mid refactor for improved rebustness and readability
This commit is contained in:
Landon Wark
@@ -5,12 +5,11 @@ from PyQt6.QtWidgets import (
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QDialogButtonBox, QDateEdit, QSizePolicy, QWidget,
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QGridLayout, QPushButton, QSpinBox,
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QScrollBar, QHBoxLayout,
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QMessageBox
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)
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from PyQt6.QtCore import Qt, QDate, QSize
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# from PyQt6.QtGui import QFontMetrics, QAction
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from tools import check_not_nan
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from backend.db import get_all_reagenttype_names, lookup_all_sample_types, create_kit_from_yaml, lookup_regent_by_type_name
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# from submissions.backend.db import lookup_regent_by_type_name_and_kit_name
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from tools import check_not_nan, extract_form_info
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from backend.db import get_all_reagenttype_names, lookup_all_sample_types, create_kit_from_yaml, lookup_regent_by_type_name, lookup_regent_by_type_name_and_kit_name
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from backend.excel.parser import SheetParser
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from jinja2 import Environment, FileSystemLoader
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import sys
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@@ -46,18 +45,19 @@ class AddReagentForm(QDialog):
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self.buttonBox = QDialogButtonBox(QBtn)
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self.buttonBox.accepted.connect(self.accept)
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self.buttonBox.rejected.connect(self.reject)
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# get lot info
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# widget to get lot info
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lot_input = QLineEdit()
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lot_input.setObjectName("lot")
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lot_input.setText(reagent_lot)
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# get expiry info
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# widget to get expiry info
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exp_input = QDateEdit(calendarPopup=True)
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exp_input.setObjectName('expiry')
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# if expiry is not passed in from gui, use today
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if expiry == None:
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exp_input.setDate(QDate.currentDate())
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else:
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exp_input.setDate(expiry)
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# get reagent type info
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# widget to get reagent type info
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type_input = QComboBox()
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type_input.setObjectName('type')
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type_input.addItems([item.replace("_", " ").title() for item in get_all_reagenttype_names(ctx=ctx)])
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@@ -97,8 +97,10 @@ class ReportDatePicker(QDialog):
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self.buttonBox.rejected.connect(self.reject)
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# widgets to ask for dates
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start_date = QDateEdit(calendarPopup=True)
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start_date.setObjectName("start_date")
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start_date.setDate(QDate.currentDate())
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end_date = QDateEdit(calendarPopup=True)
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end_date.setObjectName("end_date")
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end_date.setDate(QDate.currentDate())
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self.layout = QVBoxLayout()
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self.layout.addWidget(QLabel("Start Date"))
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@@ -121,28 +123,34 @@ class KitAdder(QWidget):
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# insert submit button at top
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self.submit_btn = QPushButton("Submit")
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self.grid.addWidget(self.submit_btn,0,0,1,1)
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# need to exclude ordinary users to mitigate garbage database entries
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# self.grid.addWidget(QLabel("Password:"),1,0)
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# self.grid.addWidget(QLineEdit(),1,1)
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self.grid.addWidget(QLabel("Kit Name:"),2,0)
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self.grid.addWidget(QLineEdit(),2,1)
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# widget to get kit name
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kit_name = QLineEdit()
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kit_name.setObjectName("kit_name")
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self.grid.addWidget(kit_name,2,1)
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self.grid.addWidget(QLabel("Used For Sample Type:"),3,0)
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# widget to get uses of kit
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used_for = QComboBox()
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used_for.setObjectName("used_for")
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# Insert all existing sample types
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used_for.addItems(lookup_all_sample_types(ctx=parent_ctx))
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used_for.setEditable(True)
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self.grid.addWidget(used_for,3,1)
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# set cost per run
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self.grid.addWidget(QLabel("Constant cost per full plate (plates, work hours, etc.):"),4,0)
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cost = QSpinBox()
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cost.setMinimum(0)
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cost.setMaximum(9999)
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self.grid.addWidget(cost,4,1)
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# widget to get constant cost
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const_cost = QSpinBox()
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const_cost.setObjectName("const_cost")
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const_cost.setMinimum(0)
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const_cost.setMaximum(9999)
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self.grid.addWidget(const_cost,4,1)
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self.grid.addWidget(QLabel("Mutable cost per full plate (tips, reagents, etc.):"),5,0)
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cost = QSpinBox()
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cost.setMinimum(0)
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cost.setMaximum(9999)
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self.grid.addWidget(cost,5,1)
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# widget to get mutable costs
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mut_cost = QSpinBox()
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mut_cost.setObjectName("mut_cost")
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mut_cost.setMinimum(0)
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mut_cost.setMaximum(9999)
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self.grid.addWidget(mut_cost,5,1)
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# button to add additional reagent types
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self.add_RT_btn = QPushButton("Add Reagent Type")
