Large scale frontend refactor
This commit is contained in:
Landon Wark
412
src/submissions/frontend/widgets/app.py
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412
src/submissions/frontend/widgets/app.py
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'''
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Constructs main application.
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TODO: Complete.
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'''
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import sys
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from PyQt6.QtWidgets import (
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QTabWidget, QWidget, QVBoxLayout,
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QHBoxLayout, QScrollArea, QMainWindow,
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QToolBar
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)
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from PyQt6.QtGui import QAction
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from pathlib import Path
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from backend.validators import PydReagent
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# from frontend.functions import (
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# add_kit_function, add_org_function, link_controls_function, export_csv_function
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# )
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from tools import check_if_app, Settings, Report
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from .pop_ups import AlertPop
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from .misc import AddReagentForm
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import logging
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from datetime import date
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import webbrowser
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from .submission_table import SubmissionsSheet
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from .submission_widget import SubmissionFormContainer
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from .controls_chart import ControlsViewer
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from .kit_creator import KitAdder
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import webbrowser
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logger = logging.getLogger(f'submissions.{__name__}')
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logger.info("Hello, I am a logger")
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class App(QMainWindow):
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def __init__(self, ctx: Settings = None):
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logger.debug(f"Initializing main window...")
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super().__init__()
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self.ctx = ctx
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self.last_dir = ctx.directory_path
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self.report = Report()
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# indicate version and connected database in title bar
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try:
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self.title = f"Submissions App (v{ctx.package.__version__}) - {ctx.database_path}"
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except (AttributeError, KeyError):
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self.title = f"Submissions App"
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# set initial app position and size
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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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# insert tabs into main app
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self.table_widget = AddSubForm(self)
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self.setCentralWidget(self.table_widget)
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# run initial setups
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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._controls_getter()
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self.show()
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self.statusBar().showMessage('Ready', 5000)
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def _createMenuBar(self):
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"""
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adds items to menu bar
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"""
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logger.debug(f"Creating menu bar...")
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menuBar = self.menuBar()
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fileMenu = menuBar.addMenu("&File")
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# Creating menus using a title
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# methodsMenu = menuBar.addMenu("&Methods")
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reportMenu = menuBar.addMenu("&Reports")
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maintenanceMenu = menuBar.addMenu("&Monthly")
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helpMenu = menuBar.addMenu("&Help")
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helpMenu.addAction(self.helpAction)
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helpMenu.addAction(self.docsAction)
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fileMenu.addAction(self.importAction)
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fileMenu.addAction(self.importPCRAction)
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# methodsMenu.addAction(self.constructFS)
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reportMenu.addAction(self.generateReportAction)
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maintenanceMenu.addAction(self.joinExtractionAction)
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maintenanceMenu.addAction(self.joinPCRAction)
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def _createToolBar(self):
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"""
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adds items to toolbar
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"""
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logger.debug(f"Creating toolbar...")
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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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toolbar.addAction(self.addOrgAction)
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def _createActions(self):
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"""
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creates actions
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"""
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logger.debug(f"Creating actions...")
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self.importAction = QAction("&Import Submission", self)
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self.importPCRAction = QAction("&Import PCR Results", 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("Import Kit", self)
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self.addOrgAction = QAction("Import Org", self)
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self.joinExtractionAction = QAction("Link Extraction Logs")
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self.joinPCRAction = QAction("Link PCR Logs")
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self.helpAction = QAction("&About", self)
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self.docsAction = QAction("&Docs", self)
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# self.constructFS = QAction("Make First Strand", self)
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def _connectActions(self):
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"""
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connect menu and tool bar item to functions
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"""
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logger.debug(f"Connecting actions...")
