Post code-cleanup

src/submissions/frontend/widgets/app.py

@@ -1,6 +1,7 @@
 """
 Constructs main application.
 """
+import getpass
 from pprint import pformat
 from PyQt6.QtCore import qInstallMessageHandler
 from PyQt6.QtWidgets import (
@@ -13,9 +14,10 @@ from pathlib import Path
 from markdown import markdown
 from __init__ import project_path
 from backend import SubmissionType, Reagent, BasicSample, Organization, KitType
-from tools import check_if_app, Settings, Report, jinja_template_loading, check_authorization, page_size, is_power_user
+from tools import (
+    check_if_app, Settings, Report, jinja_template_loading, check_authorization, page_size, is_power_user, under_development
+)
 from .functions import select_save_file, select_open_file
-# from datetime import date
 from .pop_ups import HTMLPop, AlertPop
 from .misc import Pagifier
 import logging, webbrowser, sys, shutil
@@ -84,7 +86,8 @@ class App(QMainWindow):
         maintenanceMenu.addAction(self.joinPCRAction)
         editMenu.addAction(self.editReagentAction)
         editMenu.addAction(self.manageOrgsAction)
-        # editMenu.addAction(self.manageKitsAction)
+        if getpass.getuser() == "lwark":
+            editMenu.addAction(self.manageKitsAction)
         if not is_power_user():
             editMenu.setEnabled(False)
 
@@ -119,7 +122,7 @@ class App(QMainWindow):
         connect menu and tool bar item to functions
         """
         self.importAction.triggered.connect(self.table_widget.formwidget.importSubmission)
-        self.addReagentAction.triggered.connect(self.table_widget.formwidget.new_add_reagent)
+        self.addReagentAction.triggered.connect(self.table_widget.formwidget.add_reagent)
         self.joinExtractionAction.triggered.connect(self.table_widget.sub_wid.link_extractions)
         self.joinPCRAction.triggered.connect(self.table_widget.sub_wid.link_pcr)
         self.helpAction.triggered.connect(self.showAbout)
@@ -177,6 +180,11 @@ class App(QMainWindow):
         dlg = SearchBox(self, object_type=BasicSample, extras=[])
         dlg.exec()
 
+    @check_authorization
+    def edit_reagent(self, *args, **kwargs):
+        dlg = SearchBox(parent=self, object_type=Reagent, extras=[dict(name='Role', field="role")])
+        dlg.exec()
+
     def export_ST_yaml(self):
         """
         Copies submission type yaml to file system for editing and remport
@@ -191,13 +199,18 @@ class App(QMainWindow):
         fname = select_save_file(obj=self, default_name="Submission Type Template.yml", extension="yml")
         shutil.copyfile(yaml_path, fname)
 
-    @check_authorization
-    def edit_reagent(self, *args, **kwargs):
-        dlg = SearchBox(parent=self, object_type=Reagent, extras=[dict(name='Role', field="role")])
-        dlg.exec()
-
     @check_authorization
     def import_ST_yaml(self, *args, **kwargs):
+        """
+        Imports a yml form into a submission type.
+
+        Args:
+            *args ():
+            **kwargs ():
+
+        Returns:
+
+        """
         fname = select_open_file(obj=self, file_extension="yml")
         if not fname:
             logger.info(f"Import cancelled.")
@@ -220,9 +233,11 @@ class App(QMainWindow):
         dlg = ManagerWindow(parent=self, object_type=Organization, extras=[])
         if dlg.exec():
             new_org = dlg.parse_form()
+            new_org.save()
             # logger.debug(new_org.__dict__)
 
-    def manage_kits(self):
+    @under_development
+    def manage_kits(self, *args, **kwargs):
         dlg = ManagerWindow(parent=self, object_type=KitType, extras=[])
         if dlg.exec():
             print(dlg.parse_form())

src/submissions/frontend/widgets/controls_chart.py

@@ -99,18 +99,24 @@ class ControlsViewer(InfoPane):
             self.mode_sub_type = self.mode_sub_typer.currentText()
         months = self.diff_month(self.start_date, self.end_date)
         # NOTE: query all controls using the type/start and end dates from the gui
-        chart_settings = dict(sub_type=self.con_sub_type, start_date=self.start_date, end_date=self.end_date,
-                              mode=self.mode,
-                              sub_mode=self.mode_sub_type, parent=self, months=months)
+        chart_settings = dict(
+            sub_type=self.con_sub_type,
+            start_date=self.start_date,
+            end_date=self.end_date,
+            mode=self.mode,
+            sub_mode=self.mode_sub_type,
+            parent=self,
+            months=months
+        )
         self.fig = self.archetype.instance_class.make_chart(chart_settings=chart_settings, parent=self, ctx=self.app.ctx)
         self.report_obj = ChartReportMaker(df=self.fig.df, sheet_name=self.archetype.name)
         if issubclass(self.fig.__class__, CustomFigure):
             self.save_button.setEnabled(True)
         # NOTE: construct html for webview
-        try:
-            html = self.fig.to_html()
-        except AttributeError:
-            html = ""
-        self.webview.setHtml(html)
+        # try:
+        #     html = self.fig.html
+        # except AttributeError:
+        #     html = ""
+        self.webview.setHtml(self.fig.html)
         self.webview.update()
         return report

src/submissions/frontend/widgets/equipment_usage.py

@@ -3,8 +3,9 @@ Creates forms that the user can enter equipment info into.
 '''
 from pprint import pformat
 from PyQt6.QtCore import Qt, QSignalBlocker
-from PyQt6.QtWidgets import (QDialog, QComboBox, QCheckBox,
-                             QLabel, QWidget, QVBoxLayout, QDialogButtonBox, QGridLayout)
+from PyQt6.QtWidgets import (
+    QDialog, QComboBox, QCheckBox, QLabel, QWidget, QVBoxLayout, QDialogButtonBox, QGridLayout
+)
 from backend.db.models import Equipment, BasicSubmission, Process
 from backend.validators.pydant import PydEquipment, PydEquipmentRole, PydTips
 import logging
@@ -36,8 +37,8 @@ class EquipmentUsage(QDialog):
         self.buttonBox.rejected.connect(self.reject)
         label = self.LabelRow(parent=self)
         self.layout.addWidget(label)
-        for eq in self.opt_equipment:
-            widg = eq.to_form(parent=self, used=self.used_equipment)
+        for equipment in self.opt_equipment:
+            widg = equipment.to_form(parent=self, used=self.used_equipment)
             self.layout.addWidget(widg)
             widg.update_processes()
         self.layout.addWidget(self.buttonBox)
@@ -64,6 +65,7 @@ class EquipmentUsage(QDialog):
                     continue
 
     class LabelRow(QWidget):
+        """Provides column headers"""
 
         def __init__(self, parent) -> None:
             super().__init__(parent)

src/submissions/frontend/widgets/functions.py

@@ -1,8 +1,11 @@
-'''
+"""
 functions used by all windows in the application's frontend
-'''
+"""
 from pathlib import Path
 import logging
+from PyQt6.QtCore import QMarginsF
+from PyQt6.QtGui import QPageLayout, QPageSize
+from PyQt6.QtWebEngineWidgets import QWebEngineView
 from PyQt6.QtWidgets import QMainWindow, QFileDialog
 
 logger = logging.getLogger(f"submissions.{__name__}")
@@ -60,3 +63,21 @@ def select_save_file(obj: QMainWindow, default_name: str, extension: str) -> Pat
     fname = Path(QFileDialog.getSaveFileName(obj, "Save File", home_dir, filter=f"{extension}(*.{extension})")[0])
     obj.last_dir = fname.parent
     return fname
+
+
+def save_pdf(obj: QWebEngineView, filename: Path):
+    """
+    Handles printing to PDF
+
+    Args:
+        obj (): Parent object
+        filename (): Where to save pdf.
+
+    Returns:
+        None
+    """
+    page_layout = QPageLayout()
+    page_layout.setPageSize(QPageSize(QPageSize.PageSizeId.A4))
+    page_layout.setOrientation(QPageLayout.Orientation.Portrait)
+    page_layout.setMargins(QMarginsF(25, 25, 25, 25))
+    obj.page().printToPdf(filename.absolute().__str__(), page_layout)

src/submissions/frontend/widgets/gel_checker.py

@@ -2,15 +2,13 @@
 Gel box for artic quality control
 """
 from operator import itemgetter
-from PyQt6.QtWidgets import (QWidget, QDialog, QGridLayout,
-                             QLabel, QLineEdit, QDialogButtonBox,
-                             QTextEdit, QComboBox
-                             )
+from PyQt6.QtWidgets import (
+    QWidget, QDialog, QGridLayout, QLabel, QLineEdit, QDialogButtonBox, QTextEdit, QComboBox
+)
 import pyqtgraph as pg
 from PyQt6.QtGui import QIcon
 from PIL import Image
-import numpy as np
-import logging
+import logging, numpy as np
 from pprint import pformat
 from typing import Tuple, List
 from pathlib import Path
@@ -103,7 +101,8 @@ class ControlsForm(QWidget):
         except TypeError:
             tt_text = None
         for iii, item in enumerate(
-                ["Negative Control Key", "Description", "Results - 65 C", "Results - 63 C", "Results - Spike"]):
+                ["Negative Control Key", "Description", "Results - 65 C", "Results - 63 C", "Results - Spike"]
+        ):
             label = QLabel(item)
             self.layout.addWidget(label, 0, iii, 1, 1)
             if iii > 1:

src/submissions/frontend/widgets/info_tab.py

@@ -6,8 +6,8 @@ from PyQt6.QtCore import QSignalBlocker
 from PyQt6.QtWebEngineWidgets import QWebEngineView
 from PyQt6.QtWidgets import QWidget, QGridLayout
 from tools import Report, report_result, Result
-from .misc import StartEndDatePicker, save_pdf
-from .functions import select_save_file
+from .misc import StartEndDatePicker
+from .functions import select_save_file, save_pdf
 import logging
 
 logger = logging.getLogger(f"submissions.{__name__}")
@@ -38,8 +38,7 @@ class InfoPane(QWidget):
             lastmonth = self.datepicker.end_date.date().addDays(-31)
             msg = f"Start date after end date is not allowed! Setting to {lastmonth.toString()}."
             logger.warning(msg)
-            # NOTE: block signal that will rerun controls getter and set start date
-            # Without triggering this function again
+            # NOTE: block signal that will rerun controls getter and set start date without triggering this function again
             with QSignalBlocker(self.datepicker.start_date) as blocker:
                 self.datepicker.start_date.setDate(lastmonth)
             self.update_data()

src/submissions/frontend/widgets/misc.py

@@ -3,12 +3,10 @@ Contains miscellaneous widgets for frontend functions
 """
 import math
 from datetime import date
-from PyQt6.QtGui import QPageLayout, QPageSize, QStandardItem, QIcon
-from PyQt6.QtWebEngineWidgets import QWebEngineView
+from PyQt6.QtGui import QStandardItem, QIcon
 from PyQt6.QtWidgets import (
-    QLabel, QVBoxLayout,
-    QLineEdit, QComboBox, QDialog,
-    QDialogButtonBox, QDateEdit, QPushButton, QWidget, QHBoxLayout, QSizePolicy
+    QLabel, QLineEdit, QComboBox, QDateEdit, QPushButton, QWidget,
+    QHBoxLayout, QSizePolicy
 )
 from PyQt6.QtCore import Qt, QDate, QSize, QMarginsF
 from tools import jinja_template_loading
@@ -20,96 +18,98 @@ logger = logging.getLogger(f"submissions.{__name__}")
 env = jinja_template_loading()
 
