Large scale refactor to improve db efficiency

src/submissions/frontend/__init__.py

@@ -12,9 +12,8 @@ from PyQt6.QtGui import QAction
 from PyQt6.QtWebEngineWidgets import QWebEngineView
 from pathlib import Path
 from backend.db import (
-    construct_reagent, get_all_Control_Types_names, get_all_available_modes, store_reagent 
+    construct_reagent, store_object, lookup_control_types, lookup_modes
 )
-# from .main_window_functions import *
 from .all_window_functions import extract_form_info
 from tools import check_if_app, Settings
 from frontend.custom_widgets import SubmissionsSheet, AlertPop, AddReagentForm, KitAdder, ControlsDatePicker
@@ -63,7 +62,7 @@ class App(QMainWindow):
         menuBar = self.menuBar()
         fileMenu = menuBar.addMenu("&File")
         # Creating menus using a title
-        editMenu = menuBar.addMenu("&Edit")
+        # editMenu = menuBar.addMenu("&Edit")
         methodsMenu = menuBar.addMenu("&Methods")
         reportMenu = menuBar.addMenu("&Reports")
         maintenanceMenu = menuBar.addMenu("&Monthly")
@@ -213,13 +212,12 @@ class App(QMainWindow):
         if dlg.exec():
             # extract form info
             info = extract_form_info(dlg)
-            logger.debug(f"dictionary from form: {info}")
-            # return None
             logger.debug(f"Reagent info: {info}")
             # create reagent object
             reagent = construct_reagent(ctx=self.ctx, info_dict=info)
             # send reagent to db
-            store_reagent(ctx=self.ctx, reagent=reagent)
+            # store_reagent(ctx=self.ctx, reagent=reagent)
+            result = store_object(ctx=self.ctx, object=reagent)
             return reagent
 
     def generateReport(self):
@@ -302,6 +300,14 @@ class App(QMainWindow):
         self, result = construct_first_strand_function(self)
         self.result_reporter(result)
 
+    def scrape_reagents(self, *args, **kwargs):
+        from .main_window_functions import scrape_reagents
+        logger.debug(f"Args: {args}")
+        logger.debug(F"kwargs: {kwargs}")
+        self, result = scrape_reagents(self, args[0])
+        self.kit_integrity_completion()
+        self.result_reporter(result)
+
 class AddSubForm(QWidget):
     
     def __init__(self, parent):
@@ -348,11 +354,13 @@ class AddSubForm(QWidget):
         self.tab2.layout = QVBoxLayout(self)
         self.control_typer = QComboBox()
         # fetch types of controls 
-        con_types = get_all_Control_Types_names(ctx=parent.ctx)
+        # con_types = get_all_Control_Types_names(ctx=parent.ctx)
+        con_types = [item.name for item in lookup_control_types(ctx=parent.ctx)]
         self.control_typer.addItems(con_types)
         # create custom widget to get types of analysis
         self.mode_typer = QComboBox()
-        mode_types = get_all_available_modes(ctx=parent.ctx)
+        # mode_types = get_all_available_modes(ctx=parent.ctx)
+        mode_types = lookup_modes(ctx=parent.ctx)
         self.mode_typer.addItems(mode_types)
         # create custom widget to get subtypes of analysis
         self.sub_typer = QComboBox()

src/submissions/frontend/all_window_functions.py

@@ -22,14 +22,12 @@ def select_open_file(obj:QMainWindow, file_extension:str) -> Path:
     Returns:
         Path: Path of file to be opened
     """    
-    # home_dir = str(Path(obj.ctx["directory_path"]))
     try:
         home_dir = Path(obj.ctx.directory_path).resolve().__str__()
     except FileNotFoundError:
         home_dir = Path.home().resolve().__str__()
     fname = Path(QFileDialog.getOpenFileName(obj, 'Open file', home_dir, filter = f"{file_extension}(*.{file_extension})")[0])
     # fname = Path(QFileDialog.getOpenFileName(obj, 'Open file', filter = f"{file_extension}(*.{file_extension})")[0])
-
     return fname
 
 def select_save_file(obj:QMainWindow, default_name:str, extension:str) -> Path:
@@ -45,7 +43,6 @@ def select_save_file(obj:QMainWindow, default_name:str, extension:str) -> Path:
         Path: Path of file to be opened
     """    
     try:
-        # home_dir = Path(obj.ctx["directory_path"]).joinpath(default_name).resolve().__str__()
         home_dir = Path(obj.ctx.directory_path).joinpath(default_name).resolve().__str__()
     except FileNotFoundError:
         home_dir = Path.home().joinpath(default_name).resolve().__str__()

src/submissions/frontend/custom_widgets/misc.py

@@ -12,8 +12,8 @@ from PyQt6.QtWidgets import (
 from PyQt6.QtCore import Qt, QDate, QSize
 from tools import check_not_nan, jinja_template_loading, Settings
 from ..all_window_functions import extract_form_info
-from backend.db import get_all_reagenttype_names, lookup_all_sample_types, create_kit_from_yaml, \
-    lookup_regent_by_type_name, lookup_last_used_reagenttype_lot, lookup_all_reagent_names_by_role
+from backend.db import construct_kit_from_yaml, \
+    lookup_reagent_types, lookup_reagents, lookup_submission_type, lookup_reagenttype_kittype_association
 import logging
 import numpy as np
 from .pop_ups import AlertPop
@@ -27,7 +27,7 @@ class AddReagentForm(QDialog):
     """
     dialog to add gather info about new reagent
     """    
-    def __init__(self, ctx:dict, reagent_lot:str|None, reagent_type:str|None, expiry:date|None=None, reagent_name:str|None=None) -> None:
+    def __init__(self, ctx:dict, 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:
@@ -60,7 +60,7 @@ class AddReagentForm(QDialog):
         # widget to get reagent type info
         self.type_input = QComboBox()
         self.type_input.setObjectName('type')
-        self.type_input.addItems([item for item in get_all_reagenttype_names(ctx=ctx)])
+        self.type_input.addItems([item.name for item in lookup_reagent_types(ctx=ctx)])
         logger.debug(f"Trying to find index of {reagent_type}")
         # convert input to user friendly string?
         try:
@@ -85,9 +85,13 @@ class AddReagentForm(QDialog):
         self.type_input.currentTextChanged.connect(self.update_names)
 
     def update_names(self):
+        """
+        Updates reagent names form field with examples from reagent type
+        """        
         logger.debug(self.type_input.currentText())
         self.name_input.clear()
-        self.name_input.addItems(item for item in lookup_all_reagent_names_by_role(ctx=self.ctx, role_name=self.type_input.currentText().replace(" ", "_").lower()))
+        lookup = lookup_reagents(ctx=self.ctx, reagent_type=self.type_input.currentText())
+        self.name_input.addItems(list(set([item.name for item in lookup])))
 
