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Pre-frontend refactor.

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This commit is contained in:
Landon Wark
2023-11-09 09:55:51 -06:00
parent 5570d87b7c
commit bf4149b1b3
25 changed files with 1002 additions and 784 deletions
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121
src/submissions/frontend/__init__.py
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@@ -6,23 +6,27 @@ from PyQt6.QtWidgets import (
QMainWindow, QToolBar,
QTabWidget, QWidget, QVBoxLayout,
QComboBox, QHBoxLayout,
QScrollArea, QLineEdit, QDateEdit
QScrollArea
)
from PyQt6.QtCore import pyqtSignal
from PyQt6.QtGui import QAction
from PyQt6.QtWebEngineWidgets import QWebEngineView
from pathlib import Path
from backend.db.functions import (
lookup_control_types, lookup_modes
)
from backend.db.models import ControlType, Control
from backend.validators import PydSubmission, PydReagent
from tools import check_if_app, Settings
from frontend.custom_widgets import SubmissionsSheet, AlertPop, AddReagentForm, KitAdder, ControlsDatePicker, ReagentFormWidget
from .functions import (
import_submission_function, kit_reload_function, kit_integrity_completion_function,
submit_new_sample_function, generate_report_function, add_kit_function, add_org_function,
controls_getter_function, chart_maker_function, link_controls_function, link_extractions_function,
link_pcr_function, autofill_excel, scrape_reagents, export_csv_function, import_pcr_results_function
)
from tools import check_if_app, Settings, Report
from frontend.custom_widgets import SubmissionsSheet, AlertPop, AddReagentForm, KitAdder, ControlsDatePicker
import logging
from datetime import date
import webbrowser
from pathlib import Path
from typing import List
logger = logging.getLogger(f'submissions.{__name__}')
logger.info("Hello, I am a logger")
@@ -34,6 +38,7 @@ class App(QMainWindow):
super().__init__()
self.ctx = ctx
self.last_dir = ctx.directory_path
self.report = Report()
# indicate version and connected database in title bar
try:
self.title = f"Submissions App (v{ctx.package.__version__}) - {ctx.database_path}"
@@ -58,7 +63,6 @@ class App(QMainWindow):
self.show()
self.statusBar().showMessage('Ready', 5000)
def _createMenuBar(self):
"""
adds items to menu bar
@@ -67,7 +71,7 @@ class App(QMainWindow):
menuBar = self.menuBar()
fileMenu = menuBar.addMenu("&File")
# Creating menus using a title
methodsMenu = menuBar.addMenu("&Methods")
# methodsMenu = menuBar.addMenu("&Methods")
reportMenu = menuBar.addMenu("&Reports")
maintenanceMenu = menuBar.addMenu("&Monthly")
helpMenu = menuBar.addMenu("&Help")
@@ -75,7 +79,7 @@ class App(QMainWindow):
helpMenu.addAction(self.docsAction)
fileMenu.addAction(self.importAction)
fileMenu.addAction(self.importPCRAction)
methodsMenu.addAction(self.constructFS)
# methodsMenu.addAction(self.constructFS)
reportMenu.addAction(self.generateReportAction)
maintenanceMenu.addAction(self.joinExtractionAction)
maintenanceMenu.addAction(self.joinPCRAction)
@@ -106,8 +110,7 @@ class App(QMainWindow):
self.joinPCRAction = QAction("Link PCR Logs")
self.helpAction = QAction("&About", self)
self.docsAction = QAction("&Docs", self)
self.constructFS = QAction("Make First Strand", self)
# self.constructFS = QAction("Make First Strand", self)
def _connectActions(self):
"""
@@ -128,7 +131,7 @@ class App(QMainWindow):
self.joinPCRAction.triggered.connect(self.linkPCR)
self.helpAction.triggered.connect(self.showAbout)
self.docsAction.triggered.connect(self.openDocs)
self.constructFS.triggered.connect(self.construct_first_strand)
# self.constructFS.triggered.connect(self.construct_first_strand)
self.table_widget.formwidget.import_drag.connect(self.importSubmission)
def showAbout(self):
@@ -150,7 +153,7 @@ class App(QMainWindow):
logger.debug(f"Attempting to open {url}")
webbrowser.get('windows-default').open(f"file://{url.__str__()}")
def result_reporter(self, result:dict|None=None):
def result_reporter(self):
# def result_reporter(self, result:TypedDict[]|None=None):
"""
Report any anomolous results - if any - to the user
@@ -158,31 +161,41 @@ class App(QMainWindow):
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.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!")
for result in self.report.results:
logger.debug(f"Showing result: {result}")
if result != None:
alert = result.report()
if alert.exec():
pass
self.report = Report()
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
# from .main_window_functions import import_submission_function
self.raise_()
self.activateWindow()
self, result = import_submission_function(self, fname)
logger.debug(f"Import result: {result}")
self.result_reporter(result)
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, result = kit_reload_function(self)
self.result_reporter(result)
# from .main_window_functions import kit_reload_function
self = kit_reload_function(self)
self.result_reporter()
def kit_integrity_completion(self):
"""
@@ -190,15 +203,15 @@ class App(QMainWindow):
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, result = kit_integrity_completion_function(self)
self.result_reporter(result)
# 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
# from .main_window_functions import submit_new_sample_function
self, result = submit_new_sample_function(self)
self.result_reporter(result)
@@ -237,7 +250,7 @@ class App(QMainWindow):
"""
Action to create a summary of sheet data per client
"""
from .main_window_functions import generate_report_function
# from .main_window_functions import generate_report_function
self, result = generate_report_function(self)
self.result_reporter(result)
@@ -245,7 +258,7 @@ class App(QMainWindow):
"""
Constructs new kit from yaml and adds to DB.
"""
from .main_window_functions import add_kit_function
# from .main_window_functions import add_kit_function
self, result = add_kit_function(self)
self.result_reporter(result)
@@ -253,7 +266,7 @@ class App(QMainWindow):
"""
Constructs new kit from yaml and adds to DB.
"""
from .main_window_functions import add_org_function
# from .main_window_functions import add_org_function
self, result = add_org_function(self)
self.result_reporter(result)
@@ -261,24 +274,24 @@ class App(QMainWindow):
"""
Lookup controls from database and send to chartmaker
"""
from .main_window_functions import controls_getter_function
self, result = controls_getter_function(self)
self.result_reporter(result)
# 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, result = chart_maker_function(self)
self.result_reporter(result)
# 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
# from .main_window_functions import link_controls_function
self, result = link_controls_function(self)
self.result_reporter(result)
@@ -286,7 +299,7 @@ class App(QMainWindow):
"""
Links extraction logs from .csv files to relevant submissions.
"""
from .main_window_functions import link_extractions_function
# from .main_window_functions import link_extractions_function
self, result = link_extractions_function(self)
self.result_reporter(result)
@@ -294,7 +307,7 @@ class App(QMainWindow):
"""
Links PCR logs from .csv files to relevant submissions.
"""
from .main_window_functions import link_pcr_function
# from .main_window_functions import link_pcr_function
self, result = link_pcr_function(self)
self.result_reporter(result)
@@ -302,25 +315,29 @@ class App(QMainWindow):
"""
Imports results exported from Design and Analysis .eds files
"""
from .main_window_functions import import_pcr_results_function
# 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 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
# from .main_window_functions import scrape_reagents
logger.debug(f"Args: {args}")
logger.debug(F"kwargs: {kwargs}")
self, result = scrape_reagents(self, args[0])
self = scrape_reagents(self, args[0])
self.kit_integrity_completion()
self.result_reporter(result)
self.result_reporter()
def export_csv(self, fname:Path|None=None):
from .main_window_functions import export_csv_function
export_csv_function(self, fname)
class AddSubForm(QWidget):