 
-class AddReagentForm(QDialog):
-    """
-    dialog to add gather info about new reagent
-    """
-
-    def __init__(self, reagent_lot: str | None = None, reagent_role: str | None = None, expiry: date | None = None,
-                 reagent_name: str | None = None, kit: str | KitType | None = None) -> None:
-        super().__init__()
-        if reagent_name is None:
-            reagent_name = reagent_role
-        self.setWindowTitle("Add Reagent")
-        QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
-        self.buttonBox = QDialogButtonBox(QBtn)
-        self.buttonBox.accepted.connect(self.accept)
-        self.buttonBox.rejected.connect(self.reject)
-        # NOTE: widget to get lot info
-        self.name_input = QComboBox()
-        self.name_input.setObjectName("name")
-        self.name_input.setEditable(True)
-        self.name_input.setCurrentText(reagent_name)
-        self.lot_input = QLineEdit()
-        self.lot_input.setObjectName("lot")
-        self.lot_input.setText(reagent_lot)
-        # NOTE: widget to get expiry info
-        self.exp_input = QDateEdit(calendarPopup=True)
-        self.exp_input.setObjectName('expiry')
-        # NOTE: if expiry is not passed in from gui, use today
-        if expiry is None:
-            self.exp_input.setDate(QDate(1970, 1, 1))
-        else:
-            try:
-                self.exp_input.setDate(expiry)
-            except TypeError:
-                self.exp_input.setDate(QDate(1970, 1, 1))
-        # NOTE: widget to get reagent type info
-        self.type_input = QComboBox()
-        self.type_input.setObjectName('role')
-        if kit:
-            match kit:
-                case str():
-                    kit = KitType.query(name=kit)
-                case _:
-                    pass
-            self.type_input.addItems([item.name for item in ReagentRole.query() if kit in item.kit_types])
-        else:
-            self.type_input.addItems([item.name for item in ReagentRole.query()])
-        # NOTE: convert input to user-friendly string?
-        try:
-            reagent_role = reagent_role.replace("_", " ").title()
-        except AttributeError:
-            reagent_role = None
-        # NOTE: set parsed reagent type to top of list
-        index = self.type_input.findText(reagent_role, Qt.MatchFlag.MatchEndsWith)
-        if index >= 0:
-            self.type_input.setCurrentIndex(index)
-        self.layout = QVBoxLayout()
-        self.layout.addWidget(QLabel("Name:"))
-        self.layout.addWidget(self.name_input)
-        self.layout.addWidget(QLabel("Lot:"))
-        self.layout.addWidget(self.lot_input)
-        self.layout.addWidget(
-            QLabel("Expiry:\n(use exact date on reagent.\nEOL will be calculated from kit automatically)"))
-        self.layout.addWidget(self.exp_input)
-        self.layout.addWidget(QLabel("Type:"))
-        self.layout.addWidget(self.type_input)
-        self.layout.addWidget(self.buttonBox)
-        self.setLayout(self.layout)
-        self.type_input.currentTextChanged.connect(self.update_names)
-
-    def parse_form(self) -> dict:
-        """
-        Converts information in form to dict.
-
-        Returns:
-            dict: Output info
-        """
-        return dict(name=self.name_input.currentText().strip(),
-                    lot=self.lot_input.text().strip(),
-                    expiry=self.exp_input.date().toPyDate(),
-                    role=self.type_input.currentText().strip())
-
-    def update_names(self):
-        """
-        Updates reagent names form field with examples from reagent type
-        """
-        self.name_input.clear()
-        lookup = Reagent.query(role=self.type_input.currentText())
-        self.name_input.addItems(list(set([item.name for item in lookup])))
-
-
+# class AddReagentForm(QDialog):
+#     """
+#     dialog to add gather info about new reagent (Defunct)
+#     """
+#
+#     def __init__(self, reagent_lot: str | None = None, reagent_role: str | None = None, expiry: date | None = None,
+#                  reagent_name: str | None = None, kit: str | KitType | None = None) -> None:
+#         super().__init__()
+#         if reagent_name is None:
+#             reagent_name = reagent_role
+#         self.setWindowTitle("Add Reagent")
+#         QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
+#         self.buttonBox = QDialogButtonBox(QBtn)
+#         self.buttonBox.accepted.connect(self.accept)
+#         self.buttonBox.rejected.connect(self.reject)
+#         # NOTE: widget to get lot info
+#         self.name_input = QComboBox()
+#         self.name_input.setObjectName("name")
+#         self.name_input.setEditable(True)
+#         self.name_input.setCurrentText(reagent_name)
+#         self.lot_input = QLineEdit()
+#         self.lot_input.setObjectName("lot")
+#         self.lot_input.setText(reagent_lot)
+#         # NOTE: widget to get expiry info
+#         self.expiry_input = QDateEdit(calendarPopup=True)
+#         self.expiry_input.setObjectName('expiry')
+#         # NOTE: if expiry is not passed in from gui, use today
+#         if expiry is None:
+#             logger.warning(f"Did not receive expiry, setting to 1970, 1, 1")
+#             self.expiry_input.setDate(QDate(1970, 1, 1))
+#         else:
+#             try:
+#                 self.expiry_input.setDate(expiry)
+#             except TypeError:
+#                 self.expiry_input.setDate(QDate(1970, 1, 1))
+#         # NOTE: widget to get reagent type info
+#         self.role_input = QComboBox()
+#         self.role_input.setObjectName('role')
+#         if kit:
+#             match kit:
+#                 case str():
+#                     kit = KitType.query(name=kit)
+#                 case _:
+#                     pass
+#             self.role_input.addItems([item.name for item in ReagentRole.query() if kit in item.kit_types])
+#         else:
+#             self.role_input.addItems([item.name for item in ReagentRole.query()])
+#         # NOTE: convert input to user-friendly string?
+#         try:
+#             reagent_role = reagent_role.replace("_", " ").title()
+#         except AttributeError:
+#             reagent_role = None
+#         # NOTE: set parsed reagent type to top of list
+#         index = self.role_input.findText(reagent_role, Qt.MatchFlag.MatchEndsWith)
+#         if index >= 0:
+#             self.role_input.setCurrentIndex(index)
+#         self.layout = QVBoxLayout()
+#         self.layout.addWidget(QLabel("Name:"))
+#         self.layout.addWidget(self.name_input)
+#         self.layout.addWidget(QLabel("Lot:"))
+#         self.layout.addWidget(self.lot_input)
+#         self.layout.addWidget(
+#             QLabel("Expiry:\n(use exact date on reagent.\nEOL will be calculated from kit automatically)")
+#         )
+#         self.layout.addWidget(self.expiry_input)
+#         self.layout.addWidget(QLabel("Type:"))
+#         self.layout.addWidget(self.role_input)
+#         self.layout.addWidget(self.buttonBox)
+#         self.setLayout(self.layout)
+#         self.role_input.currentTextChanged.connect(self.update_names)
+#
+#     def parse_form(self) -> dict:
+#         """
+#         Converts information in form to dict.
+#
+#         Returns:
+#             dict: Output info
+#         """
+#         return dict(name=self.name_input.currentText().strip(),
+#                     lot=self.lot_input.text().strip(),
+#                     expiry=self.expiry_input.date().toPyDate(),
+#                     role=self.role_input.currentText().strip())
+#
+#     def update_names(self):
+#         """
+#         Updates reagent names form field with examples from reagent type
+#         """
+#         self.name_input.clear()
+#         lookup = Reagent.query(role=self.role_input.currentText())
+#         self.name_input.addItems(list(set([item.name for item in lookup])))
+#
+#
 class StartEndDatePicker(QWidget):
     """
     custom widget to pick start and end dates for controls graphs
@@ -135,12 +135,12 @@ class StartEndDatePicker(QWidget):
         return QSize(80, 20)
 
 
-def save_pdf(obj: QWebEngineView, filename: Path):
-    page_layout = QPageLayout()
-    page_layout.setPageSize(QPageSize(QPageSize.PageSizeId.A4))
-    page_layout.setOrientation(QPageLayout.Orientation.Portrait)
-    page_layout.setMargins(QMarginsF(25, 25, 25, 25))
-    obj.page().printToPdf(filename.absolute().__str__(), page_layout)
+# def save_pdf(obj: QWebEngineView, filename: Path):
+#     page_layout = QPageLayout()
+#     page_layout.setPageSize(QPageSize(QPageSize.PageSizeId.A4))
+#     page_layout.setOrientation(QPageLayout.Orientation.Portrait)
+#     page_layout.setMargins(QMarginsF(25, 25, 25, 25))
+#     obj.page().printToPdf(filename.absolute().__str__(), page_layout)
 
