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@@ -2,27 +2,18 @@
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Contains miscellaneous widgets for frontend functions
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'''
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from datetime import date
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from pprint import pformat
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from PyQt6 import QtCore
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from PyQt6.QtWidgets import (
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QLabel, QVBoxLayout,
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QLineEdit, QComboBox, QDialog,
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QDialogButtonBox, QDateEdit, QSizePolicy, QWidget,
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QGridLayout, QPushButton, QSpinBox, QDoubleSpinBox,
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QHBoxLayout, QScrollArea, QFormLayout
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QDialogButtonBox, QDateEdit, QPushButton, QFormLayout
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)
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from PyQt6.QtCore import Qt, QDate, QSize, pyqtSignal
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from tools import check_not_nan, jinja_template_loading, Settings, Result
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from PyQt6.QtCore import Qt, QDate
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from tools import jinja_template_loading, Settings
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from backend.db.models import *
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from sqlalchemy import FLOAT, INTEGER
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import logging
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import numpy as np
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from .pop_ups import AlertPop, QuestionAsker
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from backend.validators import PydReagent, PydKit, PydReagentType, PydSubmission
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from typing import Tuple, List
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from pprint import pformat
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import difflib
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from .pop_ups import AlertPop
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from .functions import select_open_file
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from tools import readInChunks
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logger = logging.getLogger(f"submissions.{__name__}")
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@@ -137,235 +128,6 @@ class ReportDatePicker(QDialog):
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def parse_form(self):
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return dict(start_date=self.start_date.date().toPyDate(), end_date = self.end_date.date().toPyDate())
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# class KitAdder(QWidget):
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# """
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# dialog to get information to add kit
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# """
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# def __init__(self) -> None:
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# super().__init__()
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# # self.ctx = parent_ctx
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# main_box = QVBoxLayout(self)
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# scroll = QScrollArea(self)
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# main_box.addWidget(scroll)
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# scroll.setWidgetResizable(True)
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# scrollContent = QWidget(scroll)
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# self.grid = QGridLayout()
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# # self.setLayout(self.grid)
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# scrollContent.setLayout(self.grid)
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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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# self.grid.addWidget(QLabel("Kit Name:"),2,0)
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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 Submission 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([item.name for item in lookup_submission_type(ctx=parent_ctx)])
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# used_for.addItems([item.name for item in SubmissionType.query()])
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# used_for.setEditable(True)
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# self.grid.addWidget(used_for,3,1)
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# # Get all fields in SubmissionTypeKitTypeAssociation
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# self.columns = [item for item in SubmissionTypeKitTypeAssociation.__table__.columns if len(item.foreign_keys) == 0]
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# for iii, column in enumerate(self.columns):
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# idx = iii + 4
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# # convert field name to human readable.
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# field_name = column.name.replace("_", " ").title()
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# self.grid.addWidget(QLabel(field_name),idx,0)
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# match column.type:
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# case FLOAT():
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# add_widget = QDoubleSpinBox()
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# add_widget.setMinimum(0)
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# add_widget.setMaximum(9999)
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# case INTEGER():
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# add_widget = QSpinBox()
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# add_widget.setMinimum(0)
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# add_widget.setMaximum(9999)
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# case _:
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# add_widget = QLineEdit()
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# add_widget.setObjectName(column.name)
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# self.grid.addWidget(add_widget, idx,1)
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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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# self.add_RT_btn.clicked.connect(self.add_RT)
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# self.submit_btn.clicked.connect(self.submit)
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# scroll.setWidget(scrollContent)
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# self.ignore = [None, "", "qt_spinbox_lineedit", "qt_scrollarea_viewport", "qt_scrollarea_hcontainer",
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# "qt_scrollarea_vcontainer", "submit_btn"
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# ]
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# def add_RT(self) -> None:
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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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# reg_form = ReagentTypeForm()
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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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# self.grid.addWidget(reg_form, maxrow,0,1,4)
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# def submit(self) -> None:
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# """
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# send kit to database
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# """
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# # get form info
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# info, reagents = self.parse_form()
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# # info, reagents = extract_form_info(self)
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# info = {k:v for k,v in info.items() if k in [column.name for column in self.columns] + ['kit_name', 'used_for']}
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# logger.debug(f"kit info: {pformat(info)}")
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# logger.debug(f"kit reagents: {pformat(reagents)}")
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# info['reagent_types'] = reagents
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# logger.debug(pformat(info))
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# # send to kit constructor
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# kit = PydKit(name=info['kit_name'])
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# for reagent in info['reagent_types']:
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# uses = {
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# info['used_for']:
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# {'sheet':reagent['sheet'],
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# 'name':reagent['name'],
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# 'lot':reagent['lot'],
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# 'expiry':reagent['expiry']
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# }}
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# kit.reagent_types.append(PydReagentType(name=reagent['rtname'], eol_ext=reagent['eol'], uses=uses))
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# logger.debug(f"Output pyd object: {kit.__dict__}")
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# # result = construct_kit_from_yaml(ctx=self.ctx, kit_dict=info)
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# sqlobj, result = kit.toSQL(self.ctx)
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# sqlobj.save()
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# msg = AlertPop(message=result['message'], status=result['status'])
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# msg.exec()
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# self.__init__(self.ctx)
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# def parse_form(self) -> Tuple[dict, list]:
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# logger.debug(f"Hello from {self.__class__} parser!")
