Removed logger.debugs for proven functions.

2024-12-12 12:17:21 -06:00
parent b174eb1221
commit 67520cb784
32 changed files with 80 additions and 758 deletions
--- a/src/submissions/frontend/widgets/app.py
+++ b/src/submissions/frontend/widgets/app.py
@@ -27,13 +27,11 @@ from .turnaround import TurnaroundTime
 from .omni_search import SearchBox

 logger = logging.getLogger(f'submissions.{__name__}')
-# logger.info("Hello, I am a logger")


 class App(QMainWindow):

    def __init__(self, ctx: Settings = None):
-        # logger.debug(f"Initializing main window...")
        super().__init__()
        qInstallMessageHandler(lambda x, y, z: None)
        self.ctx = ctx
@@ -68,7 +66,6 @@ class App(QMainWindow):
        """
        adds items to menu bar
        """
-        # logger.debug(f"Creating menu bar...")
        menuBar = self.menuBar()
        fileMenu = menuBar.addMenu("&File")
        editMenu = menuBar.addMenu("&Edit")
@@ -82,7 +79,6 @@ class App(QMainWindow):
        fileMenu.addAction(self.importAction)
        fileMenu.addAction(self.yamlExportAction)
        fileMenu.addAction(self.yamlImportAction)
-        # methodsMenu.addAction(self.searchLog)
        methodsMenu.addAction(self.searchSample)
        maintenanceMenu.addAction(self.joinExtractionAction)
        maintenanceMenu.addAction(self.joinPCRAction)
@@ -92,27 +88,20 @@ class App(QMainWindow):
        """
        adds items to toolbar
        """
-        # logger.debug(f"Creating toolbar...")
        toolbar = QToolBar("My main toolbar")
        self.addToolBar(toolbar)
        toolbar.addAction(self.addReagentAction)
-        # toolbar.addAction(self.addKitAction)
-        # toolbar.addAction(self.addOrgAction)

    def _createActions(self):
        """
        creates actions
        """
-        # logger.debug(f"Creating actions...")
        self.importAction = QAction("&Import Submission", self)
        self.addReagentAction = QAction("Add Reagent", self)
-        # self.addKitAction = QAction("Import Kit", self)
-        # self.addOrgAction = QAction("Import Org", self)
        self.joinExtractionAction = QAction("Link Extraction Logs")
        self.joinPCRAction = QAction("Link PCR Logs")
        self.helpAction = QAction("&About", self)
        self.docsAction = QAction("&Docs", self)
-        # self.searchLog = QAction("Search Log", self)
        self.searchSample = QAction("Search Sample", self)
        self.githubAction = QAction("Github", self)
        self.yamlExportAction = QAction("Export Type Example", self)
@@ -123,14 +112,12 @@ class App(QMainWindow):
        """
        connect menu and tool bar item to functions
        """
-        # logger.debug(f"Connecting actions...")
        self.importAction.triggered.connect(self.table_widget.formwidget.importSubmission)
        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)
        self.docsAction.triggered.connect(self.openDocs)
-        # self.searchLog.triggered.connect(self.runSearch)
        self.searchSample.triggered.connect(self.runSampleSearch)
        self.githubAction.triggered.connect(self.openGithub)
        self.yamlExportAction.triggered.connect(self.export_ST_yaml)
@@ -145,7 +132,6 @@ class App(QMainWindow):
        j_env = jinja_template_loading()
        template = j_env.get_template("project.html")
        html = template.render(info=self.ctx.package.__dict__)
-        # logger.debug(html)
        about = HTMLPop(html=html, title="About")
        about.exec()

@@ -157,7 +143,6 @@ class App(QMainWindow):
            url = Path(sys._MEIPASS).joinpath("files", "docs", "index.html")
        else:
            url = Path("docs\\build\\index.html").absolute()
-        # logger.debug(f"Attempting to open {url}")
        webbrowser.get('windows-default').open(f"file://{url.__str__()}")

    def openGithub(self):
@@ -177,10 +162,6 @@ class App(QMainWindow):
        instr = HTMLPop(html=html, title="Instructions")
        instr.exec()

-    # def runSearch(self):
-    #     dlg = LogParser(self)
-    #     dlg.exec()
-
    def runSampleSearch(self):
        """
        Create a search for samples.
@@ -253,7 +234,6 @@ class App(QMainWindow):
 class AddSubForm(QWidget):

    def __init__(self, parent: QWidget):
-        # logger.debug(f"Initializating subform...")
        super(QWidget, self).__init__(parent)
        self.layout = QVBoxLayout(self)
        # NOTE: Initialize tab screen
--- a/src/submissions/frontend/widgets/controls_chart.py
+++ b/src/submissions/frontend/widgets/controls_chart.py
@@ -6,7 +6,6 @@ from PyQt6.QtWidgets import (
    QWidget, QComboBox, QPushButton
 )
 from PyQt6.QtCore import QSignalBlocker
-
 from backend import ChartReportMaker
 from backend.db import ControlType, IridaControl
 import logging
@@ -21,12 +20,9 @@ class ControlsViewer(InfoPane):

    def __init__(self, parent: QWidget, archetype: str) -> None:
        super().__init__(parent)
-        logger.debug(f"Incoming Archetype: {archetype}")
        self.archetype = ControlType.query(name=archetype)
        if not self.archetype:
            return
-        logger.debug(f"Archetype set as: {self.archetype}")
-        # logger.debug(f"\n\n{self.app}\n\n")
        # NOTE: set tab2 layout
        self.control_sub_typer = QComboBox()
        # NOTE: fetch types of controls
@@ -54,12 +50,6 @@ class ControlsViewer(InfoPane):
        self.save_button.pressed.connect(self.save_png)
        self.export_button.pressed.connect(self.save_excel)