 
 # NOTE: subclass

src/submissions/frontend/widgets/omni_add_edit.py

@@ -1,17 +1,18 @@
+"""
+A widget to handle adding/updating any database object.
+"""
 from datetime import date
 from pprint import pformat
-from typing import Any, List, Tuple
+from typing import Any, Tuple
 from pydantic import BaseModel
 from PyQt6.QtWidgets import (
-    QLabel, QDialog, QTableView, QWidget, QLineEdit, QGridLayout, QComboBox, QPushButton, QDialogButtonBox, QDateEdit
+    QLabel, QDialog, QWidget, QLineEdit, QGridLayout, QComboBox, QDialogButtonBox, QDateEdit, QSpinBox, QDoubleSpinBox
 )
-from sqlalchemy import String, TIMESTAMP
+from sqlalchemy import String, TIMESTAMP, INTEGER, FLOAT
 from sqlalchemy.orm import InstrumentedAttribute, ColumnProperty
 import logging
-
 from sqlalchemy.orm.relationships import _RelationshipDeclared
-
-from tools import Report, Result, report_result
+from tools import Report, report_result
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -23,7 +24,6 @@ class AddEdit(QDialog):
         self.instance = instance
         self.object_type = instance.__class__
         self.layout = QGridLayout(self)
-        # logger.debug(f"Manager: {manager}")
         QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
         self.buttonBox = QDialogButtonBox(QBtn)
         self.buttonBox.accepted.connect(self.accept)
@@ -36,7 +36,6 @@ class AddEdit(QDialog):
             fields = {'name': fields.pop('name'), **fields}
         except KeyError:
             pass
-        # logger.debug(pformat(fields, indent=4))
         height_counter = 0
         for key, field in fields.items():
             try:
@@ -45,9 +44,6 @@ class AddEdit(QDialog):
                 value = None
             try:
                 logger.debug(f"{key} property: {type(field['class_attr'].property)}")
-                # widget = EditProperty(self, key=key, column_type=field.property.expression.type,
-                #                           value=getattr(self.instance, key))
-                # logger.debug(f"Column type: {field}, Value: {value}")
                 widget = EditProperty(self, key=key, column_type=field, value=value)
             except AttributeError as e:
                 logger.error(f"Problem setting widget {key}: {e}")
@@ -64,15 +60,11 @@ class AddEdit(QDialog):
     def parse_form(self) -> Tuple[BaseModel, Report]:
         report = Report()
         parsed = {result[0].strip(":"): result[1] for result in [item.parse_form() for item in self.findChildren(EditProperty)] if result[0]}
-        logger.debug(parsed)
+        # logger.debug(parsed)
         model = self.object_type.pydantic_model
         # NOTE: Hand-off to pydantic model for validation.
         # NOTE: Also, why am I not just using the toSQL method here. I could write one for contacts.
         model = model(**parsed)
-        # output, result = model.to_sql()
-        # report.add_result(result)
-        # if len(report.results) < 1:
-        #     report.add_result(Result(msg="Added new regeant.", icon="Information", owner=__name__))
         return model, report
 
 
@@ -84,7 +76,7 @@ class EditProperty(QWidget):
         self.label = QLabel(key.title().replace("_", " "))
         self.layout = QGridLayout()
         self.layout.addWidget(self.label, 0, 0, 1, 1)
-        self.setObjectName(f"{key}:")
+        self.setObjectName(key)
         match column_type['class_attr'].property:
             case ColumnProperty():
                 self.column_property_set(column_type, value=value)
@@ -97,15 +89,15 @@ class EditProperty(QWidget):
         self.setLayout(self.layout)
 
     def relationship_property_set(self, relationship_property, value=None):
-        # print(relationship_property)
         self.property_class = relationship_property['class_attr'].property.entity.class_
         self.is_list = relationship_property['class_attr'].property.uselist
-        choices = [item.name for item in self.property_class.query()]
+        choices = [""] + [item.name for item in self.property_class.query()]
         try:
-            instance_value = getattr(self.parent().instance, self.name)
+            instance_value = getattr(self.parent().instance, self.objectName())
         except AttributeError:
-            logger.error(f"Unable to get instance {self.parent().instance} attribute: {self.name}")
+            logger.error(f"Unable to get instance {self.parent().instance} attribute: {self.objectName()}")
             instance_value = None
+        # NOTE: get the value for the current instance and move it to the front.
         if isinstance(instance_value, list):
             instance_value = next((item.name for item in instance_value), None)
         if instance_value:
@@ -120,6 +112,16 @@ class EditProperty(QWidget):
                     value = ""
                 self.widget = QLineEdit(self)
                 self.widget.setText(value)
+            case INTEGER():
+                if not value:
+                    value = 1
+                self.widget = QSpinBox()
+                self.widget.setValue(value)
+            case FLOAT():
+                if not value:
+                    value = 1.0
+                self.widget = QDoubleSpinBox()
+                self.widget.setValue(value)
             case TIMESTAMP():
                 self.widget = QDateEdit(self, calendarPopup=True)
                 if not value:
@@ -129,12 +131,13 @@ class EditProperty(QWidget):
                 logger.error(f"{column_property} not a supported property.")
                 self.widget = None
         try:
-            tooltip_text = self.parent().object_type.add_edit_tooltips[self.name]
+            tooltip_text = self.parent().object_type.add_edit_tooltips[self.objectName()]
             self.widget.setToolTip(tooltip_text)
         except KeyError:
             pass
 
     def parse_form(self):
+        # NOTE: Make sure there's a widget.
         try:
             check = self.widget
         except AttributeError:
@@ -146,10 +149,12 @@ class EditProperty(QWidget):
                 value = self.widget.date().toPyDate()
             case QComboBox():
                 value = self.widget.currentText()
+            case QSpinBox() | QDoubleSpinBox():
+                value = self.widget.value()
                 # if self.is_list:
                 #     value = [self.property_class.query(name=prelim)]
                 # else:
                 #     value = self.property_class.query(name=prelim)
             case _:
                 value = None
-        return self.name, value
+        return self.objectName(), value

src/submissions/frontend/widgets/omni_manager.py

@@ -1,4 +1,6 @@
-from operator import itemgetter
+"""
+Provides a screen for managing all attributes of a database object.
+"""
 from typing import Any, List
 from PyQt6.QtCore import QSortFilterProxyModel, Qt
 from PyQt6.QtGui import QAction, QCursor
@@ -49,21 +51,22 @@ class ManagerWindow(QDialog):
             self.layout.addWidget(self.sub_class, 0, 0)
         else:
             self.sub_class = None
-        # self.layout.addWidget(self.buttonBox, self.layout.rowCount(), 0)
         self.options = QComboBox(self)
         self.options.setObjectName("options")
         self.update_options()
         self.setLayout(self.layout)
         self.setWindowTitle(f"Manage {self.object_type.__name__}")
 
-    def update_options(self):
+    def update_options(self) -> None:
         """
         Changes form inputs based on sample type
         """
-
         if self.sub_class:
             self.object_type = getattr(db, self.sub_class.currentText())
         options = [item.name for item in self.object_type.query()]
+        logger.debug(f"self.instance: {self.instance}")
+        if self.instance:
+            options.insert(0, options.pop(options.index(self.instance.name)))
         self.options.clear()
         self.options.addItems(options)
         self.options.setEditable(False)
@@ -75,23 +78,34 @@ class ManagerWindow(QDialog):
         self.add_button.clicked.connect(self.add_new)
         self.update_data()
 
-    def update_data(self):
+    def update_data(self) -> None:
+        """
+        Performs updating of widgets on first run and after options change.
+
+        Returns:
+            None
+        """
+        # NOTE: Remove all old widgets.
         deletes = [item for item in self.findChildren(EditProperty)] + \
                   [item for item in self.findChildren(EditRelationship)] + \
                   [item for item in self.findChildren(QDialogButtonBox)]
         for item in deletes:
             item.setParent(None)
+        # NOTE: Find the instance this manager will update
         self.instance = self.object_type.query(name=self.options.currentText())
         fields = {k: v for k, v in self.object_type.__dict__.items() if
                   isinstance(v, InstrumentedAttribute) and k != "id"}
         for key, field in fields.items():
-            # logger.debug(f"Key: {key}, Value: {field}")
             match field.property:
+                # NOTE: ColumnProperties will be directly edited.
                 case ColumnProperty():
+                    # NOTE: field.property.expression.type gives db column type eg. STRING or TIMESTAMP
                     widget = EditProperty(self, key=key, column_type=field.property.expression.type,
                                           value=getattr(self.instance, key))
+                # NOTE: RelationshipDeclareds will be given a list of existing related objects.
                 case _RelationshipDeclared():
                     if key != "submissions":
+                        # NOTE: field.comparator.entity.class_ gives the relationship class
                         widget = EditRelationship(self, key=key, entity=field.comparator.entity.class_,
                                                   value=getattr(self.instance, key))
                     else:
@@ -100,11 +114,18 @@ class ManagerWindow(QDialog):
                     continue
             if widget:
                 self.layout.addWidget(widget, self.layout.rowCount(), 0, 1, 2)
+        # NOTE: Add OK|Cancel to bottom of dialog.
         self.layout.addWidget(self.buttonBox, self.layout.rowCount(), 0, 1, 2)
 
-    def parse_form(self):
+    def parse_form(self) -> Any:
+        """
+        Returns the instance associated with this window.
+
+        Returns:
+            Any: The instance with updated fields.
+        """
+        # TODO: Need Relationship property here too?
         results = [item.parse_form() for item in self.findChildren(EditProperty)]
-        # logger.debug(results)
         for result in results:
             # logger.debug(result)
             self.instance.__setattr__(result[0], result[1])
@@ -113,9 +134,10 @@ class ManagerWindow(QDialog):
     def add_new(self):
         dlg = AddEdit(parent=self, instance=self.object_type(), manager=self.object_type.__name__.lower())
         if dlg.exec():
-            new_instance = dlg.parse_form()
-            # logger.debug(new_instance.__dict__)
+            new_pyd = dlg.parse_form()
+            new_instance = new_pyd.to_sql()
             new_instance.save()
+            self.instance = new_instance
             self.update_options()
 
 
@@ -222,10 +244,13 @@ class EditRelationship(QWidget):
             self.data['id'] = self.data['id'].apply(str)
             self.data['id'] = self.data['id'].str.zfill(4)
         except KeyError as e:
-            logger.error(f"Could not alter id to string due to {e}")
+            logger.error(f"Could not alter id to string due to KeyError: {e}")
         proxy_model = QSortFilterProxyModel()
         proxy_model.setSourceModel(pandasModel(self.data))
         self.table.setModel(proxy_model)
+        self.table.resizeColumnsToContents()
+        self.table.resizeRowsToContents()
+        self.table.setSortingEnabled(True)
         self.table.doubleClicked.connect(self.parse_row)
 
     def contextMenuEvent(self, event):

src/submissions/frontend/widgets/omni_search.py

@@ -2,9 +2,9 @@
 Search box that performs fuzzy search for various object types
 """
 from pprint import pformat
-from typing import Tuple, Any, List
+from typing import Tuple, Any, List, Generator
 from pandas import DataFrame
-from PyQt6.QtCore import QSortFilterProxyModel
+from PyQt6.QtCore import QSortFilterProxyModel, QModelIndex
 from PyQt6.QtWidgets import (
     QLabel, QVBoxLayout, QDialog,
     QTableView, QWidget, QLineEdit, QGridLayout, QComboBox, QDialogButtonBox
@@ -74,7 +74,6 @@ class SearchBox(QDialog):
             search_fields = []
         for iii, searchable in enumerate(search_fields):
             widget = FieldSearch(parent=self, label=searchable['label'], field_name=searchable['field'])
-            # widget = FieldSearch(parent=self, label=k, field_name=v)
             widget.setObjectName(searchable['field'])
             self.layout.addWidget(widget, 1 + iii, 0)
             widget.search_widget.textChanged.connect(self.update_data)
@@ -100,11 +99,17 @@ class SearchBox(QDialog):
         # NOTE: Setting results moved to here from __init__ 202411118
         self.results.setData(df=data)
 
-    def return_selected_rows(self):
-        rows = sorted(set(index.row() for index in
-                          self.results.selectedIndexes()))
+    def return_selected_rows(self) -> Generator[dict, None, None]:
+        """
+        Yields data from selected rows
+
+        Returns:
+            dict: Dictionary of column name: data
+        """
+        rows = sorted(set(index.row() for index in self.results.selectedIndexes()))
         for index in rows:
-            output = {column:self.results.model().data(self.results.model().index(index, ii)) for ii, column in enumerate(self.results.data.columns)}
+            output = {column: self.results.model().data(self.results.model().index(index, ii)) for ii, column in
+                      enumerate(self.results.data.columns)}
             yield output
 
 
@@ -130,7 +135,13 @@ class FieldSearch(QWidget):
         """
         self.parent().update_data()
 
