = self.get_processes(submission_type=submission_type, extraction_kit=kit_type)
         return dict(role=self.name, processes=[item for item in processes])
 
+    def to_omni(self, expand: bool = False) -> "OmniEquipmentRole":
+        from backend.validators.omni_gui_objects import OmniEquipmentRole
+        return OmniEquipmentRole(instance_object=self, name=self.name)
+
 
 class SubmissionEquipmentAssociation(BaseClass):
     """
@@ -1949,6 +2184,20 @@ class Process(BaseClass):
                 if value not in field:
                     field.append(value)
 
+    @classmethod
+    def query_or_create(cls, **kwargs) -> Tuple[Process, bool]:
+        new = False
+        disallowed = ['expiry']
+        sanitized_kwargs = {k: v for k, v in kwargs.items() if k not in disallowed}
+        instance = cls.query(**sanitized_kwargs)
+        if not instance or isinstance(instance, list):
+            instance = cls()
+            new = True
+        for k, v in sanitized_kwargs.items():
+            setattr(instance, k, v)
+        logger.info(f"Instance from query or create: {instance}")
+        return instance, new
+
     @classmethod
     @setup_lookup
     def query(cls,
@@ -2013,7 +2262,15 @@ class Process(BaseClass):
     def save(self):
         super().save()
 
-    # @classmethod
+    def to_omni(self, expand: bool = False):
+        from backend.validators.omni_gui_objects import OmniProcess
+        return OmniProcess(
+            instance_object=self,
+            name=self.name,
+            submission_types=[item.to_omni() for item in self.submission_types],
+            equipment_roles=[item.to_omni() for item in self.equipment_roles],
+            tip_roles=[item.to_omni() for item in self.tip_roles]
+        )
 
 
 class TipRole(BaseClass):
@@ -2034,13 +2291,51 @@ class TipRole(BaseClass):
 
     submission_types = association_proxy("tiprole_submissiontype_associations", "submission_type")
 
+    @hybrid_property
+    def tips(self):
+        return self.instances
+
     def __repr__(self):
         return f"<TipRole({self.name})>"
 
+    @classmethod
+    def query_or_create(cls, **kwargs) -> Tuple[TipRole, bool]:
+        new = False
+        disallowed = ['expiry']
+        sanitized_kwargs = {k: v for k, v in kwargs.items() if k not in disallowed}
+        instance = cls.query(**sanitized_kwargs)
+        if not instance or isinstance(instance, list):
+            instance = cls()
+            new = True
+        for k, v in sanitized_kwargs.items():
+            setattr(instance, k, v)
+        logger.info(f"Instance from query or create: {instance}")
+        return instance, new
+
+    @classmethod
+    @setup_lookup
+    def query(cls, name: str | None = None, limit: int = 0, **kwargs) -> TipRole | List[TipRole]:
+        query = cls.__database_session__.query(cls)
+        match name:
+            case str():
+                query = query.filter(cls.name == name)
+                limit = 1
+            case _:
+                pass
+        return cls.execute_query(query=query, limit=limit)
+
     @check_authorization
     def save(self):
         super().save()
 
+    def to_omni(self, expand: bool = False):
+        from backend.validators.omni_gui_objects import OmniTipRole
+        return OmniTipRole(
+            instance_object=self,
+            name=self.name,
+            tips=[item.to_omni() for item in self.tips]
+        )
+
 
 class Tips(BaseClass, LogMixin):
     """
@@ -2070,6 +2365,20 @@ class Tips(BaseClass, LogMixin):
     def __repr__(self):
         return f"<Tips({self.name})>"
 
+    @classmethod
+    def query_or_create(cls, **kwargs) -> Tuple[Tips, bool]:
+        new = False
+        disallowed = ['expiry']
+        sanitized_kwargs = {k: v for k, v in kwargs.items() if k not in disallowed}
+        instance = cls.query(**sanitized_kwargs)
+        if not instance or isinstance(instance, list):
+            instance = cls()
+            new = True
+        for k, v in sanitized_kwargs.items():
+            setattr(instance, k, v)
+        logger.info(f"Instance from query or create: {instance}")
+        return instance, new
+
     @classmethod
     def query(cls, name: str | None = None, lot: str | None = None, limit: int = 0, **kwargs) -> Tips | List[Tips]:
         """
@@ -2101,6 +2410,13 @@ class Tips(BaseClass, LogMixin):
     def save(self):
         super().save()
 
