325 lines
13 KiB
Python
325 lines
13 KiB
Python
"""
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Constructs main application.
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"""
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import getpass, logging, webbrowser, sys, shutil
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from pprint import pformat
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from PyQt6.QtCore import qInstallMessageHandler
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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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# import pickle
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from PyQt6.QtGui import QAction
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from pathlib import Path
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from markdown import markdown
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from __init__ import project_path
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from backend import SubmissionType, Reagent, BasicSample, Organization, KitType
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from tools import (
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check_if_app, Settings, Report, jinja_template_loading, check_authorization, page_size, is_power_user, under_development
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)
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from .functions import select_save_file, select_open_file
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from .pop_ups import HTMLPop, AlertPop
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from .misc import Pagifier
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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 .summary import Summary
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from .turnaround import TurnaroundTime
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from .concentrations import Concentrations
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from .omni_search import SearchBox
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from .omni_manager import ManagerWindow
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logger = logging.getLogger(f'submissions.{__name__}')
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class App(QMainWindow):
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def __init__(self, ctx: Settings = None):
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super().__init__()
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qInstallMessageHandler(lambda x, y, z: None)
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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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# NOTE: 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}/{ctx.database_name}"
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except (AttributeError, KeyError):
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self.title = f"Submissions App"
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# NOTE: 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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self.page_size = page_size
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# NOTE: 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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# NOTE: 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.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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menuBar = self.menuBar()
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fileMenu = menuBar.addMenu("&File")
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editMenu = menuBar.addMenu("&Edit")
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# NOTE: Creating menus using a title
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methodsMenu = menuBar.addMenu("&Search")
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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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helpMenu.addAction(self.githubAction)
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fileMenu.addAction(self.importAction)
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fileMenu.addAction(self.yamlExportAction)
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fileMenu.addAction(self.yamlImportAction)
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methodsMenu.addAction(self.searchSample)
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maintenanceMenu.addAction(self.joinExtractionAction)
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maintenanceMenu.addAction(self.joinPCRAction)
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editMenu.addAction(self.editReagentAction)
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editMenu.addAction(self.manageOrgsAction)
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if getpass.getuser() == "lwark":
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editMenu.addAction(self.manageKitsAction)
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if not is_power_user():
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editMenu.setEnabled(False)
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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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toolbar = QToolBar("My main toolbar")
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self.addToolBar(toolbar)
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toolbar.addAction(self.addReagentAction)
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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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self.importAction = QAction("&Import Submission", self)
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self.addReagentAction = QAction("Add Reagent", 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.searchSample = QAction("Search Sample", self)
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self.githubAction = QAction("Github", self)
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self.yamlExportAction = QAction("Export Type Example", self)
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self.yamlImportAction = QAction("Import Type Template", self)
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self.editReagentAction = QAction("Edit Reagent", self)
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self.manageOrgsAction = QAction("Manage Clients", self)
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self.manageKitsAction = QAction("Manage Kits", 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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self.importAction.triggered.connect(self.table_widget.formwidget.importSubmission)
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self.addReagentAction.triggered.connect(self.table_widget.formwidget.add_reagent)
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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.searchSample.triggered.connect(self.runSampleSearch)
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self.githubAction.triggered.connect(self.openGithub)
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self.yamlExportAction.triggered.connect(self.export_ST_yaml)
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self.yamlImportAction.triggered.connect(self.import_ST_yaml)
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self.table_widget.pager.current_page.textChanged.connect(self.update_data)
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self.editReagentAction.triggered.connect(self.edit_reagent)
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self.manageOrgsAction.triggered.connect(self.manage_orgs)
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self.manageKitsAction.triggered.connect(self.manage_kits)
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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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j_env = jinja_template_loading()
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template = j_env.get_template("project.html")
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html = template.render(info=self.ctx.package.__dict__)
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about = HTMLPop(html=html, title="About")
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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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webbrowser.get('windows-default').open(f"file://{url.__str__()}")
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def openGithub(self):
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"""
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Opens the github page
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"""
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url = "https://github.com/landowark/submissions"
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webbrowser.get('windows-default').open(url)
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def openInstructions(self):
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if check_if_app():
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url = Path(sys._MEIPASS).joinpath("files", "README.md")
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else:
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url = Path("README.md")
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with open(url, "r", encoding="utf-8") as f:
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html = markdown(f.read())
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instr = HTMLPop(html=html, title="Instructions")
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instr.exec()
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def runSampleSearch(self):
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"""
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Create a search for samples.
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"""
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dlg = SearchBox(self, object_type=BasicSample, extras=[])
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dlg.exec()
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@check_authorization
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def edit_reagent(self, *args, **kwargs):
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dlg = SearchBox(parent=self, object_type=Reagent, extras=[dict(name='Role', field="role")])
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dlg.exec()
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def export_ST_yaml(self):
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"""
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Copies submission type yaml to file system for editing and remport
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Returns:
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None
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"""
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if check_if_app():
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yaml_path = Path(sys._MEIPASS).joinpath("files", "resources", "viral_culture.yml")
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else:
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yaml_path = project_path.joinpath("src", "submissions", "resources", "viral_culture.yml")
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fname = select_save_file(obj=self, default_name="Submission Type Template.yml", extension="yml")
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shutil.copyfile(yaml_path, fname)
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@check_authorization
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def import_ST_yaml(self, *args, **kwargs):
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"""
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Imports a yml form into a submission type.
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Args:
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*args ():
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**kwargs ():
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Returns:
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"""
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fname = select_open_file(obj=self, file_extension="yml")
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if not fname:
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logger.info(f"Import cancelled.")
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return
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ap = AlertPop(message="This function will proceed in the debug window.", status="Warning", owner=self)
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ap.exec()
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st = SubmissionType.import_from_json(filepath=fname)
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if st:
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# NOTE: Do not delete the print statement below.
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choice = input("Save the above submission type? [y/N]: ")
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if choice.lower() == "y":
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pass
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else:
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logger.warning("Save of submission type cancelled.")
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def update_data(self):
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self.table_widget.sub_wid.setData(page=self.table_widget.pager.page_anchor, page_size=page_size)
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def manage_orgs(self):
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dlg = ManagerWindow(parent=self, object_type=Organization, extras=[], add_edit='edit', managers=set())
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if dlg.exec():
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new_org = dlg.parse_form()
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new_org.save()
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# logger.debug(new_org.__dict__)
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@under_development
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def manage_kits(self, *args, **kwargs):
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from frontend.widgets.omni_manager_pydant import ManagerWindow as ManagerWindowPyd
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dlg = ManagerWindowPyd(parent=self, object_type=KitType, extras=[], add_edit='edit', managers=set())
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if dlg.exec():
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logger.debug("\n\nBeginning parsing\n\n")
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output = dlg.parse_form()
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logger.debug(f"Kit output: {pformat(output.__dict__)}")
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# with open(f"{output.name}.obj", "wb") as f:
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# pickle.dump(output, f)
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logger.debug("\n\nBeginning transformation\n\n")
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sql = output.to_sql()
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assert isinstance(sql, KitType)
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# with open(f"{output.name}.sql", "wb") as f:
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# pickle.dump(sql, f)
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sql.save()
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class AddSubForm(QWidget):
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def __init__(self, parent: QWidget):
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super(QWidget, self).__init__(parent)
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self.layout = QVBoxLayout(self)
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# NOTE: 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.tab4 = QWidget()
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self.tab5 = QWidget()
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self.tab6 = QWidget()
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self.tabs.resize(300, 200)
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# NOTE: Add tabs
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self.tabs.addTab(self.tab1, "Submissions")
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self.tabs.addTab(self.tab2, "Irida Controls")
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self.tabs.addTab(self.tab6, "Concentrations")
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self.tabs.addTab(self.tab3, "PCR Controls")
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self.tabs.addTab(self.tab4, "Cost Report")
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self.tabs.addTab(self.tab5, "Turnaround Times")
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# NOTE: 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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# NOTE: 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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# NOTE: 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.pager = Pagifier(page_max=self.sub_wid.total_count / page_size)
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self.sheetlayout.addWidget(self.sub_wid)
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self.sheetlayout.addWidget(self.pager)
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# NOTE: 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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self.tab2.layout = QVBoxLayout(self)
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self.irida_viewer = ControlsViewer(self, archetype="Irida Control")
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self.tab2.layout.addWidget(self.irida_viewer)
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self.tab2.setLayout(self.tab2.layout)
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self.tab3.layout = QVBoxLayout(self)
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self.pcr_viewer = ControlsViewer(self, archetype="PCR Control")
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self.tab3.layout.addWidget(self.pcr_viewer)
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self.tab3.setLayout(self.tab3.layout)
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summary_report = Summary(self)
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self.tab4.layout = QVBoxLayout(self)
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self.tab4.layout.addWidget(summary_report)
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self.tab4.setLayout(self.tab4.layout)
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turnaround = TurnaroundTime(self)
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self.tab5.layout = QVBoxLayout(self)
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self.tab5.layout.addWidget(turnaround)
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self.tab5.setLayout(self.tab5.layout)
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concentration = Concentrations(self)
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self.tab6.layout = QVBoxLayout(self)
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self.tab6.layout.addWidget(concentration)
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self.tab6.setLayout(self.tab6.layout)
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# NOTE: 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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