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self.grid.addWidget(self.add_RT_btn)
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@@ -153,8 +161,11 @@ class KitAdder(QWidget):
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"""
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insert new reagent type row
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"""
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# get bottommost row
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maxrow = self.grid.rowCount()
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self.grid.addWidget(ReagentTypeForm(parent_ctx=self.ctx), maxrow + 1,0,1,2)
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reg_form = ReagentTypeForm(parent_ctx=self.ctx)
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reg_form.setObjectName(f"ReagentForm_{maxrow}")
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self.grid.addWidget(reg_form, maxrow + 1,0,1,2)
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def submit(self) -> None:
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@@ -162,80 +173,65 @@ class KitAdder(QWidget):
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send kit to database
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"""
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# get form info
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labels, values, reagents = self.extract_form_info(self)
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info = {item[0]:item[1] for item in zip(labels, values)}
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logger.debug(info)
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info, reagents = extract_form_info(self)
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logger.debug(f"kit info: {info}")
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yml_type = {}
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try:
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yml_type['password'] = info['password']
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except KeyError:
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pass
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used = info['used_for_sample_type'].replace(" ", "_").lower()
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used = info['used_for'].replace(" ", "_").lower()
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yml_type[used] = {}
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yml_type[used]['kits'] = {}
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yml_type[used]['kits'][info['kit_name']] = {}
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yml_type[used]['kits'][info['kit_name']]['constant_cost'] = info["Constant cost per full plate (plates, work hours, etc.)"]
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yml_type[used]['kits'][info['kit_name']]['mutable_cost'] = info["Mutable cost per full plate (tips, reagents, etc.)"]
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yml_type[used]['kits'][info['kit_name']]['constant_cost'] = info["const_cost"]
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yml_type[used]['kits'][info['kit_name']]['mutable_cost'] = info["mut_cost"]
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yml_type[used]['kits'][info['kit_name']]['reagenttypes'] = reagents
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logger.debug(yml_type)
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# send to kit constructor
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result = create_kit_from_yaml(ctx=self.ctx, exp=yml_type)
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# result = create_kit_from_yaml(ctx=self.ctx, exp=exp)
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msg = AlertPop(message=result['message'], status=result['status'])
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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()
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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(m)
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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 extract_form_info(self, object):
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"""
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retrieves arbitrary number of labels, values from form
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Args:
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object (_type_): the object to extract info from
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Returns:
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_type_: _description_
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"""
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labels = []
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values = []
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reagents = {}
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for item in object.findChildren(QWidget):
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logger.debug(item.parentWidget())
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# if not isinstance(item.parentWidget(), ReagentTypeForm):
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match item:
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case QLabel():
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labels.append(item.text().replace(" ", "_").strip(":").lower())
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case QLineEdit():
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# ad hoc check to prevent double reporting of qdatedit under lineedit for some reason
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if not isinstance(prev_item, QDateEdit) and not isinstance(prev_item, QComboBox) and not isinstance(prev_item, QSpinBox) and not isinstance(prev_item, QScrollBar):
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logger.debug(f"Previous: {prev_item}")
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logger.debug(f"Item: {item}, {item.text()}")
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values.append(item.text().strip())
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case QComboBox():
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values.append(item.currentText().strip())
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case QDateEdit():
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values.append(item.date().toPyDate())
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case QSpinBox():
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values.append(item.value())
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case ReagentTypeForm():
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re_labels, re_values, _ = self.extract_form_info(item)
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reagent = {item[0]:item[1] for item in zip(re_labels, re_values)}
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logger.debug(reagent)
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# reagent = {reagent['name:']:{'eol':reagent['extension_of_life_(months):']}}
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reagents[reagent["name_(*exactly*_as_it_appears_in_the_excel_submission_form)"].strip()] = {'eol_ext':int(reagent['extension_of_life_(months)'])}
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prev_item = item
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return labels, values, reagents
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# def extract_form_info(self, object):
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# """
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# retrieves arbitrary number of labels, values from form
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# Args:
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# object (_type_): the object to extract info from
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# Returns:
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# _type_: _description_
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# """
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# labels = []
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# values = []
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# reagents = {}
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# for item in object.findChildren(QWidget):
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# logger.debug(item.parentWidget())
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# # if not isinstance(item.parentWidget(), ReagentTypeForm):
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# match item:
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# case QLabel():
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# labels.append(item.text().replace(" ", "_").strip(":").lower())
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# case QLineEdit():
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# # ad hoc check to prevent double reporting of qdatedit under lineedit for some reason
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# if not isinstance(prev_item, QDateEdit) and not isinstance(prev_item, QComboBox) and not isinstance(prev_item, QSpinBox) and not isinstance(prev_item, QScrollBar):
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# logger.debug(f"Previous: {prev_item}")
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# logger.debug(f"Item: {item}, {item.text()}")
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# values.append(item.text().strip())
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# case QComboBox():
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# values.append(item.currentText().strip())
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# case QDateEdit():
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# values.append(item.date().toPyDate())
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# case QSpinBox():
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# values.append(item.value())
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# case ReagentTypeForm():
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# re_labels, re_values, _ = self.extract_form_info(item)
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# reagent = {item[0]:item[1] for item in zip(re_labels, re_values)}
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# logger.debug(reagent)
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# # reagent = {reagent['name:']:{'eol':reagent['extension_of_life_(months):']}}
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# reagents[reagent["name_(*exactly*_as_it_appears_in_the_excel_submission_form)"].strip()] = {'eol_ext':int(reagent['extension_of_life_(months)'])}
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# prev_item = item
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# return labels, values, reagents
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class ReagentTypeForm(QWidget):
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"""
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@@ -246,14 +242,17 @@ class ReagentTypeForm(QWidget):
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grid = QGridLayout()
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self.setLayout(grid)
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grid.addWidget(QLabel("Name (*Exactly* as it appears in the excel submission form):"),0,0)
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# Widget to get reagent info
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reagent_getter = QComboBox()
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reagent_getter.setObjectName("name")
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# lookup all reagent type names from db
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reagent_getter.addItems(get_all_reagenttype_names(ctx=parent_ctx))
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reagent_getter.setEditable(True)
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grid.addWidget(reagent_getter,0,1)
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grid.addWidget(QLabel("Extension of Life (months):"),0,2)
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# get extension of life
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# widget toget extension of life
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eol = QSpinBox()
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eol.setObjectName('eol')
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eol.setMinimum(0)
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grid.addWidget(eol, 0,3)
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@@ -277,7 +276,6 @@ class ControlsDatePicker(QWidget):
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self.layout.addWidget(self.start_date)
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self.layout.addWidget(QLabel("End Date"))
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self.layout.addWidget(self.end_date)
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self.setLayout(self.layout)
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self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Fixed)
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@@ -304,15 +302,17 @@ class ImportReagent(QComboBox):
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logger.debug(f"Attempting lookup of reagents by type: {query_var}")
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# below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work.
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relevant_reagents = [item.__str__() for item in lookup_regent_by_type_name(ctx=ctx, type_name=query_var)]#, kit_name=prsr.sub['extraction_kit'])]
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# relevant_reagents = [item.__str__() for item in lookup_regent_by_type_name_and_kit_name(ctx=ctx, type_name=query_var, kit_name=prsr.sub['extraction_kit'])]
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output_reg = []
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for reagent in relevant_reagents:
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# extract strings from any sets.
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if isinstance(reagent, set):
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for thing in reagent:
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output_reg.append(thing)
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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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# if reagent in sheet is not found insert it into items
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# if reagent in sheet is not found insert it into the front of relevant reagents so it shows
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if prsr != None:
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logger.debug(f"Relevant reagents for {prsr.sub[item]}: {relevant_reagents}")
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if str(prsr.sub[item]['lot']) not in relevant_reagents and prsr.sub[item]['lot'] != 'nan':
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@@ -1,12 +1,7 @@
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# from datetime import date
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from PyQt6.QtWidgets import (
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QLabel, QVBoxLayout, QDialog,
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QDialogButtonBox, QMessageBox
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)
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# from PyQt6.QtCore import Qt, QDate, QSize
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# from PyQt6.QtGui import QFontMetrics, QAction
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# from backend.db import get_all_reagenttype_names, lookup_all_sample_types, create_kit_from_yaml
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from jinja2 import Environment, FileSystemLoader
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import sys
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from pathlib import Path
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@@ -14,6 +9,7 @@ import logging
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logger = logging.getLogger(f"submissions.{__name__}")
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# determine if pyinstaller launcher is being used
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if getattr(sys, 'frozen', False):
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loader_path = Path(sys._MEIPASS).joinpath("files", "templates")
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else:
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@@ -22,50 +18,6 @@ loader = FileSystemLoader(loader_path)
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env = Environment(loader=loader)
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# class AddReagentQuestion(QDialog):
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# """
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# dialog to ask about adding a new reagne to db
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# """
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# def __init__(self, reagent_type:str, reagent_lot:str) -> QDialog:
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# super().__init__()
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# self.setWindowTitle(f"Add {reagent_lot}?")
