Before addition of tips.

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

@@ -2,7 +2,6 @@
 All kit and reagent related models
 """
 from __future__ import annotations
-from copy import copy
 from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT, BLOB
 from sqlalchemy.orm import relationship, validates, Query
 from sqlalchemy.ext.associationproxy import association_proxy

src/submissions/backend/excel/parser.py

@@ -8,8 +8,6 @@ from pprint import pformat
 from typing import List
 import pandas as pd
 from openpyxl import load_workbook, Workbook
-from openpyxl.worksheet.protection import SheetProtection
-import numpy as np
 from pathlib import Path
 from backend.db.models import *
 from backend.validators import PydSubmission, PydReagent, RSLNamer, PydSample, PydEquipment
@@ -17,14 +15,12 @@ import logging, re
 from collections import OrderedDict
 from datetime import date
 from dateutil.parser import parse, ParserError
-from tools import check_not_nan, convert_nans_to_nones, row_map, row_keys, is_missing, remove_key_from_list_of_dicts
+from tools import check_not_nan, convert_nans_to_nones, is_missing, remove_key_from_list_of_dicts
 
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
 
-# row_keys = {v:k for k,v in row_map.items()}
-
 class SheetParser(object):
     """
     object to pull and contain data from excel file

src/submissions/backend/excel/writer.py

@@ -1,12 +1,10 @@
 import logging
 from copy import copy
-from pathlib import Path
+# from pathlib import Path
 from pprint import pformat
 from typing import List
-
 from openpyxl import load_workbook, Workbook
-from tools import row_keys
+from backend.db.models import SubmissionType, KitType, BasicSubmission
-from backend.db.models import SubmissionType, KitType, BasicSample, BasicSubmission
 from backend.validators.pydant import PydSubmission
 from io import BytesIO
 from collections import OrderedDict

src/submissions/backend/validators/pydant.py

@@ -2,7 +2,6 @@
 Contains pydantic models and accompanying validators
 '''
 from __future__ import annotations
-
 import sys
 from operator import attrgetter
 import uuid, re, logging

src/submissions/frontend/widgets/functions.py

@@ -8,6 +8,7 @@ from PyQt6.QtWidgets import QMainWindow, QFileDialog
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
+
 def select_open_file(obj:QMainWindow, file_extension:str) -> Path:
     """
     File dialog to select a file to read from
@@ -29,6 +30,7 @@ def select_open_file(obj:QMainWindow, file_extension:str) -> Path:
     obj.last_dir = fname.parent
     return fname
 
+
 def select_save_file(obj:QMainWindow, default_name:str, extension:str) -> Path:
     """
     File dialog to select a file to write to

src/submissions/frontend/widgets/gel_checker.py

@@ -5,9 +5,8 @@ from PyQt6.QtWidgets import (QWidget, QDialog, QGridLayout,
                              QLabel, QLineEdit, QDialogButtonBox,
                              QTextEdit
                              )
-import numpy as np
 import pyqtgraph as pg
-from PyQt6.QtGui import QIcon, QFont
+from PyQt6.QtGui import QIcon
 from PIL import Image
 import numpy as np
 import logging
@@ -18,6 +17,7 @@ from backend.db.models import WastewaterArtic
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
+
 # Main window class
 class GelBox(QDialog):
 
@@ -86,7 +86,8 @@ class GelBox(QDialog):
         gel_barcode = self.gel_barcode.text()
         values, comment = self.form.parse_form()
         return dna_core_submission_number, gel_barcode, self.img_path, values, comment
-        
+
+
 class ControlsForm(QWidget):
 
     def __init__(self, parent, control_info:List=None) -> None:

src/submissions/frontend/widgets/kit_creator.py

@@ -138,7 +138,8 @@ class KitAdder(QWidget):
                 case QDateEdit():
                     info[widget.objectName()] = widget.date().toPyDate()
         return info, reagents
-        
+
+
 class ReagentRoleForm(QWidget):
     """
     custom widget to add information about a new reagenttype

src/submissions/frontend/widgets/misc.py

@@ -13,12 +13,12 @@ from backend.db.models import *
 import logging
 from .pop_ups import AlertPop
 from .functions import select_open_file
-from tools import Settings
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
 env = jinja_template_loading()
 
+
 class AddReagentForm(QDialog):
     """
     dialog to add gather info about new reagent
@@ -102,6 +102,7 @@ class AddReagentForm(QDialog):
         lookup = Reagent.query(reagent_role=self.type_input.currentText())
         self.name_input.addItems(list(set([item.name for item in lookup])))
 
+
 class ReportDatePicker(QDialog):
     """
     custom dialog to ask for report start/stop dates
@@ -138,6 +139,7 @@ class ReportDatePicker(QDialog):
         """        
         return dict(start_date=self.start_date.date().toPyDate(), end_date = self.end_date.date().toPyDate())
 
+
 class FirstStrandSalvage(QDialog):
 
     def __init__(self, ctx:Settings, submitter_id:str, rsl_plate_num:str|None=None) -> None:
@@ -178,6 +180,7 @@ class FirstStrandSalvage(QDialog):
         """              
         return dict(plate=self.rsl_plate_num.text(), submitter_id=self.submitter_id_input.text(), well=f"{self.row_letter.currentText()}{self.column_number.currentText()}")
 
+
 class LogParser(QDialog):
 
     def __init__(self, parent):
@@ -197,7 +200,6 @@ class LogParser(QDialog):
         self.btn.clicked.connect(self.runsearch)
         self.setMinimumWidth(400)
 
-
     def filelookup(self):
         """
         Select file to search

src/submissions/frontend/widgets/pop_ups.py

@@ -14,6 +14,7 @@ logger = logging.getLogger(f"submissions.{__name__}")
 
 env = jinja_template_loading()
 
+
 class QuestionAsker(QDialog):
     """
     dialog to ask yes/no questions
@@ -33,6 +34,7 @@ class QuestionAsker(QDialog):
         self.layout.addWidget(self.buttonBox)
         self.setLayout(self.layout)
 
+
 class AlertPop(QMessageBox):
     """
     Dialog to show an alert.
@@ -45,6 +47,7 @@ class AlertPop(QMessageBox):
         self.setInformativeText(message)
         self.setWindowTitle(f"{owner} - {status.title()}")
 
+
 class ObjectSelector(QDialog):
     """
     dialog to input BaseClass type manually
@@ -79,70 +82,3 @@ class ObjectSelector(QDialog):
             str: KitType as str
         """        
         return self.widget.currentText()
-
-# class KitSelector(QDialog):
-#     """
-#     dialog to input KitType manually
-#     """    
-#     def __init__(self, title:str, message:str) -> QDialog:
-#         super().__init__()
-#         self.setWindowTitle(title)
-#         self.widget = QComboBox()
-#         kits = [item.name for item in KitType.query()]
-#         self.widget.addItems(kits)
-#         self.widget.setEditable(False)
-#         # set yes/no buttons
-#         QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
-#         self.buttonBox = QDialogButtonBox(QBtn)
-#         self.buttonBox.accepted.connect(self.accept)
-#         self.buttonBox.rejected.connect(self.reject)
-#         self.layout = QVBoxLayout()
-#         # Text for the yes/no question
-#         message = QLabel(message)
-#         self.layout.addWidget(message)
-#         self.layout.addWidget(self.widget)
-#         self.layout.addWidget(self.buttonBox)
-#         self.setLayout(self.layout)
-
-#     def getValues(self) -> str:
-#         """
-#         Get KitType(str) from widget
-
-#         Returns:
-#             str: KitType as str
-#         """        
-#         return self.widget.currentText()
-
-# class SubmissionTypeSelector(QDialog):
-#     """
-#     dialog to input SubmissionType manually
-#     """    
-#     def __init__(self, title:str, message:str) -> 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 SubmissionType.query()]
-#         self.widget.addItems(sub_type)
-#         self.widget.setEditable(False)
-#         # set yes/no buttons
-#         QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
-#         self.buttonBox = QDialogButtonBox(QBtn)
-#         self.buttonBox.accepted.connect(self.accept)
-#         self.buttonBox.rejected.connect(self.reject)
-#         self.layout = QVBoxLayout()
-#         # Text for the yes/no question
-#         message = QLabel(message)
-#         self.layout.addWidget(message)
-#         self.layout.addWidget(self.widget)
-#         self.layout.addWidget(self.buttonBox)
-#         self.setLayout(self.layout)
-
-#     def parse_form(self) -> str:
-#         """
-#         Pulls SubmissionType(str) from widget
-
-#         Returns:
-#             str: SubmissionType as str
-#         """
-#         return self.widget.currentText()

src/submissions/frontend/widgets/sample_search.py

@@ -1,14 +1,13 @@
 from pprint import pformat
 from typing import Tuple
 from pandas import DataFrame
-from PyQt6.QtCore import QAbstractTableModel, Qt, QEvent, QSortFilterProxyModel
+from PyQt6.QtCore import QSortFilterProxyModel
 from PyQt6.QtWidgets import (
     QLabel, QVBoxLayout, QDialog,
-    QDialogButtonBox, QMessageBox, QComboBox, QTableView, QWidget, QLineEdit, QGridLayout
+    QComboBox, QTableView, QWidget, QLineEdit, QGridLayout
 )
 from backend.db.models import BasicSample
 from .submission_table import pandasModel
-from .submission_details import SubmissionDetails
 import logging
 
 logger = logging.getLogger(f"submissions.{__name__}")

src/submissions/frontend/widgets/submission_details.py

@@ -21,6 +21,7 @@ from typing import List
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
+
 class SubmissionDetails(QDialog):
     """
     a window showing text details of submission
@@ -92,8 +93,8 @@ class SubmissionDetails(QDialog):
         self.base_dict, self.template = submission.get_details_template(base_dict=self.base_dict)
         self.html = self.template.render(sub=self.base_dict, signing_permission=is_power_user())
         self.webview.setHtml(self.html)
-        with open("test.html", "w") as f:
+        # with open("test.html", "w") as f:
-            f.write(self.html)
+        #     f.write(self.html)
         self.setWindowTitle(f"Submission Details - {submission.rsl_plate_num}")
 
     @pyqtSlot(str)
@@ -125,8 +126,6 @@ class SubmissionDetails(QDialog):
         del self.base_dict['platemap']
         self.html2 = self.template.render(sub=self.base_dict)
         try:
-            # with open(fname, "w+b") as f:
-            #     pisa.CreatePDF(self.html2, dest=f)
             html_to_pdf(html=self.html2, output_file=fname)
         except PermissionError as e:
             logger.error(f"Error saving pdf: {e}")
@@ -135,7 +134,8 @@ class SubmissionDetails(QDialog):
             msg.setInformativeText(f"Looks like {fname.__str__()} is open.\nPlease close it and try again.")
             msg.setWindowTitle("Permission Error")
             msg.exec()
-        
+
+
 class SubmissionComment(QDialog):
     """
     a window for adding comment text to a submission
@@ -174,4 +174,3 @@ class SubmissionComment(QDialog):
         full_comment = {"name":commenter, "time": dt, "text": comment}
         # logger.debug(f"Full comment: {full_comment}")
         return full_comment
-

src/submissions/frontend/widgets/submission_table.py

@@ -9,7 +9,6 @@ from PyQt6.QtGui import QAction, QCursor
 from backend.db.models import BasicSubmission
 from backend.excel import make_report_html, make_report_xlsx
 from tools import Report, Result, row_map, get_first_blank_df_row, html_to_pdf
-# from xhtml2pdf import pisa
 from .functions import select_save_file, select_open_file
 from .misc import ReportDatePicker
 import pandas as pd
@@ -17,6 +16,7 @@ from openpyxl.worksheet.worksheet import Worksheet
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
+
 class pandasModel(QAbstractTableModel):
     """
     pandas model for inserting summary sheet into gui
@@ -60,7 +60,8 @@ class pandasModel(QAbstractTableModel):
         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

src/submissions/frontend/widgets/submission_type_creator.py

@@ -12,6 +12,7 @@ from .functions import select_open_file
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
+
 class SubmissionTypeAdder(QWidget):
 
     def __init__(self, parent) -> None:
@@ -80,6 +81,7 @@ class SubmissionTypeAdder(QWidget):
         self.template_path = select_open_file(obj=self, file_extension="xlsx")
         self.template_label.setText(self.template_path.__str__())
 
+
 class InfoWidget(QWidget):
 
     def __init__(self, parent: QWidget, key) -> None:

src/submissions/tools.py

@@ -4,7 +4,6 @@ Contains miscellaenous functions used by both frontend and backend.
 from __future__ import annotations
 
 import json
-from pathlib import Path
 import numpy as np
 import logging, re, yaml, sys, os, stat, platform, getpass, inspect, csv
 import pandas as pd
@@ -16,7 +15,7 @@ from sqlalchemy import create_engine, text
 from pydantic import field_validator, BaseModel, Field
 from pydantic_settings import BaseSettings, SettingsConfigDict
 from typing import Any, Tuple, Literal, List
-from PyQt6.QtGui import QTextDocument, QPageSize
+from PyQt6.QtGui import QPageSize
 from PyQt6.QtWebEngineWidgets import QWebEngineView
 from openpyxl.worksheet.worksheet import Worksheet