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Debugged reports.

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This commit is contained in:
lwark
2025-03-24 13:42:39 -05:00
parent d796dc4b8d
commit 6404bc499b
5 changed files with 23 additions and 110 deletions
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4
CHANGELOG.md
View File

@@ -1,3 +1,7 @@
# 202503.05
- Added concentrations chart tab.
# 202503.04
- Kit editor debugging.

7
src/submissions/backend/excel/reports.py
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@@ -1,6 +1,6 @@
'''
"""
Contains functions for generating summary reports
'''
"""
import itertools
import sys
from pprint import pformat
@@ -10,7 +10,7 @@ from pathlib import Path
from datetime import date
from typing import Tuple
from backend.db.models import BasicSubmission, IridaControl
from tools import jinja_template_loading, get_first_blank_df_row, row_map, ctx
from tools import jinja_template_loading, get_first_blank_df_row, row_map
from PyQt6.QtWidgets import QWidget
from openpyxl.worksheet.worksheet import Worksheet
@@ -36,6 +36,7 @@ class ReportArchetype(object):
filename = Path(filename)
filename = filename.absolute()
self.writer = ExcelWriter(filename.with_suffix(".xlsx"), engine='openpyxl')
self.df.index += 1
self.df.to_excel(self.writer, sheet_name=self.sheet_name)
self.writer.close()

88
src/submissions/backend/validators/omni_gui_objects.py
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@@ -22,86 +22,6 @@ class BaseOmni(BaseModel):
def aliases(cls):
return cls.class_object.aliases
# NOTE: Okay, this will not work for editing, since by definition not all attributes will line up.
# def check_all_attributes(self, attributes: dict) -> bool:
# """
# Checks this instance against a dictionary of attributes to determine if they are a match.
#
# Args:
# attributes (dict): A dictionary of attributes to be check for equivalence
#
# Returns:
# bool: If a single unequivocal value is found will be false, else true.
# """
# logger.debug(f"Incoming attributes: {attributes}")
# for key, value in attributes.items():
# logger.debug(f"Comparing value class: {value.__class__} to omni class")
# if isinstance(value, str):
# try:
# check = value.lower() == "none"
# except AttributeError:
# continue
# if check:
# value = None
# logger.debug(f"Attempting to grab attribute: {key}")
# try:
# self_value = getattr(self, key)
# class_attr = getattr(self.class_object, key)
# except AttributeError:
# continue
# try:
# logger.debug(f"Check if {self_value.__class__} is subclass of {BaseOmni}")
# check = issubclass(self_value.__class__, BaseOmni)
# except TypeError as e:
# logger.error(f"Couldn't check if {self_value.__class__} is subclass of {BaseOmni} due to {e}")
# check = False
# if check:
# logger.debug(f"Checking for subclass name.")
# self_value = self_value.name
# try:
# logger.debug(f"Check if {value.__class__} is subclass of {BaseOmni}")
# check = issubclass(value.__class__, BaseOmni)
# except TypeError as e:
# logger.error(f"Couldn't check if {value.__class__} is subclass of {BaseOmni} due to {e}")
# check = False
# if check:
# logger.debug(f"Checking for subclass name.")
# value = value.name
# logger.debug(f"Self value: {self_value}, class attr: {class_attr} of type: {type(class_attr)}")
# if isinstance(class_attr, property):
# filter = "property"
# else:
# filter = class_attr.property
# match filter:
# case ColumnProperty():
# match class_attr.type:
# case INTEGER():
# if value.lower() == "true":
# value = 1
# elif value.lower() == "false":
# value = 0
# else:
# value = int(value)
# case FLOAT():
# value = float(value)
# case "property":
# pass
# case _RelationshipDeclared():
# logger.debug(f"Checking relationship value: {self_value}")
# try:
# self_value = self_value.name
# except AttributeError:
# pass
# if class_attr.property.uselist:
# self_value = self_value.__str__()
# logger.debug(
# f"Checking self_value {self_value} of type {type(self_value)} against attribute {value} of type {type(value)}")
# if self_value != value:
# output = False
# logger.debug(f"Value {key} is False, returning.")
# return output
# return True
def check_all_attributes(self, attributes: dict) -> bool:
logger.debug(f"Incoming attributes: {attributes}")
attributes = {k : v for k, v in attributes.items() if k in self.list_searchables.keys()}
@@ -122,7 +42,6 @@ class BaseOmni(BaseModel):
logger.debug("Everything checks out, these are the same object.")
return True
def __setattr__(self, key, value):
try:
class_value = getattr(self.class_object, key)
@@ -395,6 +314,13 @@ class OmniKitTypeReagentRoleAssociation(BaseOmni):
return {}
return value
@field_validator("required", mode="before")
@classmethod
def rescue_required_none(cls, value):
if not value:
value = 1
return value
def __init__(self, instance_object: Any, **data):
super().__init__(**data)
self.instance_object = instance_object

