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

Minor bug fixes.

Browse Source
This commit is contained in:
Landon Wark
2023-12-07 12:50:03 -06:00
parent cbf36a5b0b
commit 0dd51827a0
22 changed files with 308 additions and 370 deletions
Download Patch File Download Diff File Expand all files Collapse all files

67
src/submissions/frontend/visualizations/control_charts.py
View File

@@ -194,73 +194,6 @@ def construct_chart(df:pd.DataFrame, modes:list, ytitle:str|None=None) -> Figure
fig.add_traces(bar.data)
return generic_figure_markers(fig=fig, modes=modes, ytitle=ytitle)
# Below are the individual construction functions. They must be named "construct_{mode}_chart" and
# take only json_in and mode to hook into the main processor.
# def construct_refseq_chart(df:pd.DataFrame, group_name:str, mode:str) -> Figure:
# """
# Constructs intial refseq chart for both contains and matches (depreciated).
# Args:
# df (pd.DataFrame): dataframe containing all sample data for the group.
# group_name (str): name of the group being processed.
# mode (str): contains or matches, overwritten by hardcoding, so don't think about it too hard.
# Returns:
# Figure: initial figure with contains and matches traces.
# """
# # This overwrites the mode from the signature, might get confusing.
# fig = Figure()
# modes = ['contains', 'matches']
# for ii, mode in enumerate(modes):
# bar = px.bar(df, x="submitted_date",
# y=f"{mode}_ratio",
# color="target",
# title=f"{group_name}_{mode}",
# barmode='stack',
# hover_data=["genus", "name", f"{mode}_hashes"],
# text="genera"
# )
# bar.update_traces(visible = ii == 0)
# # Plotly express returns a full figure, so we have to use the data from that figure only.
# fig.add_traces(bar.data)
# # sys.exit(f"number of traces={len(fig.data)}")
# return generic_figure_markers(fig=fig, modes=modes)
# def construct_kraken_chart(settings:dict, df:pd.DataFrame, group_name:str, mode:str) -> Figure:
# """
# Constructs intial refseq chart for each mode in the kraken config settings. (depreciated)
# Args:
# settings (dict): settings passed down from click.
# df (pd.DataFrame): dataframe containing all sample data for the group.
# group_name (str): name of the group being processed.
# mode (str): kraken modes retrieved from config file by setup.
# Returns:
# Figure: initial figure with traces for modes
# """
# df[f'{mode}_count'] = pd.to_numeric(df[f'{mode}_count'],errors='coerce')
# df = df.groupby('submitted_date')[f'{mode}_count'].nlargest(2)
# # The actual percentage from kraken was off due to exclusion of NaN, recalculating.
# df[f'{mode}_percent'] = 100 * df[f'{mode}_count'] / df.groupby('submitted_date')[f'{mode}_count'].transform('sum')
# modes = settings['modes'][mode]
# # This overwrites the mode from the signature, might get confusing.
# fig = Figure()
# for ii, entry in enumerate(modes):
# bar = px.bar(df, x="submitted_date",
# y=entry,
# color="genus",
# title=f"{group_name}_{entry}",
# barmode="stack",
# hover_data=["genus", "name", "target"],
# text="genera",
# )
# bar.update_traces(visible = ii == 0)
# fig.add_traces(bar.data)
# return generic_figure_markers(fig=fig, modes=modes)
def divide_chunks(input_list:list, chunk_count:int):
"""
Divides a list into {chunk_count} equal parts

3
src/submissions/frontend/visualizations/plate_map.py
View File

@@ -1,9 +1,8 @@
from pathlib import Path
import sys
from PIL import Image, ImageDraw, ImageFont
import numpy as np
from tools import check_if_app, jinja_template_loading
import logging
import logging, sys
logger = logging.getLogger(f"submissions.{__name__}")

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

@@ -1,8 +1,6 @@
'''
Constructs main application.
TODO: Complete.
'''
import sys
from PyQt6.QtWidgets import (
QTabWidget, QWidget, QVBoxLayout,
QHBoxLayout, QScrollArea, QMainWindow,
@@ -14,14 +12,12 @@ from backend.validators import PydReagent
from tools import check_if_app, Settings, Report
from .pop_ups import AlertPop
from .misc import AddReagentForm, LogParser
import logging
import logging, webbrowser, sys
from datetime import date
import webbrowser
from .submission_table import SubmissionsSheet
from .submission_widget import SubmissionFormContainer
from .controls_chart import ControlsViewer
from .kit_creator import KitAdder
import webbrowser
logger = logging.getLogger(f'submissions.{__name__}')
logger.info("Hello, I am a logger")

7
src/submissions/frontend/widgets/controls_chart.py
View File

@@ -3,8 +3,8 @@ from PyQt6.QtWidgets import (
QWidget, QVBoxLayout, QComboBox, QHBoxLayout,
QDateEdit, QLabel, QSizePolicy
)
from PyQt6.QtCore import QSignalBlocker, QLoggingCategory
from backend.db import ControlType, Control, get_control_subtypes
from PyQt6.QtCore import QSignalBlocker
from backend.db import ControlType, Control#, get_control_subtypes
from PyQt6.QtCore import QDate, QSize
import logging, sys
from tools import Report, Result
@@ -88,7 +88,8 @@ class ControlsViewer(QWidget):
self.mode = self.mode_typer.currentText()
self.sub_typer.clear()
# lookup subtypes
sub_types = get_control_subtypes(type=self.con_type, mode=self.mode)
# sub_types = get_control_subtypes(type=self.con_type, mode=self.mode)
sub_types = ControlType.query(name=self.con_type).get_subtypes(mode=self.mode)
# sub_types = lookup_controls(ctx=obj.ctx, control_type=obj.con_type)
if sub_types != []:
# block signal that will rerun controls getter and update sub_typer

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

@@ -15,7 +15,6 @@ from PyQt6.QtWidgets import (
from PyQt6.QtWebEngineWidgets import QWebEngineView
from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel
from PyQt6.QtGui import QAction, QCursor, QPixmap, QPainter
from backend.db.functions import submissions_to_df
from backend.db.models import BasicSubmission
from backend.excel import make_report_html, make_report_xlsx
from tools import check_if_app, Report, Result, jinja_template_loading, get_first_blank_df_row, row_map
@@ -102,7 +101,8 @@ class SubmissionsSheet(QTableView):
"""
sets data in model
"""
self.data = submissions_to_df()
# self.data = submissions_to_df()
self.data = BasicSubmission.submissions_to_df()
try:
self.data['id'] = self.data['id'].apply(str)
self.data['id'] = self.data['id'].str.zfill(3)

39
src/submissions/frontend/widgets/submission_widget.py
View File

@@ -5,23 +5,20 @@ from PyQt6.QtWidgets import (
from PyQt6.QtCore import pyqtSignal
from pathlib import Path
from . import select_open_file, select_save_file
import logging
import logging, difflib, inspect, json, sys
from pathlib import Path
from tools import Report, Result, check_not_nan
from backend.excel.parser import SheetParser, PCRParser
from backend.validators import PydSubmission, PydReagent
from backend.db import (
check_kit_integrity, KitType, Organization, SubmissionType, Reagent,
KitType, Organization, SubmissionType, Reagent,
ReagentType, KitTypeReagentTypeAssociation, BasicSubmission
)
from pprint import pformat
from .pop_ups import QuestionAsker, AlertPop
# from .misc import ReagentFormWidget
from typing import List, Tuple
import difflib
from datetime import date
import inspect
import json
logger = logging.getLogger(f"submissions.{__name__}")
@@ -143,14 +140,14 @@ class SubmissionFormContainer(QWidget):
return
except AttributeError:
self.prsr = SheetParser(ctx=self.app.ctx, filepath=fname)
try:
logger.debug(f"Submission dictionary:\n{pformat(self.prsr.sub)}")
self.pyd = self.prsr.to_pydantic()
logger.debug(f"Pydantic result: \n\n{pformat(self.pyd)}\n\n")
except Exception as e:
report.add_result(Result(msg=f"Problem creating pydantic model:\n\n{e}", status="Critical"))
self.report.add_result(report)
return
# try:
logger.debug(f"Submission dictionary:\n{pformat(self.prsr.sub)}")
self.pyd = self.prsr.to_pydantic()
logger.debug(f"Pydantic result: \n\n{pformat(self.pyd)}\n\n")
# except Exception as e:
# report.add_result(Result(msg=f"Problem creating pydantic model:\n\n{e}", status="Critical"))
# self.report.add_result(report)
# return
self.form = self.pyd.toForm(parent=self)
self.layout().addWidget(self.form)
kit_widget = self.form.find_widgets(object_name="extraction_kit")[0].input
@@ -265,7 +262,8 @@ class SubmissionFormContainer(QWidget):
self.pyd: PydSubmission = self.form.parse_form()
logger.debug(f"Submission: {pformat(self.pyd)}")
logger.debug("Checking kit integrity...")
result = check_kit_integrity(sub=self.pyd)
# result = check_kit_integrity(sub=self.pyd)
result = self.pyd.check_kit_integrity()
report.add_result(result)
if len(result.results) > 0:
self.report.add_result(report)
@@ -417,7 +415,8 @@ class SubmissionFormWidget(QWidget):
# self.ignore = [None, "", "qt_spinbox_lineedit", "qt_scrollarea_viewport", "qt_scrollarea_hcontainer",
# "qt_scrollarea_vcontainer", "submit_btn"
# ]
self.ignore = ['filepath', 'samples', 'reagents', 'csv', 'ctx']
self.ignore = ['filepath', 'samples', 'reagents', 'csv', 'ctx', 'comment']
self.recover = ['filepath', 'samples', 'csv', 'comment']
layout = QVBoxLayout()
for k, v in kwargs.items():
if k not in self.ignore:
@@ -448,8 +447,6 @@ class SubmissionFormWidget(QWidget):
logger.debug(f"Hello from form parser!")
info = {}
reagents = []
if hasattr(self, 'csv'):
info['csv'] = self.csv
for widget in self.findChildren(QWidget):
# logger.debug(f"Parsed widget of type {type(widget)}")
match widget:
@@ -463,9 +460,13 @@ class SubmissionFormWidget(QWidget):
info[field] = value
logger.debug(f"Info: {pformat(info)}")
logger.debug(f"Reagents: {pformat(reagents)}")
# sys.exit()
# logger.debug(f"Attrs not in info: {[k for k, v in self.__dict__.items() if k not in info.keys()]}")
for item in self.recover:
if hasattr(self, item):
info[item] = getattr(self, item)
# app = self.parent().parent().parent().parent().parent().parent().parent().parent
submission = PydSubmission(filepath=self.filepath, reagents=reagents, samples=self.samples, **info)
# submission = PydSubmission(filepath=self.filepath, reagents=reagents, samples=self.samples, **info)
submission = PydSubmission(reagents=reagents, **info)
return submission
class InfoItem(QWidget):