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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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79
src/submissions/frontend/__init__.py
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@@ -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}")