-    def parse_form(self) -> Tuple:
+    def parse_form(self) -> Tuple[str, str]:
+        """
+        Gets object name and widget value.
+
+        Returns:
+            Tuple(str, str): Key, value to be used in constructing a dictionary.
+        """
         field_value = self.search_widget.text()
         if field_value == "":
             field_value = None
@@ -147,6 +158,7 @@ class SearchResults(QTableView):
         self.context = kwargs
         self.parent = parent
         self.object_type = object_type
+
         try:
             self.extras = extras + self.object_type.searchables
         except AttributeError:
@@ -160,7 +172,8 @@ class SearchResults(QTableView):
 
         self.data = df
         try:
-            self.columns_of_interest = [dict(name=item['field'], column=self.data.columns.get_loc(item['field'])) for item in self.extras]
+            self.columns_of_interest = [dict(name=item['field'], column=self.data.columns.get_loc(item['field'])) for
+                                        item in self.extras]
         except KeyError:
             self.columns_of_interest = []
         try:
@@ -171,9 +184,21 @@ class SearchResults(QTableView):
         proxy_model = QSortFilterProxyModel()
         proxy_model.setSourceModel(pandasModel(self.data))
         self.setModel(proxy_model)
+        self.resizeColumnsToContents()
+        self.resizeRowsToContents()
+        self.setSortingEnabled(True)
         self.doubleClicked.connect(self.parse_row)
 
-    def parse_row(self, x):
+    def parse_row(self, x: QModelIndex) -> None:
+        """
+        Runs the self.object_type edit from search method for row X.
+
+        Args:
+            x (QModelIndex): Row to be parsed.
+
+        Returns:
+            None
+        """
         context = {item['name']: x.sibling(x.row(), item['column']).data() for item in self.columns_of_interest}
         try:
             object = self.object_type.query(**context)

src/submissions/frontend/widgets/submission_details.py

@@ -8,9 +8,8 @@ from PyQt6.QtWebChannel import QWebChannel
 from PyQt6.QtCore import Qt, pyqtSlot
 from jinja2 import TemplateNotFound
 from backend.db.models import BasicSubmission, BasicSample, Reagent, KitType
-from tools import is_power_user, jinja_template_loading, timezone
-from .functions import select_save_file
-from .misc import save_pdf
+from tools import is_power_user, jinja_template_loading, timezone, get_application_from_parent
+from .functions import select_save_file, save_pdf
 from pathlib import Path
 import logging
 from getpass import getuser
@@ -30,13 +29,11 @@ class SubmissionDetails(QDialog):
     def __init__(self, parent, sub: BasicSubmission | BasicSample | Reagent) -> None:
 
         super().__init__(parent)
-        try:
-            self.app = parent.parent().parent().parent().parent().parent().parent()
-        except AttributeError:
-            self.app = None
+        self.app = get_application_from_parent(parent)
         self.webview = QWebEngineView(parent=self)
         self.webview.setMinimumSize(900, 500)
         self.webview.setMaximumWidth(900)
+        # NOTE: Decide if exporting should be allowed.
         self.webview.loadFinished.connect(self.activate_export)
         self.layout = QGridLayout()
         # NOTE: button to export a pdf version
@@ -61,9 +58,16 @@ class SubmissionDetails(QDialog):
                 self.sample_details(sample=sub)
             case Reagent():
                 self.reagent_details(reagent=sub)
+        # NOTE: Used to maintain javascript functions.
         self.webview.page().setWebChannel(self.channel)
 
-    def activate_export(self):
+    def activate_export(self) -> None:
+        """
+        Determines if export pdf should be active.
+
+        Returns:
+            None
+        """
         title = self.webview.title()
         self.setWindowTitle(title)
         if "Submission" in title:
@@ -103,6 +107,13 @@ class SubmissionDetails(QDialog):
 
     @pyqtSlot(str, str)
     def reagent_details(self, reagent: str | Reagent, kit: str | KitType):
+        """
+        Changes details view to summary of Reagent
+
+        Args:
+            kit (str | KitType): Name of kit.
+            reagent (str | Reagent): Lot number of the reagent
+        """
         if isinstance(reagent, str):
             reagent = Reagent.query(lot=reagent)
         if isinstance(kit, str):
@@ -124,6 +135,17 @@ class SubmissionDetails(QDialog):
 
     @pyqtSlot(str, str, str)
     def update_reagent(self, old_lot: str, new_lot: str, expiry: str):
+        """
+        Designed to allow editing reagent in details view (depreciated)
+
+        Args:
+            old_lot ():
+            new_lot ():
+            expiry ():
+
+        Returns:
+
+        """
         expiry = datetime.strptime(expiry, "%Y-%m-%d")
         reagent = Reagent.query(lot=old_lot)
         if reagent:
@@ -157,7 +179,16 @@ class SubmissionDetails(QDialog):
         self.webview.setHtml(self.html)
 
     @pyqtSlot(str)
-    def sign_off(self, submission: str | BasicSubmission):
+    def sign_off(self, submission: str | BasicSubmission) -> None:
+        """
+        Allows power user to signify a submission is complete.
+
+        Args:
+            submission (str | BasicSubmission): Submission to be completed
+
+        Returns:
+            None
+        """
         logger.info(f"Signing off on {submission} - ({getuser()})")
         if isinstance(submission, str):
             submission = BasicSubmission.query(rsl_plate_num=submission)
@@ -183,10 +214,7 @@ class SubmissionComment(QDialog):
     def __init__(self, parent, submission: BasicSubmission) -> None:
 
         super().__init__(parent)
-        try:
-            self.app = parent.parent().parent().parent().parent().parent().parent
-        except AttributeError:
-            pass
+        self.app = get_application_from_parent(parent)
         self.submission = submission
         self.setWindowTitle(f"{self.submission.rsl_plate_num} Submission Comment")
         # NOTE: create text field

src/submissions/frontend/widgets/submission_table.py

@@ -65,12 +65,6 @@ class SubmissionsSheet(QTableView):
     """
 
     def __init__(self, parent) -> None:
-        """
-        initialize
-
-        Args:
-            ctx (dict): settings passed from gui
-        """
         super().__init__(parent)
         self.app = self.parent()
         self.report = Report()
@@ -107,7 +101,9 @@ class SubmissionsSheet(QTableView):
         Args:
             event (_type_): the item of interest
         """
+        # NOTE: Get current row index
         id = self.selectionModel().currentIndex()
+        # NOTE: Convert to data in id column (i.e. column 0)
         id = id.sibling(id.row(), 0).data()
         submission = BasicSubmission.query(id=id)
         self.menu = QMenu(self)

