Large scale frontend refactor
This commit is contained in:
Landon Wark
747
src/submissions/frontend/widgets/submission_widget.py
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747
src/submissions/frontend/widgets/submission_widget.py
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@@ -0,0 +1,747 @@
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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
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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, PCRParser
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from backend.validators import PydSubmission, PydReagent
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from backend.db import (
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check_kit_integrity, update_last_used, KitType, Organization, SubmissionType, Reagent,
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ReagentType, KitTypeReagentTypeAssociation, BasicSubmission, update_subsampassoc_with_pcr
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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 ReagentFormWidget
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from typing import List, Tuple
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import difflib
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from datetime import date
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import inspect
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import json
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logger = logging.getLogger(f"submissions.{__name__}")
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class SubmissionFormContainer(QWidget):
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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#().parent().parent().parent().parent().parent
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self.report = Report()
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# self.parent = parent
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self.setAcceptDrops(True)
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self.import_drag.connect(self.importSubmission)
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def dragEnterEvent(self, event):
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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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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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# from .main_window_functions import import_submission_function
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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 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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print(f"\n\n{inspect.stack()[1].function}\n\n")
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self.scrape_reagents_function(args[0])
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self.kit_integrity_completion()
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self.app.report.add_result(self.report)
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self.report = Report()
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match inspect.stack()[1].function:
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case "import_submission_function":
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pass
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case _:
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self.app.result_reporter()
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# def kit_reload_function(self):
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# """
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# Reload the fields in the form
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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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# report = Report()
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# # for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
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# logger.debug(f"Attempting to clear {obj.form.find_widgets()}")
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# for item in self.form.find_widgets():
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# if isinstance(item, ReagentFormWidget):
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# item.setParent(None)
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# self.kit_integrity_completion_function()
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# self.report.add_result(report)
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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()
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self.app.report.add_result(self.report)
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self.report = Report()
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match inspect.stack()[1].function:
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case "import_submission_function":
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pass
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case _:
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self.app.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()
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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 export_csv(self, fname:Path|None=None):
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# from .main_window_functions import export_csv_function
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self.export_csv_function(fname)
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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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# logger.debug(obj.ctx)
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# initialize samples
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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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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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# result = dict(message=f"File {fname.__str__()} not found.", status="critical")
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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(ctx=self.ctx, 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(ctx=self.app.ctx, filepath=fname)
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try:
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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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except Exception as e:
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report.add_result(Result(msg=f"Problem creating pydantic model:\n\n{e}", status="Critical"))
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self.report.add_result(report)
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return
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self.form = self.pyd.toForm(parent=self)
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self.layout().addWidget(self.form)
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kit_widget = self.form.find_widgets(object_name="extraction_kit")[0].input
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logger.debug(f"Kitwidget {kit_widget}")
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self.scrape_reagents(kit_widget.currentText())
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kit_widget.currentTextChanged.connect(self.scrape_reagents)
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# compare obj.reagents with expected reagents in kit
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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 scrape_reagents_function(self, extraction_kit:str):
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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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report = Report()
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logger.debug(f"Extraction kit: {extraction_kit}")
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# obj.reagents = []
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# obj.missing_reagents = []
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# Remove previous reagent widgets
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try:
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old_reagents = self.form.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, ReagentFormWidget) or isinstance(reagent, QPushButton):
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reagent.setParent(None)
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# reagents = obj.prsr.parse_reagents(extraction_kit=extraction_kit)
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# logger.debug(f"Got reagents: {reagents}")
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# for reagent in obj.prsr.sub['reagents']:
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# # create label
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# if reagent.parsed:
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# obj.reagents.append(reagent)
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# else:
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# obj.missing_reagents.append(reagent)
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self.form.reagents = self.prsr.sub['reagents']
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# logger.debug(f"Imported reagents: {obj.reagents}")
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# logger.debug(f"Missing reagents: {obj.missing_reagents}")
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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 kit_integrity_completion_function(self):
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"""
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Compare kit contents to parsed contents
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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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kit_widget = self.form.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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# for reagent in obj.pyd.reagents:
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for reagent in self.form.reagents:
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add_widget = ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.ext_kit)
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# add_widget.setParent(sub_form_container.form)
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self.form.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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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.form.layout().addWidget(export_csv_btn)
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export_csv_btn.clicked.connect(self.export_csv)
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submit_btn = QPushButton("Submit")
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submit_btn.setObjectName("submit_btn")
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self.form.layout().addWidget(submit_btn)
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submit_btn.clicked.connect(self.submit_new_sample)
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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 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.form.parse_form()
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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 = check_kit_integrity(sub=self.pyd)
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report.add_result(result)
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if len(result.results) > 0:
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self.report.add_result(report)
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return
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base_submission, result = self.pyd.toSQL()
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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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self.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['message'])
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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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self.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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self.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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update_last_used(reagent=reagent, 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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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.form.setParent(None)
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logger.debug(f"All attributes of obj: {pformat(self.__dict__)}")
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wkb = self.pyd.autofill_excel()
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if wkb != None:
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fname = select_save_file(obj=self, default_name=self.pyd.construct_filename(), extension="xlsx")
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try:
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wkb.save(filename=fname.__str__())
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except PermissionError:
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logger.error("Hit a permission error when saving workbook. Cancelled?")
