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moved frontend function check_not_nan to tools

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This commit is contained in:
Landon Wark
2023-02-15 09:29:03 -06:00
parent a9ce9514fc
commit 85dad791ec
15 changed files with 275 additions and 156 deletions
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97
src/submissions/frontend/__init__.py
View File

@@ -19,21 +19,23 @@ from xhtml2pdf import pisa
# import plotly.express as px
import yaml
import pprint
import numpy as np
from backend.excel.parser import SheetParser
from backend.excel.reports import convert_control_by_mode, convert_data_list_to_df
from backend.db import (construct_submission_info, lookup_reagent,
construct_reagent, store_reagent, store_submission, lookup_kittype_by_use,
lookup_regent_by_type_name, lookup_all_orgs, lookup_submissions_by_date_range,
get_all_Control_Types_names, create_kit_from_yaml, get_all_available_modes, get_all_controls_by_type,
get_control_subtypes, lookup_all_submissions_by_type, get_all_controls, lookup_submission_by_rsl_num
get_control_subtypes, lookup_all_submissions_by_type, get_all_controls, lookup_submission_by_rsl_num,
create_org_from_yaml
)
from .functions import check_kit_integrity, check_not_nan
from .functions import check_kit_integrity
from tools import check_not_nan
from backend.excel.reports import make_report_xlsx, make_report_html
import numpy
from frontend.custom_widgets.sub_details import SubmissionsSheet
from frontend.custom_widgets.pop_ups import AddReagentQuestion, OverwriteSubQuestion, AlertPop
from frontend.custom_widgets.pop_ups import AlertPop, QuestionAsker
from frontend.custom_widgets import AddReagentForm, ReportDatePicker, KitAdder, ControlsDatePicker
import logging
import difflib
@@ -96,6 +98,7 @@ class App(QMainWindow):
self.addToolBar(toolbar)
toolbar.addAction(self.addReagentAction)
toolbar.addAction(self.addKitAction)
toolbar.addAction(self.addOrgAction)
def _createActions(self):
"""
@@ -105,6 +108,7 @@ class App(QMainWindow):
self.addReagentAction = QAction("Add Reagent", self)
self.generateReportAction = QAction("Make Report", self)
self.addKitAction = QAction("Add Kit", self)
self.addOrgAction = QAction("Add Org", self)
self.joinControlsAction = QAction("Link Controls")
self.joinExtractionAction = QAction("Link Ext Logs")
@@ -117,6 +121,7 @@ class App(QMainWindow):
self.addReagentAction.triggered.connect(self.add_reagent)
self.generateReportAction.triggered.connect(self.generateReport)
self.addKitAction.triggered.connect(self.add_kit)
self.addOrgAction.triggered.connect(self.add_org)
self.table_widget.control_typer.currentIndexChanged.connect(self._controls_getter)
self.table_widget.mode_typer.currentIndexChanged.connect(self._controls_getter)
self.table_widget.datepicker.start_date.dateChanged.connect(self._controls_getter)
@@ -183,7 +188,7 @@ class App(QMainWindow):
# create label
self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
# if extraction kit not available, all other values fail
if np.isnan(prsr.sub[item]):
if not check_not_nan(prsr.sub[item]):
msg = AlertPop(message="Make sure to check your extraction kit!", status="warning")
msg.exec()
# create combobox to hold looked up kits
@@ -231,7 +236,7 @@ class App(QMainWindow):
elif isinstance(reagent, str):
output_reg.append(reagent)
relevant_reagents = output_reg
logger.debug(f"Relevant reagents: {relevant_reagents}")
logger.debug(f"Relevant reagents for {prsr.sub[item]}: {relevant_reagents}")
# if reagent in sheet is not found insert it into items
if str(prsr.sub[item]['lot']) not in relevant_reagents and prsr.sub[item]['lot'] != 'nan':
if check_not_nan(prsr.sub[item]['lot']):
@@ -272,11 +277,13 @@ class App(QMainWindow):
logger.debug(f"Looked up reagent: {wanted_reagent}")
# if reagent not found offer to add to database
if wanted_reagent == None:
dlg = AddReagentQuestion(reagent_type=reagent, reagent_lot=reagents[reagent])
# dlg = AddReagentQuestion(reagent_type=reagent, reagent_lot=reagents[reagent])
r_lot = reagents[reagent]
dlg = QuestionAsker(title=f"Add {r_lot}?", message=f"Couldn't find reagent type {reagent.replace('_', ' ').title().strip('Lot')}: {r_lot} in the database.\n\nWould you like to add it?")
if dlg.exec():
logger.debug(f"checking reagent: {reagent} in self.reagents. Result: {self.reagents[reagent]}")
expiry_date = self.reagents[reagent]['exp']
wanted_reagent = self.add_reagent(reagent_lot=reagents[reagent], reagent_type=reagent.replace("lot_", ""), expiry=expiry_date)
wanted_reagent = self.add_reagent(reagent_lot=r_lot, reagent_type=reagent.replace("lot_", ""), expiry=expiry_date)
else:
logger.debug("Will not add reagent.")
if wanted_reagent != None:
@@ -287,14 +294,23 @@ class App(QMainWindow):
info['uploaded_by'] = getuser()
# construct submission object
logger.debug(f"Here is the info_dict: {pprint.pformat(info)}")
base_submission, output = construct_submission_info(ctx=self.ctx, info_dict=info)
base_submission, result = construct_submission_info(ctx=self.ctx, info_dict=info)
# check output message for issues
if output['message'] != None:
dlg = OverwriteSubQuestion(output['message'], base_submission.rsl_plate_num)
if dlg.exec():
base_submission.reagents = []
else:
match result['code']:
case 1:
# if output['code'] > 0:
# dlg = OverwriteSubQuestion(output['message'], base_submission.rsl_plate_num)
dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_num}?", message=result['message'])
if dlg.exec():
base_submission.reagents = []
else:
return
case 2:
dlg = AlertPop(message=result['message'], status='critical')
dlg.exec()
return
case _:
pass
# add reagents to submission object
for reagent in parsed_reagents:
base_submission.reagents.append(reagent)
@@ -447,20 +463,59 @@ class App(QMainWindow):
return
# send to kit creator function
result = create_kit_from_yaml(ctx=self.ctx, exp=exp)
msg = QMessageBox()
# msg = QMessageBox()
# msg.setIcon(QMessageBox.critical)
match result['code']:
case 0:
msg.setText("Kit added")
msg.setInformativeText(result['message'])
msg.setWindowTitle("Kit added")
msg = AlertPop(message=result['message'], status='info')
# msg.setText("Kit added")
# msg.setInformativeText(result['message'])
# msg.setWindowTitle("Kit added")
case 1:
msg.setText("Permission Error")
msg.setInformativeText(result['message'])
msg.setWindowTitle("Permission Error")
msg = AlertPop(message=result['message'], status='critical')
# msg.setText("Permission Error")
# msg.setInformativeText(result['message'])
# msg.setWindowTitle("Permission Error")
msg.exec()
def add_org(self):
"""
Constructs new kit from yaml and adds to DB.
"""
# setup file dialog to find yaml flie
home_dir = str(Path(self.ctx["directory_path"]))
fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir, filter = "yml(*.yml)")[0])
assert fname.exists()
# read yaml file
try:
with open(fname.__str__(), "r") as stream:
try:
org = yaml.load(stream, Loader=yaml.Loader)
except yaml.YAMLError as exc:
logger.error(f'Error reading yaml file {fname}: {exc}')
return {}
except PermissionError:
return
# send to kit creator function
result = create_org_from_yaml(ctx=self.ctx, org=org)
# msg = QMessageBox()
# msg.setIcon(QMessageBox.critical)
match result['code']:
case 0:
msg = AlertPop(message=result['message'], status='information')
# msg.setText("Organization added")
# msg.setInformativeText(result['message'])
# msg.setWindowTitle("Kit added")
case 1:
msg = AlertPop(message=result['message'], status='critical')
# msg.setText("Permission Error")
# msg.setInformativeText(result['message'])
# msg.setWindowTitle("Permission Error")
msg.exec()
def _controls_getter(self):
"""

