492 lines
22 KiB
Python
492 lines
22 KiB
Python
import re
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from PyQt6.QtWidgets import (
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QMainWindow, QLabel, QToolBar, QStatusBar,
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QTabWidget, QWidget, QVBoxLayout,
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QPushButton, QMenuBar, QFileDialog,
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QLineEdit, QMessageBox, QComboBox, QDateEdit, QHBoxLayout,
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QSpinBox, QScrollArea, QScrollBar, QSizePolicy
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)
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from PyQt6.QtGui import QAction, QIcon
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from PyQt6.QtCore import pyqtSlot, QDateTime, QDate, QSignalBlocker, Qt
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from PyQt6.QtWebEngineWidgets import QWebEngineView
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import pandas as pd
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from pathlib import Path
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import plotly
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import plotly.express as px
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import yaml
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from backend.excel.parser import SheetParser
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from backend.excel.reports import convert_control_by_mode, convert_data_list_to_df
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from backend.db import (construct_submission_info, lookup_reagent,
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construct_reagent, store_reagent, store_submission, lookup_kittype_by_use,
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lookup_regent_by_type_name_and_kit_name, lookup_all_orgs, lookup_submissions_by_date_range,
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get_all_Control_Types_names, create_kit_from_yaml, get_all_available_modes, get_all_controls_by_type,
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get_control_subtypes
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)
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from backend.excel.reports import make_report_xlsx
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import numpy
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from frontend.custom_widgets import AddReagentQuestion, AddReagentForm, SubmissionsSheet, ReportDatePicker, KitAdder, ControlsDatePicker, OverwriteSubQuestion
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import logging
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import difflib
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from frontend.visualizations.charts import create_charts
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logger = logging.getLogger(__name__)
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logger.info("Hello, I am a logger")
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class App(QMainWindow):
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# class App(QScrollArea):
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def __init__(self, ctx: dict = {}):
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super().__init__()
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self.ctx = ctx
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self.title = 'Submissions App - PyQT6'
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self.left = 0
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self.top = 0
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self.width = 1300
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self.height = 1000
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self.setWindowTitle(self.title)
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self.setGeometry(self.left, self.top, self.width, self.height)
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self.table_widget = AddSubForm(self)
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self.setCentralWidget(self.table_widget)
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self._createActions()
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self._createMenuBar()
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self._createToolBar()
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self._connectActions()
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# self.renderPage()
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self.controls_getter()
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self.show()
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def _createMenuBar(self):
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menuBar = self.menuBar()
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fileMenu = menuBar.addMenu("&File")
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# menuBar.addMenu(fileMenu)
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# Creating menus using a title
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editMenu = menuBar.addMenu("&Edit")
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reportMenu = menuBar.addMenu("&Reports")
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helpMenu = menuBar.addMenu("&Help")
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fileMenu.addAction(self.importAction)
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reportMenu.addAction(self.generateReportAction)
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def _createToolBar(self):
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toolbar = QToolBar("My main toolbar")
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self.addToolBar(toolbar)
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toolbar.addAction(self.addReagentAction)
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toolbar.addAction(self.addKitAction)
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def _createActions(self):
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self.importAction = QAction("&Import", self)
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self.addReagentAction = QAction("Add Reagent", self)
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self.generateReportAction = QAction("Make Report", self)
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self.addKitAction = QAction("Add Kit", self)
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def _connectActions(self):
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self.importAction.triggered.connect(self.importSubmission)
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self.addReagentAction.triggered.connect(self.add_reagent)
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self.generateReportAction.triggered.connect(self.generateReport)
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self.addKitAction.triggered.connect(self.add_kit)
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self.table_widget.control_typer.currentIndexChanged.connect(self.controls_getter)
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self.table_widget.mode_typer.currentIndexChanged.connect(self.controls_getter)
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self.table_widget.datepicker.start_date.dateChanged.connect(self.controls_getter)
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self.table_widget.datepicker.end_date.dateChanged.connect(self.controls_getter)
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def importSubmission(self):