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if hasattr(self.pyd, 'csv'):
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dlg = QuestionAsker("Export CSV?", "Would you like to export the csv file?")
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if dlg.exec():
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fname = select_save_file(self, f"{self.pyd.construct_filename()}.csv", 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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self.report.add_result(report)
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def export_csv_function(self, fname:Path|None=None):
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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 import_pcr_results(self):
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self.import_pcr_results_function()
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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_pcr_results_function(self):
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"""
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Import Quant-studio PCR data to an imported submission
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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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report = Report()
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fname = select_open_file(self, file_extension="xlsx")
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parser = PCRParser(filepath=fname)
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logger.debug(f"Attempting lookup for {parser.plate_num}")
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# sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=parser.plate_num)
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sub = BasicSubmission.query(rsl_number=parser.plate_num)
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try:
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logger.debug(f"Found submission: {sub.rsl_plate_num}")
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except AttributeError:
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# If no plate is found, may be because this is a repeat. Lop off the '-1' or '-2' and repeat
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logger.error(f"Submission of number {parser.plate_num} not found. Attempting rescue of plate repeat.")
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parser.plate_num = "-".join(parser.plate_num.split("-")[:-1])
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# sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=parser.plate_num)
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# sub = lookup_submissions(ctx=obj.ctx, rsl_number=parser.plate_num)
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sub = BasicSubmission.query(rsl_number=parser.plate_num)
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try:
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logger.debug(f"Found submission: {sub.rsl_plate_num}")
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except AttributeError:
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logger.error(f"Rescue of {parser.plate_num} failed.")
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# return obj, dict(message="Couldn't find a submission with that RSL number.", status="warning")
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self.report.add_result(Result(msg="Couldn't find a submission with that RSL number.", status="Warning"))
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return
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# Check if PCR info already exists
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if hasattr(sub, 'pcr_info') and sub.pcr_info != None:
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existing = json.loads(sub.pcr_info)
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else:
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existing = None
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if existing != None:
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# update pcr_info
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try:
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logger.debug(f"Updating {type(existing)}: {existing} with {type(parser.pcr)}: {parser.pcr}")
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if json.dumps(parser.pcr) not in sub.pcr_info:
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existing.append(parser.pcr)
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logger.debug(f"Setting: {existing}")
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sub.pcr_info = json.dumps(existing)
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except TypeError:
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logger.error(f"Error updating!")
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sub.pcr_info = json.dumps([parser.pcr])
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logger.debug(f"Final pcr info for {sub.rsl_plate_num}: {sub.pcr_info}")
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else:
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sub.pcr_info = json.dumps([parser.pcr])
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# obj.ctx.database_session.add(sub)
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logger.debug(f"Existing {type(sub.pcr_info)}: {sub.pcr_info}")
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logger.debug(f"Inserting {type(json.dumps(parser.pcr))}: {json.dumps(parser.pcr)}")
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sub.save()
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logger.debug(f"Got {len(parser.samples)} samples to update!")
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logger.debug(f"Parser samples: {parser.samples}")
|
||||
for sample in sub.samples:
|
||||
logger.debug(f"Running update on: {sample}")
|
||||
try:
|
||||
sample_dict = [item for item in parser.samples if item['sample']==sample.rsl_number][0]
|
||||
except IndexError:
|
||||
continue
|
||||
update_subsampassoc_with_pcr(submission=sub, sample=sample, input_dict=sample_dict)
|
||||
self.report.add_result(Result(msg=f"We added PCR info to {sub.rsl_plate_num}.", status='Information'))
|
||||
# return obj, result
|
||||
|
||||
class SubmissionFormWidget(QWidget):
|
||||
|
||||
def __init__(self, parent: QWidget, **kwargs) -> None:
|
||||
super().__init__(parent)
|
||||
# self.ignore = [None, "", "qt_spinbox_lineedit", "qt_scrollarea_viewport", "qt_scrollarea_hcontainer",
|
||||
# "qt_scrollarea_vcontainer", "submit_btn"
|
||||
# ]
|
||||
self.ignore = ['filepath', 'samples', 'reagents', 'csv', 'ctx']
|
||||
layout = QVBoxLayout()
|
||||
for k, v in kwargs.items():
|
||||
if k not in self.ignore:
|
||||
add_widget = self.create_widget(key=k, value=v, submission_type=kwargs['submission_type'])
|
||||
if add_widget != None:
|
||||
layout.addWidget(add_widget)
|
||||
else:
|
||||
setattr(self, k, v)
|
||||
|
||||
self.setLayout(layout)
|
||||
|
||||
def create_widget(self, key:str, value:dict, submission_type:str|None=None):
|
||||
if key not in self.ignore:
|
||||
return self.InfoItem(self, key=key, value=value, submission_type=submission_type)
|
||||
return None
|
||||
|
||||
def clear_form(self):
|
||||
for item in self.findChildren(QWidget):
|
||||
item.setParent(None)
|
||||
|
||||
def find_widgets(self, object_name:str|None=None) -> List[QWidget]:
|
||||
query = self.findChildren(QWidget)
|
||||
if object_name != None:
|
||||
query = [widget for widget in query if widget.objectName()==object_name]
|
||||
return query
|
||||
|
||||
def parse_form(self) -> PydSubmission:
|
||||
logger.debug(f"Hello from form parser!")
