Created WastewaterArticAssociation, added tip handling.

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

@@ -1520,6 +1520,9 @@ class Process(BaseClass):
 
 
 class TipRole(BaseClass):
+    """
+    An abstract role that a tip fills during a process
+    """    
     id = Column(INTEGER, primary_key=True)  #: primary key
     name = Column(String(64))  #: name of reagent type
     instances = relationship("Tips", back_populates="role",
@@ -1539,6 +1542,9 @@ class TipRole(BaseClass):
 
 
 class Tips(BaseClass):
+    """
+    A concrete instance of tips.
+    """    
     id = Column(INTEGER, primary_key=True)  #: primary key
     role = relationship("TipRole", back_populates="instances",
                         secondary=tiproles_tips)  #: joined parent reagent type
@@ -1560,7 +1566,18 @@ class Tips(BaseClass):
         return f"<Tips({self.name})>"
 
     @classmethod
-    def query(cls, name: str | None = None, lot: str | None = None, limit: int = 0, **kwargs) -> Any | List[Any]:
+    def query(cls, name: str | None = None, lot: str | None = None, limit: int = 0, **kwargs) -> Tips | List[Tips]:
+        """
+        Lookup tips
+
+        Args:
+            name (str | None, optional): Informal name of tips. Defaults to None.
+            lot (str | None, optional): Lot number. Defaults to None.
+            limit (int, optional): Maximum number of results to return (0=all). Defaults to 0.
+
+        Returns:
+            Tips | List[Tips]: Tips matching criteria
+        """        
         query = cls.__database_session__.query(cls)
         match name:
             case str():
@@ -1595,6 +1612,9 @@ class SubmissionTypeTipRoleAssociation(BaseClass):
 
 
 class SubmissionTipsAssociation(BaseClass):
+    """
+    Association between a concrete submission instance and concrete tips
+    """    
     tip_id = Column(INTEGER, ForeignKey("_tips.id"), primary_key=True)  #: id of associated equipment
     submission_id = Column(INTEGER, ForeignKey("_basicsubmission.id"), primary_key=True)  #: id of associated submission
     submission = relationship("BasicSubmission",
@@ -1605,5 +1625,11 @@ class SubmissionTipsAssociation(BaseClass):
 
     # role = relationship(TipRole)
 
-    def to_sub_dict(self):
+    def to_sub_dict(self) -> dict:
+        """
+        This item as a dictionary
+
+        Returns:
+            dict: Values of this object
+        """        
         return dict(role=self.role_name, name=self.tips.name, lot=self.tips.lot)

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

@@ -2576,6 +2576,10 @@ class SubmissionSampleAssociation(BaseClass):
 
 
 class WastewaterAssociation(SubmissionSampleAssociation):
+    """
+    table containing wastewater specific submission/sample associations
+    DOC: https://docs.sqlalchemy.org/en/14/orm/extensions/associationproxy.html
+    """
     id = Column(INTEGER, ForeignKey("_submissionsampleassociation.id"), primary_key=True)
     ct_n1 = Column(FLOAT(2))  #: AKA ct for N1
     ct_n2 = Column(FLOAT(2))  #: AKA ct for N2
@@ -2635,7 +2639,10 @@ class WastewaterAssociation(SubmissionSampleAssociation):
 
 
 class WastewaterArticAssociation(SubmissionSampleAssociation):
-
+    """
+    table containing wastewater artic specific submission/sample associations
+    DOC: https://docs.sqlalchemy.org/en/14/orm/extensions/associationproxy.html
+    """
     id = Column(INTEGER, ForeignKey("_submissionsampleassociation.id"), primary_key=True)
     source_plate = Column(String(16))
     source_plate_number = Column(INTEGER)

src/submissions/backend/excel/parser.py

@@ -68,7 +68,6 @@ class SheetParser(object):
         parser = InfoParser(xl=self.xl, submission_type=self.submission_type, sub_object=self.sub_object)
         info = parser.parse_info()
         self.info_map = parser.map
-        # exclude_from_info = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.sub['submission_type']).exclude_from_info_parser()
         for k, v in info.items():
             match k:
                 case "sample":
@@ -96,7 +95,6 @@ class SheetParser(object):
         """
         parser = SampleParser(xl=self.xl, submission_type=self.submission_type)
         self.sub['samples'] = parser.reconcile_samples()
-        # self.plate_map = parser.plate_map
 
     def parse_equipment(self):
         parser = EquipmentParser(xl=self.xl, submission_type=self.submission_type)
@@ -126,8 +124,6 @@ class SheetParser(object):
         """
         Run custom final validations of data for submission subclasses.
         """
-        # finisher = BasicSubmission.find_polymorphic_subclass(
-        #     polymorphic_identity=self.sub['submission_type']).finalize_parse
         self.sub = self.sub_object.finalize_parse(input_dict=self.sub, xl=self.xl, info_map=self.info_map)
 
     def to_pydantic(self) -> PydSubmission:
@@ -264,16 +260,15 @@ class ReagentParser(object):
         if isinstance(extraction_kit, dict):
             extraction_kit = extraction_kit['value']
         self.kit_object = KitType.query(name=extraction_kit)
-        self.map = self.fetch_kit_info_map(extraction_kit=extraction_kit, submission_type=submission_type)
+        self.map = self.fetch_kit_info_map(submission_type=submission_type)
         # logger.debug(f"Reagent Parser map: {self.map}")
         self.xl = xl
 
