Mid code cleanup

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

@@ -11,7 +11,7 @@ from typing import Any, List
 from pathlib import Path
 from tools import report_result
 
-# Load testing environment
+# NOTE: Load testing environment
 if 'pytest' in sys.modules:
     sys.path.append(Path(__file__).parents[4].absolute().joinpath("tests").__str__())
 
@@ -24,7 +24,7 @@ class BaseClass(Base):
     """
     Abstract class to pass ctx values to all SQLAlchemy objects.
     """
-    __abstract__ = True  #: Will not be added to DB
+    __abstract__ = True  #: NOTE: Will not be added to DB
 
     __table_args__ = {'extend_existing': True}  #: Will only add new columns
 
@@ -168,6 +168,7 @@ class BaseClass(Base):
             logger.error(f"Error message: {type(e)}")
             self.__database_session__.rollback()
             report.add_result(Result(msg=e, status="Critical"))
+        return report
 
 
 class ConfigItem(BaseClass):
@@ -202,5 +203,6 @@ from .organizations import *
 from .kits import *
 from .submissions import *
 
-# NOTE: Add a creator to the submission for reagent association.
+# NOTE: Add a creator to the submission for reagent association. Assigned here due to circular import constraints.
+# https://docs.sqlalchemy.org/en/20/orm/extensions/associationproxy.html#sqlalchemy.ext.associationproxy.association_proxy.params.creator
 BasicSubmission.reagents.creator = lambda reg: SubmissionReagentAssociation(reagent=reg)

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

@@ -161,7 +161,7 @@ class Control(BaseClass):
         }
         return output
 
-    def convert_by_mode(self, mode: Literal['kraken', 'matches', 'contains']) -> list[dict]:
+    def convert_by_mode(self, mode: Literal['kraken', 'matches', 'contains']) -> List[dict]:
         """
         split this instance into analysis types for controls graphs
 
@@ -169,7 +169,7 @@ class Control(BaseClass):
             mode (str): analysis type, 'contains', etc
 
         Returns:
-            list[dict]: list of records
+            List[dict]: list of records
         """
         output = []
         # logger.debug("load json string for mode (i.e. contains, matches, kraken2)")

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

@@ -263,7 +263,6 @@ class KitType(BaseClass):
         for k, v in self.construct_xl_map_for_use(submission_type=submission_type):
             # logger.debug(f"Value: {v}")
             try:
-                # assoc = [item for item in self.kit_reagentrole_associations if item.reagent_role.name == k][0]
                 assoc = next(item for item in self.kit_reagentrole_associations if item.reagent_role.name == k)
             except StopIteration as e:
                 continue
@@ -272,10 +271,8 @@ class KitType(BaseClass):
             base_dict['reagent roles'].append(v)
         for k, v in submission_type.construct_equipment_map():
             try:
-                # assoc = [item for item in submission_type.submissiontype_equipmentrole_associations if
-                #          item.equipment_role.name == k][0]
                 assoc = next(item for item in submission_type.submissiontype_equipmentrole_associations if
-                          item.equipment_role.name == k)
+                             item.equipment_role.name == k)
             except StopIteration:
                 continue
             for kk, vv in assoc.to_export_dict(kit_type=self).items():
@@ -292,7 +289,7 @@ class ReagentRole(BaseClass):
     """
 
     id = Column(INTEGER, primary_key=True)  #: primary key
-    name = Column(String(64))  #: name of reagent type
+    name = Column(String(64))  #: name of role reagent plays
     instances = relationship("Reagent", back_populates="role",
                              secondary=reagentroles_reagents)  #: concrete instances of this reagent type
     eol_ext = Column(Interval())  #: extension of life interval
@@ -747,15 +744,12 @@ class SubmissionType(BaseClass):
         Returns:
             dict: Map equipment locations in excel sheet
         """
-        # output = {}
         # logger.debug("Iterating through equipment roles")
         for item in self.submissiontype_equipmentrole_associations:
             emap = item.uses
             if emap is None:
                 emap = {}
-            # output[item.equipment_role.name] = emap
             yield item.equipment_role.name, emap
-        # return output
 
     def construct_tips_map(self) -> Generator[str, dict]:
         """
@@ -764,14 +758,11 @@ class SubmissionType(BaseClass):
         Returns:
             dict: Tip locations in the excel sheet.
         """
-        # output = {}
         for item in self.submissiontype_tiprole_associations:
             tmap = item.uses
             if tmap is None:
                 tmap = {}
-            # output[item.tip_role.name] = tmap
             yield item.tip_role.name, tmap
-        # return output
 
     def get_equipment(self, extraction_kit: str | KitType | None = None) -> List['PydEquipmentRole']:
         """
@@ -1035,7 +1026,7 @@ class SubmissionTypeKitTypeAssociation(BaseClass):
         exclude = ['_sa_instance_state', 'submission_types_id', 'kits_id', 'submission_type', 'kit_type']
         base_dict = {k: v for k, v in self.__dict__.items() if k not in exclude}
         base_dict['kit_type'] = self.kit_type.to_export_dict(submission_type=self.submission_type)
-        logger.debug(f"STKTA returning: {base_dict}")
+        # logger.debug(f"STKTA returning: {base_dict}")
         return base_dict
 
