Code cleanup and documentation

2024-02-09 14:03:35 -06:00
parent eda62fba5a
commit a534d229a8
30 changed files with 1558 additions and 1347 deletions
--- a/src/submissions/frontend/visualizations/init.py
+++ b/src/submissions/frontend/visualizations/init.py
@@ -2,5 +2,3 @@
 Contains all operations for creating charts, graphs and visual effects.
 '''
 from .control_charts import *
-from .barcode import *
-from .plate_map import *
--- a/src/submissions/frontend/visualizations/barcode.py
+++ b/src/submissions/frontend/visualizations/barcode.py
@@ -1,19 +0,0 @@
-from reportlab.graphics.barcode import createBarcodeImageInMemory
-from reportlab.graphics.shapes import Drawing
-from reportlab.lib.units import mm
-
-
-def make_plate_barcode(text:str, width:int=100, height:int=25) -> Drawing:
-    """
-    Creates a barcode image for a given str.
-
-    Args:
-        text (str): Input string
-        width (int, optional): Width (pixels) of image. Defaults to 100.
-        height (int, optional): Height (pixels) of image. Defaults to 25.
-
-    Returns:
-        Drawing: image object
-    """    
-    # return createBarcodeDrawing('Code128', value=text, width=200, height=50, humanReadable=True)
-    return createBarcodeImageInMemory('Code128', value=text, width=width*mm, height=height*mm, humanReadable=True, format="png")
--- a/src/submissions/frontend/visualizations/control_charts.py
+++ b/src/submissions/frontend/visualizations/control_charts.py
@@ -12,7 +12,6 @@ from frontend.widgets.functions import select_save_file

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

-
 def create_charts(ctx:Settings, df:pd.DataFrame, ytitle:str|None=None) -> Figure:
    """
    Constructs figures based on parsed pandas dataframe.
@@ -40,7 +39,6 @@ def create_charts(ctx:Settings, df:pd.DataFrame, ytitle:str|None=None) -> Figure
            genera.append("")
    df['genus'] = df['genus'].replace({'\*':''}, regex=True).replace({"NaN":"Unknown"})
    df['genera'] = genera
-    # df = df.dropna()
    # remove original runs, using reruns if applicable
    df = drop_reruns_from_df(ctx=ctx, df=df)
    # sort by and exclude from
@@ -224,4 +222,4 @@ def construct_html(figure:Figure) -> str:
    else:
        html += "<h1>No data was retrieved for the given parameters.</h1>"
    html += '</body></html>'
-    return html
+    return html
--- a/src/submissions/frontend/visualizations/plate_map.py
+++ b/src/submissions/frontend/visualizations/plate_map.py
@@ -1,121 +0,0 @@
-from pathlib import Path
-from PIL import Image, ImageDraw, ImageFont
-import numpy as np
-from tools import check_if_app, jinja_template_loading
-import logging, sys
-
-logger = logging.getLogger(f"submissions.{__name__}")
-
-def make_plate_map(sample_list:list) -> Image:
-    """
-    Makes a pillow image of a plate from hitpicks 
-
-    Args:
-        sample_list (list): list of sample dictionaries from the hitpicks
-
-    Returns:
-        Image: Image of the 96 well plate with positive samples in red.
-    """  
-    # If we can't get a plate number, do nothing  
-    try:
-        plate_num = sample_list[0]['plate_name']
-    except IndexError as e:
-        logger.error(f"Couldn't get a plate number. Will not make plate.")
-        return None
-    except TypeError as e:
-        logger.error(f"No samples for this plate. Nothing to do.")
-        return None
-    # Make an 8 row, 12 column, 3 color ints array, filled with white by default
-    grid = np.full((8,12,3),255, dtype=np.uint8)
-    # Go through samples and change its row/column to red if positive, else blue
-    for sample in sample_list:
-        logger.debug(f"sample keys: {list(sample.keys())}")
-        # set color of square
-        if sample['positive']:
-            colour = [255,0,0]
-        else:
-            if 'colour' in sample.keys():
-                colour = sample['colour']
-            else:
-                colour = [0,0,255]
-        grid[int(sample['row'])-1][int(sample['column'])-1] = colour
-    # Create pixel image from the grid and enlarge
-    img = Image.fromarray(grid).resize((1200, 800), resample=Image.NEAREST)
-    # create a drawer over the image
-    draw = ImageDraw.Draw(img)
-    # draw grid over the image
-    y_start = 0
-    y_end = img.height
-    step_size = int(img.width / 12)
-    for x in range(0, img.width, step_size):
-        line = ((x, y_start), (x, y_end))
-        draw.line(line, fill=128)
-    x_start = 0
-    x_end = img.width
-    step_size = int(img.height / 8)
-    for y in range(0, img.height, step_size):
-        line = ((x_start, y), (x_end, y))
-        draw.line(line, fill=128)
-    del draw
-    old_size = img.size
-    new_size = (1300, 900)
-    # create a new, larger white image to hold the annotations
-    new_img = Image.new("RGB", new_size, "White")
-    box = tuple((n - o) // 2 for n, o in zip(new_size, old_size))
-    # paste plate map into the new image
-    new_img.paste(img, box)
-    # create drawer over the new image
-    draw = ImageDraw.Draw(new_img)
-    if check_if_app():
-        font_path = Path(sys._MEIPASS).joinpath("files", "resources")
-    else:
-        font_path = Path(__file__).parents[2].joinpath('resources').absolute()
-        logger.debug(f"Font path: {font_path}")
-    font = ImageFont.truetype(font_path.joinpath('arial.ttf').__str__(), 32)
-    row_dict = ["A", "B", "C", "D", "E", "F", "G", "H"]
-    # write the plate number on the image
-    draw.text((100, 850),plate_num,(0,0,0),font=font)
-    # write column numbers
-    for num in range(1,13):
-        x = (num * 100) - 10
-        draw.text((x, 0), str(num), (0,0,0),font=font)
-    # write row letters
-    for num in range(1,9):
-        letter = row_dict[num-1]
-        y = (num * 100) - 10
-        draw.text((10, y), letter, (0,0,0),font=font)
-    return new_img
-
-def make_plate_map_html(sample_list:list, plate_rows:int=8, plate_columns=12) -> str:
-    """
-    Constructs an html based plate map.
-
-    Args:
-        sample_list (list): List of submission samples
-        plate_rows (int, optional): Number of rows in the plate. Defaults to 8.
-        plate_columns (int, optional): Number of columns in the plate. Defaults to 12.
-
-    Returns:
-        str: html output string.
-    """    
-    for sample in sample_list:
-        if sample['positive']:
-            sample['background_color'] = "#f10f07"
-        else:
-            if "colour" in sample.keys():
-                sample['background_color'] = "#69d84f"
-            else:
-                sample['background_color'] = "#80cbc4"
-    output_samples = []
-    for column in range(1, plate_columns+1):
-        for row in range(1, plate_rows+1):
-            try:
-                well = [item for item in sample_list if item['row'] == row and item['column']==column][0]
-            except IndexError:
-                well = dict(name="", row=row, column=column, background_color="#ffffff")
-            output_samples.append(well)
-    env = jinja_template_loading()
-    template = env.get_template("plate_map.html")
-    html = template.render(samples=output_samples, PLATE_ROWS=plate_rows, PLATE_COLUMNS=plate_columns)
-    return html
-
--- a/src/submissions/frontend/widgets/app.py
+++ b/src/submissions/frontend/widgets/app.py
@@ -52,7 +52,6 @@ class App(QMainWindow):
        self._createMenuBar()
        self._createToolBar()
        self._connectActions()
-        # self._controls_getter()
        self.show()
        self.statusBar().showMessage('Ready', 5000)
        