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# info = {}
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# reagents = []
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# widgets = [widget for widget in self.findChildren(QWidget) if widget.objectName() not in self.ignore and not isinstance(widget.parent(), ReagentTypeForm)]
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# for widget in widgets:
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# # logger.debug(f"Parsed widget: {widget.objectName()} of type {type(widget)} with parent {widget.parent()}")
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# match widget:
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# case ReagentTypeForm():
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# reagents.append(widget.parse_form())
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# case QLineEdit():
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# info[widget.objectName()] = widget.text()
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# case QComboBox():
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# info[widget.objectName()] = widget.currentText()
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# case QDateEdit():
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# info[widget.objectName()] = widget.date().toPyDate()
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# return info, reagents
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# class ReagentTypeForm(QWidget):
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# """
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# custom widget to add information about a new reagenttype
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# """
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# def __init__(self) -> None:
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# super().__init__()
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# grid = QGridLayout()
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# self.setLayout(grid)
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# grid.addWidget(QLabel("Reagent Type Name"),0,0)
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# # Widget to get reagent info
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# self.reagent_getter = QComboBox()
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# self.reagent_getter.setObjectName("rtname")
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# # lookup all reagent type names from db
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# # lookup = lookup_reagent_types(ctx=ctx)
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# lookup = ReagentType.query()
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# logger.debug(f"Looked up ReagentType names: {lookup}")
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# self.reagent_getter.addItems([item.__str__() for item in lookup])
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# self.reagent_getter.setEditable(True)
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# grid.addWidget(self.reagent_getter,0,1)
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# grid.addWidget(QLabel("Extension of Life (months):"),0,2)
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# # widget to get extension of life
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# self.eol = QSpinBox()
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# self.eol.setObjectName('eol')
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# self.eol.setMinimum(0)
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# grid.addWidget(self.eol, 0,3)
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# grid.addWidget(QLabel("Excel Location Sheet Name:"),1,0)
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# self.location_sheet_name = QLineEdit()
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# self.location_sheet_name.setObjectName("sheet")
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# self.location_sheet_name.setText("e.g. 'Reagent Info'")
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# grid.addWidget(self.location_sheet_name, 1,1)
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# for iii, item in enumerate(["Name", "Lot", "Expiry"]):
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# idx = iii + 2
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# grid.addWidget(QLabel(f"{item} Row:"), idx, 0)
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# row = QSpinBox()
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# row.setFixedWidth(50)
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# row.setObjectName(f'{item.lower()}_row')
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# row.setMinimum(0)
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# grid.addWidget(row, idx, 1)
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# grid.addWidget(QLabel(f"{item} Column:"), idx, 2)
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# col = QSpinBox()
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# col.setFixedWidth(50)
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# col.setObjectName(f'{item.lower()}_column')
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# col.setMinimum(0)
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# grid.addWidget(col, idx, 3)
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# self.setFixedHeight(175)
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# max_row = grid.rowCount()
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# self.r_button = QPushButton("Remove")
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# self.r_button.clicked.connect(self.remove)
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# grid.addWidget(self.r_button,max_row,0,1,1)
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# self.ignore = [None, "", "qt_spinbox_lineedit", "qt_scrollarea_viewport", "qt_scrollarea_hcontainer",
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# "qt_scrollarea_vcontainer", "submit_btn", "eol", "sheet", "rtname"
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# ]
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# def remove(self):
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# self.setParent(None)
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# self.destroy()
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# def parse_form(self) -> dict:
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# logger.debug(f"Hello from {self.__class__} parser!")