 
@@ -1073,7 +1064,7 @@ class KitTypeReagentRoleAssociation(BaseClass):
         return f"<KitTypeReagentRoleAssociation({self.kit_type} & {self.reagent_role})>"
 
     @validates('required')
-    def validate_age(self, key, value):
+    def validate_required(self, key, value):
         """
         Ensures only 1 & 0 used in 'required'
 
@@ -1243,7 +1234,6 @@ class SubmissionReagentAssociation(BaseClass):
         match submission:
             case BasicSubmission() | str():
                 if isinstance(submission, str):
-                    # submission = BasicSubmission.query(rsl_number=submission)
                     submission = BasicSubmission.query(rsl_plate_num=submission)
                 # logger.debug(f"Lookup SubmissionReagentAssociation by submission BasicSubmission {submission}")
                 query = query.filter(cls.submission == submission)
@@ -1424,7 +1414,7 @@ class Equipment(BaseClass):
                           re.VERBOSE)
 
     @classmethod
-    def assign_equipment(cls, equipment_role: EquipmentRole|str) -> List[Equipment]:
+    def assign_equipment(cls, equipment_role: EquipmentRole | str) -> List[Equipment]:
         """
         Creates a list of equipment from user input to be used in Submission Type creation
 
@@ -1581,10 +1571,11 @@ class EquipmentRole(BaseClass):
         Returns:
             dict: dictionary of Association and related reagent role
         """
-        base_dict = {}
+        return dict(role=self.name,
-        base_dict['role'] = self.name
+                    processes=self.get_processes(submission_type=submission_type, extraction_kit=kit_type))
-        base_dict['processes'] = self.get_processes(submission_type=submission_type, extraction_kit=kit_type)
+        # base_dict['role'] = self.name
-        return base_dict
+        # base_dict['processes'] = self.get_processes(submission_type=submission_type, extraction_kit=kit_type)
+        # return base_dict
 
 
 class SubmissionEquipmentAssociation(BaseClass):
@@ -1621,6 +1612,7 @@ class SubmissionEquipmentAssociation(BaseClass):
         Returns:
             dict: This SubmissionEquipmentAssociation as a dictionary
         """
+        # TODO: Currently this will only fetch a single process, even if multiple are selectable.
         try:
             process = self.process.name
         except AttributeError:
@@ -1707,9 +1699,9 @@ class SubmissionTypeEquipmentRoleAssociation(BaseClass):
         super().save()
 
     def to_export_dict(self, kit_type: KitType):
-        base_dict = dict(static=self.static)
+        base_dict = {k: v for k, v in self.equipment_role.to_export_dict(submission_type=self.submission_type,
-        for k, v in self.equipment_role.to_export_dict(submission_type=self.submission_type, kit_type=kit_type).items():
+                                                                         kit_type=kit_type).items()}
-            base_dict[k] = v
+        base_dict['static'] = self.static
         return base_dict
 
 

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

@@ -132,7 +132,7 @@ class BasicSubmission(BaseClass):
             str: Representation of this BasicSubmission
         """
         submission_type = self.submission_type or "Basic"
-        return f"{submission_type}Submission({self.rsl_plate_num})"
+        return f"<{submission_type}Submission({self.rsl_plate_num})>"
 
     @classmethod
     def jsons(cls) -> List[str]:
@@ -231,6 +231,9 @@ class BasicSubmission(BaseClass):
         """
         Gets the SubmissionType associated with this class
 
+        Args:
+            sub_type (str | SubmissionType, Optional): Identity of the submission type to retrieve. Defaults to None.
+
         Returns:
             SubmissionType: SubmissionType with name equal to this polymorphic identity
         """
@@ -421,8 +424,6 @@ class BasicSubmission(BaseClass):
         except Exception as e:
             logger.error(f"Column count error: {e}")
         # NOTE: Get kit associated with this submission
-        # assoc = [item for item in self.extraction_kit.kit_submissiontype_associations if
-        #          item.submission_type == self.submission_type][0]
         assoc = next((item for item in self.extraction_kit.kit_submissiontype_associations if item.submission_type == self.submission_type),
                       None)
         # logger.debug(f"Came up with association: {assoc}")
@@ -445,7 +446,7 @@ class BasicSubmission(BaseClass):
         Returns positve sample locations for plate
 
         Returns:
-            list: list of htipick dictionaries for each sample
+            list: list of hitpick dictionaries for each sample
         """
         output_list = [assoc.to_hitpick() for assoc in self.submission_sample_associations]
         return output_list
@@ -468,8 +469,7 @@ class BasicSubmission(BaseClass):
         for column in range(1, plate_columns + 1):
             for row in range(1, plate_rows + 1):
                 try:
-                    # well = [item for item in sample_list if item['row'] == row and item['column'] == column][0]
+                    well = next((item for item in sample_list if item['row'] == row and item['column'] == column), dict(name="", row=row, column=column, background_color="#ffffff"))
-                    well = next(item for item in sample_list if item['row'] == row and item['column'] == column)
                 except StopIteration:
                     well = dict(name="", row=row, column=column, background_color="#ffffff")
                 output_samples.append(well)
@@ -2788,16 +2788,17 @@ class SubmissionSampleAssociation(BaseClass):
         if isinstance(polymorphic_identity, dict):
             polymorphic_identity = polymorphic_identity['value']
         if polymorphic_identity is None:
-            output = cls
+            model = cls
         else:
             try:
-                output = [item for item in cls.__subclasses__() if
+                # output = [item for item in cls.__subclasses__() if
-                          item.__mapper_args__['polymorphic_identity'] == polymorphic_identity][0]
+                #           item.__mapper_args__['polymorphic_identity'] == polymorphic_identity][0]
+                model = cls.__mapper__.polymorphic_map[polymorphic_identity].class_
             except Exception as e:
                 logger.error(f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}")
-                output = cls
+                model = cls
         # logger.debug(f"Using SubmissionSampleAssociation subclass: {output}")
-        return output
+        return model
 
     @classmethod
     @setup_lookup
@@ -2986,7 +2987,7 @@ class WastewaterAssociation(SubmissionSampleAssociation):
         return sample
 
     @classmethod
-    def autoincrement_id(cls) -> int:
+    def autoincrement_id_local(cls) -> int:
         """
         Increments the association id automatically. Overrides parent
 
@@ -2994,12 +2995,17 @@ class WastewaterAssociation(SubmissionSampleAssociation):
             int: incremented id
         """
         try:
-            parent = [base for base in cls.__bases__ if base.__name__ == "SubmissionSampleAssociation"][0]
+            parent = next((base for base in cls.__bases__ if base.__name__=="SubmissionSampleAssociation"),
+                          SubmissionSampleAssociation)
             return max([item.id for item in parent.query()]) + 1
-        except ValueError as e:
+        except StopIteration as e:
             logger.error(f"Problem incrementing id: {e}")
             return 1
         
+    @classmethod
+    def autoincrement_id(cls) -> int:
+        return super().autoincrement_id()
+
 
 class WastewaterArticAssociation(SubmissionSampleAssociation):
     """
@@ -3040,8 +3046,9 @@ class WastewaterArticAssociation(SubmissionSampleAssociation):
             int: incremented id
         """
         try:
-            parent = [base for base in cls.__bases__ if base.__name__ == "SubmissionSampleAssociation"][0]
+            parent = next((base for base in cls.__bases__ if base.__name__ == "SubmissionSampleAssociation"),
+                          SubmissionSampleAssociation)
             return max([item.id for item in parent.query()]) + 1
-        except ValueError as e:
+        except StopIteration as e:
             logger.error(f"Problem incrementing id: {e}")
             return 1

src/submissions/backend/excel/writer.py

@@ -547,23 +547,9 @@ class DocxWriter(object):
         if columns == 0:
             columns = max([sample['column'] for sample in sample_list])
         for row in range(0, rows):
-            # NOTE: Create a list with length equal to columns length
+            # NOTE: Create a list with length equal to columns length, padding with '' where necessary
-            # contents = [''] * columns
             contents = [next((item['submitter_id'] for item in sample_list if item['row'] == row + 1 and
                               item['column'] == column + 1), '') for column in range(0, columns)]
-            # for column in range(0, columns):
-            #     contents[column] = next((item['submitter_id'] for item in sample_list if item['row'] == row + 1 and item['column'] == column), '')
-                # try:
-                #     # ooi = [item for item in sample_list if item['row'] == row + 1 and item['column'] == column + 1][0]
-                #     ooi = next(item for item in sample_list if item['row'] == row + 1 and item['column'] == column)
-                # except StopIteration:
-                #     continue
-                # contents[column] = ooi['submitter_id']
-            # NOTE: Pad length of contents to reflect columns
-            # if len(contents) < columns:
-            #     contents += [''] * (columns - len(contents))
-            # if not contents:
-            #     contents = [''] * columns
             yield contents
 
     def create_merged_template(self, *args) -> BytesIO:

src/submissions/frontend/widgets/submission_details.py

@@ -177,10 +177,10 @@ class SubmissionDetails(QDialog):
         writer = DocxWriter(base_dict=base_dict)
         fname = select_save_file(obj=self, default_name=base_dict['plate_number'], extension="docx")
         writer.save(fname)
-        try:
+        # try:
-            html_to_pdf(html=self.html, output_file=fname)
+        #     html_to_pdf(html=self.html, output_file=fname)
-        except PermissionError as e:
+        # except PermissionError as e:
-            logger.error(f"Error saving pdf: {e}")
+        #     logger.error(f"Error saving pdf: {e}")
 
 
 class SubmissionComment(QDialog):