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logger.debug(self.ctx)
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self.samples = []
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home_dir = str(Path(self.ctx["directory_path"]))
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fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir)[0])
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logger.debug(f"Attempting to parse file: {fname}")
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assert fname.exists()
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try:
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prsr = SheetParser(fname, **self.ctx)
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except PermissionError:
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return
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logger.debug(f"prsr.sub = {prsr.sub}")
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# replace formlayout with tab1.layout
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# self.form = self.table_widget.formlayout
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for item in self.table_widget.formlayout.parentWidget().findChildren(QWidget):
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item.setParent(None)
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variable_parser = re.compile(r"""
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# (?x)
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(?P<extraction_kit>^extraction_kit$) |
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(?P<submitted_date>^submitted_date$) |
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(?P<submitting_lab>)^submitting_lab$ |
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(?P<samples>)^samples$ |
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(?P<reagent>^lot_.*$)
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""", re.VERBOSE)
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for item in prsr.sub:
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logger.debug(f"Item: {item}")
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try:
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mo = variable_parser.fullmatch(item).lastgroup
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except AttributeError:
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mo = "other"
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logger.debug(f"Mo: {mo}")
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match mo:
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case 'submitting_lab':
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self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
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logger.debug(f"{item}: {prsr.sub[item]}")
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add_widget = QComboBox()
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labs = [item.__str__() for item in lookup_all_orgs(ctx=self.ctx)]
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try:
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labs = difflib.get_close_matches(prsr.sub[item], labs, len(labs), 0)
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except (TypeError, ValueError):
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pass
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add_widget.addItems(labs)
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case 'extraction_kit':
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self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
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if prsr.sub[item] == 'nan':
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msg = QMessageBox()
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# msg.setIcon(QMessageBox.critical)
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msg.setText("Error")
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msg.setInformativeText('You need to enter a value for extraction kit.')
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msg.setWindowTitle("Error")
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msg.exec()
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break
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add_widget = QComboBox()
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uses = [item.__str__() for item in lookup_kittype_by_use(ctx=self.ctx, used_by=prsr.sub['submission_type'])]
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if len(uses) > 0:
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add_widget.addItems(uses)
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else:
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add_widget.addItems(['bacterial_culture'])
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case 'submitted_date':
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self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
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add_widget = QDateEdit(calendarPopup=True)
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# add_widget.setDateTime(QDateTime.date(prsr.sub[item]))
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add_widget.setDate(prsr.sub[item])
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case 'reagent':
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self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
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add_widget = QComboBox()
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add_widget.setEditable(True)
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# Ensure that all reagenttypes have a name that matches the items in the excel parser
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query_var = item.replace("lot_", "")
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logger.debug(f"Query for: {query_var}")
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if isinstance(prsr.sub[item], numpy.float64):
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logger.debug(f"{prsr.sub[item]} is a numpy float!")
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try:
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prsr.sub[item] = int(prsr.sub[item])
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except ValueError:
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pass
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relevant_reagents = [item.__str__() for item in lookup_regent_by_type_name_and_kit_name(ctx=self.ctx, type_name=query_var, kit_name=prsr.sub['extraction_kit'])]
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logger.debug(f"Relevant reagents: {relevant_reagents}")
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if prsr.sub[item] not in relevant_reagents and prsr.sub[item] != 'nan':
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try:
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check = not numpy.isnan(prsr.sub[item])
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except TypeError:
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check = True
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if check:
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relevant_reagents.insert(0, str(prsr.sub[item]))
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logger.debug(f"Relevant reagents: {relevant_reagents}")
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add_widget.addItems(relevant_reagents)
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# TODO: make samples not appear in frame.