-    def fetch_kit_info_map(self, extraction_kit: dict, submission_type: str) -> dict:
+    def fetch_kit_info_map(self, submission_type: str) -> dict:
         """
         Gets location of kit reagents from database
 
         Args:
-            extraction_kit (dict): Relevant kit information.
             submission_type (str): Name of submission type.
 
         Returns:
@@ -388,47 +383,6 @@ class SampleParser(object):
             sample_info_map = sample_map
         return sample_info_map
 
-    # def construct_plate_map(self, plate_map_location: dict) -> pd.DataFrame:
-    #     """
-    #     Gets location of samples from plate map grid in excel sheet.
-    #
-    #     Args:
-    #         plate_map_location (dict): sheet name, start/end row/column
-    #
-    #     Returns:
-    #         pd.DataFrame: Plate map grid
-    #     """
-    #     logger.debug(f"Plate map location: {plate_map_location}")
-    #     df = self.xl.parse(plate_map_location['sheet'], header=None, dtype=object)
-    #     df = df.iloc[plate_map_location['start_row'] - 1:plate_map_location['end_row'],
-    #          plate_map_location['start_column'] - 1:plate_map_location['end_column']]
-    #     df = pd.DataFrame(df.values[1:], columns=df.iloc[0])
-    #     df = df.set_index(df.columns[0])
-    #     logger.debug(f"Vanilla platemap: {df}")
-    #     # custom_mapper = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
-    #     df = self.sub_object.custom_platemap(self.xl, df)
-    #     # logger.debug(f"Custom platemap:\n{df}")
-    #     return df
-    #
-    # def construct_lookup_table(self, lookup_table_location: dict) -> pd.DataFrame:
-    #     """
-    #     Gets table of misc information from excel book
-    #
-    #     Args:
-    #         lookup_table_location (dict): sheet name, start/end row
-    #
-    #     Returns:
-    #         pd.DataFrame: _description_
-    #     """
-    #     try:
-    #         df = self.xl.parse(lookup_table_location['sheet'], header=None, dtype=object)
-    #     except KeyError:
-    #         return None
-    #     df = df.iloc[lookup_table_location['start_row'] - 1:lookup_table_location['end_row']]
-    #     df = pd.DataFrame(df.values[1:], columns=df.iloc[0])
-    #     df = df.reset_index(drop=True)
-    #     return df
-
     def parse_plate_map(self):
         """
         Parse sample location/name from plate map
@@ -614,6 +568,8 @@ class EquipmentParser(object):
                 asset = self.get_asset_number(input=asset)
                 logger.debug(f"asset: {asset}")
                 eq = Equipment.query(asset_number=asset)
+                if eq is None:
+                    eq = Equipment.query(name=asset)
                 process = ws.cell(row=v['process']['row'], column=v['process']['column']).value
                 try:
                     output.append(
@@ -674,7 +630,6 @@ class TipParser(object):
                     previous_asset = asset
                 logger.debug(f"asset: {asset}")
                 eq = Tips.query(lot=lot, name=asset, limit=1)
-                # process = ws.cell(row=v['process']['row'], column=v['process']['column']).value
                 try:
                     output.append(
                         dict(name=eq.name, role=k, lot=lot))
@@ -705,7 +660,7 @@ class PCRParser(object):
                 logger.error(f'Incorrect value: {e}')
                 self.xl = None
             except PermissionError:
-                logger.error(f'Couldn\'t get permissions for {filepath.__str__()}. Operation might have been cancelled.')
+                logger.error(f"Couldn't get permissions for {filepath.__str__()}. Operation might have been cancelled.")
                 return None
         if submission is None:
             self.submission_obj = Wastewater

src/submissions/frontend/widgets/equipment_usage.py

@@ -128,7 +128,9 @@ class RoleComboBox(QWidget):
         self.process.addItems([item for item in equip2.processes if item in self.role.processes])
 
     def update_tips(self):
-
+        """
+        Changes what tips are available when process is changed
+        """        
         process = self.process.currentText()
         logger.debug(f"Checking process: {process}")
         process = Process.query(name=process)