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added kraken data to details.

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This commit is contained in:
Landon Wark
2023-02-06 13:39:35 -06:00
parent 7fb5bb12f3
commit 963ac7d4a4
11 changed files with 177 additions and 24 deletions
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20
src/submissions/frontend/__init__.py
View File

@@ -35,6 +35,7 @@ import numpy
from frontend.custom_widgets import AddReagentQuestion, AddReagentForm, SubmissionsSheet, ReportDatePicker, KitAdder, ControlsDatePicker, OverwriteSubQuestion
import logging
import difflib
from getpass import getuser
from datetime import date
from frontend.visualizations.charts import create_charts
@@ -65,7 +66,7 @@ class App(QMainWindow):
self._createMenuBar()
self._createToolBar()
self._connectActions()
self.controls_getter()
self._controls_getter()
self.show()
@@ -109,10 +110,10 @@ class App(QMainWindow):
self.addReagentAction.triggered.connect(self.add_reagent)
self.generateReportAction.triggered.connect(self.generateReport)
self.addKitAction.triggered.connect(self.add_kit)
self.table_widget.control_typer.currentIndexChanged.connect(self.controls_getter)
self.table_widget.mode_typer.currentIndexChanged.connect(self.controls_getter)
self.table_widget.datepicker.start_date.dateChanged.connect(self.controls_getter)
self.table_widget.datepicker.end_date.dateChanged.connect(self.controls_getter)
self.table_widget.control_typer.currentIndexChanged.connect(self._controls_getter)
self.table_widget.mode_typer.currentIndexChanged.connect(self._controls_getter)
self.table_widget.datepicker.start_date.dateChanged.connect(self._controls_getter)
self.table_widget.datepicker.end_date.dateChanged.connect(self._controls_getter)
def importSubmission(self):
@@ -268,6 +269,7 @@ class App(QMainWindow):
# logger.debug(info)
# move samples into preliminary submission dict
info['samples'] = self.samples
info['uploaded_by'] = getuser()
# construct submission object
logger.debug(f"Here is the info_dict: {pprint.pformat(info)}")
base_submission, output = construct_submission_info(ctx=self.ctx, info_dict=info)
@@ -445,7 +447,7 @@ class App(QMainWindow):
def controls_getter(self):
def _controls_getter(self):
"""
Lookup controls from database and send to chartmaker
"""
@@ -476,14 +478,14 @@ class App(QMainWindow):
with QSignalBlocker(self.table_widget.sub_typer) as blocker:
self.table_widget.sub_typer.addItems(sub_types)
self.table_widget.sub_typer.setEnabled(True)
self.table_widget.sub_typer.currentTextChanged.connect(self.chart_maker)
self.table_widget.sub_typer.currentTextChanged.connect(self._chart_maker)
else:
self.table_widget.sub_typer.clear()
self.table_widget.sub_typer.setEnabled(False)
self.chart_maker()
self._chart_maker()
def chart_maker(self):
def _chart_maker(self):
"""
Creates plotly charts for webview
"""

52
src/submissions/frontend/custom_widgets/__init__.py
View File

@@ -5,14 +5,14 @@ from PyQt6.QtWidgets import (
QTextEdit, QSizePolicy, QWidget,
QGridLayout, QPushButton, QSpinBox,
QScrollBar, QScrollArea, QHBoxLayout,
QMessageBox
QMessageBox, QFileDialog, QToolBar
)
from PyQt6.QtCore import Qt, QDate, QAbstractTableModel, QSize
from PyQt6.QtGui import QFontMetrics
from PyQt6.QtGui import QFontMetrics, QAction
from backend.db import get_all_reagenttype_names, submissions_to_df, lookup_submission_by_id, lookup_all_sample_types, create_kit_from_yaml
from jinja2 import Environment, FileSystemLoader
from xhtml2pdf import pisa
import sys
from pathlib import Path
import logging
@@ -212,23 +212,25 @@ class SubmissionDetails(QDialog):
def __init__(self, ctx:dict, id:int) -> None:
super().__init__()
self.ctx = ctx
self.setWindowTitle("Submission Details")
# create scrollable interior
interior = QScrollArea()
interior.setParent(self)
# get submision from db
data = lookup_submission_by_id(ctx=ctx, id=id)
base_dict = data.to_dict()
self.base_dict = data.to_dict()
logger.debug(f"Base dict: {self.base_dict}")
# don't want id
del base_dict['id']
del self.base_dict['id']
# convert sub objects to dicts
base_dict['reagents'] = [item.to_sub_dict() for item in data.reagents]
base_dict['samples'] = [item.to_sub_dict() for item in data.samples]
self.base_dict['reagents'] = [item.to_sub_dict() for item in data.reagents]
self.base_dict['samples'] = [item.to_sub_dict() for item in data.samples]
# retrieve jinja template
template = env.get_template("submission_details.txt")
# render using object dict
text = template.render(sub=base_dict)
text = template.render(sub=self.base_dict)
# create text field
txt_editor = QTextEdit(self)
txt_editor.setReadOnly(True)
@@ -247,7 +249,37 @@ class SubmissionDetails(QDialog):
interior.setWidget(txt_editor)
self.layout = QVBoxLayout()
self.setFixedSize(w, 900)
self.layout.addWidget(interior)
btn = QPushButton("Export PDF")
btn.setParent(self)
btn.setFixedWidth(w)
btn.clicked.connect(self.export)
# def _create_actions(self):
# self.exportAction = QAction("Export", self)
def export(self):
template = env.get_template("submission_details.html")
html = template.render(sub=self.base_dict)
# logger.debug(f"Submission details: {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])
# logger.debug(f"report output name: {fname}")
# df.to_excel(fname, engine='openpyxl')
if fname.__str__() == ".":
logger.debug("Saving pdf was cancelled.")
return
try:
with open(fname, "w+b") as f:
pisa.CreatePDF(html, 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()

2
src/submissions/frontend/visualizations/charts.py
View File

@@ -94,7 +94,7 @@ def generic_figure_markers(fig:Figure, modes:list=[], ytitle:str|None=None) -> F
])
)
)
logger.debug(f"Returning figure {fig}")
# logger.debug(f"Returning figure {fig}")
assert type(fig) == Figure
return fig