278 lines
11 KiB
Python
278 lines
11 KiB
Python
from datetime import date
|
|
from PyQt6.QtWidgets import (
|
|
QLabel, QVBoxLayout,
|
|
QLineEdit, QComboBox, QDialog,
|
|
QDialogButtonBox, QDateEdit, QSizePolicy, QWidget,
|
|
QGridLayout, QPushButton, QSpinBox,
|
|
QScrollBar, QHBoxLayout,
|
|
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 AddReagentForm(QDialog):
|
|
"""
|
|
dialog to add gather info about new reagent
|
|
"""
|
|
def __init__(self, ctx:dict, reagent_lot:str|None, reagent_type:str|None, expiry:date|None=None) -> None:
|
|
super().__init__()
|
|
|
|
if reagent_lot == None:
|
|
reagent_lot = ""
|
|
|
|
self.setWindowTitle("Add Reagent")
|
|
|
|
QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
|
|
|
|
self.buttonBox = QDialogButtonBox(QBtn)
|
|
self.buttonBox.accepted.connect(self.accept)
|
|
self.buttonBox.rejected.connect(self.reject)
|
|
# get lot info
|
|
lot_input = QLineEdit()
|
|
lot_input.setText(reagent_lot)
|
|
# get expiry info
|
|
exp_input = QDateEdit(calendarPopup=True)
|
|
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)])
|
|
logger.debug(f"Trying to find index of {reagent_type}")
|
|
# convert input to user friendly string?
|
|
try:
|
|
reagent_type = reagent_type.replace("_", " ").title()
|
|
except AttributeError:
|
|
reagent_type = None
|
|
# set parsed reagent type to top of list
|
|
index = type_input.findText(reagent_type, Qt.MatchFlag.MatchEndsWith)
|
|
if index >= 0:
|
|
type_input.setCurrentIndex(index)
|
|
self.layout = QVBoxLayout()
|
|
self.layout.addWidget(QLabel("Lot"))
|
|
self.layout.addWidget(lot_input)
|
|
self.layout.addWidget(QLabel("Expiry"))
|
|
self.layout.addWidget(exp_input)
|
|
self.layout.addWidget(QLabel("Type"))
|
|
self.layout.addWidget(type_input)
|
|
self.layout.addWidget(self.buttonBox)
|
|
self.setLayout(self.layout)
|
|
|
|
|
|
class ReportDatePicker(QDialog):
|
|
"""
|
|
custom dialog to ask for report start/stop dates
|
|
"""
|
|
def __init__(self) -> None:
|
|
super().__init__()
|
|
|
|
self.setWindowTitle("Select Report Date Range")
|
|
# make confirm/reject buttons
|
|
QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
|
|
self.buttonBox = QDialogButtonBox(QBtn)
|
|
self.buttonBox.accepted.connect(self.accept)
|
|
self.buttonBox.rejected.connect(self.reject)
|
|
# widgets to ask for dates
|
|
start_date = QDateEdit(calendarPopup=True)
|
|
start_date.setDate(QDate.currentDate())
|
|
end_date = QDateEdit(calendarPopup=True)
|
|
end_date.setDate(QDate.currentDate())
|
|
self.layout = QVBoxLayout()
|
|
self.layout.addWidget(QLabel("Start Date"))
|
|
self.layout.addWidget(start_date)
|
|
self.layout.addWidget(QLabel("End Date"))
|
|
self.layout.addWidget(end_date)
|
|
self.layout.addWidget(self.buttonBox)
|
|
self.setLayout(self.layout)
|
|
|
|
|
|
class KitAdder(QWidget):
|
|
"""
|
|
dialog to get information to add kit
|
|
"""
|
|
def __init__(self, parent_ctx:dict) -> None:
|
|
super().__init__()
|
|
self.ctx = parent_ctx
|
|
self.grid = QGridLayout()
|
|
self.setLayout(self.grid)
|
|
# insert submit button at top
|
|
self.submit_btn = QPushButton("Submit")
|
|
self.grid.addWidget(self.submit_btn,0,0,1,1)
|
|
# need to exclude ordinary users to mitigate garbage database entries
|
|
# self.grid.addWidget(QLabel("Password:"),1,0)
|
|
# self.grid.addWidget(QLineEdit(),1,1)
|
|
self.grid.addWidget(QLabel("Kit Name:"),2,0)
|
|
self.grid.addWidget(QLineEdit(),2,1)
|
|
self.grid.addWidget(QLabel("Used For Sample Type:"),3,0)
|
|
used_for = QComboBox()
|
|
# Insert all existing sample types
|
|
used_for.addItems(lookup_all_sample_types(ctx=parent_ctx))
|
|
used_for.setEditable(True)
|
|
self.grid.addWidget(used_for,3,1)
|
|
# set cost per run
|
|
self.grid.addWidget(QLabel("Constant cost per full plate (plates, work hours, etc.):"),4,0)
|
|
cost = QSpinBox()
|
|
cost.setMinimum(0)
|
|
cost.setMaximum(9999)
|
|
self.grid.addWidget(cost,4,1)
|
|
self.grid.addWidget(QLabel("Mutable cost per full plate (tips, reagents, etc.):"),5,0)
|
|
cost = QSpinBox()
|
|
cost.setMinimum(0)
|
|
cost.setMaximum(9999)
|
|
self.grid.addWidget(cost,5,1)
|
|
# button to add additional reagent types
|
|
self.add_RT_btn = QPushButton("Add Reagent Type")
|
|
self.grid.addWidget(self.add_RT_btn)
|
|
self.add_RT_btn.clicked.connect(self.add_RT)
|
|
self.submit_btn.clicked.connect(self.submit)
|
|
|
|
def add_RT(self) -> None:
|
|
"""
|
|
insert new reagent type row
|
|
"""
|
|
maxrow = self.grid.rowCount()
|
|
self.grid.addWidget(ReagentTypeForm(parent_ctx=self.ctx), maxrow + 1,0,1,2)
|
|
|
|
|
|
def submit(self) -> None:
|
|
"""
|
|
send kit to database
|
|
"""
|
|
# get form info
|
|
labels, values, reagents = self.extract_form_info(self)
|
|
info = {item[0]:item[1] for item in zip(labels, values)}
|
|
logger.debug(info)
|
|
yml_type = {}
|
|
try:
|
|
yml_type['password'] = info['password']
|
|
except KeyError:
|
|
pass
|
|
used = info['used_for_sample_type'].replace(" ", "_").lower()
|
|
yml_type[used] = {}
|
|
yml_type[used]['kits'] = {}
|
|
yml_type[used]['kits'][info['kit_name']] = {}
|
|
yml_type[used]['kits'][info['kit_name']]['constant_cost'] = info["Constant cost per full plate (plates, work hours, etc.)"]
|
|
yml_type[used]['kits'][info['kit_name']]['mutable_cost'] = info["Mutable cost per full plate (tips, reagents, etc.)"]
|
|
yml_type[used]['kits'][info['kit_name']]['reagenttypes'] = reagents
|
|
logger.debug(yml_type)
|
|
# send to kit constructor
|
|
result = create_kit_from_yaml(ctx=self.ctx, exp=yml_type)
|
|
# result = create_kit_from_yaml(ctx=self.ctx, exp=exp)
|
|
msg = QMessageBox()
|
|
# msg.setIcon(QMessageBox.critical)
|
|
match result['code']:
|
|
case 0:
|
|
msg.setText("Kit added")
|
|
msg.setInformativeText(result['message'])
|
|
msg.setWindowTitle("Kit added")
|
|
case 1:
|
|
msg.setText("Permission Error")
|
|
msg.setInformativeText(result['message'])
|
|
msg.setWindowTitle("Permission Error")
|
|
msg.exec()
|
|
|
|
def extract_form_info(self, object):
|
|
"""
|
|
retrieves arbitrary number of labels, values from form
|
|
|
|
Args:
|
|
object (_type_): the object to extract info from
|
|
|
|
Returns:
|
|
_type_: _description_
|
|
"""
|
|
labels = []
|
|
values = []
|
|
reagents = {}
|
|
for item in object.findChildren(QWidget):
|
|
logger.debug(item.parentWidget())
|
|
# if not isinstance(item.parentWidget(), ReagentTypeForm):
|
|
match item:
|
|
case QLabel():
|
|
labels.append(item.text().replace(" ", "_").strip(":").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) and not isinstance(prev_item, QScrollBar):
|
|
logger.debug(f"Previous: {prev_item}")
|
|
logger.debug(f"Item: {item}, {item.text()}")
|
|
values.append(item.text().strip())
|
|
case QComboBox():
|
|
values.append(item.currentText().strip())
|
|
case QDateEdit():
|
|
values.append(item.date().toPyDate())
|
|
case QSpinBox():
|
|
values.append(item.value())
|
|
case ReagentTypeForm():
|
|
re_labels, re_values, _ = self.extract_form_info(item)
|
|
reagent = {item[0]:item[1] for item in zip(re_labels, re_values)}
|
|
logger.debug(reagent)
|
|
# reagent = {reagent['name:']:{'eol':reagent['extension_of_life_(months):']}}
|
|
reagents[reagent["name_(*exactly*_as_it_appears_in_the_excel_submission_form)"].strip()] = {'eol_ext':int(reagent['extension_of_life_(months)'])}
|
|
prev_item = item
|
|
return labels, values, reagents
|
|
|
|
|
|
|
|
class ReagentTypeForm(QWidget):
|
|
"""
|
|
custom widget to add information about a new reagenttype
|
|
"""
|
|
def __init__(self, parent_ctx:dict) -> None:
|
|
super().__init__()
|
|
grid = QGridLayout()
|
|
self.setLayout(grid)
|
|
grid.addWidget(QLabel("Name (*Exactly* as it appears in the excel submission form):"),0,0)
|
|
reagent_getter = QComboBox()
|
|
# lookup all reagent type names from db
|
|
reagent_getter.addItems(get_all_reagenttype_names(ctx=parent_ctx))
|
|
reagent_getter.setEditable(True)
|
|
grid.addWidget(reagent_getter,0,1)
|
|
grid.addWidget(QLabel("Extension of Life (months):"),0,2)
|
|
# get extension of life
|
|
eol = QSpinBox()
|
|
eol.setMinimum(0)
|
|
grid.addWidget(eol, 0,3)
|
|
|
|
|
|
class ControlsDatePicker(QWidget):
|
|
"""
|
|
custom widget to pick start and end dates for controls graphs
|
|
"""
|
|
def __init__(self) -> None:
|
|
super().__init__()
|
|
|
|
self.start_date = QDateEdit(calendarPopup=True)
|
|
# start date is three month prior to end date by default
|
|
threemonthsago = QDate.currentDate().addDays(-60)
|
|
self.start_date.setDate(threemonthsago)
|
|
self.end_date = QDateEdit(calendarPopup=True)
|
|
self.end_date.setDate(QDate.currentDate())
|
|
self.layout = QHBoxLayout()
|
|
self.layout.addWidget(QLabel("Start Date"))
|
|
self.layout.addWidget(self.start_date)
|
|
self.layout.addWidget(QLabel("End Date"))
|
|
self.layout.addWidget(self.end_date)
|
|
|
|
self.setLayout(self.layout)
|
|
self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Fixed)
|
|
|
|
def sizeHint(self) -> QSize:
|
|
return QSize(80,20)
|