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commit before refactor to use pyqt6 input field names

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This commit is contained in:
Landon Wark
2023-03-14 13:13:10 -05:00
parent 285ccecd73
commit fc334155ff
11 changed files with 193 additions and 150 deletions
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66
src/submissions/frontend/__init__.py
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@@ -1,5 +1,6 @@
import json
import re
from typing import Tuple
from PyQt6.QtWidgets import (
QMainWindow, QLabel, QToolBar,
QTabWidget, QWidget, QVBoxLayout,
@@ -30,14 +31,14 @@ from backend.db import (construct_submission_info, lookup_reagent,
)
from backend.db import lookup_kittype_by_name
from .functions import check_kit_integrity, insert_reagent_import
from tools import check_not_nan, create_reagent_list
from .functions import check_kit_integrity
from tools import check_not_nan
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
from frontend.custom_widgets import AddReagentForm, ReportDatePicker, KitAdder, ControlsDatePicker, ImportReagent
import logging
import difflib
from getpass import getuser
@@ -172,7 +173,6 @@ class App(QMainWindow):
(?P<samples>)^samples$ |
(?P<reagent>^lot_.*$)
""", re.VERBOSE)
# reagents = []
for item in prsr.sub:
logger.debug(f"Item: {item}")
# attempt to match variable name to regex group
@@ -201,16 +201,16 @@ class App(QMainWindow):
self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
# if extraction kit not available, all other values fail
if not check_not_nan(prsr.sub[item]):
msg = AlertPop(message="Make sure to check your extraction kit!", status="warning")
msg = AlertPop(message="Make sure to check your extraction kit in the excel sheet!", status="warning")
msg.exec()
# create combobox to hold looked up kits
add_widget = QComboBox()
# lookup existing kits by 'submission_type' decided on by sheetparser
uses = [item.__str__() for item in lookup_kittype_by_use(ctx=self.ctx, used_by=prsr.sub['submission_type'])]
if len(uses) > 0:
add_widget.addItems(uses)
else:
add_widget.addItems(['bacterial_culture'])
# if len(uses) > 0:
add_widget.addItems(uses)
# else:
# add_widget.addItems(['bacterial_culture'])
self.ext_kit = prsr.sub[item]
case 'submitted_date':
# create label
@@ -224,40 +224,10 @@ class App(QMainWindow):
except:
add_widget.setDate(date.today())
case 'reagent':
# create label
self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
# add_widget = QComboBox()
# add_widget.setEditable(True)
# # Ensure that all reagenttypes have a name that matches the items in the excel parser
# 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]['lot']} is a numpy float!")
# try:
# 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}")
# # 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 = []
# for reagent in relevant_reagents:
# if isinstance(reagent, set):
# for thing in reagent:
# output_reg.append(thing)
# elif isinstance(reagent, str):
# output_reg.append(reagent)
# relevant_reagents = output_reg
# logger.debug(f"Relevant reagents for {prsr.sub[item]}: {relevant_reagents}")
# # if reagent in sheet is not found insert it into items
# 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)
add_widget = insert_reagent_import(ctx=self.ctx, item=item, prsr=prsr)
# create reagent choice widget
add_widget = ImportReagent(ctx=self.ctx, item=item, prsr=prsr)
self.reagents[item] = prsr.sub[item]
case 'samples':
# hold samples in 'self' until form submitted
@@ -278,7 +248,7 @@ class App(QMainWindow):
msg.exec()
for item in kit_integrity['missing']:
self.table_widget.formlayout.addWidget(QLabel(f"Lot {item.replace('_', ' ').title()}"))
add_widget = insert_reagent_import(ctx=self.ctx, item=item)
add_widget = ImportReagent(ctx=self.ctx, item=item)
self.table_widget.formlayout.addWidget(add_widget)
# create submission button
submit_btn = QPushButton("Submit")
@@ -302,7 +272,6 @@ class App(QMainWindow):
logger.debug(f"Looked up reagent: {wanted_reagent}")
# if reagent not found offer to add to database
if wanted_reagent == None:
# dlg = AddReagentQuestion(reagent_type=reagent, reagent_lot=reagents[reagent])
r_lot = reagents[reagent]
dlg = QuestionAsker(title=f"Add {r_lot}?", message=f"Couldn't find reagent type {reagent.replace('_', ' ').title().strip('Lot')}: {r_lot} in the database.\n\nWould you like to add it?")
if dlg.exec():
@@ -310,10 +279,10 @@ class App(QMainWindow):
expiry_date = self.reagents[reagent]['exp']
wanted_reagent = self.add_reagent(reagent_lot=r_lot, reagent_type=reagent.replace("lot_", ""), expiry=expiry_date)
else:
# In this case we will have an empty reagent and the submission will fail kit integrity check
logger.debug("Will not add reagent.")
if wanted_reagent != None:
parsed_reagents.append(wanted_reagent)
# logger.debug(info)
# move samples into preliminary submission dict
info['samples'] = self.samples
info['uploaded_by'] = getuser()
@@ -322,14 +291,14 @@ class App(QMainWindow):
base_submission, result = construct_submission_info(ctx=self.ctx, info_dict=info)
# check output message for issues
match result['code']:
# code 1: ask for overwrite
case 1:
# if output['code'] > 0:
# dlg = OverwriteSubQuestion(output['message'], base_submission.rsl_plate_num)
dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_num}?", message=result['message'])
if dlg.exec():
base_submission.reagents = []
else:
return
# code 2: No RSL plate number given
case 2:
dlg = AlertPop(message=result['message'], status='critical')
dlg.exec()
@@ -386,12 +355,12 @@ class App(QMainWindow):
return reagent
def extract_form_info(self, object):
def extract_form_info(self, object) -> Tuple[list, list]:
"""
retrieves arbitrary number of labels, values from form
Args:
object (_type_): _description_
object (_type_): the form widget
Returns:
_type_: _description_
@@ -399,6 +368,7 @@ class App(QMainWindow):
labels = []
values = []
# grab all widgets in form
prev_item = None
for item in object.layout.parentWidget().findChildren(QWidget):
match item:
case QLabel():