Code cleanup, dependency update, various bug fixes

2024-05-24 13:02:46 -05:00
parent 2814be8980
commit e047d1a9ee
24 changed files with 403 additions and 561 deletions
--- a/src/submissions/frontend/visualizations/control_charts.py
+++ b/src/submissions/frontend/visualizations/control_charts.py
@@ -48,7 +48,7 @@ def create_charts(ctx:Settings, df:pd.DataFrame, ytitle:str|None=None) -> Figure
    # Set descending for any columns that have "{mode}" in the header.
    ascending = [False if item == "target" else True for item in sorts]
    df = df.sort_values(by=sorts, ascending=ascending)
-    logger.debug(df[df.isna().any(axis=1)])
+    # logger.debug(df[df.isna().any(axis=1)])
    # actual chart construction is done by
    fig = construct_chart(df=df, modes=modes, ytitle=ytitle)
    return fig
--- a/src/submissions/frontend/widgets/app.py
+++ b/src/submissions/frontend/widgets/app.py
@@ -25,7 +25,7 @@ logger.info("Hello, I am a logger")
 class App(QMainWindow):

    def __init__(self, ctx: Settings = None):
-        logger.debug(f"Initializing main window...")
+        # logger.debug(f"Initializing main window...")
        super().__init__()
        self.ctx = ctx
        self.last_dir = ctx.directory_path
@@ -58,7 +58,7 @@ class App(QMainWindow):
        """
        adds items to menu bar
        """        
-        logger.debug(f"Creating menu bar...")
+        # logger.debug(f"Creating menu bar...")
        menuBar = self.menuBar()
        fileMenu = menuBar.addMenu("&File")
        # Creating menus using a title
@@ -79,7 +79,7 @@ class App(QMainWindow):
        """
        adds items to toolbar
        """        
-        logger.debug(f"Creating toolbar...")
+        # logger.debug(f"Creating toolbar...")
        toolbar = QToolBar("My main toolbar")
        self.addToolBar(toolbar)
        toolbar.addAction(self.addReagentAction)
@@ -90,7 +90,7 @@ class App(QMainWindow):
        """
        creates actions
        """        
-        logger.debug(f"Creating actions...")
+        # logger.debug(f"Creating actions...")
        self.importAction = QAction("&Import Submission", self)
        # self.importPCRAction = QAction("&Import PCR Results", self)
        self.addReagentAction = QAction("Add Reagent", self)
@@ -107,7 +107,7 @@ class App(QMainWindow):
        """
        connect menu and tool bar item to functions
        """
-        logger.debug(f"Connecting actions...")
+        # logger.debug(f"Connecting actions...")
        self.importAction.triggered.connect(self.table_widget.formwidget.importSubmission)
        # self.importPCRAction.triggered.connect(self.table_widget.formwidget.import_pcr_results)
        self.addReagentAction.triggered.connect(self.table_widget.formwidget.add_reagent)
@@ -134,7 +134,7 @@ 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}")
+        # logger.debug(f"Attempting to open {url}")
        webbrowser.get('windows-default').open(f"file://{url.__str__()}")

    def result_reporter(self):
@@ -144,11 +144,11 @@ class App(QMainWindow):
        Args:
            result (dict | None, optional): The result from a function. Defaults to None.
        """        
-        logger.debug(f"Running results reporter for: {self.report.results}")
+        # logger.debug(f"Running results reporter for: {self.report.results}")
        if len(self.report.results) > 0:
-            logger.debug(f"We've got some results!")
+            # logger.debug(f"We've got some results!")
            for result in self.report.results:
-                logger.debug(f"Showing result: {result}")
+                # logger.debug(f"Showing result: {result}")
                if result != None:
                    alert = result.report()
                    if alert.exec():
@@ -164,17 +164,17 @@ class App(QMainWindow):
    def backup_database(self):
        month = date.today().strftime("%Y-%m")
        # day = date.today().strftime("%Y-%m-%d")
-        logger.debug(f"Here is the db directory: {self.ctx.database_path}")
-        logger.debug(f"Here is the backup directory: {self.ctx.backup_path}")
+        # logger.debug(f"Here is the db directory: {self.ctx.database_path}")
+        # logger.debug(f"Here is the backup directory: {self.ctx.backup_path}")
        current_month_bak = Path(self.ctx.backup_path).joinpath(f"submissions_backup-{month}").resolve().with_suffix(".db")
        if not current_month_bak.exists() and "demo" not in self.ctx.database_path.__str__():
-            logger.debug("No backup found for this month, backing up database.")
+            logger.info("No backup found for this month, backing up database.")
            shutil.copyfile(self.ctx.database_path, current_month_bak)

 class AddSubForm(QWidget):
    
