Commit pre-refactor for code cleanup.

src/submissions/__init__.py

@@ -1,4 +1,4 @@
 # __init__.py
 
 # Version of the realpython-reader package
-__version__ = "1.2.2"
+__version__ = "1.2.3"

src/submissions/backend/db/__init__.py

@@ -329,7 +329,7 @@ def lookup_all_submissions_by_type(ctx:dict, type:str|None=None) -> list[models.
     if type == None:
         subs = ctx['database_session'].query(models.BasicSubmission).all()
     else:
-        subs = ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.submission_type==type).all()
+        subs = ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.submission_type==type.lower().replace(" ", "_")).all()
     return subs
 
 def lookup_all_orgs(ctx:dict) -> list[models.Organization]:

src/submissions/backend/db/functions/__init__.py

@@ -0,0 +1,21 @@
+from ..models import *
+import logging
+
+logger = logging.getLogger(f"submissions.{__name__}")
+
+def check_kit_integrity(sub:BasicSubmission):
+    ext_kit_rtypes = [reagenttype.name for reagenttype in sub.extraction_kit.reagent_types]
+    logger.debug(f"Kit reagents: {ext_kit_rtypes}")
+    reagenttypes = [reagent.type.name for reagent in sub.reagents]
+    logger.debug(f"Submission reagents: {reagenttypes}")
+    check = set(ext_kit_rtypes) == set(reagenttypes)
+    logger.debug(f"Checking if reagents match kit contents: {check}")
+    common = list(set(ext_kit_rtypes).intersection(reagenttypes))
+    logger.debug(f"common reagents types: {common}")
+    if check:
+        result = None
+    else:
+        result = {'message' : f"Couldn't verify reagents match listed kit components.\n\nIt looks like you are missing: {[x.upper for x in ext_kit_rtypes if x not in common]}\n\nAlternatively, you may have set the wrong extraction kit."}
+    return result
+    
+    

src/submissions/backend/db/models/kits.py

@@ -78,7 +78,7 @@ class Reagent(Base):
         Returns:
             str: string representing this object's lot number
         """        
-        return self.lot
+        return str(self.lot)
 
     def to_sub_dict(self) -> dict:
         """

src/submissions/backend/excel/parser.py

@@ -7,6 +7,7 @@ import re
 import numpy as np
 from datetime import date
 import uuid
+from frontend.functions import check_not_nan
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -60,6 +61,7 @@ class SheetParser(object):
         """
         Dummy function to handle unknown excel structures
         """    
+        logger.error(f"Unknown excel workbook structure. Cannot parse.")    
         self.sub = None
     
 
@@ -96,11 +98,11 @@ class SheetParser(object):
                 if ii == 11:
                     continue
                 logger.debug(f"Running reagent parse for {row[1]} with type {type(row[1])} and value: {row[2]} with type {type(row[2])}")
-                try:
+                # try:
-                    check = not np.isnan(row[1])
+                #     check = not np.isnan(row[1])
-                except TypeError:
+                # except TypeError:
-                    check = True
+                #     check = True
-                if not isinstance(row[2], float) and check:
+                if not isinstance(row[2], float) and check_not_nan(row[1]):
                     # must be prefixed with 'lot_' to be recognized by gui
                     try:
                         reagent_type = row[1].replace(' ', '_').lower().strip()
@@ -114,7 +116,18 @@ class SheetParser(object):
                         logger.debug(f"Couldn't upperize {row[2]}, must be a number")
                         output_var = row[2]
                     logger.debug(f"Output variable is {output_var}")
-                    self.sub[f"lot_{reagent_type}"] = output_var
+                    # self.sub[f"lot_{reagent_type}"] = output_var
+                    # update 2023-02-10 to above allowing generation of expiry date in adding reagent to db.
+                    logger.debug(f"Expiry date for imported reagent: {row[3]}")
+                    try:
+                        check = not np.isnan(row[3])
+                    except TypeError:
+                        check = True
+                    if check:
+                        expiry = row[3].date()
+                    else:
+                        expiry = date.today()
+                    self.sub[f"lot_{reagent_type}"] = {'lot':output_var, 'exp':expiry}
 
         submission_info = self._parse_generic("Sample List")
         # iloc is [row][column] and the first row is set as header row so -2

src/submissions/backend/excel/reports.py

@@ -33,7 +33,9 @@ def make_report_xlsx(records:list[dict]) -> DataFrame:
     # put submissions with the same lab together
     df = df.sort_values("Submitting Lab")
     # aggregate cost and sample count columns
-    df2 = df.groupby(["Submitting Lab", "Extraction Kit"]).agg({'Cost': ['sum', 'count'], 'Sample Count':['sum']})
+    df2 = df.groupby(["Submitting Lab", "Extraction Kit"]).agg({'Extraction Kit':'count', 'Cost': 'sum', 'Sample Count':'sum'})
+    df2 = df2.rename(columns={"Extraction Kit": 'Kit Count'})
+    logger.debug(f"Output daftaframe for xlsx: {df2.columns}")
     # apply formating to cost column
     # df2.iloc[:, (df2.columns.get_level_values(1)=='sum') & (df2.columns.get_level_values(0)=='Cost')] = df2.iloc[:, (df2.columns.get_level_values(1)=='sum') & (df2.columns.get_level_values(0)=='Cost')].applymap('${:,.2f}'.format)
     return df2
@@ -54,11 +56,14 @@ def make_report_html(df:DataFrame, start_date:date, end_date:date) -> str:
     """    
     old_lab = ""
     output = []
+    logger.debug(f"Report DataFrame: {df}")
     for ii, row in enumerate(df.iterrows()):
         row = [item for item in row]
+        logger.debug(f"Row: {row}")
+        
         lab = row[0][0]
         logger.debug(f"Old lab: {old_lab}, Current lab: {lab}")
-        kit = dict(name=row[0][1], cost=row[1][('Cost', 'sum')], plate_count=int(row[1][('Cost', 'count')]), sample_count=int(row[1][('Sample Count', 'sum')]))
+        kit = dict(name=row[0][1], cost=row[1]['Cost'], plate_count=int(row[1]['Kit Count']), sample_count=int(row[1]['Sample Count']))
         if lab == old_lab:
             output[ii-1]['kits'].append(kit)
             output[ii-1]['total_cost'] += kit['cost']

src/submissions/frontend/__init__.py

@@ -10,9 +10,7 @@ from PyQt6.QtWidgets import (
 from PyQt6.QtGui import QAction
 from PyQt6.QtCore import QSignalBlocker
 from PyQt6.QtWebEngineWidgets import QWebEngineView
-
 # import pandas as pd
-
 from pathlib import Path
 import plotly
 import pandas as pd
@@ -21,7 +19,7 @@ from xhtml2pdf import pisa
 # import plotly.express as px
 import yaml
 import pprint
-
+import numpy as np
 from backend.excel.parser import SheetParser
 from backend.excel.reports import convert_control_by_mode, convert_data_list_to_df
 from backend.db import (construct_submission_info, lookup_reagent, 
@@ -30,9 +28,13 @@ from backend.db import (construct_submission_info, lookup_reagent,
     get_all_Control_Types_names, create_kit_from_yaml, get_all_available_modes, get_all_controls_by_type,
     get_control_subtypes, lookup_all_submissions_by_type, get_all_controls, lookup_submission_by_rsl_num
 )
+from .functions import check_kit_integrity, check_not_nan
 from backend.excel.reports import make_report_xlsx, make_report_html
+
 import numpy
-from frontend.custom_widgets import AddReagentQuestion, AddReagentForm, SubmissionsSheet, ReportDatePicker, KitAdder, ControlsDatePicker, OverwriteSubQuestion
+from frontend.custom_widgets.sub_details import SubmissionsSheet
+from frontend.custom_widgets.pop_ups import AddReagentQuestion, OverwriteSubQuestion, AlertPop
+from frontend.custom_widgets import AddReagentForm, ReportDatePicker, KitAdder, ControlsDatePicker
 import logging
 import difflib
 from getpass import getuser
@@ -130,6 +132,7 @@ class App(QMainWindow):
         logger.debug(self.ctx)
         # initialize samples
         self.samples = []
+        self.reagents = {}
         # set file dialog
         home_dir = str(Path(self.ctx["directory_path"]))
         fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir)[0])
@@ -180,14 +183,9 @@ class App(QMainWindow):
                     # create label
                     self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
                     # if extraction kit not available, all other values fail
-                    if prsr.sub[item] == 'nan':
+                    if np.isnan(prsr.sub[item]):
-                        msg = QMessageBox()
+                        msg = AlertPop(message="Make sure to check your extraction kit!", status="warning")
-                        # msg.setIcon(QMessageBox.critical)
-                        msg.setText("Error")
-                        msg.setInformativeText('You need to enter a value for extraction kit.')
-                        msg.setWindowTitle("Error")
                         msg.exec()
-                        break
                     # create combobox to hold looked up kits
                     add_widget = QComboBox()
                     # lookup existing kits by 'submission_type' decided on by sheetparser
@@ -216,13 +214,13 @@ class App(QMainWindow):
                     query_var = item.replace("lot_", "")
                     logger.debug(f"Query for: {query_var}")
                     if isinstance(prsr.sub[item], numpy.float64):
-                        logger.debug(f"{prsr.sub[item]} is a numpy float!")
+                        logger.debug(f"{prsr.sub[item]['lot']} is a numpy float!")
                         try:
-                            prsr.sub[item] = int(prsr.sub[item])
+                            prsr.sub[item] = int(prsr.sub[item]['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} and kit: {prsr.sub['extraction_kit']}")
+                    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=self.ctx, type_name=query_var)]#, kit_name=prsr.sub['extraction_kit'])]
                     output_reg = []
@@ -235,15 +233,12 @@ class App(QMainWindow):
                     relevant_reagents = output_reg
                     logger.debug(f"Relevant reagents: {relevant_reagents}")
                     # if reagent in sheet is not found insert it into items
-                    if prsr.sub[item] not in relevant_reagents and prsr.sub[item] != 'nan':
+                    if str(prsr.sub[item]['lot']) not in relevant_reagents and prsr.sub[item]['lot'] != 'nan':
-                        try:
+                        if check_not_nan(prsr.sub[item]['lot']):
-                            check = not numpy.isnan(prsr.sub[item])
+                            relevant_reagents.insert(0, str(prsr.sub[item]['lot']))
-                        except TypeError:
+                    logger.debug(f"New relevant reagents: {relevant_reagents}")
-                            check = True
-                        if check:
-                            relevant_reagents.insert(0, str(prsr.sub[item]))
-                    logger.debug(f"Relevant reagents: {relevant_reagents}")
                     add_widget.addItems(relevant_reagents)
+                    self.reagents[item] = prsr.sub[item]
                 # TODO: make samples not appear in frame.
                 case 'samples':
                     # hold samples in 'self' until form submitted
@@ -259,6 +254,7 @@ class App(QMainWindow):
         submit_btn = QPushButton("Submit")
         self.table_widget.formlayout.addWidget(submit_btn)
         submit_btn.clicked.connect(self.submit_new_sample)
+        logger.debug(f"Imported reagents: {self.reagents}")
         
     def submit_new_sample(self):
         """
@@ -278,7 +274,9 @@ class App(QMainWindow):
             if wanted_reagent == None:
                 dlg = AddReagentQuestion(reagent_type=reagent, reagent_lot=reagents[reagent])
                 if dlg.exec():
-                    wanted_reagent = self.add_reagent(reagent_lot=reagents[reagent], reagent_type=reagent.replace("lot_", ""))
+                    logger.debug(f"checking reagent: {reagent} in self.reagents. Result: {self.reagents[reagent]}")
+                    expiry_date = self.reagents[reagent]['exp']
+                    wanted_reagent = self.add_reagent(reagent_lot=reagents[reagent], reagent_type=reagent.replace("lot_", ""), expiry=expiry_date)
                 else:
                     logger.debug("Will not add reagent.")
             if wanted_reagent != None:
@@ -301,15 +299,17 @@ class App(QMainWindow):
         for reagent in parsed_reagents:
             base_submission.reagents.append(reagent)
             # base_submission.reagents_id = reagent.id
+        logger.debug("Checking kit integrity...")
+        kit_integrity = check_kit_integrity(base_submission)
+        if kit_integrity != None:
+            msg = AlertPop(message=kit_integrity['message'], status="critical")
+            msg.exec()
+            return
         logger.debug(f"Sending submission: {base_submission.rsl_plate_num} to database.")
         result = store_submission(ctx=self.ctx, base_submission=base_submission)
-        # check result of storing for issues
+        # # check result of storing for issues
         if result != None:
-            msg = QMessageBox()
+            msg = AlertPop(result['message'])
-            # msg.setIcon(QMessageBox.critical)
-            msg.setText("Error")
-            msg.setInformativeText(result['message'])
-            msg.setWindowTitle("Error")
             msg.exec()
         # update summary sheet
         self.table_widget.sub_wid.setData()
@@ -318,7 +318,7 @@ class App(QMainWindow):
             item.setParent(None)
 
 
-    def add_reagent(self, reagent_lot:str|None=None, reagent_type:str|None=None):
+    def add_reagent(self, reagent_lot:str|None=None, reagent_type:str|None=None, expiry:date|None=None):
         """
         Action to create new reagent in DB.
 
@@ -332,7 +332,7 @@ class App(QMainWindow):
         if isinstance(reagent_lot, bool):
             reagent_lot = ""
         # create form
-        dlg = AddReagentForm(ctx=self.ctx, reagent_lot=reagent_lot, reagent_type=reagent_type)
+        dlg = AddReagentForm(ctx=self.ctx, reagent_lot=reagent_lot, reagent_type=reagent_type, expiry=expiry)
         if dlg.exec():
             # extract form info
             labels, values = self.extract_form_info(dlg)
@@ -341,7 +341,7 @@ class App(QMainWindow):
             # 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)
             return reagent
             
 
@@ -417,19 +417,16 @@ class App(QMainWindow):
                 # set_column(idx, idx, max_len)  # set column width
             # colu = worksheet.column_dimensions["C"]
             # style = NamedStyle(name="custom_currency", number_format='Currency')
-            for cell in worksheet['C']:
+            for cell in worksheet['D']:
                 # try:
                 #     check = int(cell.row)
                 # except TypeError:
                 #     continue
-                if cell.row > 3:
+                if cell.row > 1:
                     cell.style = 'Currency'
             writer.close()
                   
 
-            
-            
-
     def add_kit(self):
         """
         Constructs new kit from yaml and adds to DB.
@@ -477,7 +474,7 @@ class App(QMainWindow):
         # correct start date being more recent than end date and rerun
         if self.table_widget.datepicker.start_date.date() > self.table_widget.datepicker.end_date.date():
             logger.warning("Start date after end date is not allowed!")
-            threemonthsago = self.table_widget.datepicker.end_date.date().addDays(-90)
+            threemonthsago = self.table_widget.datepicker.end_date.date().addDays(-60)
             # block signal that will rerun controls getter and set start date
             with QSignalBlocker(self.table_widget.datepicker.start_date) as blocker:
                 self.table_widget.datepicker.start_date.setDate(threemonthsago)
@@ -572,12 +569,14 @@ class App(QMainWindow):
                 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 sample not in ac_list:
+                if not any([ac.startswith(sample) for ac in ac_list]):
                     continue
                 else:
                     for control in all_controls:
                         diff = difflib.SequenceMatcher(a=sample, b=control.name).ratio()
-                        if diff > 0.955:
+                        # if diff > 0.955:
+                        if control.name.startswith(sample):
                             logger.debug(f"Checking {sample} against {control.name}... {diff}")
                         # if sample == control.name:
                             logger.debug(f"Found match:\n\tSample: {sample}\n\tControl: {control.name}\n\tDifference: {diff}")

src/submissions/frontend/custom_widgets/__init__.py

@@ -1,18 +1,17 @@
+from datetime import date
 from PyQt6.QtWidgets import (
     QLabel, QVBoxLayout,
     QLineEdit, QComboBox, QDialog, 
-    QDialogButtonBox, QDateEdit, QTableView,
+    QDialogButtonBox, QDateEdit, QSizePolicy, QWidget,
-    QTextEdit, QSizePolicy, QWidget,
     QGridLayout, QPushButton, QSpinBox,
-    QScrollBar, QScrollArea, QHBoxLayout,
+    QScrollBar, QHBoxLayout,
-    QMessageBox, QFileDialog, QToolBar
+    QMessageBox
 )
-from PyQt6.QtCore import Qt, QDate, QAbstractTableModel, QSize
+from PyQt6.QtCore import Qt, QDate, QSize
-from PyQt6.QtGui import QFontMetrics, QAction
+# from PyQt6.QtGui import QFontMetrics, QAction
 
-from backend.db import get_all_reagenttype_names, submissions_to_df, lookup_submission_by_id, lookup_all_sample_types, create_kit_from_yaml
+from backend.db import get_all_reagenttype_names, lookup_all_sample_types, create_kit_from_yaml
 from jinja2 import Environment, FileSystemLoader
-from xhtml2pdf import pisa
 import sys
 from pathlib import Path
 import logging
@@ -26,55 +25,12 @@ else:
 loader = FileSystemLoader(loader_path)
 env = Environment(loader=loader)
 
-class AddReagentQuestion(QDialog):
-    """
-    dialog to ask about adding a new reagne to db
-    """    
-    def __init__(self, reagent_type:str, reagent_lot:str) -> None:
-        super().__init__()
-
-        self.setWindowTitle(f"Add {reagent_lot}?")
-
-        QBtn = QDialogButtonBox.StandardButton.Yes | QDialogButtonBox.StandardButton.No
-
-        self.buttonBox = QDialogButtonBox(QBtn)
-        self.buttonBox.accepted.connect(self.accept)
-        self.buttonBox.rejected.connect(self.reject)
-
-        self.layout = QVBoxLayout()
-        message = QLabel(f"Couldn't find reagent type {reagent_type.replace('_', ' ').title().strip('Lot')}: {reagent_lot} in the database.\nWould you like to add it?")
-        self.layout.addWidget(message)
-        self.layout.addWidget(self.buttonBox)
-        self.setLayout(self.layout)
-
-
-class OverwriteSubQuestion(QDialog):
-    """
-    dialog to ask about overwriting existing submission
-    """    
-    def __init__(self, message:str, rsl_plate_num:str) -> None:
-        super().__init__()
-
-        self.setWindowTitle(f"Overwrite {rsl_plate_num}?")
-
-        QBtn = QDialogButtonBox.StandardButton.Yes | QDialogButtonBox.StandardButton.No
-
-        self.buttonBox = QDialogButtonBox(QBtn)
-        self.buttonBox.accepted.connect(self.accept)
-        self.buttonBox.rejected.connect(self.reject)
-
-        self.layout = QVBoxLayout()
-        message = QLabel(message)
-        self.layout.addWidget(message)
-        self.layout.addWidget(self.buttonBox)
-        self.setLayout(self.layout)
-
 
 class AddReagentForm(QDialog):
     """
     dialog to add gather info about new reagent
     """    
-    def __init__(self, ctx:dict, reagent_lot:str|None, reagent_type:str|None) -> None:
+    def __init__(self, ctx:dict, reagent_lot:str|None, reagent_type:str|None, expiry:date|None=None) -> None:
         super().__init__()
 
         if reagent_lot == None:
@@ -92,7 +48,10 @@ class AddReagentForm(QDialog):
         lot_input.setText(reagent_lot)
         # get expiry info
         exp_input = QDateEdit(calendarPopup=True)
+        if expiry == None:
             exp_input.setDate(QDate.currentDate())
+        else:
+            exp_input.setDate(expiry)
         # get reagent type info
         type_input = QComboBox()
         type_input.addItems([item.replace("_", " ").title() for item in get_all_reagenttype_names(ctx=ctx)])
@@ -117,172 +76,6 @@ class AddReagentForm(QDialog):
         self.setLayout(self.layout)
 
 
-
-class pandasModel(QAbstractTableModel):
-    """
-    pandas model for inserting summary sheet into gui
-    """
-    def __init__(self, data) -> None:
-        QAbstractTableModel.__init__(self)
-        self._data = data
-
-    def rowCount(self, parent=None) -> int:
-        """
-        does what it says
-
-        Args:
-            parent (_type_, optional): _description_. Defaults to None.
-
-        Returns:
-            int: number of rows in data
-        """
-        return self._data.shape[0]
-
-    def columnCount(self, parnet=None) -> int:
-        """
-        does what it says
-
-        Args:
-            parnet (_type_, optional): _description_. Defaults to None.
-
-        Returns:
-            int: number of columns in data
-        """        
-        return self._data.shape[1]
-
-    def data(self, index, role=Qt.ItemDataRole.DisplayRole) -> str|None:
-        if index.isValid():
-            if role == Qt.ItemDataRole.DisplayRole:
-                return str(self._data.iloc[index.row(), index.column()])
-        return None
-
-    def headerData(self, col, orientation, role):
-        if orientation == Qt.Orientation.Horizontal and role == Qt.ItemDataRole.DisplayRole:
-            return self._data.columns[col]
-        return None
-        
-
-class SubmissionsSheet(QTableView):
-    """
-    presents submission summary to user in tab1
-    """    
-    def __init__(self, ctx:dict) -> None:
-        """
-        initialize
-
-        Args:
-            ctx (dict): settings passed from gui
-        """        
-        super().__init__()
-        self.ctx = ctx
-        self.setData()
-        self.resizeColumnsToContents()
-        self.resizeRowsToContents()
-        # self.clicked.connect(self.test)
-        self.doubleClicked.connect(self.show_details)
- 
-    def setData(self) -> None: 
-        """
-        sets data in model
-        """        
-        self.data = submissions_to_df(ctx=self.ctx)
-        self.model = pandasModel(self.data)
-        self.setModel(self.model)
-        # self.resize(800,600)
-
-    def show_details(self) -> None:
-        """
-        creates detailed data to show in seperate window
-        """        
-        index=(self.selectionModel().currentIndex())
-        # logger.debug(index)
-        value=index.sibling(index.row(),0).data()
-        dlg = SubmissionDetails(ctx=self.ctx, id=value)
-        # dlg.show()
-        if dlg.exec():
-            pass
-
-
-
-    
-class SubmissionDetails(QDialog):
-    """
-    a window showing text details of submission
-    """    
-    def __init__(self, ctx:dict, id:int) -> None:
-
-        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)
-        self.base_dict = data.to_dict()
-        logger.debug(f"Base dict: {self.base_dict}")
-        # don't want id
-        del self.base_dict['id']
-        # convert sub objects to dicts
-        self.base_dict['reagents'] = [item.to_sub_dict() for item in data.reagents]
-        self.base_dict['samples'] = [item.to_sub_dict() for item in data.samples]
-        # 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)
-        self.layout = QVBoxLayout()
-        self.setFixedSize(w, 900)
-        btn = QPushButton("Export PDF")
-        btn.setParent(self)
-        btn.setFixedWidth(w)
-        btn.clicked.connect(self.export)
-        
-
-    # def _create_actions(self):
-    #     self.exportAction = QAction("Export", self)
-        
-
-    def export(self):
-        template = env.get_template("submission_details.html")
-        html = template.render(sub=self.base_dict)
-        # logger.debug(f"Submission details: {self.base_dict}")
-        home_dir = Path(self.ctx["directory_path"]).joinpath(f"Submission_Details_{self.base_dict['Plate Number']}.pdf").resolve().__str__()
-        fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".pdf")[0])
-        # logger.debug(f"report output name: {fname}")
-        # df.to_excel(fname, engine='openpyxl')
-        if fname.__str__() == ".":
-            logger.debug("Saving pdf was cancelled.")
-            return
-        try:
-            with open(fname, "w+b") as f:
-                pisa.CreatePDF(html, dest=f)
-        except PermissionError as e:
-            logger.error(f"Error saving pdf: {e}")
-            msg = QMessageBox()
-            msg.setText("Permission Error")
-            msg.setInformativeText(f"Looks like {fname.__str__()} is open.\nPlease close it and try again.")
-            msg.setWindowTitle("Permission Error")
-            msg.exec()
-        
-
-
 class ReportDatePicker(QDialog):
     """
     custom dialog to ask for report start/stop dates
@@ -467,7 +260,7 @@ class ControlsDatePicker(QWidget):
 
         self.start_date = QDateEdit(calendarPopup=True)
         # start date is three month prior to end date by default
-        threemonthsago = QDate.currentDate().addDays(-90)
+        threemonthsago = QDate.currentDate().addDays(-60)
         self.start_date.setDate(threemonthsago)
         self.end_date = QDateEdit(calendarPopup=True)
         self.end_date.setDate(QDate.currentDate())

src/submissions/frontend/custom_widgets/pop_ups.py

@@ -0,0 +1,78 @@
+# from datetime import date
+from PyQt6.QtWidgets import (
+    QLabel, QVBoxLayout, QDialog, 
+    QDialogButtonBox, QMessageBox
+)
+# from PyQt6.QtCore import Qt, QDate, QSize
+# from PyQt6.QtGui import QFontMetrics, QAction
+
+# from backend.db import get_all_reagenttype_names, lookup_all_sample_types, create_kit_from_yaml
+from jinja2 import Environment, FileSystemLoader
+import sys
+from pathlib import Path
+import logging
+
+logger = logging.getLogger(f"submissions.{__name__}")
+
+if getattr(sys, 'frozen', False):
+    loader_path = Path(sys._MEIPASS).joinpath("files", "templates")
+else:
+    loader_path = Path(__file__).parents[2].joinpath('templates').absolute().__str__()
+loader = FileSystemLoader(loader_path)
+env = Environment(loader=loader)
+
+
+class AddReagentQuestion(QDialog):
+    """
+    dialog to ask about adding a new reagne to db
+    """    
+    def __init__(self, reagent_type:str, reagent_lot:str) -> QDialog:
+        super().__init__()
+
+        self.setWindowTitle(f"Add {reagent_lot}?")
+
+        QBtn = QDialogButtonBox.StandardButton.Yes | QDialogButtonBox.StandardButton.No
+
+        self.buttonBox = QDialogButtonBox(QBtn)
+        self.buttonBox.accepted.connect(self.accept)
+        self.buttonBox.rejected.connect(self.reject)
+
+        self.layout = QVBoxLayout()
+        message = QLabel(f"Couldn't find reagent type {reagent_type.replace('_', ' ').title().strip('Lot')}: {reagent_lot} in the database.\n\nWould you like to add it?")
+        self.layout.addWidget(message)
+        self.layout.addWidget(self.buttonBox)
+        self.setLayout(self.layout)
+
+
+class OverwriteSubQuestion(QDialog):
+    """
+    dialog to ask about overwriting existing submission
+    """    
+    def __init__(self, message:str, rsl_plate_num:str) -> QDialog:
+        super().__init__()
+
+        self.setWindowTitle(f"Overwrite {rsl_plate_num}?")
+
+        QBtn = QDialogButtonBox.StandardButton.Yes | QDialogButtonBox.StandardButton.No
+
+        self.buttonBox = QDialogButtonBox(QBtn)
+        self.buttonBox.accepted.connect(self.accept)
+        self.buttonBox.rejected.connect(self.reject)
+
+        self.layout = QVBoxLayout()
+        message = QLabel(message)
+        self.layout.addWidget(message)
+        self.layout.addWidget(self.buttonBox)
+        self.setLayout(self.layout)
+
+
+class AlertPop(QMessageBox):
+
+    def __init__(self, message:str, status:str) -> QMessageBox:
+        super().__init__()
+        icon = getattr(QMessageBox.Icon, status.title())
+        self.setIcon(icon)
+        # msg.setText("Error")
+        self.setInformativeText(message)
+        self.setWindowTitle(status.title())
+

src/submissions/frontend/custom_widgets/sub_details.py

@@ -0,0 +1,188 @@
+from datetime import date
+from PyQt6.QtWidgets import (
+    QVBoxLayout, QDialog, QTableView,
+    QTextEdit, QPushButton, QScrollArea, 
+    QMessageBox, QFileDialog
+)
+from PyQt6.QtCore import Qt, QAbstractTableModel
+from PyQt6.QtGui import QFontMetrics
+
+from backend.db import submissions_to_df, lookup_submission_by_id, lookup_all_sample_types, create_kit_from_yaml
+from jinja2 import Environment, FileSystemLoader
+from xhtml2pdf import pisa
+import sys
+from pathlib import Path
+import logging
+
+logger = logging.getLogger(f"submissions.{__name__}")
+
+if getattr(sys, 'frozen', False):
+    loader_path = Path(sys._MEIPASS).joinpath("files", "templates")
+else:
+    loader_path = Path(__file__).parents[2].joinpath('templates').absolute().__str__()
+loader = FileSystemLoader(loader_path)
+env = Environment(loader=loader)
+
+class pandasModel(QAbstractTableModel):
+    """
+    pandas model for inserting summary sheet into gui
+    """
+    def __init__(self, data) -> None:
+        QAbstractTableModel.__init__(self)
+        self._data = data
+
+    def rowCount(self, parent=None) -> int:
+        """
+        does what it says
+
+        Args:
+            parent (_type_, optional): _description_. Defaults to None.
+
+        Returns:
+            int: number of rows in data
+        """
+        return self._data.shape[0]
+
+    def columnCount(self, parnet=None) -> int:
+        """
+        does what it says
+
+        Args:
+            parnet (_type_, optional): _description_. Defaults to None.
+
+        Returns:
+            int: number of columns in data
+        """        
+        return self._data.shape[1]
+
+    def data(self, index, role=Qt.ItemDataRole.DisplayRole) -> str|None:
+        if index.isValid():
+            if role == Qt.ItemDataRole.DisplayRole:
+                return str(self._data.iloc[index.row(), index.column()])
+        return None
+
+    def headerData(self, col, orientation, role):
+        if orientation == Qt.Orientation.Horizontal and role == Qt.ItemDataRole.DisplayRole:
+            return self._data.columns[col]
+        return None
+        
+
+class SubmissionsSheet(QTableView):
+    """
+    presents submission summary to user in tab1
+    """    
+    def __init__(self, ctx:dict) -> None:
+        """
+        initialize
+
+        Args:
+            ctx (dict): settings passed from gui
+        """        
+        super().__init__()
+        self.ctx = ctx
+        self.setData()
+        self.resizeColumnsToContents()
+        self.resizeRowsToContents()
+        # self.clicked.connect(self.test)
+        self.doubleClicked.connect(self.show_details)
+ 
+    def setData(self) -> None: 
+        """
+        sets data in model
+        """        
+        self.data = submissions_to_df(ctx=self.ctx)
+        self.model = pandasModel(self.data)
+        self.setModel(self.model)
+        # self.resize(800,600)
+
+    def show_details(self) -> None:
+        """
+        creates detailed data to show in seperate window
+        """        
+        index=(self.selectionModel().currentIndex())
+        # logger.debug(index)
+        value=index.sibling(index.row(),0).data()
+        dlg = SubmissionDetails(ctx=self.ctx, id=value)
+        # dlg.show()
+        if dlg.exec():
+            pass
+
+
+
+    
+class SubmissionDetails(QDialog):
+    """
+    a window showing text details of submission
+    """    
+    def __init__(self, ctx:dict, id:int) -> None:
+
+        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)
+        self.base_dict = data.to_dict()
+        logger.debug(f"Base dict: {self.base_dict}")
+        # don't want id
+        del self.base_dict['id']
+        # convert sub objects to dicts
+        self.base_dict['reagents'] = [item.to_sub_dict() for item in data.reagents]
+        self.base_dict['samples'] = [item.to_sub_dict() for item in data.samples]
+        # 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)
+        self.layout = QVBoxLayout()
+        self.setFixedSize(w, 900)
+        btn = QPushButton("Export PDF")
+        btn.setParent(self)
+        btn.setFixedWidth(w)
+        btn.clicked.connect(self.export)
+        
+
+    # def _create_actions(self):
+    #     self.exportAction = QAction("Export", self)
+        
+
+    def export(self):
+        template = env.get_template("submission_details.html")
+        html = template.render(sub=self.base_dict)
+        # logger.debug(f"Submission details: {self.base_dict}")
+        home_dir = Path(self.ctx["directory_path"]).joinpath(f"Submission_Details_{self.base_dict['Plate Number']}.pdf").resolve().__str__()
+        fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".pdf")[0])
+        # logger.debug(f"report output name: {fname}")
+        # df.to_excel(fname, engine='openpyxl')
+        if fname.__str__() == ".":
+            logger.debug("Saving pdf was cancelled.")
+            return
+        try:
+            with open(fname, "w+b") as f:
+                pisa.CreatePDF(html, dest=f)
+        except PermissionError as e:
+            logger.error(f"Error saving pdf: {e}")
+            msg = QMessageBox()
+            msg.setText("Permission Error")
+            msg.setInformativeText(f"Looks like {fname.__str__()} is open.\nPlease close it and try again.")
+            msg.setWindowTitle("Permission Error")
+            msg.exec()
+        

src/submissions/frontend/functions.py

@@ -0,0 +1,31 @@
+# from ..models import *
+from backend.db.models import *
+import logging
+import numpy as np
+
+logger = logging.getLogger(f"submissions.{__name__}")
+
+def check_kit_integrity(sub:BasicSubmission):
+    ext_kit_rtypes = [reagenttype.name for reagenttype in sub.extraction_kit.reagent_types]
+    logger.debug(f"Kit reagents: {ext_kit_rtypes}")
+    reagenttypes = [reagent.type.name for reagent in sub.reagents]
+    logger.debug(f"Submission reagents: {reagenttypes}")
+    check = set(ext_kit_rtypes) == set(reagenttypes)
+    logger.debug(f"Checking if reagents match kit contents: {check}")
+    common = list(set(ext_kit_rtypes).intersection(reagenttypes))
+    logger.debug(f"common reagents types: {common}")
+    if check:
+        result = None
+    else:
+        result = {'message' : f"Couldn't verify reagents match listed kit components.\n\nIt looks like you are missing: {[x.upper() for x in ext_kit_rtypes if x not in common]}\n\nAlternatively, you may have set the wrong extraction kit."}
+    return result
+    
+
+def check_not_nan(cell_contents) -> bool:
+    try:
+        return not np.isnan(cell_contents)
+    except ValueError:
+        return True
+    except Exception as e:
+        logger.debug(f"Check encounteded unknown error: {e}")
+        return False