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