Pre-major refactor

src/submissions/frontend/__init__.py

@@ -1,7 +1,6 @@
 '''
 Constructs main application.
 '''
-from pprint import pformat
 import sys
 from PyQt6.QtWidgets import (
     QMainWindow, QToolBar, 
@@ -16,9 +15,10 @@ from pathlib import Path
 from backend.db.functions import (
     lookup_control_types, lookup_modes
 )
+from backend.db.models import ControlType, Control
 from backend.validators import PydSubmission, PydReagent
 from tools import check_if_app, Settings
-from frontend.custom_widgets import SubmissionsSheet, AlertPop, AddReagentForm, KitAdder, ControlsDatePicker, ImportReagent, ReagentFormWidget
+from frontend.custom_widgets import SubmissionsSheet, AlertPop, AddReagentForm, KitAdder, ControlsDatePicker, ReagentFormWidget
 import logging
 from datetime import date
 import webbrowser
@@ -228,7 +228,7 @@ class App(QMainWindow):
             # send reagent to db
             # store_reagent(ctx=self.ctx, reagent=reagent)
             sqlobj, result = reagent.toSQL()
-            sqlobj.save(ctx=self.ctx)
+            sqlobj.save()
             # result = store_object(ctx=self.ctx, object=reagent.toSQL()[0])
             self.result_reporter(result=result)
             return reagent
@@ -369,12 +369,14 @@ class AddSubForm(QWidget):
         self.control_typer = QComboBox()
         # fetch types of controls 
         # con_types = get_all_Control_Types_names(ctx=parent.ctx)
-        con_types = [item.name for item in lookup_control_types(ctx=parent.ctx)]
+        # con_types = [item.name for item in lookup_control_types(ctx=parent.ctx)]
+        con_types = [item.name for item in ControlType.query()]
         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 = lookup_modes(ctx=parent.ctx)
+        # mode_types = lookup_modes(ctx=parent.ctx)
+        mode_types = Control.get_modes()
         self.mode_typer.addItems(mode_types)
         # create custom widget to get subtypes of analysis
         self.sub_typer = QComboBox()

src/submissions/frontend/custom_widgets/misc.py

@@ -13,10 +13,9 @@ from PyQt6.QtWidgets import (
 )
 from PyQt6.QtCore import Qt, QDate, QSize, pyqtSignal
 from tools import check_not_nan, jinja_template_loading, Settings
-from backend.db.functions import \
-    lookup_reagent_types, lookup_reagents, lookup_submission_type, lookup_reagenttype_kittype_association, \
-    lookup_submissions, lookup_organizations, lookup_kit_types
-from backend.db.models import SubmissionTypeKitTypeAssociation
+from backend.db.functions import (lookup_reagent_types, lookup_reagents, lookup_submission_type, lookup_reagenttype_kittype_association, \
+    lookup_submissions, lookup_organizations, lookup_kit_types)
+from backend.db.models import *
 from sqlalchemy import FLOAT, INTEGER
 import logging
 import numpy as np
@@ -26,6 +25,7 @@ from typing import Tuple, List
 from pprint import pformat
 import difflib
 
+
 logger = logging.getLogger(f"submissions.{__name__}")
 
 env = jinja_template_loading()
@@ -67,7 +67,8 @@ 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 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?
         try:
@@ -103,7 +104,8 @@ class AddReagentForm(QDialog):
         """        
         logger.debug(self.type_input.currentText())
         self.name_input.clear()
-        lookup = lookup_reagents(ctx=self.ctx, reagent_type=self.type_input.currentText())
+        # lookup = lookup_reagents(ctx=self.ctx, reagent_type=self.type_input.currentText())
+        lookup = Reagent.query(reagent_type=self.type_input.currentText())
         self.name_input.addItems(list(set([item.name for item in lookup])))
 
 class ReportDatePicker(QDialog):
@@ -165,7 +167,8 @@ class KitAdder(QWidget):
         used_for = QComboBox()
         used_for.setObjectName("used_for")
         # Insert all existing sample types
-        used_for.addItems([item.name for item in lookup_submission_type(ctx=parent_ctx)])
+        # used_for.addItems([item.name for item in lookup_submission_type(ctx=parent_ctx)])
+        used_for.addItems([item.name for item in SubmissionType.query()])
         used_for.setEditable(True)
         self.grid.addWidget(used_for,3,1)
         # Get all fields in SubmissionTypeKitTypeAssociation
@@ -188,28 +191,6 @@ class KitAdder(QWidget):
                     add_widget = QLineEdit()
             add_widget.setObjectName(column.name)
             self.grid.addWidget(add_widget, idx,1)
-        # self.grid.addWidget(QLabel("Constant cost per full plate (plates, work hours, etc.):"),4,0)
-        # # widget to get constant cost
-        # const_cost = QDoubleSpinBox() #QSpinBox()
-        # const_cost.setObjectName("const_cost")
-        # const_cost.setMinimum(0)
-        # const_cost.setMaximum(9999)
-        # self.grid.addWidget(const_cost,4,1)
-        # self.grid.addWidget(QLabel("Cost per column (multidrop reagents, etc.):"),5,0)
-        # # widget to get mutable costs per column
-        # mut_cost_col = QDoubleSpinBox() #QSpinBox()
-        # mut_cost_col.setObjectName("mut_cost_col")
-        # mut_cost_col.setMinimum(0)
-        # mut_cost_col.setMaximum(9999)
-        # self.grid.addWidget(mut_cost_col,5,1)
-        # self.grid.addWidget(QLabel("Cost per sample (tips, reagents, etc.):"),6,0)
-        # # widget to get mutable costs per column
-        # mut_cost_samp = QDoubleSpinBox() #QSpinBox()
-        # mut_cost_samp.setObjectName("mut_cost_samp")
-        # mut_cost_samp.setMinimum(0)
-        # mut_cost_samp.setMaximum(9999)
-        # self.grid.addWidget(mut_cost_samp,6,1)
-        # button to add additional reagent types
         self.add_RT_btn = QPushButton("Add Reagent Type")
         self.grid.addWidget(self.add_RT_btn)
         self.add_RT_btn.clicked.connect(self.add_RT)
@@ -259,7 +240,7 @@ class KitAdder(QWidget):
         logger.debug(f"Output pyd object: {kit.__dict__}")
         # result = construct_kit_from_yaml(ctx=self.ctx, kit_dict=info)
         sqlobj, result = kit.toSQL(self.ctx)
-        sqlobj.save(ctx=self.ctx)
+        sqlobj.save()
         msg = AlertPop(message=result['message'], status=result['status'])
         msg.exec()
         self.__init__(self.ctx)
@@ -295,7 +276,8 @@ class ReagentTypeForm(QWidget):
         self.reagent_getter = QComboBox()
         self.reagent_getter.setObjectName("rtname")
         # lookup all reagent type names from db
-        lookup = lookup_reagent_types(ctx=ctx)
+        # lookup = lookup_reagent_types(ctx=ctx)
+        lookup = ReagentType.query()
         logger.debug(f"Looked up ReagentType names: {lookup}")
         self.reagent_getter.addItems([item.__str__() for item in lookup])
         self.reagent_getter.setEditable(True)
@@ -387,66 +369,6 @@ class ControlsDatePicker(QWidget):
     def sizeHint(self) -> QSize:
         return QSize(80,20)  
 
-class ImportReagent(QComboBox):
-
-    """
-    NOTE: Depreciated in favour of ReagentFormWidget
-    """
-
-    def __init__(self, ctx:Settings, reagent:dict|PydReagent, extraction_kit:str):
-        super().__init__()
-        self.setEditable(True)
-        if isinstance(reagent, dict):
-            reagent = PydReagent(ctx=ctx, **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 {query_var}")
-        if isinstance(reagent.lot, np.float64):
-            logger.debug(f"{reagent.lot} is a numpy float!")
-            try:
-                reagent.lot = int(reagent.lot)
-            except ValueError:
-                pass
-        # 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.
-        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.
-            if isinstance(rel_reagent, set):
-                for thing in rel_reagent:
-                    output_reg.append(thing)
-            elif isinstance(rel_reagent, str):
-                output_reg.append(rel_reagent)
-        relevant_reagents = output_reg
-        # if reagent in sheet is not found insert it into the front of relevant reagents so it shows 
-        logger.debug(f"Relevant reagents for {reagent.lot}: {relevant_reagents}")
-        if str(reagent.lot) not in relevant_reagents:
-            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=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))
-                    relevant_reagents.insert(0, str(looked_up_reg.lot))
-        else:
-            if len(relevant_reagents) > 1:
-                logger.debug(f"Found {reagent.lot} in relevant reagents: {relevant_reagents}. Moving to front of list.")
-                idx = relevant_reagents.index(str(reagent.lot))
-                logger.debug(f"The index we got for {reagent.lot} in {relevant_reagents} was {idx}")
-                moved_reag = relevant_reagents.pop(idx)
-                relevant_reagents.insert(0, moved_reag)
-            else:
-                logger.debug(f"Found {reagent.lot} in relevant reagents: {relevant_reagents}. But no need to move due to short list.")
-        logger.debug(f"New relevant reagents: {relevant_reagents}")
-        self.setObjectName(f"lot_{reagent.type}")
-        self.addItems(relevant_reagents)
-
 class FirstStrandSalvage(QDialog):
 
     def __init__(self, ctx:Settings, submitter_id:str, rsl_plate_num:str|None=None) -> None:
@@ -492,7 +414,8 @@ class FirstStrandPlateList(QDialog):
         self.buttonBox = QDialogButtonBox(QBtn)
         self.buttonBox.accepted.connect(self.accept)
         self.buttonBox.rejected.connect(self.reject)
-        ww = [item.rsl_plate_num for item in lookup_submissions(ctx=ctx, submission_type="Wastewater")]
+        # ww = [item.rsl_plate_num for item in lookup_submissions(ctx=ctx, submission_type="Wastewater")]
+        ww = [item.rsl_plate_num for item in BasicSubmission.query(submission_type="Wastewater")]
         self.plate1 = QComboBox()
         self.plate2 = QComboBox()
         self.plate3 = QComboBox()
@@ -532,7 +455,8 @@ class ReagentFormWidget(QWidget):
 
     def parse_form(self) -> Tuple[PydReagent, dict]:
         lot = self.lot.currentText()
-        wanted_reagent = lookup_reagents(ctx=self.ctx, lot_number=lot, reagent_type=self.reagent.type)
+        # 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?")
@@ -546,10 +470,12 @@ 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, 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 = 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(ctx=self.ctx, name=wanted_reagent.name, lot=wanted_reagent.lot, type=rt.name, expiry=wanted_reagent.expiry, parsed=not self.missing), None
 
     def updated(self):
@@ -584,7 +510,8 @@ class ReagentFormWidget(QWidget):
             #     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 = lookup_reagents(ctx=self.ctx, reagent_type=reagent.type)
+            lookup = Reagent.query(reagent_type=reagent.type)
             relevant_reagents = [item.__str__() for item in lookup]
             output_reg = []
             for rel_reagent in relevant_reagents:
@@ -602,9 +529,11 @@ class ReagentFormWidget(QWidget):
                     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 = 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 = 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
                     logger.debug(f"Because there was no reagent listed for {reagent.lot}, we will insert the last lot used: {looked_up_reg}")
@@ -743,7 +672,8 @@ class SubmissionFormWidget(QWidget):
                 case 'submitting_lab':
                     add_widget = QComboBox()
                     # lookup organizations suitable for submitting_lab (ctx: self.InfoItem.SubmissionFormWidget.SubmissionFormContainer.AddSubForm )
-                    labs = [item.__str__() for item in lookup_organizations(ctx=obj.ctx)]
+                    # labs = [item.__str__() for item in lookup_organizations(ctx=obj.ctx)]
+                    labs = [item.__str__() for item in Organization.query()]
                     # try to set closest match to top of list
                     try:
                         labs = difflib.get_close_matches(value, labs, len(labs), 0)
@@ -760,7 +690,8 @@ class SubmissionFormWidget(QWidget):
                     add_widget = QComboBox()
                     # lookup existing kits by 'submission_type' decided on by sheetparser
                     logger.debug(f"Looking up kits used for {submission_type}")
-                    uses = [item.__str__() for item in lookup_kit_types(ctx=obj.ctx, used_for=submission_type)]
+                    # uses = [item.__str__() for item in lookup_kit_types(ctx=obj.ctx, used_for=submission_type)]
+                    uses = [item.__str__() for item in KitType.query(used_for=submission_type)]
                     obj.uses = uses
                     logger.debug(f"Kits received for {submission_type}: {uses}")
                     if check_not_nan(value):
@@ -786,7 +717,8 @@ 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 lookup_submission_type(ctx=obj.ctx)]
+                    cats += [item.name for item in SubmissionType.query()]
                     try:
                         cats.insert(0, cats.pop(cats.index(value)))
                     except ValueError:

src/submissions/frontend/custom_widgets/pop_ups.py

@@ -8,6 +8,7 @@ from PyQt6.QtWidgets import (
 from tools import jinja_template_loading
 import logging
 from backend.db.functions import lookup_kit_types, lookup_submission_type
+from backend.db.models import KitType, SubmissionType
 from typing import Literal
 
 logger = logging.getLogger(f"submissions.{__name__}")
@@ -53,7 +54,8 @@ class KitSelector(QDialog):
         super().__init__()
         self.setWindowTitle(title)
         self.widget = QComboBox()
-        kits = [item.__str__() for item in lookup_kit_types(ctx=ctx)]
+        # kits = [item.__str__() for item in lookup_kit_types(ctx=ctx)]
+        kits = [item.__str__() for item in KitType.query()]
         self.widget.addItems(kits)
         self.widget.setEditable(False)
         # set yes/no buttons
@@ -80,7 +82,8 @@ class SubmissionTypeSelector(QDialog):
         super().__init__()
         self.setWindowTitle(title)
         self.widget = QComboBox()
-        sub_type = [item.name for item in lookup_submission_type(ctx=ctx)]
+        # sub_type = [item.name for item in lookup_submission_type(ctx=ctx)]
+        sub_type = [item.name for item in SubmissionType.query()]
         self.widget.addItems(sub_type)
         self.widget.setEditable(False)
         # set yes/no buttons

src/submissions/frontend/custom_widgets/sub_details.py

@@ -15,7 +15,8 @@ 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.functions import submissions_to_df, delete_submission, lookup_submissions
+from backend.db.functions import submissions_to_df
+from backend.db.models import BasicSubmission
 from backend.excel import make_hitpicks
 from tools import check_if_app, Settings
 from tools import jinja_template_loading
@@ -98,7 +99,7 @@ class SubmissionsSheet(QTableView):
         """
         sets data in model
         """        
-        self.data = submissions_to_df(ctx=self.ctx)
+        self.data = submissions_to_df()
         try:
             self.data['id'] = self.data['id'].apply(str)
             self.data['id'] = self.data['id'].str.zfill(3)
@@ -180,7 +181,8 @@ class SubmissionsSheet(QTableView):
         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(ctx=self.ctx, id=value)
+            # delete_submission(id=value)
+            BasicSubmission.query(id=value).delete()
         else:
             return
         self.setData()
@@ -199,7 +201,8 @@ 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_submissions(ctx=self.ctx, id=id) for id in indices]
+        # subs = [lookup_submissions(ctx=self.ctx, id=id) for id in indices]
+        subs = [BasicSubmission.query(id=id) for id in indices]
         # full list of samples
         dicto = []
         # list to contain plate images
@@ -256,7 +259,8 @@ class SubmissionDetails(QDialog):
         interior = QScrollArea()
         interior.setParent(self)
         # get submision from db
-        sub = lookup_submissions(ctx=ctx, id=id)
+        # sub = lookup_submissions(ctx=ctx, id=id)
+        sub = BasicSubmission.query(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
@@ -427,7 +431,8 @@ class SubmissionComment(QDialog):
         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_submissions(ctx = self.ctx, rsl_number=self.rsl)
+        # sub = lookup_submissions(ctx = self.ctx, rsl_number=self.rsl)
+        sub = BasicSubmission.query(rsl_number=self.rsl)
         try:
             sub.comment.append(full_comment)
         except AttributeError:

src/submissions/frontend/main_window_functions.py

@@ -281,7 +281,7 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
     obj.pyd: PydSubmission = obj.form.parse_form()
     logger.debug(f"Submission: {pprint.pformat(obj.pyd)}")
     logger.debug("Checking kit integrity...")
-    kit_integrity = check_kit_integrity(ctx=obj.ctx, sub=obj.pyd)
+    kit_integrity = check_kit_integrity(sub=obj.pyd)
     if kit_integrity != None:
         return obj, dict(message=kit_integrity['message'], status="critical")
     base_submission, result = obj.pyd.toSQL()
@@ -307,11 +307,11 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
             pass
     # add reagents to submission object
     for reagent in base_submission.reagents:
-        update_last_used(ctx=obj.ctx, reagent=reagent, kit=base_submission.extraction_kit)
+        update_last_used(reagent=reagent, kit=base_submission.extraction_kit)
     logger.debug(f"Here is the final submission: {pprint.pformat(base_submission.__dict__)}")
     logger.debug(f"Parsed reagents: {pprint.pformat(base_submission.reagents)}")    
     logger.debug(f"Sending submission: {base_submission.rsl_plate_num} to database.")
-    base_submission.save(ctx=obj.ctx)
+    base_submission.save()
     # update summary sheet
     obj.table_widget.sub_wid.setData()
     # reset form
@@ -319,12 +319,12 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
     logger.debug(f"All attributes of obj: {pprint.pformat(obj.__dict__)}")
     wkb = obj.pyd.autofill_excel()
     if wkb != None:
-        fname = select_save_file(obj=obj, default_name=obj.pyd.rsl_plate_num['value'], extension="xlsx")
+        fname = select_save_file(obj=obj, default_name=obj.pyd.construct_filename(), extension="xlsx")
         wkb.save(filename=fname.__str__())
     if hasattr(obj.pyd, 'csv'):
         dlg = QuestionAsker("Export CSV?", "Would you like to export the csv file?")
         if dlg.exec():
-            fname = select_save_file(obj, f"{base_submission.rsl_plate_num}.csv", extension="csv")
+            fname = select_save_file(obj, f"{obj.pyd.rsl_plate_num['value']}.csv", extension="csv")
             try:
                 obj.csv.to_csv(fname.__str__(), index=False)
             except PermissionError:
@@ -348,7 +348,8 @@ def generate_report_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
         info = dlg.parse_form()
         logger.debug(f"Report info: {info}")
         # find submissions based on date range
-        subs = lookup_submissions(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'])
+        subs = BasicSubmission.query(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
@@ -468,7 +469,7 @@ def controls_getter_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
     obj.mode = obj.table_widget.mode_typer.currentText()
     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 = get_control_subtypes(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
@@ -502,7 +503,8 @@ def chart_maker_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
     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 = lookup_controls(ctx=obj.ctx, control_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)
+    controls = Control.query(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
@@ -544,10 +546,12 @@ def link_controls_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
     """    
     result = None
     # all_bcs = lookup_all_submissions_by_type(obj.ctx, "Bacterial Culture")
-    all_bcs = lookup_submissions(ctx=obj.ctx, submission_type="Bacterial Culture")
+    # all_bcs = lookup_submissions(ctx=obj.ctx, submission_type="Bacterial Culture")
+    all_bcs = BasicSubmission.query(submission_type="Bacterial Culture")
     logger.debug(all_bcs)
     # all_controls = get_all_controls(obj.ctx)
-    all_controls = lookup_controls(ctx=obj.ctx)
+    # all_controls = lookup_controls(ctx=obj.ctx)
+    all_controls = Control.query()
     ac_list = [control.name for control in all_controls]
     count = 0
     for bcs in all_bcs:
@@ -615,7 +619,8 @@ def link_extractions_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
             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_submissions(ctx=obj.ctx, rsl_number=new_run['rsl_plate_num'])
+        # sub = lookup_submissions(ctx=obj.ctx, rsl_number=new_run['rsl_plate_num'])
+        sub = BasicSubmission.query(rsl_number=new_run['rsl_plate_num'])
         # If no such submission exists, move onto the next run
         if sub == None:
             continue
@@ -680,7 +685,8 @@ def link_pcr_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
             )
         # lookup imported submission
         # sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=new_run['rsl_plate_num'])
-        sub = lookup_submissions(ctx=obj.ctx, rsl_number=new_run['rsl_plate_num'])
+        # sub = lookup_submissions(ctx=obj.ctx, rsl_number=new_run['rsl_plate_num'])
+        sub = BasicSubmission.query(rsl_number=new_run['rsl_plate_num'])
         # if imported submission doesn't exist move on to next run
         if sub == None:
             continue
@@ -734,7 +740,7 @@ def import_pcr_results_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
     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_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:
@@ -742,7 +748,8 @@ def import_pcr_results_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
         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 = 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:
@@ -779,7 +786,7 @@ 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
-        update_subsampassoc_with_pcr(ctx=obj.ctx, submission=sub, sample=sample, input_dict=sample_dict)
+        update_subsampassoc_with_pcr(submission=sub, sample=sample, input_dict=sample_dict)
 
     result = dict(message=f"We added PCR info to {sub.rsl_plate_num}.", status='information')
     return obj, result
@@ -877,8 +884,6 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
     fname = select_save_file(obj=obj, default_name=info['rsl_plate_num'], extension="xlsx")
     workbook.save(filename=fname.__str__())
 
-
-
 def construct_first_strand_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
     """
     Generates a csv file from client submitted xlsx file.
@@ -891,13 +896,16 @@ def construct_first_strand_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]
     """    
     def get_plates(input_sample_number:str, plates:list) -> Tuple[int, str]:
         logger.debug(f"Looking up {input_sample_number} in {plates}")
-        samp = lookup_samples(ctx=obj.ctx, ww_processing_num=input_sample_number)
+        # samp = lookup_samples(ctx=obj.ctx, ww_processing_num=input_sample_number)
+        samp = BasicSample.query(ww_processing_num=input_sample_number)
         if samp ==  None:
-            samp = lookup_samples(ctx=obj.ctx, submitter_id=input_sample_number)
+            # samp = lookup_samples(ctx=obj.ctx, submitter_id=input_sample_number)
+            samp = BasicSample.query(submitter_id=input_sample_number)
         if samp == None:
             return None, None
         logger.debug(f"Got sample: {samp}")
-        new_plates = [(iii+1, lookup_submission_sample_association(ctx=obj.ctx, sample=samp, submission=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)]
+        new_plates = [(iii+1, SubmissionSampleAssociation.query(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])