Commit pre-refactor for code cleanup.
This commit is contained in:
Landon Wark
@@ -1,18 +1,17 @@
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from datetime import date
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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, QTableView,
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QTextEdit, QSizePolicy, QWidget,
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QDialogButtonBox, QDateEdit, QSizePolicy, QWidget,
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QGridLayout, QPushButton, QSpinBox,
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QScrollBar, QScrollArea, QHBoxLayout,
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QMessageBox, QFileDialog, QToolBar
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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, QAbstractTableModel, QSize
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from PyQt6.QtGui import QFontMetrics, QAction
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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, submissions_to_df, lookup_submission_by_id, lookup_all_sample_types, create_kit_from_yaml
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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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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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@@ -26,55 +25,12 @@ else:
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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) -> None:
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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.\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) -> None:
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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 AddReagentForm(QDialog):
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"""
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dialog to add gather info about new reagent
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"""
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def __init__(self, ctx:dict, reagent_lot:str|None, reagent_type:str|None) -> None:
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def __init__(self, ctx:dict, reagent_lot:str|None, reagent_type:str|None, expiry:date|None=None) -> None:
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super().__init__()
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if reagent_lot == None:
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@@ -92,7 +48,10 @@ class AddReagentForm(QDialog):
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lot_input.setText(reagent_lot)
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# get expiry info
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exp_input = QDateEdit(calendarPopup=True)
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exp_input.setDate(QDate.currentDate())
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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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type_input = QComboBox()
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type_input.addItems([item.replace("_", " ").title() for item in get_all_reagenttype_names(ctx=ctx)])
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@@ -117,172 +76,6 @@ class AddReagentForm(QDialog):
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self.setLayout(self.layout)
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class pandasModel(QAbstractTableModel):
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"""
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pandas model for inserting summary sheet into gui
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"""
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def __init__(self, data) -> None:
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QAbstractTableModel.__init__(self)
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self._data = data
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def rowCount(self, parent=None) -> int:
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"""
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does what it says
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Args:
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parent (_type_, optional): _description_. Defaults to None.
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Returns:
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int: number of rows in data
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"""
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return self._data.shape[0]
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def columnCount(self, parnet=None) -> int:
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"""
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does what it says
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Args:
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parnet (_type_, optional): _description_. Defaults to None.
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Returns:
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int: number of columns in data
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"""
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return self._data.shape[1]
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def data(self, index, role=Qt.ItemDataRole.DisplayRole) -> str|None:
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if index.isValid():
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if role == Qt.ItemDataRole.DisplayRole:
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return str(self._data.iloc[index.row(), index.column()])
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return None
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def headerData(self, col, orientation, role):
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if orientation == Qt.Orientation.Horizontal and role == Qt.ItemDataRole.DisplayRole:
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return self._data.columns[col]
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return None
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class SubmissionsSheet(QTableView):
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"""
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presents submission summary to user in tab1
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"""
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def __init__(self, ctx:dict) -> None:
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"""
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initialize
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Args:
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ctx (dict): settings passed from gui
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"""
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super().__init__()
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self.ctx = ctx
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self.setData()
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self.resizeColumnsToContents()
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self.resizeRowsToContents()
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# self.clicked.connect(self.test)
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self.doubleClicked.connect(self.show_details)
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def setData(self) -> None:
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"""
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sets data in model
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"""
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self.data = submissions_to_df(ctx=self.ctx)
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self.model = pandasModel(self.data)
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self.setModel(self.model)
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# self.resize(800,600)
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def show_details(self) -> None:
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"""
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creates detailed data to show in seperate window
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"""
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index=(self.selectionModel().currentIndex())
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# logger.debug(index)
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value=index.sibling(index.row(),0).data()
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dlg = SubmissionDetails(ctx=self.ctx, id=value)
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# dlg.show()
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if dlg.exec():
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pass
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class SubmissionDetails(QDialog):
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"""
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a window showing text details of submission
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"""
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def __init__(self, ctx:dict, id:int) -> None:
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super().__init__()
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self.ctx = ctx
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self.setWindowTitle("Submission Details")
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# create scrollable interior
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interior = QScrollArea()
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interior.setParent(self)
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# get submision from db
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data = lookup_submission_by_id(ctx=ctx, id=id)
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self.base_dict = data.to_dict()
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logger.debug(f"Base dict: {self.base_dict}")
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# don't want id
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del self.base_dict['id']
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# convert sub objects to dicts
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self.base_dict['reagents'] = [item.to_sub_dict() for item in data.reagents]
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self.base_dict['samples'] = [item.to_sub_dict() for item in data.samples]
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# retrieve jinja template
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template = env.get_template("submission_details.txt")
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# render using object dict
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text = template.render(sub=self.base_dict)
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# create text field
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txt_editor = QTextEdit(self)
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txt_editor.setReadOnly(True)
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txt_editor.document().setPlainText(text)
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# resize
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font = txt_editor.document().defaultFont()
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fontMetrics = QFontMetrics(font)
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textSize = fontMetrics.size(0, txt_editor.toPlainText())
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w = textSize.width() + 10
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h = textSize.height() + 10
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txt_editor.setMinimumSize(w, h)
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txt_editor.setMaximumSize(w, h)
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txt_editor.resize(w, h)
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interior.resize(w,900)
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txt_editor.setText(text)
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interior.setWidget(txt_editor)
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self.layout = QVBoxLayout()
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self.setFixedSize(w, 900)
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btn = QPushButton("Export PDF")
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btn.setParent(self)
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btn.setFixedWidth(w)
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btn.clicked.connect(self.export)
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# def _create_actions(self):
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# self.exportAction = QAction("Export", self)
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def export(self):
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template = env.get_template("submission_details.html")
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html = template.render(sub=self.base_dict)
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# logger.debug(f"Submission details: {self.base_dict}")
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home_dir = Path(self.ctx["directory_path"]).joinpath(f"Submission_Details_{self.base_dict['Plate Number']}.pdf").resolve().__str__()
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fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".pdf")[0])
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# logger.debug(f"report output name: {fname}")
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# df.to_excel(fname, engine='openpyxl')
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if fname.__str__() == ".":
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logger.debug("Saving pdf was cancelled.")
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return
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try:
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with open(fname, "w+b") as f:
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pisa.CreatePDF(html, dest=f)
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except PermissionError as e:
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logger.error(f"Error saving pdf: {e}")
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msg = QMessageBox()
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msg.setText("Permission Error")
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msg.setInformativeText(f"Looks like {fname.__str__()} is open.\nPlease close it and try again.")
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msg.setWindowTitle("Permission Error")
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msg.exec()
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class ReportDatePicker(QDialog):
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"""
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custom dialog to ask for report start/stop dates
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@@ -467,7 +260,7 @@ class ControlsDatePicker(QWidget):
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self.start_date = QDateEdit(calendarPopup=True)
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# start date is three month prior to end date by default
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threemonthsago = QDate.currentDate().addDays(-90)
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threemonthsago = QDate.currentDate().addDays(-60)
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self.start_date.setDate(threemonthsago)
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self.end_date = QDateEdit(calendarPopup=True)
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self.end_date.setDate(QDate.currentDate())
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