+    def to_omni(self, expand: bool = True):
+        from backend.validators.omni_gui_objects import OmniTips
+        return OmniTips(
+            instance_object=self,
+            name=self.name
+        )
+
 
 class SubmissionTypeTipRoleAssociation(BaseClass):
     """
@@ -2129,6 +2445,9 @@ class SubmissionTypeTipRoleAssociation(BaseClass):
     def save(self):
         super().save()
 
+    def to_omni(self):
+        pass
+
 
 class SubmissionTipsAssociation(BaseClass):
     """

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

@@ -10,9 +10,7 @@ from zipfile import ZipFile, BadZipfile
 from tempfile import TemporaryDirectory, TemporaryFile
 from operator import itemgetter
 from pprint import pformat
-
 from sqlalchemy.ext.hybrid import hybrid_property
-
 from . import BaseClass, Reagent, SubmissionType, KitType, Organization, Contact, LogMixin, SubmissionReagentAssociation
 from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case, func
 from sqlalchemy.orm import relationship, validates, Query
@@ -24,7 +22,7 @@ from sqlite3 import OperationalError as SQLOperationalError, IntegrityError as S
 from openpyxl import Workbook
 from openpyxl.drawing.image import Image as OpenpyxlImage
 from tools import row_map, setup_lookup, jinja_template_loading, rreplace, row_keys, check_key_or_attr, Result, Report, \
-    report_result, create_holidays_for_year
+    report_result, create_holidays_for_year, check_dictionary_inclusion_equality
 from datetime import datetime, date, timedelta
 from typing import List, Any, Tuple, Literal, Generator, Type
 from dateutil.parser import parse
@@ -558,12 +556,14 @@ class BasicSubmission(BaseClass, LogMixin):
                         existing = value
                     case _:
                         existing = self.__getattribute__(key)
+                        logger.debug(f"Existing value is {pformat(existing)}")
                         if value in ['', 'null', None]:
                             logger.error(f"No value given, not setting.")
                             return
                         if existing is None:
                             existing = []
-                        if value in existing:
+                        # if value in existing:
+                        if check_dictionary_inclusion_equality(existing, value):
                             logger.warning("Value already exists. Preventing duplicate addition.")
                             return
                         else:
@@ -572,6 +572,7 @@ class BasicSubmission(BaseClass, LogMixin):
                             else:
                                 if value:
                                     existing.append(value)
+
                 self.__setattr__(key, existing)
                 # NOTE: Make sure this gets updated by telling SQLAlchemy it's been modified.
                 flag_modified(self, key)
@@ -1223,10 +1224,19 @@ class BasicSubmission(BaseClass, LogMixin):
             if "submitted_date" not in kwargs.keys():
                 instance.submitted_date = date.today()
         else:
+            from frontend.widgets.pop_ups import QuestionAsker
             logger.warning(f"Found existing instance: {instance}, asking to overwrite.")
-            code = 1
-            msg = "This submission already exists.\nWould you like to overwrite?"
-        report.add_result(Result(msg=msg, code=code))
+        #     code = 1
+        #     msg = "This submission already exists.\nWould you like to overwrite?"
+        # report.add_result(Result(msg=msg, code=code))
+            dlg = QuestionAsker(title="Overwrite?", message="This submission already exists.\nWould you like to overwrite?")
+            if dlg.exec():
+                pass
+            else:
+                code = 1
+                msg = "This submission already exists.\nWould you like to overwrite?"
+                report.add_result(Result(msg=msg, code=code))
+                return None, report
         return instance, report
 
     # NOTE: Custom context events for the ui
@@ -1528,6 +1538,7 @@ class Wastewater(BasicSubmission):
                 dummy_samples.append(thing)
             output['origin_plate'] = self.__class__.make_plate_map(sample_list=dummy_samples, plate_rows=4,
                                                                    plate_columns=6)
+        # logger.debug(f"PCR info: {output['pcr_info']}")
         return output
 