    def __init__(self, parent:QWidget):
-        logger.debug(f"Initializating subform...")
+        # logger.debug(f"Initializating subform...")
        super(QWidget, self).__init__(parent)
        self.layout = QVBoxLayout(self)
        # Initialize tab screen
--- a/src/submissions/frontend/widgets/controls_chart.py
+++ b/src/submissions/frontend/widgets/controls_chart.py
@@ -112,13 +112,13 @@ class ControlsViewer(QWidget):
            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_type}\n\tMode: {self.mode}\n\tStart Date: {self.start_date}\n\tEnd Date: {self.end_date}")
+        # logger.debug(f"Control getter context: \n\tControl type: {self.con_type}\n\tMode: {self.mode}\n\tStart Date: {self.start_date}\n\tEnd Date: {self.end_date}")
        # set the subtype for kraken
        if self.sub_typer.currentText() == "":
            self.subtype = None
        else:
            self.subtype = self.sub_typer.currentText()
-        logger.debug(f"Subtype: {self.subtype}")
+        # logger.debug(f"Subtype: {self.subtype}")
        # query all controls using the type/start and end dates from the gui
        controls = Control.query(control_type=self.con_type, start_date=self.start_date, end_date=self.end_date)
        # if no data found from query set fig to none for reporting in webview
@@ -129,7 +129,7 @@ class ControlsViewer(QWidget):
            data = [control.convert_by_mode(mode=self.mode) for control in controls]
            # flatten data to one dimensional list
            data = [item for sublist in data for item in sublist]
-            logger.debug(f"Control objects going into df conversion: {type(data)}")
+            # logger.debug(f"Control objects going into df conversion: {type(data)}")
            if data == []:
                self.report.add_result(Result(status="Critical", msg="No data found for controls in given date range."))
                return
@@ -141,13 +141,13 @@ class ControlsViewer(QWidget):
                title = f"{self.mode} - {self.subtype}"
            # send dataframe to chart maker
            fig = create_charts(ctx=self.app.ctx, df=df, ytitle=title)
-        logger.debug(f"Updating figure...")
+        # logger.debug(f"Updating figure...")
        # construct html for webview
        html = construct_html(figure=fig)
-        logger.debug(f"The length of html code is: {len(html)}")
+        # logger.debug(f"The length of html code is: {len(html)}")
        self.webengineview.setHtml(html)
        self.webengineview.update()
-        logger.debug("Figure updated... I hope.")
+        # logger.debug("Figure updated... I hope.")
        self.report.add_result(report)

 class ControlsDatePicker(QWidget):
--- a/src/submissions/frontend/widgets/equipment_usage.py
+++ b/src/submissions/frontend/widgets/equipment_usage.py
@@ -17,9 +17,9 @@ class EquipmentUsage(QDialog):
        self.setWindowTitle("Equipment Checklist")
        self.used_equipment = self.submission.get_used_equipment()
        self.kit = self.submission.extraction_kit
-        logger.debug(f"Existing equipment: {self.used_equipment}")
+        # logger.debug(f"Existing equipment: {self.used_equipment}")
        self.opt_equipment = submission.submission_type.get_equipment()
-        logger.debug(f"EquipmentRoles: {self.opt_equipment}")
+        # logger.debug(f"EquipmentRoles: {self.opt_equipment}")
        self.layout = QVBoxLayout()
        self.setLayout(self.layout)
        self.populate_form()
@@ -115,9 +115,9 @@ class RoleComboBox(QWidget):
        Changes processes when equipment is changed
        """        
        equip = self.box.currentText()
-        logger.debug(f"Updating equipment: {equip}")
+        # logger.debug(f"Updating equipment: {equip}")
        equip2 = [item for item in self.role.equipment if item.name==equip][0]
-        logger.debug(f"Using: {equip2}")
+        # logger.debug(f"Using: {equip2}")
        self.process.clear()
        self.process.addItems([item for item in equip2.processes if item in self.role.processes])

--- a/src/submissions/frontend/widgets/gel_checker.py
+++ b/src/submissions/frontend/widgets/gel_checker.py
@@ -145,5 +145,5 @@ class ControlsForm(QWidget):
            dicto['values'].append(dict(name=label[1], value=le.text()))
            if label[0] not in [item['name'] for item in output]:
                output.append(dicto)
-        logger.debug(pformat(output))
+        # logger.debug(pformat(output))
        return output, self.comment_field.toPlainText()
--- a/src/submissions/frontend/widgets/kit_creator.py
+++ b/src/submissions/frontend/widgets/kit_creator.py
@@ -93,10 +93,10 @@ class KitAdder(QWidget):
        # get form info
        info, reagents = self.parse_form()
        info = {k:v for k,v in info.items() if k in [column.name for column in self.columns] + ['kit_name', 'used_for']}
-        logger.debug(f"kit info: {pformat(info)}")
-        logger.debug(f"kit reagents: {pformat(reagents)}")
+        # logger.debug(f"kit info: {pformat(info)}")
+        # logger.debug(f"kit reagents: {pformat(reagents)}")
        info['reagent_types'] = reagents
-        logger.debug(pformat(info))
+        # logger.debug(pformat(info))
        # send to kit constructor
        kit = PydKit(name=info['kit_name'])
        for reagent in info['reagent_types']:
@@ -108,7 +108,7 @@ class KitAdder(QWidget):
                     'expiry':reagent['expiry']
                    }}
            kit.reagent_types.append(PydReagentType(name=reagent['rtname'], eol_ext=reagent['eol'], uses=uses))
-        logger.debug(f"Output pyd object: {kit.__dict__}")
+        # logger.debug(f"Output pyd object: {kit.__dict__}")
        sqlobj, result = kit.toSQL(self.ctx)
        report.add_result(result=result)
        sqlobj.save()
@@ -122,7 +122,7 @@ class KitAdder(QWidget):
        Returns:
            Tuple[dict, list]: dict=info, list=reagents
        """        
-        logger.debug(f"Hello from {self.__class__} parser!")
+        # logger.debug(f"Hello from {self.__class__} parser!")
        info = {}
        reagents = []
        widgets = [widget for widget in self.findChildren(QWidget) if widget.objectName() not in self.ignore and not isinstance(widget.parent(), ReagentTypeForm)]
@@ -153,7 +153,7 @@ class ReagentTypeForm(QWidget):
        self.reagent_getter.setObjectName("rtname")
        # lookup all reagent type names from db
        lookup = ReagentType.query()
-        logger.debug(f"Looked up ReagentType names: {lookup}")
+        # logger.debug(f"Looked up ReagentType names: {lookup}")
        self.reagent_getter.addItems([item.name for item in lookup])
        self.reagent_getter.setEditable(True)
        grid.addWidget(self.reagent_getter,0,1)
@@ -205,14 +205,14 @@ class ReagentTypeForm(QWidget):
        Returns:
            dict: _description_
        """        
-        logger.debug(f"Hello from {self.__class__} parser!")
+        # logger.debug(f"Hello from {self.__class__} parser!")
        info = {}
        info['eol'] = self.eol.value()
        info['sheet'] = self.location_sheet_name.text()
        info['rtname'] = self.reagent_getter.currentText()
        widgets = [widget for widget in self.findChildren(QWidget) if widget.objectName() not in self.ignore]
        for widget in widgets:
-            logger.debug(f"Parsed widget: {widget.objectName()} of type {type(widget)} with parent {widget.parent()}")
+            # logger.debug(f"Parsed widget: {widget.objectName()} of type {type(widget)} with parent {widget.parent()}")
            match widget:
                case QLineEdit():
                    info[widget.objectName()] = widget.text()
@@ -225,7 +225,7 @@ class ReagentTypeForm(QWidget):
                        key, sub_key = widget.objectName().split("_")
                        if key not in info.keys():
                            info[key] = {}
-                            logger.debug(f"Adding key {key}, {sub_key} and value {widget.value()} to {info}")
+                            # logger.debug(f"Adding key {key}, {sub_key} and value {widget.value()} to {info}")
                        info[key][sub_key] = widget.value()        
        return info

--- a/src/submissions/frontend/widgets/misc.py
+++ b/src/submissions/frontend/widgets/misc.py
@@ -58,7 +58,7 @@ class AddReagentForm(QDialog):
        self.type_input = QComboBox()
        self.type_input.setObjectName('type')
        self.type_input.addItems([item.name for item in ReagentType.query()])
-        logger.debug(f"Trying to find index of {reagent_type}")
+        # logger.debug(f"Trying to find index of {reagent_type}")
        # convert input to user friendly string?
        try:
            reagent_type = reagent_type.replace("_", " ").title()
@@ -97,7 +97,7 @@ class AddReagentForm(QDialog):
        """
        Updates reagent names form field with examples from reagent type
        """        
-        logger.debug(self.type_input.currentText())
+        # logger.debug(self.type_input.currentText())
        self.name_input.clear()
        lookup = Reagent.query(reagent_type=self.type_input.currentText())
        self.name_input.addItems(list(set([item.name for item in lookup])))
@@ -210,7 +210,7 @@ class LogParser(QDialog):
        """        
        count: int = 0
        total: int = 0
-        logger.debug(f"Current search term: {self.phrase_looker.currentText()}")
+        # logger.debug(f"Current search term: {self.phrase_looker.currentText()}")
        try:
            with open(self.fname, "r") as f:
                for chunk in readInChunks(fileObj=f):
--- a/src/submissions/frontend/widgets/submission_details.py
+++ b/src/submissions/frontend/widgets/submission_details.py
@@ -1,4 +1,4 @@
-from PyQt6.QtWidgets import (QDialog, QScrollArea, QPushButton, QVBoxLayout, QMessageBox,
+from PyQt6.QtWidgets import (QDialog, QPushButton, QVBoxLayout, QMessageBox,
                             QDialogButtonBox, QTextEdit)
 from PyQt6.QtWebEngineWidgets import QWebEngineView
 from PyQt6.QtWebChannel import QWebChannel
@@ -10,7 +10,6 @@ from .functions import select_save_file
 from io import BytesIO
 from tempfile import TemporaryFile, TemporaryDirectory
 from pathlib import Path
-# from xhtml2pdf import pisa
 import logging, base64
 from getpass import getuser
 from datetime import datetime
@@ -33,24 +32,19 @@ class SubmissionDetails(QDialog):
            self.app = parent.parent().parent().parent().parent().parent().parent()
        except AttributeError:
            self.app = None
-        # self.setWindowTitle(f"Submission Details - {sub.rsl_plate_num}")
-        # create scrollable interior
-        interior = QScrollArea()
-        interior.setParent(self)
        self.webview = QWebEngineView(parent=self)
        self.webview.setMinimumSize(900, 500)
        self.webview.setMaximumSize(900, 500)
-        # self.webview.setHtml(self.html)
        self.layout = QVBoxLayout()
-        interior.resize(900, 500)
-        interior.setWidget(self.webview)
        self.setFixedSize(900, 500)
-        # button to export a pdf version
+        # NOTE: button to export a pdf version
        btn = QPushButton("Export PDF")
-        btn.setParent(self)
-        btn.setFixedWidth(900)
+        btn.setFixedWidth(875)
        btn.clicked.connect(self.export)
-        # setup channel
+        self.layout.addWidget(btn)
+        self.layout.addWidget(self.webview)
+        self.setLayout(self.layout)
+        # NOTE: setup channel
        self.channel = QWebChannel()
        self.channel.registerObject('backend', self)
        self.submission_details(submission=sub)
@@ -80,31 +74,25 @@ class SubmissionDetails(QDialog):
        Args:
            submission (str | BasicSubmission): Submission of interest.
        """        
-        logger.debug(f"Details for: {submission}")
+        # logger.debug(f"Details for: {submission}")
        if isinstance(submission, str):
-            # submission = BasicSubmission.query(rsl_number=submission)
            submission = BasicSubmission.query(rsl_plate_num=submission)
        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 != 'samples'})}")
-        # don't want id
+        # logger.debug(f"Submission details data:\n{pformat({k:v for k,v in self.base_dict.items() if k != 'samples'})}")
+        # NOTE: don't want id
        del self.base_dict['id']
        # logger.debug(f"Creating barcode.")
-        # if not check_if_app():
-        #     self.base_dict['barcode'] = base64.b64encode(submission.make_plate_barcode(width=120, height=30)).decode('utf-8')
-        logger.debug(f"Making platemap...")
+        # logger.debug(f"Making platemap...")
        self.base_dict['platemap'] = submission.make_plate_map()
        self.base_dict, self.template = submission.get_details_template(base_dict=self.base_dict)
        self.html = self.template.render(sub=self.base_dict, signing_permission=is_power_user())
        self.webview.setHtml(self.html)
        self.setWindowTitle(f"Submission Details - {submission.rsl_plate_num}")
-        # with open("details.html", "w") as f:
-        #     f.write(self.html)