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case 'samples':
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logger.debug(f"{item}: {prsr.sub[item]}")
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self.samples = prsr.sub[item]
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case _:
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self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
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add_widget = QLineEdit()
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add_widget.setText(str(prsr.sub[item]).replace("_", " "))
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self.table_widget.formlayout.addWidget(add_widget)
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submit_btn = QPushButton("Submit")
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self.table_widget.formlayout.addWidget(submit_btn)
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submit_btn.clicked.connect(self.submit_new_sample)
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# self.table_widget.interior.setSizePolicy(QSizePolicy.Policy.Preferred, QSizePolicy.Policy.MinimumExpanding)
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print(self.table_widget.formwidget.size())
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# def renderPage(self):
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# """
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# Test function for plotly chart rendering
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# """
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# df = pd.read_excel("C:\\Users\\lwark\\Desktop\\test_df.xlsx", engine="openpyxl")
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# fig = px.bar(df, x="submitted_date", y="kraken_percent", color="genus", title="Long-Form Input")
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# fig.update_layout(
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# xaxis_title="Submitted Date (* - Date parsed from fastq file creation date)",
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# yaxis_title="Kraken Percent",
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# showlegend=True,
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# barmode='stack'
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# )
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# html = '<html><body>'
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# html += plotly.offline.plot(fig, output_type='div', include_plotlyjs='cdn', auto_open=True, image = 'png', image_filename='plot_image')
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# html += '</body></html>'
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# self.table_widget.webengineview.setHtml(html)
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# self.table_widget.webengineview.update()
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def submit_new_sample(self):
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labels, values = self.extract_form_info(self.table_widget.tab1)
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info = {item[0]:item[1] for item in zip(labels, values) if not item[0].startswith("lot_")}
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reagents = {item[0]:item[1] for item in zip(labels, values) if item[0].startswith("lot_")}
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logger.debug(f"Reagents: {reagents}")
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parsed_reagents = []
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for reagent in reagents:
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wanted_reagent = lookup_reagent(ctx=self.ctx, reagent_lot=reagents[reagent])
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logger.debug(wanted_reagent)
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if wanted_reagent == None:
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dlg = AddReagentQuestion(reagent_type=reagent, reagent_lot=reagents[reagent])
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if dlg.exec():
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wanted_reagent = self.add_reagent(reagent_lot=reagents[reagent], reagent_type=reagent.replace("lot_", ""))
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else:
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logger.debug("Will not add reagent.")
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if wanted_reagent != None:
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parsed_reagents.append(wanted_reagent)
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logger.debug(info)
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info['samples'] = self.samples
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base_submission, output = construct_submission_info(ctx=self.ctx, info_dict=info)
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if output['message'] != None:
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dlg = OverwriteSubQuestion(output['message'], base_submission.rsl_plate_num)
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if dlg.exec():
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base_submission.reagents = []
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else:
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return
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for reagent in parsed_reagents:
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base_submission.reagents.append(reagent)
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logger.debug(f"Sending submission: {base_submission.rsl_plate_num} to database.")
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result = store_submission(ctx=self.ctx, base_submission=base_submission)
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if result != None:
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msg = QMessageBox()
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# msg.setIcon(QMessageBox.critical)
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msg.setText("Error")
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msg.setInformativeText(result['message'])
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msg.setWindowTitle("Error")
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msg.show()
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msg.exec()
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self.table_widget.sub_wid.setData()
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for item in self.table_widget.formlayout.parentWidget().findChildren(QWidget):
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item.setParent(None)
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def add_reagent(self, reagent_lot:str|None=None, reagent_type:str|None=None):
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if isinstance(reagent_lot, bool):
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reagent_lot = ""
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dlg = AddReagentForm(ctx=self.ctx, reagent_lot=reagent_lot, reagent_type=reagent_type)
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if dlg.exec():
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labels, values = self.extract_form_info(dlg)
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info = {item[0]:item[1] for item in zip(labels, values)}
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logger.debug(f"Reagent info: {info}")
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reagent = construct_reagent(ctx=self.ctx, info_dict=info)
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store_reagent(ctx=self.ctx, reagent=reagent)
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return reagent
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def extract_form_info(self, object):
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labels = []
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values = []
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for item in object.layout.parentWidget().findChildren(QWidget):
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match item:
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case QLabel():
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labels.append(item.text().replace(" ", "_").lower())
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case QLineEdit():
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# ad hoc check to prevent double reporting of qdatedit under lineedit for some reason