 class ReportDatePicker(QDialog):
     """
@@ -103,17 +107,17 @@ class ReportDatePicker(QDialog):
         self.buttonBox.accepted.connect(self.accept)
         self.buttonBox.rejected.connect(self.reject)
         # widgets to ask for dates 
-        start_date = QDateEdit(calendarPopup=True)
-        start_date.setObjectName("start_date")
-        start_date.setDate(QDate.currentDate())
-        end_date = QDateEdit(calendarPopup=True)
-        end_date.setObjectName("end_date")
-        end_date.setDate(QDate.currentDate())
+        self.start_date = QDateEdit(calendarPopup=True)
+        self.start_date.setObjectName("start_date")
+        self.start_date.setDate(QDate.currentDate())
+        self.end_date = QDateEdit(calendarPopup=True)
+        self.end_date.setObjectName("end_date")
+        self.end_date.setDate(QDate.currentDate())
         self.layout = QVBoxLayout()
         self.layout.addWidget(QLabel("Start Date"))
-        self.layout.addWidget(start_date)
+        self.layout.addWidget(self.start_date)
         self.layout.addWidget(QLabel("End Date"))
-        self.layout.addWidget(end_date)
+        self.layout.addWidget(self.end_date)
         self.layout.addWidget(self.buttonBox)
         self.setLayout(self.layout)
 
@@ -139,7 +143,8 @@ class KitAdder(QWidget):
         used_for = QComboBox()
         used_for.setObjectName("used_for")
         # Insert all existing sample types
-        used_for.addItems(lookup_all_sample_types(ctx=parent_ctx))
+        # used_for.addItems(lookup_all_sample_types(ctx=parent_ctx))
+        used_for.addItems([item.name for item in lookup_submission_type(ctx=parent_ctx)])
         used_for.setEditable(True)
         self.grid.addWidget(used_for,3,1)
         # set cost per run
@@ -203,7 +208,7 @@ class KitAdder(QWidget):
         yml_type[used]['kits'][info['kit_name']]['reagenttypes'] = reagents
         logger.debug(yml_type)
         # send to kit constructor
-        result = create_kit_from_yaml(ctx=self.ctx, exp=yml_type)
+        result = construct_kit_from_yaml(ctx=self.ctx, exp=yml_type)
         msg = AlertPop(message=result['message'], status=result['status'])
         msg.exec()
         self.__init__(self.ctx)
@@ -212,20 +217,22 @@ class ReagentTypeForm(QWidget):
     """
     custom widget to add information about a new reagenttype
     """    
-    def __init__(self, parent_ctx:dict) -> None:
+    def __init__(self, ctx:dict) -> None:
         super().__init__()
         grid = QGridLayout()
         self.setLayout(grid)
         grid.addWidget(QLabel("Name (*Exactly* as it appears in the excel submission form):"),0,0)
         # Widget to get reagent info
-        reagent_getter = QComboBox()
-        reagent_getter.setObjectName("name")
+        self.reagent_getter = QComboBox()
+        self.reagent_getter.setObjectName("name")
         # lookup all reagent type names from db
-        reagent_getter.addItems(get_all_reagenttype_names(ctx=parent_ctx))
-        reagent_getter.setEditable(True)
-        grid.addWidget(reagent_getter,0,1)
+        lookup = lookup_reagent_types(ctx=ctx)
+        logger.debug(f"Looked up ReagentType names: {lookup}")
+        self.reagent_getter.addItems([item.__str__() for item in lookup])
+        self.reagent_getter.setEditable(True)
+        grid.addWidget(self.reagent_getter,0,1)
         grid.addWidget(QLabel("Extension of Life (months):"),0,2)
-        # widget toget extension of life
+        # widget to get extension of life
         eol = QSpinBox()
         eol.setObjectName('eol')
         eol.setMinimum(0)
@@ -257,12 +264,14 @@ class ControlsDatePicker(QWidget):
 
 class ImportReagent(QComboBox):
 
-    def __init__(self, ctx:dict, reagent:PydReagent, extraction_kit:str):
+    def __init__(self, ctx:Settings, reagent:dict|PydReagent, extraction_kit:str):
         super().__init__()
         self.setEditable(True)
+        if isinstance(reagent, dict):
+            reagent = PydReagent(**reagent)
         # Ensure that all reagenttypes have a name that matches the items in the excel parser
         query_var = reagent.type
-        logger.debug(f"Import Reagent is looking at: {reagent.lot} for {reagent.type}")
+        logger.debug(f"Import Reagent is looking at: {reagent.lot} for {query_var}")
         if isinstance(reagent.lot, np.float64):
             logger.debug(f"{reagent.lot} is a numpy float!")
             try:
@@ -272,7 +281,8 @@ class ImportReagent(QComboBox):
         # query for reagents using type name from sheet and kit from sheet
         logger.debug(f"Attempting lookup of reagents by type: {query_var}")
         # below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work.
-        relevant_reagents = [item.__str__() for item in lookup_regent_by_type_name(ctx=ctx, type_name=query_var)]
+        lookup = lookup_reagents(ctx=ctx, reagent_type=query_var)
+        relevant_reagents = [item.__str__() for item in lookup]
         output_reg = []
         for rel_reagent in relevant_reagents:
             # extract strings from any sets.
@@ -289,7 +299,8 @@ class ImportReagent(QComboBox):
                 relevant_reagents.insert(0, str(reagent.lot))
             else:
                 # TODO: look up the last used reagent of this type in the database
-                looked_up_reg = lookup_last_used_reagenttype_lot(ctx=ctx, type_name=reagent.type, extraction_kit=extraction_kit)
+                looked_up_rt = lookup_reagenttype_kittype_association(ctx=ctx, reagent_type=reagent.type, kit_type=extraction_kit)
+                looked_up_reg = lookup_reagents(ctx=ctx, lot_number=looked_up_rt.last_used)
                 logger.debug(f"Because there was no reagent listed for {reagent}, we will insert the last lot used: {looked_up_reg}")
                 if looked_up_reg != None:
                     relevant_reagents.remove(str(looked_up_reg.lot))
@@ -309,12 +320,14 @@ class ImportReagent(QComboBox):
 
 class ParsedQLabel(QLabel):
 
-    def __init__(self, input_object, field_name, title:bool=True):
+    def __init__(self, input_object, field_name, title:bool=True, label_name:str|None=None):
         super().__init__()
         try:
             check = input_object['parsed']
         except:
             return
+        if label_name != None:
+            self.setObjectName(label_name)
         if title:
             output = field_name.replace('_', ' ').title()
         else:

src/submissions/frontend/custom_widgets/pop_ups.py

@@ -7,13 +7,12 @@ from PyQt6.QtWidgets import (
 )
 from tools import jinja_template_loading
 import logging
-from backend.db.functions import lookup_kittype_by_use, lookup_all_sample_types
+from backend.db.functions import lookup_kit_types, lookup_submission_type
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
 env = jinja_template_loading()
 
-
 class QuestionAsker(QDialog):
     """
     dialog to ask yes/no questions
@@ -28,8 +27,8 @@ class QuestionAsker(QDialog):
         self.buttonBox.rejected.connect(self.reject)
         self.layout = QVBoxLayout()
         # Text for the yes/no question
-        message = QLabel(message)
-        self.layout.addWidget(message)
+        self.message = QLabel(message)
+        self.layout.addWidget(self.message)
         self.layout.addWidget(self.buttonBox)
         self.setLayout(self.layout)
 
@@ -53,7 +52,7 @@ class KitSelector(QDialog):
         super().__init__()
         self.setWindowTitle(title)
         self.widget = QComboBox()
-        kits = [item.__str__() for item in lookup_kittype_by_use(ctx=ctx)]
+        kits = [item.__str__() for item in lookup_kit_types(ctx=ctx)]
         self.widget.addItems(kits)
         self.widget.setEditable(False)
         # set yes/no buttons
@@ -72,14 +71,6 @@ class KitSelector(QDialog):
     def getValues(self):
         return self.widget.currentText()
 
-    # @staticmethod
-    # def launch(parent):
-    #     dlg = KitSelector(parent)
-    #     r = dlg.exec_()
-    #     if r:
-    #         return dlg.getValues()
-    #     return None
-
 class SubmissionTypeSelector(QDialog):
     """
     dialog to ask yes/no questions
@@ -88,7 +79,7 @@ class SubmissionTypeSelector(QDialog):
         super().__init__()
         self.setWindowTitle(title)
         self.widget = QComboBox()
-        sub_type = lookup_all_sample_types(ctx=ctx)
+        sub_type = [item.name for item in lookup_submission_type(ctx=ctx)]
         self.widget.addItems(sub_type)
         self.widget.setEditable(False)
         # set yes/no buttons

src/submissions/frontend/custom_widgets/sub_details.py

@@ -15,7 +15,7 @@ from PyQt6.QtWidgets import (
 from PyQt6.QtWebEngineWidgets import QWebEngineView
 from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel
 from PyQt6.QtGui import QAction, QCursor, QPixmap, QPainter
-from backend.db import submissions_to_df, lookup_submission_by_id, delete_submission_by_id, lookup_submission_by_rsl_num, hitpick_plate
+from backend.db.functions import submissions_to_df, delete_submission, lookup_submissions
 from backend.excel import make_hitpicks
 from tools import check_if_app, Settings
 from tools import jinja_template_loading
@@ -33,6 +33,7 @@ env = jinja_template_loading()
 class pandasModel(QAbstractTableModel):
     """
     pandas model for inserting summary sheet into gui
+    NOTE: Copied from Stack Overflow. I have no idea how it actually works.
     """
     def __init__(self, data) -> None:
         QAbstractTableModel.__init__(self)
@@ -73,7 +74,6 @@ class pandasModel(QAbstractTableModel):
             return self._data.columns[col]
         return None
         
-
 class SubmissionsSheet(QTableView):
     """
     presents submission summary to user in tab1
@@ -98,24 +98,13 @@ class SubmissionsSheet(QTableView):
         """
         sets data in model
         """        
-        self.data = submissions_to_df(ctx=self.ctx, limit=100)
+        self.data = submissions_to_df(ctx=self.ctx)
         try:
             self.data['id'] = self.data['id'].apply(str)
             self.data['id'] = self.data['id'].str.zfill(3)
         except KeyError:
             pass
-        try:
-            del self.data['samples']
-        except KeyError:
-            pass
-        try:
-            del self.data['reagents']
-        except KeyError:
-            pass
-        try:
-            del self.data['comments']
-        except KeyError:
-            pass
+        
         proxyModel = QSortFilterProxyModel()
         proxyModel.setSourceModel(pandasModel(self.data))
         self.setModel(proxyModel)
@@ -132,6 +121,9 @@ class SubmissionsSheet(QTableView):
             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}")
@@ -140,6 +132,9 @@ class SubmissionsSheet(QTableView):
             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}")
@@ -147,7 +142,6 @@ class SubmissionsSheet(QTableView):
         if dlg.exec():
             dlg.add_comment()
 
-
     def contextMenuEvent(self, event):
         """
         Creates actions for right click menu events.
@@ -174,25 +168,23 @@ class SubmissionsSheet(QTableView):
         # add other required actions
         self.menu.popup(QCursor.pos())
 
-
     def delete_item(self, event):
         """
         Confirms user deletion and sends id to backend for deletion.
 
         Args:
-            event (_type_): _description_
+            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")
         if msg.exec():
-            delete_submission_by_id(ctx=self.ctx, id=value)
+            delete_submission(ctx=self.ctx, id=value)
         else:
             return
         self.setData()
 
