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Pre-code cleanup.

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This commit is contained in:
lwark
2025-03-25 15:25:14 -05:00
parent 6404bc499b
commit 3ec79fdcfe
7 changed files with 40 additions and 128 deletions
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1
CHANGELOG.md
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@@ -1,6 +1,7 @@
# 202503.05
- Added concentrations chart tab.
- Saving report xlsx/pdf now inserts report class name in file name.
# 202503.04

33
src/submissions/backend/db/models/__init__.py
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@@ -56,23 +56,23 @@ class BaseClass(Base):
omni_inheritable = []
searchables = []
@classproperty
def skip_on_edit(cls):
if "association" in cls.__name__.lower() or cls.__name__.lower() == "discount":
return True
else:
return False
# @classproperty
# def skip_on_edit(cls):
# if "association" in cls.__name__.lower() or cls.__name__.lower() == "discount":
# return True
# else:
# return False
@classproperty
def aliases(cls):
return [cls.query_alias]
@classproperty
def level(cls):
if "association" in cls.__name__.lower() or cls.__name__.lower() == "discount":
return 2
else:
return 1
# @classproperty
# def level(cls):
# if "association" in cls.__name__.lower() or cls.__name__.lower() == "discount":
# return 2
# else:
# return 1
@classproperty
def query_alias(cls):
@@ -187,8 +187,9 @@ class BaseClass(Base):
return query.limit(50).all()
@classmethod
def results_to_df(cls, objects: list, **kwargs) -> DataFrame:
def results_to_df(cls, objects: list|None=None, **kwargs) -> DataFrame:
"""
Converts class sub_dicts into a Dataframe for all instances of the class.
Args:
objects (list): Objects to be converted to dataframe.
@@ -197,6 +198,12 @@ class BaseClass(Base):
Returns:
Dataframe
"""
if not objects:
try:
records = [obj.to_sub_dict(**kwargs) for obj in cls.query()]
except AttributeError:
records = [obj.to_dict(**kwargs) for obj in cls.query(page_size=0)]
else:
try:
records = [obj.to_sub_dict(**kwargs) for obj in objects]
except AttributeError:

5
src/submissions/backend/db/models/controls.py
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@@ -262,7 +262,7 @@ class Control(BaseClass):
try:
model = next(subclass for subclass in cls.__subclasses__() if
all([hasattr(subclass, attr) for attr in attrs.keys()]))
except StopIteration as e:
except StopIteration:
raise AttributeError(
f"Couldn't find existing class/subclass of {cls} with all attributes:\n{pformat(attrs.keys())}")
return model
@@ -286,6 +286,7 @@ class Control(BaseClass):
Dummy operation to be overridden by child classes.
Args:
parent (QWidget): widget to add chart to.
chart_settings (dict): settings passed down from chart widget
ctx (Settings): settings passed down from gui
"""
@@ -663,7 +664,7 @@ class IridaControl(Control):
return df, previous_dates
# NOTE: if date was changed, rerun with new date
else:
logger.warning(f"Date check failed, running recursion")
logger.warning(f"Date check failed, running recursion.")
df, previous_dates = cls.check_date(df, item, previous_dates)
return df, previous_dates

10
src/submissions/backend/db/models/submissions.py
View File

@@ -31,7 +31,6 @@ from jinja2.exceptions import TemplateNotFound
from jinja2 import Template
from PIL import Image
logger = logging.getLogger(f"submissions.{__name__}")
@@ -1584,7 +1583,7 @@ class Wastewater(BasicSubmission):
continue
thing['tooltip'] = f"Sample Name: {thing['name']}\nWell: {thing['sample_location']}"
dummy_samples.append(thing)
logger.debug(f"Dummy samples for 24 well: {pformat(dummy_samples)}")
# logger.debug(f"Dummy samples for 24 well: {pformat(dummy_samples)}")
output['origin_plate'] = self.__class__.make_plate_map(sample_list=dummy_samples, plate_rows=4,
plate_columns=6)
# logger.debug(f"PCR info: {output['pcr_info']}")
@@ -2772,7 +2771,12 @@ class BacterialCultureSample(BasicSample):
sample['concentration'] = self.concentration
if self.control is not None:
sample['colour'] = [0, 128, 0]
sample['tooltip'] = f"Control: {self.control.controltype.name} - {self.control.controltype.targets}"
target = next((v for k,v in self.control.controltype.targets.items() if k == self.control.subtype), "Not Available")
try:
target = ", ".join(target)
except:
target = "None"
sample['tooltip'] = f"\nControl: {self.control.controltype.name} - {target}"
return sample

2
src/submissions/frontend/visualizations/__init__.py
View File

@@ -134,3 +134,5 @@ class CustomFigure(Figure):
from .irida_charts import IridaFigure
from .pcr_charts import PCRFigure
from .concentrations_chart import ConcentrationsChart
from .turnaround_chart import TurnaroundChart

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

@@ -60,12 +60,12 @@ class InfoPane(QWidget):
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")
fname = select_save_file(self, default_name=f"{self.__class__.__name__} 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)
def save_pdf(self):
fname = select_save_file(obj=self,
default_name=f"Report {self.start_date.strftime('%Y%m%d')} - {self.end_date.strftime('%Y%m%d')}",
default_name=f"{self.__class__.__name__} Report {self.start_date.strftime('%Y%m%d')} - {self.end_date.strftime('%Y%m%d')}",
extension="pdf")
save_pdf(obj=self.webview, filename=fname)

105
src/submissions/frontend/widgets/misc.py
View File

@@ -2,13 +2,12 @@
Contains miscellaneous widgets for frontend functions
"""
import math
from datetime import date
from PyQt6.QtGui import QStandardItem, QIcon
from PyQt6.QtWidgets import (
QLabel, QLineEdit, QComboBox, QDateEdit, QPushButton, QWidget,
QHBoxLayout, QSizePolicy
)
from PyQt6.QtCore import Qt, QDate, QSize, QMarginsF
from PyQt6.QtCore import Qt, QDate, QSize
from tools import jinja_template_loading
from backend.db.models import *
import logging
@@ -18,98 +17,6 @@ logger = logging.getLogger(f"submissions.{__name__}")
env = jinja_template_loading()
# class AddReagentForm(QDialog):
# """
# dialog to add gather info about new reagent (Defunct)
# """
#
# def __init__(self, reagent_lot: str | None = None, reagent_role: str | None = None, expiry: date | None = None,
# reagent_name: str | None = None, kit: str | KitType | None = None) -> None:
# super().__init__()
# if reagent_name is None:
# reagent_name = reagent_role
# self.setWindowTitle("Add Reagent")
# QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
# self.buttonBox = QDialogButtonBox(QBtn)
# self.buttonBox.accepted.connect(self.accept)
# self.buttonBox.rejected.connect(self.reject)
# # NOTE: widget to get lot info
# self.name_input = QComboBox()
# self.name_input.setObjectName("name")
# self.name_input.setEditable(True)
# self.name_input.setCurrentText(reagent_name)
# self.lot_input = QLineEdit()
# self.lot_input.setObjectName("lot")
# self.lot_input.setText(reagent_lot)
# # NOTE: widget to get expiry info
# self.expiry_input = QDateEdit(calendarPopup=True)
# self.expiry_input.setObjectName('expiry')
# # NOTE: if expiry is not passed in from gui, use today
# if expiry is None:
# logger.warning(f"Did not receive expiry, setting to 1970, 1, 1")
# self.expiry_input.setDate(QDate(1970, 1, 1))
# else:
# try:
# self.expiry_input.setDate(expiry)
# except TypeError:
# self.expiry_input.setDate(QDate(1970, 1, 1))
# # NOTE: widget to get reagent type info
# self.role_input = QComboBox()
# self.role_input.setObjectName('role')
# if kit:
# match kit:
# case str():
# kit = KitType.query(name=kit)
# case _:
# pass
# self.role_input.addItems([item.name for item in ReagentRole.query() if kit in item.kit_types])
# else:
# self.role_input.addItems([item.name for item in ReagentRole.query()])
# # NOTE: convert input to user-friendly string?
# try:
# reagent_role = reagent_role.replace("_", " ").title()
# except AttributeError:
# reagent_role = None
# # NOTE: set parsed reagent type to top of list
# index = self.role_input.findText(reagent_role, Qt.MatchFlag.MatchEndsWith)
# if index >= 0:
# self.role_input.setCurrentIndex(index)
# self.layout = QVBoxLayout()
# self.layout.addWidget(QLabel("Name:"))
# self.layout.addWidget(self.name_input)
# self.layout.addWidget(QLabel("Lot:"))
# self.layout.addWidget(self.lot_input)
# self.layout.addWidget(
# QLabel("Expiry:\n(use exact date on reagent.\nEOL will be calculated from kit automatically)")
# )
# self.layout.addWidget(self.expiry_input)
# self.layout.addWidget(QLabel("Type:"))
# self.layout.addWidget(self.role_input)
# self.layout.addWidget(self.buttonBox)
# self.setLayout(self.layout)
# self.role_input.currentTextChanged.connect(self.update_names)
#
# def parse_form(self) -> dict:
# """
# Converts information in form to dict.
#
# Returns:
# dict: Output info
# """
# return dict(name=self.name_input.currentText().strip(),
# lot=self.lot_input.text().strip(),
# expiry=self.expiry_input.date().toPyDate(),
# role=self.role_input.currentText().strip())
#
# def update_names(self):
# """
# Updates reagent names form field with examples from reagent type
# """
# self.name_input.clear()
# lookup = Reagent.query(role=self.role_input.currentText())
# self.name_input.addItems(list(set([item.name for item in lookup])))
#
#
class StartEndDatePicker(QWidget):
"""
custom widget to pick start and end dates for controls graphs
@@ -135,16 +42,6 @@ class StartEndDatePicker(QWidget):
return QSize(80, 20)
# def save_pdf(obj: QWebEngineView, filename: Path):
# page_layout = QPageLayout()
# page_layout.setPageSize(QPageSize(QPageSize.PageSizeId.A4))
# page_layout.setOrientation(QPageLayout.Orientation.Portrait)
# page_layout.setMargins(QMarginsF(25, 25, 25, 25))
# obj.page().printToPdf(filename.absolute().__str__(), page_layout)
# NOTE: subclass
class CheckableComboBox(QComboBox):
# once there is a checkState set, it is rendered
# here we assume default Unchecked