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# info = {}
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# info['eol'] = self.eol.value()
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# info['sheet'] = self.location_sheet_name.text()
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# info['rtname'] = self.reagent_getter.currentText()
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# widgets = [widget for widget in self.findChildren(QWidget) if widget.objectName() not in self.ignore]
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# for widget in widgets:
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# logger.debug(f"Parsed widget: {widget.objectName()} of type {type(widget)} with parent {widget.parent()}")
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# match widget:
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# case QLineEdit():
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# info[widget.objectName()] = widget.text()
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# case QComboBox():
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# info[widget.objectName()] = widget.currentText()
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# case QDateEdit():
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# info[widget.objectName()] = widget.date().toPyDate()
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# case QSpinBox() | QDoubleSpinBox():
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# if "_" in widget.objectName():
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# key, sub_key = widget.objectName().split("_")
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# if key not in info.keys():
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# info[key] = {}
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# logger.debug(f"Adding key {key}, {sub_key} and value {widget.value()} to {info}")
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# info[key][sub_key] = widget.value()
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# return info
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# class ControlsDatePicker(QWidget):
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# """
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# custom widget to pick start and end dates for controls graphs
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# """
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# def __init__(self) -> None:
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# super().__init__()
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# self.start_date = QDateEdit(calendarPopup=True)
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# # start date is two months prior to end date by default
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# twomonthsago = QDate.currentDate().addDays(-60)
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# self.start_date.setDate(twomonthsago)
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# self.end_date = QDateEdit(calendarPopup=True)
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# self.end_date.setDate(QDate.currentDate())
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# self.layout = QHBoxLayout()
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# self.layout.addWidget(QLabel("Start Date"))
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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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# def sizeHint(self) -> QSize:
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# return QSize(80,20)
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class FirstStrandSalvage(QDialog):
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def __init__(self, ctx:Settings, submitter_id:str, rsl_plate_num:str|None=None) -> None:
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@@ -429,321 +191,46 @@ class FirstStrandPlateList(QDialog):
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output.append(plate.currentText())
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return output
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# class ReagentFormWidget(QWidget):
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class LogParser(QDialog):
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# def __init__(self, parent:QWidget, reagent:PydReagent, extraction_kit:str):
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# super().__init__(parent)
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# # self.setParent(parent)
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# self.reagent = reagent
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# self.extraction_kit = extraction_kit
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# # self.ctx = reagent.ctx
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# layout = QVBoxLayout()
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# self.label = self.ReagentParsedLabel(reagent=reagent)
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# layout.addWidget(self.label)
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# self.lot = self.ReagentLot(reagent=reagent, extraction_kit=extraction_kit)
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# layout.addWidget(self.lot)
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# # Remove spacing between reagents
|
|
|
|
|
# layout.setContentsMargins(0,0,0,0)
|
|
|
|
|
# self.setLayout(layout)
|
|
|
|
|
# self.setObjectName(reagent.name)
|
|
|
|
|
# self.missing = reagent.missing
|
|
|
|
|
# # If changed set self.missing to True and update self.label
|
|
|
|
|
# self.lot.currentTextChanged.connect(self.updated)
|
|
|
|
|
|
|
|
|
|
# def parse_form(self) -> Tuple[PydReagent, dict]:
|
|
|
|
|
# lot = self.lot.currentText()
|
|
|
|
|
# # wanted_reagent = lookup_reagents(ctx=self.ctx, lot_number=lot, reagent_type=self.reagent.type)
|
|
|
|
|
# wanted_reagent = Reagent.query(lot_number=lot, reagent_type=self.reagent.type)
|
|
|
|
|
# # if reagent doesn't exist in database, off to add it (uses App.add_reagent)
|
|
|
|
|
# if wanted_reagent == None:
|
|
|
|
|
# dlg = QuestionAsker(title=f"Add {lot}?", message=f"Couldn't find reagent type {self.reagent.type}: {lot} in the database.\n\nWould you like to add it?")
