Large scale frontend refactor
This commit is contained in:
Landon Wark
646
src/submissions/frontend/widgets/submission_table.py
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646
src/submissions/frontend/widgets/submission_table.py
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@@ -0,0 +1,646 @@
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'''
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Contains widgets specific to the submission summary and submission details.
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'''
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import base64
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from datetime import datetime
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from io import BytesIO
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import pprint
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from PyQt6 import QtPrintSupport
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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, QLabel,
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QDialogButtonBox, QToolBar
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)
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from PyQt6.QtWebEngineWidgets import QWebEngineView
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from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel
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from PyQt6.QtGui import QAction, QCursor, QPixmap, QPainter
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from backend.db.functions import submissions_to_df
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from backend.db.models import BasicSubmission
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from backend.excel import make_hitpicks, make_report_html, make_report_xlsx
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from tools import check_if_app, Settings, Report, Result
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from tools import jinja_template_loading
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from xhtml2pdf import pisa
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from pathlib import Path
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import logging
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from .pop_ups import QuestionAsker, AlertPop
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from ..visualizations import make_plate_barcode, make_plate_map, make_plate_map_html
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from .functions import select_save_file, select_open_file
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from .misc import ReportDatePicker
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import pandas as pd
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from getpass import getuser
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import json
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logger = logging.getLogger(f"submissions.{__name__}")
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env = jinja_template_loading()
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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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NOTE: Copied from Stack Overflow. I have no idea how it actually works.
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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, 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 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, parent) -> 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__(parent)
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self.app = self.parent()
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# self.ctx = ctx
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self.report = Report()
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self.setData()
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self.resizeColumnsToContents()
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self.resizeRowsToContents()
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self.setSortingEnabled(True)
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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()
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try:
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self.data['id'] = self.data['id'].apply(str)
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self.data['id'] = self.data['id'].str.zfill(3)
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except KeyError:
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pass
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proxyModel = QSortFilterProxyModel()
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proxyModel.setSourceModel(pandasModel(self.data))
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self.setModel(proxyModel)
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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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logger.debug(f"Sheet.app: {self.app}")
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index = (self.selectionModel().currentIndex())
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value = index.sibling(index.row(),0).data()
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dlg = SubmissionDetails(parent=self, id=value)
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if dlg.exec():
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pass
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def create_barcode(self) -> None:
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"""
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Generates a window for displaying barcode
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"""
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index = (self.selectionModel().currentIndex())
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value = index.sibling(index.row(),1).data()
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logger.debug(f"Selected value: {value}")
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dlg = BarcodeWindow(value)
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if dlg.exec():
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dlg.print_barcode()
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def add_comment(self) -> None:
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"""
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Generates a text editor window.
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"""
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index = (self.selectionModel().currentIndex())
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value = index.sibling(index.row(),1).data()
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logger.debug(f"Selected value: {value}")
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dlg = SubmissionComment(ctx=self.ctx, rsl=value)
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if dlg.exec():
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dlg.add_comment()
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def contextMenuEvent(self, event):
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"""
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Creates actions for right click menu events.
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Args:
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event (_type_): the item of interest
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"""
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self.menu = QMenu(self)
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renameAction = QAction('Delete', self)
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detailsAction = QAction('Details', self)
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barcodeAction = QAction("Print Barcode", self)
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commentAction = QAction("Add Comment", self)
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hitpickAction = QAction("Hitpicks", self)
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renameAction.triggered.connect(lambda: self.delete_item(event))
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detailsAction.triggered.connect(lambda: self.show_details())
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barcodeAction.triggered.connect(lambda: self.create_barcode())
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commentAction.triggered.connect(lambda: self.add_comment())
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hitpickAction.triggered.connect(lambda: self.hit_pick())
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self.menu.addAction(detailsAction)
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self.menu.addAction(renameAction)
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self.menu.addAction(barcodeAction)
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self.menu.addAction(commentAction)
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self.menu.addAction(hitpickAction)
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# add other required actions
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self.menu.popup(QCursor.pos())
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def delete_item(self, event):
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"""
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Confirms user deletion and sends id to backend for deletion.
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Args:
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event (_type_): the item of interest
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"""
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index = (self.selectionModel().currentIndex())
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value = index.sibling(index.row(),0).data()
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logger.debug(index)
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msg = QuestionAsker(title="Delete?", message=f"Are you sure you want to delete {index.sibling(index.row(),1).data()}?\n")
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if msg.exec():
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# delete_submission(id=value)
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BasicSubmission.query(id=value).delete()
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else:
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return
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self.setData()
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def hit_pick(self):
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"""
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Extract positive samples from submissions with PCR results and export to csv.
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NOTE: For this to work for arbitrary samples, positive samples must have 'positive' in their name
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"""
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# Get all selected rows
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indices = self.selectionModel().selectedIndexes()
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# convert to id numbers
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indices = [index.sibling(index.row(), 0).data() for index in indices]
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# biomek can handle 4 plates maximum
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if len(indices) > 4:
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logger.error(f"Error: Had to truncate number of plates to 4.")
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indices = indices[:4]
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# lookup ids in the database
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# subs = [lookup_submissions(ctx=self.ctx, id=id) for id in indices]
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subs = [BasicSubmission.query(id=id) for id in indices]
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# full list of samples
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dicto = []
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# list to contain plate images
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images = []
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for iii, sub in enumerate(subs):
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# second check to make sure there aren't too many plates
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if iii > 3:
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logger.error(f"Error: Had to truncate number of plates to 4.")
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continue
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plate_dicto = sub.hitpick_plate(plate_number=iii+1)
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if plate_dicto == None:
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continue
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image = make_plate_map(plate_dicto)
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images.append(image)
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for item in plate_dicto:
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if len(dicto) < 94:
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dicto.append(item)
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else:
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logger.error(f"We had to truncate the number of samples to 94.")
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logger.debug(f"We found {len(dicto)} to hitpick")
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# convert all samples to dataframe
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df = make_hitpicks(dicto)
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df = df[df.positive != False]
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logger.debug(f"Size of the dataframe: {df.shape[0]}")
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msg = AlertPop(message=f"We found {df.shape[0]} samples to hitpick", status="INFORMATION")
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msg.exec()
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if df.size == 0:
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return
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date = datetime.strftime(datetime.today(), "%Y-%m-%d")
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# ask for filename and save as csv.
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home_dir = Path(self.ctx.directory_path).joinpath(f"Hitpicks_{date}.csv").resolve().__str__()
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fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".csv")[0])
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if fname.__str__() == ".":
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logger.debug("Saving csv was cancelled.")
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return
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df.to_csv(fname.__str__(), index=False)
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# show plate maps
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for image in images:
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try:
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image.show()
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except Exception as e:
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logger.error(f"Could not show image: {e}.")
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def link_extractions(self):
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self.link_extractions_function()
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self.app.report.add_result(self.report)
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self.report = Report()
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self.app.result_reporter()
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def link_extractions_function(self):
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"""
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Link extractions from runlogs to imported submissions
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Args:
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obj (QMainWindow): original app window
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Returns:
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Tuple[QMainWindow, dict]: Collection of new main app window and result dict
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"""
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fname = select_open_file(self, file_extension="csv")
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with open(fname.__str__(), 'r') as f:
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# split csv on commas
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runs = [col.strip().split(",") for col in f.readlines()]
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count = 0
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for run in runs:
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new_run = dict(
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start_time=run[0].strip(),
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rsl_plate_num=run[1].strip(),
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sample_count=run[2].strip(),
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status=run[3].strip(),
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experiment_name=run[4].strip(),
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end_time=run[5].strip()
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)
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# elution columns are item 6 in the comma split list to the end
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for ii in range(6, len(run)):
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new_run[f"column{str(ii-5)}_vol"] = run[ii]
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# Lookup imported submissions
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# sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=new_run['rsl_plate_num'])
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# sub = lookup_submissions(ctx=obj.ctx, rsl_number=new_run['rsl_plate_num'])
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sub = BasicSubmission.query(rsl_number=new_run['rsl_plate_num'])
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# If no such submission exists, move onto the next run
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if sub == None:
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continue
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try:
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logger.debug(f"Found submission: {sub.rsl_plate_num}")
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count += 1
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except AttributeError:
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continue
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if sub.extraction_info != None:
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existing = json.loads(sub.extraction_info)
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else:
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existing = None
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# Check if the new info already exists in the imported submission
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try:
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if json.dumps(new_run) in sub.extraction_info:
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logger.debug(f"Looks like we already have that info.")
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continue
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except TypeError:
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pass
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# Update or create the extraction info
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if existing != None:
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try:
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logger.debug(f"Updating {type(existing)}: {existing} with {type(new_run)}: {new_run}")
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existing.append(new_run)
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logger.debug(f"Setting: {existing}")
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sub.extraction_info = json.dumps(existing)
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except TypeError:
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logger.error(f"Error updating!")
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sub.extraction_info = json.dumps([new_run])
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logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.extraction_info}")
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else:
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sub.extraction_info = json.dumps([new_run])
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sub.save()
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self.report.add_result(Result(msg=f"We added {count} logs to the database.", status='Information'))
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def link_pcr(self):
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self.link_pcr_function()
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self.app.report.add_result(self.report)
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self.report = Report()
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self.app.result_reporter()
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def link_pcr_function(self):
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"""
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Link PCR data from run logs to an imported submission
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Args:
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obj (QMainWindow): original app window
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Returns:
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Tuple[QMainWindow, dict]: Collection of new main app window and result dict
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"""
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fname = select_open_file(self, file_extension="csv")
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with open(fname.__str__(), 'r') as f:
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# split csv rows on comma
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runs = [col.strip().split(",") for col in f.readlines()]
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count = 0
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for run in runs:
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new_run = dict(
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start_time=run[0].strip(),
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rsl_plate_num=run[1].strip(),
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biomek_status=run[2].strip(),
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quant_status=run[3].strip(),
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experiment_name=run[4].strip(),
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end_time=run[5].strip()
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)
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# lookup imported submission
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# sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=new_run['rsl_plate_num'])
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# sub = lookup_submissions(ctx=obj.ctx, rsl_number=new_run['rsl_plate_num'])
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sub = BasicSubmission.query(rsl_number=new_run['rsl_plate_num'])
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# if imported submission doesn't exist move on to next run
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if sub == None:
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continue
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try:
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logger.debug(f"Found submission: {sub.rsl_plate_num}")
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except AttributeError:
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continue
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# check if pcr_info already exists
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if hasattr(sub, 'pcr_info') and sub.pcr_info != None:
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existing = json.loads(sub.pcr_info)
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else:
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existing = None
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# check if this entry already exists in imported submission
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try:
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if json.dumps(new_run) in sub.pcr_info:
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logger.debug(f"Looks like we already have that info.")
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continue
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else:
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count += 1
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except TypeError:
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logger.error(f"No json to dump")
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if existing != None:
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try:
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logger.debug(f"Updating {type(existing)}: {existing} with {type(new_run)}: {new_run}")
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existing.append(new_run)
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logger.debug(f"Setting: {existing}")
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sub.pcr_info = json.dumps(existing)
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except TypeError:
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logger.error(f"Error updating!")
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sub.pcr_info = json.dumps([new_run])
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logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.pcr_info}")
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else:
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sub.pcr_info = json.dumps([new_run])
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sub.save()
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self.report.add_result(Result(msg=f"We added {count} logs to the database.", status='Information'))
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def generate_report(self):
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self.generate_report_function()
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self.app.report.add_result(self.report)
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self.report = Report()
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self.app.result_reporter()
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def generate_report_function(self):
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"""
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Generate a summary of activities for a time period
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Args:
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obj (QMainWindow): original app window
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Returns:
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Tuple[QMainWindow, dict]: Collection of new main app window and result dict
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"""
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report = Report()
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# ask for date ranges
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dlg = ReportDatePicker()
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if dlg.exec():
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info = dlg.parse_form()
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logger.debug(f"Report info: {info}")
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# find submissions based on date range
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subs = BasicSubmission.query(start_date=info['start_date'], end_date=info['end_date'])
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# convert each object to dict
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records = [item.report_dict() for item in subs]
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# make dataframe from record dictionaries
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detailed_df, summary_df = make_report_xlsx(records=records)
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html = make_report_html(df=summary_df, start_date=info['start_date'], end_date=info['end_date'])
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# get save location of report
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fname = select_save_file(obj=self, default_name=f"Submissions_Report_{info['start_date']}-{info['end_date']}.pdf", extension="pdf")
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with open(fname, "w+b") as f:
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pisa.CreatePDF(html, dest=f)
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writer = pd.ExcelWriter(fname.with_suffix(".xlsx"), engine='openpyxl')
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summary_df.to_excel(writer, sheet_name="Report")
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detailed_df.to_excel(writer, sheet_name="Details", index=False)
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worksheet = writer.sheets['Report']
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for idx, col in enumerate(summary_df): # loop through all columns
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series = summary_df[col]
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max_len = max((
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series.astype(str).map(len).max(), # len of largest item
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len(str(series.name)) # len of column name/header
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)) + 20 # adding a little extra space
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try:
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worksheet.column_dimensions[get_column_letter(idx)].width = max_len
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except ValueError:
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pass
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for cell in worksheet['D']:
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if cell.row > 1:
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cell.style = 'Currency'
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writer.close()
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self.report.add_result(report)
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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, parent, id:int) -> None:
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||||
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||||
super().__init__(parent)
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||||
# self.ctx = ctx
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||||
self.setWindowTitle("Submission Details")
|
||||
# create scrollable interior
|
||||
interior = QScrollArea()
|
||||
interior.setParent(self)
|
||||
# get submision from db
|
||||
# sub = lookup_submissions(ctx=ctx, id=id)
|
||||
sub = BasicSubmission.query(id=id)
|
||||
logger.debug(f"Submission details data:\n{pprint.pformat(sub.to_dict())}")
|
||||
self.base_dict = sub.to_dict(full_data=True)
|
||||
# don't want id
|
||||
del self.base_dict['id']
|
||||
logger.debug(f"Creating barcode.")
|
||||
if not check_if_app():
|
||||
self.base_dict['barcode'] = base64.b64encode(make_plate_barcode(self.base_dict['Plate Number'], width=120, height=30)).decode('utf-8')
|
||||
logger.debug(f"Hitpicking plate...")
|
||||
self.plate_dicto = sub.hitpick_plate()
|
||||
logger.debug(f"Making platemap...")
|
||||
self.base_dict['platemap'] = make_plate_map_html(self.plate_dicto)
|
||||
# logger.debug(f"Platemap: {self.base_dict['platemap']}")
|
||||
# logger.debug(f"platemap: {platemap}")
|
||||
# image_io = BytesIO()
|
||||
# try:
|
||||
# platemap.save(image_io, 'JPEG')
|
||||
# except AttributeError:
|
||||
# logger.error(f"No plate map found for {sub.rsl_plate_num}")
|
||||
# self.base_dict['platemap'] = base64.b64encode(image_io.getvalue()).decode('utf-8')
|
||||
self.template = env.get_template("submission_details.html")
|
||||
self.html = self.template.render(sub=self.base_dict)
|
||||
webview = QWebEngineView()
|
||||
webview.setMinimumSize(900, 500)
|
||||
webview.setMaximumSize(900, 500)
|
||||
webview.setHtml(self.html)
|
||||
self.layout = QVBoxLayout()
|
||||
interior.resize(900, 500)
|
||||
interior.setWidget(webview)
|
||||
self.setFixedSize(900, 500)
|
||||
# button to export a pdf version
|
||||
btn = QPushButton("Export PDF")
|
||||
btn.setParent(self)
|
||||
btn.setFixedWidth(900)
|
||||
btn.clicked.connect(self.export)
|
||||
|
||||
def export(self):
|
||||
"""
|
||||
Renders submission to html, then creates and saves .pdf file to user selected file.
|
||||
"""
|
||||
# try:
|
||||
# home_dir = Path(self.ctx.directory_path).joinpath(f"Submission_Details_{self.base_dict['Plate Number']}.pdf").resolve().__str__()
|
||||
# except FileNotFoundError:
|
||||
# home_dir = Path.home().resolve().__str__()
|
||||
# fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".pdf")[0])
|
||||
# if fname.__str__() == ".":
|
||||
# logger.debug("Saving pdf was cancelled.")
|
||||
# return
|
||||
fname = select_save_file(obj=self, default_name=self.base_dict['Plate Number'], extension="pdf")
|
||||
del self.base_dict['platemap']
|
||||
export_map = make_plate_map(self.plate_dicto)
|
||||
image_io = BytesIO()
|
||||
try:
|
||||
export_map.save(image_io, 'JPEG')
|
||||
except AttributeError:
|
||||
logger.error(f"No plate map found")
|
||||
self.base_dict['export_map'] = base64.b64encode(image_io.getvalue()).decode('utf-8')
|
||||
self.html2 = self.template.render(sub=self.base_dict)
|
||||
try:
|
||||
with open(fname, "w+b") as f:
|
||||
pisa.CreatePDF(self.html2, dest=f)
|
||||
except PermissionError as e:
|
||||
logger.error(f"Error saving pdf: {e}")
|
||||
msg = QMessageBox()
|
||||
msg.setText("Permission Error")
|
||||
msg.setInformativeText(f"Looks like {fname.__str__()} is open.\nPlease close it and try again.")
|
||||
msg.setWindowTitle("Permission Error")
|
||||
msg.exec()
|
||||
|
||||
class BarcodeWindow(QDialog):
|
||||
|
||||
def __init__(self, rsl_num:str):
|
||||
super().__init__()
|
||||
# set the title
|
||||
self.setWindowTitle("Image")
|
||||
self.layout = QVBoxLayout()
|
||||
# setting the geometry of window
|
||||
self.setGeometry(0, 0, 400, 300)
|
||||
# creating label
|
||||
self.label = QLabel()
|
||||
self.img = make_plate_barcode(rsl_num)
|
||||
self.pixmap = QPixmap()
|
||||
self.pixmap.loadFromData(self.img)
|
||||
# adding image to label
|
||||
self.label.setPixmap(self.pixmap)
|
||||
# show all the widgets]
|
||||
QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
|
||||
self.buttonBox = QDialogButtonBox(QBtn)
|
||||
self.buttonBox.accepted.connect(self.accept)
|
||||
self.buttonBox.rejected.connect(self.reject)
|
||||
self.layout.addWidget(self.label)
|
||||
self.layout.addWidget(self.buttonBox)
|
||||
self.setLayout(self.layout)
|
||||
self._createActions()
|
||||
self._createToolBar()
|
||||
self._connectActions()
|
||||
|
||||
|
||||
|
||||
def _createToolBar(self):
|
||||
"""
|
||||
adds items to menu bar
|
||||
"""
|
||||
toolbar = QToolBar("My main toolbar")
|
||||
toolbar.addAction(self.printAction)
|
||||
|
||||
|
||||
def _createActions(self):
|
||||
"""
|
||||
creates actions
|
||||
"""
|
||||
self.printAction = QAction("&Print", self)
|
||||
|
||||
|
||||
def _connectActions(self):
|
||||
"""
|
||||
connect menu and tool bar item to functions
|
||||
"""
|
||||
self.printAction.triggered.connect(self.print_barcode)
|
||||
|
||||
|
||||
def print_barcode(self):
|
||||
"""
|
||||
Sends barcode image to printer.
|
||||
"""
|
||||
printer = QtPrintSupport.QPrinter()
|
||||
dialog = QtPrintSupport.QPrintDialog(printer)
|
||||
if dialog.exec():
|
||||
self.handle_paint_request(printer, self.pixmap.toImage())
|
||||
|
||||
|
||||
def handle_paint_request(self, printer:QtPrintSupport.QPrinter, im):
|
||||
logger.debug(f"Hello from print handler.")
|
||||
painter = QPainter(printer)
|
||||
image = QPixmap.fromImage(im)
|
||||
painter.drawPixmap(120, -20, image)
|
||||
painter.end()
|
||||
|
||||
class SubmissionComment(QDialog):
|
||||
"""
|
||||
a window for adding comment text to a submission
|
||||
"""
|
||||
def __init__(self, ctx:Settings, rsl:str) -> None:
|
||||
|
||||
super().__init__()
|
||||
self.ctx = ctx
|
||||
self.rsl = rsl
|
||||
self.setWindowTitle(f"{self.rsl} Submission Comment")
|
||||
# create text field
|
||||
self.txt_editor = QTextEdit(self)
|
||||
self.txt_editor.setReadOnly(False)
|
||||
self.txt_editor.setText("Add Comment")
|
||||
QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
|
||||
self.buttonBox = QDialogButtonBox(QBtn)
|
||||
self.buttonBox.accepted.connect(self.accept)
|
||||
self.buttonBox.rejected.connect(self.reject)
|
||||
self.layout = QVBoxLayout()
|
||||
self.setFixedSize(400, 300)
|
||||
self.layout.addWidget(self.txt_editor)
|
||||
self.layout.addWidget(self.buttonBox, alignment=Qt.AlignmentFlag.AlignBottom)
|
||||
self.setLayout(self.layout)
|
||||
|
||||
def add_comment(self):
|
||||
"""
|
||||
Adds comment to submission object.
|
||||
"""
|
||||
commenter = getuser()
|
||||
comment = self.txt_editor.toPlainText()
|
||||
dt = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M:%S")
|
||||
full_comment = {"name":commenter, "time": dt, "text": comment}
|
||||
logger.debug(f"Full comment: {full_comment}")
|
||||
# sub = lookup_submission_by_rsl_num(ctx = self.ctx, rsl_num=self.rsl)
|
||||
# sub = lookup_submissions(ctx = self.ctx, rsl_number=self.rsl)
|
||||
sub = BasicSubmission.query(rsl_number=self.rsl)
|
||||
try:
|
||||
sub.comment.append(full_comment)
|
||||
except AttributeError:
|
||||
sub.comment = [full_comment]
|
||||
logger.debug(sub.__dict__)
|
||||
self.ctx.database_session.add(sub)
|
||||
self.ctx.database_session.commit()
|
||||
|
||||
|
||||
Reference in New Issue
Block a user