-
     def hit_pick(self):
         """
         Extract positive samples from submissions with PCR results and export to csv.
@@ -207,7 +199,7 @@ class SubmissionsSheet(QTableView):
             logger.error(f"Error: Had to truncate number of plates to 4.")
             indices = indices[:4]
         # lookup ids in the database
-        subs = [lookup_submission_by_id(self.ctx, id) for id in indices]
+        subs = [lookup_submissions(ctx=self.ctx, id=id) for id in indices]
         # full list of samples
         dicto = []
         # list to contain plate images
@@ -217,7 +209,6 @@ class SubmissionsSheet(QTableView):
             if iii > 3: 
                 logger.error(f"Error: Had to truncate number of plates to 4.")
                 continue
-            # plate_dicto = hitpick_plate(submission=sub, plate_number=iii+1)
             plate_dicto = sub.hitpick_plate(plate_number=iii+1)
             if plate_dicto == None:
                 continue
@@ -251,8 +242,7 @@ class SubmissionsSheet(QTableView):
                 image.show()
             except Exception as e:
                 logger.error(f"Could not show image: {e}.")
-        
-    
+          
 class SubmissionDetails(QDialog):
     """
     a window showing text details of submission
@@ -262,41 +252,18 @@ class SubmissionDetails(QDialog):
         super().__init__()
         self.ctx = ctx
         self.setWindowTitle("Submission Details")
-        
         # create scrollable interior
         interior = QScrollArea()
         interior.setParent(self)
         # get submision from db
-        data = lookup_submission_by_id(ctx=ctx, id=id)
-        logger.debug(f"Submission details data:\n{pprint.pformat(data.to_dict())}")
-        self.base_dict = data.to_dict(full_data=True)
+        sub = lookup_submissions(ctx=ctx, id=id)
+        logger.debug(f"Submission details data:\n{pprint.pformat(sub.to_dict())}")
+        self.base_dict = sub.to_dict(full_data=True)
         # don't want id
         del self.base_dict['id']
-        # retrieve jinja template
-        # template = env.get_template("submission_details.txt")
-        # render using object dict
-        # text = template.render(sub=self.base_dict)
-        # create text field
-        # txt_editor = QTextEdit(self)
-        # txt_editor.setReadOnly(True)
-        # txt_editor.document().setPlainText(text)
-        # resize
-        # font = txt_editor.document().defaultFont()
-        # fontMetrics = QFontMetrics(font)
-        # textSize = fontMetrics.size(0, txt_editor.toPlainText())
-        # w = textSize.width() + 10
-        # h = textSize.height() + 10
-        # txt_editor.setMinimumSize(w, h)
-        # txt_editor.setMaximumSize(w, h)
-        # txt_editor.resize(w, h)
-        # interior.resize(w,900)
-        # txt_editor.setText(text)
-        # interior.setWidget(txt_editor)
         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')
-        sub = lookup_submission_by_rsl_num(ctx=self.ctx, rsl_num=self.base_dict['Plate Number'])
-        # plate_dicto = hitpick_plate(sub)
         logger.debug(f"Hitpicking plate...")
         plate_dicto = sub.hitpick_plate()
         logger.debug(f"Making platemap...")
@@ -307,7 +274,6 @@ class SubmissionDetails(QDialog):
             platemap.save(image_io, 'JPEG')
         except AttributeError:
             logger.error(f"No plate map found for {sub.rsl_plate_num}")
-        # platemap.save("test.jpg", 'JPEG')
         self.base_dict['platemap'] = base64.b64encode(image_io.getvalue()).decode('utf-8')
         template = env.get_template("submission_details.html")
         self.html = template.render(sub=self.base_dict)
@@ -325,31 +291,11 @@ class SubmissionDetails(QDialog):
         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.
         """        
-        # template = env.get_template("submission_details.html")
-        # # make barcode because, reasons
-        # self.base_dict['barcode'] = base64.b64encode(make_plate_barcode(self.base_dict['Plate Number'], width=120, height=30)).decode('utf-8')
-        # sub = lookup_submission_by_rsl_num(ctx=self.ctx, rsl_num=self.base_dict['Plate Number'])
-        # plate_dicto = hitpick_plate(sub)
-        # platemap = make_plate_map(plate_dicto)
-        # logger.debug(f"platemap: {platemap}")
-        # image_io = BytesIO()
-        # try:
-        #     platemap.save(image_io, 'JPEG')
-        # except AttributeError:
-        #     logger.error(f"No plate map found for {sub.rsl_plate_num}")
-        # # platemap.save("test.jpg", 'JPEG')
-        # self.base_dict['platemap'] = base64.b64encode(image_io.getvalue()).decode('utf-8')
-        # logger.debug(self.base_dict)
-        # html = template.render(sub=self.base_dict)
-        # with open("test.html", "w") as f:
-        #     f.write(html)
         try:
-            # home_dir = Path(self.ctx["directory_path"]).joinpath(f"Submission_Details_{self.base_dict['Plate Number']}.pdf").resolve().__str__()
             home_dir = Path(self.ctx.directory_path).joinpath(f"Submission_Details_{self.base_dict['Plate Number']}.pdf").resolve().__str__()
         except FileNotFoundError:
             home_dir = Path.home().resolve().__str__()
@@ -421,6 +367,9 @@ class BarcodeWindow(QDialog):
 
 
     def print_barcode(self):
+        """
+        Sends barcode image to printer.
+        """        
         printer = QtPrintSupport.QPrinter()
         dialog = QtPrintSupport.QPrintDialog(printer)
         if dialog.exec():
@@ -439,7 +388,7 @@ class SubmissionComment(QDialog):
     """
     a window for adding comment text to a submission
     """    
-    def __init__(self, ctx:dict, rsl:str) -> None:
+    def __init__(self, ctx:Settings, rsl:str) -> None:
 
         super().__init__()
         self.ctx = ctx
@@ -460,18 +409,22 @@ class SubmissionComment(QDialog):
         self.setLayout(self.layout)
         
     def add_comment(self):
+        """
+        Adds comment to submission object.
+        """        
         commenter = getuser()
         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}")
-        sub = lookup_submission_by_rsl_num(ctx = self.ctx, rsl_num=self.rsl)
+        # sub = lookup_submission_by_rsl_num(ctx = self.ctx, rsl_num=self.rsl)
+        sub = lookup_submissions(ctx = self.ctx, rsl_number=self.rsl)
         try:
             sub.comment.append(full_comment)
         except AttributeError:
             sub.comment = [full_comment]
         logger.debug(sub.__dict__)
-        self.ctx['database_session'].add(sub)
-        self.ctx['database_session'].commit()
+        self.ctx.database_session.add(sub)
+        self.ctx.database_session.commit()
 
         

src/submissions/frontend/main_window_functions.py

@@ -22,16 +22,12 @@ from PyQt6.QtWidgets import (
 from .all_window_functions import extract_form_info, select_open_file, select_save_file
 from PyQt6.QtCore import QSignalBlocker
 from backend.db.functions import (
-    lookup_all_orgs, lookup_kittype_by_use, lookup_kittype_by_name, 
-    construct_submission_info, lookup_reagent, store_submission, lookup_submissions_by_date_range, 
-    create_kit_from_yaml, create_org_from_yaml, get_control_subtypes, get_all_controls_by_type,
-    lookup_all_submissions_by_type, get_all_controls, lookup_submission_by_rsl_num, update_subsampassoc_with_pcr,
-    check_kit_integrity, lookup_sub_samp_association_by_plate_sample, lookup_ww_sample_by_processing_number,
-    lookup_sample_by_submitter_id, update_last_used
+    construct_submission_info, lookup_reagents, construct_kit_from_yaml, construct_org_from_yaml, get_control_subtypes,
+    update_subsampassoc_with_pcr, check_kit_integrity, update_last_used, lookup_organizations, lookup_kit_types, 
+    lookup_submissions, lookup_controls, lookup_samples, lookup_submission_sample_association, store_object
 )
 from backend.excel.parser import SheetParser, PCRParser, SampleParser
 from backend.excel.reports import make_report_html, make_report_xlsx, convert_data_list_to_df
-from backend.pydant import PydReagent
 from tools import check_not_nan, convert_well_to_row_column
 from .custom_widgets.pop_ups import AlertPop, QuestionAsker
 from .custom_widgets import ReportDatePicker
@@ -55,8 +51,7 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
     logger.debug(obj.ctx)
     # initialize samples
     obj.samples = []
-    obj.reagents = []
-    obj.missing_reagents = []
+    
     obj.missing_info = []
     
     # set file dialog
@@ -67,31 +62,20 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
         return obj, result
     # create sheetparser using excel sheet and context from gui
     try:
-        prsr = SheetParser(ctx=obj.ctx, filepath=fname)
+        obj.prsr = SheetParser(ctx=obj.ctx, filepath=fname)
     except PermissionError:
         logger.error(f"Couldn't get permission to access file: {fname}")
         return obj, result
-    # prsr.sub = import_validation_check(ctx=obj.ctx, parser_sub=prsr.sub)
-    # obj.column_count = prsr.column_count
     try:
-        logger.debug(f"Submission dictionary:\n{pprint.pformat(prsr.sub)}")
-        pyd = prsr.to_pydantic()
+        logger.debug(f"Submission dictionary:\n{pprint.pformat(obj.prsr.sub)}")
+        pyd = obj.prsr.to_pydantic()
         logger.debug(f"Pydantic result: \n\n{pprint.pformat(pyd)}\n\n")
     except Exception as e:
         return obj, dict(message= f"Problem creating pydantic model:\n\n{e}", status="critical")
-    try:
-        obj.xl = prsr.filepath
-    except Exception as e:
-        logger.error(f"Unable to make obj xl.")
-    # for sample in pyd.samples:
-    #     if hasattr(sample, "elution_well"):
-    #         logger.debug(f"Sample from import: {sample.elution_well}")
-    # I don't remember why this is here.
-    
-    obj.current_submission_type = pyd.submission_type['value']
     # destroy any widgets from previous imports
     for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
         item.setParent(None)
+    obj.current_submission_type = pyd.submission_type['value']
     # Get list of fields from pydantic model.
     fields = list(pyd.model_fields.keys()) + list(pyd.model_extra.keys())
     fields.remove('filepath')
@@ -107,13 +91,11 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
         label = ParsedQLabel(value, field)
         match field:
             case 'submitting_lab':
-                # create label
-                # label = QLabel(field.replace("_", " ").title())
-                # label = ParsedQLabel(value, field)
                 logger.debug(f"{field}: {value['value']}")
                 # create combobox to hold looked up submitting labs
                 add_widget = QComboBox()
-                labs = [item.__str__() for item in lookup_all_orgs(ctx=obj.ctx)]
+                # labs = [item.__str__() for item in lookup_all_orgs(ctx=obj.ctx)]
+                labs = [item.__str__() for item in lookup_organizations(ctx=obj.ctx)]
                 # try to set closest match to top of list
                 try:
                     labs = difflib.get_close_matches(value['value'], labs, len(labs), 0)
@@ -122,9 +104,6 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
                 # set combobox values to lookedup values
                 add_widget.addItems(labs)
             case 'extraction_kit':
-                # create label
-                # label = QLabel(field.replace("_", " ").title())
-                
                 # if extraction kit not available, all other values fail
                 if not check_not_nan(value['value']):
                     msg = AlertPop(message="Make sure to check your extraction kit in the excel sheet!", status="warning")
@@ -132,21 +111,21 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
                 # create combobox to hold looked up kits
                 add_widget = QComboBox()
                 # lookup existing kits by 'submission_type' decided on by sheetparser
-                # uses = [item.__str__() for item in lookup_kittype_by_use(ctx=obj.ctx, used_by=pyd.submission_type['value'].lower())]
                 logger.debug(f"Looking up kits used for {pyd.submission_type['value']}")
-                uses = [item.__str__() for item in lookup_kittype_by_use(ctx=obj.ctx, used_for=pyd.submission_type['value'])]
+                # uses = [item.__str__() for item in lookup_kittype_by_use(ctx=obj.ctx, used_for=pyd.submission_type['value'])]
+                uses = [item.__str__() for item in lookup_kit_types(ctx=obj.ctx, used_for=pyd.submission_type['value'])]
                 logger.debug(f"Kits received for {pyd.submission_type['value']}: {uses}")
                 if check_not_nan(value['value']):
                     logger.debug(f"The extraction kit in parser was: {value['value']}")
                     uses.insert(0, uses.pop(uses.index(value['value'])))
                     obj.ext_kit = value['value']
                 else:
-                    logger.error(f"Couldn't find {prsr.sub['extraction_kit']}")
+                    logger.error(f"Couldn't find {obj.prsr.sub['extraction_kit']}")
                     obj.ext_kit = uses[0]
-                add_widget.addItems(uses)
+                # Run reagent scraper whenever extraction kit is changed.
+                add_widget.currentTextChanged.connect(obj.scrape_reagents)
+                # add_widget.addItems(uses)
             case 'submitted_date':
-                # create label
-                # label = QLabel(field.replace("_", " ").title())
                 # uses base calendar
                 add_widget = QDateEdit(calendarPopup=True)
                 # sets submitted date based on date found in excel sheet
@@ -163,40 +142,10 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
             case "ctx":
                 continue
             case 'reagents':
-                for reagent in value:
-                    # create label
-                    # reg_label = QLabel(reagent['type'].replace("_", " ").title())
-                    reg_label = ParsedQLabel(reagent, reagent['value'].type, title=False)
-                    if reagent['parsed']:
-                        # try:
-                        #     reg_label = QLabel(f"Parsed Lot: {reagent['value'].type}")
-                        obj.reagents.append(reagent['value'])
-                        # except AttributeError:
-                            # continue
-                    else:
-                        # try:
-                        #     reg_label = QLabel(f"MISSING Lot: {reagent['value'].type}")
-                        obj.missing_reagents.append(reagent['value'])
-                        continue
-                        # except AttributeError:
-                        #     continue
-                    # reg_label.setObjectName(f"lot_{reagent['type']}_label")
-                    reg_label.setObjectName(f"lot_{reagent['value'].type}_label")
-                    # create reagent choice widget
-                    add_widget = ImportReagent(ctx=obj.ctx, reagent=reagent['value'], extraction_kit=pyd.extraction_kit['value'])
-                    add_widget.setObjectName(f"lot_{reagent['value'].type}")
-                    logger.debug(f"Widget name set to: {add_widget.objectName()}")
-                    obj.table_widget.formlayout.addWidget(reg_label)
-                    obj.table_widget.formlayout.addWidget(add_widget)
+                # NOTE: This is now set to run when the extraction kit is updated.
                 continue
-            # case "rsl_plate_num":
-            #     label = QLabel(field.replace("_", " ").title())
-            #     add_widget = QLineEdit()
-            #     logger.debug(f"Setting widget text to {str(value['value']).replace('_', ' ')}")
-            #     add_widget.setText(str(value['value']).replace("_", " "))
             case _:
                 # anything else gets added in as a line edit
-                # label = QLabel(field.replace("_", " ").title())
                 add_widget = QLineEdit()
