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Added in charts for BC control concentrations.

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This commit is contained in:
lwark
2025-03-24 08:58:26 -05:00
parent ea24a8ffd4
commit d796dc4b8d
5 changed files with 169 additions and 15 deletions
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4
src/submissions/backend/db/models/controls.py
View File

@@ -725,3 +725,7 @@ class IridaControl(Control):
"""
from backend.validators import PydIridaControl
return PydIridaControl(**self.__dict__)
@property
def is_positive_control(self):
return not self.subtype.lower().startswith("en")

31
src/submissions/backend/excel/reports.py
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@@ -1,6 +1,7 @@
'''
Contains functions for generating summary reports
'''
import itertools
import sys
from pprint import pformat
from pandas import DataFrame, ExcelWriter
@@ -8,7 +9,7 @@ import logging
from pathlib import Path
from datetime import date
from typing import Tuple
from backend.db.models import BasicSubmission
from backend.db.models import BasicSubmission, IridaControl
from tools import jinja_template_loading, get_first_blank_df_row, row_map, ctx
from PyQt6.QtWidgets import QWidget
from openpyxl.worksheet.worksheet import Worksheet
@@ -156,7 +157,8 @@ class TurnaroundMaker(ReportArchetype):
self.start_date = start_date
self.end_date = end_date
# NOTE: Set page size to zero to override limiting query size.
self.subs = BasicSubmission.query(start_date=start_date, end_date=end_date, submission_type_name=submission_type, page_size=0)
self.subs = BasicSubmission.query(start_date=start_date, end_date=end_date,
submission_type_name=submission_type, page_size=0)
records = [self.build_record(sub) for sub in self.subs]
self.df = DataFrame.from_records(records)
self.sheet_name = "Turnaround"
@@ -191,9 +193,32 @@ class TurnaroundMaker(ReportArchetype):
completed_date=sub.completed_date, acceptable=tat_ok)
class ConcentrationMaker(ReportArchetype):
def __init__(self, start_date: date, end_date: date, submission_type: str = "Bacterial Culture"):
self.start_date = start_date
self.end_date = end_date
# NOTE: Set page size to zero to override limiting query size.
self.subs = BasicSubmission.query(start_date=start_date, end_date=end_date,
submission_type_name=submission_type, page_size=0)
self.controls = list(itertools.chain.from_iterable([sub.controls for sub in self.subs]))
self.records = [self.build_record(control) for control in self.controls]
self.df = DataFrame.from_records(self.records)
self.sheet_name = "Concentration"
@classmethod
def build_record(cls, control: IridaControl) -> dict:
positive = control.is_positive_control
concentration = control.sample.concentration
if not concentration:
concentration = 0
return dict(name=control.name,
submission=str(control.submission.rsl_plate_num), concentration=concentration,
submitted_date=control.submitted_date, positive=positive)
class ChartReportMaker(ReportArchetype):
def __init__(self, df: DataFrame, sheet_name):
self.df = df
self.sheet_name = sheet_name

65
src/submissions/frontend/visualizations/concentrations_chart.py Normal file
View File

@@ -0,0 +1,65 @@
"""
Construct turnaround time charts
"""
from pprint import pformat
from . import CustomFigure
import plotly.express as px
import pandas as pd
from PyQt6.QtWidgets import QWidget
import logging
from operator import itemgetter
logger = logging.getLogger(f"submissions.{__name__}")
class ConcentrationsChart(CustomFigure):
def __init__(self, df: pd.DataFrame, modes: list, settings: dict,
ytitle: str | None = None,
parent: QWidget | None = None,
months: int = 6):
super().__init__(df=df, modes=modes, settings=settings)
self.df = df
self.construct_chart()
# if threshold:
# self.add_hline(y=threshold)
self.update_layout(showlegend=False)
def construct_chart(self, df: pd.DataFrame | None = None):
if df:
self.df = df
# logger.debug(f"Constructing concentration chart with df:\n{self.df}")
try:
self.df = self.df[self.df.concentration.notnull()]
self.df = self.df.sort_values(['submitted_date', 'submission'], ascending=[True, True]).reset_index(drop=True)
self.df = self.df.reset_index().rename(columns={"index": "idx"})
# logger.debug(f"DF after changes:\n{self.df}")
scatter = px.scatter(data_frame=self.df, x='submission', y="concentration",
hover_data=["name", "submission", "submitted_date", "concentration"],
color="positive", color_discrete_map={True: "red", False: "green"}
)
except (ValueError, AttributeError) as e:
logger.error(f"Error constructing chart: {e}")
scatter = px.scatter()
# logger.debug(f"Scatter data: {scatter.data}")
# self.add_traces(scatter.data)
# NOTE: For some reason if data is allowed to sort itself it leads to wrong ordering of x axis.
traces = sorted(scatter.data, key=itemgetter("name"))
for trace in traces:
self.add_trace(trace)
try:
tickvals = self.df['submission'].tolist()
except KeyError:
tickvals = []
try:
ticklabels = self.df['submission'].tolist()
except KeyError:
ticklabels = []
self.update_layout(
xaxis=dict(
tickmode='array',
tickvals=tickvals,
ticktext=ticklabels,
)
)
self.update_traces(marker={'size': 15})

24
src/submissions/frontend/widgets/app.py
View File

@@ -1,7 +1,7 @@
"""
Constructs main application.
"""
import getpass
import getpass, logging, webbrowser, sys, shutil
from pprint import pformat
from PyQt6.QtCore import qInstallMessageHandler
from PyQt6.QtWidgets import (
@@ -9,7 +9,7 @@ from PyQt6.QtWidgets import (
QHBoxLayout, QScrollArea, QMainWindow,
QToolBar
)
import pickle
# import pickle
from PyQt6.QtGui import QAction
from pathlib import Path
from markdown import markdown
@@ -21,12 +21,12 @@ from tools import (
from .functions import select_save_file, select_open_file
from .pop_ups import HTMLPop, AlertPop
from .misc import Pagifier
import logging, webbrowser, sys, shutil
from .submission_table import SubmissionsSheet
from .submission_widget import SubmissionFormContainer
from .controls_chart import ControlsViewer
from .summary import Summary
from .turnaround import TurnaroundTime
from .concentrations import Concentrations
from .omni_search import SearchBox
from .omni_manager import ManagerWindow
@@ -244,16 +244,14 @@ class App(QMainWindow):
if dlg.exec():
logger.debug("\n\nBeginning parsing\n\n")
output = dlg.parse_form()
# assert isinstance(output, KitType)
# output.save()
logger.debug(f"Kit output: {pformat(output.__dict__)}")
# output.to_sql()
with open(f"{output.name}.obj", "wb") as f:
pickle.dump(output, f)
# with open(f"{output.name}.obj", "wb") as f:
# pickle.dump(output, f)
logger.debug("\n\nBeginning transformation\n\n")
sql = output.to_sql()
with open(f"{output.name}.sql", "wb") as f:
pickle.dump(sql, f)
assert isinstance(sql, KitType)
# with open(f"{output.name}.sql", "wb") as f:
# pickle.dump(sql, f)
sql.save()
@@ -269,10 +267,12 @@ class AddSubForm(QWidget):
self.tab3 = QWidget()
self.tab4 = QWidget()
self.tab5 = QWidget()
self.tab6 = QWidget()
self.tabs.resize(300, 200)
# NOTE: Add tabs
self.tabs.addTab(self.tab1, "Submissions")
self.tabs.addTab(self.tab2, "Irida Controls")
self.tabs.addTab(self.tab6, "Concentrations")
self.tabs.addTab(self.tab3, "PCR Controls")
self.tabs.addTab(self.tab4, "Cost Report")
self.tabs.addTab(self.tab5, "Turnaround Times")
@@ -315,6 +315,10 @@ class AddSubForm(QWidget):
self.tab5.layout = QVBoxLayout(self)
self.tab5.layout.addWidget(turnaround)
self.tab5.setLayout(self.tab5.layout)
concentration = Concentrations(self)
self.tab6.layout = QVBoxLayout(self)
self.tab6.layout.addWidget(concentration)
self.tab6.setLayout(self.tab6.layout)
# NOTE: add tabs to main widget
self.layout.addWidget(self.tabs)
self.setLayout(self.layout)

56
src/submissions/frontend/widgets/concentrations.py Normal file
View File

@@ -0,0 +1,56 @@
"""
Pane showing turnaround time summary.
"""
from PyQt6.QtWidgets import QWidget, QPushButton, QComboBox, QLabel
from .info_tab import InfoPane
from backend.excel.reports import ConcentrationMaker
from frontend.visualizations.concentrations_chart import ConcentrationsChart
import logging
logger = logging.getLogger(f"submissions.{__name__}")
class Concentrations(InfoPane):
def __init__(self, parent: QWidget):
super().__init__(parent)
self.save_button = QPushButton("Save Chart", parent=self)
self.save_button.pressed.connect(self.save_png)
self.layout.addWidget(self.save_button, 0, 2, 1, 1)
self.export_button = QPushButton("Save Data", parent=self)
self.export_button.pressed.connect(self.save_excel)
self.layout.addWidget(self.export_button, 0, 3, 1, 1)
self.fig = None
self.report_object = None
# self.submission_typer = QComboBox(self)
# subs = ["All"] + [item.name for item in SubmissionType.query()]
# self.submission_typer.addItems(subs)
# self.layout.addWidget(QLabel("Submission Type"), 1, 0, 1, 1)
# self.layout.addWidget(self.submission_typer, 1, 1, 1, 3)
# self.submission_typer.currentTextChanged.connect(self.update_data)
self.update_data()
def update_data(self) -> None:
"""
Sets data in the info pane
Returns:
None
"""
super().update_data()
months = self.diff_month(self.start_date, self.end_date)
chart_settings = dict(start_date=self.start_date, end_date=self.end_date)
# if self.submission_typer.currentText() == "All":
# submission_type = None
# subtype_obj = None
# else:
# submission_type = self.submission_typer.currentText()
# subtype_obj = SubmissionType.query(name = submission_type)
# self.report_obj = ConcentrationMaker(start_date=self.start_date, end_date=self.end_date)#, submission_type=submission_type)
self.report_obj = ConcentrationMaker(**chart_settings)
# if subtype_obj:
# threshold = subtype_obj.defaults['turnaround_time'] + 0.5
# else:
# threshold = None
self.fig = ConcentrationsChart(df=self.report_obj.df, settings=chart_settings, modes=[], months=months)
self.webview.setHtml(self.fig.html)