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hitpicking complete, pre-addition of WW-Arctic parsers and models.

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Landon Wark
2023-05-31 09:44:20 -05:00
parent 01d95e80f5
commit 1d6823705c
17 changed files with 334 additions and 247 deletions
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101
src/submissions/frontend/custom_widgets/sub_details.py
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@@ -3,6 +3,8 @@ Contains widgets specific to the submission summary and submission details.
'''
import base64
from datetime import datetime
from io import BytesIO
import math
from PyQt6 import QtPrintSupport
from PyQt6.QtWidgets import (
QVBoxLayout, QDialog, QTableView,
@@ -10,16 +12,18 @@ from PyQt6.QtWidgets import (
QMessageBox, QFileDialog, QMenu, QLabel,
QDialogButtonBox, QToolBar, QMainWindow
)
from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel
from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel, QItemSelectionModel
from PyQt6.QtGui import QFontMetrics, QAction, QCursor, QPixmap, QPainter
from backend.db import submissions_to_df, lookup_submission_by_id, delete_submission_by_id, lookup_submission_by_rsl_num
from backend.db import submissions_to_df, lookup_submission_by_id, delete_submission_by_id, lookup_submission_by_rsl_num, hitpick_plate
# from backend.misc import hitpick_plate
from backend.excel import make_hitpicks
from jinja2 import Environment, FileSystemLoader
from xhtml2pdf import pisa
import sys
from pathlib import Path
import logging
from .pop_ups import QuestionAsker
from ..visualizations import make_plate_barcode
from .pop_ups import QuestionAsker, AlertPop
from ..visualizations import make_plate_barcode, make_plate_map
from getpass import getuser
logger = logging.getLogger(f"submissions.{__name__}")
@@ -92,6 +96,7 @@ class SubmissionsSheet(QTableView):
self.resizeColumnsToContents()
self.resizeRowsToContents()
self.setSortingEnabled(True)
self.doubleClicked.connect(self.show_details)
def setData(self) -> None:
@@ -111,10 +116,8 @@ class SubmissionsSheet(QTableView):
pass
proxyModel = QSortFilterProxyModel()
proxyModel.setSourceModel(pandasModel(self.data))
# self.model = pandasModel(self.data)
# self.setModel(self.model)
self.setModel(proxyModel)
# self.resize(800,600)
def show_details(self) -> None:
"""
@@ -124,7 +127,7 @@ class SubmissionsSheet(QTableView):
value = index.sibling(index.row(),0).data()
dlg = SubmissionDetails(ctx=self.ctx, id=value)
if dlg.exec():
pass
pass
def create_barcode(self) -> None:
index = (self.selectionModel().currentIndex())
@@ -155,14 +158,17 @@ class SubmissionsSheet(QTableView):
detailsAction = QAction('Details', self)
barcodeAction = QAction("Print Barcode", self)
commentAction = QAction("Add Comment", self)
hitpickAction = QAction("Hitpicks", self)
renameAction.triggered.connect(lambda: self.delete_item(event))
detailsAction.triggered.connect(lambda: self.show_details())
barcodeAction.triggered.connect(lambda: self.create_barcode())
commentAction.triggered.connect(lambda: self.add_comment())
hitpickAction.triggered.connect(lambda: self.hit_pick())
self.menu.addAction(detailsAction)
self.menu.addAction(renameAction)
self.menu.addAction(barcodeAction)
self.menu.addAction(commentAction)
self.menu.addAction(hitpickAction)
# add other required actions
self.menu.popup(QCursor.pos())
@@ -185,7 +191,63 @@ class SubmissionsSheet(QTableView):
self.setData()
def hit_pick(self):
"""
Extract positive samples from submissions with PCR results and export to csv.
NOTE: For this to work for arbitrary samples, positive samples must have 'positive' in their name
"""
# Get all selected rows
indices = self.selectionModel().selectedIndexes()
# convert to id numbers
indices = [index.sibling(index.row(), 0).data() for index in indices]
# biomek can handle 4 plates maximum
if len(indices) > 4:
logger.error(f"Error: Had to truncate number of plates to 4.")
indices = indices[:4]
# lookup ids in the database
subs = [lookup_submission_by_id(self.ctx, id) for id in indices]
# full list of samples
dicto = []
# list to contain plate images
images = []
for iii, sub in enumerate(subs):
# second check to make sure there aren't too many plates
if iii > 3:
logger.error(f"Error: Had to truncate number of plates to 4.")
continue
plate_dicto = hitpick_plate(submission=sub, plate_number=iii+1)
if plate_dicto == None:
continue
image = make_plate_map(plate_dicto)
images.append(image)
for item in plate_dicto:
if len(dicto) < 94:
dicto.append(item)
else:
logger.error(f"We had to truncate the number of samples to 94.")
logger.debug(f"We found {len(dicto)} to hitpick")
msg = AlertPop(message=f"We found {len(dicto)} samples to hitpick", status="INFORMATION")
msg.exec()
# convert all samples to dataframe
df = make_hitpicks(dicto)
logger.debug(f"Size of the dataframe: {df.size}")
if df.size == 0:
return
date = datetime.strftime(datetime.today(), "%Y-%m-%d")
# ask for filename and save as csv.
home_dir = Path(self.ctx["directory_path"]).joinpath(f"Hitpicks_{date}.csv").resolve().__str__()
fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".csv")[0])
if fname.__str__() == ".":
logger.debug("Saving csv was cancelled.")
return
df.to_csv(fname.__str__(), index=False)
# show plate maps
for image in images:
try:
image.show()
except Exception as e:
logger.error(f"Could not show image: {e}.")
class SubmissionDetails(QDialog):
"""
@@ -239,7 +301,17 @@ class SubmissionDetails(QDialog):
Renders submission to html, then creates and saves .pdf file to user selected file.
"""
template = env.get_template("submission_details.html")
# make barcode because, reasons
self.base_dict['barcode'] = base64.b64encode(make_plate_barcode(self.base_dict['Plate Number'], width=120, height=30)).decode('utf-8')
sub = lookup_submission_by_rsl_num(ctx=self.ctx, rsl_num=self.base_dict['Plate Number'])
plate_dicto = hitpick_plate(sub)
platemap = make_plate_map(plate_dicto)
logger.debug(f"platemap: {platemap}")
image_io = BytesIO()
platemap.save(image_io, 'JPEG')
platemap.save("test.jpg", 'JPEG')
self.base_dict['platemap'] = base64.b64encode(image_io.getvalue()).decode('utf-8')
logger.debug(self.base_dict)
html = template.render(sub=self.base_dict)
home_dir = Path(self.ctx["directory_path"]).joinpath(f"Submission_Details_{self.base_dict['Plate Number']}.pdf").resolve().__str__()
fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".pdf")[0])
@@ -269,18 +341,10 @@ class BarcodeWindow(QDialog):
# creating label
self.label = QLabel()
self.img = make_plate_barcode(rsl_num)
# logger.debug(dir(img), img.contents[0])
# fp = BytesIO().read()
# img.save(formats=['png'], fnRoot=fp)
# pixmap = QPixmap("C:\\Users\\lwark\\Documents\\python\\submissions\\src\\Drawing000.png")
self.pixmap = QPixmap()
# self.pixmap.loadFromData(self.img.asString("bmp"))
self.pixmap.loadFromData(self.img)
# adding image to label
self.label.setPixmap(self.pixmap)
# Optional, resize label to image size
# self.label.resize(self.pixmap.width(), self.pixmap.height())
# self.label.resize(200, 200)
# show all the widgets]
QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
self.buttonBox = QDialogButtonBox(QBtn)
@@ -300,8 +364,6 @@ class BarcodeWindow(QDialog):
adds items to menu bar
"""
toolbar = QToolBar("My main toolbar")
# self.addToolBar(toolbar)
# self.layout.setToolBar(toolbar)
toolbar.addAction(self.printAction)
@@ -321,7 +383,6 @@ class BarcodeWindow(QDialog):
def print_barcode(self):
printer = QtPrintSupport.QPrinter()
dialog = QtPrintSupport.QPrintDialog(printer)
if dialog.exec():
self.handle_paint_request(printer, self.pixmap.toImage())