    @pyqtSlot(str)
    def sign_off(self, submission:str|BasicSubmission):
-        logger.debug(f"Signing off on {submission} - ({getuser()})")
+        # logger.debug(f"Signing off on {submission} - ({getuser()})")
        if isinstance(submission, str):
-            # submission = BasicSubmission.query(rsl_number=submission)
            submission = BasicSubmission.query(rsl_plate_num=submission)
        submission.signed_by = getuser()
        submission.save()
@@ -177,6 +165,6 @@ class SubmissionComment(QDialog):
        comment = self.txt_editor.toPlainText()
        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}")
+        # 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
@@ -110,7 +110,7 @@ class SubmissionsSheet(QTableView):
        self.menu = QMenu(self)
        self.con_actions = submission.custom_context_events()
        for k in self.con_actions.keys():
-            logger.debug(f"Adding {k}")
+            # 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)
@@ -124,8 +124,8 @@ 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]}")
+        # 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)

@@ -162,50 +162,20 @@ class SubmissionsSheet(QTableView):
                    experiment_name=run[4].strip(),
                    end_time=run[5].strip()
                )
-            # elution columns are item 6 in the comma split list to the end
+            # NOTE: elution columns are item 6 in the comma split list to the end
            for ii in range(6, len(run)):
                new_run[f"column{str(ii-5)}_vol"] = run[ii]
-            # Lookup imported submissions
-            # sub = BasicSubmission.query(rsl_number=new_run['rsl_plate_num'])
+            # NOTE: Lookup imported submissions
            sub = BasicSubmission.query(rsl_plate_num=new_run['rsl_plate_num'])
-            # If no such submission exists, move onto the next run
+            # NOTE: If no such submission exists, move onto the next run
            if sub == None:
                continue
            try:
-                logger.debug(f"Found submission: {sub.rsl_plate_num}")
+                # logger.debug(f"Found submission: {sub.rsl_plate_num}")
                count += 1
            except AttributeError:
                continue
            sub.set_attribute('extraction_info', new_run)
-            # if sub.extraction_info != None:
-            #     # existing = json.loads(sub.extraction_info)
-            #     existing = sub.extraction_info
-            # else:
-            #     existing = None
-            # # Check if the new info already exists in the imported submission
-            # try:
-            #     # if json.dumps(new_run) in sub.extraction_info:
-            #     if new_run in sub.extraction_info:
-            #         logger.debug(f"Looks like we already have that info.")
-            #         continue
-            # except TypeError:
-            #     pass
-            # # Update or create the extraction info
-            # if existing != None:
-            #     try:
-            #         logger.debug(f"Updating {type(existing)}: {existing} with {type(new_run)}: {new_run}")
-            #         existing.append(new_run)
-            #         logger.debug(f"Setting: {existing}")
-            #         # sub.extraction_info = json.dumps(existing)
-            #         sub.extraction_info = existing
-            #     except TypeError:
-            #         logger.error(f"Error updating!")
-            #         # sub.extraction_info = json.dumps([new_run])
-            #         sub.extraction_info = [new_run]
-            #     logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.extraction_info}")
-            # else:
-            #     # sub.extraction_info = json.dumps([new_run])
-            #     sub.extraction_info = [new_run]
            sub.save()
        self.report.add_result(Result(msg=f"We added {count} logs to the database.", status='Information'))