|
|
|
|
|
# if dlg.exec():
|
|
|
|
|
# wanted_reagent = self.parent().parent().parent().parent().parent().parent().parent().parent().parent.add_reagent(reagent_lot=lot, reagent_type=self.reagent.type, expiry=self.reagent.expiry, name=self.reagent.name)
|
|
|
|
|
# return wanted_reagent, None
|
|
|
|
|
# else:
|
|
|
|
|
# # In this case we will have an empty reagent and the submission will fail kit integrity check
|
|
|
|
|
# logger.debug("Will not add reagent.")
|
|
|
|
|
# return None, Result(msg="Failed integrity check", status="Critical")
|
|
|
|
|
# else:
|
|
|
|
|
# # Since this now gets passed in directly from the parser -> pyd -> form and the parser gets the name
|
|
|
|
|
# # from the db, it should no longer be necessary to query the db with reagent/kit, but with rt name directly.
|
|
|
|
|
# # rt = lookup_reagent_types(ctx=self.ctx, name=self.reagent.type)
|
|
|
|
|
# # rt = lookup_reagent_types(ctx=self.ctx, kit_type=self.extraction_kit, reagent=wanted_reagent)
|
|
|
|
|
# rt = ReagentType.query(name=self.reagent.type)
|
|
|
|
|
# if rt == None:
|
|
|
|
|
# # rt = lookup_reagent_types(ctx=self.ctx, kit_type=self.extraction_kit, reagent=wanted_reagent)
|
|
|
|
|
# rt = ReagentType.query(kit_type=self.extraction_kit, reagent=wanted_reagent)
|
|
|
|
|
# return PydReagent(name=wanted_reagent.name, lot=wanted_reagent.lot, type=rt.name, expiry=wanted_reagent.expiry, parsed=not self.missing), None
|
|
|
|
|
|
|
|
|
|
# def updated(self):
|
|
|
|
|
# self.missing = True
|
|
|
|
|
# self.label.updated(self.reagent.type)
|
|
|
|
|
def __init__(self, parent):
|
|
|
|
|
super().__init__(parent)
|
|
|
|
|
self.app = self.parent()
|
|
|
|
|
self.filebutton = QPushButton(self)
|
|
|
|
|
self.filebutton.setText("Import File")
|
|
|
|
|
self.phrase_looker = QComboBox(self)
|
|
|
|
|
self.phrase_looker.setEditable(True)
|
|
|
|
|
self.btn = QPushButton(self)
|
|
|
|
|
self.btn.setText("Search")
|
|
|
|
|
self.layout = QFormLayout(self)
|
|
|
|
|
self.layout.addRow(self.tr("&File:"), self.filebutton)
|
|
|
|
|
self.layout.addRow(self.tr("&Search Term:"), self.phrase_looker)
|
|
|
|
|
self.layout.addRow(self.btn)
|
|
|
|
|
self.filebutton.clicked.connect(self.filelookup)
|
|
|
|
|
self.btn.clicked.connect(self.runsearch)
|
|
|
|
|
self.setMinimumWidth(400)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
# class ReagentParsedLabel(QLabel):
|
|
|
|
|
|
|
|
|
|
# def __init__(self, reagent:PydReagent):
|
|
|
|
|
# super().__init__()
|
|
|
|
|
# try:
|
|
|
|
|
# check = not reagent.missing
|
|
|
|
|
# except:
|
|
|
|
|
# check = False
|
|
|
|
|
# self.setObjectName(f"{reagent.type}_label")
|
|
|
|
|
# if check:
|
|
|
|
|
# self.setText(f"Parsed {reagent.type}")
|
|
|
|
|
# else:
|
|
|
|
|
# self.setText(f"MISSING {reagent.type}")
|
|
|
|
|
|
|
|
|
|
# def updated(self, reagent_type:str):
|
|
|
|
|
# self.setText(f"UPDATED {reagent_type}")
|
|
|
|
|
def filelookup(self):
|
|
|
|
|
self.fname = select_open_file(self, "tabular")
