754 lines
34 KiB
Python
754 lines
34 KiB
Python
from PyQt6.QtWidgets import (
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QWidget, QPushButton, QVBoxLayout,
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QComboBox, QDateEdit, QLineEdit, QLabel
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)
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from PyQt6.QtCore import pyqtSignal
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from pathlib import Path
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from . import select_open_file, select_save_file
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import logging, difflib, inspect
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from pathlib import Path
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from tools import Report, Result, check_not_nan
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from backend.excel.parser import SheetParser
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from backend.validators import PydSubmission, PydReagent
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from backend.db import (
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KitType, Organization, SubmissionType, Reagent,
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ReagentType, KitTypeReagentTypeAssociation
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)
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from pprint import pformat
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from .pop_ups import QuestionAsker, AlertPop
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from .misc import AddReagentForm
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from typing import List, Tuple
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from datetime import date
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logger = logging.getLogger(f"submissions.{__name__}")
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class SubmissionFormContainer(QWidget):
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# A signal carrying a path
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import_drag = pyqtSignal(Path)
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def __init__(self, parent: QWidget) -> None:
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logger.debug(f"Setting form widget...")
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super().__init__(parent)
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self.app = self.parent().parent()
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self.report = Report()
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self.setAcceptDrops(True)
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# if import_drag is emitted, importSubmission will fire
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self.import_drag.connect(self.importSubmission)
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def dragEnterEvent(self, event):
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"""
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Allow drag if file.
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"""
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if event.mimeData().hasUrls():
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event.accept()
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else:
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event.ignore()
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def dropEvent(self, event):
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"""
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Sets filename when file dropped
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"""
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fname = Path([u.toLocalFile() for u in event.mimeData().urls()][0])
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logger.debug(f"App: {self.app}")
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self.app.last_dir = fname.parent
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self.import_drag.emit(fname)
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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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self.app.raise_()
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self.app.activateWindow()
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self.import_submission_function(fname)
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logger.debug(f"Result from result reporter: {self.report.results}")
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self.app.report.add_result(self.report)
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self.report = Report()
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self.app.result_reporter()
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def import_submission_function(self, fname:Path|None=None):
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"""
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Import a new submission to the app window
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Args:
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obj (QMainWindow): original app window
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Returns:
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Tuple[QMainWindow, dict|None]: Collection of new main app window and result dict
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"""
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logger.debug(f"\n\nStarting Import...\n\n")
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report = Report()
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try:
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self.form.setParent(None)
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except AttributeError:
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pass
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# initialize samples
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self.samples = []
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self.missing_info = []
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# set file dialog
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if isinstance(fname, bool) or fname == None:
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fname = select_open_file(self, file_extension="xlsx")
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logger.debug(f"Attempting to parse file: {fname}")
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if not fname.exists():
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report.add_result(Result(msg=f"File {fname.__str__()} not found.", status="critical"))
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self.report.add_result(report)
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return
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# create sheetparser using excel sheet and context from gui
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try:
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self.prsr = SheetParser(filepath=fname)
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except PermissionError:
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logger.error(f"Couldn't get permission to access file: {fname}")
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return
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except AttributeError:
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self.prsr = SheetParser(filepath=fname)
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logger.debug(f"Submission dictionary:\n{pformat(self.prsr.sub)}")
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self.pyd = self.prsr.to_pydantic()
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logger.debug(f"Pydantic result: \n\n{pformat(self.pyd)}\n\n")
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self.form = self.pyd.toForm(parent=self)
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self.layout().addWidget(self.form)
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if self.prsr.sample_result != None:
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report.add_result(msg=self.prsr.sample_result, status="Warning")
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self.report.add_result(report)
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logger.debug(f"Outgoing report: {self.report.results}")
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logger.debug(f"All attributes of submission container:\n{pformat(self.__dict__)}")
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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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expiry (date | None, optional): Parsed reagent expiry data. Defaults to None.
