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Various bug fixes and streamlining.

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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
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15
src/submissions/frontend/widgets/app.py
View File

@@ -189,8 +189,8 @@ class App(QMainWindow):
"""
month = date.today().strftime("%Y-%m")
current_month_bak = Path(self.ctx.backup_path).joinpath(f"submissions_backup-{month}").resolve()
logger.debug(f"Here is the db directory: {self.ctx.database_path}")
logger.debug(f"Here is the backup directory: {self.ctx.backup_path}")
logger.info(f"Here is the db directory: {self.ctx.database_path}")
logger.info(f"Here is the backup directory: {self.ctx.backup_path}")
match self.ctx.database_schema:
case "sqlite":
db_path = self.ctx.database_path.joinpath(self.ctx.database_name).with_suffix(".db")
@@ -206,15 +206,17 @@ class App(QMainWindow):
current_month_bak = current_month_bak.with_suffix(".psql")
def export_ST_yaml(self):
"""
Copies submission type yaml to file system for editing and remport
Returns:
None
"""
if check_if_app():
yaml_path = Path(sys._MEIPASS).joinpath("resources", "viral_culture.yml")
else:
yaml_path = project_path.joinpath("src", "submissions", "resources", "viral_culture.yml")
# with open(yaml_path, "r") as f:
# data = yaml.safe_load(f)
fname = select_save_file(obj=self, default_name="Submission Type Template.yml", extension="yml")
# with open(fname, "w") as f:
# yaml.safe_dump(data=data, stream=f)
shutil.copyfile(yaml_path, fname)
@check_authorization
@@ -230,7 +232,6 @@ class App(QMainWindow):
print(pformat(st.to_export_dict()))
choice = input("Save the above submission type? [y/N]: ")
if choice.lower() == "y":
# st.save()
pass
else:
logger.warning("Save of submission type cancelled.")

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)

30
src/submissions/frontend/widgets/equipment_usage.py
View File

@@ -8,7 +8,7 @@ from PyQt6.QtWidgets import (QDialog, QComboBox, QCheckBox,
from backend.db.models import Equipment, BasicSubmission, Process
from backend.validators.pydant import PydEquipment, PydEquipmentRole, PydTips
import logging
from typing import List
from typing import List, Generator
logger = logging.getLogger(f"submissions.{__name__}")
@@ -45,26 +45,26 @@ class EquipmentUsage(QDialog):
widg.update_processes()
self.layout.addWidget(self.buttonBox)
def parse_form(self) -> List[PydEquipment]:
def parse_form(self) -> Generator[PydEquipment, None, None]:
"""
Pull info from all RoleComboBox widgets
Returns:
List[PydEquipment]: All equipment pulled from widgets
"""
output = []
for widget in self.findChildren(QWidget):
match widget:
case RoleComboBox():
if widget.check.isChecked():
output.append(widget.parse_form())
item = widget.parse_form()
if item:
yield item
else:
continue
else:
continue
case _:
pass
# logger.debug(f"parsed output of Equsage form: {pformat(output)}")
try:
return [item.strip() for item in output if item is not None]
except AttributeError:
return [item for item in output if item is not None]
continue
class LabelRow(QWidget):
@@ -93,14 +93,10 @@ class RoleComboBox(QWidget):
def __init__(self, parent, role: PydEquipmentRole, used: list) -> None:
super().__init__(parent)
# self.layout = QHBoxLayout()
self.layout = QGridLayout()
self.role = role
self.check = QCheckBox()
# if role.name in used:
self.check.setChecked(False)
# else:
# self.check.setChecked(True)
self.check.stateChanged.connect(self.toggle_checked)
self.box = QComboBox()
self.box.setMaximumWidth(200)
@@ -129,7 +125,6 @@ class RoleComboBox(QWidget):
"""
equip = self.box.currentText()
# logger.debug(f"Updating equipment: {equip}")
# equip2 = [item for item in self.role.equipment if item.name == equip][0]
equip2 = next((item for item in self.role.equipment if item.name == equip), self.role.equipment[0])
# logger.debug(f"Using: {equip2}")
self.process.clear()
@@ -158,7 +153,10 @@ class RoleComboBox(QWidget):
widget.setMinimumWidth(200)
widget.setMaximumWidth(200)
self.layout.addWidget(widget, 0, 4)
widget.setEnabled(self.check.isChecked())
try:
widget.setEnabled(self.check.isChecked())
except NameError:
pass
def parse_form(self) -> PydEquipment | None:
"""