@@ -114,14 +113,10 @@ class App(QMainWindow):
        self.importPCRAction.triggered.connect(self.table_widget.formwidget.import_pcr_results)
        self.addReagentAction.triggered.connect(self.add_reagent)
        self.generateReportAction.triggered.connect(self.table_widget.sub_wid.generate_report)
-        # self.addKitAction.triggered.connect(self.add_kit)
-        # self.addOrgAction.triggered.connect(self.add_org)
        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.constructFS.triggered.connect(self.construct_first_strand)
-        # self.table_widget.formwidget.import_drag.connect(self.importSubmission)
        self.searchLog.triggered.connect(self.runSearch)

    def showAbout(self):
--- a/src/submissions/frontend/widgets/controls_chart.py
+++ b/src/submissions/frontend/widgets/controls_chart.py
@@ -4,9 +4,9 @@ from PyQt6.QtWidgets import (
    QDateEdit, QLabel, QSizePolicy
 )
 from PyQt6.QtCore import QSignalBlocker
-from backend.db import ControlType, Control#, get_control_subtypes
+from backend.db import ControlType, Control
 from PyQt6.QtCore import QDate, QSize
-import logging, sys
+import logging
 from tools import Report, Result
 from backend.excel.reports import convert_data_list_to_df
 from frontend.visualizations.control_charts import create_charts, construct_html
@@ -88,9 +88,7 @@ class ControlsViewer(QWidget):
        self.mode = self.mode_typer.currentText()
        self.sub_typer.clear()
        # lookup subtypes
-        # sub_types = get_control_subtypes(type=self.con_type, mode=self.mode)
        sub_types = ControlType.query(name=self.con_type).get_subtypes(mode=self.mode)
-        # sub_types = lookup_controls(ctx=obj.ctx, control_type=obj.con_type)
        if sub_types != []:
            # block signal that will rerun controls getter and update sub_typer
            with QSignalBlocker(self.sub_typer) as blocker: 
@@ -103,7 +101,6 @@ class ControlsViewer(QWidget):
        self.chart_maker()
        self.report.add_result(report)
        
-
    def chart_maker_function(self):
        """
        Create html chart for controls reporting
--- a/src/submissions/frontend/widgets/equipment_usage.py
+++ b/src/submissions/frontend/widgets/equipment_usage.py
@@ -2,9 +2,10 @@ from PyQt6.QtCore import Qt
 from PyQt6.QtWidgets import (QDialog, QComboBox, QCheckBox, 
                             QLabel, QWidget, QHBoxLayout, 
                             QVBoxLayout, QDialogButtonBox)
-from backend.db.models import SubmissionType, Equipment, BasicSubmission
+from backend.db.models import Equipment, BasicSubmission
 from backend.validators.pydant import PydEquipment, PydEquipmentRole
 import logging
+from typing import List

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

@@ -24,19 +25,29 @@ class EquipmentUsage(QDialog):
        self.populate_form()

    def populate_form(self):
+        """
+        Create form widgets
+        """        
        QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
        self.buttonBox = QDialogButtonBox(QBtn)
        self.buttonBox.accepted.connect(self.accept)
        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.toForm(parent=self, submission_type=self.submission.submission_type, used=self.used_equipment)
+            widg = eq.toForm(parent=self, used=self.used_equipment)
            self.layout.addWidget(widg)
            widg.update_processes()
        self.layout.addWidget(self.buttonBox)

-    def parse_form(self):
+    def parse_form(self) -> List[PydEquipment]:
+        """
+        Pull info from all RoleComboBox widgets
+
+        Returns:
+            List[PydEquipment]: All equipment pulled from widgets
+        """        
        output = []
        for widget in self.findChildren(QWidget):
            match widget:
@@ -63,43 +74,18 @@ class EquipmentUsage(QDialog):
            self.setLayout(self.layout)

        def check_all(self):
+            """
+            Toggles all checkboxes in the form
+            """            
            for object in self.parent().findChildren(QCheckBox):
                object.setChecked(self.check.isChecked())
-            
-class EquipmentCheckBox(QWidget):
-
-    def __init__(self, parent, equipment:PydEquipment) -> None:
-        super().__init__(parent)
-        self.layout = QHBoxLayout()
-        self.label = QLabel()
-        self.label.setMaximumWidth(125)
-        self.label.setMinimumWidth(125)
-        self.check = QCheckBox()
-        if equipment.static:
-            self.check.setChecked(True)
-        if equipment.nickname != None:
-            text = f"{equipment.name} ({equipment.nickname})"
-        else:
-            text = equipment.name
-        self.setObjectName(equipment.name)
-        self.label.setText(text)
-        self.layout.addWidget(self.label)
-        self.layout.addWidget(self.check)
-        self.setLayout(self.layout)
-
-    def parse_form(self) -> str|None:
-        if self.check.isChecked():
-            return self.objectName()
-        else:
-            return None

+# TODO: Figure out how this is working again
 class RoleComboBox(QWidget):

-    def __init__(self, parent, role:PydEquipmentRole, submission_type:SubmissionType, used:list) -> None:
+    def __init__(self, parent, role:PydEquipmentRole, used:list) -> None:
        super().__init__(parent)
        self.layout = QHBoxLayout()
-        # label = QLabel()
-        # label.setText(pool.name)
        self.role = role
        self.check = QCheckBox()
        if role.name in used:
@@ -111,14 +97,10 @@ class RoleComboBox(QWidget):
        self.box.setMinimumWidth(200)
        self.box.addItems([item.name for item in role.equipment])
        self.box.currentTextChanged.connect(self.update_processes)
-        # self.check = QCheckBox()
-        # self.layout.addWidget(label)
        self.process = QComboBox()
        self.process.setMaximumWidth(200)
        self.process.setMinimumWidth(200)
        self.process.setEditable(True)
-        # self.process.addItems(submission_type.get_processes_for_role(equipment_role=role.name))
-        # self.process.addItems(role.processes)
        self.layout.addWidget(self.check)
        label = QLabel(f"{role.name}:")
        label.setMinimumWidth(200)
@@ -127,11 +109,12 @@ class RoleComboBox(QWidget):
        self.layout.addWidget(label)
        self.layout.addWidget(self.box)
        self.layout.addWidget(self.process)
-        # self.layout.addWidget(self.check)
        self.setLayout(self.layout)
-        # self.update_processes()
        
    def update_processes(self):
+        """
+        Changes processes when equipment is changed
+        """        
        equip = self.box.currentText()
        logger.debug(f"Updating equipment: {equip}")
        equip2 = [item for item in self.role.equipment if item.name==equip][0]
@@ -139,10 +122,16 @@ class RoleComboBox(QWidget):
        self.process.clear()
        self.process.addItems([item for item in equip2.processes if item in self.role.processes])

-    def parse_form(self) -> str|None:
+    def parse_form(self) -> PydEquipment|None:
+        """
+        Creates PydEquipment for values in form
+
+        Returns:
+            PydEquipment|None: PydEquipment matching form
+        """        
        eq = Equipment.query(name=self.box.currentText())
-        # if self.check.isChecked():
-        return PydEquipment(name=eq.name, processes=[self.process.currentText()], role=self.role.name, asset_number=eq.asset_number, nickname=eq.nickname)
-        # else:
-        #     return None
+        try:
+            return PydEquipment(name=eq.name, processes=[self.process.currentText()], role=self.role.name, asset_number=eq.asset_number, nickname=eq.nickname)
+        except Exception as e:
+            logger.error(f"Could create PydEquipment due to: {e}")
        
--- a/src/submissions/frontend/widgets/gel_checker.py
+++ b/src/submissions/frontend/widgets/gel_checker.py
@@ -1,7 +1,7 @@
-# import required modules
-# from PyQt6.QtCore import Qt
+"""
+Gel box for artic quality control
+"""
 from PyQt6.QtWidgets import *
-# import sys
 from PyQt6.QtWidgets import QWidget
 import numpy as np
 import pyqtgraph as pg
@@ -9,11 +9,17 @@ from PyQt6.QtGui import *
 from PyQt6.QtCore import *
 from PIL import Image
 import numpy as np
+import logging
+from pprint import pformat
+from typing import Tuple, List
+from pathlib import Path
+
+logger = logging.getLogger(f"submissions.{__name__}")

 # Main window class
 class GelBox(QDialog):

-    def __init__(self, parent, img_path):
+    def __init__(self, parent, img_path:str|Path):
        super().__init__(parent)
        # setting title
        self.setWindowTitle("PyQtGraph")
@@ -27,11 +33,12 @@ class GelBox(QDialog):
        # calling method
        self.UiComponents()
        # showing all the widgets
-        # self.show()

    # method for components
    def UiComponents(self):
-        # widget = QWidget()
+        """
+        Create widgets in ui
+        """        
        # setting configuration options
        pg.setConfigOptions(antialias=True)
        # creating image view object
@@ -39,33 +46,41 @@ class GelBox(QDialog):
        img = np.array(Image.open(self.img_path).rotate(-90).transpose(Image.FLIP_LEFT_RIGHT))
        self.imv.setImage(img)#, xvals=np.linspace(1., 3., data.shape[0]))
        layout = QGridLayout()
+        layout.addWidget(QLabel("DNA Core Submission Number"),0,1)
+        self.core_number = QLineEdit()
+        layout.addWidget(self.core_number, 0,2)
        # setting this layout to the widget
-        # widget.setLayout(layout)
        # plot window goes on right side, spanning 3 rows
-        layout.addWidget(self.imv, 0, 0,20,20)
+        layout.addWidget(self.imv, 1, 1,20,20)
        # setting this widget as central widget of the main window
        self.form = ControlsForm(parent=self)
-        layout.addWidget(self.form,21,1,1,4)
+        layout.addWidget(self.form,22,1,1,4)
        QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
        self.buttonBox = QDialogButtonBox(QBtn)
        self.buttonBox.accepted.connect(self.accept)
        self.buttonBox.rejected.connect(self.reject)
-        layout.addWidget(self.buttonBox, 21, 5, 1, 1)#, alignment=Qt.AlignmentFlag.AlignTop)
-        # self.buttonBox.clicked.connect(self.submit)
+        layout.addWidget(self.buttonBox, 22, 5, 1, 1)#, alignment=Qt.AlignmentFlag.AlignTop)
        self.setLayout(layout)

-    def parse_form(self):
-        return self.img_path, self.form.parse_form()
-        
+    def parse_form(self) -> Tuple[str, str|Path, list]:
+        """
+        Get relevant values from self/form

+        Returns:
+            Tuple[str, str|Path, list]: output values
+        """        
+        dna_core_submission_number = self.core_number.text()
+        return dna_core_submission_number, self.img_path, self.form.parse_form()
+        
 class ControlsForm(QWidget):

    def __init__(self, parent) -> None:
        super().__init__(parent)
        self.layout = QGridLayout()
+        
        columns = []
        rows = []
-        for iii, item in enumerate(["Negative Control Key", "Description", "Results - 65 C",	"Results - 63 C", "Results - Spike"]):
+        for iii, item in enumerate(["Negative Control Key", "Description", "Results - 65 C", "Results - 63 C", "Results - Spike"]):
            label = QLabel(item)
            self.layout.addWidget(label, 0, iii,1,1)
            if iii > 1:
@@ -85,11 +100,22 @@ class ControlsForm(QWidget):
                self.layout.addWidget(widge, iii+1, jjj+2, 1, 1)
        self.setLayout(self.layout)

-    def parse_form(self):
-        dicto = {}
+    def parse_form(self) -> List[dict]:
+        """
+        Pulls the controls statuses from the form.
+
+        Returns:
+            List[dict]: output of values
+        """        
+        output = []
        for le in self.findChildren(QLineEdit):
            label = [item.strip() for item in le.objectName().split(" : ")]
-            if label[0] not in dicto.keys():
-                dicto[label[0]] = {}
-            dicto[label[0]][label[1]] = le.text()
-        return dicto
+            try:
+                dicto = [item for item in output if item['name']==label[0]][0]
+            except IndexError:
+                dicto = dict(name=label[0], values=[])
+            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))
+        return output
--- a/src/submissions/frontend/widgets/kit_creator.py
+++ b/src/submissions/frontend/widgets/kit_creator.py
@@ -79,12 +79,10 @@ class KitAdder(QWidget):
        """
        insert new reagent type row
        """        
-        print(self.app)
        # get bottommost row
        maxrow = self.grid.rowCount()
        reg_form = ReagentTypeForm(parent=self)
        reg_form.setObjectName(f"ReagentForm_{maxrow}")
-        # self.grid.addWidget(reg_form, maxrow + 1,0,1,2)
        self.grid.addWidget(reg_form, maxrow,0,1,4)
        
    def submit(self) -> None:
@@ -118,6 +116,12 @@ class KitAdder(QWidget):
        self.__init__(self.parent())

    def parse_form(self) -> Tuple[dict, list]:
+        """
+        Pulls reagent and general info from form
+
+        Returns:
+            Tuple[dict, list]: dict=info, list=reagents
+        """        
        logger.debug(f"Hello from {self.__class__} parser!")
        info = {}
        reagents = []
@@ -188,10 +192,19 @@ class ReagentTypeForm(QWidget):
                       ]

    def remove(self):
+        """
+        Destroys this row of reagenttype from the form
+        """        
        self.setParent(None)
        self.destroy()

    def parse_form(self) -> dict:
+        """
+        Pulls ReagentType info from the form.
+
+        Returns:
+            dict: _description_
+        """        
        logger.debug(f"Hello from {self.__class__} parser!")
        info = {}
        info['eol'] = self.eol.value()
--- a/src/submissions/frontend/widgets/misc.py
+++ b/src/submissions/frontend/widgets/misc.py
@@ -25,7 +25,6 @@ class AddReagentForm(QDialog):
    """    
    def __init__(self, reagent_lot:str|None=None, reagent_type:str|None=None, expiry:date|None=None, reagent_name:str|None=None) -> None:
        super().__init__()
-        # self.ctx = ctx
        if reagent_lot == None:
            reagent_lot = reagent_type

@@ -41,7 +40,6 @@ class AddReagentForm(QDialog):
        self.name_input.setObjectName("name")
        self.name_input.setEditable(True)
        self.name_input.setCurrentText(reagent_name)
-        # self.name_input.setText(reagent_name)
        self.lot_input = QLineEdit()
        self.lot_input.setObjectName("lot")
        self.lot_input.setText(reagent_lot)
@@ -56,7 +54,6 @@ class AddReagentForm(QDialog):
        # widget to get reagent type info
        self.type_input = QComboBox()
        self.type_input.setObjectName('type')
-        # self.type_input.addItems([item.name for item in lookup_reagent_types(ctx=ctx)])
        self.type_input.addItems([item.name for item in ReagentType.query()])
        logger.debug(f"Trying to find index of {reagent_type}")
        # convert input to user friendly string?
@@ -169,7 +166,13 @@ class FirstStrandSalvage(QDialog):
        self.layout.addWidget(self.buttonBox)
        self.setLayout(self.layout)

-    def parse_form(self):
+    def parse_form(self) -> dict:
+        """
+        Pulls first strand info from form.
+
+        Returns:
+            dict: Output info
+        """              
        return dict(plate=self.rsl_plate_num.text(), submitter_id=self.submitter_id_input.text(), well=f"{self.row_letter.currentText()}{self.column_number.currentText()}")

 class LogParser(QDialog):
@@ -193,9 +196,15 @@ class LogParser(QDialog):


    def filelookup(self):
+        """
+        Select file to search
+        """        
        self.fname = select_open_file(self, "tabular")

    def runsearch(self):
+        """
+        Gets total/percent occurences of string in tabular file.
+        """        
        count: int = 0
        total: int = 0
        logger.debug(f"Current search term: {self.phrase_looker.currentText()}")
--- a/src/submissions/frontend/widgets/pop_ups.py
+++ b/src/submissions/frontend/widgets/pop_ups.py
@@ -47,7 +47,7 @@ class AlertPop(QMessageBox):

 class KitSelector(QDialog):
    """
-    dialog to ask yes/no questions
+    dialog to input KitType manually
    """    
    def __init__(self, title:str, message:str) -> QDialog:
        super().__init__()
@@ -69,12 +69,18 @@ class KitSelector(QDialog):
        self.layout.addWidget(self.buttonBox)
        self.setLayout(self.layout)

-    def getValues(self):
+    def getValues(self) -> str:
+        """
+        Get KitType(str) from widget
+
+        Returns:
+            str: KitType as str
+        """        
        return self.widget.currentText()

 class SubmissionTypeSelector(QDialog):
    """
-    dialog to ask yes/no questions
+    dialog to input SubmissionType manually
    """    
    def __init__(self, title:str, message:str) -> QDialog:
        super().__init__()
@@ -97,5 +103,11 @@ class SubmissionTypeSelector(QDialog):
        self.layout.addWidget(self.buttonBox)
        self.setLayout(self.layout)