@@ -230,7 +200,7 @@ class SubmissionsSheet(QTableView):
        """    
        fname = select_open_file(self, file_extension="csv")
        with open(fname.__str__(), 'r') as f:
-            # split csv rows on comma
+            # NOTE: split csv rows on comma
            runs = [col.strip().split(",") for col in f.readlines()]
        count = 0
        for run in runs:
@@ -242,49 +212,17 @@ class SubmissionsSheet(QTableView):
                    experiment_name=run[4].strip(),
                    end_time=run[5].strip()
                )
-            # lookup imported submission
-            # sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=new_run['rsl_plate_num'])
-            # sub = lookup_submissions(ctx=obj.ctx, rsl_number=new_run['rsl_plate_num'])
+            # NOTE: lookup imported submission
            sub = BasicSubmission.query(rsl_number=new_run['rsl_plate_num'])
-            # if imported submission doesn't exist move on to next run
+            # NOTE: if imported submission doesn't exist move on to next run
            if sub == None:
                continue
-            try:
-                logger.debug(f"Found submission: {sub.rsl_plate_num}")
-            except AttributeError:
-                continue
-            sub.set_attribute('pcr_info', new_run)
-            # # check if pcr_info already exists
-            # if hasattr(sub, 'pcr_info') and sub.pcr_info != None:
-            #     # existing = json.loads(sub.pcr_info)
-            #     existing = sub.pcr_info
-            # else:
-            #     existing = None
-            # # check if this entry already exists in imported submission
            # try:
-            #     # if json.dumps(new_run) in sub.pcr_info:
-            #     if new_run in sub.pcr_info:
-            #         logger.debug(f"Looks like we already have that info.")
-            #         continue
-            #     else:
-            #         count += 1
-            # except TypeError:
-            #     logger.error(f"No json to dump")
-            # if existing is not None:
-            #     try:
-            #         logger.debug(f"Updating {type(existing)}: {existing} with {type(new_run)}: {new_run}")
-            #         existing.append(new_run)
-            #         logger.debug(f"Setting: {existing}")
-            #         # sub.pcr_info = json.dumps(existing)
-            #         sub.pcr_info = existing
-            #     except TypeError:
-            #         logger.error(f"Error updating!")
-            #         # sub.pcr_info = json.dumps([new_run])
-            #         sub.pcr_info = [new_run]
-            #     logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.pcr_info}")
-            # else:
-            #     # sub.pcr_info = json.dumps([new_run])
-            #     sub.pcr_info = [new_run]
+            #     logger.debug(f"Found submission: {sub.rsl_plate_num}")
+            # except AttributeError:
+            #     continue
+            sub.set_attribute('pcr_info', new_run)
+            # NOTE: check if pcr_info already exists
            sub.save()
        self.report.add_result(Result(msg=f"We added {count} logs to the database.", status='Information'))
        
@@ -308,23 +246,21 @@ class SubmissionsSheet(QTableView):
            Tuple[QMainWindow, dict]: Collection of new main app window and result dict
        """    
        report = Report()
-        # ask for date ranges
+        # NOTE: ask for date ranges
        dlg = ReportDatePicker()
        if dlg.exec():
            info = dlg.parse_form()
-            logger.debug(f"Report info: {info}")
-            # find submissions based on date range
+            # logger.debug(f"Report info: {info}")
+            # NOTE: find submissions based on date range
            subs = BasicSubmission.query(start_date=info['start_date'], end_date=info['end_date'])
-            # convert each object to dict
+            # NOTE: convert each object to dict
            records = [item.to_dict(report=True) for item in subs]
            logger.debug(f"Records: {pformat(records)}")
-            # make dataframe from record dictionaries
+            # NOTE: make dataframe from record dictionaries
            detailed_df, summary_df = make_report_xlsx(records=records)
            html = make_report_html(df=summary_df, start_date=info['start_date'], end_date=info['end_date'])
-            # get save location of report
+            # NOTE: get save location of report
            fname = select_save_file(obj=self, default_name=f"Submissions_Report_{info['start_date']}-{info['end_date']}.pdf", extension="pdf")
-            # with open(fname, "w+b") as f:
-            #     pisa.CreatePDF(html, dest=f)
            html_to_pdf(html=html, output_file=fname)
            writer = pd.ExcelWriter(fname.with_suffix(".xlsx"), engine='openpyxl')
            summary_df.to_excel(writer, sheet_name="Report")
@@ -337,14 +273,13 @@ class SubmissionsSheet(QTableView):
                    len(str(series.name))  # len of column name/header
                    )) + 20  # adding a little extra space
                try:
-                    # worksheet.column_dimensions[get_column_letter(idx=idx)].width = max_len
-                    # Convert idx to letter
+                    # NOTE: Convert idx to letter
                    col_letter = chr(ord('@') + idx)
                    worksheet.column_dimensions[col_letter].width = max_len
                except ValueError:
                    pass
            blank_row = get_first_blank_df_row(summary_df) + 1
-            logger.debug(f"Blank row index = {blank_row}")
+            # logger.debug(f"Blank row index = {blank_row}")
            for col in range(3,6):
                col_letter = row_map[col]
                worksheet.cell(row=blank_row, column=col, value=f"=SUM({col_letter}2:{col_letter}{str(blank_row-1)})")
--- a/src/submissions/frontend/widgets/submission_type_creator.py
+++ b/src/submissions/frontend/widgets/submission_type_creator.py
@@ -26,11 +26,11 @@ class SubmissionTypeAdder(QWidget):
        scrollContent = QWidget(scroll)
        self.grid = QGridLayout()
        scrollContent.setLayout(self.grid)
-        # insert submit button at top
+        # NOTE: insert submit button at top
        self.submit_btn = QPushButton("Submit")
        self.grid.addWidget(self.submit_btn,0,0,1,1)
        self.grid.addWidget(QLabel("Submission Type Name:"),2,0)
-        # widget to get kit name
+        # NOTE: widget to get kit name
        self.st_name = QLineEdit()
        self.st_name.setObjectName("submission_type_name")
        self.grid.addWidget(self.st_name,2,1,1,2)
@@ -39,7 +39,7 @@ class SubmissionTypeAdder(QWidget):
        self.grid.addWidget(template_selector,3,1)
        self.template_label = QLabel("None")
        self.grid.addWidget(self.template_label,3,2)
-        # widget to get uses of kit
+        # NOTE: widget to get uses of kit
        exclude = ['id', 'submitting_lab_id', 'extraction_kit_id', 'reagents_id', 'extraction_info', 'pcr_info', 'run_cost']
        self.columns = {key:value for key, value in BasicSubmission.__dict__.items() if isinstance(value, InstrumentedAttribute)}
        self.columns = {key:value for key, value in self.columns.items() if hasattr(value, "type") and key not in exclude}
--- a/src/submissions/frontend/widgets/submission_widget.py
+++ b/src/submissions/frontend/widgets/submission_widget.py
@@ -30,7 +30,7 @@ class SubmissionFormContainer(QWidget):
    import_drag = pyqtSignal(Path)

