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Commit pre-refactor for code cleanup.

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This commit is contained in:
Landon Wark
2023-02-10 10:22:39 -06:00
parent c3db706e7c
commit a9ce9514fc
11 changed files with 400 additions and 272 deletions
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2
src/submissions/__init__.py
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@@ -1,4 +1,4 @@
# __init__.py
# Version of the realpython-reader package
__version__ = "1.2.2"
__version__ = "1.2.3"

2
src/submissions/backend/db/__init__.py
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@@ -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]:

21
src/submissions/backend/db/functions/__init__.py
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@@ -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

2
src/submissions/backend/db/models/kits.py
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@@ -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:
"""

27
src/submissions/backend/excel/parser.py
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@@ -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__}")
@@ -59,7 +60,8 @@ class SheetParser(object):
def _parse_unknown(self) -> None:
"""
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:
check = not np.isnan(row[1])
except TypeError:
check = True
if not isinstance(row[2], float) and check:
# try:
# check = not np.isnan(row[1])
# except TypeError:
# check = True
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

9
src/submissions/backend/excel/reports.py
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@@ -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']

79
src/submissions/frontend/__init__.py
View File

@@ -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':
msg = QMessageBox()
# msg.setIcon(QMessageBox.critical)
msg.setText("Error")
msg.setInformativeText('You need to enter a value for extraction kit.')
msg.setWindowTitle("Error")
if np.isnan(prsr.sub[item]):
msg = AlertPop(message="Make sure to check your extraction kit!", status="warning")
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':
try:
check = not numpy.isnan(prsr.sub[item])
except TypeError:
check = True
if check:
relevant_reagents.insert(0, str(prsr.sub[item]))
logger.debug(f"Relevant reagents: {relevant_reagents}")
if str(prsr.sub[item]['lot']) not in relevant_reagents and prsr.sub[item]['lot'] != 'nan':
if check_not_nan(prsr.sub[item]['lot']):
relevant_reagents.insert(0, str(prsr.sub[item]['lot']))
logger.debug(f"New 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.setIcon(QMessageBox.critical)
msg.setText("Error")
msg.setInformativeText(result['message'])
msg.setWindowTitle("Error")
msg = AlertPop(result['message'])
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}")

233
src/submissions/frontend/custom_widgets/__init__.py
View File

@@ -1,18 +1,17 @@
from datetime import date
from PyQt6.QtWidgets import (
QLabel, QVBoxLayout,
QLineEdit, QComboBox, QDialog,
QDialogButtonBox, QDateEdit, QTableView,
QTextEdit, QSizePolicy, QWidget,
QDialogButtonBox, QDateEdit, QSizePolicy, QWidget,
QGridLayout, QPushButton, QSpinBox,
QScrollBar, QScrollArea, QHBoxLayout,
QMessageBox, QFileDialog, QToolBar
QScrollBar, QHBoxLayout,
QMessageBox
)
from PyQt6.QtCore import Qt, QDate, QAbstractTableModel, QSize
from PyQt6.QtGui import QFontMetrics, QAction
from PyQt6.QtCore import Qt, QDate, QSize
# 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)
exp_input.setDate(QDate.currentDate())
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())

78
src/submissions/frontend/custom_widgets/pop_ups.py Normal file
View File

@@ -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())

188
src/submissions/frontend/custom_widgets/sub_details.py Normal file
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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()

31
src/submissions/frontend/functions.py Normal file
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# 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