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Pre-sample/control connect

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This commit is contained in:
Landon Wark
2023-12-05 10:20:46 -06:00
parent 283e77fee5
commit cddb947ec8
29 changed files with 1357 additions and 1042 deletions
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171
src/submissions/frontend/widgets/app.py
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@@ -11,9 +11,6 @@ from PyQt6.QtWidgets import (
from PyQt6.QtGui import QAction
from pathlib import Path
from backend.validators import PydReagent
# from frontend.functions import (
# add_kit_function, add_org_function, link_controls_function, export_csv_function
# )
from tools import check_if_app, Settings, Report
from .pop_ups import AlertPop
from .misc import AddReagentForm, LogParser
@@ -149,17 +146,12 @@ class App(QMainWindow):
webbrowser.get('windows-default').open(f"file://{url.__str__()}")
def result_reporter(self):
# def result_reporter(self, result:TypedDict[]|None=None):
"""
Report any anomolous results - if any - to the user
Args:
result (dict | None, optional): The result from a function. Defaults to None.
"""
# logger.info(f"We got the result: {result}")
# if result != None:
# msg = AlertPop(message=result['message'], status=result['status'])
# msg.exec()
logger.debug(f"Running results reporter for: {self.report.results}")
if len(self.report.results) > 0:
logger.debug(f"We've got some results!")
@@ -173,43 +165,6 @@ class App(QMainWindow):
else:
self.statusBar().showMessage("Action completed sucessfully.", 5000)
# def importSubmission(self, fname:Path|None=None):
# """
# import submission from excel sheet into form
# """
# # from .main_window_functions import import_submission_function
# self.raise_()
# self.activateWindow()
# self = import_submission_function(self, fname)
# logger.debug(f"Result from result reporter: {self.report.results}")
# self.result_reporter()
# def kit_reload(self):
# """
# Removes all reagents from form before running kit integrity completion.
# """
# # from .main_window_functions import kit_reload_function
# self = kit_reload_function(self)
# self.result_reporter()
# def kit_integrity_completion(self):
# """
# Performs check of imported reagents
# NOTE: this will not change self.reagents which should be fine
# since it's only used when looking up
# """
# # from .main_window_functions import kit_integrity_completion_function
# self = kit_integrity_completion_function(self)
# self.result_reporter()
# def submit_new_sample(self):
# """
# Attempt to add sample to database when 'submit' button clicked
# """
# # from .main_window_functions import submit_new_sample_function
# self = submit_new_sample_function(self)
# self.result_reporter()
def add_reagent(self, reagent_lot:str|None=None, reagent_type:str|None=None, expiry:date|None=None, name:str|None=None):
"""
Action to create new reagent in DB.
@@ -217,6 +172,8 @@ class App(QMainWindow):
Args:
reagent_lot (str | None, optional): Parsed reagent from import form. Defaults to None.
reagent_type (str | None, optional): Parsed reagent type from import form. Defaults to None.
expiry (date | None, optional): Parsed reagent expiry data. Defaults to None.
name (str | None, optional): Parsed reagent name. Defaults to None.
Returns:
models.Reagent: the constructed reagent object to add to submission
@@ -225,117 +182,20 @@ class App(QMainWindow):
if isinstance(reagent_lot, bool):
reagent_lot = ""
# create form
dlg = AddReagentForm(ctx=self.ctx, reagent_lot=reagent_lot, reagent_type=reagent_type, expiry=expiry, reagent_name=name)
dlg = AddReagentForm(reagent_lot=reagent_lot, reagent_type=reagent_type, expiry=expiry, reagent_name=name)
if dlg.exec():
# extract form info
# info = extract_form_info(dlg)
info = dlg.parse_form()
logger.debug(f"Reagent info: {info}")
# create reagent object
# reagent = construct_reagent(ctx=self.ctx, info_dict=info)
reagent = PydReagent(ctx=self.ctx, **info)
# send reagent to db
# store_reagent(ctx=self.ctx, reagent=reagent)
sqlobj, result = reagent.toSQL()
sqlobj.save()
# result = store_object(ctx=self.ctx, object=reagent.toSQL()[0])
report.add_result(result)
self.result_reporter()