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# QBtn = QDialogButtonBox.StandardButton.Yes | QDialogButtonBox.StandardButton.No
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# self.buttonBox = QDialogButtonBox(QBtn)
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# self.buttonBox.accepted.connect(self.accept)
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# self.buttonBox.rejected.connect(self.reject)
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# self.layout = QVBoxLayout()
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# 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?")
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# self.layout.addWidget(message)
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# self.layout.addWidget(self.buttonBox)
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# self.setLayout(self.layout)
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# class OverwriteSubQuestion(QDialog):
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# """
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# dialog to ask about overwriting existing submission
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# """
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# def __init__(self, message:str, rsl_plate_num:str) -> QDialog:
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# super().__init__()
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# self.setWindowTitle(f"Overwrite {rsl_plate_num}?")
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# QBtn = QDialogButtonBox.StandardButton.Yes | QDialogButtonBox.StandardButton.No
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# self.buttonBox = QDialogButtonBox(QBtn)
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# self.buttonBox.accepted.connect(self.accept)
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# self.buttonBox.rejected.connect(self.reject)
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# self.layout = QVBoxLayout()
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# message = QLabel(message)
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# self.layout.addWidget(message)
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# self.layout.addWidget(self.buttonBox)
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# self.setLayout(self.layout)
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class QuestionAsker(QDialog):
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"""
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dialog to ask yes/no questions
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@@ -73,23 +25,27 @@ class QuestionAsker(QDialog):
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def __init__(self, title:str, message:str) -> QDialog:
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super().__init__()
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self.setWindowTitle(title)
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# set yes/no buttons
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QBtn = QDialogButtonBox.StandardButton.Yes | QDialogButtonBox.StandardButton.No
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self.buttonBox = QDialogButtonBox(QBtn)
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self.buttonBox.accepted.connect(self.accept)
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self.buttonBox.rejected.connect(self.reject)
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self.layout = QVBoxLayout()
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# Text for the yes/no question
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message = QLabel(message)
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self.layout.addWidget(message)
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self.layout.addWidget(self.buttonBox)
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self.setLayout(self.layout)
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class AlertPop(QMessageBox):
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"""
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Dialog to show an alert.
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"""
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def __init__(self, message:str, status:str) -> QMessageBox:
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super().__init__()
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# select icon by string
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icon = getattr(QMessageBox.Icon, status.title())
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self.setIcon(icon)
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# msg.setText("Error")
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self.setInformativeText(message)
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self.setWindowTitle(status.title())
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@@ -1,20 +1,17 @@
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from datetime import date
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from PyQt6.QtWidgets import (
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QVBoxLayout, QDialog, QTableView,
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QTextEdit, QPushButton, QScrollArea,
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QMessageBox, QFileDialog, QMenu
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)
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from PyQt6.QtCore import Qt, QAbstractTableModel
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from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel
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from PyQt6.QtGui import QFontMetrics, QAction, QCursor
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from backend.db import submissions_to_df, lookup_submission_by_id, delete_submission_by_id
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from jinja2 import Environment, FileSystemLoader
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from xhtml2pdf import pisa
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import sys
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from pathlib import Path
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import logging
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from .pop_ups import AlertPop, QuestionAsker
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from tools import check_is_power_user
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from .pop_ups import QuestionAsker
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logger = logging.getLogger(f"submissions.{__name__}")
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|
||||
@@ -45,7 +42,7 @@ class pandasModel(QAbstractTableModel):
|
||||
"""
|
||||
return self._data.shape[0]
|
||||
|
||||
def columnCount(self, parnet=None) -> int:
|
||||
def columnCount(self, parent=None) -> int:
|
||||
"""
|
||||
does what it says
|
||||
|
||||
@@ -85,7 +82,7 @@ class SubmissionsSheet(QTableView):
|
||||
self.setData()
|
||||
self.resizeColumnsToContents()
|
||||
self.resizeRowsToContents()
|
||||
# self.clicked.connect(self.test)
|
||||
self.setSortingEnabled(True)
|
||||
self.doubleClicked.connect(self.show_details)
|
||||
|
||||
def setData(self) -> None:
|
||||
@@ -93,6 +90,8 @@ class SubmissionsSheet(QTableView):
|
||||
sets data in model
|
||||
"""
|
||||
self.data = submissions_to_df(ctx=self.ctx)
|
||||
self.data['id'] = self.data['id'].apply(str)
|
||||
self.data['id'] = self.data['id'].str.zfill(3)
|
||||
try:
|
||||
del self.data['samples']
|
||||
except KeyError:
|
||||
@@ -101,8 +100,11 @@ class SubmissionsSheet(QTableView):
|
||||
del self.data['reagents']
|
||||
except KeyError:
|
||||
pass
|
||||
self.model = pandasModel(self.data)
|
||||
self.setModel(self.model)
|
||||
proxyModel = QSortFilterProxyModel()
|
||||
proxyModel.setSourceModel(pandasModel(self.data))
|
||||
# self.model = pandasModel(self.data)
|
||||
# self.setModel(self.model)
|
||||
self.setModel(proxyModel)
|
||||
# self.resize(800,600)
|
||||
|
||||
def show_details(self) -> None:
|
||||
@@ -110,22 +112,22 @@ class SubmissionsSheet(QTableView):
|
||||
creates detailed data to show in seperate window
|
||||
"""
|
||||
index = (self.selectionModel().currentIndex())
|
||||
# logger.debug(index)
|
||||
value = index.sibling(index.row(),0).data()
|
||||
dlg = SubmissionDetails(ctx=self.ctx, id=value)
|
||||
# dlg.show()
|
||||
if dlg.exec():
|
||||
pass
|
||||
|
||||
|
||||
def contextMenuEvent(self, event):
|
||||
"""
|
||||
Creates actions for right click menu events.
|
||||
|
||||
Args:
|
||||
event (_type_): the item of interest
|
||||
"""
|
||||
self.menu = QMenu(self)
|
||||
renameAction = QAction('Delete', self)
|
||||
detailsAction = QAction('Details', self)
|
||||
# Originally I intended to limit deletions to power users.
|
||||
# renameAction.setEnabled(False)
|
||||
# if check_is_power_user(ctx=self.ctx):
|
||||
# renameAction.setEnabled(True)
|
||||
renameAction.triggered.connect(lambda: self.delete_item(event))
|
||||
detailsAction.triggered.connect(lambda: self.show_details())
|
||||
self.menu.addAction(detailsAction)
|
||||
@@ -164,12 +166,8 @@ class SubmissionDetails(QDialog):
|
||||
# get submision from db
|
||||
data = lookup_submission_by_id(ctx=ctx, id=id)
|
||||
self.base_dict = data.to_dict()
|
||||
# logger.debug(f"Base dict: {self.base_dict}")
|
||||
# don't want id
|
||||
del self.base_dict['id']
|
||||
# convert sub objects to dicts
|
||||
# self.base_dict['reagents'] = [item.to_sub_dict() for item in data.reagents]
|
||||
# self.base_dict['samples'] = [item.to_sub_dict() for item in data.samples]
|
||||
# retrieve jinja template
|
||||
template = env.get_template("submission_details.txt")
|
||||
# render using object dict
|
||||
@@ -192,24 +190,18 @@ class SubmissionDetails(QDialog):
|
||||
interior.setWidget(txt_editor)
|
||||
self.layout = QVBoxLayout()
|
||||
self.setFixedSize(w, 900)
|
||||
# button to export a pdf version
|
||||
btn = QPushButton("Export PDF")
|
||||
btn.setParent(self)
|
||||
btn.setFixedWidth(w)
|
||||
btn.clicked.connect(self.export)
|
||||
|
||||
|
||||
# def _create_actions(self):
|
||||
# self.exportAction = QAction("Export", self)
|
||||
|
||||
|
||||
def export(self):
|
||||
template = env.get_template("submission_details.html")
|
||||
html = template.render(sub=self.base_dict)
|
||||
# logger.debug(f"Submission details: {self.base_dict}")
|
||||
home_dir = Path(self.ctx["directory_path"]).joinpath(f"Submission_Details_{self.base_dict['Plate Number']}.pdf").resolve().__str__()
|
||||
fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".pdf")[0])
|
||||
# logger.debug(f"report output name: {fname}")
|
||||
# df.to_excel(fname, engine='openpyxl')
|
||||
if fname.__str__() == ".":
|
||||
logger.debug("Saving pdf was cancelled.")
|
||||
return
|
||||
@@ -223,4 +215,3 @@ class SubmissionDetails(QDialog):
|
||||
msg.setInformativeText(f"Looks like {fname.__str__()} is open.\nPlease close it and try again.")
|
||||
msg.setWindowTitle("Permission Error")
|
||||
msg.exec()
|
||||
|
||||
|
||||
Reference in New Issue
Block a user