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name (str | None, optional): Parsed reagent name. 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(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 = 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 = PydReagent(ctx=self.app.ctx, **info)
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# send reagent to db
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sqlobj, result = reagent.toSQL()
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sqlobj.save()
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report.add_result(result)
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self.app.result_reporter()
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return reagent
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class SubmissionFormWidget(QWidget):
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def __init__(self, parent: QWidget, submission:PydSubmission) -> None:
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super().__init__(parent)
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# self.report = Report()
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self.app = parent.app
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self.pyd = submission
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# self.input = [{k:v} for k,v in kwargs.items()]
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# self.samples = []
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self.missing_info = []
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self.ignore = ['filepath', 'samples', 'reagents', 'csv', 'ctx', 'comment',
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'equipment', 'gel_controls', 'id', 'cost', 'extraction_info',
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'controls', 'pcr_info', 'gel_info', 'gel_image']
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self.recover = ['filepath', 'samples', 'csv', 'comment', 'equipment']
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self.layout = QVBoxLayout()
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# for k, v in kwargs.items():
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for k in list(self.pyd.model_fields.keys()) + list(self.pyd.model_extra.keys()):
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if k not in self.ignore:
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try:
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value = self.pyd.__getattribute__(k)
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except AttributeError:
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logger.error(f"Couldn't get attribute from pyd: {k}")
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value = dict(value=None, missing=True)
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add_widget = self.create_widget(key=k, value=value, submission_type=self.pyd.submission_type['value'])
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if add_widget != None:
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self.layout.addWidget(add_widget)
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if k == "extraction_kit":
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add_widget.input.currentTextChanged.connect(self.scrape_reagents)
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# else:
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# self.__setattr__(k, v)
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# self.scrape_reagents(self.extraction_kit['value'])
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self.scrape_reagents(self.pyd.extraction_kit)
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# extraction kit must be added last so widget order makes sense.
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# self.layout.addWidget(self.create_widget(key="extraction_kit", value=self.extraction_kit, submission_type=self.submission_type))
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# if hasattr(self.pyd, "csv"):
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# export_csv_btn = QPushButton("Export CSV")
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# export_csv_btn.setObjectName("export_csv_btn")
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# self.layout.addWidget(export_csv_btn)
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# export_csv_btn.clicked.connect(self.export_csv_function)
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# submit_btn = QPushButton("Submit")
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# submit_btn.setObjectName("submit_btn")
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# self.layout.addWidget(submit_btn)
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# submit_btn.clicked.connect(self.submit_new_sample_function)
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# self.setLayout(self.layout)
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# self.app.report.add_result(self.report)
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# self.app.result_reporter()
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def create_widget(self, key:str, value:dict|PydReagent, submission_type:str|None=None, extraction_kit:str|None=None) -> "self.InfoItem":
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"""
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Make an InfoItem widget to hold a field
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Args:
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key (str): Name of the field
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value (dict): Value of field
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submission_type (str | None, optional): Submissiontype as str. Defaults to None.
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Returns:
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self.InfoItem: Form widget to hold name:value
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"""
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if key not in self.ignore:
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match value:
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case PydReagent():
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if value.name.lower() != "not applicable":
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widget = self.ReagentFormWidget(self, reagent=value, extraction_kit=extraction_kit)
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else:
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widget = None
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case _:
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widget = self.InfoItem(self, key=key, value=value, submission_type=submission_type)
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return widget
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return None
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def scrape_reagents(self, *args, **kwargs):#extraction_kit:str, caller:str|None=None):
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"""
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Extracted scrape reagents function that will run when
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form 'extraction_kit' widget is updated.
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Args:
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obj (QMainWindow): updated main application
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extraction_kit (str): name of extraction kit (in 'extraction_kit' widget)
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Returns:
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Tuple[QMainWindow, dict]: Updated application and result
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"""
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extraction_kit = args[0]
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caller = inspect.stack()[1].function.__repr__().replace("'", "")
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# self.reagents = []
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# logger.debug(f"Self.reagents: {self.reagents}")
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logger.debug(f"\n\n{pformat(caller)}\n\n")
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# logger.debug(f"SubmissionType: {self.submission_type}")
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report = Report()
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logger.debug(f"Extraction kit: {extraction_kit}")
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# Remove previous reagent widgets
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try:
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old_reagents = self.find_widgets()
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except AttributeError:
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logger.error(f"Couldn't find old reagents.")
