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Post code clean-up, before attempt to upgrade controls to FigureWidgets

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lwark
2024-10-21 08:17:43 -05:00
parent 495d1a5a7f
commit 1f83b61c81
29 changed files with 441 additions and 1089 deletions
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104
src/submissions/backend/db/models/controls.py
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@@ -3,14 +3,12 @@ All control related models.
"""
from __future__ import annotations
from pprint import pformat
from PyQt6.QtWidgets import QWidget, QCheckBox, QLabel
from pandas import DataFrame
from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, case, FLOAT
from sqlalchemy.orm import relationship, Query, validates
import logging, re
from operator import itemgetter
from . import BaseClass
from tools import setup_lookup, report_result, Result, Report, Settings, get_unique_values_in_df_column, super_splitter
from datetime import date, datetime, timedelta
@@ -73,7 +71,6 @@ class ControlType(BaseClass):
if not self.instances:
return
jsoner = getattr(self.instances[0], mode)
# logger.debug(f"JSON retrieved: {jsoner.keys()}")
try:
# NOTE: Pick genera (all should have same subtypes)
genera = list(jsoner.keys())[0]
@@ -81,10 +78,15 @@ class ControlType(BaseClass):
return []
# NOTE: remove items that don't have relevant data
subtypes = [item for item in jsoner[genera] if "_hashes" not in item and "_ratio" not in item]
# logger.debug(f"subtypes out: {pformat(subtypes)}")
return subtypes
def get_instance_class(self):
def get_instance_class(self) -> Control:
"""
Retrieves the Control class associated with this controltype
Returns:
Control: Associated Control class
"""
return Control.find_polymorphic_subclass(polymorphic_identity=self.name)
@classmethod
@@ -93,7 +95,7 @@ class ControlType(BaseClass):
Gets list of Control types if they have targets
Returns:
List[ControlType]: Control types that have targets
Generator[str, None, None]: Control types that have targets
"""
ct = cls.query(name=control_type).targets
return (item for item in ct.keys() if ct[item])
@@ -106,7 +108,6 @@ class ControlType(BaseClass):
Returns:
Pattern: Constructed pattern
"""
# strings = list(set([item.name.split("-")[0] for item in cls.get_positive_control_types()]))
strings = list(set([super_splitter(item, "-", 0) for item in cls.get_positive_control_types(control_type)]))
return re.compile(rf"(^{'|^'.join(strings)})-.*", flags=re.IGNORECASE)
@@ -144,7 +145,7 @@ class Control(BaseClass):
@classmethod
def find_polymorphic_subclass(cls, polymorphic_identity: str | ControlType | None = None,
attrs: dict | None = None):
attrs: dict | None = None) -> Control:
"""
Find subclass based on polymorphic identity or relevant attributes.
@@ -153,7 +154,7 @@ class Control(BaseClass):
attrs (str | SubmissionType | None, optional): Attributes of the relevant class. Defaults to None.
Returns:
_type_: Subclass of interest.
Control: Subclass of interest.
"""
if isinstance(polymorphic_identity, dict):
# logger.debug(f"Controlling for dict value")
@@ -184,7 +185,8 @@ class Control(BaseClass):
@classmethod
def make_parent_buttons(cls, parent: QWidget) -> None:
"""
Super that will make buttons in a CustomFigure. Made to be overrided.
Args:
parent (QWidget): chart holding widget to add buttons to.
@@ -196,13 +198,11 @@ class Control(BaseClass):
@classmethod
def make_chart(cls, parent, chart_settings: dict, ctx):
"""
Dummy operation to be overridden by child classes.
Args:
chart_settings (dict): settings passed down from chart widget
ctx (Settings): settings passed down from gui
Returns:
"""
return None
@@ -220,7 +220,13 @@ class PCRControl(Control):
polymorphic_load="inline",
inherit_condition=(id == Control.id))
def to_sub_dict(self):
def to_sub_dict(self) -> dict:
"""
Creates dictionary of fields for this object
Returns:
dict: Output dict of name, ct, subtype, target, reagent_lot and submitted_date
"""
return dict(name=self.name, ct=self.ct, subtype=self.subtype, target=self.target, reagent_lot=self.reagent_lot,
submitted_date=self.submitted_date.date())
@@ -237,15 +243,16 @@ class PCRControl(Control):
Lookup control objects in the database based on a number of parameters.
Args:
sub_type (models.ControlType | str | None, optional): Control archetype. Defaults to None.
sub_type (str | None, optional): Control archetype. Defaults to None.
start_date (date | str | int | None, optional): Beginning date to search by. Defaults to 2023-01-01 if end_date not None.
end_date (date | str | int | None, optional): End date to search by. Defaults to today if start_date not None.
control_name (str | None, optional): Name of control. Defaults to None.
limit (int, optional): Maximum number of results to return (0 = all). Defaults to 0.
Returns:
models.Control|List[models.Control]: Control object of interest.
PCRControl|List[PCRControl]: Control object of interest.