                 logger.debug(f"Setting widget text to {str(value['value']).replace('_', ' ')}")
                 add_widget.setText(str(value['value']).replace("_", " "))
@@ -207,13 +156,11 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
             obj.table_widget.formlayout.addWidget(add_widget)
         except AttributeError as e:
             logger.error(e)
+    kit_widget = obj.table_widget.formlayout.parentWidget().findChild(QComboBox, 'extraction_kit')
+    kit_widget.addItems(uses)
     # compare obj.reagents with expected reagents in kit
-    if hasattr(obj, 'ext_kit'):
-        obj.kit_integrity_completion()
-        # obj.missing_reagents = obj.missing_reagents + missing_info
-    logger.debug(f"Imported reagents: {obj.reagents}")
-    if prsr.sample_result != None:
-        msg = AlertPop(message=prsr.sample_result, status="WARNING")
+    if obj.prsr.sample_result != None:
+        msg = AlertPop(message=obj.prsr.sample_result, status="WARNING")
         msg.exec()
     logger.debug(f"Pydantic extra fields: {pyd.model_extra}")
     if "csv" in pyd.model_extra:
@@ -255,31 +202,30 @@ def kit_integrity_completion_function(obj:QMainWindow) -> Tuple[QMainWindow, dic
     """    
     result = None
     logger.debug(inspect.currentframe().f_back.f_code.co_name)
-    # find the widget that contains lit info
+    # find the widget that contains kit info
     kit_widget = obj.table_widget.formlayout.parentWidget().findChild(QComboBox, 'extraction_kit')
     logger.debug(f"Kit selector: {kit_widget}")
-    # get current kit info
+    # get current kit being used
     obj.ext_kit = kit_widget.currentText()
+    for item in obj.reagents:
+        obj.table_widget.formlayout.addWidget(ParsedQLabel({'parsed':True}, item.type, title=False, label_name=f"lot_{item.type}_label"))
+        reagent = dict(type=item.type, lot=item.lot, exp=item.exp, name=item.name)
+        add_widget = ImportReagent(ctx=obj.ctx, reagent=reagent, extraction_kit=obj.ext_kit)
+        obj.table_widget.formlayout.addWidget(add_widget)
     logger.debug(f"Checking integrity of {obj.ext_kit}")
-    # get the kit from database using current kit info
-    # kit = lookup_kittype_by_name(ctx=obj.ctx, name=obj.ext_kit)
-    # get all reagents stored in the QWindow object
-    # reagents_to_lookup = [item.name for item in obj.missing_reagents]
-    # logger.debug(f"Reagents for lookup for {kit.name}: {reagents_to_lookup}")
-    # make sure kit contains all necessary info
-    # kit_integrity = check_kit_integrity(kit, reagents_to_lookup)
-    # if kit integrity comes back with an error, make widgets with missing reagents using default info
-    # if kit_integrity != None:
-    # result = dict(message=kit_integrity['message'], status="Warning")
-        # obj.missing_reagents = kit_integrity['missing']
-    # for item in kit_integrity['missing']:
+    # see if there are any missing reagents
     if len(obj.missing_reagents) > 0:
         result = dict(message=f"The submission you are importing is missing some reagents expected by the kit.\n\nIt looks like you are missing: {[item.type.upper() for item in obj.missing_reagents]}\n\nAlternatively, 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!", status="Warning")
     for item in obj.missing_reagents:
-        obj.table_widget.formlayout.addWidget(ParsedQLabel({'parsed':False}, item.type, title=False))
+        # Add label that has parsed as False to show "MISSING" label.
+        obj.table_widget.formlayout.addWidget(ParsedQLabel({'parsed':False}, item.type, title=False, label_name=f"missing_{item.type}_label"))
+        # Set default parameters for the empty reagent.
         reagent = dict(type=item.type, lot=None, exp=date.today(), name=None)
-        add_widget = ImportReagent(ctx=obj.ctx, reagent=PydReagent(**reagent), extraction_kit=obj.ext_kit)#item=item)
+        # create and add widget
+        # add_widget = ImportReagent(ctx=obj.ctx, reagent=PydReagent(**reagent), extraction_kit=obj.ext_kit)
+        add_widget = ImportReagent(ctx=obj.ctx, reagent=reagent, extraction_kit=obj.ext_kit)
         obj.table_widget.formlayout.addWidget(add_widget)
+    # Add submit button to the form.
     submit_btn = QPushButton("Submit")
     submit_btn.setObjectName("lot_submit_btn")
     obj.table_widget.formlayout.addWidget(submit_btn)
@@ -309,7 +255,7 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
     # compare reagents in form to reagent database
     for reagent in reagents:
         # Lookup any existing reagent of this type with this lot number
-        wanted_reagent = lookup_reagent(ctx=obj.ctx, reagent_lot=reagents[reagent], type_name=reagent)
+        wanted_reagent = lookup_reagents(ctx=obj.ctx, lot_number=reagents[reagent], reagent_type=reagent)
         logger.debug(f"Looked up reagent: {wanted_reagent}")
         # if reagent not found offer to add to database
         if wanted_reagent == None:
@@ -362,8 +308,7 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
     if kit_integrity != None:
         return obj, dict(message=kit_integrity['message'], status="critical")
     logger.debug(f"Sending submission: {base_submission.rsl_plate_num} to database.")
-    result = store_submission(ctx=obj.ctx, base_submission=base_submission)
-    # check result of storing for issues
+    result = store_object(ctx=obj.ctx, object=base_submission)
     # update summary sheet
     obj.table_widget.sub_wid.setData()
     # reset form
@@ -372,7 +317,7 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
     logger.debug(f"All attributes of obj: {pprint.pformat(obj.__dict__)}")
     if len(obj.missing_reagents + obj.missing_info) > 0:
         logger.debug(f"We have blank reagents in the excel sheet.\n\tLet's try to fill them in.") 
-        extraction_kit = lookup_kittype_by_name(obj.ctx, name=obj.ext_kit)
+        extraction_kit = lookup_kit_types(ctx=obj.ctx, name=obj.ext_kit)
         logger.debug(f"We have the extraction kit: {extraction_kit.name}")
         excel_map = extraction_kit.construct_xl_map_for_use(obj.current_submission_type)
         logger.debug(f"Extraction kit map:\n\n{pprint.pformat(excel_map)}")
@@ -410,7 +355,8 @@ def generate_report_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
         info = extract_form_info(dlg)
         logger.debug(f"Report info: {info}")
         # find submissions based on date range
-        subs = lookup_submissions_by_date_range(ctx=obj.ctx, start_date=info['start_date'], end_date=info['end_date'])
+        # subs = lookup_submissions_by_date_range(ctx=obj.ctx, start_date=info['start_date'], end_date=info['end_date'])
+        subs = lookup_submissions(ctx=obj.ctx, start_date=info['start_date'], end_date=info['end_date'])
         # convert each object to dict
         records = [item.report_dict() for item in subs]
         # make dataframe from record dictionaries
@@ -452,7 +398,7 @@ def add_kit_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
         Tuple[QMainWindow, dict]: Collection of new main app window and result dict
     """    
     result = None
-    # setup file dialog to find yaml flie
+    # setup file dialog to find yaml file
     fname = select_open_file(obj, file_extension="yml")
     assert fname.exists()
     # read yaml file
@@ -466,7 +412,7 @@ def add_kit_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
     except PermissionError:
         return
     # send to kit creator function
-    result = create_kit_from_yaml(ctx=obj.ctx, exp=exp)
+    result = construct_kit_from_yaml(ctx=obj.ctx, exp=exp)
     return obj, result
 
 def add_org_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
@@ -494,7 +440,7 @@ def add_org_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
     except PermissionError:
         return obj, result
     # send to kit creator function
-    result = create_org_from_yaml(ctx=obj.ctx, org=org)
+    result = construct_org_from_yaml(ctx=obj.ctx, org=org)
     return obj, result
 
 def controls_getter_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
@@ -531,6 +477,7 @@ def controls_getter_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
     obj.table_widget.sub_typer.clear()
     # lookup subtypes
     sub_types = get_control_subtypes(ctx=obj.ctx, type=obj.con_type, mode=obj.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(obj.table_widget.sub_typer) as blocker: 
@@ -562,7 +509,8 @@ def chart_maker_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
         obj.subtype = obj.table_widget.sub_typer.currentText()
     logger.debug(f"Subtype: {obj.subtype}")
     # query all controls using the type/start and end dates from the gui
-    controls = get_all_controls_by_type(ctx=obj.ctx, con_type=obj.con_type, start_date=obj.start_date, end_date=obj.end_date)
+    # controls = get_all_controls_by_type(ctx=obj.ctx, con_type=obj.con_type, start_date=obj.start_date, end_date=obj.end_date)
+    controls = lookup_controls(ctx=obj.ctx, control_type=obj.con_type, start_date=obj.start_date, end_date=obj.end_date)
     # if no data found from query set fig to none for reporting in webview
     if controls == None:
         fig = None
@@ -602,9 +550,11 @@ def link_controls_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
         Tuple[QMainWindow, dict]: Collection of new main app window and result dict
     """    
     result = None
-    all_bcs = lookup_all_submissions_by_type(obj.ctx, "Bacterial Culture")
+    # all_bcs = lookup_all_submissions_by_type(obj.ctx, "Bacterial Culture")
+    all_bcs = lookup_submissions(ctx=obj.ctx, submission_type="Bacterial Culture")
     logger.debug(all_bcs)
-    all_controls = get_all_controls(obj.ctx)
+    # all_controls = get_all_controls(obj.ctx)
+    all_controls = lookup_controls(ctx=obj.ctx)
     ac_list = [control.name for control in all_controls]
     count = 0
     for bcs in all_bcs:
@@ -617,7 +567,6 @@ def link_controls_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
             if " " in sample:
                 logger.warning(f"There is not supposed to be a space in the sample name!!!")
                 sample = sample.replace(" ", "")
-            # if sample not in ac_list:
             if not any([ac.startswith(sample) for ac in ac_list]):
                 continue
             else:
@@ -632,24 +581,15 @@ def link_controls_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
                         else:
                             logger.debug(f"Adding {control.name} to {bcs.rsl_plate_num} as control")
                             bcs.controls.append(control)
-                            # bcs.control_id.append(control.id)
                             control.submission = bcs
                             control.submission_id = bcs.id
-                            # obj.ctx["database_session"].add(control)
                             obj.ctx.database_session.add(control)
                             count += 1
-        # obj.ctx["database_session"].add(bcs)
         obj.ctx.database_session.add(bcs)
         logger.debug(f"Here is the new control: {[control.name for control in bcs.controls]}")
     result = dict(message=f"We added {count} controls to bacterial cultures.", status="information")
     logger.debug(result)
-    # obj.ctx['database_session'].commit()
     obj.ctx.database_session.commit()
-    # msg = QMessageBox()
-    # msg.setText("Controls added")
-    # msg.setInformativeText(result)
-    # msg.setWindowTitle("Controls added")
-    # msg.exec()
     return obj, result
 
 def link_extractions_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
@@ -681,7 +621,8 @@ def link_extractions_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
         for ii in range(6, len(run)):
             new_run[f"column{str(ii-5)}_vol"] = run[ii]
         # Lookup imported submissions
-        sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=new_run['rsl_plate_num'])
+        # 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'])
         # If no such submission exists, move onto the next run
         try:
             logger.debug(f"Found submission: {sub.rsl_plate_num}")
@@ -712,8 +653,6 @@ def link_extractions_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
             logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.extraction_info}")
         else:
             sub.extraction_info = json.dumps([new_run])        
-        # obj.ctx['database_session'].add(sub)
-        # obj.ctx["database_session"].commit()
         obj.ctx.database_session.add(sub)
         obj.ctx.database_session.commit()
     result = dict(message=f"We added {count} logs to the database.", status='information') 
@@ -745,7 +684,8 @@ def link_pcr_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
                 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_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'])
         # if imported submission doesn't exist move on to next run
         try:
             logger.debug(f"Found submission: {sub.rsl_plate_num}")
@@ -777,8 +717,6 @@ def link_pcr_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
             logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.pcr_info}")
         else:
             sub.pcr_info = json.dumps([new_run])        
-        # obj.ctx['database_session'].add(sub)
-        # obj.ctx["database_session"].commit()
         obj.ctx.database_session.add(sub)
         obj.ctx.database_session.commit()
     result = dict(message=f"We added {count} logs to the database.", status='information')
@@ -798,14 +736,16 @@ def import_pcr_results_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
     fname = select_open_file(obj, file_extension="xlsx")
     parser = PCRParser(ctx=obj.ctx, 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 = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=parser.plate_num)
+    sub = lookup_submissions(ctx=obj.ctx, rsl_number=parser.plate_num)
     try:
         logger.debug(f"Found submission: {sub.rsl_plate_num}")
     except AttributeError:
         # 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_submission_by_rsl_num(ctx=obj.ctx, rsl_num=parser.plate_num)
+        sub = lookup_submissions(ctx=obj.ctx, rsl_number=parser.plate_num)
         try:
             logger.debug(f"Found submission: {sub.rsl_plate_num}")
         except AttributeError:
@@ -830,11 +770,9 @@ def import_pcr_results_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
         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)
     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)}")
-    # obj.ctx["database_session"].commit()
     obj.ctx.database_session.commit()
     logger.debug(f"Got {len(parser.samples)} samples to update!")
     logger.debug(f"Parser samples: {parser.samples}")
@@ -844,8 +782,6 @@ def import_pcr_results_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
             sample_dict = [item for item in parser.samples if item['sample']==sample.rsl_number][0]
         except IndexError:
             continue
-        # sample['plate_rsl'] = sub.rsl_plate_num
-        # update_ww_sample(ctx=obj.ctx, sample_obj=sample)
         update_subsampassoc_with_pcr(ctx=obj.ctx, submission=sub, sample=sample, input_dict=sample_dict)
 
     result = dict(message=f"We added PCR info to {sub.rsl_plate_num}.", status='information')
@@ -909,8 +845,8 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
         new_info.append(new_item)
     logger.debug(f"New reagents: {new_reagents}")
     logger.debug(f"New info: {new_info}")
-    # open the workbook using openpyxl
-    workbook = load_workbook(obj.xl)
+    # open a new workbook using openpyxl
+    workbook = load_workbook(obj.prsr.xl.io)
     # get list of sheet names
     sheets = workbook.sheetnames
     # logger.debug(workbook.sheetnames)
@@ -941,22 +877,25 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
     workbook.save(filename=fname.__str__())
 
 def construct_first_strand_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
+    """
+    Generates a csv file from client submitted xlsx file.
 
+    Args:
+        obj (QMainWindow): Main application
+
+    Returns:
+        Tuple[QMainWindow, dict]: Updated main application and result
+    """    
     def get_plates(input_sample_number:str, plates:list) -> Tuple[int, str]:
         logger.debug(f"Looking up {input_sample_number} in {plates}")
-        samp = lookup_ww_sample_by_processing_number(ctx=obj.ctx, processing_number=input_sample_number)
+        # samp = lookup_ww_sample_by_processing_number(ctx=obj.ctx, processing_number=input_sample_number)
+        samp = lookup_samples(ctx=obj.ctx, ww_processing_num=input_sample_number)
         if samp ==  None:
-            samp = lookup_sample_by_submitter_id(ctx=obj.ctx, submitter_id=input_sample_number)
+            # samp = lookup_sample_by_submitter_id(ctx=obj.ctx, submitter_id=input_sample_number)
+            samp = lookup_samples(ctx=obj.ctx, submitter_id=input_sample_number)
         logger.debug(f"Got sample: {samp}")
-        # if samp != None:
-        new_plates = [(iii+1, lookup_sub_samp_association_by_plate_sample(ctx=obj.ctx, rsl_sample_num=samp, rsl_plate_num=lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=plate))) for iii, plate in enumerate(plates)]
-            # for iii, plate in enumerate(plates):
-            #     lplate = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=plate)
-            #     if lplate == None:
-            #         continue
-            #     else:
-            #         logger.debug(f"Got a plate: {lplate}")
-            #         new_plates.append((iii, lookup_sub_samp_association_by_plate_sample(ctx=obj.ctx, rsl_sample_num=samp, rsl_plate_num=lplate)))
+        # new_plates = [(iii+1, lookup_sub_samp_association_by_plate_sample(ctx=obj.ctx, rsl_sample_num=samp, rsl_plate_num=lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=plate))) for iii, plate in enumerate(plates)]
+        new_plates = [(iii+1, lookup_submission_sample_association(ctx=obj.ctx, sample=samp, submission=plate)) for iii, plate in enumerate(plates)]
         logger.debug(f"Associations: {pprint.pformat(new_plates)}")
         try:
             plate_num, plate = next(assoc for assoc in new_plates if assoc[1] is not None)
@@ -964,8 +903,6 @@ def construct_first_strand_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]
             plate_num, plate = None, None
         logger.debug(f"Plate number {plate_num} is {plate}")
         return plate_num, plate
-        
-        
     fname = select_open_file(obj=obj, file_extension="xlsx")
     xl = pd.ExcelFile(fname)
     sprsr = SampleParser(ctx=obj.ctx, xl=xl, submission_type="First Strand")
@@ -988,7 +925,6 @@ def construct_first_strand_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]
         else:
             new_dict['destination_row'] = item['row']
             new_dict['destination_column'] = item['column']
-        # assocs = [(iii, lookup_ww_sample_by_processing_number_and_plate(ctx=obj.ctx, processing_number=new_dict['sample'], plate_number=plate)) for iii, plate in enumerate(plates)]
         plate_num, plate = get_plates(input_sample_number=new_dict['sample'], plates=plates)
         if plate_num == None:
             plate_num = str(old_plate_number) + "*"
@@ -1015,3 +951,34 @@ def construct_first_strand_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]
     df.to_csv(ofname, index=False)
     return obj, None
 
+def scrape_reagents(obj:QMainWindow, extraction_kit:str) -> Tuple[QMainWindow, dict]:
+    """
+    Extracted scrape reagents function that will run when 
+    form 'extraction_kit' widget is updated.
+
+    Args:
+        obj (QMainWindow): updated main application
+        extraction_kit (str): name of extraction kit (in 'extraction_kit' widget)
+
+    Returns:
+        Tuple[QMainWindow, dict]: Updated application and result
+    """    
+    logger.debug("\n\nHello from reagent scraper!!\n\n")
+    logger.debug(f"Extraction kit: {extraction_kit}")
+    obj.reagents = []
+    obj.missing_reagents = []
+    [item.setParent(None) for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget) if item.objectName().startswith("lot_") or item.objectName().startswith("missing_")]
+    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['value'])
+        else:
+            obj.missing_reagents.append(reagent['value'])
+    logger.debug(f"Imported reagents: {obj.reagents}")
+    logger.debug(f"Missing reagents: {obj.missing_reagents}")
+    return obj, None
+    
+
+