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old_reagents = []
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# logger.debug(f"\n\nAttempting to clear: {old_reagents}\n\n")
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for reagent in old_reagents:
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if isinstance(reagent, self.ReagentFormWidget) or isinstance(reagent, QPushButton):
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reagent.setParent(None)
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# match caller:
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# case "import_submission_function":
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# self.reagents = self.prsr.sub['reagents']
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# case _:
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# already_have = [reagent for reagent in self.prsr.sub['reagents'] if not reagent.missing]
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# already_have = [reagent for reagent in self.pyd.reagents if not reagent.missing]
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# names = list(set([item.type for item in already_have]))
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# # logger.debug(f"Already have: {already_have}")
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# reagents = [item.to_pydantic() for item in KitType.query(name=extraction_kit).get_reagents(submission_type=self.pyd.submission_type) if item.name not in names]
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# # logger.debug(f"Missing: {reagents}")
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# self.pyd.reagents = already_have + reagents
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# logger.debug(f"Reagents: {self.reagents}")
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# self.kit_integrity_completion_function(extraction_kit=extraction_kit)
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reagents, integrity_report = self.pyd.check_kit_integrity(extraction_kit=extraction_kit)
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# logger.debug(f"Missing reagents: {obj.missing_reagents}")
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for reagent in reagents:
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add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.pyd.extraction_kit)
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self.layout.addWidget(add_widget)
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report.add_result(integrity_report)
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logger.debug(f"Outgoing report: {report.results}")
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if hasattr(self.pyd, "csv"):
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export_csv_btn = QPushButton("Export CSV")
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export_csv_btn.setObjectName("export_csv_btn")
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self.layout.addWidget(export_csv_btn)
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export_csv_btn.clicked.connect(self.export_csv_function)
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submit_btn = QPushButton("Submit")
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submit_btn.setObjectName("submit_btn")
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self.layout.addWidget(submit_btn)
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submit_btn.clicked.connect(self.submit_new_sample_function)
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self.setLayout(self.layout)
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self.app.report.add_result(report)
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self.app.result_reporter()
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def kit_integrity_completion_function(self, extraction_kit:str|None=None):
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"""
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Compare kit contents to parsed contents and creates widgets.
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Args:
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obj (QMainWindow): The original app window
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Returns:
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Tuple[QMainWindow, dict]: Collection of new main app window and result dict
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"""
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report = Report()
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missing_reagents = []
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# logger.debug(inspect.currentframe().f_back.f_code.co_name)
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# find the widget that contains kit info
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if extraction_kit is None:
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kit_widget = self.find_widgets(object_name="extraction_kit")[0].input
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logger.debug(f"Kit selector: {kit_widget}")
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# get current kit being used
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self.ext_kit = kit_widget.currentText()
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else:
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self.ext_kit = extraction_kit
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for reagent in self.reagents:
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logger.debug(f"Creating widget for {reagent}")
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add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.ext_kit)
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# self.form.layout().addWidget(add_widget)
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self.layout.addWidget(add_widget)
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if reagent.missing:
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missing_reagents.append(reagent)
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logger.debug(f"Checking integrity of {self.ext_kit}")
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# TODO: put check_kit_integrity here instead of what's here?
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# see if there are any missing reagents
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if len(missing_reagents) > 0:
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result = Result(msg=f"""The submission you are importing is missing some reagents expected by the kit.\n\n
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It looks like you are missing: {[item.type.upper() for item in missing_reagents]}\n\n
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Alternatively, you may have set the wrong extraction kit.\n\nThe program will populate lists using existing reagents.
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\n\nPlease make sure you check the lots carefully!""".replace(" ", ""), status="Warning")
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report.add_result(result)
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self.report.add_result(report)
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logger.debug(f"Outgoing report: {self.report.results}")
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def clear_form(self):
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"""
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Removes all form widgets
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"""
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for item in self.findChildren(QWidget):
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item.setParent(None)
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def find_widgets(self, object_name:str|None=None) -> List[QWidget]:
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"""
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Gets all widgets filtered by object name
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Args:
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object_name (str | None, optional): name to filter by. Defaults to None.
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Returns:
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List[QWidget]: Widgets matching filter
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"""
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query = self.findChildren(QWidget)
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if object_name != None:
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query = [widget for widget in query if widget.objectName()==object_name]
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return query
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def submit_new_sample_function(self) -> QWidget:
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"""
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Parse forms and add sample to the database.
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Args:
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obj (QMainWindow): original app window
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Returns:
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Tuple[QMainWindow, dict]: Collection of new main app window and result dict
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"""
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logger.debug(f"\n\nBeginning Submission\n\n")
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report = Report()
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# self.pyd: PydSubmission = self.parse_form()
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result = self.parse_form()
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report.add_result(result)
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logger.debug(f"Submission: {pformat(self.pyd)}")
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logger.debug("Checking kit integrity...")
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_, result = self.pyd.check_kit_integrity()
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report.add_result(result)
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if len(result.results) > 0:
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self.app.report.add_result(report)
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self.app.result_reporter()
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return
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logger.debug(f"PYD before transformation into SQL:\n\n{self.pyd}\n\n")
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base_submission, result = self.pyd.toSQL()
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# logger.debug(f"Base submission: {base_submission.to_dict()}")
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# check output message for issues
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match result.code:
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# code 0: everything is fine.
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case 0:
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report.add_result(None)
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# code 1: ask for overwrite
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case 1:
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dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_num}?", message=result.msg)
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if dlg.exec():
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# Do not add duplicate reagents.
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# base_submission.reagents = []
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result = None
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else:
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self.app.ctx.database_session.rollback()
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report.add_result(Result(msg="Overwrite cancelled", status="Information"))
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return
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# code 2: No RSL plate number given
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case 2:
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report.add_result(result)
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return
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case _:
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pass
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# add reagents to submission object
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for reagent in base_submission.reagents:
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# logger.debug(f"Updating: {reagent} with {reagent.lot}")
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reagent.update_last_used(kit=base_submission.extraction_kit)
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# logger.debug(f"Here is the final submission: {pformat(base_submission.__dict__)}")
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# logger.debug(f"Parsed reagents: {pformat(base_submission.reagents)}")
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# logger.debug(f"Sending submission: {base_submission.rsl_plate_num} to database.")
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# logger.debug(f"Samples from pyd: {pformat(self.pyd.samples)}")
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# logger.debug(f"Samples SQL: {pformat([item.__dict__ for item in base_submission.samples])}")
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# logger.debug(f"")
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base_submission.save()
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# update summary sheet
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self.app.table_widget.sub_wid.setData()
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# reset form
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self.setParent(None)
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# logger.debug(f"All attributes of obj: {pformat(self.__dict__)}")
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self.app.report.add_result(report)
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self.app.result_reporter()
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def export_csv_function(self, fname:Path|None=None):
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"""
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Save the submission's csv file.
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Args:
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fname (Path | None, optional): Input filename. Defaults to None.
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"""
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self.parse_form()
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if isinstance(fname, bool) or fname == None:
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fname = select_save_file(obj=self, default_name=self.pyd.construct_filename(), extension="csv")
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try:
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self.pyd.csv.to_csv(fname.__str__(), index=False)
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except PermissionError:
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logger.debug(f"Could not get permissions to {fname}. Possibly the request was cancelled.")
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def parse_form(self) -> PydSubmission:
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"""
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Transforms form info into PydSubmission
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Returns:
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PydSubmission: Pydantic submission object
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"""
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report = Report()
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logger.debug(f"Hello from form parser!")
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info = {}
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reagents = []
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for widget in self.findChildren(QWidget):
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# logger.debug(f"Parsed widget of type {type(widget)}")
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match widget:
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case self.ReagentFormWidget():
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reagent, _ = widget.parse_form()
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if reagent != None:
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reagents.append(reagent)
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case self.InfoItem():
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field, value = widget.parse_form()
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if field != None:
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info[field] = value
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logger.debug(f"Info: {pformat(info)}")
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logger.debug(f"Reagents: {pformat(reagents)}")
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self.pyd.reagents = reagents
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|
# logger.debug(f"Attrs not in info: {[k for k, v in self.__dict__.items() if k not in info.keys()]}")
|
|
for item in self.recover:
|
|
logger.debug(f"Attempting to recover: {item}")
|
|
if hasattr(self, item):
|
|
value = getattr(self, item)
|
|
logger.debug(f"Setting {item}")
|
|
info[item] = value
|
|
# submission = PydSubmission(reagents=reagents, **info)
|
|
for k,v in info.items():
|
|
self.pyd.set_attribute(key=k, value=v)
|
|
# return submission
|
|
report.add_result(report)
|
|
return report
|
|
|
|
class InfoItem(QWidget):
|
|
|
|
def __init__(self, parent: QWidget, key:str, value:dict, submission_type:str|None=None) -> None:
|
|
super().__init__(parent)
|
|
layout = QVBoxLayout()
|
|
self.label = self.ParsedQLabel(key=key, value=value)
|
|
self.input: QWidget = self.set_widget(parent=self, key=key, value=value, submission_type=submission_type)
|
|
self.setObjectName(key)
|
|
try:
|
|
self.missing:bool = value['missing']
|
|
except (TypeError, KeyError):
|
|
self.missing:bool = True
|
|
if self.input != None:
|
|
layout.addWidget(self.label)
|
|
layout.addWidget(self.input)
|
|
layout.setContentsMargins(0,0,0,0)
|
|
self.setLayout(layout)
|
|
match self.input:
|
|
case QComboBox():
|
|
self.input.currentTextChanged.connect(self.update_missing)
|
|
case QDateEdit():
|
|
self.input.dateChanged.connect(self.update_missing)
|
|
case QLineEdit():
|
|
self.input.textChanged.connect(self.update_missing)
|
|
|
|
def parse_form(self) -> Tuple[str, dict]:
|
|
"""
|
|
Pulls info from widget into dict
|
|
|
|
Returns:
|
|
Tuple[str, dict]: name of field, {value, missing}
|
|
"""
|
|
match self.input:
|
|
case QLineEdit():
|
|
value = self.input.text()
|
|
case QComboBox():
|
|
value = self.input.currentText()
|
|
case QDateEdit():
|
|
value = self.input.date().toPyDate()
|
|
case _:
|
|
return None, None
|
|
return self.input.objectName(), dict(value=value, missing=self.missing)
|
|
|
|
def set_widget(self, parent: QWidget, key:str, value:dict, submission_type:str|None=None) -> QWidget:
|
|
"""
|
|
Creates form widget
|
|
|
|
Args:
|
|
parent (QWidget): parent widget
|
|
key (str): name of field
|
|
value (dict): value, and is it missing from scrape
|
|
submission_type (str | None, optional): SubmissionType as str. Defaults to None.
|
|
|
|
Returns:
|
|
QWidget: Form object
|
|
"""
|
|
try:
|
|
value = value['value']
|
|
except (TypeError, KeyError):
|
|
pass
|
|
obj = parent.parent().parent()
|
|
logger.debug(f"Creating widget for: {key}")
|
|
match key:
|
|
case 'submitting_lab':
|
|
add_widget = QComboBox()
|
|
# lookup organizations suitable for submitting_lab (ctx: self.InfoItem.SubmissionFormWidget.SubmissionFormContainer.AddSubForm )
|