     @classmethod

src/submissions/backend/validators/pydant.py

@@ -483,7 +483,6 @@ class PydSubmission(BaseModel, extra='allow'):
         value['value'] = output.replace(tzinfo=timezone)
         return value
 
-
     @field_validator("submitting_lab", mode="before")
     @classmethod
     def rescue_submitting_lab(cls, value):
@@ -772,7 +771,7 @@ class PydSubmission(BaseModel, extra='allow'):
         return missing_info, missing_reagents
 
     @report_result
-    def to_sql(self) -> Tuple[BasicSubmission, Report]:
+    def to_sql(self) -> Tuple[BasicSubmission | None, Report]:
         """
         Converts this instance into a backend.db.models.submissions.BasicSubmission instance
 
@@ -782,12 +781,19 @@ class PydSubmission(BaseModel, extra='allow'):
         report = Report()
         dicto = self.improved_dict()
         logger.debug(f"Pydantic submission type: {self.submission_type['value']}")
+        logger.debug(f"Pydantic improved_dict: {pformat(dicto)}")
+        # At this point, pcr_info is not duplicated
         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}")
+        # logger.debug(f"Created or queried instance: {instance}")
+        if instance is None:
+            report.add_result(Result(msg="Overwrite Cancelled."))
+            return None, report
         report.add_result(result)
         self.handle_duplicate_samples()
         for key, value in dicto.items():
+            logger.debug(f"Checking key {key}, value {value}")
+            # At this point, pcr_info is not duplicated.
             if isinstance(value, dict):
                 try:
                     value = value['value']
@@ -843,6 +849,8 @@ class PydSubmission(BaseModel, extra='allow'):
                         value = value
                     instance.set_attribute(key=key, value=value)
                 case item if item in instance.jsons:
+                    # At this point pcr_info is not duplicated
+                    logger.debug(f"Validating json value: {item} to value:{pformat(value)}")
                     try:
                         ii = value.items()
                     except AttributeError:
@@ -851,7 +859,9 @@ class PydSubmission(BaseModel, extra='allow'):
                         if isinstance(v, datetime):
                             value[k] = v.strftime("%Y-%m-%d %H:%M:%S")
                         else:
-                            value[k] = v
+                            pass
+                    logger.debug(f"Setting json value: {item} to value:{pformat(value)}")
+                    # At this point, pcr_info is not duplicated.
                     instance.set_attribute(key=key, value=value)
                 case _:
                     try:
@@ -899,6 +909,10 @@ class PydSubmission(BaseModel, extra='allow'):
             SubmissionFormWidget: Submission form widget
         """
         from frontend.widgets.submission_widget import SubmissionFormWidget
+        try:
+            logger.debug(f"PCR info: {self.pcr_info}")
+        except AttributeError:
+            pass
         return SubmissionFormWidget(parent=parent, submission=self, disable=disable)
 
     def to_writer(self) -> "SheetWriter":
@@ -1124,7 +1138,7 @@ class PydReagentRole(BaseModel):
 
 class PydKitType(BaseModel):
     name: str
-    reagent_roles: List[PydReagentRole] = []
+    reagent_roles: List[PydReagent] = []
 
     @report_result
     def to_sql(self) -> Tuple[KitType, Report]:

src/submissions/frontend/widgets/app.py

@@ -9,6 +9,7 @@ from PyQt6.QtWidgets import (
     QHBoxLayout, QScrollArea, QMainWindow,
     QToolBar
 )
+import pickle
 from PyQt6.QtGui import QAction
 from pathlib import Path
 from markdown import markdown
@@ -238,11 +239,17 @@ class App(QMainWindow):
 
     @under_development
     def manage_kits(self, *args, **kwargs):
-        dlg = ManagerWindow(parent=self, object_type=KitType, extras=[], add_edit='edit', managers=set())
+        from frontend.widgets.omni_manager_pydant import ManagerWindow as ManagerWindowPyd
+        dlg = ManagerWindowPyd(parent=self, object_type=KitType, extras=[], add_edit='edit', managers=set())
         if dlg.exec():
             output = dlg.parse_form()
-            assert isinstance(output, KitType)
-            output.save()
+            # assert isinstance(output, KitType)
+            # output.save()
+            logger.debug(f"Kit output: {pformat(output.__dict__)}")
+            # output.to_sql()
+            with open(f"{output.name}.obj", "wb") as f:
+                pickle.dump(output, f)
+
 
 class AddSubForm(QWidget):
 

src/submissions/frontend/widgets/omni_manager.py

@@ -211,7 +211,7 @@ class ManagerWindow(QDialog):
                 else:
                     value = current_value + [data]
             setattr(self.instance, name, value)
-            self.instance.save()
+            # self.instance.save()
 
     def toggle_textedit(self, caller_child=None):
         already_exists = self.findChildren(LargeTextEdit)
@@ -369,7 +369,7 @@ class EditRelationship(QWidget):
             new_instance = dlg.parse_form()
             # NOTE: My custom __setattr__ should take care of any list problems.
             self.parent().instance.__setattr__(self.objectName(), new_instance)
-            self.parent().instance.save()
+            # self.parent().instance.save()
             self.parent().update_data()
 
     def add_existing(self):
@@ -381,7 +381,7 @@ class EditRelationship(QWidget):
                 instance = self.class_object.query(**row)
                 # NOTE: My custom __setattr__ should take care of any list problems.
                 self.parent().instance.__setattr__(self.objectName(), instance)
-                self.parent().instance.save()
+                # self.parent().instance.save()
                 self.parent().update_data()
 
     def set_data(self) -> None:

src/submissions/frontend/widgets/submission_widget.py

@@ -371,6 +371,9 @@ class SubmissionFormWidget(QWidget):
             case _:
                 pass
         # NOTE: add reagents to submission object
+        if base_submission is None:
+            # self.app.table_widget.sub_wid.setData()
+            return
         for reagent in base_submission.reagents:
             reagent.update_last_used(kit=base_submission.extraction_kit)
         save_output = base_submission.save()

src/submissions/tools/__init__.py

@@ -821,7 +821,7 @@ def check_object_in_manager(manager: list, object_name: object) -> Tuple[Any, bo
     # for manager in managers:
     if manager is None:
         return None, False
-    logger.debug(f"Manager: {manager}, aliases: {manager.aliases}, Key: {object_name}")
+    # logger.debug(f"Manager: {manager}, aliases: {manager.aliases}, Key: {object_name}")
     if object_name in manager.aliases:
         return manager, True
     relationships = [getattr(manager.__class__, item) for item in dir(manager.__class__)
@@ -1113,7 +1113,7 @@ def report_result(func):
 
     @wraps(func)
     def wrapper(*args, **kwargs):
-        logger.info(f"Report result being called by {func.__name__}")
+        # logger.info(f"Report result being called by {func.__name__}")
         output = func(*args, **kwargs)
         match output:
             case Report():
@@ -1201,6 +1201,28 @@ def create_holidays_for_year(year: int | None = None) -> List[date]:
     return sorted(holidays)
 
 
+def check_dictionary_inclusion_equality(listo: List[dict] | dict, dicto: dict) -> bool:
+    """
+    Determines if a dictionary is in a list of dictionaries (possible ordering issue with just using dict in list)
+
+    Args:
+        listo (List[dict): List of dictionaries to compare to.
+        dicto (dict): Dictionary to compare.
+
+    Returns:
+        bool: True if dicto is equal to any dictionary in the list.
+    """
+    logger.debug(f"Comparing: {listo} and {dicto}")
+    if isinstance(dicto, list) and isinstance(listo, list):
+        return listo == dicto
+    elif isinstance(dicto, dict) and isinstance(listo, dict):
+        return listo == dicto
+    elif isinstance(dicto, dict) and isinstance(listo, list):
+        return any([dicto == d for d in listo])
+    else:
+        raise TypeError(f"Unsupported variable: {type(listo)}")
+
+
 class classproperty(property):
     def __get__(self, owner_self, owner_cls):
         return self.fget(owner_cls)