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Post code-cleanup.

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This commit is contained in:
lwark
2024-12-06 14:45:22 -06:00
parent 4ed5502c60
commit 51c419e470
11 changed files with 195 additions and 175 deletions
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6
src/submissions/__init__.py
View File

@@ -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

2
src/submissions/backend/db/models/controls.py
View File

@@ -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)

44
src/submissions/backend/excel/reports.py
View File

@@ -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:
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="Turnaround")
# logger.debug(f"Writing report to: {filename}")
self.writer.close()
class ChartReportMaker(ReportArchetype):
def __init__(self, df: DataFrame, sheet_name):
self.df = df
self.sheet_name = sheet_name

119
src/submissions/frontend/visualizations/__init__.py
View File

@@ -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 ():
settings (dict): settings passed down from click
fig (Figure): input figure object
group_name (str): controltype
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)
output = select_save_file(obj=parent, default_name=group_name, extension="png")
self.write_image(output.absolute().__str__(), engine="kaleido")
def make_plotly_buttons(self, months: int = 6) -> Generator[dict, None, None]:
"""
Creates html buttons to zoom in on date areas
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)
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},
])
# 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:
"""

94
src/submissions/frontend/visualizations/irida_charts.py
View File

@@ -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},
])

1
src/submissions/frontend/visualizations/pcr_charts.py
View File

@@ -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:

48
src/submissions/frontend/widgets/controls_chart.py
View File

@@ -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.datepicker.end_date.dateChanged.connect(self.update_data)
self.save_button.pressed.connect(self.save_chart_function)
self.export_button.pressed.connect(self.save_data_function)
self.save_button.pressed.connect(self.save_png)
self.export_button.pressed.connect(self.save_excel)
def save_chart_function(self):
self.fig.save_figure(parent=self)
def save_data_function(self):
self.fig.save_data(parent=self)
# def save_chart_function(self):
# self.fig.save_figure(parent=self)
#
# def save_data_function(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...")

18
src/submissions/frontend/widgets/info_tab.py
View File

@@ -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)

14
src/submissions/frontend/widgets/turnaround.py
View File

@@ -1,10 +1,10 @@
from PyQt6.QtCore import QSignalBlocker
from PyQt6.QtWebEngineWidgets import QWebEngineView
from PyQt6.QtWidgets import QWidget, QGridLayout, QPushButton, QLabel, QComboBox
"""
Pane showing turnaround time summary.
"""
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 BasicSubmission, SubmissionType
from backend.db import 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())

22
src/submissions/tools/__init__.py
View File

@@ -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)