13
src/submissions/frontend/visualizations/concentrations_chart.py
View File

@@ -1,5 +1,5 @@
"""
Construct turnaround time charts
Construct BC control concentration charts
"""
from pprint import pformat
from . import CustomFigure
@@ -21,17 +21,15 @@ class ConcentrationsChart(CustomFigure):
super().__init__(df=df, modes=modes, settings=settings)
self.df = df
self.construct_chart()
# if threshold:
# self.add_hline(y=threshold)
self.update_layout(showlegend=False)
def construct_chart(self, df: pd.DataFrame | None = None):
if df:
self.df = df
# logger.debug(f"Constructing concentration chart with df:\n{self.df}")
try:
self.df = self.df[self.df.concentration.notnull()]
self.df = self.df.sort_values(['submitted_date', 'submission'], ascending=[True, True]).reset_index(drop=True)
self.df = self.df.sort_values(['submitted_date', 'submission'], ascending=[True, True]).reset_index(
drop=True)
self.df = self.df.reset_index().rename(columns={"index": "idx"})
# logger.debug(f"DF after changes:\n{self.df}")
scatter = px.scatter(data_frame=self.df, x='submission', y="concentration",
@@ -41,8 +39,6 @@ class ConcentrationsChart(CustomFigure):
except (ValueError, AttributeError) as e:
logger.error(f"Error constructing chart: {e}")
scatter = px.scatter()
# logger.debug(f"Scatter data: {scatter.data}")
# self.add_traces(scatter.data)
# NOTE: For some reason if data is allowed to sort itself it leads to wrong ordering of x axis.
traces = sorted(scatter.data, key=itemgetter("name"))
for trace in traces:
@@ -60,6 +56,9 @@ class ConcentrationsChart(CustomFigure):
tickmode='array',
tickvals=tickvals,
ticktext=ticklabels,
),
yaxis=dict(
rangemode="nonnegative"
)
)
self.update_traces(marker={'size': 15})

21
src/submissions/frontend/widgets/concentrations.py
View File

@@ -1,7 +1,7 @@
"""
Pane showing turnaround time summary.
Pane showing BC control concentrations summary.
"""
from PyQt6.QtWidgets import QWidget, QPushButton, QComboBox, QLabel
from PyQt6.QtWidgets import QWidget, QPushButton
from .info_tab import InfoPane
from backend.excel.reports import ConcentrationMaker
from frontend.visualizations.concentrations_chart import ConcentrationsChart
@@ -22,12 +22,6 @@ class Concentrations(InfoPane):
self.layout.addWidget(self.export_button, 0, 3, 1, 1)
self.fig = None
self.report_object = None
# 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) -> None:
@@ -40,17 +34,6 @@ class Concentrations(InfoPane):
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
# subtype_obj = None
# else:
# submission_type = self.submission_typer.currentText()
# subtype_obj = SubmissionType.query(name = submission_type)
# self.report_obj = ConcentrationMaker(start_date=self.start_date, end_date=self.end_date)#, submission_type=submission_type)
self.report_obj = ConcentrationMaker(**chart_settings)
# if subtype_obj:
# threshold = subtype_obj.defaults['turnaround_time'] + 0.5
# else:
# threshold = None
self.fig = ConcentrationsChart(df=self.report_obj.df, settings=chart_settings, modes=[], months=months)
self.webview.setHtml(self.fig.html)