-    # def save_chart_function(self):
-    #     self.fig.save_figure(parent=self)
-    #
-    # def save_data_function(self):
-    #     self.fig.save_data(parent=self)
-
    @report_result
    def update_data(self, *args, **kwargs):
        """
@@ -71,20 +61,6 @@ class ControlsViewer(InfoPane):
            self.mode_sub_typer.disconnect()
        except TypeError:
            pass
-        # NOTE: correct start date being more recent than end date and rerun
-        # if self.datepicker.start_date.date() > self.datepicker.end_date.date():
-        #     threemonthsago = self.datepicker.end_date.date().addDays(-60)
-        #     msg = f"Start date after end date is not allowed! Setting to {threemonthsago.toString()}."
-        #     logger.warning(msg)
-        #     # 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(threemonthsago)
-        #     self.update_data()
-        #     report.add_result(Result(owner=self.__str__(), msg=msg, status="Warning"))
-        #     return report
-        # # NOTE: convert to python useable date objects
-        # self.start_date = self.datepicker.start_date.date().toPyDate()
-        # self.end_date = self.datepicker.end_date.date().toPyDate()
        self.con_sub_type = self.control_sub_typer.currentText()
        self.mode = self.mode_typer.currentText()
        self.mode_sub_typer.clear()
@@ -104,7 +80,6 @@ class ControlsViewer(InfoPane):
            self.mode_sub_typer.clear()
            self.mode_sub_typer.setEnabled(False)
        self.chart_maker_function()
-        # return report

    @report_result
    def chart_maker_function(self, *args, **kwargs):
@@ -119,14 +94,11 @@ class ControlsViewer(InfoPane):
            Tuple[QMainWindow, dict]: Collection of new main app window and result dict
        """
        report = Report()
-        # logger.debug(f"Control getter context: \n\tControl type: {self.con_sub_type}\n\tMode: {self.mode}\n\tStart \
-        #     Date: {self.start_date}\n\tEnd Date: {self.end_date}")
        # NOTE: set the mode_sub_type for kraken
        if self.mode_sub_typer.currentText() == "":
            self.mode_sub_type = None
        else:
            self.mode_sub_type = self.mode_sub_typer.currentText()
-        logger.debug(f"Subtype: {self.mode_sub_type}")
        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,
@@ -136,14 +108,11 @@ class ControlsViewer(InfoPane):
        self.report_obj = ChartReportMaker(df=self.fig.df, sheet_name=self.archetype.name)
        if issubclass(self.fig.__class__, CustomFigure):
            self.save_button.setEnabled(True)
-        # logger.debug(f"Updating figure...")
        # NOTE: construct html for webview
        try:
            html = self.fig.to_html()
        except AttributeError:
            html = ""
-        # logger.debug(f"The length of html code is: {len(html)}")
        self.webview.setHtml(html)
        self.webview.update()
-        # logger.debug("Figure updated... I hope.")
        return report
--- a/src/submissions/frontend/widgets/equipment_usage.py
+++ b/src/submissions/frontend/widgets/equipment_usage.py
@@ -21,9 +21,7 @@ class EquipmentUsage(QDialog):
        self.setWindowTitle(f"Equipment Checklist - {submission.rsl_plate_num}")
        self.used_equipment = self.submission.get_used_equipment()
        self.kit = self.submission.extraction_kit
-        # logger.debug(f"Existing equipment: {self.used_equipment}")
        self.opt_equipment = submission.submission_type.get_equipment()
-        # logger.debug(f"EquipmentRoles: {self.opt_equipment}")
        self.layout = QVBoxLayout()
        self.setLayout(self.layout)
        self.populate_form()
@@ -38,7 +36,6 @@ class EquipmentUsage(QDialog):
        self.buttonBox.rejected.connect(self.reject)
        label = self.LabelRow(parent=self)
        self.layout.addWidget(label)
-        # logger.debug("Creating widgets for equipment")
        for eq in self.opt_equipment:
            widg = eq.to_form(parent=self, used=self.used_equipment)
            self.layout.addWidget(widg)
@@ -124,9 +121,7 @@ class RoleComboBox(QWidget):
        Changes processes when equipment is changed
        """
        equip = self.box.currentText()
-        # logger.debug(f"Updating equipment: {equip}")
        equip2 = next((item for item in self.role.equipment if item.name == equip), self.role.equipment[0])
-        # logger.debug(f"Using: {equip2}")
        with QSignalBlocker(self.process) as blocker:
            self.process.clear()
        self.process.addItems([item for item in equip2.processes if item in self.role.processes])
@@ -136,7 +131,6 @@ class RoleComboBox(QWidget):
        Changes what tips are available when process is changed
        """
        process = self.process.currentText().strip()
-        # logger.debug(f"Checking process: {process} for equipment {self.role.name}")
        process = Process.query(name=process)
        if process.tip_roles:
            for iii, tip_role in enumerate(process.tip_roles):
@@ -144,7 +138,6 @@ class RoleComboBox(QWidget):
                tip_choices = [item.name for item in tip_role.instances]
                widget.setEditable(False)
                widget.addItems(tip_choices)
-                # logger.debug(f"Tiprole: {tip_role.__dict__}")
                widget.setObjectName(f"tips_{tip_role.name}")
                widget.setMinimumWidth(200)
                widget.setMaximumWidth(200)
@@ -169,7 +162,6 @@ class RoleComboBox(QWidget):
        eq = Equipment.query(name=self.box.currentText())
        tips = [PydTips(name=item.currentText(), role=item.objectName().lstrip("tips").lstrip("_")) for item in
                self.findChildren(QComboBox) if item.objectName().startswith("tips")]
-        # logger.debug(tips)
        try:
            return PydEquipment(
                name=eq.name,
--- a/src/submissions/frontend/widgets/gel_checker.py
+++ b/src/submissions/frontend/widgets/gel_checker.py
@@ -148,5 +148,4 @@ class ControlsForm(QWidget):
            dicto['values'].append(dict(name=label[1], value=le.currentText()))
            if label[0] not in [item['name'] for item in output]:
                output.append(dicto)
-        # logger.debug(pformat(output))
        return output, self.comment_field.toPlainText()
--- a/src/submissions/frontend/widgets/info_tab.py
+++ b/src/submissions/frontend/widgets/info_tab.py
@@ -18,7 +18,6 @@ class InfoPane(QWidget):
    def __init__(self, parent: QWidget) -> None:
        super().__init__(parent)
        self.app = self.parent().parent()
-        # logger.debug(f"\n\n{self.app}\n\n")
        self.report = Report()
        self.datepicker = StartEndDatePicker(default_start=-180)
        self.webview = QWebEngineView()
@@ -75,4 +74,4 @@ class InfoPane(QWidget):
        fname = select_save_file(obj=self,
                                 default_name=f"Plotly {self.start_date.strftime('%Y%m%d')} - {self.end_date.strftime('%Y%m%d')}",
                                 extension="png")
-        self.fig.write_image(fname.absolute().__str__(), engine="kaleido")
+        self.fig.write_image(fname.absolute().__str__(), engine="kaleido")
--- a/src/submissions/frontend/widgets/misc.py
+++ b/src/submissions/frontend/widgets/misc.py
@@ -1,6 +1,6 @@
-'''
+"""
 Contains miscellaneous widgets for frontend functions
-'''
+"""
 import math
 from datetime import date
 from PyQt6.QtGui import QPageLayout, QPageSize, QStandardItem, QIcon
@@ -8,7 +8,7 @@ from PyQt6.QtWebEngineWidgets import QWebEngineView
 from PyQt6.QtWidgets import (
    QLabel, QVBoxLayout,
    QLineEdit, QComboBox, QDialog,
-    QDialogButtonBox, QDateEdit, QPushButton, QFormLayout, QWidget, QHBoxLayout, QSizePolicy
+    QDialogButtonBox, QDateEdit, QPushButton, QWidget, QHBoxLayout, QSizePolicy
 )
 from PyQt6.QtCore import Qt, QDate, QSize, QMarginsF
 from tools import jinja_template_loading
@@ -66,7 +66,6 @@ class AddReagentForm(QDialog):
            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()])
-        # logger.debug(f"Trying to find index of {reagent_type}")
        # NOTE: convert input to user-friendly string?
        try:
            reagent_role = reagent_role.replace("_", " ").title()
@@ -106,7 +105,6 @@ class AddReagentForm(QDialog):
        """
        Updates reagent names form field with examples from reagent type
        """
-        # logger.debug(self.type_input.currentText())
        self.name_input.clear()
        lookup = Reagent.query(role=self.type_input.currentText())
        self.name_input.addItems(list(set([item.name for item in lookup])))
@@ -145,7 +143,8 @@ def save_pdf(obj: QWebEngineView, filename: Path):
    obj.page().printToPdf(filename.absolute().__str__(), page_layout)


-# subclass
+# NOTE: subclass
+
 class CheckableComboBox(QComboBox):
    # once there is a checkState set, it is rendered
    # here we assume default Unchecked
@@ -162,7 +161,6 @@ class CheckableComboBox(QComboBox):
        return item.checkState() == Qt.CheckState.Checked

    def changed(self):
-        logger.debug("emitting updated")
        self.updated.emit()


--- a/src/submissions/frontend/widgets/omni_search.py
+++ b/src/submissions/frontend/widgets/omni_search.py
@@ -1,6 +1,6 @@
-'''
+"""
 Search box that performs fuzzy search for samples
-'''
+"""
 from pprint import pformat
 from typing import Tuple, Any, List
 from pandas import DataFrame
@@ -39,7 +39,6 @@ class SearchBox(QDialog):
        else:
            self.sub_class = None
        self.results = SearchResults(parent=self, object_type=self.object_type, extras=self.extras, **kwargs)
-        # logger.debug(f"results: {self.results}")
        self.layout.addWidget(self.results, 5, 0)
        self.setLayout(self.layout)
        self.setWindowTitle(f"Search {self.object_type.__name__}")
@@ -51,7 +50,6 @@ class SearchBox(QDialog):
        Changes form inputs based on sample type
        """
        deletes = [item for item in self.findChildren(FieldSearch)]
-        # logger.debug(deletes)
        for item in deletes:
            item.setParent(None)
        # NOTE: Handle any subclasses
@@ -62,7 +60,6 @@ class SearchBox(QDialog):
                self.object_type = self.original_type
            else:
                self.object_type = self.original_type.find_regular_subclass(self.sub_class.currentText())
-        logger.debug(f"{self.object_type} searchables: {self.object_type.searchables}")
        for iii, searchable in enumerate(self.object_type.searchables):
            widget = FieldSearch(parent=self, label=searchable, field_name=searchable)
            widget.setObjectName(searchable)
@@ -85,10 +82,9 @@ class SearchBox(QDialog):
        Shows dataframe of relevant samples.
        """
        fields = self.parse_form()
-        # logger.debug(f"Got fields: {fields}")
        sample_list_creator = self.object_type.fuzzy_search(**fields)
        data = self.object_type.results_to_df(objects=sample_list_creator)
-        # Setting results moved to here from __init__ 202411118
+        # NOTE: Setting results moved to here from __init__ 202411118
        self.results.setData(df=data)


@@ -154,7 +150,6 @@ class SearchResults(QTableView):

    def parse_row(self, x):
        context = {item['name']: x.sibling(x.row(), item['column']).data() for item in self.columns_of_interest}
-        logger.debug(f"Context: {context}")
        try:
            object = self.object_type.query(**context)
        except KeyError:
--- a/src/submissions/frontend/widgets/pop_ups.py
+++ b/src/submissions/frontend/widgets/pop_ups.py
@@ -9,7 +9,7 @@ from PyQt6.QtWebEngineWidgets import QWebEngineView
 from tools import jinja_template_loading
 import logging
 from backend.db import models
-from typing import Any, Literal
+from typing import Literal

 logger = logging.getLogger(f"submissions.{__name__}")

--- a/src/submissions/frontend/widgets/submission_details.py
+++ b/src/submissions/frontend/widgets/submission_details.py
@@ -45,7 +45,6 @@ class SubmissionDetails(QDialog):
        self.btn.clicked.connect(self.save_pdf)
        self.back = QPushButton("Back")
        self.back.setFixedWidth(100)
-        # self.back.clicked.connect(self.back_function)
        self.back.clicked.connect(self.webview.back)
        self.layout.addWidget(self.back, 0, 0, 1, 1)
        self.layout.addWidget(self.btn, 0, 1, 1, 9)
@@ -70,7 +69,6 @@ class SubmissionDetails(QDialog):
        if "Submission" in title:
            self.btn.setEnabled(True)
            self.export_plate = title.split(" ")[-1]
-            # logger.debug(f"Updating export plate to: {self.export_plate}")
        else:
            self.btn.setEnabled(False)
        try:
@@ -78,7 +76,6 @@ class SubmissionDetails(QDialog):
        except IndexError as e:
            check = title
        if title == check:
-            # logger.debug("Disabling back button")
            self.back.setEnabled(False)
        else:
            self.back.setEnabled(True)
@@ -91,7 +88,6 @@ class SubmissionDetails(QDialog):
        Args:
            sample (str): Submitter Id of the sample.
        """
-        # logger.debug(f"Details: {sample}")
        if isinstance(sample, str):
            sample = BasicSample.query(submitter_id=sample)
        base_dict = sample.to_sub_dict(full_data=True)
@@ -114,7 +110,6 @@ class SubmissionDetails(QDialog):
        base_dict = reagent.to_sub_dict(extraction_kit=self.kit, full_data=True)
        env = jinja_template_loading()
        temp_name = "reagent_details.html"
-        # logger.debug(f"Returning template: {temp_name}")
        try:
            template = env.get_template(temp_name)
        except TemplateNotFound as e:
@@ -147,29 +142,23 @@ class SubmissionDetails(QDialog):
        Args:
            submission (str | BasicSubmission): Submission of interest.
        """
-        # logger.debug(f"Details for: {submission}")
        if isinstance(submission, str):
            submission = BasicSubmission.query(rsl_plate_num=submission)
        self.rsl_plate_num = submission.rsl_plate_num
        self.base_dict = submission.to_dict(full_data=True)
-        # logger.debug(f"Submission details data:\n{pformat({k:v for k,v in self.base_dict.items() if k == 'reagents'})}")
        # NOTE: don't want id
-        # logger.debug(f"Creating barcode.")
-        # logger.debug(f"Making platemap...")
        self.base_dict['platemap'] = submission.make_plate_map(sample_list=submission.hitpick_plate())
        self.base_dict['excluded'] = submission.get_default_info("details_ignore")
        self.base_dict, self.template = submission.get_details_template(base_dict=self.base_dict)
        template_path = Path(self.template.environment.loader.__getattribute__("searchpath")[0])
        with open(template_path.joinpath("css", "styles.css"), "r") as f:
            css = f.read()
-        # logger.debug(f"Submission_details: {pformat(self.base_dict)}")
-        # logger.debug(f"User is power user: {is_power_user()}")
        self.html = self.template.render(sub=self.base_dict, permission=is_power_user(), css=css)
        self.webview.setHtml(self.html)

    @pyqtSlot(str)
    def sign_off(self, submission: str | BasicSubmission):
-        logger.debug(f"Signing off on {submission} - ({getuser()})")
+        logger.info(f"Signing off on {submission} - ({getuser()})")
        if isinstance(submission, str):
            submission = BasicSubmission.query(rsl_plate_num=submission)
        submission.signed_by = getuser()
@@ -195,7 +184,6 @@ class SubmissionComment(QDialog):
        super().__init__(parent)
        try:
            self.app = parent.parent().parent().parent().parent().parent().parent
-            # logger.debug(f"App: {self.app}")
        except AttributeError:
            pass
        self.submission = submission
@@ -225,5 +213,4 @@ class SubmissionComment(QDialog):
            return None
        dt = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M:%S")
        full_comment = {"name": commenter, "time": dt, "text": comment}
-        # logger.debug(f"Full comment: {full_comment}")
        return full_comment
--- a/src/submissions/frontend/widgets/submission_table.py
+++ b/src/submissions/frontend/widgets/submission_table.py
@@ -1,6 +1,6 @@
-'''
+"""
 Contains widgets specific to the submission summary and submission details.
-'''
+"""
 import logging
 from pprint import pformat
 from PyQt6.QtWidgets import QTableView, QMenu
@@ -107,20 +107,16 @@ class SubmissionsSheet(QTableView):
        Args:
            event (_type_): the item of interest
        """
-        # logger.debug(event.__dict__)
        id = self.selectionModel().currentIndex()
        id = id.sibling(id.row(), 0).data()
        submission = BasicSubmission.query(id=id)
-        # logger.debug(f"Event submission: {submission}")
        self.menu = QMenu(self)
        self.con_actions = submission.custom_context_events()
-        # logger.debug(f"Menu options: {self.con_actions}")
        for k in self.con_actions.keys():
-            # logger.debug(f"Adding {k}")
            action = QAction(k, self)
            action.triggered.connect(lambda _, action_name=k: self.triggered_action(action_name=action_name))
            self.menu.addAction(action)
-        # add other required actions
+        # NOTE: add other required actions
        self.menu.popup(QCursor.pos())

    def triggered_action(self, action_name: str):
@@ -130,8 +126,6 @@ class SubmissionsSheet(QTableView):
        Args:
            action_name (str): name of the action from the menu
        """
-        # logger.debug(f"Action: {action_name}")
-        # logger.debug(f"Responding with {self.con_actions[action_name]}")
        func = self.con_actions[action_name]
        func(obj=self)

@@ -179,7 +173,6 @@ class SubmissionsSheet(QTableView):
            if sub is None:
                continue
            try:
-                # logger.debug(f"Found submission: {sub.rsl_plate_num}")
                count += 1
            except AttributeError:
                continue
--- a/src/submissions/frontend/widgets/submission_widget.py
+++ b/src/submissions/frontend/widgets/submission_widget.py
@@ -1,9 +1,9 @@
-'''
+"""
 Contains all submission related frontend functions
-'''
+"""
 from PyQt6.QtWidgets import (
    QWidget, QPushButton, QVBoxLayout,
-    QComboBox, QDateEdit, QLineEdit, QLabel, QCheckBox, QBoxLayout, QHBoxLayout, QGridLayout
+    QComboBox, QDateEdit, QLineEdit, QLabel, QCheckBox, QHBoxLayout, QGridLayout
 )
 from PyQt6.QtCore import pyqtSignal, Qt, QSignalBlocker
 from . import select_open_file, select_save_file
@@ -34,7 +34,6 @@ class MyQComboBox(QComboBox):
        super(MyQComboBox, self).__init__(*args, **kwargs)
        self.scrollWidget = scrollWidget
        self.setFocusPolicy(Qt.FocusPolicy.StrongFocus)
-        logger.debug(f"Scrollwidget: {scrollWidget}")

    def wheelEvent(self, *args, **kwargs):
        if self.hasFocus():
@@ -61,14 +60,12 @@ class MyQDateEdit(QDateEdit):


 class SubmissionFormContainer(QWidget):
-    # A signal carrying a path
+    # NOTE: A signal carrying a path
    import_drag = pyqtSignal(Path)

    def __init__(self, parent: QWidget) -> None:
-        # logger.debug(f"Setting form widget...")
        super().__init__(parent)
        self.app = self.parent().parent()
-        # logger.debug(f"App: {self.app}")
        self.report = Report()
        self.setStyleSheet('background-color: light grey;')
        self.setAcceptDrops(True)
@@ -89,7 +86,6 @@ class SubmissionFormContainer(QWidget):
        Sets filename when file dropped
        """
        fname = Path([u.toLocalFile() for u in event.mimeData().urls()][0])
-        # logger.debug(f"App: {self.app}")
        self.app.last_dir = fname.parent
        self.import_drag.emit(fname)

@@ -127,7 +123,6 @@ class SubmissionFormContainer(QWidget):
        # NOTE: set file dialog
        if isinstance(fname, bool) or fname is None:
            fname = select_open_file(self, file_extension="xlsx")
-        # logger.debug(f"Attempting to parse file: {fname}")
        if not fname:
            report.add_result(Result(msg=f"File {fname.__str__()} not found.", status="critical"))
            return report
@@ -139,14 +134,10 @@ class SubmissionFormContainer(QWidget):
            return
        except AttributeError:
            self.prsr = SheetParser(filepath=fname)
-        # logger.debug(f"Submission dictionary:\n{pformat(self.prsr.sub)}")
        self.pyd = self.prsr.to_pydantic()
-        # logger.debug(f"Pydantic result: \n\n{pformat(self.pyd)}\n\n")
        self.form = self.pyd.to_form(parent=self)
        self.layout().addWidget(self.form)
        return report
-        # logger.debug(f"Outgoing report: {self.report.results}")
-        # logger.debug(f"All attributes of submission container:\n{pformat(self.__dict__)}")

    @report_result
    def add_reagent(self, reagent_lot: str | None = None, reagent_role: str | None = None, expiry: date | None = None,
@@ -172,14 +163,12 @@ class SubmissionFormContainer(QWidget):
        if dlg.exec():
            # NOTE: extract form info
            info = dlg.parse_form()
-            # logger.debug(f"Reagent info: {info}")
            # NOTE: create reagent object
            reagent = PydReagent(ctx=self.app.ctx, **info, missing=False)
            # NOTE: send reagent to db
            sqlobj, result = reagent.toSQL()
            sqlobj.save()
            report.add_result(result)
-            # logger.debug(f"Reagent: {reagent}, Report: {report}")
            return reagent, report


@@ -189,7 +178,6 @@ class SubmissionFormWidget(QWidget):

    def __init__(self, parent: QWidget, submission: PydSubmission, disable: list | None = None) -> None:
        super().__init__(parent)
-        # logger.debug(f"Disable: {disable}")
        if disable is None:
            disable = []
        self.app = parent.app
@@ -200,17 +188,13 @@ class SubmissionFormWidget(QWidget):
        defaults = st.get_default_info("form_recover", "form_ignore", submission_type=self.pyd.submission_type['value'])
        self.recover = defaults['form_recover']
        self.ignore = defaults['form_ignore']
-        # logger.debug(f"Attempting to extend ignore list with {self.pyd.submission_type['value']}")
        self.layout = QVBoxLayout()
        for k in list(self.pyd.model_fields.keys()) + list(self.pyd.model_extra.keys()):
-            # logger.debug(f"Creating widget: {k}")
            if k in self.ignore:
                logger.warning(f"{k} in form_ignore {self.ignore}, not creating widget")
                continue
            try:
-                # logger.debug(f"Key: {k}, Disable: {disable}")
                check = k in disable
-                # logger.debug(f"Check: {check}")
            except TypeError:
                check = False
            try:
@@ -225,7 +209,6 @@ class SubmissionFormWidget(QWidget):
                                            sub_obj=st, disable=check)
            if add_widget is not None:
                self.layout.addWidget(add_widget)
-            # if k == "extraction_kit":
            if k in self.__class__.update_reagent_fields:
                add_widget.input.currentTextChanged.connect(self.scrape_reagents)
                self.disabler = self.DisableReagents(self)
@@ -236,15 +219,10 @@ class SubmissionFormWidget(QWidget):
        self.scrape_reagents(self.extraction_kit)

    def disable_reagents(self):
+        """
+        Disables all ReagentFormWidgets in this form/
+        """
        for reagent in self.findChildren(self.ReagentFormWidget):
-            # if self.disabler.checkbox.isChecked():
-            #     # reagent.setVisible(True)
-            #     # with QSignalBlocker(self.disabler.checkbox) as b:
-            #     reagent.flip_check()
-            # else:
-            #     # reagent.setVisible(False)
-            #     # with QSignalBlocker(self.disabler.checkbox) as b:
-            #     reagent.check.setChecked(False)
            reagent.flip_check(self.disabler.checkbox.isChecked())


@@ -263,7 +241,6 @@ class SubmissionFormWidget(QWidget):
        Returns:
            self.InfoItem: Form widget to hold name:value
        """
-        # logger.debug(f"Key: {key}, Disable: {disable}")
        if isinstance(submission_type, str):
            submission_type = SubmissionType.query(name=submission_type)
        if key not in self.ignore:
@@ -276,7 +253,6 @@ class SubmissionFormWidget(QWidget):
                case _:
                    widget = self.InfoItem(parent=self, key=key, value=value, submission_type=submission_type,
                                           sub_obj=sub_obj)
-            # logger.debug(f"Setting widget enabled to: {not disable}")
            if disable:
                widget.input.setEnabled(False)
                widget.input.setToolTip("Widget disabled to protect database integrity.")
@@ -298,24 +274,20 @@ class SubmissionFormWidget(QWidget):
        """
        self.extraction_kit = args[0]
        report = Report()
-        logger.debug(f"Extraction kit: {self.extraction_kit}")
        # NOTE: Remove previous reagent widgets
        try:
            old_reagents = self.find_widgets()
        except AttributeError:
            logger.error(f"Couldn't find old reagents.")
            old_reagents = []
-        # logger.debug(f"\n\nAttempting to clear: {old_reagents}\n\n")
        for reagent in old_reagents:
            if isinstance(reagent, self.ReagentFormWidget) or isinstance(reagent, QPushButton):
                reagent.setParent(None)
        reagents, integrity_report = self.pyd.check_kit_integrity(extraction_kit=self.extraction_kit)
-        # logger.debug(f"Got reagents: {pformat(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)
-        # logger.debug(f"Outgoing report: {report.results}")
        if hasattr(self.pyd, "csv"):
            export_csv_btn = QPushButton("Export CSV")
            export_csv_btn.setObjectName("export_csv_btn")
@@ -326,6 +298,7 @@ class SubmissionFormWidget(QWidget):
        self.layout.addWidget(submit_btn)
        submit_btn.clicked.connect(self.submit_new_sample_function)
        self.setLayout(self.layout)
+        self.disabler.checkbox.setChecked(True)
        return report

    def clear_form(self):
@@ -365,23 +338,16 @@ class SubmissionFormWidget(QWidget):
        report = Report()
        result = self.parse_form()
        report.add_result(result)
-        # logger.debug(f"Submission: {pformat(self.pyd)}")
-        # logger.debug("Checking kit integrity...")
        if self.disabler.checkbox.isChecked():
            _, result = self.pyd.check_kit_integrity()
            report.add_result(result)
        if len(result.results) > 0:
            return
-        # logger.debug(f"PYD before transformation into SQL:\n\n{self.pyd}\n\n")
        base_submission, result = self.pyd.to_sql()
-        # logger.debug(f"SQL object: {pformat(base_submission.__dict__)}")
-        # logger.debug(f"Base submission: {base_submission.to_dict()}")
        # NOTE: check output message for issues
-        # logger.debug(f"Result of to_sql: {result}")
        try:
            trigger = result.results[-1]
            code = trigger.code
-            # logger.debug(f"Code from return: {code}")
        except IndexError as e:
            logger.error(result.results)
            logger.error(f"Problem getting error code: {e}")
@@ -408,11 +374,8 @@ class SubmissionFormWidget(QWidget):
                pass
        # NOTE: add reagents to submission object
        for reagent in base_submission.reagents:
-            # logger.debug(f"Updating: {reagent} with {reagent.lot}")
            reagent.update_last_used(kit=base_submission.extraction_kit)
-        # logger.debug(f"Final reagents: {pformat(base_submission.reagents)}")
        save_output = base_submission.save()
-        # logger.debug(f"Save output: {save_output}")
        # NOTE: update summary sheet
        self.app.table_widget.sub_wid.setData()
        # NOTE: reset form
@@ -423,7 +386,6 @@ class SubmissionFormWidget(QWidget):
            check = True
        if check:
            self.setParent(None)
-        # logger.debug(f"All attributes of obj: {pformat(self.__dict__)}")
        return report

    def export_csv_function(self, fname: Path | None = None):
@@ -454,7 +416,6 @@ class SubmissionFormWidget(QWidget):
        info = {}
        reagents = []
        for widget in self.findChildren(QWidget):
-            # logger.debug(f"Parsed widget of type {type(widget)}")
            match widget:
                case self.ReagentFormWidget():
                    reagent, _ = widget.parse_form()
@@ -464,16 +425,10 @@ class SubmissionFormWidget(QWidget):
                    field, value = widget.parse_form()
                    if field is not None:
                        info[field] = value
-        # logger.debug(f"Info: {pformat(info)}")
-        logger.debug(f"Reagents going into pyd: {pformat(reagents)}")
        self.pyd.reagents = reagents
-        logger.debug(f"Reagents after insertion in pyd: {pformat(self.pyd.reagents)}")
-        # logger.debug(f"Attrs not in info: {[k for k, v in self.__dict__.items() if k not in info.keys()]}")
        for item in self.recover:
-            # logger.debug(f"Attempting to recover: {item}")
            if hasattr(self, item):
                value = getattr(self, item)
-                # logger.debug(f"Setting {item}")
                info[item] = value
        for k, v in info.items():
            self.pyd.set_attribute(key=k, value=v)
@@ -551,9 +506,6 @@ class SubmissionFormWidget(QWidget):
            except (TypeError, KeyError):
                pass
            obj = parent.parent().parent()
-            # logger.debug(f"Object: {obj}")
-            # logger.debug(f"Parent: {parent.parent()}")
-            # logger.debug(f"Creating widget for: {key}")
            match key:
                case 'submitting_lab':
                    add_widget = MyQComboBox(scrollWidget=parent)
@@ -567,7 +519,6 @@ class SubmissionFormWidget(QWidget):
                        looked_up_lab = Organization.query(name=value, limit=1)
                    except AttributeError:
                        looked_up_lab = None
-                    # logger.debug(f"\n\nLooked up lab: {looked_up_lab}")
                    if looked_up_lab:
                        try:
                            labs.remove(str(looked_up_lab.name))
@@ -586,12 +537,9 @@ class SubmissionFormWidget(QWidget):
                    # NOTE: create combobox to hold looked up kits
                    add_widget = MyQComboBox(scrollWidget=parent)
                    # NOTE: lookup existing kits by 'submission_type' decided on by sheetparser
-                    # logger.debug(f"Looking up kits used for {submission_type}")
                    uses = [item.name for item in submission_type.kit_types]
                    obj.uses = uses
-                    # logger.debug(f"Kits received for {submission_type}: {uses}")
                    if check_not_nan(value):
-                        # logger.debug(f"The extraction kit in parser was: {value}")
                        try:
                            uses.insert(0, uses.pop(uses.index(value)))
                        except ValueError:
@@ -626,7 +574,6 @@ class SubmissionFormWidget(QWidget):
                    else:
                        # NOTE: anything else gets added in as a line edit
                        add_widget = QLineEdit()
-                        # logger.debug(f"Setting widget text to {str(value).replace('_', ' ')}")
                        add_widget.setText(str(value).replace("_", " "))
                        add_widget.setToolTip(f"Enter value for {key}")
            if add_widget is not None:
@@ -725,7 +672,6 @@ class SubmissionFormWidget(QWidget):
            if not self.lot.isEnabled():
                return None, report
            lot = self.lot.currentText()
-            # logger.debug(f"Using this lot for the reagent {self.reagent}: {lot}")
            wanted_reagent = Reagent.query(lot=lot, role=self.reagent.role)
            # NOTE: if reagent doesn't exist in database, offer to add it (uses App.add_reagent)
            if wanted_reagent is None:
@@ -741,7 +687,6 @@ class SubmissionFormWidget(QWidget):
                    return wanted_reagent, report
                else:
                    # NOTE: In this case we will have an empty reagent and the submission will fail kit integrity check
-                    # logger.debug("Will not add reagent.")
                    report.add_result(Result(msg="Failed integrity check", status="Critical"))
                    return None, report
            else:
@@ -791,7 +736,6 @@ class SubmissionFormWidget(QWidget):
                looked_up_rt = KitTypeReagentRoleAssociation.query(reagent_role=reagent.role,
                                                                   kit_type=extraction_kit)
                relevant_reagents = [str(item.lot) for item in looked_up_rt.get_all_relevant_reagents()]
-                logger.debug(f"Relevant reagents for {reagent}: {relevant_reagents}")
                # NOTE: if reagent in sheet is not found insert it into the front of relevant reagents so it shows
                if str(reagent.lot) not in relevant_reagents:
                    if check_not_nan(reagent.lot):
@@ -803,7 +747,6 @@ class SubmissionFormWidget(QWidget):
                            looked_up_reg = None
                        if isinstance(looked_up_reg, list):
                            looked_up_reg = None
-                        # logger.debug(f"Because there was no reagent listed for {reagent.lot}, we will insert the last lot used: {looked_up_reg}")
                        if looked_up_reg:
                            try:
                                relevant_reagents.remove(str(looked_up_reg.lot))
@@ -812,15 +755,11 @@ class SubmissionFormWidget(QWidget):
                            relevant_reagents.insert(0, str(looked_up_reg.lot))
                else:
                    if len(relevant_reagents) > 1:
-                        # logger.debug(f"Found {reagent.lot} in relevant reagents: {relevant_reagents}. Moving to front of list.")
                        idx = relevant_reagents.index(str(reagent.lot))
-                        # logger.debug(f"The index we got for {reagent.lot} in {relevant_reagents} was {idx}")
                        moved_reag = relevant_reagents.pop(idx)
                        relevant_reagents.insert(0, moved_reag)
                    else:
-                        # logger.debug(f"Found {reagent.lot} in relevant reagents: {relevant_reagents}. But no need to move due to short list.")
                        pass
-                logger.debug(f"New relevant reagents: {relevant_reagents}")
                self.setObjectName(f"lot_{reagent.role}")
                self.addItems(relevant_reagents)
                self.setToolTip(f"Enter lot number for the reagent used for {reagent.role}")
--- a/src/submissions/frontend/widgets/summary.py
+++ b/src/submissions/frontend/widgets/summary.py
@@ -35,7 +35,6 @@ class Summary(InfoPane):
    def update_data(self):
        super().update_data()
        orgs = [self.org_select.itemText(i) for i in range(self.org_select.count()) if self.org_select.itemChecked(i)]
-        # logger.debug(f"Getting report from {self.start_date} to {self.end_date} using {orgs}")
        self.report_obj = ReportMaker(start_date=self.start_date, end_date=self.end_date, organizations=orgs)
        self.webview.setHtml(self.report_obj.html)
        if self.report_obj.subs: