Added in charts for BC control concentrations.

src/submissions/backend/db/models/controls.py

@@ -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")

src/submissions/backend/excel/reports.py

@@ -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
-

src/submissions/frontend/visualizations/concentrations_chart.py

@@ -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})

src/submissions/frontend/widgets/app.py

@@ -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:
-            with open(f"{output.name}.obj", "wb") as f:
+            #     pickle.dump(output, 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:
+            assert isinstance(sql, KitType)
-                pickle.dump(sql, f)
+            # 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)

src/submissions/frontend/widgets/concentrations.py

@@ -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)