src/submissions/frontend/widgets/submission_widget.py

@@ -9,16 +9,15 @@ from PyQt6.QtCore import pyqtSignal, Qt, QSignalBlocker
 from .functions import select_open_file, select_save_file
 import logging
 from pathlib import Path
-from tools import Report, Result, check_not_nan, main_form_style, report_result
+from tools import Report, Result, check_not_nan, main_form_style, report_result, get_application_from_parent
 from backend.excel.parser import SheetParser
 from backend.validators import PydSubmission, PydReagent
 from backend.db import (
-    KitType, Organization, SubmissionType, Reagent,
+    Organization, SubmissionType, Reagent,
     ReagentRole, KitTypeReagentRoleAssociation, BasicSubmission
 )
 from pprint import pformat
 from .pop_ups import QuestionAsker, AlertPop
-from .misc import AddReagentForm
 from .omni_add_edit import AddEdit
 from typing import List, Tuple
 from datetime import date
@@ -67,7 +66,6 @@ class SubmissionFormContainer(QWidget):
     def __init__(self, parent: QWidget) -> None:
         super().__init__(parent)
         self.app = self.parent().parent()
-        self.report = Report()
         self.setStyleSheet('background-color: light grey;')
         self.setAcceptDrops(True)
         # NOTE: if import_drag is emitted, importSubmission will fire
@@ -97,12 +95,12 @@ class SubmissionFormContainer(QWidget):
         """
         self.app.raise_()
         self.app.activateWindow()
-        self.report = Report()
+        report = Report()
         self.import_submission_function(fname)
-        return self.report
+        return report
 
     @report_result
-    def import_submission_function(self, fname: Path | None = None):
+    def import_submission_function(self, fname: Path | None = None) -> Report:
         """
         Import a new submission to the app window
 
@@ -110,10 +108,11 @@ class SubmissionFormContainer(QWidget):
             obj (QMainWindow): original app window
 
         Returns:
-            Tuple[QMainWindow, dict|None]: Collection of new main app window and result dict
+            Report: Object to give results of import.
         """
         logger.info(f"\n\nStarting Import...\n\n")
         report = Report()
+        # NOTE: Clear any previous forms.
         try:
             self.form.setParent(None)
         except AttributeError:
@@ -141,7 +140,16 @@ class SubmissionFormContainer(QWidget):
         return report
 
     @report_result
-    def new_add_reagent(self, instance: Reagent | None = None):
+    def add_reagent(self, instance: Reagent | None = None):
+        """
+        Action to create new reagent in DB.
+
+        Args:
+            instance (Reagent | None): Blank reagent instance to be edited and then added.
+
+        Returns:
+            models.Reagent: the constructed reagent object to add to submission
+        """
         report = Report()
         if not instance:
             instance = Reagent()
@@ -149,48 +157,12 @@ class SubmissionFormContainer(QWidget):
         if dlg.exec():
             reagent = dlg.parse_form()
             reagent.missing = False
-            # logger.debug(f"Reagent: {reagent}, result: {result}")
-            # report.add_result(result)
             # NOTE: send reagent to db
             sqlobj = reagent.to_sql()
             sqlobj.save()
-            logger.debug(f"Reagent added!")
             report.add_result(Result(owner=__name__, code=0, msg="New reagent created.", status="Information"))
-            # report.add_result(result)
             return reagent, report
 
-    @report_result
-    def add_reagent(self, reagent_lot: str | None = None, reagent_role: str | None = None, expiry: date | None = None,
-                    name: str | None = None, kit: str | KitType | None = None) -> Tuple[PydReagent, Report]:
-        """
-        Action to create new reagent in DB.
-
-        Args:
-            reagent_lot (str | None, optional): Parsed reagent from import form. Defaults to None.
-            reagent_role (str | None, optional): Parsed reagent type from import form. Defaults to None.
-            expiry (date | None, optional): Parsed reagent expiry data. Defaults to None.
-            name (str | None, optional): Parsed reagent name. Defaults to None.
-
-        Returns:
-            models.Reagent: the constructed reagent object to add to submission
-        """
-        report = Report()
-        if isinstance(reagent_lot, bool):
-            reagent_lot = ""
-        # NOTE: create form
-        dlg = AddReagentForm(reagent_lot=reagent_lot, reagent_role=reagent_role, expiry=expiry, reagent_name=name,
-                             kit=kit)
-        if dlg.exec():
-            # NOTE: extract form info
-            info = dlg.parse_form()
-            # NOTE: create reagent object
-            reagent = PydReagent(ctx=self.app.ctx, **info, missing=False)
-            # NOTE: send reagent to db
-            sqlobj = reagent.to_sql()
-            sqlobj.save()
-            # report.add_result(result)
-            return reagent
-
 
 class SubmissionFormWidget(QWidget):
     update_reagent_fields = ['extraction_kit']
@@ -199,12 +171,12 @@ class SubmissionFormWidget(QWidget):
         super().__init__(parent)
         if disable is None:
             disable = []
-        self.app = parent.app
+        self.app = get_application_from_parent(parent)
         self.pyd = submission
         self.missing_info = []
         self.submission_type = SubmissionType.query(name=self.pyd.submission_type['value'])
-        st = self.submission_type.submission_class
-        defaults = st.get_default_info("form_recover", "form_ignore", submission_type=self.pyd.submission_type['value'])
+        basic_submission_class = self.submission_type.submission_class
+        defaults = basic_submission_class.get_default_info("form_recover", "form_ignore", submission_type=self.pyd.submission_type['value'])
         self.recover = defaults['form_recover']
         self.ignore = defaults['form_ignore']
         self.layout = QVBoxLayout()
@@ -225,7 +197,7 @@ class SubmissionFormWidget(QWidget):
                 except KeyError:
                     value = dict(value=None, missing=True)
             add_widget = self.create_widget(key=k, value=value, submission_type=self.submission_type,
-                                            sub_obj=st, disable=check)
+                                            sub_obj=basic_submission_class, disable=check)
             if add_widget is not None:
                 self.layout.addWidget(add_widget)
             if k in self.__class__.update_reagent_fields:
@@ -302,10 +274,9 @@ class SubmissionFormWidget(QWidget):
             if isinstance(reagent, self.ReagentFormWidget) or isinstance(reagent, QPushButton):
                 reagent.setParent(None)
         reagents, integrity_report, missing_reagents = self.pyd.check_kit_integrity(extraction_kit=self.extraction_kit)
-        logger.debug(f"Reagents: {reagents}")
+        # logger.debug(f"Reagents: {reagents}")
         expiry_report = self.pyd.check_reagent_expiries(exempt=missing_reagents)
         for reagent in reagents:
-
             add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.extraction_kit)
             self.layout.addWidget(add_widget)
         report.add_result(integrity_report)
@@ -340,9 +311,12 @@ class SubmissionFormWidget(QWidget):
         Returns:
             List[QWidget]: Widgets matching filter
         """
-        query = self.findChildren(QWidget)
-        if object_name is not None:
-            query = [widget for widget in query if widget.objectName() == object_name]
+        if object_name:
+            query = self.findChildren(QWidget, name=object_name)
+        else:
+            query = self.findChildren(QWidget)
+        # if object_name is not None:
+        #     query = [widget for widget in query if widget.objectName() == object_name]
         return query
 
     @report_result
@@ -581,13 +555,13 @@ class SubmissionFormWidget(QWidget):
                     parent.extraction_kit = add_widget.currentText()
                 case 'submission_category':
                     add_widget = MyQComboBox(scrollWidget=parent)
-                    cats = ['Diagnostic', "Surveillance", "Research"]
-                    cats += [item.name for item in SubmissionType.query()]
+                    categories = ['Diagnostic', "Surveillance", "Research"]
+                    categories += [item.name for item in SubmissionType.query()]
                     try:
-                        cats.insert(0, cats.pop(cats.index(value)))
+                        categories.insert(0, categories.pop(categories.index(value)))
                     except ValueError:
-                        cats.insert(0, cats.pop(cats.index(submission_type)))
-                    add_widget.addItems(cats)
+                        categories.insert(0, categories.pop(categories.index(submission_type)))
+                    add_widget.addItems(categories)
                     add_widget.setToolTip("Enter submission category or select from list.")
                 case _:
                     if key in sub_obj.timestamps:
@@ -655,7 +629,8 @@ class SubmissionFormWidget(QWidget):
 
         def __init__(self, parent: QWidget, reagent: PydReagent, extraction_kit: str):
             super().__init__(parent)
-            self.app = self.parent().parent().parent().parent().parent().parent().parent().parent()
+            self.parent = parent
+            self.app = get_application_from_parent(parent)
             self.reagent = reagent
             self.extraction_kit = extraction_kit
             layout = QGridLayout()
@@ -684,10 +659,11 @@ class SubmissionFormWidget(QWidget):
         def disable(self):
             self.lot.setEnabled(self.check.isChecked())
             self.label.setEnabled(self.check.isChecked())
-            if not any([item.lot.isEnabled() for item in self.parent().findChildren(self.__class__)]):
-                self.parent().disabler.checkbox.setChecked(False)
-            else:
-                self.parent().disabler.checkbox.setChecked(True)
+            with QSignalBlocker(self.parent.disabler.checkbox) as blocker:
+                if any([item.lot.isEnabled() for item in self.parent.findChildren(self.__class__)]):
+                    self.parent.disabler.checkbox.setChecked(True)
+                else:
+                    self.parent.disabler.checkbox.setChecked(False)
 
         @report_result
         def parse_form(self) -> Tuple[PydReagent | None, Report]:
@@ -703,31 +679,23 @@ class SubmissionFormWidget(QWidget):
             lot = self.lot.currentText()
             wanted_reagent, new = Reagent.query_or_create(lot=lot, role=self.reagent.role, expiry=self.reagent.expiry)
             # NOTE: if reagent doesn't exist in database, offer to add it (uses App.add_reagent)
-            logger.debug(f"Wanted reagent: {wanted_reagent}, New: {new}")
-            # if wanted_reagent is None:
             if new:
                 dlg = QuestionAsker(title=f"Add {lot}?",
                                     message=f"Couldn't find reagent type {self.reagent.role}: {lot} in the database.\n\nWould you like to add it?")
 
                 if dlg.exec():
                     wanted_reagent = self.parent().parent().new_add_reagent(instance=wanted_reagent)
-                    logger.debug(f"Reagent added!")
-                    report.add_result(Result(owner=__name__, code=0, msg="New reagent created.", status="Information"))
                     return wanted_reagent, report
                 else:
                     # NOTE: In this case we will have an empty reagent and the submission will fail kit integrity check
-
                     return None, report
             else:
-                # NOTE: Since this now gets passed in directly from the parser -> pyd -> form and the parser gets the name
-                # from the db, it should no longer be necessary to query the db with reagent/kit, but with rt name directly.
+                # NOTE: Since this now gets passed in directly from the parser -> pyd -> form and the parser gets the name from the db, it should no longer be necessary to query the db with reagent/kit, but with rt name directly.
                 rt = ReagentRole.query(name=self.reagent.role)
-                logger.debug(f"Reagent role: {rt}")
                 if rt is None:
                     rt = ReagentRole.query(kit_type=self.extraction_kit, reagent=wanted_reagent)
                 final = PydReagent(name=wanted_reagent.name, lot=wanted_reagent.lot, role=rt.name,
                                    expiry=wanted_reagent.expiry.date(), missing=False)
-                logger.debug(f"Final Reagent: {final}")
                 return final, report
 
         def updated(self):
@@ -781,10 +749,11 @@ class SubmissionFormWidget(QWidget):
                             looked_up_reg = None
                         if looked_up_reg:
                             try:
-                                relevant_reagents.remove(str(looked_up_reg.lot))
+                                # relevant_reagents.remove(str(looked_up_reg.lot))
+                                relevant_reagents.insert(0, relevant_reagents.pop(relevant_reagents.index(looked_up_reg.lot)))
                             except ValueError as e:
                                 logger.error(f"Error reordering relevant reagents: {e}")
-                            relevant_reagents.insert(0, str(looked_up_reg.lot))
+                            # relevant_reagents.insert(0, str(looked_up_reg.lot))
                 else:
                     if len(relevant_reagents) > 1:
                         idx = relevant_reagents.index(str(reagent.lot))

src/submissions/frontend/widgets/summary.py

@@ -32,7 +32,13 @@ class Summary(InfoPane):
         self.update_data()
 
 
-    def update_data(self):
+    def update_data(self) -> None:
+        """
+        Sets data in the info pane
+
+        Returns:
+            None
+        """
         super().update_data()
         orgs = [self.org_select.itemText(i) for i in range(self.org_select.count()) if self.org_select.itemChecked(i)]
         self.report_obj = ReportMaker(start_date=self.start_date, end_date=self.end_date, organizations=orgs)

src/submissions/frontend/widgets/turnaround.py

@@ -31,7 +31,13 @@ class TurnaroundTime(InfoPane):
         self.submission_typer.currentTextChanged.connect(self.update_data)
         self.update_data()
 
-    def update_data(self):
+    def update_data(self) -> None:
+        """
+        Sets data in the info pane
+
+        Returns:
+            None
+        """
         super().update_data()
         months = self.diff_month(self.start_date, self.end_date)
         chart_settings = dict(start_date=self.start_date, end_date=self.end_date)
@@ -47,4 +53,4 @@ class TurnaroundTime(InfoPane):
         else:
             threshold = None
         self.fig = TurnaroundChart(df=self.report_obj.df, settings=chart_settings, modes=[], threshold=threshold, months=months)
-        self.webview.setHtml(self.fig.to_html())
+        self.webview.setHtml(self.fig.html)