-    def parse_form(self):
+    def parse_form(self) -> str:
+        """
+        Pulls SubmissionType(str) from widget
+
+        Returns:
+            str: SubmissionType as str
+        """
        return self.widget.currentText()
--- a/src/submissions/frontend/widgets/submission_details.py
+++ b/src/submissions/frontend/widgets/submission_details.py
@@ -1,25 +1,25 @@
 from PyQt6.QtWidgets import (QDialog, QScrollArea, QPushButton, QVBoxLayout, QMessageBox,
-                             QLabel, QDialogButtonBox, QToolBar, QTextEdit)
-from PyQt6.QtGui import QAction, QPixmap
+                             QDialogButtonBox, QTextEdit)
 from PyQt6.QtWebEngineWidgets import QWebEngineView
 from PyQt6.QtCore import Qt
-from PyQt6 import QtPrintSupport
 from backend.db.models import BasicSubmission
-from ..visualizations import make_plate_barcode, make_plate_map, make_plate_map_html
-from tools import check_if_app, jinja_template_loading
+from tools import check_if_app
 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
 from pprint import pformat
+from html2image import Html2Image
+from PIL import Image
+from typing import List


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

-env = jinja_template_loading()
-
 class SubmissionDetails(QDialog):
    """
    a window showing text details of submission
@@ -27,7 +27,6 @@ class SubmissionDetails(QDialog):
    def __init__(self, parent, sub:BasicSubmission) -> None:

        super().__init__(parent)
-        # self.ctx = ctx
        try:
            self.app = parent.parent().parent().parent().parent().parent().parent()
        except AttributeError:
@@ -36,19 +35,16 @@ class SubmissionDetails(QDialog):
        # create scrollable interior
        interior = QScrollArea()
        interior.setParent(self)
-        # sub = BasicSubmission.query(id=id)
        self.base_dict = sub.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
        del self.base_dict['id']
        logger.debug(f"Creating barcode.")
        if not check_if_app():
-            self.base_dict['barcode'] = base64.b64encode(make_plate_barcode(self.base_dict['Plate Number'], width=120, height=30)).decode('utf-8')
-        logger.debug(f"Hitpicking plate...")
-        self.plate_dicto = sub.hitpick_plate()
+            self.base_dict['barcode'] = base64.b64encode(sub.make_plate_barcode(width=120, height=30)).decode('utf-8')
        logger.debug(f"Making platemap...")
-        self.base_dict['platemap'] = make_plate_map_html(self.plate_dicto)
-        self.template = env.get_template("submission_details.html")
+        self.base_dict['platemap'] = sub.make_plate_map()
+        self.base_dict, self.template = sub.get_details_template(base_dict=self.base_dict)
        self.html = self.template.render(sub=self.base_dict)
        webview = QWebEngineView()
        webview.setMinimumSize(900, 500)
@@ -63,21 +59,29 @@ class SubmissionDetails(QDialog):
        btn.setParent(self)
        btn.setFixedWidth(900)
        btn.clicked.connect(self.export)
-        
+
+           
    def export(self):
        """
        Renders submission to html, then creates and saves .pdf file to user selected file.
        """        
        fname = select_save_file(obj=self, default_name=self.base_dict['Plate Number'], extension="pdf")
-        del self.base_dict['platemap']
-        export_map = make_plate_map(self.plate_dicto)
        image_io = BytesIO()
+        temp_dir = Path(TemporaryDirectory().name)
+        hti = Html2Image(output_path=temp_dir, size=(1200, 750))
+        temp_file = Path(TemporaryFile(dir=temp_dir, suffix=".png").name)
+        screenshot = hti.screenshot(self.base_dict['platemap'], save_as=temp_file.name)
+        export_map = Image.open(screenshot[0])
+        export_map = export_map.convert('RGB')
        try:
            export_map.save(image_io, 'JPEG')
        except AttributeError:
            logger.error(f"No plate map found")
        self.base_dict['export_map'] = base64.b64encode(image_io.getvalue()).decode('utf-8')
+        del self.base_dict['platemap']
        self.html2 = self.template.render(sub=self.base_dict)
+        with open("test.html", "w") as fw:
+            fw.write(self.html2)
        try:
            with open(fname, "w+b") as f:
                pisa.CreatePDF(self.html2, dest=f)
@@ -88,73 +92,6 @@ class SubmissionDetails(QDialog):
            msg.setInformativeText(f"Looks like {fname.__str__()} is open.\nPlease close it and try again.")
            msg.setWindowTitle("Permission Error")
            msg.exec()
-
-class BarcodeWindow(QDialog):
-
-    def __init__(self, rsl_num:str):
-        super().__init__()
-        # set the title
-        self.setWindowTitle("Image")
-        self.layout = QVBoxLayout()
-        # setting  the geometry of window
-        self.setGeometry(0, 0, 400, 300)
-        # creating label
-        self.label = QLabel()
-        self.img = make_plate_barcode(rsl_num)
-        self.pixmap = QPixmap()
-        self.pixmap.loadFromData(self.img)
-        # adding image to label
-        self.label.setPixmap(self.pixmap)
-        # show all the widgets]
-        QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
-        self.buttonBox = QDialogButtonBox(QBtn)
-        self.buttonBox.accepted.connect(self.accept)
-        self.buttonBox.rejected.connect(self.reject)
-        self.layout.addWidget(self.label)
-        self.layout.addWidget(self.buttonBox)
-        self.setLayout(self.layout)
-        self._createActions()
-        self._createToolBar()
-        self._connectActions()
-        
-    def _createToolBar(self):
-        """
-        adds items to menu bar
-        """    
-        toolbar = QToolBar("My main toolbar")
-        toolbar.addAction(self.printAction)
-        
-
-    def _createActions(self):
-        """
-        creates actions
-        """        
-        self.printAction = QAction("&Print", self)
-
-
-    def _connectActions(self):
-        """
-        connect menu and tool bar item to functions
-        """
-        self.printAction.triggered.connect(self.print_barcode)
-
-
-    def print_barcode(self):
-        """
-        Sends barcode image to printer.
-        """        
-        printer = QtPrintSupport.QPrinter()
-        dialog = QtPrintSupport.QPrintDialog(printer)
-        if dialog.exec():
-            self.handle_paint_request(printer, self.pixmap.toImage())
-
-
-    def handle_paint_request(self, printer:QtPrintSupport.QPrinter, im):
-        logger.debug(f"Hello from print handler.")
-        painter = QPainter(printer)
-        image = QPixmap.fromImage(im)
-        painter.drawPixmap(120, -20, image)
-        painter.end()
        
 class SubmissionComment(QDialog):
    """
@@ -163,7 +100,6 @@ class SubmissionComment(QDialog):
    def __init__(self, parent, submission:BasicSubmission) -> None:

        super().__init__(parent)
-        # self.ctx = ctx
        try:
            self.app = parent.parent().parent().parent().parent().parent().parent
            print(f"App: {self.app}")
@@ -185,7 +121,7 @@ class SubmissionComment(QDialog):
        self.layout.addWidget(self.buttonBox, alignment=Qt.AlignmentFlag.AlignBottom)
        self.setLayout(self.layout)
        
-    def parse_form(self):
+    def parse_form(self) -> List[dict]:
        """
        Adds comment to submission object.
        """        
--- a/src/submissions/frontend/widgets/submission_table.py
+++ b/src/submissions/frontend/widgets/submission_table.py
@@ -1,37 +1,22 @@
 '''
 Contains widgets specific to the submission summary and submission details.
 '''
-import base64, logging, json
-from datetime import datetime
-from io import BytesIO
+import logging, json
 from pprint import pformat
-from PyQt6 import QtPrintSupport
-from PyQt6.QtWidgets import (
-    QVBoxLayout, QDialog, QTableView,
-    QTextEdit, QPushButton, QScrollArea, 
-    QMessageBox, QMenu, QLabel,
-    QDialogButtonBox, QToolBar
-)
-from PyQt6.QtWebEngineWidgets import QWebEngineView
+from PyQt6.QtWidgets import QTableView, QMenu
 from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel
-from PyQt6.QtGui import QAction, QCursor, QPixmap, QPainter
-from backend.db.models import BasicSubmission, Equipment
+from PyQt6.QtGui import QAction, QCursor
+from backend.db.models import BasicSubmission
 from backend.excel import make_report_html, make_report_xlsx
-from tools import check_if_app, Report, Result, jinja_template_loading, get_first_blank_df_row, row_map
+from tools import Report, Result, get_first_blank_df_row, row_map
 from xhtml2pdf import pisa
-from .pop_ups import QuestionAsker
-from .equipment_usage import EquipmentUsage
-from ..visualizations import make_plate_barcode, make_plate_map, make_plate_map_html
 from .functions import select_save_file, select_open_file
 from .misc import ReportDatePicker
 import pandas as pd
 from openpyxl.worksheet.worksheet import Worksheet
-from getpass import getuser