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if not isinstance(prev_item, QDateEdit) and not isinstance(prev_item, QComboBox) and not isinstance(prev_item, QSpinBox):
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logger.debug(f"Previous: {prev_item}")
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logger.debug(f"Item: {item}")
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values.append(item.text())
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case QComboBox():
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values.append(item.currentText())
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case QDateEdit():
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values.append(item.date().toPyDate())
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prev_item = item
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return labels, values
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def generateReport(self):
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dlg = ReportDatePicker()
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if dlg.exec():
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labels, values = self.extract_form_info(dlg)
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info = {item[0]:item[1] for item in zip(labels, values)}
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subs = lookup_submissions_by_date_range(ctx=self.ctx, start_date=info['start_date'], end_date=info['end_date'])
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records = [item.report_dict() for item in subs]
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df = make_report_xlsx(records=records)
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home_dir = Path(self.ctx["directory_path"]).joinpath(f"Submissions_{info['start_date']}-{info['end_date']}.xlsx").resolve().__str__()
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fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".xlsx")[0])
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try:
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df.to_excel(fname, engine="openpyxl")
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except PermissionError:
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pass
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def add_kit(self):
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home_dir = str(Path(self.ctx["directory_path"]))
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fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir, filter = "yml(*.yml)")[0])
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assert fname.exists()
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try:
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with open(fname.__str__(), "r") as stream:
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try:
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exp = yaml.load(stream, Loader=yaml.Loader)
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except yaml.YAMLError as exc:
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logger.error(f'Error reading yaml file {fname}: {exc}')
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return {}
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except PermissionError:
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return
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create_kit_from_yaml(ctx=self.ctx, exp=exp)
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def controls_getter(self):
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# self.table_widget.webengineview.setHtml("")
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try:
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self.table_widget.sub_typer.disconnect()
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except TypeError:
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pass
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if self.table_widget.datepicker.start_date.date() > self.table_widget.datepicker.end_date.date():
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logger.warning("Start date after end date is not allowed!")
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# self.table_widget.datepicker.start_date.setDate(e_date)
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threemonthsago = self.table_widget.datepicker.end_date.date().addDays(-90)
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with QSignalBlocker(self.table_widget.datepicker.start_date) as blocker:
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self.table_widget.datepicker.start_date.setDate(threemonthsago)
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self.controls_getter()
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return
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self.start_date = self.table_widget.datepicker.start_date.date().toPyDate()
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self.end_date = self.table_widget.datepicker.end_date.date().toPyDate()
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self.con_type = self.table_widget.control_typer.currentText()
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self.mode = self.table_widget.mode_typer.currentText()
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self.table_widget.sub_typer.clear()
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sub_types = get_control_subtypes(ctx=self.ctx, type=self.con_type, mode=self.mode)
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if sub_types != []:
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with QSignalBlocker(self.table_widget.sub_typer) as blocker:
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self.table_widget.sub_typer.addItems(sub_types)
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self.table_widget.sub_typer.setEnabled(True)
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self.table_widget.sub_typer.currentTextChanged.connect(self.chart_maker)
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else:
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self.table_widget.sub_typer.clear()
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self.table_widget.sub_typer.setEnabled(False)
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self.chart_maker()
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def chart_maker(self):
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logger.debug(f"Control getter context: \n\tControl type: {self.con_type}\n\tMode: {self.mode}\n\tStart Date: {self.start_date}\n\tEnd Date: {self.end_date}")
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if self.table_widget.sub_typer.currentText() == "":
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self.subtype = None
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else:
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self.subtype = self.table_widget.sub_typer.currentText()
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logger.debug(f"Subtype: {self.subtype}")
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controls = get_all_controls_by_type(ctx=self.ctx, con_type=self.con_type, start_date=self.start_date, end_date=self.end_date)
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if controls == None:
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return
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data = []
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for control in controls:
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dicts = convert_control_by_mode(ctx=self.ctx, control=control, mode=self.mode)
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data.append(dicts)
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data = [item for sublist in data for item in sublist]
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# logger.debug(data)
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df = convert_data_list_to_df(ctx=self.ctx, input=data, subtype=self.subtype)
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if self.subtype == None:
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title = self.mode
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else:
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title = f"{self.mode} - {self.subtype}"
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fig = create_charts(ctx=self.ctx, df=df, ytitle=title)
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logger.debug(f"Updating figure...")