|
|
|
|
|
|
|
|
|
|
# class ReagentLot(QComboBox):
|
|
|
|
|
|
|
|
|
|
# def __init__(self, reagent, extraction_kit:str) -> None:
|
|
|
|
|
# super().__init__()
|
|
|
|
|
# # self.ctx = reagent.ctx
|
|
|
|
|
# self.setEditable(True)
|
|
|
|
|
# # if reagent.parsed:
|
|
|
|
|
# # pass
|
|
|
|
|
# logger.debug(f"Attempting lookup of reagents by type: {reagent.type}")
|
|
|
|
|
# # below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work.
|
|
|
|
|
# # lookup = lookup_reagents(ctx=self.ctx, reagent_type=reagent.type)
|
|
|
|
|
# lookup = Reagent.query(reagent_type=reagent.type)
|
|
|
|
|
# relevant_reagents = [item.__str__() for item in lookup]
|
|
|
|
|
# output_reg = []
|
|
|
|
|
# for rel_reagent in relevant_reagents:
|
|
|
|
|
# # extract strings from any sets.
|
|
|
|
|
# if isinstance(rel_reagent, set):
|
|
|
|
|
# for thing in rel_reagent:
|
|
|
|
|
# output_reg.append(thing)
|
|
|
|
|
# elif isinstance(rel_reagent, str):
|
|
|
|
|
# output_reg.append(rel_reagent)
|
|
|
|
|
# relevant_reagents = output_reg
|
|
|
|
|
# # if reagent in sheet is not found insert it into the front of relevant reagents so it shows
|
|
|
|
|
# logger.debug(f"Relevant reagents for {reagent.lot}: {relevant_reagents}")
|
|
|
|
|
# if str(reagent.lot) not in relevant_reagents:
|
|
|
|
|
# if check_not_nan(reagent.lot):
|
|
|
|
|
# relevant_reagents.insert(0, str(reagent.lot))
|
|
|
|
|
# else:
|
|
|
|
|
# # TODO: look up the last used reagent of this type in the database
|
|
|
|
|
# # looked_up_rt = lookup_reagenttype_kittype_association(ctx=self.ctx, reagent_type=reagent.type, kit_type=extraction_kit)
|
|
|
|
|
# looked_up_rt = KitTypeReagentTypeAssociation.query(reagent_type=reagent.type, kit_type=extraction_kit)
|
|
|
|
|
# try:
|
|
|
|
|
# # looked_up_reg = lookup_reagents(ctx=self.ctx, lot_number=looked_up_rt.last_used)
|
|
|
|
|
# looked_up_reg = Reagent.query(lot_number=looked_up_rt.last_used)
|
|
|
|
|
# except AttributeError:
|
|
|
|
|
# looked_up_reg = None
|
|
|
|
|
# logger.debug(f"Because there was no reagent listed for {reagent.lot}, we will insert the last lot used: {looked_up_reg}")
|
|
|
|
|
# if looked_up_reg != None:
|
|
|
|
|
# relevant_reagents.remove(str(looked_up_reg.lot))
|
|
|
|
|
# relevant_reagents.insert(0, str(looked_up_reg.lot))
|
|
|
|
|
# else:
|
|
|
|
|
# if len(relevant_reagents) > 1:
|
|
|
|
|
# logger.debug(f"Found {reagent.lot} in relevant reagents: {relevant_reagents}. Moving to front of list.")
|
|
|
|
|
# idx = relevant_reagents.index(str(reagent.lot))
|
|
|
|
|
# logger.debug(f"The index we got for {reagent.lot} in {relevant_reagents} was {idx}")
|
|
|
|
|
# moved_reag = relevant_reagents.pop(idx)
|
|
|
|
|
# relevant_reagents.insert(0, moved_reag)
|
|
|
|
|
# else:
|
|
|
|
|
# logger.debug(f"Found {reagent.lot} in relevant reagents: {relevant_reagents}. But no need to move due to short list.")
|
|
|
|
|
# logger.debug(f"New relevant reagents: {relevant_reagents}")
|
|
|
|
|
# self.setObjectName(f"lot_{reagent.type}")
|
|
|
|
|
# self.addItems(relevant_reagents)
|
|
|
|
|
|
|
|
|
|
# class SubmissionFormWidget(QWidget):
|
|
|
|
|
|
|
|
|
|
# def __init__(self, parent: QWidget, **kwargs) -> None:
|
|
|
|
|
# super().__init__(parent)
|
|
|
|
|
# # self.ignore = [None, "", "qt_spinbox_lineedit", "qt_scrollarea_viewport", "qt_scrollarea_hcontainer",
|
|
|
|
|
# # "qt_scrollarea_vcontainer", "submit_btn"
|
|
|
|
|
# # ]
|
|
|
|
|
# self.ignore = ['filepath', 'samples', 'reagents', 'csv', 'ctx']
|
|
|
|
|
# layout = QVBoxLayout()
|
|
|
|
|
# for k, v in kwargs.items():
|
|
|
|
|
# if k not in self.ignore:
|
|
|
|
|
# add_widget = self.create_widget(key=k, value=v, submission_type=kwargs['submission_type'])
|
|
|
|
|
# if add_widget != None:
|
|
|
|
|
# layout.addWidget(add_widget)
|
|
|
|
|
# else:
|
|
|
|
|
# setattr(self, k, v)
|
|
|
|
|
|
|
|
|
|
# self.setLayout(layout)
|
|
|
|
|
|
|
|
|
|
# def create_widget(self, key:str, value:dict, submission_type:str|None=None):
|
|
|
|
|
# if key not in self.ignore:
|
|
|
|
|
# return self.InfoItem(self, key=key, value=value, submission_type=submission_type)
|
|
|
|
|
# return None
|
|
|
|
|
|
|
|
|
|
# def clear_form(self):
|
|
|
|
|
# for item in self.findChildren(QWidget):
|
|
|
|
|
# item.setParent(None)
|
|
|
|
|
|
|
|
|
|
# def find_widgets(self, object_name:str|None=None) -> List[QWidget]:
|
|
|
|
|
# query = self.findChildren(QWidget)
|
|
|
|
|
# if object_name != None:
|
|
|
|
|
# query = [widget for widget in query if widget.objectName()==object_name]
|
|
|
|
|
# return query
|
|
|
|
|
|
|
|
|
|
# def parse_form(self) -> PydSubmission:
|
|
|
|
|
# logger.debug(f"Hello from form parser!")
|
|
|
|
|
# info = {}
|
|
|
|
|
# reagents = []
|
|
|
|
|
# if hasattr(self, 'csv'):
|
|
|
|
|
# info['csv'] = self.csv
|
|
|
|
|
# for widget in self.findChildren(QWidget):
|
|
|
|
|
# # logger.debug(f"Parsed widget of type {type(widget)}")
|
|
|
|
|
# match widget:
|
|
|
|
|
# case ReagentFormWidget():
|
|
|
|
|
# reagent, _ = widget.parse_form()
|
|
|
|
|
# if reagent != None:
|
|
|
|
|
# reagents.append(reagent)
|
|
|
|
|
# case self.InfoItem():
|
|
|
|
|
# field, value = widget.parse_form()
|
|
|
|
|
# if field != None:
|
|
|
|
|
# info[field] = value
|
|
|
|
|
# logger.debug(f"Info: {pformat(info)}")
|
|
|
|
|
# logger.debug(f"Reagents: {pformat(reagents)}")
|
|
|
|
|
# # app = self.parent().parent().parent().parent().parent().parent().parent().parent
|
|
|
|
|
# submission = PydSubmission(filepath=self.filepath, reagents=reagents, samples=self.samples, **info)
|
|
|
|
|
# return submission
|
|
|
|
|
|
|
|
|
|
# class InfoItem(QWidget):
|
|
|
|
|
|
|
|
|
|
# def __init__(self, parent: QWidget, key:str, value:dict, submission_type:str|None=None) -> None:
|
|
|
|
|
# super().__init__(parent)
|
|
|
|
|
# layout = QVBoxLayout()
|
|
|
|
|
# self.label = self.ParsedQLabel(key=key, value=value)
|
|
|
|
|
# self.input: QWidget = self.set_widget(parent=self, key=key, value=value, submission_type=submission_type['value'])
|
|
|
|
|
# self.setObjectName(key)
|
|
|
|
|
# try:
|
|
|
|
|
# self.missing:bool = value['missing']
|
|
|
|
|
# except (TypeError, KeyError):
|
|
|
|
|
# self.missing:bool = True
|
|
|
|
|
# if self.input != None:
|
|
|
|
|
# layout.addWidget(self.label)
|
|
|
|
|
# layout.addWidget(self.input)
|
|
|
|
|
# layout.setContentsMargins(0,0,0,0)
|
|
|
|
|
# self.setLayout(layout)
|
|
|
|
|
# match self.input:
|
|
|
|
|
# case QComboBox():
|
|
|
|
|
# self.input.currentTextChanged.connect(self.update_missing)
|
|
|
|
|
# case QDateEdit():
|
|
|
|
|
# self.input.dateChanged.connect(self.update_missing)
|
|
|
|
|
# case QLineEdit():
|
|
|
|
|
# self.input.textChanged.connect(self.update_missing)
|
|
|
|
|
|
|
|
|
|
# def parse_form(self):
|
|
|
|
|
# match self.input:
|
|
|
|
|
# case QLineEdit():
|
|
|
|
|
# value = self.input.text()
|
|
|
|
|
# case QComboBox():
|
|
|
|
|
# value = self.input.currentText()
|
|
|
|
|
# case QDateEdit():
|
|
|
|
|
# value = self.input.date().toPyDate()
|
|
|
|
|
# case _:
|
|
|
|
|
# return None, None
|
|
|
|
|
# return self.input.objectName(), dict(value=value, missing=self.missing)
|
|
|
|
|
|
|
|
|
|
# def set_widget(self, parent: QWidget, key:str, value:dict, submission_type:str|None=None) -> QWidget:
|
|
|
|
|
# try:
|
|
|
|
|
# value = value['value']
|
|
|
|
|
# except (TypeError, KeyError):
|
|
|
|
|
# pass
|
|
|
|
|
# obj = parent.parent().parent()
|
|
|
|
|
# logger.debug(f"Creating widget for: {key}")
|
|
|
|
|
# match key:
|
|
|
|
|
# case 'submitting_lab':
|
|
|
|
|
# add_widget = QComboBox()
|
|
|
|
|
# # lookup organizations suitable for submitting_lab (ctx: self.InfoItem.SubmissionFormWidget.SubmissionFormContainer.AddSubForm )
|
|
|
|
|
# labs = [item.__str__() for item in Organization.query()]
|
|
|
|
|
# # try to set closest match to top of list
|
|
|
|
|
# try:
|
|
|
|
|
# labs = difflib.get_close_matches(value, labs, len(labs), 0)
|
|
|
|
|
# except (TypeError, ValueError):
|
|
|
|
|
# pass
|
|
|
|
|
# # set combobox values to lookedup values
|
|
|
|
|
# add_widget.addItems(labs)
|
|
|
|
|
# case 'extraction_kit':
|
|
|
|
|
# # if extraction kit not available, all other values fail
|
|
|
|
|
# if not check_not_nan(value):
|
|
|
|
|
# msg = AlertPop(message="Make sure to check your extraction kit in the excel sheet!", status="warning")
|
|
|
|
|
# msg.exec()
|
|
|
|
|
# # create combobox to hold looked up kits
|
|
|
|
|
# add_widget = QComboBox()
|
|
|
|
|
# # lookup existing kits by 'submission_type' decided on by sheetparser
|
|
|
|
|
# logger.debug(f"Looking up kits used for {submission_type}")
|
|
|
|
|
# uses = [item.__str__() for item in KitType.query(used_for=submission_type)]
|
|
|
|
|
# obj.uses = uses
|
|
|
|
|
# logger.debug(f"Kits received for {submission_type}: {uses}")
|
|
|
|
|
# if check_not_nan(value):
|
|
|
|
|
# logger.debug(f"The extraction kit in parser was: {value}")
|
|
|
|
|
# uses.insert(0, uses.pop(uses.index(value)))
|
|
|
|
|
# obj.ext_kit = value
|
|
|
|
|
# else:
|
|
|
|
|
# logger.error(f"Couldn't find {obj.prsr.sub['extraction_kit']}")
|
|
|
|
|
# obj.ext_kit = uses[0]
|
|
|
|
|
# add_widget.addItems(uses)
|
|
|
|
|
# # Run reagent scraper whenever extraction kit is changed.
|
|
|
|
|
# # add_widget.currentTextChanged.connect(obj.scrape_reagents)
|
|
|
|
|
# case 'submitted_date':
|
|
|
|
|
# # uses base calendar
|
|
|
|
|
# add_widget = QDateEdit(calendarPopup=True)
|
|
|
|
|
# # sets submitted date based on date found in excel sheet
|
|
|
|
|
# try:
|
|
|
|
|
# add_widget.setDate(value)
|
|
|
|
|
# # if not found, use today
|
|
|
|
|
# except:
|
|
|
|
|
# add_widget.setDate(date.today())
|
|
|
|
|
# case 'submission_category':
|
|
|
|
|
# add_widget = QComboBox()
|
|
|
|
|
# cats = ['Diagnostic', "Surveillance", "Research"]
|
|
|
|
|
# # cats += [item.name for item in lookup_submission_type(ctx=obj.ctx)]
|
|
|
|
|
# cats += [item.name for item in SubmissionType.query()]
|
|
|
|
|
# try:
|
|
|
|
|
# cats.insert(0, cats.pop(cats.index(value)))
|
|
|
|
|
# except ValueError:
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# cats.insert(0, cats.pop(cats.index(submission_type)))
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# add_widget.addItems(cats)
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# case _:
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# # anything else gets added in as a line edit
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# add_widget = QLineEdit()
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# logger.debug(f"Setting widget text to {str(value).replace('_', ' ')}")
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# add_widget.setText(str(value).replace("_", " "))
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# if add_widget != None:
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# add_widget.setObjectName(key)
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# add_widget.setParent(parent)
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# return add_widget
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# def update_missing(self):
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# self.missing = True
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# self.label.updated(self.objectName())
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# class ParsedQLabel(QLabel):
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# def __init__(self, key:str, value:dict, title:bool=True, label_name:str|None=None):
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# super().__init__()
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# try:
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# check = not value['missing']
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# except:
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|
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# check = True
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# if label_name != None:
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|
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# self.setObjectName(label_name)
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# else:
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# self.setObjectName(f"{key}_label")
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# if title:
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|
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# output = key.replace('_', ' ').title()
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# else:
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|
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# output = key.replace('_', ' ')
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# if check:
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|
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# self.setText(f"Parsed {output}")
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# else:
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|
|
# self.setText(f"MISSING {output}")
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|
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# def updated(self, key:str, title:bool=True):
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|
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# if title:
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|
|
# output = key.replace('_', ' ').title()
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|
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# else:
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|
|
# output = key.replace('_', ' ')
|
|
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|
|
# self.setText(f"UPDATED {output}")
|
|
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|
|
def runsearch(self):
|
|
|
|
|
count: int = 0
|
|
|
|
|
total: int = 0
|
|
|
|
|
logger.debug(f"Current search term: {self.phrase_looker.currentText()}")
|
|
|
|
|
try:
|
|
|
|
|
with open(self.fname, "r") as f:
|
|
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|
|
for chunk in readInChunks(fileObj=f):
|
|
|
|
|
total += len(chunk)
|
|
|
|
|
for line in chunk:
|
|
|
|
|
if self.phrase_looker.currentText().lower() in line.lower():
|
|
|
|
|
count += 1
|
|
|
|
|
percent = (count/total)*100
|
|
|
|
|
msg = f"I found {count} instances of the search phrase out of {total} = {percent:.2f}%."
|
|
|
|
|
status = "Information"
|
|
|
|
|
except AttributeError:
|
|
|
|
|
msg = f"No file was selected."
|
|
|
|
|
status = "Error"
|
|
|
|
|
dlg = AlertPop(message=msg, status=status)
|
|
|
|
|
dlg.exec()
|
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Landon Wark