    def __init__(self, parent: QWidget) -> None:
-        logger.debug(f"Setting form widget...")
+        # logger.debug(f"Setting form widget...")
        super().__init__(parent)
        self.app = self.parent().parent()
        self.report = Report()
@@ -52,7 +52,7 @@ 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}")
+        # logger.debug(f"App: {self.app}")
        self.app.last_dir = fname.parent
        self.import_drag.emit(fname)

@@ -63,7 +63,7 @@ class SubmissionFormContainer(QWidget):
        self.app.raise_()
        self.app.activateWindow()
        self.import_submission_function(fname)
-        logger.debug(f"Result from result reporter: {self.report.results}")
+        # logger.debug(f"Result from result reporter: {self.report.results}")
        self.app.report.add_result(self.report)
        self.report = Report()
        self.app.result_reporter()
@@ -78,7 +78,7 @@ class SubmissionFormContainer(QWidget):
        Returns:
            Tuple[QMainWindow, dict|None]: Collection of new main app window and result dict
        """    
-        logger.debug(f"\n\nStarting Import...\n\n")
+        logger.info(f"\n\nStarting Import...\n\n")
        report = Report()
        try:
            self.form.setParent(None)
@@ -90,7 +90,7 @@ class SubmissionFormContainer(QWidget):
        # set file dialog
        if isinstance(fname, bool) or fname == None:
            fname = select_open_file(self, file_extension="xlsx")
-        logger.debug(f"Attempting to parse file: {fname}")
+        # logger.debug(f"Attempting to parse file: {fname}")
        if not fname.exists():
            report.add_result(Result(msg=f"File {fname.__str__()} not found.", status="critical"))
            self.report.add_result(report)
@@ -103,16 +103,16 @@ class SubmissionFormContainer(QWidget):
            return
        except AttributeError:
            self.prsr = SheetParser(filepath=fname)
-        logger.debug(f"Submission dictionary:\n{pformat(self.prsr.sub)}")
+        # 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")
+        # 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)
        # if self.prsr.sample_result != None:
        #     report.add_result(msg=self.prsr.sample_result, status="Warning")
        self.report.add_result(report)
-        logger.debug(f"Outgoing report: {self.report.results}")
-        logger.debug(f"All attributes of submission container:\n{pformat(self.__dict__)}")
+        # logger.debug(f"Outgoing report: {self.report.results}")
+        # logger.debug(f"All attributes of submission container:\n{pformat(self.__dict__)}")

    def add_reagent(self, reagent_lot:str|None=None, reagent_type:str|None=None, expiry:date|None=None, name:str|None=None):
        """
@@ -135,7 +135,7 @@ class SubmissionFormContainer(QWidget):
        if dlg.exec():
            # extract form info
            info = dlg.parse_form()
-            logger.debug(f"Reagent info: {info}")
+            # logger.debug(f"Reagent info: {info}")
            # create reagent object
            reagent = PydReagent(ctx=self.app.ctx, **info, missing=False)
            # send reagent to db
@@ -216,10 +216,10 @@ class SubmissionFormWidget(QWidget):
        caller = inspect.stack()[1].function.__repr__().replace("'", "")
        # self.reagents = []
        # logger.debug(f"Self.reagents: {self.reagents}")
-        logger.debug(f"\n\n{pformat(caller)}\n\n")
+        # logger.debug(f"\n\n{pformat(caller)}\n\n")
        # logger.debug(f"SubmissionType: {self.submission_type}")
        report = Report()
-        logger.debug(f"Extraction kit: {extraction_kit}")
+        # logger.debug(f"Extraction kit: {extraction_kit}")
        # Remove previous reagent widgets
        try:
            old_reagents = self.find_widgets()
@@ -249,7 +249,7 @@ class SubmissionFormWidget(QWidget):
            add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.pyd.extraction_kit)
            self.layout.addWidget(add_widget)
        report.add_result(integrity_report)
-        logger.debug(f"Outgoing report: {report.results}")
+        # 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")
@@ -263,46 +263,6 @@ class SubmissionFormWidget(QWidget):
        self.app.report.add_result(report)
        self.app.result_reporter()

-    # def kit_integrity_completion_function(self, extraction_kit:str|None=None):
-    #     """
-    #     Compare kit contents to parsed contents and creates widgets.
-    #
-    #     Args:
-    #         obj (QMainWindow): The original app window
-    #
-    #     Returns:
-    #         Tuple[QMainWindow, dict]: Collection of new main app window and result dict
-    #     """
-    #     report = Report()
-    #     missing_reagents = []
-    #     # logger.debug(inspect.currentframe().f_back.f_code.co_name)
-    #     # find the widget that contains kit info
-    #     if extraction_kit is None:
-    #         kit_widget = self.find_widgets(object_name="extraction_kit")[0].input
-    #         logger.debug(f"Kit selector: {kit_widget}")
-    #         # get current kit being used
-    #         self.ext_kit = kit_widget.currentText()
-    #     else:
-    #         self.ext_kit = extraction_kit
-    #     for reagent in self.reagents:
-    #         logger.debug(f"Creating widget for {reagent}")
-    #         add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.ext_kit)
-    #         # self.form.layout().addWidget(add_widget)
-    #         self.layout.addWidget(add_widget)
-    #         if reagent.missing:
-    #             missing_reagents.append(reagent)
-    #     logger.debug(f"Checking integrity of {self.ext_kit}")
-    #     # TODO: put check_kit_integrity here instead of what's here?
-    #     # see if there are any missing reagents
-    #     if len(missing_reagents) > 0:
-    #         result = Result(msg=f"""The submission you are importing is missing some reagents expected by the kit.\n\n
-    #                         It looks like you are missing: {[item.type.upper() for item in missing_reagents]}\n\n
-    #                         Alternatively, you may have set the wrong extraction kit.\n\nThe program will populate lists using existing reagents.
-    #                         \n\nPlease make sure you check the lots carefully!""".replace("  ", ""), status="Warning")
-    #         report.add_result(result)
-    #     self.report.add_result(report)
-    #     logger.debug(f"Outgoing report: {self.report.results}")
-        
    def clear_form(self):
        """
        Removes all form widgets
@@ -335,24 +295,23 @@ class SubmissionFormWidget(QWidget):
        Returns:
            Tuple[QMainWindow, dict]: Collection of new main app window and result dict
        """    
-        logger.debug(f"\n\nBeginning Submission\n\n")
+        logger.info(f"\n\nBeginning Submission\n\n")
        report = Report()
-        # self.pyd: PydSubmission = self.parse_form()
        result = self.parse_form()
        report.add_result(result)
-        logger.debug(f"Submission: {pformat(self.pyd)}")
-        logger.debug("Checking kit integrity...")
+        # logger.debug(f"Submission: {pformat(self.pyd)}")
+        # logger.debug("Checking kit integrity...")
        _, result = self.pyd.check_kit_integrity()
        report.add_result(result)
        if len(result.results) > 0:
            self.app.report.add_result(report)
            self.app.result_reporter()
            return
-        logger.debug(f"PYD before transformation into SQL:\n\n{self.pyd}\n\n")
+        # 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"SQL object: {pformat(base_submission.__dict__)}")
        # logger.debug(f"Base submission: {base_submission.to_dict()}")
-        # check output message for issues
+        # NOTE: check output message for issues
        match result.code:
            # code 0: everything is fine.
            case 0:
@@ -379,11 +338,10 @@ class SubmissionFormWidget(QWidget):
            # 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)}")
-        # sys.exit("Programmed stop submission_widget.py, line 381")
        base_submission.save()
-        # update summary sheet
+        # NOTE: update summary sheet
        self.app.table_widget.sub_wid.setData()
-        # reset form
+        # NOTE: reset form
        self.setParent(None)
        # logger.debug(f"All attributes of obj: {pformat(self.__dict__)}")
        self.app.report.add_result(report)
@@ -396,16 +354,14 @@ class SubmissionFormWidget(QWidget):
        Args:
            fname (Path | None, optional): Input filename. Defaults to None.
        """        
-        # self.parse_form()
        if isinstance(fname, bool) or fname == None:
            fname = select_save_file(obj=self, default_name=self.pyd.construct_filename(), extension="csv")
        try:

-            # logger.debug(f'')
            # self.pyd.csv.to_csv(fname.__str__(), index=False)
            workbook_2_csv(worksheet=self.pyd.csv, filename=fname)
        except PermissionError:
-            logger.debug(f"Could not get permissions to {fname}. Possibly the request was cancelled.")
+            logger.warning(f"Could not get permissions to {fname}. Possibly the request was cancelled.")
        except AttributeError:
            logger.error(f"No csv file found in the submission at this point.")

@@ -417,7 +373,7 @@ class SubmissionFormWidget(QWidget):
            Report: Report on status of parse.
        """        
        report = Report()
-        logger.debug(f"Hello from form parser!")
+        logger.info(f"Hello from form parser!")
        info = {}
        reagents = []
        for widget in self.findChildren(QWidget):
@@ -431,21 +387,19 @@ 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)}")
+        # logger.debug(f"Info: {pformat(info)}")
+        # logger.debug(f"Reagents going into pyd: {pformat(reagents)}")
        self.pyd.reagents = 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}")
+            # logger.debug(f"Attempting to recover: {item}")
            if hasattr(self, item):
                value = getattr(self, item)
-                logger.debug(f"Setting {item}")
+                # logger.debug(f"Setting {item}")
                info[item] = value
-        # submission = PydSubmission(reagents=reagents, **info)
        for k,v in info.items():
            self.pyd.set_attribute(key=k, value=v)
-        # return submission
+        # NOTE: return submission
        report.add_result(report)
        return report
    
@@ -510,7 +464,7 @@ class SubmissionFormWidget(QWidget):
            except (TypeError, KeyError):
                pass
            obj = parent.parent().parent()
-            logger.debug(f"Creating widget for: {key}")
+            # logger.debug(f"Creating widget for: {key}")
            match key:
                case 'submitting_lab':
                    add_widget = QComboBox()
@@ -531,12 +485,12 @@ class SubmissionFormWidget(QWidget):
                    # create combobox to hold looked up kits
                    add_widget = QComboBox()
                    # lookup existing kits by 'submission_type' decided on by sheetparser
-                    logger.debug(f"Looking up kits used for {submission_type}")
+                    # logger.debug(f"Looking up kits used for {submission_type}")
                    uses = [item.name for item in KitType.query(used_for=submission_type)]
                    obj.uses = uses
-                    logger.debug(f"Kits received for {submission_type}: {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}")
+                        # logger.debug(f"The extraction kit in parser was: {value}")
                        uses.insert(0, uses.pop(uses.index(value)))
                        obj.ext_kit = value
                    else:
@@ -565,7 +519,7 @@ class SubmissionFormWidget(QWidget):
                case _:
                    # anything else gets added in as a line edit
                    add_widget = QLineEdit()
-                    logger.debug(f"Setting widget text to {str(value).replace('_', ' ')}")
+                    # logger.debug(f"Setting widget text to {str(value).replace('_', ' ')}")
                    add_widget.setText(str(value).replace("_", " "))
            if add_widget != None:
                add_widget.setObjectName(key)
@@ -639,14 +593,6 @@ class SubmissionFormWidget(QWidget):
            # If changed set self.missing to True and update self.label
            self.lot.currentTextChanged.connect(self.updated)

-        # def check_uncheck(self):
-        #     if self.check_box.isChecked():
-        #         self.lot.setCurrentIndex(0)
-        #         self.lot.setEnabled(True)
-        #     else:
-        #         self.lot.setCurrentText("Not Applicable")
-        #         self.lot.setEnabled(False)
-
        def parse_form(self) -> Tuple[PydReagent, dict]:
            """
            Pulls form info into PydReagent
@@ -657,17 +603,17 @@ class SubmissionFormWidget(QWidget):
            # if not self.check_box.isChecked():
            #     return None, None
            lot = self.lot.currentText()
-            logger.debug(f"Using this lot for the reagent {self.reagent}: {lot}")
+            # logger.debug(f"Using this lot for the reagent {self.reagent}: {lot}")
            wanted_reagent = Reagent.query(lot_number=lot, reagent_type=self.reagent.type)
-            # if reagent doesn't exist in database, offer to add it (uses App.add_reagent)
+            # NOTE: if reagent doesn't exist in database, offer to add it (uses App.add_reagent)
            if wanted_reagent == None:
                dlg = QuestionAsker(title=f"Add {lot}?", message=f"Couldn't find reagent type {self.reagent.type}: {lot} in the database.\n\nWould you like to add it?")
                if dlg.exec():
                    wanted_reagent = self.parent().parent().add_reagent(reagent_lot=lot, reagent_type=self.reagent.type, expiry=self.reagent.expiry, name=self.reagent.name)
                    return wanted_reagent, None
                else:
-                    # In this case we will have an empty reagent and the submission will fail kit integrity check
-                    logger.debug("Will not add reagent.")
+                    # NOTE: In this case we will have an empty reagent and the submission will fail kit integrity check
+                    # logger.debug("Will not add reagent.")
                    return None, Result(msg="Failed integrity check", status="Critical")
            else:
                # Since this now gets passed in directly from the parser -> pyd -> form and the parser gets the name
@@ -712,8 +658,8 @@ class SubmissionFormWidget(QWidget):
            def __init__(self, reagent, extraction_kit:str) -> None:
                super().__init__()
                self.setEditable(True)
-                logger.debug(f"Attempting lookup of reagents by type: {reagent.type}")
-                # below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work.
+                # logger.debug(f"Attempting lookup of reagents by type: {reagent.type}")
+                # NOTE: below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work.
                lookup = Reagent.query(reagent_type=reagent.type)
                relevant_reagents = [str(item.lot) for item in lookup]
                output_reg = []
@@ -725,8 +671,8 @@ class SubmissionFormWidget(QWidget):
                    elif isinstance(rel_reagent, str):
                        output_reg.append(rel_reagent)
                relevant_reagents = output_reg
-                # if reagent in sheet is not found insert it into the front of relevant reagents so it shows 
-                logger.debug(f"Relevant reagents for {reagent.lot}: {relevant_reagents}")
+                # NOTE: if reagent in sheet is not found insert it into the front of relevant reagents so it shows
+                # logger.debug(f"Relevant reagents for {reagent.lot}: {relevant_reagents}")
                if str(reagent.lot) not in relevant_reagents:
                    if check_not_nan(reagent.lot):
                        relevant_reagents.insert(0, str(reagent.lot))