return reagent
# def generateReport(self):
# """
# Action to create a summary of sheet data per client
# """
# # from .main_window_functions import generate_report_function
# self, result = generate_report_function(self)
# self.result_reporter(result)
# def add_kit(self):
# """
# Constructs new kit from yaml and adds to DB.
# """
# # from .main_window_functions import add_kit_function
# self, result = add_kit_function(self)
# self.result_reporter(result)
# def add_org(self):
# """
# Constructs new kit from yaml and adds to DB.
# """
# # from .main_window_functions import add_org_function
# self, result = add_org_function(self)
# self.result_reporter(result)
# def _controls_getter(self):
# """
# Lookup controls from database and send to chartmaker
# """
# # from .main_window_functions import controls_getter_function
# self = controls_getter_function(self)
# self.result_reporter()
# def _chart_maker(self):
# """
# Creates plotly charts for webview
# """
# # from .main_window_functions import chart_maker_function
# self = chart_maker_function(self)
# self.result_reporter()
# def linkControls(self):
# """
# Adds controls pulled from irida to relevant submissions
# NOTE: Depreciated due to improvements in controls scraper.
# """
# # from .main_window_functions import link_controls_function
# self, result = link_controls_function(self)
# self.result_reporter(result)
# def linkExtractions(self):
# """
# Links extraction logs from .csv files to relevant submissions.
# """
# # from .main_window_functions import link_extractions_function
# self, result = link_extractions_function(self)
# self.result_reporter(result)
# def linkPCR(self):
# """
# Links PCR logs from .csv files to relevant submissions.
# """
# # from .main_window_functions import link_pcr_function
# self, result = link_pcr_function(self)
# self.result_reporter(result)
# def importPCRResults(self):
# """
# Imports results exported from Design and Analysis .eds files
# """
# # from .main_window_functions import import_pcr_results_function
# self, result = import_pcr_results_function(self)
# self.result_reporter(result)
# def construct_first_strand(self):
# """
# Converts first strand excel sheet to Biomek CSV
# """
# from .main_window_functions import construct_first_strand_function
# self, result = construct_first_strand_function(self)
# self.result_reporter(result)
# def scrape_reagents(self, *args, **kwargs):
# # from .main_window_functions import scrape_reagents
# logger.debug(f"Args: {args}")
# logger.debug(F"kwargs: {kwargs}")
# self = scrape_reagents(self, args[0])
# self.kit_integrity_completion()
# self.result_reporter()
# def export_csv(self, fname:Path|None=None):
# # from .main_window_functions import export_csv_function
# export_csv_function(self, fname)
def runSearch(self):
dlg = LogParser(self)
dlg.exec()
@@ -377,32 +237,7 @@ class AddSubForm(QWidget):
self.tab1.setLayout(self.tab1.layout)
self.tab1.layout.addWidget(self.interior)
self.tab1.layout.addWidget(self.sheetwidget)
# create widgets for tab 2
# self.datepicker = ControlsDatePicker()
# self.webengineview = QWebEngineView()
# set tab2 layout
self.tab2.layout = QVBoxLayout(self)
# self.control_typer = QComboBox()
# fetch types of controls
# con_types = get_all_Control_Types_names(ctx=parent.ctx)
# con_types = [item.name for item in lookup_control_types(ctx=parent.ctx)]
# con_types = [item.name for item in ControlType.query()]
# self.control_typer.addItems(con_types)
# create custom widget to get types of analysis
# self.mode_typer = QComboBox()
# mode_types = get_all_available_modes(ctx=parent.ctx)
# mode_types = lookup_modes(ctx=parent.ctx)
# mode_types = Control.get_modes()
# self.mode_typer.addItems(mode_types)
# create custom widget to get subtypes of analysis
# self.sub_typer = QComboBox()
# self.sub_typer.setEnabled(False)
# add widgets to tab2 layout
# self.tab2.layout.addWidget(self.datepicker)
# self.tab2.layout.addWidget(self.control_typer)
# self.tab2.layout.addWidget(self.mode_typer)
# self.tab2.layout.addWidget(self.sub_typer)
# self.tab2.layout.addWidget(self.webengineview)
self.controls_viewer = ControlsViewer(self)
self.tab2.layout.addWidget(self.controls_viewer)
self.tab2.setLayout(self.tab2.layout)