Pre-sample/control connect
This commit is contained in:
Landon Wark
@@ -1,15 +1,15 @@
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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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import base64, logging, json
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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 pprint import pformat
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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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QMessageBox, 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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@@ -17,19 +17,16 @@ 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, Report, Result
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from tools import jinja_template_loading
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from backend.excel import make_report_html, make_report_xlsx
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from tools import check_if_app, Report, Result, jinja_template_loading, get_first_blank_df_row, row_map
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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 .pop_ups import QuestionAsker
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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 openpyxl.worksheet.worksheet import Worksheet
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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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@@ -161,16 +158,19 @@ class SubmissionsSheet(QTableView):
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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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backupAction = QAction("Backup", 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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backupAction.triggered.connect(lambda: self.regenerate_submission_form())
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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(backupAction)
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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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@@ -193,64 +193,64 @@ class SubmissionsSheet(QTableView):
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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 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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@@ -420,6 +420,7 @@ class SubmissionsSheet(QTableView):
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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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logger.debug(f"Records: {pformat(records)}")
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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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@@ -430,23 +431,42 @@ class SubmissionsSheet(QTableView):
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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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worksheet: Worksheet = writer.sheets['Report']
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for idx, col in enumerate(summary_df, start=1): # 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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# worksheet.column_dimensions[get_column_letter(idx=idx)].width = max_len
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# Convert idx to letter
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col_letter = chr(ord('@') + idx)
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worksheet.column_dimensions[col_letter].width = max_len
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except ValueError:
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pass
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blank_row = get_first_blank_df_row(summary_df) + 1
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logger.debug(f"Blank row index = {blank_row}")
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for col in range(3,6):
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col_letter = row_map[col]
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worksheet.cell(row=blank_row, column=col, value=f"=SUM({col_letter}2:{col_letter}{str(blank_row-1)})")
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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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def regenerate_submission_form(self):
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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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sub = BasicSubmission.query(id=value)
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fname = select_save_file(self, default_name=sub.to_pydantic().construct_filename(), extension="xlsx")
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sub.backup(fname=fname)
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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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@@ -466,7 +486,7 @@ class SubmissionDetails(QDialog):
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# get submision from db
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# sub = lookup_submissions(ctx=ctx, id=id)
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sub = BasicSubmission.query(id=id)
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logger.debug(f"Submission details data:\n{pprint.pformat(sub.to_dict())}")
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logger.debug(f"Submission details data:\n{pformat(sub.to_dict())}")
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self.base_dict = sub.to_dict(full_data=True)
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# don't want id
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del self.base_dict['id']
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@@ -611,8 +631,11 @@ class SubmissionComment(QDialog):
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super().__init__(parent)
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# self.ctx = ctx
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self.app = parent.parent().parent().parent().parent().parent().parent
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print(f"App: {self.app}")
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try:
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self.app = parent.parent().parent().parent().parent().parent().parent
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print(f"App: {self.app}")
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except AttributeError:
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pass
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self.rsl = rsl
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self.setWindowTitle(f"{self.rsl} Submission Comment")
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# create text field
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