|
||||
info = {}
|
||||
reagents = []
|
||||
if hasattr(self, 'csv'):
|
||||
info['csv'] = self.csv
|
||||
for widget in self.findChildren(QWidget):
|
||||
# logger.debug(f"Parsed widget of type {type(widget)}")
|
||||
match widget:
|
||||
case ReagentFormWidget():
|
||||
reagent, _ = widget.parse_form()
|
||||
if reagent != None:
|
||||
reagents.append(reagent)
|
||||
case self.InfoItem():
|
||||
field, value = widget.parse_form()
|
||||
if field != None:
|
||||
info[field] = value
|
||||
logger.debug(f"Info: {pformat(info)}")
|
||||
logger.debug(f"Reagents: {pformat(reagents)}")
|
||||
# app = self.parent().parent().parent().parent().parent().parent().parent().parent
|
||||
submission = PydSubmission(filepath=self.filepath, reagents=reagents, samples=self.samples, **info)
|
||||
return submission
|
||||
|
||||
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['value'])
|
||||
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):
|
||||
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:
|
||||
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.__str__() 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.__str__() 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)
|
||||
# Run reagent scraper whenever extraction kit is changed.
|
||||
# add_widget.currentTextChanged.connect(obj.scrape_reagents)
|
||||
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 lookup_submission_type(ctx=obj.ctx)]
|
||||
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):
|
||||
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):
|
||||
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.setParent(parent)
|
||||
self.reagent = reagent
|
||||
self.extraction_kit = extraction_kit
|
||||
# self.ctx = reagent.ctx
|
||||
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]:
|
||||
lot = self.lot.currentText()
|
||||
# wanted_reagent = lookup_reagents(ctx=self.ctx, lot_number=lot, reagent_type=self.reagent.type)
|
||||
wanted_reagent = Reagent.query(lot_number=lot, reagent_type=self.reagent.type)
|
||||
# if reagent doesn't exist in database, off 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().parent().parent().parent().parent().parent().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 = lookup_reagent_types(ctx=self.ctx, name=self.reagent.type)
|
||||
# rt = lookup_reagent_types(ctx=self.ctx, kit_type=self.extraction_kit, reagent=wanted_reagent)
|
||||
rt = ReagentType.query(name=self.reagent.type)
|
||||
if rt == None:
|
||||
# rt = lookup_reagent_types(ctx=self.ctx, kit_type=self.extraction_kit, reagent=wanted_reagent)
|
||||
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):
|
||||
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):
|
||||
self.setText(f"UPDATED {reagent_type}")
|
||||
|
||||
class ReagentLot(QComboBox):
|
||||
|
||||
def __init__(self, reagent, extraction_kit:str) -> None:
|
||||
super().__init__()
|
||||
# self.ctx = reagent.ctx
|
||||
self.setEditable(True)
|
||||
# if reagent.parsed:
|
||||
# pass
|
||||
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 = lookup_reagents(ctx=self.ctx, reagent_type=reagent.type)
|
||||
lookup = Reagent.query(reagent_type=reagent.type)
|
||||
relevant_reagents = [item.__str__() 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:
|
||||
# TODO: look up the last used reagent of this type in the database
|
||||
# looked_up_rt = lookup_reagenttype_kittype_association(ctx=self.ctx, reagent_type=reagent.type, kit_type=extraction_kit)
|
||||
looked_up_rt = KitTypeReagentTypeAssociation.query(reagent_type=reagent.type, kit_type=extraction_kit)
|
||||
try:
|
||||
# looked_up_reg = lookup_reagents(ctx=self.ctx, lot_number=looked_up_rt.last_used)
|
||||
looked_up_reg = Reagent.query(lot_number=looked_up_rt.last_used)
|
||||
except AttributeError:
|
||||
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.")
|
||||
logger.debug(f"New relevant reagents: {relevant_reagents}")
|
||||
self.setObjectName(f"lot_{reagent.type}")
|
||||
self.addItems(relevant_reagents)
|
||||
|
||||
Reference in New Issue
Block a user