79
src/submissions/frontend/custom_widgets/pop_ups.py
View File

@@ -22,50 +22,67 @@ loader = FileSystemLoader(loader_path)
env = Environment(loader=loader)
class AddReagentQuestion(QDialog):
# class AddReagentQuestion(QDialog):
# """
# dialog to ask about adding a new reagne to db
# """
# def __init__(self, reagent_type:str, reagent_lot:str) -> QDialog:
# super().__init__()
# self.setWindowTitle(f"Add {reagent_lot}?")
# QBtn = QDialogButtonBox.StandardButton.Yes | QDialogButtonBox.StandardButton.No
# self.buttonBox = QDialogButtonBox(QBtn)
# self.buttonBox.accepted.connect(self.accept)
# self.buttonBox.rejected.connect(self.reject)
# self.layout = QVBoxLayout()
# message = QLabel(f"Couldn't find reagent type {reagent_type.replace('_', ' ').title().strip('Lot')}: {reagent_lot} in the database.\n\nWould you like to add it?")
# self.layout.addWidget(message)
# self.layout.addWidget(self.buttonBox)
# self.setLayout(self.layout)
# class OverwriteSubQuestion(QDialog):
# """
# dialog to ask about overwriting existing submission
# """
# def __init__(self, message:str, rsl_plate_num:str) -> QDialog:
# super().__init__()
# self.setWindowTitle(f"Overwrite {rsl_plate_num}?")
# QBtn = QDialogButtonBox.StandardButton.Yes | QDialogButtonBox.StandardButton.No
# self.buttonBox = QDialogButtonBox(QBtn)
# self.buttonBox.accepted.connect(self.accept)
# self.buttonBox.rejected.connect(self.reject)
# self.layout = QVBoxLayout()
# message = QLabel(message)
# self.layout.addWidget(message)
# self.layout.addWidget(self.buttonBox)
# self.setLayout(self.layout)
class QuestionAsker(QDialog):
"""
dialog to ask about adding a new reagne to db
dialog to ask yes/no questions
"""
def __init__(self, reagent_type:str, reagent_lot:str) -> QDialog:
def __init__(self, title:str, message:str) -> QDialog:
super().__init__()
self.setWindowTitle(f"Add {reagent_lot}?")
self.setWindowTitle(title)
QBtn = QDialogButtonBox.StandardButton.Yes | QDialogButtonBox.StandardButton.No
self.buttonBox = QDialogButtonBox(QBtn)
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
self.layout = QVBoxLayout()
message = QLabel(f"Couldn't find reagent type {reagent_type.replace('_', ' ').title().strip('Lot')}: {reagent_lot} in the database.\n\nWould you like to add it?")
self.layout.addWidget(message)
self.layout.addWidget(self.buttonBox)
self.setLayout(self.layout)
class OverwriteSubQuestion(QDialog):
"""
dialog to ask about overwriting existing submission
"""
def __init__(self, message:str, rsl_plate_num:str) -> QDialog:
super().__init__()
self.setWindowTitle(f"Overwrite {rsl_plate_num}?")
QBtn = QDialogButtonBox.StandardButton.Yes | QDialogButtonBox.StandardButton.No
self.buttonBox = QDialogButtonBox(QBtn)
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
self.layout = QVBoxLayout()
message = QLabel(message)
self.layout.addWidget(message)
self.layout.addWidget(self.buttonBox)
self.setLayout(self.layout)
class AlertPop(QMessageBox):
def __init__(self, message:str, status:str) -> QMessageBox:

8
src/submissions/frontend/functions.py
View File

@@ -21,11 +21,3 @@ def check_kit_integrity(sub:BasicSubmission):
return result
def check_not_nan(cell_contents) -> bool:
try:
return not np.isnan(cell_contents)
except ValueError:
return True
except Exception as e:
logger.debug(f"Check encounteded unknown error: {e}")
return False