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

-env = jinja_template_loading()
-
 class pandasModel(QAbstractTableModel):
    """
    pandas model for inserting summary sheet into gui
@@ -89,20 +74,17 @@ class SubmissionsSheet(QTableView):
        """        
        super().__init__(parent)
        self.app = self.parent()
-        # self.ctx = ctx
        self.report = Report()
        self.setData()
        self.resizeColumnsToContents()
        self.resizeRowsToContents()
        self.setSortingEnabled(True)
-        # self.doubleClicked.connect(self.show_details)
        self.doubleClicked.connect(lambda x: BasicSubmission.query(id=x.sibling(x.row(), 0).data()).show_details(self))
 
    def setData(self) -> None: 
        """
        sets data in model
        """        
-        # self.data = submissions_to_df()
        self.data = BasicSubmission.submissions_to_df()
        try:
            self.data['id'] = self.data['id'].apply(str)
@@ -114,39 +96,6 @@ class SubmissionsSheet(QTableView):
        proxyModel.setSourceModel(pandasModel(self.data))
        self.setModel(proxyModel)
        
-    # def show_details(self, submission:BasicSubmission) -> None:
-    #     """
-    #     creates detailed data to show in seperate window
-    #     """        
-    #     logger.debug(f"Sheet.app: {self.app}")
-    #     # index = (self.selectionModel().currentIndex())
-    #     # value = index.sibling(index.row(),0).data()
-    #     dlg = SubmissionDetails(parent=self, sub=submission)
-    #     if dlg.exec():
-    #         pass  
-
-    def create_barcode(self) -> None:
-        """
-        Generates a window for displaying barcode
-        """        
-        index = (self.selectionModel().currentIndex())
-        value = index.sibling(index.row(),1).data()
-        logger.debug(f"Selected value: {value}")
-        dlg = BarcodeWindow(value)
-        if dlg.exec():
-            dlg.print_barcode()
-
-    def add_comment(self) -> None:
-        """
-        Generates a text editor window.
-        """        
-        index = (self.selectionModel().currentIndex())
-        value = index.sibling(index.row(),1).data()
-        logger.debug(f"Selected value: {value}")
-        dlg = SubmissionComment(parent=self, rsl=value)
-        if dlg.exec():
-            dlg.add_comment()
-
    def contextMenuEvent(self, event):
        """
        Creates actions for right click menu events.
@@ -158,21 +107,6 @@ class SubmissionsSheet(QTableView):
        id = id.sibling(id.row(),0).data()
        submission = BasicSubmission.query(id=id)
        self.menu = QMenu(self)
-        # renameAction = QAction('Delete', self)
-        # detailsAction = QAction('Details', self)
-        # commentAction = QAction("Add Comment", self)
-        # equipAction = QAction("Add Equipment", self)
-        # backupAction = QAction("Export", self)
-        # renameAction.triggered.connect(lambda: self.delete_item(submission))
-        # detailsAction.triggered.connect(lambda: self.show_details(submission))
-        # commentAction.triggered.connect(lambda: self.add_comment(submission))
-        # backupAction.triggered.connect(lambda: self.regenerate_submission_form(submission))
-        # equipAction.triggered.connect(lambda: self.add_equipment(submission))
-        # self.menu.addAction(detailsAction)
-        # self.menu.addAction(renameAction)
-        # self.menu.addAction(commentAction)
-        # self.menu.addAction(backupAction)
-        # self.menu.addAction(equipAction)
        self.con_actions = submission.custom_context_events()
        for k in self.con_actions.keys():
            logger.debug(f"Adding {k}")
@@ -183,57 +117,21 @@ class SubmissionsSheet(QTableView):
        self.menu.popup(QCursor.pos())

    def triggered_action(self, action_name:str):
+        """
+        Calls the triggered action from the context menu
+
+        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)

-    def add_equipment(self):
-        index = (self.selectionModel().currentIndex())
-        value = index.sibling(index.row(),0).data()
-        self.add_equipment_function(rsl_plate_id=value)
-
-    def add_equipment_function(self, submission:BasicSubmission):
-        # submission = BasicSubmission.query(id=rsl_plate_id)
-        submission_type = submission.submission_type_name
-        dlg = EquipmentUsage(parent=self, submission_type=submission_type, submission=submission)
-        if dlg.exec():
-            equipment = dlg.parse_form()
-            logger.debug(f"We've got equipment: {equipment}")
-            for equip in equipment:
-                e = Equipment.query(name=equip.name)
-                # assoc = SubmissionEquipmentAssociation(submission=submission, equipment=e)
-                # process = Process.query(name=equip.processes)
-                # assoc.process = process
-                # assoc.role = equip.role
-                _, assoc = equip.toSQL(submission=submission)
-                # submission.submission_equipment_associations.append(assoc)
-                logger.debug(f"Appending SubmissionEquipmentAssociation: {assoc}")
-                # submission.save()
-                assoc.save()
-        else:
-            pass
-
-    def delete_item(self, submission:BasicSubmission):
-        """
-        Confirms user deletion and sends id to backend for deletion.
-
-        Args:
-            event (_type_): the item of interest
-        """        
-        # index = (self.selectionModel().currentIndex())
-        # value = index.sibling(index.row(),0).data()
-        # logger.debug(index)
-        # msg = QuestionAsker(title="Delete?", message=f"Are you sure you want to delete {index.sibling(index.row(),1).data()}?\n")
-        msg = QuestionAsker(title="Delete?", message=f"Are you sure you want to delete {submission.rsl_plate_num}?\n")
-        if msg.exec():
-            # delete_submission(id=value)
-            submission.delete()
-        else:
-            return
-        self.setData()
-
    def link_extractions(self):
+        """
+        Pull extraction logs into the db
+        """        
        self.link_extractions_function()
        self.app.report.add_result(self.report)
        self.report = Report()
@@ -306,6 +204,9 @@ class SubmissionsSheet(QTableView):
        self.report.add_result(Result(msg=f"We added {count} logs to the database.", status='Information'))

    def link_pcr(self):
+        """
+        Pull pcr logs into the db
+        """        
        self.link_pcr_function()
        self.app.report.add_result(self.report)
        self.report = Report()
@@ -376,6 +277,9 @@ class SubmissionsSheet(QTableView):
        self.report.add_result(Result(msg=f"We added {count} logs to the database.", status='Information'))
        
    def generate_report(self):
+        """
+        Make a report
+        """        
        self.generate_report_function()
        self.app.report.add_result(self.report)
        self.report = Report()
@@ -436,12 +340,3 @@ class SubmissionsSheet(QTableView):
                    cell.style = 'Currency'
            writer.close()
        self.report.add_result(report)
-
-    def regenerate_submission_form(self, submission:BasicSubmission):
-        # index = (self.selectionModel().currentIndex())
-        # value = index.sibling(index.row(),0).data()
-        # logger.debug(index)
-        # sub = BasicSubmission.query(id=value)
-        fname = select_save_file(self, default_name=submission.to_pydantic().construct_filename(), extension="xlsx")
-        submission.backup(fname=fname, full_backup=False)
-
--- a/src/submissions/frontend/widgets/submission_type_creator.py
+++ b/src/submissions/frontend/widgets/submission_type_creator.py
@@ -2,21 +2,14 @@ from PyQt6.QtCore import Qt
 from PyQt6.QtWidgets import (
    QWidget, QVBoxLayout, QScrollArea,
    QGridLayout, QPushButton, QLabel,
-    QLineEdit, QComboBox, QDoubleSpinBox,
-    QSpinBox, QDateEdit
+    QLineEdit, QSpinBox
 )
-from sqlalchemy import FLOAT, INTEGER
 from sqlalchemy.orm.attributes import InstrumentedAttribute
-from backend.db import SubmissionType, Equipment, SubmissionTypeEquipmentRoleAssociation, BasicSubmission
-from backend.validators import PydReagentType, PydKit
+from backend.db import SubmissionType, BasicSubmission
 import logging
-from pprint import pformat
 from tools import Report
-from typing import Tuple
 from .functions import select_open_file