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self.importAction.triggered.connect(self.table_widget.formwidget.importSubmission)
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self.importPCRAction.triggered.connect(self.table_widget.formwidget.import_pcr_results)
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self.addReagentAction.triggered.connect(self.add_reagent)
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self.generateReportAction.triggered.connect(self.table_widget.sub_wid.generate_report)
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# self.addKitAction.triggered.connect(self.add_kit)
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# self.addOrgAction.triggered.connect(self.add_org)
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self.joinExtractionAction.triggered.connect(self.table_widget.sub_wid.link_extractions)
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self.joinPCRAction.triggered.connect(self.table_widget.sub_wid.link_pcr)
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self.helpAction.triggered.connect(self.showAbout)
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self.docsAction.triggered.connect(self.openDocs)
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# self.constructFS.triggered.connect(self.construct_first_strand)
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# self.table_widget.formwidget.import_drag.connect(self.importSubmission)
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def showAbout(self):
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"""
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Show the 'about' message
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"""
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output = f"Version: {self.ctx.package.__version__}\n\nAuthor: {self.ctx.package.__author__['name']} - {self.ctx.package.__author__['email']}\n\nCopyright: {self.ctx.package.__copyright__}"
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about = AlertPop(message=output, status="information")
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about.exec()
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def openDocs(self):
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"""
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Open the documentation html pages
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"""
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if check_if_app():
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url = Path(sys._MEIPASS).joinpath("files", "docs", "index.html")
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else:
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url = Path("docs\\build\\index.html").absolute()
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logger.debug(f"Attempting to open {url}")
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webbrowser.get('windows-default').open(f"file://{url.__str__()}")
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def result_reporter(self):
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# def result_reporter(self, result:TypedDict[]|None=None):
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"""
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Report any anomolous results - if any - to the user
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Args:
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result (dict | None, optional): The result from a function. Defaults to None.
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"""
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# logger.info(f"We got the result: {result}")
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# if result != None:
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# msg = AlertPop(message=result['message'], status=result['status'])
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# msg.exec()
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logger.debug(f"Running results reporter for: {self.report.results}")
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if len(self.report.results) > 0:
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logger.debug(f"We've got some results!")
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for result in self.report.results:
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logger.debug(f"Showing result: {result}")
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if result != None:
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alert = result.report()
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if alert.exec():
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pass
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self.report = Report()
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else:
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self.statusBar().showMessage("Action completed sucessfully.", 5000)
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# def importSubmission(self, fname:Path|None=None):
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# """
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# import submission from excel sheet into form
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# """
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# # from .main_window_functions import import_submission_function
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# self.raise_()
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# self.activateWindow()
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# self = import_submission_function(self, fname)
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# logger.debug(f"Result from result reporter: {self.report.results}")
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# self.result_reporter()
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# def kit_reload(self):
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# """
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# Removes all reagents from form before running kit integrity completion.
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# """
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# # from .main_window_functions import kit_reload_function
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# self = kit_reload_function(self)
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# self.result_reporter()
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# def kit_integrity_completion(self):
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# """
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# Performs check of imported reagents
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# NOTE: this will not change self.reagents which should be fine
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# since it's only used when looking up
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# """
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# # from .main_window_functions import kit_integrity_completion_function
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# self = kit_integrity_completion_function(self)
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# self.result_reporter()
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# def submit_new_sample(self):
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# """
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# Attempt to add sample to database when 'submit' button clicked
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# """
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# # from .main_window_functions import submit_new_sample_function
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# self = submit_new_sample_function(self)
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# self.result_reporter()
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def add_reagent(self, reagent_lot:str|None=None, reagent_type:str|None=None, expiry:date|None=None, name:str|None=None):
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"""
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Action to create new reagent in DB.
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Args:
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reagent_lot (str | None, optional): Parsed reagent from import form. Defaults to None.
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reagent_type (str | None, optional): Parsed reagent type from import form. Defaults to None.
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Returns:
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models.Reagent: the constructed reagent object to add to submission
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"""
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report = Report()
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if isinstance(reagent_lot, bool):
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reagent_lot = ""
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# create form
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dlg = AddReagentForm(ctx=self.ctx, reagent_lot=reagent_lot, reagent_type=reagent_type, expiry=expiry, reagent_name=name)
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if dlg.exec():
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# extract form info
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# info = extract_form_info(dlg)
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info = dlg.parse_form()
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logger.debug(f"Reagent info: {info}")
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# create reagent object
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# reagent = construct_reagent(ctx=self.ctx, info_dict=info)
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reagent = PydReagent(ctx=self.ctx, **info)
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# send reagent to db
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# store_reagent(ctx=self.ctx, reagent=reagent)
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sqlobj, result = reagent.toSQL()
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sqlobj.save()
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# result = store_object(ctx=self.ctx, object=reagent.toSQL()[0])
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report.add_result(result)
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self.result_reporter()
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return reagent
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# def generateReport(self):
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# """
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# Action to create a summary of sheet data per client
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# """
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# # from .main_window_functions import generate_report_function
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# self, result = generate_report_function(self)
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# self.result_reporter(result)
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# def add_kit(self):
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# """
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# Constructs new kit from yaml and adds to DB.