|
labs = [item.name for item in Organization.query()]
|
|
# try to set closest match to top of list
|
|
try:
|
|
labs = difflib.get_close_matches(value, labs, len(labs), 0)
|
|
except (TypeError, ValueError):
|
|
pass
|
|
# set combobox values to lookedup values
|
|
add_widget.addItems(labs)
|
|
case 'extraction_kit':
|
|
# if extraction kit not available, all other values fail
|
|
if not check_not_nan(value):
|
|
msg = AlertPop(message="Make sure to check your extraction kit in the excel sheet!", status="warning")
|
|
msg.exec()
|
|
# create combobox to hold looked up kits
|
|
add_widget = QComboBox()
|
|
# lookup existing kits by 'submission_type' decided on by sheetparser
|
|
logger.debug(f"Looking up kits used for {submission_type}")
|
|
uses = [item.name for item in KitType.query(used_for=submission_type)]
|
|
obj.uses = uses
|
|
logger.debug(f"Kits received for {submission_type}: {uses}")
|
|
if check_not_nan(value):
|
|
logger.debug(f"The extraction kit in parser was: {value}")
|
|
uses.insert(0, uses.pop(uses.index(value)))
|
|
obj.ext_kit = value
|
|
else:
|
|
logger.error(f"Couldn't find {obj.prsr.sub['extraction_kit']}")
|
|
obj.ext_kit = uses[0]
|
|
add_widget.addItems(uses)
|
|
|
|
case 'submitted_date':
|
|
# uses base calendar
|
|
add_widget = QDateEdit(calendarPopup=True)
|
|
# sets submitted date based on date found in excel sheet
|
|
try:
|
|
add_widget.setDate(value)
|
|
# if not found, use today
|
|
except:
|
|
add_widget.setDate(date.today())
|
|
case 'submission_category':
|
|
add_widget = QComboBox()
|
|
cats = ['Diagnostic', "Surveillance", "Research"]
|
|
cats += [item.name for item in SubmissionType.query()]
|
|
try:
|
|
cats.insert(0, cats.pop(cats.index(value)))
|
|
except ValueError:
|
|
cats.insert(0, cats.pop(cats.index(submission_type)))
|
|
add_widget.addItems(cats)
|
|
case _:
|
|
# anything else gets added in as a line edit
|
|
add_widget = QLineEdit()
|
|
logger.debug(f"Setting widget text to {str(value).replace('_', ' ')}")
|
|
add_widget.setText(str(value).replace("_", " "))
|
|
if add_widget != None:
|
|
add_widget.setObjectName(key)
|
|
add_widget.setParent(parent)
|
|
return add_widget
|
|
|
|
def update_missing(self):
|
|
"""
|
|
Set widget status to updated
|
|
"""
|
|
self.missing = True
|
|
self.label.updated(self.objectName())
|
|
|
|
class ParsedQLabel(QLabel):
|
|
|
|
def __init__(self, key:str, value:dict, title:bool=True, label_name:str|None=None):
|
|
super().__init__()
|
|
try:
|
|
check = not value['missing']
|
|
except:
|
|
check = True
|
|
if label_name != None:
|
|
self.setObjectName(label_name)
|
|
else:
|
|
self.setObjectName(f"{key}_label")
|
|
if title:
|
|
output = key.replace('_', ' ').title()
|
|
else:
|
|
output = key.replace('_', ' ')
|
|
if check:
|
|
self.setText(f"Parsed {output}")
|
|
else:
|
|
self.setText(f"MISSING {output}")
|
|
|
|
def updated(self, key:str, title:bool=True):
|
|
"""
|
|
Mark widget as updated
|
|
|
|
Args:
|
|
key (str): Name of the field
|
|
title (bool, optional): Use title case. Defaults to True.
|
|
"""
|
|
if title:
|
|
output = key.replace('_', ' ').title()
|
|
else:
|
|
output = key.replace('_', ' ')
|
|
self.setText(f"UPDATED {output}")
|
|
|
|
class ReagentFormWidget(QWidget):
|
|
|
|
def __init__(self, parent:QWidget, reagent:PydReagent, extraction_kit:str):
|
|
super().__init__(parent)
|
|
self.app = self.parent().parent().parent().parent().parent().parent().parent().parent()
|
|
self.reagent = reagent
|
|
self.extraction_kit = extraction_kit
|
|
layout = QVBoxLayout()
|
|
self.label = self.ReagentParsedLabel(reagent=reagent)
|
|
layout.addWidget(self.label)
|
|
self.lot = self.ReagentLot(reagent=reagent, extraction_kit=extraction_kit)
|
|
layout.addWidget(self.lot)
|
|
# Remove spacing between reagents
|
|
layout.setContentsMargins(0,0,0,0)
|
|
self.setLayout(layout)
|
|
self.setObjectName(reagent.name)
|
|
self.missing = reagent.missing
|
|
# If changed set self.missing to True and update self.label
|
|
self.lot.currentTextChanged.connect(self.updated)
|
|
|
|
def parse_form(self) -> Tuple[PydReagent, dict]:
|
|
"""
|
|
Pulls form info into PydReagent
|
|
|
|
Returns:
|
|
Tuple[PydReagent, dict]: PydReagent and Report(?)
|
|
"""
|
|
lot = self.lot.currentText()
|
|
logger.debug(f"Using this lot for the reagent {self.reagent}: {lot}")
|
|
wanted_reagent = Reagent.query(lot_number=lot, reagent_type=self.reagent.type)
|
|
# if reagent doesn't exist in database, offer to add it (uses App.add_reagent)
|
|
if wanted_reagent == None:
|
|
dlg = QuestionAsker(title=f"Add {lot}?", message=f"Couldn't find reagent type {self.reagent.type}: {lot} in the database.\n\nWould you like to add it?")
|
|
if dlg.exec():
|
|
wanted_reagent = self.parent().parent().add_reagent(reagent_lot=lot, reagent_type=self.reagent.type, expiry=self.reagent.expiry, name=self.reagent.name)
|
|
return wanted_reagent, None
|
|
else:
|
|
# In this case we will have an empty reagent and the submission will fail kit integrity check
|
|
logger.debug("Will not add reagent.")
|
|
return None, Result(msg="Failed integrity check", status="Critical")
|
|
else:
|
|
# Since this now gets passed in directly from the parser -> pyd -> form and the parser gets the name
|
|
# from the db, it should no longer be necessary to query the db with reagent/kit, but with rt name directly.
|
|
rt = ReagentType.query(name=self.reagent.type)
|
|
if rt == None:
|
|
rt = ReagentType.query(kit_type=self.extraction_kit, reagent=wanted_reagent)
|
|
return PydReagent(name=wanted_reagent.name, lot=wanted_reagent.lot, type=rt.name, expiry=wanted_reagent.expiry, parsed=not self.missing), None
|
|
|
|
def updated(self):
|
|
"""
|
|
Set widget status to updated
|
|
"""
|
|
self.missing = True
|
|
self.label.updated(self.reagent.type)
|
|
|
|
class ReagentParsedLabel(QLabel):
|
|
|
|
def __init__(self, reagent:PydReagent):
|
|
super().__init__()
|
|
try:
|
|
check = not reagent.missing
|
|
except:
|
|
check = False
|
|
self.setObjectName(f"{reagent.type}_label")
|
|
if check:
|
|
self.setText(f"Parsed {reagent.type}")
|
|
else:
|
|
self.setText(f"MISSING {reagent.type}")
|
|
|
|
def updated(self, reagent_type:str):
|
|
"""
|
|
Marks widget as updated
|
|
|
|
Args:
|
|
reagent_type (str): _description_
|
|
"""
|
|
self.setText(f"UPDATED {reagent_type}")
|
|
|
|
class ReagentLot(QComboBox):
|
|
|
|
def __init__(self, reagent, extraction_kit:str) -> None:
|
|
super().__init__()
|
|
self.setEditable(True)
|
|
logger.debug(f"Attempting lookup of reagents by type: {reagent.type}")
|
|
# below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work.
|
|
lookup = Reagent.query(reagent_type=reagent.type)
|
|
relevant_reagents = [str(item.lot) for item in lookup]
|
|
output_reg = []
|
|
for rel_reagent in relevant_reagents:
|
|
# extract strings from any sets.
|
|
if isinstance(rel_reagent, set):
|
|
for thing in rel_reagent:
|
|
output_reg.append(thing)
|
|
elif isinstance(rel_reagent, str):
|
|
output_reg.append(rel_reagent)
|
|
relevant_reagents = output_reg
|
|
# if reagent in sheet is not found insert it into the front of relevant reagents so it shows
|
|
logger.debug(f"Relevant reagents for {reagent.lot}: {relevant_reagents}")
|
|
if str(reagent.lot) not in relevant_reagents:
|
|
if check_not_nan(reagent.lot):
|
|
relevant_reagents.insert(0, str(reagent.lot))
|
|
else:
|
|
looked_up_rt = KitTypeReagentTypeAssociation.query(reagent_type=reagent.type, kit_type=extraction_kit)
|
|
try:
|
|
looked_up_reg = Reagent.query(lot_number=looked_up_rt.last_used)
|
|
except AttributeError:
|
|
looked_up_reg = None
|
|
if isinstance(looked_up_reg, list):
|
|
looked_up_reg = None
|
|
# logger.debug(f"Because there was no reagent listed for {reagent.lot}, we will insert the last lot used: {looked_up_reg}")
|
|
if looked_up_reg != None:
|
|
relevant_reagents.remove(str(looked_up_reg.lot))
|
|
relevant_reagents.insert(0, str(looked_up_reg.lot))
|
|
else:
|
|
if len(relevant_reagents) > 1:
|
|
# logger.debug(f"Found {reagent.lot} in relevant reagents: {relevant_reagents}. Moving to front of list.")
|
|
idx = relevant_reagents.index(str(reagent.lot))
|
|
# logger.debug(f"The index we got for {reagent.lot} in {relevant_reagents} was {idx}")
|
|
moved_reag = relevant_reagents.pop(idx)
|
|
relevant_reagents.insert(0, moved_reag)
|
|
else:
|
|
# logger.debug(f"Found {reagent.lot} in relevant reagents: {relevant_reagents}. But no need to move due to short list.")
|
|
pass
|
|
# logger.debug(f"New relevant reagents: {relevant_reagents}")
|
|
self.setObjectName(f"lot_{reagent.type}")
|
|
self.addItems(relevant_reagents)
|