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

 class SubmissionTypeAdder(QWidget):
@@ -46,35 +39,21 @@ class SubmissionTypeAdder(QWidget):
        self.grid.addWidget(template_selector,3,1)
        self.template_label = QLabel("None")
        self.grid.addWidget(self.template_label,3,2)
-        # self.grid.addWidget(QLabel("Used For Submission Type:"),3,0)
        # 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}
        for iii, key in enumerate(self.columns):
            idx = iii + 4
-            # convert field name to human readable.
-            # field_name = key
-            # self.grid.addWidget(QLabel(field_name),idx,0)
-            # print(self.columns[key].type)
-            # match self.columns[key].type:
-            #     case FLOAT():
-            #         add_widget = QDoubleSpinBox()
-            #         add_widget.setMinimum(0)
-            #         add_widget.setMaximum(9999)
-            #     case INTEGER():
-            #         add_widget = QSpinBox()
-            #         add_widget.setMinimum(0)
-            #         add_widget.setMaximum(9999)
-            #     case _:
-            #         add_widget = QLineEdit()
-            # add_widget.setObjectName(key)
            self.grid.addWidget(InfoWidget(parent=self, key=key), idx,0,1,3)
        scroll.setWidget(scrollContent)
        self.submit_btn.clicked.connect(self.submit)
        template_selector.clicked.connect(self.get_template_path)

    def submit(self):
+        """
+        Create SubmissionType and send to db
+        """        
        info = self.parse_form()
        ST = SubmissionType(name=self.st_name.text(), info_map=info)
        try:
@@ -84,11 +63,20 @@ class SubmissionTypeAdder(QWidget):
            logger.error(f"Could not find template file: {self.template_path}")
        ST.save(ctx=self.app.ctx)

-    def parse_form(self):
+    def parse_form(self) -> dict:
+        """
+        Pulls info from form
+
+        Returns:
+            dict: information from form
+        """        
        widgets = [widget for widget in self.findChildren(QWidget) if isinstance(widget, InfoWidget)]
        return {widget.objectName():widget.parse_form() for widget in widgets}
    
    def get_template_path(self):
+        """
+        Sets path for loading a submission form template
+        """        
        self.template_path = select_open_file(obj=self, file_extension="xlsx")
        self.template_label.setText(self.template_path.__str__())

@@ -113,7 +101,13 @@ class InfoWidget(QWidget):
        self.column.setObjectName("column")
        grid.addWidget(self.column,2,3)

-    def parse_form(self):
+    def parse_form(self) -> dict:
+        """
+        Pulls info from the Info form.
+
+        Returns:
+            dict: sheets, row, column
+        """        
        return dict(
            sheets = self.sheet.text().split(","),
            row = self.row.value(),
--- a/src/submissions/frontend/widgets/submission_widget.py
+++ b/src/submissions/frontend/widgets/submission_widget.py
@@ -5,7 +5,7 @@ from PyQt6.QtWidgets import (
 from PyQt6.QtCore import pyqtSignal
 from pathlib import Path
 from . import select_open_file, select_save_file
-import logging, difflib, inspect, json, sys
+import logging, difflib, inspect, json
 from pathlib import Path
 from tools import Report, Result, check_not_nan
 from backend.excel.parser import SheetParser, PCRParser
@@ -16,7 +16,6 @@ from backend.db import (
 )
 from pprint import pformat
 from .pop_ups import QuestionAsker, AlertPop
-# from .misc import ReagentFormWidget
 from typing import List, Tuple
 from datetime import date

@@ -24,6 +23,7 @@ logger = logging.getLogger(f"submissions.{__name__}")

 class SubmissionFormContainer(QWidget):

+    # A signal carrying a path 
    import_drag = pyqtSignal(Path)

    def __init__(self, parent: QWidget) -> None:
@@ -31,19 +31,24 @@ class SubmissionFormContainer(QWidget):
        super().__init__(parent)
        self.app = self.parent().parent()
        self.report = Report()
-        # self.parent = parent
        self.setAcceptDrops(True)
+        # if import_drag is emitted, importSubmission will fire
        self.import_drag.connect(self.importSubmission)

    def dragEnterEvent(self, event):
+        """
+        Allow drag if file.
+        """        
        if event.mimeData().hasUrls():
            event.accept()
        else:
            event.ignore()

    def dropEvent(self, event):
+        """
+        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)
@@ -52,7 +57,6 @@ class SubmissionFormContainer(QWidget):
        """
        import submission from excel sheet into form
        """        
-        # from .main_window_functions import import_submission_function
        self.app.raise_()
        self.app.activateWindow()
        self.import_submission_function(fname)
@@ -62,6 +66,9 @@ class SubmissionFormContainer(QWidget):
        self.app.result_reporter()

    def scrape_reagents(self, *args, **kwargs):
+        """
+        Called when a reagent is changed.
+        """        
        caller = inspect.stack()[1].function.__repr__().replace("'", "")
        logger.debug(f"Args: {args}, kwargs: {kwargs}")
        self.scrape_reagents_function(args[0], caller=caller)
@@ -80,7 +87,6 @@ class SubmissionFormContainer(QWidget):
        NOTE: this will not change self.reagents which should be fine
        since it's only used when looking up 
        """        
-        # from .main_window_functions import kit_integrity_completion_function
        self.kit_integrity_completion_function()
        self.app.report.add_result(self.report)
        self.report = Report()
@@ -94,14 +100,12 @@ class SubmissionFormContainer(QWidget):
        """
        Attempt to add sample to database when 'submit' button clicked
        """        
-        # from .main_window_functions import submit_new_sample_function
        self.submit_new_sample_function()
        self.app.report.add_result(self.report)
        self.report = Report()
        self.app.result_reporter()

    def export_csv(self, fname:Path|None=None):
-        # from .main_window_functions import export_csv_function
        self.export_csv_function(fname)

