Post code-cleanup.

src/submissions/__init__.py

@@ -11,6 +11,12 @@ month = date.today().month
 day = date.today().day
 
 def get_week_of_month() -> int:
+    """
+    Gets the current week number of the month.
+
+    Returns:
+        int:
+    """
     for ii, week in enumerate(calendar.monthcalendar(date.today().year, date.today().month)):
         if day in week:
             return ii + 1

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

@@ -503,7 +503,7 @@ class IridaControl(Control):
 
         """
         super().make_parent_buttons(parent=parent)
-        rows = parent.layout.rowCount()
+        rows = parent.layout.rowCount() - 2
         # logger.debug(f"Parent rows: {rows}")
         checker = QCheckBox(parent)
         checker.setChecked(True)

src/submissions/backend/excel/reports.py

@@ -17,6 +17,25 @@ logger = logging.getLogger(f"submissions.{__name__}")
 env = jinja_template_loading()
 
 
+class ReportArchetype(object):
+
+    def write_report(self, filename: Path | str, obj: QWidget | None = None):
+        """
+        Writes info to files.
+
+        Args:
+            filename (Path | str): Basename of output file
+            obj (QWidget | None, optional): Parent object. Defaults to None.
+        """
+        if isinstance(filename, str):
+            filename = Path(filename)
+        filename = filename.absolute()
+        self.writer = ExcelWriter(filename.with_suffix(".xlsx"), engine='openpyxl')
+        self.df.to_excel(self.writer, sheet_name=self.sheet_name)
+        # logger.debug(f"Writing report to: {filename}")
+        self.writer.close()
+
+
 class ReportMaker(object):
 
     def __init__(self, start_date: date, end_date: date, organizations: list | None = None):
@@ -138,7 +157,7 @@ class ReportMaker(object):
             if cell.row > 1:
                 cell.style = 'Currency'
 
-class TurnaroundMaker(object):
+class TurnaroundMaker(ReportArchetype):
 
     def __init__(self, start_date: date, end_date: date, submission_type:str):
         self.start_date = start_date
@@ -147,6 +166,7 @@ class TurnaroundMaker(object):
         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"
 
     @classmethod
     def build_record(cls, sub: BasicSubmission) -> dict:
@@ -163,18 +183,12 @@ class TurnaroundMaker(object):
         return dict(name=str(sub.rsl_plate_num), days=days, submitted_date=sub.submitted_date,
                         completed_date=sub.completed_date, acceptable=tat_ok)
 
-    def write_report(self, filename: Path | str, obj: QWidget | None = None):
-        """
-        Writes info to files.
 
-        Args:
+class ChartReportMaker(ReportArchetype):
-            filename (Path | str): Basename of output file
+
-            obj (QWidget | None, optional): Parent object. Defaults to None.
+    def __init__(self, df: DataFrame, sheet_name):
-        """
+        self.df = df
-        if isinstance(filename, str):
+        self.sheet_name = sheet_name
-            filename = Path(filename)
+
-        filename = filename.absolute()
+
-        self.writer = ExcelWriter(filename.with_suffix(".xlsx"), engine='openpyxl')
+
-        self.df.to_excel(self.writer, sheet_name="Turnaround")
-        # logger.debug(f"Writing report to: {filename}")
-        self.writer.close()

src/submissions/frontend/__init__.py

@@ -2,4 +2,4 @@
 Constructs main application.
 '''
 from .widgets import *
-from .visualizations import *
+from .visualizations import *

src/submissions/frontend/visualizations/__init__.py

@@ -1,13 +1,14 @@
 '''
 Contains all operations for creating charts, graphs and visual effects.
 '''
-from datetime import timedelta
+from datetime import timedelta, date
-
+from typing import Generator
 from PyQt6.QtWidgets import QWidget
 import plotly, logging
 from plotly.graph_objects import Figure
 import pandas as pd
 from frontend.widgets.functions import select_save_file
+from tools import divide_chunks
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -18,31 +19,121 @@ class CustomFigure(Figure):
 
     def __init__(self, df: pd.DataFrame, settings: dict, modes: list, ytitle: str | None = None, parent: QWidget | None = None):
         super().__init__()
-        # self.settings = settings
         try:
             months = int(settings['months'])
         except KeyError:
             months = 6
         self.df = df
         self.update_xaxes(range=[settings['start_date'] - timedelta(days=1), settings['end_date']])
+        self.generic_figure_markers(modes=modes, ytitle=ytitle, months=months)
 
-    def save_figure(self, group_name: str = "plotly_output", parent: QWidget | None = None):
+    def generic_figure_markers(self, modes: list = [], ytitle: str | None = None, months: int = 6):
         """
-        Writes plotly figure to html file.
+        Adds standard layout to figure.
 
         Args:
-            figs ():
+            fig (Figure): Input figure.
-            settings (dict): settings passed down from click
+            modes (list, optional): List of modes included in figure. Defaults to [].
-            fig (Figure): input figure object
+            ytitle (str, optional): Title for the y-axis. Defaults to None.
-            group_name (str): controltype
+
+        Returns:
+            Figure: Output figure with updated titles, rangeslider, buttons.
         """
+        if modes:
+            ytitle = modes[0]
+        # logger.debug("Creating visibles list for each mode.")
+        self.update_layout(
+            xaxis_title="Submitted Date (* - Date parsed from fastq file creation date)",
+            yaxis_title=ytitle,
+            showlegend=True,
+            barmode='stack',
+            updatemenus=[
+                dict(
+                    type="buttons",
+                    direction="right",
+                    x=0.7,
+                    y=1.2,
+                    showactive=True,
+                    buttons=[button for button in self.make_pyqt_buttons(modes=modes)],
+                )
+            ]
+        )
+        self.update_xaxes(
+            rangeslider_visible=True,
+            rangeselector=dict(
+                buttons=[button for button in self.make_plotly_buttons(months=months)]
+            )
+        )
+        assert isinstance(self, CustomFigure)
 
-        output = select_save_file(obj=parent, default_name=group_name, extension="png")
+    def make_plotly_buttons(self, months: int = 6) -> Generator[dict, None, None]:
-        self.write_image(output.absolute().__str__(), engine="kaleido")
+        """
+        Creates html buttons to zoom in on date areas
 
-    def save_data(self, group_name: str = "plotly_export", parent:QWidget|None=None):
+        Args:
-        output = select_save_file(obj=parent, default_name=group_name, extension="xlsx")
+            months (int, optional): Number of months of data given. Defaults to 6.
-        self.df.to_excel(output.absolute().__str__(), engine="openpyxl", index=False)
+
+        Yields:
+            Generator[dict, None, None]: Button details.
+        """
+        rng = [1]
+        if months > 2:
+            rng += [iii for iii in range(3, months, 3)]
+        # logger.debug(f"Making buttons for months: {rng}")
+        buttons = [dict(count=iii, label=f"{iii}m", step="month", stepmode="backward") for iii in rng]
+        if months > date.today().month:
+            buttons += [dict(count=1, label="YTD", step="year", stepmode="todate")]
+        buttons += [dict(step="all")]
+        for button in buttons:
+            yield button
+
+    def make_pyqt_buttons(self, modes: list) -> Generator[dict, None, None]:
+        """
+        Creates list of buttons with one for each mode to be used in showing/hiding mode traces.
+
+        Args:
+            modes (list): list of modes used by main parser.
+            fig_len (int): number of traces in the figure
+
+        Returns:
+            Generator[dict, None, None]: list of buttons.
+        """
+        fig_len = len(self.data)
+        if len(modes) > 1:
+            for ii, mode in enumerate(modes):
+                # NOTE: What I need to do is create a list of bools with the same length as the fig.data
+                mode_vis = [True] * fig_len
+                # NOTE: And break it into {len(modes)} chunks
+                mode_vis = list(divide_chunks(mode_vis, len(modes)))
+                # NOTE: Then, for each chunk, if the chunk index isn't equal to the index of the current mode, set to false
+                for jj, sublist in enumerate(mode_vis):
+                    if jj != ii:
+                        mode_vis[jj] = [not elem for elem in mode_vis[jj]]
+                # NOTE: Finally, flatten list.
+                mode_vis = [item for sublist in mode_vis for item in sublist]
+                # NOTE: Now, yield button to add to list
+                yield dict(label=mode, method="update", args=[
+                    {"visible": mode_vis},
+                    {"yaxis.title.text": mode},
+                ])
+
+    # def save_figure(self, group_name: str = "plotly_output", parent: QWidget | None = None):
+    #     """
+    #     Writes plotly figure to html file.
+    #
+    #     Args:
+    #         figs ():
+    #         settings (dict): settings passed down from click
+    #         fig (Figure): input figure object
+    #         group_name (str): controltype
+    #     """
+    #
+    #     output = select_save_file(obj=parent, default_name=group_name, extension="png")
+    #     self.write_image(output.absolute().__str__(), engine="kaleido")
+    #
+    # def save_data(self, group_name: str = "plotly_export", parent:QWidget|None=None):
+    #     output = select_save_file(obj=parent, default_name=group_name, extension="xlsx")
+    #     self.df.to_excel(output.absolute().__str__(), engine="openpyxl", index=False)
 
     def to_html(self) -> str:
         """

src/submissions/frontend/visualizations/irida_charts.py

@@ -19,12 +19,13 @@ class IridaFigure(CustomFigure):
     def __init__(self, df: pd.DataFrame, modes: list, settings: dict, ytitle: str | None = None, parent: QWidget | None = None):
 
         super().__init__(df=df, modes=modes, settings=settings)
+        self.df = df
         try:
             months = int(settings['months'])
         except KeyError:
             months = 6
         self.construct_chart(df=df, modes=modes, start_date=settings['start_date'], end_date=settings['end_date'])
-        self.generic_figure_markers(modes=modes, ytitle=ytitle, months=months)
+
 
     def construct_chart(self, df: pd.DataFrame, modes: list, start_date: date, end_date:date):
         """
@@ -69,94 +70,3 @@ class IridaFigure(CustomFigure):
                          )
             bar.update_traces(visible=ii == 0)
             self.add_traces(bar.data)
-
-    def generic_figure_markers(self, modes: list = [], ytitle: str | None = None, months: int = 6):
-        """
-        Adds standard layout to figure.
-
-        Args:
-            fig (Figure): Input figure.
-            modes (list, optional): List of modes included in figure. Defaults to [].
-            ytitle (str, optional): Title for the y-axis. Defaults to None.
-
-        Returns:
-            Figure: Output figure with updated titles, rangeslider, buttons.
-        """
-        if modes:
-            ytitle = modes[0]
-        # logger.debug("Creating visibles list for each mode.")
-        self.update_layout(
-            xaxis_title="Submitted Date (* - Date parsed from fastq file creation date)",
-            yaxis_title=ytitle,
-            showlegend=True,
-            barmode='stack',
-            updatemenus=[
-                dict(
-                    type="buttons",
-                    direction="right",
-                    x=0.7,
-                    y=1.2,
-                    showactive=True,
-                    buttons=[button for button in self.make_pyqt_buttons(modes=modes)],
-                )
-            ]
-        )
-        self.update_xaxes(
-            rangeslider_visible=True,
-            rangeselector=dict(
-                buttons=[button for button in self.make_plotly_buttons(months=months)]
-            )
-        )
-        assert isinstance(self, CustomFigure)
-
-    def make_plotly_buttons(self, months: int = 6) -> Generator[dict, None, None]:
-        """
-        Creates html buttons to zoom in on date areas
-
-        Args:
-            months (int, optional): Number of months of data given. Defaults to 6.
-
-        Yields:
-            Generator[dict, None, None]: Button details.
-        """        
-        rng = [1]
-        if months > 2:
-            rng += [iii for iii in range(3, months, 3)]
-        # logger.debug(f"Making buttons for months: {rng}")
-        buttons = [dict(count=iii, label=f"{iii}m", step="month", stepmode="backward") for iii in rng]
-        if months > date.today().month:
-            buttons += [dict(count=1, label="YTD", step="year", stepmode="todate")]
-        buttons += [dict(step="all")]
-        for button in buttons:
-            yield button
-
-    def make_pyqt_buttons(self, modes: list) -> Generator[dict, None, None]:
-        """
-        Creates list of buttons with one for each mode to be used in showing/hiding mode traces.
-
-        Args:
-            modes (list): list of modes used by main parser.
-            fig_len (int): number of traces in the figure
-
-        Returns:
-            Generator[dict, None, None]: list of buttons.
-        """
-        fig_len = len(self.data)
-        if len(modes) > 1:
-            for ii, mode in enumerate(modes):
-                # NOTE: What I need to do is create a list of bools with the same length as the fig.data
-                mode_vis = [True] * fig_len
-                # NOTE: And break it into {len(modes)} chunks
-                mode_vis = list(divide_chunks(mode_vis, len(modes)))
-                # NOTE: Then, for each chunk, if the chunk index isn't equal to the index of the current mode, set to false
-                for jj, sublist in enumerate(mode_vis):
-                    if jj != ii:
-                        mode_vis[jj] = [not elem for elem in mode_vis[jj]]
-                # NOTE: Finally, flatten list.
-                mode_vis = [item for sublist in mode_vis for item in sublist]
-                # NOTE: Now, yield button to add to list
-                yield dict(label=mode, method="update", args=[
-                    {"visible": mode_vis},
-                    {"yaxis.title.text": mode},
-                ])
-

src/submissions/frontend/visualizations/pcr_charts.py

@@ -16,6 +16,7 @@ class PCRFigure(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
         try:
             months = int(settings['months'])
         except KeyError:

src/submissions/frontend/widgets/controls_chart.py

@@ -1,18 +1,17 @@
 """
 Handles display of control charts
 """
-from datetime import date
 from pprint import pformat
-from PyQt6.QtWebEngineWidgets import QWebEngineView
 from PyQt6.QtWidgets import (
-    QWidget, QComboBox, QPushButton, QGridLayout
+    QWidget, QComboBox, QPushButton
 )
 from PyQt6.QtCore import QSignalBlocker
+
+from backend import ChartReportMaker
 from backend.db import ControlType, IridaControl
 import logging
-from tools import Report, report_result, Result
+from tools import Report, report_result
 from frontend.visualizations import CustomFigure
-from .misc import StartEndDatePicker
 from .info_tab import InfoPane
 
 logger = logging.getLogger(f"submissions.{__name__}")
@@ -27,13 +26,8 @@ class ControlsViewer(InfoPane):
         if not self.archetype:
             return
         logger.debug(f"Archetype set as: {self.archetype}")
-        # self.app = self.parent().parent()
         # logger.debug(f"\n\n{self.app}\n\n")
-        # self.report = Report()
-        # self.datepicker = StartEndDatePicker(default_start=-180)
-        # self.webengineview = QWebEngineView()
         # NOTE: set tab2 layout
-        # self.layout = QGridLayout(self)
         self.control_sub_typer = QComboBox()
         # NOTE: fetch types of controls
         con_sub_types = [item for item in self.archetype.targets.keys()]
@@ -46,7 +40,6 @@ class ControlsViewer(InfoPane):
         self.mode_sub_typer = QComboBox()
         self.mode_sub_typer.setEnabled(False)
         # NOTE: add widgets to tab2 layout
-        # self.layout.addWidget(self.datepicker, 0, 0, 1, 2)
         self.save_button = QPushButton("Save Chart", parent=self)
         self.layout.addWidget(self.save_button, 0, 2, 1, 1)
         self.export_button = QPushButton("Save Data", parent=self)
@@ -55,21 +48,17 @@ class ControlsViewer(InfoPane):
         self.layout.addWidget(self.mode_typer, 2, 0, 1, 4)
         self.layout.addWidget(self.mode_sub_typer, 3, 0, 1, 4)
         self.archetype.get_instance_class().make_parent_buttons(parent=self)
-        # self.layout.addWidget(self.webengineview, self.layout.rowCount(), 0, 1, 4)
-        # self.setLayout(self.layout)
         self.update_data()
         self.control_sub_typer.currentIndexChanged.connect(self.update_data)
         self.mode_typer.currentIndexChanged.connect(self.update_data)
-        # self.datepicker.start_date.dateChanged.connect(self.update_data)
+        self.save_button.pressed.connect(self.save_png)
-        # self.datepicker.end_date.dateChanged.connect(self.update_data)
+        self.export_button.pressed.connect(self.save_excel)
-        self.save_button.pressed.connect(self.save_chart_function)
-        self.export_button.pressed.connect(self.save_data_function)
 
-    def save_chart_function(self):
+    # def save_chart_function(self):
-        self.fig.save_figure(parent=self)
+    #     self.fig.save_figure(parent=self)
-
+    #
-    def save_data_function(self):
+    # def save_data_function(self):
-        self.fig.save_data(parent=self)
+    #     self.fig.save_data(parent=self)
 
     @report_result
     def update_data(self, *args, **kwargs):
@@ -117,20 +106,6 @@ class ControlsViewer(InfoPane):
         self.chart_maker_function()
         # return report
 
-    @classmethod
-    def diff_month(self, d1: date, d2: date) -> float:
-        """
-        Gets the number of months difference between two different dates
-
-        Args:
-            d1 (date): Start date.
-            d2 (date): End date.
-
-        Returns:
-            float: Number of months difference
-        """        
-        return abs((d1.year - d2.year) * 12 + d1.month - d2.month)
-
     @report_result
     def chart_maker_function(self, *args, **kwargs):
         # TODO: Generalize this by moving as much code as possible to IridaControl
@@ -158,6 +133,7 @@ class ControlsViewer(InfoPane):
                               mode=self.mode,
                               sub_mode=self.mode_sub_type, parent=self, months=months)
         self.fig = self.archetype.get_instance_class().make_chart(chart_settings=chart_settings, parent=self, ctx=self.app.ctx)
+        self.report_obj = ChartReportMaker(df=self.fig.df, sheet_name=self.archetype.name)
         if issubclass(self.fig.__class__, CustomFigure):
             self.save_button.setEnabled(True)
         # logger.debug(f"Updating figure...")

src/submissions/frontend/widgets/info_tab.py

@@ -1,6 +1,7 @@
 """
 A pane to show info e.g. cost reports and turnaround times.
 """
+from datetime import date
 from PyQt6.QtCore import QSignalBlocker
 from PyQt6.QtWebEngineWidgets import QWebEngineView
 from PyQt6.QtWidgets import QWidget, QGridLayout
@@ -25,7 +26,8 @@ class InfoPane(QWidget):
         self.datepicker.end_date.dateChanged.connect(self.update_data)
         self.layout = QGridLayout(self)
         self.layout.addWidget(self.datepicker, 0, 0, 1, 2)
-        self.layout.addWidget(self.webview, 4, 0, 1, 4)
+        # NOTE: Placed in lower row to allow for addition of custom rows.
+        self.layout.addWidget(self.webview, 5, 0, 1, 4)
         self.setLayout(self.layout)
 
     @report_result
@@ -45,6 +47,20 @@ class InfoPane(QWidget):
             report.add_result(Result(owner=self.__str__(), msg=msg, status="Warning"))
             return report
 
+    @classmethod
+    def diff_month(self, d1: date, d2: date) -> float:
+        """
+        Gets the number of months difference between two different dates
+
+        Args:
+            d1 (date): Start date.
+            d2 (date): End date.
+
+        Returns:
+            float: Number of months difference
+        """
+        return abs((d1.year - d2.year) * 12 + d1.month - d2.month)
+
     def save_excel(self):
         fname = select_save_file(self, default_name=f"Report {self.start_date.strftime('%Y%m%d')} - {self.end_date.strftime('%Y%m%d')}", extension="xlsx")
         self.report_obj.write_report(fname, obj=self)

src/submissions/frontend/widgets/turnaround.py

@@ -1,10 +1,10 @@
-from PyQt6.QtCore import QSignalBlocker
+"""
-from PyQt6.QtWebEngineWidgets import QWebEngineView
+Pane showing turnaround time summary.
-from PyQt6.QtWidgets import QWidget, QGridLayout, QPushButton, QLabel, QComboBox
+"""
+from PyQt6.QtWidgets import QWidget, QPushButton, QComboBox, QLabel
 from .info_tab import InfoPane
 from backend.excel.reports import TurnaroundMaker
-from pandas import DataFrame
+from backend.db import SubmissionType
-from backend.db import BasicSubmission, SubmissionType
 from frontend.visualizations.turnaround_chart import TurnaroundChart
 import logging
 
@@ -26,12 +26,14 @@ class TurnaroundTime(InfoPane):
         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):
         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
@@ -44,5 +46,5 @@ class TurnaroundTime(InfoPane):
             threshold = subtype_obj.defaults['turnaround_time'] + 0.5
         else:
             threshold = None
-        self.fig = TurnaroundChart(df=self.report_obj.df, settings=chart_settings, modes=[], threshold=threshold)
+        self.fig = TurnaroundChart(df=self.report_obj.df, settings=chart_settings, modes=[], threshold=threshold, months=months)
         self.webview.setHtml(self.fig.to_html())

src/submissions/tools/__init__.py

@@ -2,7 +2,6 @@
 Contains miscellaenous functions used by both frontend and backend.
 '''
 from __future__ import annotations
-
 from datetime import date, datetime, timedelta
 from json import JSONDecodeError
 from pprint import pprint
@@ -13,7 +12,6 @@ from jinja2 import Environment, FileSystemLoader
 from logging import handlers
 from pathlib import Path
 from sqlalchemy.orm import Session
-from sqlalchemy.orm.state import InstanceState
 from sqlalchemy import create_engine, text, MetaData
 from pydantic import field_validator, BaseModel, Field
 from pydantic_settings import BaseSettings, SettingsConfigDict
@@ -893,11 +891,21 @@ def yaml_regex_creator(loader, node):
     return f"(?P<{name}>RSL(?:-|_)?{abbr}(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
 
 
-def super_splitter(input:str, ioi:str, idx:int) -> str:
+def super_splitter(ins_str:str, substring:str, idx:int) -> str:
+    """
+
+    Args:
+        ins_str (str): input string
+        substring (str): substring to split on
+        idx (int): the occurrence of the substring to return
+
+    Returns:
+
+    """
     try:
-        return input.split(ioi)[idx]
+        return ins_str.split(substring)[idx]
     except IndexError:
-        return input
+        return ins_str
 
 
 ctx = get_config(None)
@@ -1021,7 +1029,3 @@ def create_holidays_for_year(year: int|None=None) -> List[date]:
     holidays.append(easter(year) - timedelta(days=2))
     holidays.append(easter(year) + timedelta(days=1))
     return sorted(holidays)
-
-
-
-