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# """
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# # from .main_window_functions import add_kit_function
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# self, result = add_kit_function(self)
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# self.result_reporter(result)
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# def add_org(self):
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# """
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# Constructs new kit from yaml and adds to DB.
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# """
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# # from .main_window_functions import add_org_function
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# self, result = add_org_function(self)
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# self.result_reporter(result)
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# def _controls_getter(self):
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# """
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# Lookup controls from database and send to chartmaker
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# """
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# # from .main_window_functions import controls_getter_function
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# self = controls_getter_function(self)
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# self.result_reporter()
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# def _chart_maker(self):
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# """
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# Creates plotly charts for webview
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# """
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# # from .main_window_functions import chart_maker_function
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# self = chart_maker_function(self)
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# self.result_reporter()
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# def linkControls(self):
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# """
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# Adds controls pulled from irida to relevant submissions
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# NOTE: Depreciated due to improvements in controls scraper.
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# """
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# # from .main_window_functions import link_controls_function
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# self, result = link_controls_function(self)
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# self.result_reporter(result)
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# def linkExtractions(self):
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# """
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# Links extraction logs from .csv files to relevant submissions.
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# """
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# # from .main_window_functions import link_extractions_function
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# self, result = link_extractions_function(self)
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# self.result_reporter(result)
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# def linkPCR(self):
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# """
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# Links PCR logs from .csv files to relevant submissions.
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# """
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# # from .main_window_functions import link_pcr_function
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# self, result = link_pcr_function(self)
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# self.result_reporter(result)
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# def importPCRResults(self):
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# """
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# Imports results exported from Design and Analysis .eds files
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# """
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# # from .main_window_functions import import_pcr_results_function
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# self, result = import_pcr_results_function(self)
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# self.result_reporter(result)
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# def construct_first_strand(self):
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# """
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# Converts first strand excel sheet to Biomek CSV
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# """
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# from .main_window_functions import construct_first_strand_function
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# self, result = construct_first_strand_function(self)
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# self.result_reporter(result)
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# def scrape_reagents(self, *args, **kwargs):
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# # from .main_window_functions import scrape_reagents
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# logger.debug(f"Args: {args}")
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# logger.debug(F"kwargs: {kwargs}")
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# self = scrape_reagents(self, args[0])
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# self.kit_integrity_completion()
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# self.result_reporter()
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# def export_csv(self, fname:Path|None=None):
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# # from .main_window_functions import export_csv_function
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# export_csv_function(self, fname)
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class AddSubForm(QWidget):
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def __init__(self, parent:QWidget):
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logger.debug(f"Initializating subform...")
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super(QWidget, self).__init__(parent)
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self.layout = QVBoxLayout(self)
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self.parent = parent
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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 submission adder form
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self.formwidget = SubmissionFormContainer(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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# Make scrollable interior for form
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self.interior = QScrollArea(self.tab1)
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self.interior.setWidgetResizable(True)
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self.interior.setFixedWidth(325)
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self.interior.setWidget(self.formwidget)
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# Create sheet to hold existing submissions
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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=parent)
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self.sheetlayout.addWidget(self.sub_wid)
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# Create layout of first tab to hold form and sheet
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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.addWidget(self.interior)
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self.tab1.layout.addWidget(self.sheetwidget)
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# create widgets for tab 2
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# self.datepicker = ControlsDatePicker()
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# self.webengineview = QWebEngineView()
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# set tab2 layout
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self.tab2.layout = QVBoxLayout(self)
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# self.control_typer = QComboBox()
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# fetch types of controls
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# con_types = get_all_Control_Types_names(ctx=parent.ctx)
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# con_types = [item.name for item in lookup_control_types(ctx=parent.ctx)]
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# con_types = [item.name for item in ControlType.query()]
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# self.control_typer.addItems(con_types)
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# create custom widget to get types of analysis
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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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# mode_types = lookup_modes(ctx=parent.ctx)
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# mode_types = Control.get_modes()
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# self.mode_typer.addItems(mode_types)
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# create custom widget to get subtypes of analysis
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# self.sub_typer = QComboBox()
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# self.sub_typer.setEnabled(False)
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# add widgets to tab2 layout
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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.controls_viewer = ControlsViewer(self)
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self.tab2.layout.addWidget(self.controls_viewer)
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self.tab2.setLayout(self.tab2.layout)
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# create custom widget to add new tabs
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adder = KitAdder(self)
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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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# add tabs to main widget
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self.layout.addWidget(self.tabs)
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self.setLayout(self.layout)
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