Beginning prelim code cleanup.

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

@@ -8,7 +8,7 @@ from pydantic import BaseModel
 from sqlalchemy import Column, INTEGER, String, JSON
 from sqlalchemy.orm import DeclarativeMeta, declarative_base, Query, Session, InstrumentedAttribute, ColumnProperty
 from sqlalchemy.ext.declarative import declared_attr
-from sqlalchemy.exc import ArgumentError, InvalidRequestError
+from sqlalchemy.exc import ArgumentError
 from typing import Any, List
 from pathlib import Path
 
@@ -156,9 +156,6 @@ class BaseClass(Base):
             Any: Subclass of this object
 
         """
-        # if not name:
-        #     logger.warning("You need to include a name of what you're looking for.")
-        #     return cls
         if " " in name:
             search = name.title().replace(" ", "")
         else:
@@ -343,7 +340,6 @@ class BaseClass(Base):
         """
         logger.debug(f"Incoming attributes: {attributes}")
         for key, value in attributes.items():
-            # print(getattr(self.__class__, key).property)
             if value.lower() == "none":
                 value = None
             logger.debug(f"Attempting to grab attribute: {key}")
@@ -355,7 +351,6 @@ class BaseClass(Base):
             else:
                 filter = class_attr.property
             match filter:
-            # match class_attr:
                 case ColumnProperty():
                     match class_attr.type:
                         case INTEGER():
@@ -397,8 +392,6 @@ class BaseClass(Base):
         """
         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:

src/submissions/backend/validators/omni_gui_objects.py

@@ -1,7 +1,5 @@
 from __future__ import annotations
-import logging
-import sys
-
+import logging, sys
 from pydantic import BaseModel, field_validator, Field
 from typing import List, ClassVar
 from backend.db.models import *
@@ -37,7 +35,6 @@ class BaseOmni(BaseModel):
         """
         logger.debug(f"Incoming attributes: {attributes}")
         for key, value in attributes.items():
-            # print(getattr(self.__class__, key).property)
             if value.lower() == "none":
                 value = None
             logger.debug(f"Attempting to grab attribute: {key}")
@@ -127,7 +124,6 @@ class BaseOmni(BaseModel):
                             if issubclass(value.__class__, self.__class__):
                                 value = value.to_sql()
                             value = [value]
-                        # value = list(set(value))
                         logger.debug(f"Final value for {key}: {value}")
                         return super().__setattr__(key, value)
                     else:
@@ -243,7 +239,6 @@ class OmniSubmissionTypeKitTypeAssociation(BaseOmni):
     mutable_cost_column: float = Field(default=0.0, description="property")
     mutable_cost_sample: float = Field(default=0.0, description="property")
     constant_cost: float = Field(default=0.0, description="property")
-    # processes: List[OmniProcess] | List[str] = Field(default=[], description="relationship", title="Process")
 
     def __repr__(self):
         if isinstance(self.submissiontype, str):
@@ -313,7 +308,6 @@ class OmniSubmissionTypeKitTypeAssociation(BaseOmni):
         else:
             kittype = KitType.query(name=self.kittype)
         # logger.debug(f"Self kittype: {self.kittype}")
-        # kittype = KitType.query(name=self.kittype)
         logger.debug(f"Query or create with {kittype}, {submissiontype}")
         instance, is_new = self.class_object.query_or_create(kittype=kittype, submissiontype=submissiontype)
         instance.mutable_cost_column = self.mutable_cost_column
@@ -352,7 +346,6 @@ class OmniKitTypeReagentRoleAssociation(BaseOmni):
             kit_type = self.kit_type.name
         else:
             kit_type = self.kit_type
-        # name = f"{kit_type} -> {self.reagent_role}"
         # logger.debug(f"Using name: {name}")
         if isinstance(self.reagent_role, OmniReagentRole):
             reagent_role = self.reagent_role.name
@@ -360,7 +353,6 @@ class OmniKitTypeReagentRoleAssociation(BaseOmni):
             reagent_role = self.reagent_role
         return dict(
             reagent_role=reagent_role,
-            # name=self.reagent_role.name,
             submission_type=submission_type,
             kit_type=kit_type
         )
@@ -381,7 +373,6 @@ class OmniKitTypeReagentRoleAssociation(BaseOmni):
         logger.debug(f"KTRRAssoc uses: {self.uses}")
         instance.uses = self.uses
         logger.debug(f"KitTypeReagentRoleAssociation: {pformat(instance.__dict__)}")
-
         return instance
 