10
src/submissions/frontend/widgets/gel_checker.py
View File

@@ -74,7 +74,7 @@ class GelBox(QDialog):
self.buttonBox = QDialogButtonBox(QBtn)
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
layout.addWidget(self.buttonBox, 23, 1, 1, 1) #, alignment=Qt.AlignmentFlag.AlignTop)
layout.addWidget(self.buttonBox, 23, 1, 1, 1)
self.setLayout(layout)
@@ -135,7 +135,7 @@ class ControlsForm(QWidget):
self.layout.addWidget(self.comment_field, 1, 5, 4, 1)
self.setLayout(self.layout)
def parse_form(self) -> List[dict]:
def parse_form(self) -> Tuple[List[dict], str]:
"""
Pulls the controls statuses from the form.
@@ -145,11 +145,7 @@ class ControlsForm(QWidget):
output = []
for le in self.findChildren(QComboBox):
label = [item.strip() for item in le.objectName().split(" : ")]
try:
# dicto = [item for item in output if item['name'] == label[0]][0]
dicto = next(item for item in output if item['name'] == label[0])
except StopIteration:
dicto = dict(name=label[0], values=[])
dicto = next((item for item in output if item['name'] == label[0]), dict(name=label[0], values=[]))
dicto['values'].append(dict(name=label[1], value=le.currentText()))
if label[0] not in [item['name'] for item in output]:
output.append(dicto)

33
src/submissions/frontend/widgets/pop_ups.py
View File

@@ -2,11 +2,10 @@
Contains dialogs for notification and prompting.
'''
from PyQt6.QtWidgets import (
QLabel, QVBoxLayout, QDialog,
QLabel, QVBoxLayout, QDialog,
QDialogButtonBox, QMessageBox, QComboBox
)
from PyQt6.QtWebEngineWidgets import QWebEngineView
from PyQt6.QtCore import Qt
from tools import jinja_template_loading
import logging
from backend.db import models
@@ -20,8 +19,9 @@ env = jinja_template_loading()
class QuestionAsker(QDialog):
"""
dialog to ask yes/no questions
"""
def __init__(self, title:str, message:str):
"""
def __init__(self, title: str, message: str):
super().__init__()
self.setWindowTitle(title)
# NOTE: set yes/no buttons
@@ -40,8 +40,10 @@ class QuestionAsker(QDialog):
class AlertPop(QMessageBox):
"""
Dialog to show an alert.
"""
def __init__(self, message:str, status:Literal['Information', 'Question', 'Warning', 'Critical'], owner:str|None=None):
"""
def __init__(self, message: str, status: Literal['Information', 'Question', 'Warning', 'Critical'],
owner: str | None = None):
super().__init__()
# NOTE: select icon by string
icon = getattr(QMessageBox.Icon, status)
@@ -49,9 +51,10 @@ class AlertPop(QMessageBox):
self.setInformativeText(message)
self.setWindowTitle(f"{owner} - {status.title()}")
class HTMLPop(QDialog):
def __init__(self, html:str, owner:str|None=None, title:str="python"):
def __init__(self, html: str, owner: str | None = None, title: str = "python"):
super().__init__()
self.webview = QWebEngineView(parent=self)
@@ -66,14 +69,18 @@ class HTMLPop(QDialog):
class ObjectSelector(QDialog):
"""
dialog to input BaseClass type manually
"""
def __init__(self, title:str, message:str, obj_type:str|type[models.BaseClass]):
"""
def __init__(self, title: str, message: str, obj_type: str | type[models.BaseClass], values: list | None = None):
super().__init__()
self.setWindowTitle(title)
self.widget = QComboBox()
if isinstance(obj_type, str):
obj_type: models.BaseClass = getattr(models, obj_type)
items = [item.name for item in obj_type.query()]
if values:
items = values
else:
if isinstance(obj_type, str):
obj_type: models.BaseClass = getattr(models, obj_type)
items = [item.name for item in obj_type.query()]
self.widget.addItems(items)
self.widget.setEditable(False)
# NOTE: set yes/no buttons
@@ -95,5 +102,5 @@ class ObjectSelector(QDialog):
Returns:
str: KitType as str
"""
"""
return self.widget.currentText()

4
src/submissions/frontend/widgets/sample_search.py
View File

@@ -55,6 +55,7 @@ class SearchBox(QDialog):
widget = FieldSearch(parent=self, label=item['label'], field_name=item['field'])
self.layout.addWidget(widget, start_row+iii, 0)
widget.search_widget.textChanged.connect(self.update_data)
self.update_data()
def parse_form(self) -> dict:
"""
@@ -73,7 +74,8 @@ class SearchBox(QDialog):
# logger.debug(f"Running update_data with sample type: {self.type}")
fields = self.parse_form()
# logger.debug(f"Got fields: {fields}")
sample_list_creator = self.type.fuzzy_search(sample_type=self.type, **fields)
# sample_list_creator = self.type.fuzzy_search(sample_type=self.type, **fields)
sample_list_creator = self.type.fuzzy_search(**fields)
data = self.type.samples_to_df(sample_list=sample_list_creator)
# logger.debug(f"Data: {data}")
self.results.setData(df=data)

4
src/submissions/frontend/widgets/submission_details.py
View File

@@ -9,7 +9,6 @@ from PyQt6.QtWebEngineWidgets import QWebEngineView
from PyQt6.QtWebChannel import QWebChannel
from PyQt6.QtCore import Qt, pyqtSlot, QMarginsF
from jinja2 import TemplateNotFound
from backend.db.models import BasicSubmission, BasicSample, Reagent, KitType
from tools import is_power_user, html_to_pdf, jinja_template_loading
from .functions import select_save_file
@@ -18,9 +17,8 @@ import logging
from getpass import getuser
from datetime import datetime
from pprint import pformat
from typing import List
from backend.excel.writer import DocxWriter
logger = logging.getLogger(f"submissions.{__name__}")

6
src/submissions/frontend/widgets/submission_table.py
View File

@@ -11,8 +11,6 @@ from backend.excel import ReportMaker
from tools import Report, Result, report_result
from .functions import select_save_file, select_open_file
from .misc import ReportDatePicker
import pandas as pd
from openpyxl.worksheet.worksheet import Worksheet
logger = logging.getLogger(f"submissions.{__name__}")
@@ -222,10 +220,6 @@ class SubmissionsSheet(QTableView):
# NOTE: if imported submission doesn't exist move on to next run
if sub is None:
continue
# try:
# logger.debug(f"Found submission: {sub.rsl_plate_num}")
# except AttributeError:
# continue
sub.set_attribute('pcr_info', new_run)
# NOTE: check if pcr_info already exists
sub.save()

6
src/submissions/frontend/widgets/submission_widget.py
View File

@@ -9,7 +9,7 @@ from PyQt6.QtWidgets import (
)
from PyQt6.QtCore import pyqtSignal, Qt
from . import select_open_file, select_save_file
import logging, difflib, inspect
import logging, difflib
from pathlib import Path
from tools import Report, Result, check_not_nan, main_form_style, report_result, check_regex_match
from backend.excel.parser import SheetParser
@@ -163,7 +163,7 @@ class SubmissionFormContainer(QWidget):
# NOTE: create form
dlg = AddReagentForm(reagent_lot=reagent_lot, reagent_role=reagent_role, expiry=expiry, reagent_name=name)
if dlg.exec():
# extract form info
# NOTE: extract form info
info = dlg.parse_form()
# logger.debug(f"Reagent info: {info}")
# NOTE: create reagent object
@@ -180,7 +180,6 @@ class SubmissionFormWidget(QWidget):
def __init__(self, parent: QWidget, submission: PydSubmission, disable: list | None = None) -> None:
super().__init__(parent)
# self.report = Report()
# logger.debug(f"Disable: {disable}")
if disable is None:
disable = []
@@ -268,7 +267,6 @@ class SubmissionFormWidget(QWidget):
Tuple[QMainWindow, dict]: Updated application and result
"""
extraction_kit = args[0]
# caller = inspect.stack()[1].function.__repr__().replace("'", "")
report = Report()
# logger.debug(f"Extraction kit: {extraction_kit}")
# NOTE: Remove previous reagent widgets