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mid refactor for improved rebustness and readability

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This commit is contained in:
Landon Wark
2023-03-15 15:38:02 -05:00
parent fc334155ff
commit c645d3a9cf
15 changed files with 337 additions and 468 deletions
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74
src/submissions/frontend/__init__.py
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@@ -1,12 +1,11 @@
import json
import re
from typing import Tuple
from PyQt6.QtWidgets import (
QMainWindow, QLabel, QToolBar,
QTabWidget, QWidget, QVBoxLayout,
QPushButton, QFileDialog,
QLineEdit, QMessageBox, QComboBox, QDateEdit, QHBoxLayout,
QSpinBox, QScrollArea
QScrollArea
)
from PyQt6.QtGui import QAction
from PyQt6.QtCore import QSignalBlocker
@@ -27,15 +26,13 @@ from backend.db import (construct_submission_info, lookup_reagent,
lookup_regent_by_type_name, lookup_all_orgs, lookup_submissions_by_date_range,
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,
create_org_from_yaml
create_org_from_yaml, store_reagent
)
from backend.db import lookup_kittype_by_name
from .functions import check_kit_integrity
from tools import check_not_nan
from tools import check_not_nan, extract_form_info
from backend.excel.reports import make_report_xlsx, make_report_html
import numpy
from frontend.custom_widgets.sub_details import SubmissionsSheet
from frontend.custom_widgets.pop_ups import AlertPop, QuestionAsker
from frontend.custom_widgets import AddReagentForm, ReportDatePicker, KitAdder, ControlsDatePicker, ImportReagent
@@ -233,12 +230,18 @@ class App(QMainWindow):
# hold samples in 'self' until form submitted
logger.debug(f"{item}: {prsr.sub[item]}")
self.samples = prsr.sub[item]
add_widget = None
case _:
# anything else gets added in as a line edit
self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
add_widget = QLineEdit()
add_widget.setText(str(prsr.sub[item]).replace("_", " "))
self.table_widget.formlayout.addWidget(add_widget)
try:
add_widget.setObjectName(item)
logger.debug(f"Widget name set to: {add_widget.objectName()}")
self.table_widget.formlayout.addWidget(add_widget)
except AttributeError as e:
logger.error(e)
# compare self.reagents with expected reagents in kit
if hasattr(self, 'ext_kit'):
kit = lookup_kittype_by_name(ctx=self.ctx, name=self.ext_kit)
@@ -261,9 +264,10 @@ class App(QMainWindow):
Attempt to add sample to database when 'submit' button clicked
"""
# get info from form
labels, values = self.extract_form_info(self.table_widget.tab1)
info = {item[0]:item[1] for item in zip(labels, values) if not item[0].startswith("lot_")}
reagents = {item[0]:item[1] for item in zip(labels, values) if item[0].startswith("lot_")}
info = extract_form_info(self.table_widget.tab1)
reagents = {k:v for k,v in info.items() if k.startswith("lot_")}
info = {k:v for k,v in info.items() if not k.startswith("lot_")}
logger.debug(f"Info: {info}")
logger.debug(f"Reagents: {reagents}")
parsed_reagents = []
# compare reagents in form to reagent database
@@ -308,7 +312,6 @@ class App(QMainWindow):
# add reagents to submission object
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:
@@ -317,7 +320,7 @@ class App(QMainWindow):
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 = AlertPop(result['message'])
msg.exec()
@@ -345,48 +348,17 @@ class App(QMainWindow):
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)
info = {item[0]:item[1] for item in zip(labels, values)}
info = extract_form_info(dlg)
logger.debug(f"dictionary from form: {info}")
# return None
logger.debug(f"Reagent info: {info}")
# 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
def extract_form_info(self, object) -> Tuple[list, list]:
"""
retrieves arbitrary number of labels, values from form
Args:
object (_type_): the form widget
Returns:
_type_: _description_
"""
labels = []
values = []
# grab all widgets in form
prev_item = None
for item in object.layout.parentWidget().findChildren(QWidget):
match item:
case QLabel():
labels.append(item.text().replace(" ", "_").lower())
case QLineEdit():
# ad hoc check to prevent double reporting of qdatedit under lineedit for some reason
if not isinstance(prev_item, QDateEdit) and not isinstance(prev_item, QComboBox) and not isinstance(prev_item, QSpinBox):
logger.debug(f"Previous: {prev_item}")
logger.debug(f"Item: {item}")
values.append(item.text())
case QComboBox():
values.append(item.currentText())
case QDateEdit():
values.append(item.date().toPyDate())
# value for ad hoc check above
prev_item = item
return labels, values
def generateReport(self):
"""
Action to create a summary of sheet data per client
@@ -394,8 +366,10 @@ class App(QMainWindow):
# Custom two date picker for start & end dates
dlg = ReportDatePicker()
if dlg.exec():
labels, values = self.extract_form_info(dlg)
info = {item[0]:item[1] for item in zip(labels, values)}
# labels, values = extract_form_info(dlg)
# info = {item[0]:item[1] for item in zip(labels, values)}
info = extract_form_info(dlg)
logger.debug(f"Report info: {info}")
# find submissions based on date range
subs = lookup_submissions_by_date_range(ctx=self.ctx, start_date=info['start_date'], end_date=info['end_date'])
# convert each object to dict
@@ -404,7 +378,7 @@ class App(QMainWindow):
html = make_report_html(df=df, start_date=info['start_date'], end_date=info['end_date'])
# make dataframe from record dictionaries
# df = make_report_xlsx(records=records)
# # setup filedialog to handle save location of report
# setup filedialog to handle save location of report
home_dir = Path(self.ctx["directory_path"]).joinpath(f"Submissions_Report_{info['start_date']}-{info['end_date']}.pdf").resolve().__str__()
# fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".xlsx")[0])
fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".pdf")[0])