 
@@ -464,8 +455,6 @@ class OmniTipRole(BaseOmni):
         instance, new = self.class_object.query_or_create(name=self.name)
         for tips in self.tips:
             tips.to_sql()
-            # if new_assoc not in instance.instances:
-            #     instance.instances.append(new_assoc)
         return instance
 
 

src/submissions/frontend/widgets/omni_manager_pydant.py

@@ -1,8 +1,7 @@
 """
 Provides a screen for managing all attributes of a database object.
 """
-import json, logging
-import sys
+import json, logging, sys
 from json.decoder import JSONDecodeError
 from datetime import datetime, timedelta
 from pprint import pformat
@@ -108,7 +107,6 @@ class ManagerWindow(QDialog):
         self.options.setEditable(False)
         self.options.setMinimumWidth(self.minimumWidth())
         self.layout.addWidget(self.options, 1, 0, 1, 1)
-        # if len(options) > 0:
         self.add_button = QPushButton("Add New")
         self.layout.addWidget(self.add_button, 1, 1, 1, 1)
         self.add_button.clicked.connect(self.add_new)
@@ -191,7 +189,6 @@ class ManagerWindow(QDialog):
         results = [item.parse_form() for item in self.findChildren(EditRelationship)]
         for result in results:
             logger.debug(f"Incoming relationship result: {result}")
-            # if not getattr(self.omni_object, result['field']):
             setattr(self.omni_object, result['field'], result['value'])
             # logger.debug(f"Set result: {getattr(self.omni_object, result['field'])}")
         # logger.debug(f"Instance coming from parsed form: {self.omni_object.__dict__}")
@@ -242,8 +239,6 @@ class EditProperty(QWidget):
                 self.widget.setValue(value.days)
             case dict():
                 self.widget = JsonEditButton(parent=self, key=key, value=value)
-                # self.widget.viewButton.clicked.connect(lambda: self.parent().toggle_textedit(self.widget))
-                # self.widget.addButton.clicked.connect(lambda: self.parent().add_to_json(self.widget))
             case bytes():
                 self.widget = QLabel("BLOB Under construction")
             case _:
@@ -281,19 +276,12 @@ class EditRelationship(QWidget):
         self.label = QLabel(key.title().replace("_", " "))
         self.setObjectName(key)  #: key is the name of the relationship this represents
         logger.debug(f"Checking relationship for {self.parent().class_object}: {key}")
-        # try:
-        # self.relationship = getattr(self.parent().instance.__class__, key)
         self.relationship = getattr(self.parent().class_object, key)
-        #: relationship object for type differentiation
-        # except AttributeError:
-        #     logger.warning(f"Could not get relationship for: {key}.")
-        #     self.relationship = None
         self.widget = QTableView()
         self.add_button = QPushButton("Add New")
         self.add_button.clicked.connect(self.add_new)
         self.existing_button = QPushButton("Add Existing")
         self.existing_button.clicked.connect(self.add_existing)
-        # self.existing_button.setEnabled(self.class_object.level == 1)
         if not isinstance(value, list):
             if value not in [None, ""]:
                 value = [value]
@@ -305,15 +293,6 @@ class EditRelationship(QWidget):
         logger.debug(f"Parent manager: {self.parent().manager}")
         checked_manager, is_primary = check_object_in_manager(self.parent().manager, self.objectName())
         if checked_manager:
-            logger.debug(f"Checked manager for {self.objectName()}: {checked_manager}")
-            # logger.debug(f"Omni will inherit: {self.class_object.omni_inheritable} from {self.parent().class_object}")
-            # if checked_manager is not None:# and not self.data:# and self.objectName() in self.parent().class_object.omni_inheritable:
-            #     # logger.debug(f"Setting {checked_manager} in self.data")
-            #     # if isinstance(checked_manager, InstrumentedList):
-            #     #     self.data = [item.to_omni() for item in checked_manager]
-            #     # else:
-            #     #     self.data = [checked_manager.to_omni()]
-            #     self.data = [checked_manager]
             if not self.data:
                 self.data = [checked_manager]
         try:
@@ -367,7 +346,6 @@ class EditRelationship(QWidget):
         # logger.debug(f"Creating manager window for {instance}")
         manager = self.parent().manager
         # logger.debug(f"Managers going into add new: {managers}")
-        # dlg = ManagerWindow(self.parent(), object_type=instance.__class__, extras=[], manager=manager, add_edit="add")
         dlg = ManagerWindow(self.parent(), instance=instance, extras=[], manager=manager, add_edit=add_edit)
         if dlg.exec():
             new_instance = dlg.parse_form()
@@ -378,7 +356,6 @@ class EditRelationship(QWidget):
             else:
                 instance.__dict__.update(new_instance.__dict__)
             logger.debug(f"Final instance: {pformat(instance.__dict__)}")
-            # self.parent().instance.save()
             self.parent().update_data()
 
