Added in charts for BC control concentrations.
This commit is contained in:
lwark
@@ -0,0 +1,65 @@
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"""
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Construct turnaround time charts
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"""
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from pprint import pformat
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from . import CustomFigure
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import plotly.express as px
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import pandas as pd
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from PyQt6.QtWidgets import QWidget
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import logging
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from operator import itemgetter
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logger = logging.getLogger(f"submissions.{__name__}")
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class ConcentrationsChart(CustomFigure):
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def __init__(self, df: pd.DataFrame, modes: list, settings: dict,
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ytitle: str | None = None,
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parent: QWidget | None = None,
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months: int = 6):
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super().__init__(df=df, modes=modes, settings=settings)
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self.df = df
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self.construct_chart()
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# if threshold:
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# self.add_hline(y=threshold)
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self.update_layout(showlegend=False)
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def construct_chart(self, df: pd.DataFrame | None = None):
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if df:
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self.df = df
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# logger.debug(f"Constructing concentration chart with df:\n{self.df}")
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try:
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self.df = self.df[self.df.concentration.notnull()]
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self.df = self.df.sort_values(['submitted_date', 'submission'], ascending=[True, True]).reset_index(drop=True)
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self.df = self.df.reset_index().rename(columns={"index": "idx"})
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# logger.debug(f"DF after changes:\n{self.df}")
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scatter = px.scatter(data_frame=self.df, x='submission', y="concentration",
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hover_data=["name", "submission", "submitted_date", "concentration"],
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color="positive", color_discrete_map={True: "red", False: "green"}
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)
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except (ValueError, AttributeError) as e:
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logger.error(f"Error constructing chart: {e}")
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scatter = px.scatter()
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# logger.debug(f"Scatter data: {scatter.data}")
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# self.add_traces(scatter.data)
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# NOTE: For some reason if data is allowed to sort itself it leads to wrong ordering of x axis.
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traces = sorted(scatter.data, key=itemgetter("name"))
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for trace in traces:
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self.add_trace(trace)
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try:
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tickvals = self.df['submission'].tolist()
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except KeyError:
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tickvals = []
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try:
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ticklabels = self.df['submission'].tolist()
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except KeyError:
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ticklabels = []
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self.update_layout(
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xaxis=dict(
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tickmode='array',
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tickvals=tickvals,
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ticktext=ticklabels,
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)
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)
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self.update_traces(marker={'size': 15})
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@@ -1,7 +1,7 @@
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"""
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Constructs main application.
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"""
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import getpass
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import getpass, logging, webbrowser, sys, shutil
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from pprint import pformat
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from PyQt6.QtCore import qInstallMessageHandler
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from PyQt6.QtWidgets import (
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@@ -9,7 +9,7 @@ from PyQt6.QtWidgets import (
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QHBoxLayout, QScrollArea, QMainWindow,
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QToolBar
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)
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import pickle
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# import pickle
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from PyQt6.QtGui import QAction
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from pathlib import Path
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from markdown import markdown
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@@ -21,12 +21,12 @@ from tools import (
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from .functions import select_save_file, select_open_file
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from .pop_ups import HTMLPop, AlertPop
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from .misc import Pagifier
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import logging, webbrowser, sys, shutil
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from .submission_table import SubmissionsSheet
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from .submission_widget import SubmissionFormContainer
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from .controls_chart import ControlsViewer
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from .summary import Summary
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from .turnaround import TurnaroundTime
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from .concentrations import Concentrations
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from .omni_search import SearchBox
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from .omni_manager import ManagerWindow
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@@ -244,16 +244,14 @@ class App(QMainWindow):
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if dlg.exec():
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logger.debug("\n\nBeginning parsing\n\n")
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output = dlg.parse_form()
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# assert isinstance(output, KitType)
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# output.save()
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logger.debug(f"Kit output: {pformat(output.__dict__)}")
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# output.to_sql()
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with open(f"{output.name}.obj", "wb") as f:
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pickle.dump(output, f)
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# with open(f"{output.name}.obj", "wb") as f:
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# pickle.dump(output, f)
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logger.debug("\n\nBeginning transformation\n\n")
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sql = output.to_sql()
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with open(f"{output.name}.sql", "wb") as f:
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pickle.dump(sql, f)
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assert isinstance(sql, KitType)
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# with open(f"{output.name}.sql", "wb") as f:
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# pickle.dump(sql, f)
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sql.save()
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@@ -269,10 +267,12 @@ class AddSubForm(QWidget):
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self.tab3 = QWidget()
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self.tab4 = QWidget()
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self.tab5 = QWidget()
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self.tab6 = QWidget()
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self.tabs.resize(300, 200)
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# NOTE: Add tabs
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self.tabs.addTab(self.tab1, "Submissions")
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self.tabs.addTab(self.tab2, "Irida Controls")
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self.tabs.addTab(self.tab6, "Concentrations")
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self.tabs.addTab(self.tab3, "PCR Controls")
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self.tabs.addTab(self.tab4, "Cost Report")
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self.tabs.addTab(self.tab5, "Turnaround Times")
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@@ -315,6 +315,10 @@ class AddSubForm(QWidget):
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self.tab5.layout = QVBoxLayout(self)
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self.tab5.layout.addWidget(turnaround)
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self.tab5.setLayout(self.tab5.layout)
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concentration = Concentrations(self)
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self.tab6.layout = QVBoxLayout(self)
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self.tab6.layout.addWidget(concentration)
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self.tab6.setLayout(self.tab6.layout)
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# NOTE: add tabs to main widget
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self.layout.addWidget(self.tabs)
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self.setLayout(self.layout)
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56
src/submissions/frontend/widgets/concentrations.py
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56
src/submissions/frontend/widgets/concentrations.py
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@@ -0,0 +1,56 @@
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"""
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Pane showing turnaround time summary.
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"""
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from PyQt6.QtWidgets import QWidget, QPushButton, QComboBox, QLabel
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from .info_tab import InfoPane
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from backend.excel.reports import ConcentrationMaker
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from frontend.visualizations.concentrations_chart import ConcentrationsChart
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import logging
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logger = logging.getLogger(f"submissions.{__name__}")
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class Concentrations(InfoPane):
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def __init__(self, parent: QWidget):
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super().__init__(parent)
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self.save_button = QPushButton("Save Chart", parent=self)
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self.save_button.pressed.connect(self.save_png)
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self.layout.addWidget(self.save_button, 0, 2, 1, 1)
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self.export_button = QPushButton("Save Data", parent=self)
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self.export_button.pressed.connect(self.save_excel)
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self.layout.addWidget(self.export_button, 0, 3, 1, 1)
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self.fig = None
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self.report_object = None
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# self.submission_typer = QComboBox(self)
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# subs = ["All"] + [item.name for item in SubmissionType.query()]
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# self.submission_typer.addItems(subs)
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# self.layout.addWidget(QLabel("Submission Type"), 1, 0, 1, 1)
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# self.layout.addWidget(self.submission_typer, 1, 1, 1, 3)
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# self.submission_typer.currentTextChanged.connect(self.update_data)
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self.update_data()
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def update_data(self) -> None:
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"""
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Sets data in the info pane
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Returns:
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None
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"""
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super().update_data()
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months = self.diff_month(self.start_date, self.end_date)
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chart_settings = dict(start_date=self.start_date, end_date=self.end_date)
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# if self.submission_typer.currentText() == "All":
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# submission_type = None
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# subtype_obj = None
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# else:
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# submission_type = self.submission_typer.currentText()
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# subtype_obj = SubmissionType.query(name = submission_type)
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# self.report_obj = ConcentrationMaker(start_date=self.start_date, end_date=self.end_date)#, submission_type=submission_type)
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self.report_obj = ConcentrationMaker(**chart_settings)
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# if subtype_obj:
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# threshold = subtype_obj.defaults['turnaround_time'] + 0.5
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# else:
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# threshold = None
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self.fig = ConcentrationsChart(df=self.report_obj.df, settings=chart_settings, modes=[], months=months)
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self.webview.setHtml(self.fig.html)
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