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html = '<html><body>'
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if fig != None:
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html += plotly.offline.plot(fig, output_type='div', include_plotlyjs='cdn')#, image = 'png', auto_open=True, image_filename='plot_image')
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else:
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html += "<h1>No data was retrieved for the given parameters.</h1>"
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html += '</body></html>'
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# with open("C:\\Users\\lwark\\Desktop\\test.html", "w") as f:
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# f.write(html)
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self.table_widget.webengineview.setHtml(html)
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self.table_widget.webengineview.update()
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logger.debug("Figure updated... I hope.")
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# def datechange(self):
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# s_date = self.table_widget.datepicker.start_date.date()
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# e_date = self.table_widget.datepicker.end_date.date()
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# if s_date > e_date:
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# logger.debug("that is not allowed!")
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# # self.table_widget.datepicker.start_date.setDate(e_date)
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# threemonthsago = e_date.addDays(-90)
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# self.table_widget.datepicker.start_date.setDate(threemonthsago)
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# self.chart_maker()
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class AddSubForm(QWidget):
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def __init__(self, parent):
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super(QWidget, self).__init__(parent)
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self.layout = QVBoxLayout(self)
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# Initialize tab screen
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self.tabs = QTabWidget()
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self.tab1 = QWidget()
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self.tab2 = QWidget()
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self.tab3 = QWidget()
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self.tabs.resize(300,200)
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# Add tabs
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self.tabs.addTab(self.tab1,"Submissions")
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self.tabs.addTab(self.tab2,"Controls")
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self.tabs.addTab(self.tab3, "Add Kit")
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# Create first tab
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# self.scroller = QWidget()
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# self.scroller.layout = QVBoxLayout(self)
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# self.scroller.setLayout(self.scroller.layout)
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# self.tab1.setMaximumHeight(1000)
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self.formwidget = QWidget(self)
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self.formlayout = QVBoxLayout(self)
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self.formwidget.setLayout(self.formlayout)
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self.formwidget.setFixedWidth(300)
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self.interior = QScrollArea(self.tab1)
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# self.interior.verticalScrollBar()
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# self.interior.setVerticalScrollBarPolicy(Qt.ScrollBarPolicy.ScrollBarAlwaysOn)
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self.interior.setWidgetResizable(True)
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self.interior.setFixedWidth(325)
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# self.interior.setParent(self.tab1)
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self.interior.setWidget(self.formwidget)
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self.sheetwidget = QWidget(self)
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self.sheetlayout = QVBoxLayout(self)
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self.sheetwidget.setLayout(self.sheetlayout)
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self.sub_wid = SubmissionsSheet(parent.ctx)
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self.sheetlayout.addWidget(self.sub_wid)
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self.tab1.layout = QHBoxLayout(self)
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self.tab1.setLayout(self.tab1.layout)
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# self.tab1.layout.addLayout(self.formlayout)
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self.tab1.layout.addWidget(self.interior)
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# self.tab1.layout.addWidget(self.formwidget)
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self.tab1.layout.addWidget(self.sheetwidget)
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# self.tab1.layout.addLayout(self.sheetlayout)
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self.datepicker = ControlsDatePicker()
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self.webengineview = QWebEngineView()
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self.tab2.layout = QVBoxLayout(self)
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self.control_typer = QComboBox()
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con_types = get_all_Control_Types_names(ctx=parent.ctx)
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self.control_typer.addItems(con_types)
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self.mode_typer = QComboBox()
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mode_types = get_all_available_modes(ctx=parent.ctx)
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self.mode_typer.addItems(mode_types)
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self.sub_typer = QComboBox()
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self.sub_typer.setEnabled(False)
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self.tab2.layout.addWidget(self.datepicker)
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self.tab2.layout.addWidget(self.control_typer)
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self.tab2.layout.addWidget(self.mode_typer)
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self.tab2.layout.addWidget(self.sub_typer)
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self.tab2.layout.addWidget(self.webengineview)
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self.tab2.setLayout(self.tab2.layout)
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# Add tabs to widget
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adder = KitAdder(parent_ctx=parent.ctx)
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self.tab3.layout = QVBoxLayout(self)
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self.tab3.layout.addWidget(adder)
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self.tab3.setLayout(self.tab3.layout)
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self.layout.addWidget(self.tabs)
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self.setLayout(self.layout)
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print(self.tab1.layout.parentWidget().findChildren(QScrollArea))
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