     def add_existing(self):
@@ -392,7 +369,6 @@ class EditRelationship(QWidget):
                 if isinstance(instance, list):
                     instance = instance[0]
                 self.parent().omni_object.__setattr__(self.objectName(), instance.to_omni())
-                # self.parent().instance.save()
                 self.parent().update_data()
 
     def set_data(self) -> None:
@@ -401,7 +377,6 @@ class EditRelationship(QWidget):
         """
         # logger.debug(f"Self.data: {self.data}")
         try:
-            # records = [{k: v['instance_attr'] for k, v in item.omnigui_instance_dict.items()} for item in self.data]
             records = [item.to_dataframe_dict() for item in self.data]
         except AttributeError:
             records = []
@@ -423,7 +398,6 @@ class EditRelationship(QWidget):
         self.widget.resizeRowsToContents()
         self.widget.setSortingEnabled(True)
         self.widget.doubleClicked.connect(self.parse_row)
-        # self.update_buttons()
 
     def contextMenuEvent(self, event):
         """
@@ -469,18 +443,8 @@ class EditRelationship(QWidget):
 
     def remove_item(self, object):
         logger.debug(f"Attempting to remove {object} from {self.parent().instance.__dict__}")
-        # editor = getattr(self.parent().instance, self.objectName().lower())
         editor = getattr(self.parent().omni_object, self.objectName().lower())
         logger.debug(f"Editor: {editor}")
-        # if object == self.parent().manager:
-        #     logger.error(f"Can't remove manager object.")
-        #     return
-        # logger.debug(f"Object: {object}")
-        # try:
-        #     self.data.remove(object)
-        # except (AttributeError, ValueError) as e:
-        #     logger.error(f"Couldn't remove object from self.data due to: {e}")
-        #     self.data = []
         try:
             # logger.debug(f"Using remove technique")
             editor.remove(object)
@@ -492,8 +456,6 @@ class EditRelationship(QWidget):
         logger.debug(f"Setting {self.objectName()} to {editor}")
         setattr(self.parent().omni_object, self.objectName().lower(), editor)
         logger.debug(f"After set: {getattr(self.parent().omni_object, self.objectName().lower())}")
-        # self.parent().instance.save()
-        # self.parent().update_data()
         self.set_data()
         self.update_buttons()
 
@@ -551,7 +513,6 @@ class JsonEditButton(QWidget):
 
     def toggle_textedit(self):
         self.edit_box.setVisible(not self.edit_box.isVisible())
-        # data = getattr(self.omni_object, name)
         # logger.debug(f"Data: {data}")
         data = json.dumps(self.data, indent=4)
         self.edit_box.widget.setText(data)
@@ -624,7 +585,6 @@ class JsonEditScreen(QDialog):
                     output.append(value)
             else:
                 raise ValueError(f"Inappropriate data type: {type(self.json_field)}")
-            # output[key] = value
         return output