"""
from backend.db import SubmissionType
query: Query = cls.__database_session__.query(cls)
# NOTE: by date range
if start_date is not None and end_date is None:
@@ -282,7 +289,12 @@ class PCRControl(Control):
match sub_type:
case str():
from backend import BasicSubmission, SubmissionType
# logger.debug(f"Lookup controls by SubmissionType str: {sub_type}")
query = query.join(BasicSubmission).join(SubmissionType).filter(SubmissionType.name == sub_type)
case SubmissionType():
from backend import BasicSubmission
# logger.debug(f"Lookup controls by SubmissionType: {sub_type}")
query = query.join(BasicSubmission).filter(BasicSubmission.submission_type_name==sub_type.name)
case _:
pass
match control_name:
@@ -295,7 +307,18 @@ class PCRControl(Control):
return cls.execute_query(query=query, limit=limit)
@classmethod
def make_chart(cls, parent, chart_settings: dict, ctx):
def make_chart(cls, parent, chart_settings: dict, ctx: Settings) -> Tuple[Report, "PCRFigure"]:
"""
Creates a PCRFigure. Overrides parent
Args:
parent (__type__): Widget to contain the chart.
chart_settings (dict): settings passed down from chart widget
ctx (Settings): settings passed down from gui. Not used here.
Returns:
Tuple[Report, "PCRFigure"]: Report of status and resulting figure.
"""
from frontend.visualizations.pcr_charts import PCRFigure
parent.mode_typer.clear()
parent.mode_typer.setEnabled(False)
@@ -308,7 +331,7 @@ class PCRControl(Control):
df = df[df.ct > 0.0]
except AttributeError:
df = df
fig = PCRFigure(df=df, modes=None)
fig = PCRFigure(df=df, modes=[])
return report, fig
@@ -324,16 +347,26 @@ class IridaControl(Control):
sample = relationship("BacterialCultureSample", back_populates="control") #: This control's submission sample
sample_id = Column(INTEGER,
ForeignKey("_basicsample.id", ondelete="SET NULL", name="cont_BCS_id")) #: sample id key
# submission_id = Column(INTEGER, ForeignKey("_basicsubmission.id")) #: parent submission id
# submission = relationship("BacterialCulture", back_populates="controls",
# foreign_keys=[submission_id]) #: parent submission
__mapper_args__ = dict(polymorphic_identity="Irida Control",
polymorphic_load="inline",
inherit_condition=(id == Control.id))
@validates("sub_type")
def enforce_subtype_literals(self, key: str, value: str):
def enforce_subtype_literals(self, key: str, value: str) -> str:
"""
Validates sub_type field with acceptable values
Args:
key (str): Field name
value (str): Field Value
Raises:
KeyError: Raised if value is not in the acceptable list.
Returns:
str: Validated string.
"""
acceptables = ['ATCC49226', 'ATCC49619', 'EN-NOS', "EN-SSTI", "MCS-NOS", "MCS-SSTI", "SN-NOS", "SN-SSTI"]
if value.upper() not in acceptables:
raise KeyError(f"Sub-type must be in {acceptables}")
@@ -346,7 +379,6 @@ class IridaControl(Control):
Returns:
dict: output dictionary containing: Name, Type, Targets, Top Kraken results
"""
# logger.debug("loading json string into dict")
try:
kraken = self.kraken
except TypeError:
@@ -405,8 +437,6 @@ class IridaControl(Control):
k.strip("*") not in self.controltype.targets[control_sub_type])
on_tar['Off-target'] = {f"{mode}_ratio": off_tar}
data = on_tar
# logger.debug(pformat(data))
# logger.debug(f"Length of data: {len(data)}")
# logger.debug("dict keys are genera of bacteria, e.g. 'Streptococcus'")
for genus in data:
_dict = dict(
@@ -416,7 +446,6 @@ class IridaControl(Control):
target='Target' if genus.strip("*") in self.controltype.targets[control_sub_type] else "Off-target"
)
# logger.debug("get Target or Off-target of genus")
# logger.debug("set 'contains_hashes', etc for genus")
for key in data[genus]:
_dict[key] = data[genus][key]
yield _dict
@@ -462,12 +491,7 @@ class IridaControl(Control):
query: Query = cls.__database_session__.query(cls)
# NOTE: by control type
match sub_type:
# case ControlType():
# # logger.debug(f"Looking up control by control type: {sub_type}")
# query = query.filter(cls.controltype == sub_type)
case str():
# logger.debug(f"Looking up control by control type: {sub_type}")
# query = query.join(ControlType).filter(ControlType.name == sub_type)
query = query.filter(cls.sub_type == sub_type)
case _:
pass
@@ -519,8 +543,6 @@ class IridaControl(Control):
Args:
parent (QWidget): chart holding widget to add buttons to.
Returns:
"""
super().make_parent_buttons(parent=parent)
rows = parent.layout.rowCount()
@@ -536,6 +558,17 @@ class IridaControl(Control):
@classmethod
@report_result
def make_chart(cls, chart_settings: dict, parent, ctx) -> Tuple[Report, "IridaFigure" | None]:
"""
Creates a IridaFigure. Overrides parent
Args:
parent (__type__): Widget to contain the chart.
chart_settings (dict): settings passed down from chart widget
ctx (Settings): settings passed down from gui.
Returns:
Tuple[Report, "IridaFigure"]: Report of status and resulting figure.
"""
from frontend.visualizations import IridaFigure
try:
checker = parent.findChild(QCheckBox, name="irida_check")
@@ -574,8 +607,6 @@ class IridaControl(Control):
# NOTE: send dataframe to chart maker
df, modes = cls.prep_df(ctx=ctx, df=df)
# logger.debug(f"prepped df: \n {df}")
# assert modes
# logger.debug(f"modes: {modes}")
fig = IridaFigure(df=df, ytitle=title, modes=modes, parent=parent,
months=chart_settings['months'])
return report, fig
@@ -604,7 +635,6 @@ class IridaControl(Control):
else:
safe.append(column)
if "percent" in column:
# count_col = [item for item in df.columns if "count" in item][0]
try:
count_col = next(item for item in df.columns if "count" in item)
except StopIteration: