Removed logger.debugs for proven functions.

src/submissions/frontend/visualizations/__init__.py

@@ -41,7 +41,6 @@ class CustomFigure(Figure):
         """
         if modes:
             ytitle = modes[0]
-        # logger.debug("Creating visibles list for each mode.")
         self.update_layout(
             xaxis_title="Submitted Date (* - Date parsed from fastq file creation date)",
             yaxis_title=ytitle,
@@ -79,7 +78,6 @@ class CustomFigure(Figure):
         rng = [1]
         if months > 2:
             rng += [iii for iii in range(3, months, 3)]
-        # logger.debug(f"Making buttons for months: {rng}")
         buttons = [dict(count=iii, label=f"{iii}m", step="month", stepmode="backward") for iii in rng]
         if months > date.today().month:
             buttons += [dict(count=1, label="YTD", step="year", stepmode="todate")]
@@ -117,24 +115,6 @@ class CustomFigure(Figure):
                     {"yaxis.title.text": mode},
                 ])
 
-    # def save_figure(self, group_name: str = "plotly_output", parent: QWidget | None = None):
-    #     """
-    #     Writes plotly figure to html file.
-    #
-    #     Args:
-    #         figs ():
-    #         settings (dict): settings passed down from click
-    #         fig (Figure): input figure object
-    #         group_name (str): controltype
-    #     """
-    #
-    #     output = select_save_file(obj=parent, default_name=group_name, extension="png")
-    #     self.write_image(output.absolute().__str__(), engine="kaleido")
-    #
-    # def save_data(self, group_name: str = "plotly_export", parent:QWidget|None=None):
-    #     output = select_save_file(obj=parent, default_name=group_name, extension="xlsx")
-    #     self.df.to_excel(output.absolute().__str__(), engine="openpyxl", index=False)
-
     def to_html(self) -> str:
         """
         Creates final html code from plotly

src/submissions/frontend/visualizations/irida_charts.py

@@ -3,13 +3,12 @@ Functions for constructing irida controls graphs using plotly.
 """
 from datetime import date
 from pprint import pformat
-from typing import Generator
 import plotly.express as px
 import pandas as pd
 from PyQt6.QtWidgets import QWidget
 from . import CustomFigure
 import logging
-from tools import get_unique_values_in_df_column, divide_chunks
+from tools import get_unique_values_in_df_column
 
 logger = logging.getLogger(f"submissions.{__name__}")
 

src/submissions/frontend/visualizations/pcr_charts.py

@@ -21,11 +21,9 @@ class PCRFigure(CustomFigure):
             months = int(settings['months'])
         except KeyError:
             months = 6
-        # logger.debug(f"DF: {self.df}")
         self.construct_chart(df=df)
 
     def construct_chart(self, df: pd.DataFrame):
-        # logger.debug(f"PCR df:\n {df}")
         try:
             scatter = px.scatter(data_frame=df, x='submitted_date', y="ct",
                                            hover_data=["name", "target", "ct", "reagent_lot"],

src/submissions/frontend/visualizations/turnaround_chart.py

@@ -23,7 +23,6 @@ class TurnaroundChart(CustomFigure):
             months = int(settings['months'])
         except KeyError:
             months = 6
-        # logger.debug(f"DF: {self.df}")
         self.construct_chart()
         if threshold:
             self.add_hline(y=threshold)
@@ -32,11 +31,9 @@ class TurnaroundChart(CustomFigure):
     def construct_chart(self, df: pd.DataFrame | None = None):
         if df:
             self.df = df
-        # logger.debug(f"PCR df:\n {df}")
         self.df = self.df[self.df.days.notnull()]
         self.df = self.df.sort_values(['submitted_date', 'name'], ascending=[True, True]).reset_index(drop=True)
         self.df = self.df.reset_index().rename(columns={"index": "idx"})
-        # logger.debug(f"DF: {self.df}")
         try:
             scatter = px.scatter(data_frame=self.df, x='idx', y="days",
                                  hover_data=["name", "submitted_date", "completed_date", "days"],

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

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

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,

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()

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")

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()
 
 

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:

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__}")
 

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

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

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}")

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: