landon/Submissions-App
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Various bug fixes and streamlining.

Browse Source
This commit is contained in:
lwark
2024-10-03 15:09:41 -05:00
parent acab9d0f4c
commit c5470b9062
22 changed files with 222 additions and 380 deletions
Download Patch File Download Diff File Expand all files Collapse all files

87
src/submissions/frontend/widgets/controls_chart.py
View File

@@ -2,12 +2,13 @@
Handles display of control charts
"""
import re
import sys
from datetime import timedelta
from typing import Tuple
from PyQt6.QtWebEngineWidgets import QWebEngineView
from PyQt6.QtWidgets import (
QWidget, QVBoxLayout, QComboBox, QHBoxLayout,
QDateEdit, QLabel, QSizePolicy
QDateEdit, QLabel, QSizePolicy, QPushButton
)
from PyQt6.QtCore import QSignalBlocker
from backend.db import ControlType, Control
@@ -15,11 +16,11 @@ from PyQt6.QtCore import QDate, QSize
import logging
from pandas import DataFrame
from tools import Report, Result, get_unique_values_in_df_column, Settings, report_result
# from backend.excel.reports import convert_data_list_to_df
from frontend.visualizations.control_charts import CustomFigure
logger = logging.getLogger(f"submissions.{__name__}")
class ControlsViewer(QWidget):
def __init__(self, parent: QWidget) -> None:
@@ -29,7 +30,7 @@ class ControlsViewer(QWidget):
self.report = Report()
self.datepicker = ControlsDatePicker()
self.webengineview = QWebEngineView()
# set tab2 layout
# NOTE: set tab2 layout
self.layout = QVBoxLayout(self)
self.control_typer = QComboBox()
# NOTE: fetch types of controls
@@ -54,18 +55,22 @@ class ControlsViewer(QWidget):
self.mode_typer.currentIndexChanged.connect(self.controls_getter)
self.datepicker.start_date.dateChanged.connect(self.controls_getter)
self.datepicker.end_date.dateChanged.connect(self.controls_getter)
self.datepicker.save_button.pressed.connect(self.save_chart_function)
def save_chart_function(self):
self.fig.save_figure(parent=self)
def controls_getter(self):
"""
Lookup controls from database and send to chartmaker
"""
"""
self.controls_getter_function()
@report_result
def controls_getter_function(self):
"""
Get controls based on start/end dates
"""
"""
report = Report()
# NOTE: subtype defaults to disabled
try:
@@ -96,7 +101,7 @@ class ControlsViewer(QWidget):
sub_types = []
if sub_types != []:
# NOTE: block signal that will rerun controls getter and update sub_typer
with QSignalBlocker(self.sub_typer) as blocker:
with QSignalBlocker(self.sub_typer) as blocker:
self.sub_typer.addItems(sub_types)
self.sub_typer.setEnabled(True)
self.sub_typer.currentTextChanged.connect(self.chart_maker)
@@ -109,8 +114,8 @@ class ControlsViewer(QWidget):
def chart_maker(self):
"""
Creates plotly charts for webview
"""
self.chart_maker_function()
"""
self.chart_maker_function()
@report_result
def chart_maker_function(self):
@@ -122,7 +127,7 @@ class ControlsViewer(QWidget):
Returns:
Tuple[QMainWindow, dict]: Collection of new main app window and result dict
"""
"""
report = Report()
# logger.debug(f"Control getter context: \n\tControl type: {self.con_type}\n\tMode: {self.mode}\n\tStart
# Date: {self.start_date}\n\tEnd Date: {self.end_date}") NOTE: set the subtype for kraken
@@ -136,6 +141,7 @@ class ControlsViewer(QWidget):
# NOTE: if no data found from query set fig to none for reporting in webview
if controls is None:
fig = None
self.datepicker.save_button.setEnabled(False)
else:
# NOTE: change each control to list of dictionaries
data = [control.convert_by_mode(mode=self.mode) for control in controls]
@@ -153,8 +159,10 @@ class ControlsViewer(QWidget):
title = f"{self.mode} - {self.subtype}"
# NOTE: send dataframe to chart maker
df, modes = self.prep_df(ctx=self.app.ctx, df=df)
fig = CustomFigure(df=df, ytitle=title, modes=modes)
fig = CustomFigure(df=df, ytitle=title, modes=modes, parent=self)
self.datepicker.save_button.setEnabled(True)
# logger.debug(f"Updating figure...")
self.fig = fig
# NOTE: construct html for webview
html = fig.to_html()
# logger.debug(f"The length of html code is: {len(html)}")
@@ -179,6 +187,11 @@ class ControlsViewer(QWidget):
df = DataFrame.from_records(input_df)
safe = ['name', 'submitted_date', 'genus', 'target']
for column in df.columns:
if column not in safe:
if self.subtype is not None and column != self.subtype:
continue
else:
safe.append(column)
if "percent" in column:
# count_col = [item for item in df.columns if "count" in item][0]
try:
@@ -187,9 +200,9 @@ class ControlsViewer(QWidget):
continue
# NOTE: The actual percentage from kraken was off due to exclusion of NaN, recalculating.
df[column] = 100 * df[count_col] / df.groupby('name')[count_col].transform('sum')
if column not in safe:
if self.subtype is not None and column != self.subtype:
del df[column]
logger.debug(df)
logger.debug(safe)
df = df[[c for c in df.columns if c in safe]]
# NOTE: move date of sample submitted on same date as previous ahead one.
df = self.displace_date(df=df)
# NOTE: ad hoc method to make data labels more accurate.
@@ -229,12 +242,13 @@ class ControlsViewer(QWidget):
# NOTE: get submitted dates for each control
dict_list = [dict(name=item, date=df[df.name == item].iloc[0]['submitted_date']) for item in
sorted(df['name'].unique())]
previous_dates = []
for _, item in enumerate(dict_list):
previous_dates = set()
# for _, item in enumerate(dict_list):
for item in dict_list:
df, previous_dates = self.check_date(df=df, item=item, previous_dates=previous_dates)
return df
def check_date(self, df: DataFrame, item: dict, previous_dates: list) -> Tuple[DataFrame, list]:
def check_date(self, df: DataFrame, item: dict, previous_dates: set) -> Tuple[DataFrame, list]:
"""
Checks if an items date is already present in df and adjusts df accordingly
@@ -250,7 +264,7 @@ class ControlsViewer(QWidget):
check = item['date'] in previous_dates
except IndexError:
check = False
previous_dates.append(item['date'])
previous_dates.add(item['date'])
if check:
# logger.debug(f"We found one! Increment date!\n\t{item['date']} to {item['date'] + timedelta(days=1)}")
# NOTE: get df locations where name == item name
@@ -273,7 +287,7 @@ class ControlsViewer(QWidget):
df, previous_dates = self.check_date(df, item, previous_dates)
return df, previous_dates
def prep_df(self, ctx: Settings, df: DataFrame) -> DataFrame:
def prep_df(self, ctx: Settings, df: DataFrame) -> Tuple[DataFrame, list]:
"""
Constructs figures based on parsed pandas dataframe.
@@ -285,27 +299,17 @@ class ControlsViewer(QWidget):
Returns:
Figure: Plotly figure
"""
# from backend.excel import drop_reruns_from_df
# converts starred genera to normal and splits off list of starred
genera = []
# NOTE: converts starred genera to normal and splits off list of starred
if df.empty:
return None
for item in df['genus'].to_list():
try:
if item[-1] == "*":
genera.append(item[-1])
else:
genera.append("")
except IndexError:
genera.append("")
df['genus'] = df['genus'].replace({'\*': ''}, regex=True).replace({"NaN": "Unknown"})
df['genera'] = genera
df['genera'] = [item[-1] if item and item[-1] == "*" else "" for item in df['genus'].to_list()]
# NOTE: remove original runs, using reruns if applicable
df = self.drop_reruns_from_df(ctx=ctx, df=df)
# NOTE: sort by and exclude from
sorts = ['submitted_date', "target", "genus"]
exclude = ['name', 'genera']
modes = [item for item in df.columns if item not in sorts and item not in exclude] # and "_hashes" not in item]
modes = [item for item in df.columns if item not in sorts and item not in exclude]
# NOTE: Set descending for any columns that have "{mode}" in the header.
ascending = [False if item == "target" else True for item in sorts]
df = df.sort_values(by=sorts, ascending=ascending)
@@ -327,23 +331,26 @@ class ControlsViewer(QWidget):
if 'rerun_regex' in ctx:
sample_names = get_unique_values_in_df_column(df, column_name="name")
rerun_regex = re.compile(fr"{ctx.rerun_regex}")
for sample in sample_names:
if rerun_regex.search(sample):
first_run = re.sub(rerun_regex, "", sample)
df = df.drop(df[df.name == first_run].index)
exclude = [re.sub(rerun_regex, "", sample) for sample in sample_names if rerun_regex.search(sample)]
df = df[df.name not in exclude]
# for sample in sample_names:
# if rerun_regex.search(sample):
# first_run = re.sub(rerun_regex, "", sample)
# df = df.drop(df[df.name == first_run].index)
return df
class ControlsDatePicker(QWidget):
"""
custom widget to pick start and end dates for controls graphs
"""
"""
def __init__(self) -> None:
super().__init__()
self.start_date = QDateEdit(calendarPopup=True)
# NOTE: start date is two months prior to end date by default
twomonthsago = QDate.currentDate().addDays(-60)
self.start_date.setDate(twomonthsago)
sixmonthsago = QDate.currentDate().addDays(-180)
self.start_date.setDate(sixmonthsago)
self.end_date = QDateEdit(calendarPopup=True)
self.end_date.setDate(QDate.currentDate())
self.layout = QHBoxLayout()
@@ -353,6 +360,8 @@ class ControlsDatePicker(QWidget):
self.layout.addWidget(self.end_date)
self.setLayout(self.layout)
self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Fixed)
self.save_button = QPushButton("Save Chart", parent=self)
self.layout.addWidget(self.save_button)
def sizeHint(self) -> QSize:
return QSize(80,20)
return QSize(80, 20)