    def import_submission_function(self, fname:Path|None=None):
@@ -116,12 +120,11 @@ class SubmissionFormContainer(QWidget):
        """    
        logger.debug(f"\n\nStarting Import...\n\n")
        report = Report()
-        # logger.debug(obj.ctx)
-        # initialize samples
        try:
            self.form.setParent(None)
        except AttributeError:
            pass
+        # initialize samples
        self.samples = []
        self.missing_info = []
        # set file dialog
@@ -129,7 +132,6 @@ class SubmissionFormContainer(QWidget):
            fname = select_open_file(self, file_extension="xlsx")
        logger.debug(f"Attempting to parse file: {fname}")
        if not fname.exists():
-            # result = dict(message=f"File {fname.__str__()} not found.", status="critical")
            report.add_result(Result(msg=f"File {fname.__str__()} not found.", status="critical"))
            self.report.add_result(report)
            return
@@ -141,14 +143,9 @@ class SubmissionFormContainer(QWidget):
            return
        except AttributeError:
            self.prsr = SheetParser(ctx=self.app.ctx, filepath=fname)
-        # try:
        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")
-        # except Exception as e:
-        #     report.add_result(Result(msg=f"Problem creating pydantic model:\n\n{e}", status="Critical"))
-        #     self.report.add_result(report)
-        #     return
        self.form = self.pyd.toForm(parent=self)
        self.layout().addWidget(self.form)
        kit_widget = self.form.find_widgets(object_name="extraction_kit")[0].input
@@ -176,11 +173,8 @@ class SubmissionFormContainer(QWidget):
        """    
        self.form.reagents = []
        logger.debug(f"\n\n{caller}\n\n")
-        # assert caller == "import_submission_function"
        report = Report()
        logger.debug(f"Extraction kit: {extraction_kit}")
-        # obj.reagents = []
-        # obj.missing_reagents = []
        # Remove previous reagent widgets
        try:
            old_reagents = self.form.find_widgets()
@@ -191,14 +185,6 @@ class SubmissionFormContainer(QWidget):
        for reagent in old_reagents:
            if isinstance(reagent, ReagentFormWidget) or isinstance(reagent, QPushButton):
                reagent.setParent(None)
-        # reagents = obj.prsr.parse_reagents(extraction_kit=extraction_kit)
-        # logger.debug(f"Got reagents: {reagents}")
-        # for reagent in obj.prsr.sub['reagents']:
-        #     # create label
-        #     if reagent.parsed:
-        #         obj.reagents.append(reagent)
-        #     else:
-        #         obj.missing_reagents.append(reagent)
        match caller:
            case "import_submission_function":
                self.form.reagents = self.prsr.sub['reagents']
@@ -231,11 +217,9 @@ class SubmissionFormContainer(QWidget):
        logger.debug(f"Kit selector: {kit_widget}")
        # get current kit being used
        self.ext_kit = kit_widget.currentText()
-        # for reagent in obj.pyd.reagents:
        for reagent in self.form.reagents:
            logger.debug(f"Creating widget for {reagent}")
            add_widget = ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.ext_kit)
-            # add_widget.setParent(sub_form_container.form)
            self.form.layout().addWidget(add_widget)
            if reagent.missing:
                missing_reagents.append(reagent)
@@ -275,7 +259,6 @@ class SubmissionFormContainer(QWidget):
        self.pyd: PydSubmission = self.form.parse_form()
        logger.debug(f"Submission: {pformat(self.pyd)}")
        logger.debug("Checking kit integrity...")
-        # result = check_kit_integrity(sub=self.pyd)
        result = self.pyd.check_kit_integrity()
        report.add_result(result)
        if len(result.results) > 0:
@@ -283,7 +266,6 @@ class SubmissionFormContainer(QWidget):
            return
        base_submission, result = self.pyd.toSQL()
        # logger.debug(f"Base submission: {base_submission.to_dict()}")
-        # sys.exit()
        # check output message for issues
        match result.code:
            # code 0: everything is fine.
@@ -309,9 +291,7 @@ class SubmissionFormContainer(QWidget):
        # add reagents to submission object
        for reagent in base_submission.reagents:
            # logger.debug(f"Updating: {reagent} with {reagent.lot}")
-            # update_last_used(reagent=reagent, kit=base_submission.extraction_kit)
            reagent.update_last_used(kit=base_submission.extraction_kit)
-        # sys.exit()
        # logger.debug(f"Here is the final submission: {pformat(base_submission.__dict__)}")
        # logger.debug(f"Parsed reagents: {pformat(base_submission.reagents)}")    
        # logger.debug(f"Sending submission: {base_submission.rsl_plate_num} to database.")
@@ -324,24 +304,15 @@ class SubmissionFormContainer(QWidget):
        # reset form
        self.form.setParent(None)
        # logger.debug(f"All attributes of obj: {pformat(self.__dict__)}")
-        # wkb = self.pyd.autofill_excel()
-        # if wkb != None:
-        #     fname = select_save_file(obj=self, default_name=self.pyd.construct_filename(), extension="xlsx")
-        #     try:
-        #         wkb.save(filename=fname.__str__())
-        #     except PermissionError:
-        #         logger.error("Hit a permission error when saving workbook. Cancelled?")
-        # if hasattr(self.pyd, 'csv'):
-        #     dlg = QuestionAsker("Export CSV?", "Would you like to export the csv file?")
-        #     if dlg.exec():
-        #         fname = select_save_file(self, f"{self.pyd.construct_filename()}.csv", extension="csv")
-        #         try:
-        #             self.pyd.csv.to_csv(fname.__str__(), index=False)
-        #         except PermissionError:
-        #             logger.debug(f"Could not get permissions to {fname}. Possibly the request was cancelled.")
        self.report.add_result(report)

    def export_csv_function(self, fname:Path|None=None):
+        """
+        Save the submission's csv file.
+
+        Args:
+            fname (Path | None, optional): Input filename. Defaults to None.
+        """        
        if isinstance(fname, bool) or fname == None:
            fname = select_save_file(obj=self, default_name=self.pyd.construct_filename(), extension="csv")
        try:
@@ -351,6 +322,9 @@ class SubmissionFormContainer(QWidget):
            logger.debug(f"Could not get permissions to {fname}. Possibly the request was cancelled.")

    def import_pcr_results(self):
+        """
+        Pull QuantStudio results into db
+        """        
        self.import_pcr_results_function()
        self.app.report.add_result(self.report)
        self.report = Report()
@@ -370,7 +344,6 @@ class SubmissionFormContainer(QWidget):
        fname = select_open_file(self, file_extension="xlsx")
        parser = PCRParser(filepath=fname)
        logger.debug(f"Attempting lookup for {parser.plate_num}")
-        # sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=parser.plate_num)
        sub = BasicSubmission.query(rsl_number=parser.plate_num)
        try:
            logger.debug(f"Found submission: {sub.rsl_plate_num}")
@@ -378,14 +351,11 @@ class SubmissionFormContainer(QWidget):
            # If no plate is found, may be because this is a repeat. Lop off the '-1' or '-2' and repeat
            logger.error(f"Submission of number {parser.plate_num} not found. Attempting rescue of plate repeat.")
            parser.plate_num = "-".join(parser.plate_num.split("-")[:-1])
-            # sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=parser.plate_num)
-            # sub = lookup_submissions(ctx=obj.ctx, rsl_number=parser.plate_num)
            sub = BasicSubmission.query(rsl_number=parser.plate_num)
            try:
                logger.debug(f"Found submission: {sub.rsl_plate_num}")
            except AttributeError:
                logger.error(f"Rescue of {parser.plate_num} failed.")
-                # return obj, dict(message="Couldn't find a submission with that RSL number.", status="warning")
                self.report.add_result(Result(msg="Couldn't find a submission with that RSL number.", status="Warning"))
                return
        # Check if PCR info already exists
@@ -407,7 +377,6 @@ class SubmissionFormContainer(QWidget):
            logger.debug(f"Final pcr info for {sub.rsl_plate_num}: {sub.pcr_info}")
        else:
            sub.pcr_info = json.dumps([parser.pcr])
-        # obj.ctx.database_session.add(sub)
        logger.debug(f"Existing {type(sub.pcr_info)}: {sub.pcr_info}")
        logger.debug(f"Inserting {type(json.dumps(parser.pcr))}: {json.dumps(parser.pcr)}")
        sub.save(original=False)
@@ -419,18 +388,13 @@ class SubmissionFormContainer(QWidget):
                sample_dict = [item for item in parser.samples if item['sample']==sample.rsl_number][0]
            except IndexError:
                continue
-            # update_subsampassoc_with_pcr(submission=sub, sample=sample, input_dict=sample_dict)
            sub.update_subsampassoc(sample=sample, input_dict=sample_dict)
        self.report.add_result(Result(msg=f"We added PCR info to {sub.rsl_plate_num}.", status='Information'))
-        # return obj, result

 class SubmissionFormWidget(QWidget):

    def __init__(self, parent: QWidget, **kwargs) -> None:
        super().__init__(parent)
-        # self.ignore = [None, "", "qt_spinbox_lineedit", "qt_scrollarea_viewport", "qt_scrollarea_hcontainer",
-        #                "qt_scrollarea_vcontainer", "submit_btn"
-        #                ]
        self.ignore = ['filepath', 'samples', 'reagents', 'csv', 'ctx', 'comment', 'equipment']
        self.recover = ['filepath', 'samples', 'csv', 'comment', 'equipment']
        layout = QVBoxLayout()
@@ -441,25 +405,53 @@ class SubmissionFormWidget(QWidget):
                    layout.addWidget(add_widget)
            else:
                setattr(self, k, v)
-        
        self.setLayout(layout)

-    def create_widget(self, key:str, value:dict, submission_type:str|None=None):
+    def create_widget(self, key:str, value:dict, submission_type:str|None=None) -> "self.InfoItem":
+        """
+        Make an InfoItem widget to hold a field
+
+        Args:
+            key (str): Name of the field
+            value (dict): Value of field
+            submission_type (str | None, optional): Submissiontype as str. Defaults to None.
+
+        Returns:
+            self.InfoItem: Form widget to hold name:value
+        """        
        if key not in self.ignore:
            return self.InfoItem(self, key=key, value=value, submission_type=submission_type)
        return None
        
    def clear_form(self):
+        """
+        Removes all form widgets
+        """        
        for item in self.findChildren(QWidget):
            item.setParent(None)

    def find_widgets(self, object_name:str|None=None) -> List[QWidget]:
+        """
+        Gets all widgets filtered by object name
+
+        Args:
+            object_name (str | None, optional): name to filter by. Defaults to None.
+
+        Returns:
+            List[QWidget]: Widgets matching filter
+        """        
        query = self.findChildren(QWidget)
        if object_name != None:
            query = [widget for widget in query if widget.objectName()==object_name]
        return query
    
    def parse_form(self) -> PydSubmission:
+        """
+        Transforms form info into PydSubmission
+
+        Returns:
+            PydSubmission: Pydantic submission object 
+        """        
        logger.debug(f"Hello from form parser!")
        info = {}
        reagents = []
@@ -483,8 +475,6 @@ class SubmissionFormWidget(QWidget):
                value = getattr(self, item)
                logger.debug(f"Setting {item}")
                info[item] = value
-        # app = self.parent().parent().parent().parent().parent().parent().parent().parent
-        # submission = PydSubmission(filepath=self.filepath, reagents=reagents, samples=self.samples, **info)
        submission = PydSubmission(reagents=reagents, **info)
        return submission
    
@@ -513,7 +503,13 @@ class SubmissionFormWidget(QWidget):
                case QLineEdit():
                    self.input.textChanged.connect(self.update_missing)
            
-        def parse_form(self):
+        def parse_form(self) -> Tuple[str, dict]:
+            """
+            Pulls info from widget into dict
+
+            Returns:
+                Tuple[str, dict]: name of field, {value, missing}
+            """
            match self.input:
                case QLineEdit():
                    value = self.input.text()
@@ -526,6 +522,18 @@ class SubmissionFormWidget(QWidget):
            return self.input.objectName(), dict(value=value, missing=self.missing)
        
        def set_widget(self, parent: QWidget, key:str, value:dict, submission_type:str|None=None) -> QWidget:
+            """
+            Creates form widget
+
+            Args:
+                parent (QWidget): parent widget
+                key (str): name of field
+                value (dict): value, and is it missing from scrape
+                submission_type (str | None, optional): SubmissionType as str. Defaults to None.
+
+            Returns:
+                QWidget: Form object
+            """            
            try:
                value = value['value']
            except (TypeError, KeyError):
@@ -565,7 +573,6 @@ class SubmissionFormWidget(QWidget):
                        obj.ext_kit = uses[0]
                    add_widget.addItems(uses)
                    # Run reagent scraper whenever extraction kit is changed.
-                    # add_widget.currentTextChanged.connect(obj.scrape_reagents)
                case 'submitted_date':
                    # uses base calendar
                    add_widget = QDateEdit(calendarPopup=True)
@@ -578,7 +585,6 @@ class SubmissionFormWidget(QWidget):
                case 'submission_category':
                    add_widget = QComboBox()
                    cats = ['Diagnostic', "Surveillance", "Research"]
-                    # cats += [item.name for item in lookup_submission_type(ctx=obj.ctx)]
                    cats += [item.name for item in SubmissionType.query()]
                    try:
                        cats.insert(0, cats.pop(cats.index(value)))
@@ -593,10 +599,12 @@ class SubmissionFormWidget(QWidget):
            if add_widget != None:
                add_widget.setObjectName(key)
                add_widget.setParent(parent)
-                
            return add_widget
            
        def update_missing(self):
+            """
+            Set widget status to updated
+            """            
            self.missing = True
            self.label.updated(self.objectName())

@@ -622,6 +630,13 @@ class SubmissionFormWidget(QWidget):
                    self.setText(f"MISSING {output}")

            def updated(self, key:str, title:bool=True):
+                """
+                Mark widget as updated
+
+                Args:
+                    key (str): Name of the field
+                    title (bool, optional): Use title case. Defaults to True.
+                """                
                if title:
                    output = key.replace('_', ' ').title()
                else:
@@ -632,12 +647,9 @@ class ReagentFormWidget(QWidget):

    def __init__(self, parent:QWidget, reagent:PydReagent, extraction_kit:str):
        super().__init__(parent)
-        # self.setParent(parent)
        self.app = self.parent().parent().parent().parent().parent().parent().parent().parent()
-        
        self.reagent = reagent
        self.extraction_kit = extraction_kit
-        # self.ctx = reagent.ctx
        layout = QVBoxLayout()
        self.label = self.ReagentParsedLabel(reagent=reagent)
        layout.addWidget(self.label)
@@ -652,14 +664,18 @@ class ReagentFormWidget(QWidget):
        self.lot.currentTextChanged.connect(self.updated)

    def parse_form(self) -> Tuple[PydReagent, dict]:
+        """
+        Pulls form info into PydReagent
+
+        Returns:
+            Tuple[PydReagent, dict]: PydReagent and Report(?)
+        """        
        lot = self.lot.currentText()
-        # wanted_reagent = lookup_reagents(ctx=self.ctx, lot_number=lot, reagent_type=self.reagent.type)
        wanted_reagent = Reagent.query(lot_number=lot, reagent_type=self.reagent.type)
        # if reagent doesn't exist in database, off 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():
-                print(self.app)
                wanted_reagent = self.app.add_reagent(reagent_lot=lot, reagent_type=self.reagent.type, expiry=self.reagent.expiry, name=self.reagent.name)
                return wanted_reagent, None
            else:
@@ -669,15 +685,15 @@ class ReagentFormWidget(QWidget):
        else:
            # Since this now gets passed in directly from the parser -> pyd -> form and the parser gets the name
            # from the db, it should no longer be necessary to query the db with reagent/kit, but with rt name directly.
-            # rt = lookup_reagent_types(ctx=self.ctx, name=self.reagent.type)
-            # rt = lookup_reagent_types(ctx=self.ctx, kit_type=self.extraction_kit, reagent=wanted_reagent)
            rt = ReagentType.query(name=self.reagent.type)
            if rt == None:
-                # rt = lookup_reagent_types(ctx=self.ctx, kit_type=self.extraction_kit, reagent=wanted_reagent)
                rt = ReagentType.query(kit_type=self.extraction_kit, reagent=wanted_reagent)
            return PydReagent(name=wanted_reagent.name, lot=wanted_reagent.lot, type=rt.name, expiry=wanted_reagent.expiry, parsed=not self.missing), None

    def updated(self):
+        """
+        Set widget status to updated
+        """        
        self.missing = True
        self.label.updated(self.reagent.type)

@@ -696,19 +712,21 @@ class ReagentFormWidget(QWidget):
                self.setText(f"MISSING {reagent.type}")
        
        def updated(self, reagent_type:str):
+            """
+            Marks widget as updated
+
+            Args:
+                reagent_type (str): _description_
+            """            
            self.setText(f"UPDATED {reagent_type}")

    class ReagentLot(QComboBox):

        def __init__(self, reagent, extraction_kit:str) -> None:
            super().__init__()
-            # self.ctx = reagent.ctx
            self.setEditable(True)
-            # if reagent.parsed:
-            #     pass
            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.
-            # lookup = lookup_reagents(ctx=self.ctx, reagent_type=reagent.type)
            lookup = Reagent.query(reagent_type=reagent.type)
            relevant_reagents = [str(item.lot) for item in lookup]
            output_reg = []
@@ -726,11 +744,8 @@ class ReagentFormWidget(QWidget):
                if check_not_nan(reagent.lot):
                    relevant_reagents.insert(0, str(reagent.lot))
                else:
-                    # TODO: look up the last used reagent of this type in the database
-                    # looked_up_rt = lookup_reagenttype_kittype_association(ctx=self.ctx, reagent_type=reagent.type, kit_type=extraction_kit)
                    looked_up_rt = KitTypeReagentTypeAssociation.query(reagent_type=reagent.type, kit_type=extraction_kit)
                    try:
-                        # looked_up_reg = lookup_reagents(ctx=self.ctx, lot_number=looked_up_rt.last_used)
                        looked_up_reg = Reagent.query(lot_number=looked_up_rt.last_used)
                    except AttributeError:
                        looked_up_reg = None
@@ -752,4 +767,3 @@ class ReagentFormWidget(QWidget):
            logger.debug(f"New relevant reagents: {relevant_reagents}")
            self.setObjectName(f"lot_{reagent.type}")
            self.addItems(relevant_reagents)
-