Mid change in details templates

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

@@ -147,10 +147,6 @@ class BaseClass(Base):
                 case _:
                     return query.limit(limit).all()
 
-    @classmethod
-    def default_info_return(cls, info, *args):
-        return info
-
     def save(self):
         """
         Add the object to the database and commit
@@ -191,7 +187,7 @@ class ConfigItem(BaseClass):
 
 
 from .controls import *
-# import order must go: orgs, kit, subs due to circular import issues
+# NOTE: import order must go: orgs, kit, subs due to circular import issues
 from .organizations import *
 from .kits import *
 from .submissions import *

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

@@ -84,7 +84,7 @@ class ControlType(BaseClass):
         Returns:
             List[ControlType]: Control types that have targets
         """
-        return [item for item in cls.query() if item.targets != []]
+        return [item for item in cls.query() if item.targets]# != []]
 
     @classmethod
     def build_positive_regex(cls) -> Pattern:

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

@@ -743,7 +743,7 @@ class SubmissionType(BaseClass):
                             item.equipment_role == equipment_role]
             case _:
                 raise TypeError(f"Type {type(equipment_role)} is not allowed")
-        return list(set([item for items in relevant for item in items if item != None]))
+        return list(set([item for items in relevant for item in items if item is not None]))
 
     def get_submission_class(self) -> "BasicSubmission":
         """
@@ -982,7 +982,7 @@ class KitTypeReagentRoleAssociation(BaseClass):
                 query = query.join(ReagentRole).filter(ReagentRole.name == reagent_role)
             case _:
                 pass
-        if kit_type != None and reagent_role != None:
+        if kit_type is not None and reagent_role is not None:
             limit = 1
         return cls.execute_query(query=query, limit=limit)
 
@@ -1339,7 +1339,7 @@ class EquipmentRole(BaseClass):
         if isinstance(submission_type, str):
             # logger.debug(f"Checking if str {submission_type} exists")
             submission_type = SubmissionType.query(name=submission_type)
-        if submission_type != None:
+        if submission_type is not None:
             # logger.debug("Getting all processes for this EquipmentRole")
             processes = [process for process in self.processes if submission_type in process.submission_types]
         else:
@@ -1421,7 +1421,7 @@ class SubmissionTypeEquipmentRoleAssociation(BaseClass):
                                   back_populates="equipmentrole_submissiontype_associations")  #: associated equipment
 
     @validates('static')
-    def validate_age(self, key, value):
+    def validate_static(self, key, value):
         """
         Ensures only 1 & 0 used in 'static'
 
@@ -1451,7 +1451,7 @@ class SubmissionTypeEquipmentRoleAssociation(BaseClass):
         """
         processes = [equipment.get_processes(self.submission_type) for equipment in self.equipment_role.instances]
         # flatten list
-        processes = [item for items in processes for item in items if item != None]
+        processes = [item for items in processes for item in items if item is not None]
         match extraction_kit:
             case str():
                 # logger.debug(f"Filtering Processes by extraction_kit str {extraction_kit}")
@@ -1474,7 +1474,7 @@ class Process(BaseClass):
     """
 
     id = Column(INTEGER, primary_key=True)  #: Process id, primary key
-    name = Column(String(64))  #: Process name
+    name = Column(String(64), unique=True)  #: Process name
     submission_types = relationship("SubmissionType", back_populates='processes',
                                     secondary=submissiontypes_processes)  #: relation to SubmissionType
     equipment = relationship("Equipment", back_populates='processes',
@@ -1497,7 +1497,10 @@ class Process(BaseClass):
 
     @classmethod
     @setup_lookup
-    def query(cls, name: str | None = None, limit: int = 0) -> Process | List[Process]:
+    def query(cls,
+              name: str | None = None,
+              id: int = 1,
+              limit: int = 0) -> Process | List[Process]:
         """
         Lookup Processes
 
@@ -1516,9 +1519,19 @@ class Process(BaseClass):
                 limit = 1
             case _:
                 pass
+        match id:
+            case int():
+                query = query.filter(cls.id == id)
+                limit = 1
+            case _:
+                pass
         return cls.execute_query(query=query, limit=limit)
 
 
+    @check_authorization
+    def save(self):
+        super().save()
+
 class TipRole(BaseClass):
     """
     An abstract role that a tip fills during a process
@@ -1539,6 +1552,10 @@ class TipRole(BaseClass):
 
     def __repr__(self):
         return f"<TipRole({self.name})>"
+    
+    @check_authorization
+    def save(self):
+        super().save()
 
 
 class Tips(BaseClass):
@@ -1593,6 +1610,10 @@ class Tips(BaseClass):
             case _:
                 pass
         return cls.execute_query(query=query, limit=limit)
+    
+    @check_authorization
+    def save(self):
+        super().save()
 
 
 class SubmissionTypeTipRoleAssociation(BaseClass):
@@ -1609,6 +1630,10 @@ class SubmissionTypeTipRoleAssociation(BaseClass):
                                    back_populates="submissiontype_tiprole_associations")  #: associated submission
     tip_role = relationship(TipRole,
                             back_populates="tiprole_submissiontype_associations")  #: associated equipment
+    
+    @check_authorization
+    def save(self):
+        super().save()
 
 
 class SubmissionTipsAssociation(BaseClass):

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

@@ -70,7 +70,6 @@ class Organization(BaseClass):
             case _:
                 pass
         return cls.execute_query(query=query, limit=limit)
-        # return query.first()
 
     @check_authorization
     def save(self):
@@ -117,7 +116,6 @@ class Contact(BaseClass):
         Returns:
             Contact|List[Contact]: Contact(s) of interest.
         """
-        # super().query(session)
         query: Query = cls.__database_session__.query(cls)
         match name:
             case str():

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

@@ -22,7 +22,7 @@ import pandas as pd
 from openpyxl import Workbook
 from openpyxl.worksheet.worksheet import Worksheet
 from openpyxl.drawing.image import Image as OpenpyxlImage
-from tools import row_map, setup_lookup, jinja_template_loading, rreplace, row_keys
+from tools import row_map, setup_lookup, jinja_template_loading, rreplace, row_keys, check_key_or_attr
 from datetime import datetime, date
 from typing import List, Any, Tuple, Literal
 from dateutil.parser import parse
@@ -145,7 +145,6 @@ class BasicSubmission(BaseClass):
             output += BasicSubmission.timestamps()
         return output
 
-    # TODO: Beef up this to include info_map from DB
     @classmethod
     def get_default_info(cls, *args):
         # NOTE: Create defaults for all submission_types
@@ -443,7 +442,7 @@ class BasicSubmission(BaseClass):
         """
         # logger.debug(f"Querying Type: {submission_type}")
         # logger.debug(f"Using limit: {limit}")
-        # use lookup function to create list of dicts
+        # NOTE: use lookup function to create list of dicts
         subs = [item.to_dict() for item in
                 cls.query(submission_type=submission_type, limit=limit, chronologic=chronologic)]
         # logger.debug(f"Got {len(subs)} submissions.")
@@ -498,7 +497,7 @@ class BasicSubmission(BaseClass):
             case "submission_type":
                 field_value = SubmissionType.query(name=value)
             case "sample_count":
-                if value == None:
+                if value is None:
                     field_value = len(self.samples)
                 else:
                     field_value = value
@@ -607,7 +606,7 @@ class BasicSubmission(BaseClass):
         super().save()
 
     @classmethod
-    def get_regex(cls):
+    def get_regex(cls) -> str:
         return cls.construct_regex()
 
     # Polymorphic functions
@@ -742,7 +741,6 @@ class BasicSubmission(BaseClass):
             str: Updated name.
         """
         # logger.info(f"Hello from {cls.__mapper_args__['polymorphic_identity']} Enforcer!")
-        # return instr
         from backend.validators import RSLNamer
         # logger.debug(f"instr coming into {cls}: {instr}")
         # logger.debug(f"data coming into {cls}: {data}")
@@ -773,7 +771,7 @@ class BasicSubmission(BaseClass):
         # logger.debug(f"After addition of plate number the plate name is: {outstr}")
         try:
             repeat = re.search(r"-\dR(?P<repeat>\d)?", outstr).groupdict()['repeat']
-            if repeat == None:
+            if repeat is None:
                 repeat = "1"
         except AttributeError as e:
             repeat = ""
@@ -835,6 +833,15 @@ class BasicSubmission(BaseClass):
 
     @classmethod
     def adjust_autofill_samples(cls, samples: List[Any]) -> List[Any]:
+        """
+        Makes adjustments to samples before writing to excel.
+
+        Args:
+            samples (List[Any]): List of Samples
+
+        Returns:
+            List[Any]: Updated list of samples
+        """        
         logger.info(f"Hello from {cls.__mapper_args__['polymorphic_identity']} sampler")
         return samples
 
@@ -953,7 +960,7 @@ class BasicSubmission(BaseClass):
                 query = query.filter(model.submitted_date == start_date)
             else:
                 query = query.filter(model.submitted_date.between(start_date, end_date))
-        # by reagent (for some reason)
+        # NOTE: by reagent (for some reason)
         match reagent:
             case str():
                 # logger.debug(f"Looking up BasicSubmission with reagent: {reagent}")
@@ -965,7 +972,7 @@ class BasicSubmission(BaseClass):
                     SubmissionSampleAssociation.reagent).filter(Reagent.lot == reagent)
             case _:
                 pass
-        # by rsl number (returns only a single value)
+        # NOTE: by rsl number (returns only a single value)
         match rsl_plate_num:
             case str():
                 query = query.filter(model.rsl_plate_num == rsl_plate_num)
@@ -973,7 +980,7 @@ class BasicSubmission(BaseClass):
                 limit = 1
             case _:
                 pass
-        # by id (returns only a single value)
+        # NOTE: by id (returns only a single value)
         match id:
             case int():
                 # logger.debug(f"Looking up BasicSubmission with id: {id}")
@@ -1051,7 +1058,7 @@ class BasicSubmission(BaseClass):
         Performs backup and deletes this instance from database.
 
         Args:
-            obj (_type_, optional): Parent Widget. Defaults to None.
+            obj (_type_, optional): Parent widget. Defaults to None.
 
         Raises:
             e: _description_
@@ -1075,7 +1082,7 @@ class BasicSubmission(BaseClass):
         Creates Widget for showing submission details.
 
         Args:
-            obj (_type_): parent widget
+            obj (_type_): Parent widget
         """
         # logger.debug("Hello from details")
         from frontend.widgets.submission_details import SubmissionDetails
@@ -1084,6 +1091,12 @@ class BasicSubmission(BaseClass):
             pass
 
     def edit(self, obj):
+        """
+        Return submission to form widget for updating
+
+        Args:
+            obj (Widget): Parent widget 
+        """        
         from frontend.widgets.submission_widget import SubmissionFormWidget
         for widg in obj.app.table_widget.formwidget.findChildren(SubmissionFormWidget):
             # logger.debug(widg)
@@ -1224,9 +1237,9 @@ class BacterialCulture(BasicSubmission):
         """
         from . import ControlType
         input_dict = super().finalize_parse(input_dict, xl, info_map)
-        # build regex for all control types that have targets
+        # NOTE: build regex for all control types that have targets
         regex = ControlType.build_positive_regex()
-        # search samples for match
+        # NOTE: search samples for match
         for sample in input_dict['samples']:
             matched = regex.match(sample['submitter_id'])
             if bool(matched):
@@ -1311,7 +1324,7 @@ class Wastewater(BasicSubmission):
             dict: Updated sample dictionary
         """
         input_dict = super().custom_info_parser(input_dict)
-        if xl != None:
+        if xl is not None:
             input_dict['csv'] = xl["Copy to import file"]
         return input_dict
 
@@ -1355,7 +1368,7 @@ class Wastewater(BasicSubmission):
         Extends parent
         """
         try:
-            # Deal with PCR file.
+            # NOTE: Deal with PCR file.
             instr = re.sub(r"PCR(-|_)", "", instr)
         except (AttributeError, TypeError) as e:
             logger.error(f"Problem using regex: {e}")
@@ -1413,6 +1426,15 @@ class Wastewater(BasicSubmission):
 
     @classmethod
     def finalize_details(cls, input_dict: dict) -> dict:
+        """
+        Makes changes to information before display
+
+        Args:
+            input_dict (dict): Input information
+
+        Returns:
+            dict: Updated information
+        """        
         input_dict = super().finalize_details(input_dict)
         dummy_samples = []
         for item in input_dict['samples']:
@@ -1430,11 +1452,23 @@ class Wastewater(BasicSubmission):
         return input_dict
 
     def custom_context_events(self) -> dict:
+        """
+        Sets context events for main widget
+
+        Returns:
+            dict: Context menu items for this instance.
+        """        
         events = super().custom_context_events()
         events['Link PCR'] = self.link_pcr
         return events
 
     def link_pcr(self, obj):
+        """
+        Adds PCR info to this submission
+
+        Args:
+            obj (_type_): Parent widget
+        """        
         from backend.excel import PCRParser
         from frontend.widgets import select_open_file
         fname = select_open_file(obj=obj, file_extension="xlsx")
@@ -1562,7 +1596,7 @@ class WastewaterArtic(BasicSubmission):
         """
         input_dict = super().parse_samples(input_dict)
         input_dict['sample_type'] = "Wastewater Sample"
-        # Because generate_sample_object needs the submitter_id and the artic has the "({origin well})"
+        # NOTE: Because generate_sample_object needs the submitter_id and the artic has the "({origin well})"
         # at the end, this has to be done here. No moving to sqlalchemy object :(
         input_dict['submitter_id'] = re.sub(r"\s\(.+\)\s?$", "", str(input_dict['submitter_id'])).strip()
         try:
@@ -1576,9 +1610,10 @@ class WastewaterArtic(BasicSubmission):
         except KeyError:
             logger.error(f"Unable to set ww_processing_num for sample {input_dict['submitter_id']}")
         year = str(date.today().year)[-2:]
-        # if "ENC" in input_dict['submitter_id']:
+        # NOTE: Check for extraction negative control (Enterics)
         if re.search(rf"^{year}-(ENC)", input_dict['submitter_id']):
             input_dict['rsl_number'] = cls.en_adapter(input_str=input_dict['submitter_id'])
+        # NOTE: Check for extraction negative control (Robotics)
         if re.search(rf"^{year}-(RSL)", input_dict['submitter_id']):
             input_dict['rsl_number'] = cls.pbs_adapter(input_str=input_dict['submitter_id'])
         return input_dict
@@ -1595,11 +1630,11 @@ class WastewaterArtic(BasicSubmission):
             str: output name
         """
         # logger.debug(f"input string raw: {input_str}")
-        # Remove letters.
+        # NOTE: Remove letters.
         processed = input_str.replace("RSL", "")
         processed = re.sub(r"\(.*\)$", "", processed).strip()
         processed = re.sub(r"[A-QS-Z]+\d*", "", processed)
-        # Remove trailing '-' if any
+        # NOTE: Remove trailing '-' if any
         processed = processed.strip("-")
         # logger.debug(f"Processed after stripping letters: {processed}")
         try:
@@ -1632,7 +1667,7 @@ class WastewaterArtic(BasicSubmission):
     @classmethod
     def pbs_adapter(cls, input_str):
         """
-                Stopgap solution because WW names their ENs different
+                Stopgap solution because WW names their controls different
 
                 Args:
                     input_str (str): input name
@@ -1641,20 +1676,13 @@ class WastewaterArtic(BasicSubmission):
                     str: output name
                 """
         # logger.debug(f"input string raw: {input_str}")
-        # Remove letters.
+        # NOTE: Remove letters.
         processed = input_str.replace("RSL", "")
         processed = re.sub(r"\(.*\)$", "", processed).strip()
         processed = re.sub(r"[A-QS-Z]+\d*", "", processed)
-        # Remove trailing '-' if any
+        # NOTE: Remove trailing '-' if any
         processed = processed.strip("-")
         # logger.debug(f"Processed after stripping letters: {processed}")
-        # try:
-        #     en_num = re.search(r"\-\d{1}$", processed).group()
-        #     processed = rreplace(processed, en_num, "")
-        # except AttributeError:
-        #     en_num = "1"
-        # en_num = en_num.strip("-")
-        # logger.debug(f"Processed after en_num: {processed}")
         try:
             plate_num = re.search(r"\-\d{1}R?\d?$", processed).group()
             processed = rreplace(processed, plate_num, "")
@@ -1728,13 +1756,15 @@ class WastewaterArtic(BasicSubmission):
             Workbook: Updated workbook
         """
         input_excel = super().custom_info_writer(input_excel, info, backup)
-        logger.debug(f"Info:\n{pformat(info)}")
-        check = 'source_plates' in info.keys() and info['source_plates'] is not None
-        if check:
+        # logger.debug(f"Info:\n{pformat(info)}")
+        # NOTE: check for source plate information
+        # check = 'source_plates' in info.keys() and info['source_plates'] is not None
+        if check_key_or_attr(key='source_plates', interest=info, check_none=True):
             worksheet = input_excel['First Strand List']
             start_row = 8
+            # NOTE: write source plates to First strand list
             for iii, plate in enumerate(info['source_plates']['value']):
-                logger.debug(f"Plate: {plate}")
+                # logger.debug(f"Plate: {plate}")
                 row = start_row + iii
                 try:
                     worksheet.cell(row=row, column=3, value=plate['plate'])
@@ -1744,41 +1774,45 @@ class WastewaterArtic(BasicSubmission):
                     worksheet.cell(row=row, column=4, value=plate['starting_sample'])
                 except TypeError:
                     pass
-        check = 'gel_info' in info.keys() and info['gel_info']['value'] is not None
-        if check:
+        # NOTE: check for gel information
+        # check = 'gel_info' in info.keys() and info['gel_info']['value'] is not None
+        if check_key_or_attr(key='gel_info', interest=info, check_none=True):
             # logger.debug(f"Gel info check passed.")
-            if info['gel_info'] != None:
-                # logger.debug(f"Gel info not none.")
-                worksheet = input_excel['Egel results']
-                start_row = 21
-                start_column = 15
-                for row, ki in enumerate(info['gel_info']['value'], start=1):
-                    # logger.debug(f"ki: {ki}")
-                    # logger.debug(f"vi: {vi}")
-                    row = start_row + row
-                    worksheet.cell(row=row, column=start_column, value=ki['name'])
-                    for jjj, kj in enumerate(ki['values'], start=1):
-                        # logger.debug(f"kj: {kj}")
-                        # logger.debug(f"vj: {vj}")
-                        column = start_column + 2 + jjj
-                        worksheet.cell(row=start_row, column=column, value=kj['name'])
-                        # logger.debug(f"Writing {kj['name']} with value {kj['value']} to row {row}, column {column}")
-                        try:
-                            worksheet.cell(row=row, column=column, value=kj['value'])
-                        except AttributeError:
-                            logger.error(f"Failed {kj['name']} with value {kj['value']} to row {row}, column {column}")
-        check = 'gel_image' in info.keys() and info['gel_image']['value'] is not None
-        if check:
-            if info['gel_image'] != None:
-                worksheet = input_excel['Egel results']
-                # logger.debug(f"We got an image: {info['gel_image']}")
-                with ZipFile(cls.__directory_path__.joinpath("submission_imgs.zip")) as zipped:
-                    z = zipped.extract(info['gel_image']['value'], Path(TemporaryDirectory().name))
-                    img = OpenpyxlImage(z)
-                    img.height = 400  # insert image height in pixels as float or int (e.g. 305.5)
-                    img.width = 600
-                    img.anchor = 'B9'
-                    worksheet.add_image(img)
+            # if info['gel_info'] is not None:
+            # logger.debug(f"Gel info not none.")
+            # NOTE: print json field gel results to Egel results
+            worksheet = input_excel['Egel results']
+            # TODO: Move all this into a seperate function?
+            #
+            start_row = 21
+            start_column = 15
+            for row, ki in enumerate(info['gel_info']['value'], start=1):
+                # logger.debug(f"ki: {ki}")
+                # logger.debug(f"vi: {vi}")
+                row = start_row + row
+                worksheet.cell(row=row, column=start_column, value=ki['name'])
+                for jjj, kj in enumerate(ki['values'], start=1):
+                    # logger.debug(f"kj: {kj}")
+                    # logger.debug(f"vj: {vj}")
+                    column = start_column + 2 + jjj
+                    worksheet.cell(row=start_row, column=column, value=kj['name'])
+                    # logger.debug(f"Writing {kj['name']} with value {kj['value']} to row {row}, column {column}")
+                    try:
+                        worksheet.cell(row=row, column=column, value=kj['value'])
+                    except AttributeError:
+                        logger.error(f"Failed {kj['name']} with value {kj['value']} to row {row}, column {column}")
+        # check = 'gel_image' in info.keys() and info['gel_image']['value'] is not None
+        if check_key_or_attr(key='gel_image', interest=info, check_none=True):
+            # if info['gel_image'] is not None:
+            worksheet = input_excel['Egel results']
+            # logger.debug(f"We got an image: {info['gel_image']}")
+            with ZipFile(cls.__directory_path__.joinpath("submission_imgs.zip")) as zipped:
+                z = zipped.extract(info['gel_image']['value'], Path(TemporaryDirectory().name))
+                img = OpenpyxlImage(z)
+                img.height = 400  # insert image height in pixels as float or int (e.g. 305.5)
+                img.width = 600
+                img.anchor = 'B9'
+                worksheet.add_image(img)
         return input_excel
 
     @classmethod
@@ -1796,55 +1830,35 @@ class WastewaterArtic(BasicSubmission):
         base_dict['excluded'] += ['gel_info', 'gel_image', 'headers', "dna_core_submission_number", "source_plates",
                                   "gel_controls"]
         base_dict['DNA Core ID'] = base_dict['dna_core_submission_number']
-        check = 'gel_info' in base_dict.keys() and base_dict['gel_info'] != None
-        if check:
+        # check = 'gel_info' in base_dict.keys() and base_dict['gel_info'] is not None
+        if check_key_or_attr(key='gel_info', interest=base_dict, check_none=True):
             headers = [item['name'] for item in base_dict['gel_info'][0]['values']]
             base_dict['headers'] = [''] * (4 - len(headers))
             base_dict['headers'] += headers
             # logger.debug(f"Gel info: {pformat(base_dict['headers'])}")
-        check = 'gel_image' in base_dict.keys() and base_dict['gel_image'] != None
-        if check:
+        # check = 'gel_image' in base_dict.keys() and base_dict['gel_image'] is not None
+        if check_key_or_attr(key='gel_image', interest=base_dict, check_none=True):
             with ZipFile(cls.__directory_path__.joinpath("submission_imgs.zip")) as zipped:
                 base_dict['gel_image'] = base64.b64encode(zipped.read(base_dict['gel_image'])).decode('utf-8')
         return base_dict, template
 
-    def adjust_to_dict_samples(self, backup: bool = False) -> List[dict]:
-        """
-        Updates sample dictionaries with custom values
-
-        Args:
-            backup (bool, optional): Whether to perform backup. Defaults to False.
-
-        Returns:
-            List[dict]: Updated dictionaries
-        """
-        # logger.debug(f"Hello from {self.__class__.__name__} dictionary sample adjuster.")
-        output = []
-        # set_plate = None
-        for assoc in self.submission_sample_associations:
-            dicto = assoc.to_sub_dict()
-            # if self.source_plates is None:
-            #     output.append(dicto)
-            #     continue
-            # for item in self.source_plates:
-            #     if assoc.sample.id is None:
-            #         old_plate = None
-            #     else:
-            #         old_plate = WastewaterAssociation.query(submission=item['plate'], sample=assoc.sample, limit=1)
-            #     if old_plate is not None:
-            #         set_plate = old_plate.submission.rsl_plate_num
-            #         # logger.debug(f"Dictionary: {pformat(dicto)}")
-            #         if dicto['ww_processing_num'].startswith("NTC"):
-            #             dicto['well'] = dicto['ww_processing_num']
-            #         else:
-            #             dicto['well'] = f"{row_map[old_plate.row]}{old_plate.column}"
-            #         break
-            #     elif dicto['ww_processing_num'].startswith("NTC"):
-            #         dicto['well'] = dicto['ww_processing_num']
-            # dicto['plate_name'] = set_plate
-            # logger.debug(f"Here is our raw sample: {pformat(dicto)}")
-            output.append(dicto)
-        return output
+    # def adjust_to_dict_samples(self, backup: bool = False) -> List[dict]:
+    #     """
+    #     Updates sample dictionaries with custom values
+    #
+    #     Args:
+    #         backup (bool, optional): Whether to perform backup. Defaults to False.
+    #
+    #     Returns:
+    #         List[dict]: Updated dictionaries
+    #     """
+    #     # logger.debug(f"Hello from {self.__class__.__name__} dictionary sample adjuster.")
+    #     output = []
+    #
+    #     for assoc in self.submission_sample_associations:
+    #         dicto = assoc.to_sub_dict()
+    #         output.append(dicto)
+    #     return output
 
     def custom_context_events(self) -> dict:
         """
@@ -1880,7 +1894,7 @@ class WastewaterArtic(BasicSubmission):
             self.gel_info = output
             dt = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M:%S")
             com = dict(text=comment, name=getuser(), time=dt)
-            if com['text'] != None and com['text'] != "":
+            if com['text'] is not None and com['text'] != "":
                 if self.comment is not None:
                     self.comment.append(com)
                 else:
@@ -1938,7 +1952,7 @@ class BasicSample(BaseClass):
         Returns:
             str: new (or unchanged) submitter id
         """
-        if value == None:
+        if value is None:
             return uuid.uuid4().hex.upper()
         else:
             return value
@@ -2334,7 +2348,7 @@ class BacterialCultureSample(BasicSample):
         sample['name'] = self.submitter_id
         sample['organism'] = self.organism
         sample['concentration'] = self.concentration
-        if self.control != None:
+        if self.control is not None:
             sample['colour'] = [0, 128, 0]
             sample['tooltip'] = f"Control: {self.control.controltype.name} - {self.control.controltype.targets}"
         # logger.debug(f"Done converting to {self} to dict after {time()-start}")
@@ -2480,7 +2494,7 @@ class SubmissionSampleAssociation(BaseClass):
         """
         if isinstance(polymorphic_identity, dict):
             polymorphic_identity = polymorphic_identity['value']
-        if polymorphic_identity == None:
+        if polymorphic_identity is None:
             output = cls
         else:
             try: