mid code cleanup
This commit is contained in:
lwark
@@ -156,7 +156,8 @@ class Control(BaseClass):
|
||||
Lookup control objects in the database based on a number of parameters.
|
||||
|
||||
Args:
|
||||
submission_type (str | None, optional): Control archetype. Defaults to None.
|
||||
submission_type (str | None, optional): Submission type associated with control. Defaults to None.
|
||||
subtype (str | None, optional): Control subtype, eg IridaControl. 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.
|
||||
name (str | None, optional): Name of control. Defaults to None.
|
||||
@@ -198,7 +199,6 @@ class Control(BaseClass):
|
||||
end_date = date.today()
|
||||
if end_date is not None and start_date is None:
|
||||
logger.warning(f"End date with no start date, using 90 days ago.")
|
||||
# start_date = date(2023, 1, 1)
|
||||
start_date = date.today() - timedelta(days=90)
|
||||
if start_date is not None:
|
||||
match start_date:
|
||||
@@ -249,8 +249,6 @@ class Control(BaseClass):
|
||||
"""
|
||||
if isinstance(polymorphic_identity, dict):
|
||||
polymorphic_identity = polymorphic_identity['value']
|
||||
# if isinstance(polymorphic_identity, ControlType):
|
||||
# polymorphic_identity = polymorphic_identity.name
|
||||
model = cls
|
||||
match polymorphic_identity:
|
||||
case str():
|
||||
@@ -304,10 +302,10 @@ class PCRControl(Control):
|
||||
id = Column(INTEGER, ForeignKey('_control.id'), primary_key=True)
|
||||
subtype = Column(String(16)) #: PC or NC
|
||||
target = Column(String(16)) #: N1, N2, etc.
|
||||
ct = Column(FLOAT)
|
||||
ct = Column(FLOAT) #: PCR result
|
||||
reagent_lot = Column(String(64), ForeignKey("_reagent.name", ondelete="SET NULL",
|
||||
name="fk_reagent_lot"))
|
||||
reagent = relationship("Reagent", foreign_keys=reagent_lot)
|
||||
reagent = relationship("Reagent", foreign_keys=reagent_lot) #: reagent used for this control
|
||||
|
||||
__mapper_args__ = dict(polymorphic_identity="PCR Control",
|
||||
polymorphic_load="inline",
|
||||
@@ -323,83 +321,6 @@ class PCRControl(Control):
|
||||
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())
|
||||
|
||||
# @classmethod
|
||||
# @setup_lookup
|
||||
# def query(cls,
|
||||
# submission_type: str | None = None,
|
||||
# start_date: date | str | int | None = None,
|
||||
# end_date: date | str | int | None = None,
|
||||
# name: str | None = None,
|
||||
# limit: int = 0
|
||||
# ) -> Control | List[Control]:
|
||||
# """
|
||||
# Lookup control objects in the database based on a number of parameters.
|
||||
#
|
||||
# Args:
|
||||
# submission_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:
|
||||
# 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:
|
||||
# logger.warning(f"Start date with no end date, using today.")
|
||||
# end_date = date.today()
|
||||
# if end_date is not None and start_date is None:
|
||||
# logger.warning(f"End date with no start date, using 90 days ago.")
|
||||
# # start_date = date(2023, 1, 1)
|
||||
# start_date = date.today() - timedelta(days=90)
|
||||
# if start_date is not None:
|
||||
# match start_date:
|
||||
# case date():
|
||||
# # logger.debug(f"Lookup control by start date({start_date})")
|
||||
# start_date = start_date.strftime("%Y-%m-%d")
|
||||
# case int():
|
||||
# # logger.debug(f"Lookup control by ordinal start date {start_date}")
|
||||
# start_date = datetime.fromordinal(
|
||||
# datetime(1900, 1, 1).toordinal() + start_date - 2).date().strftime("%Y-%m-%d")
|
||||
# case _:
|
||||
# # logger.debug(f"Lookup control with parsed start date {start_date}")
|
||||
# start_date = parse(start_date).strftime("%Y-%m-%d")
|
||||
# match end_date:
|
||||
# case date():
|
||||
# # logger.debug(f"Lookup control by end date({end_date})")
|
||||
# end_date = end_date.strftime("%Y-%m-%d")
|
||||
# case int():
|
||||
# # logger.debug(f"Lookup control by ordinal end date {end_date}")
|
||||
# end_date = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + end_date - 2).date().strftime(
|
||||
# "%Y-%m-%d")
|
||||
# case _:
|
||||
# # logger.debug(f"Lookup control with parsed end date {end_date}")
|
||||
# end_date = parse(end_date).strftime("%Y-%m-%d")
|
||||
# # logger.debug(f"Looking up BasicSubmissions from start date: {start_date} and end date: {end_date}")
|
||||
# query = query.filter(cls.submitted_date.between(start_date, end_date))
|
||||
# match submission_type:
|
||||
# case str():
|
||||
# from backend import BasicSubmission, SubmissionType
|
||||
# # logger.debug(f"Lookup controls by SubmissionType str: {submission_type}")
|
||||
# query = query.join(BasicSubmission).join(SubmissionType).filter(SubmissionType.name == submission_type)
|
||||
# case SubmissionType():
|
||||
# from backend import BasicSubmission
|
||||
# # logger.debug(f"Lookup controls by SubmissionType: {submission_type}")
|
||||
# query = query.join(BasicSubmission).filter(BasicSubmission.submission_type_name==submission_type.name)
|
||||
# case _:
|
||||
# pass
|
||||
# match control_name:
|
||||
# case str():
|
||||
# # logger.debug(f"Lookup control by name {control_name}")
|
||||
# query = query.filter(cls.name.startswith(control_name))
|
||||
# limit = 1
|
||||
# case _:
|
||||
# pass
|
||||
# return cls.execute_query(query=query, limit=limit)
|
||||
|
||||
@classmethod
|
||||
@report_result
|
||||
def make_chart(cls, parent, chart_settings: dict, ctx: Settings) -> Tuple[Report, "PCRFigure"]:
|
||||
@@ -418,7 +339,7 @@ class PCRControl(Control):
|
||||
parent.mode_typer.clear()
|
||||
parent.mode_typer.setEnabled(False)
|
||||
report = Report()
|
||||
logger.debug(f"Chart settings: {pformat(chart_settings)}")
|
||||
# logger.debug(f"Chart settings: {pformat(chart_settings)}")
|
||||
controls = cls.query(submission_type=chart_settings['sub_type'], start_date=chart_settings['start_date'],
|
||||
end_date=chart_settings['end_date'])
|
||||
data = [control.to_sub_dict() for control in controls]
|
||||
@@ -569,77 +490,6 @@ class IridaControl(Control):
|
||||
cols = []
|
||||
return cols
|
||||
|
||||
# @classmethod
|
||||
# @setup_lookup
|
||||
# def query(cls,
|
||||
# sub_type: str | None = None,
|
||||
# start_date: date | str | int | None = None,
|
||||
# end_date: date | str | int | None = None,
|
||||
# control_name: str | None = None,
|
||||
# limit: int = 0
|
||||
# ) -> Control | List[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.
|
||||
# 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.
|
||||
# """
|
||||
# query: Query = cls.__database_session__.query(cls)
|
||||
# # NOTE: by control type
|
||||
# match sub_type:
|
||||
# case str():
|
||||
# query = query.filter(cls.subtype == sub_type)
|
||||
# case _:
|
||||
# pass
|
||||
# # NOTE: If one date exists, we need the other one to exist as well.
|
||||
# if start_date is not None and end_date is None:
|
||||
# logger.warning(f"Start date with no end date, using today.")
|
||||
# end_date = date.today()
|
||||
# if end_date is not None and start_date is None:
|
||||
# logger.warning(f"End date with no start date, using 90 days ago.")
|
||||
# # start_date = date(2023, 1, 1)
|
||||
# start_date = date.today() - timedelta(days=90)
|
||||
# if start_date is not None:
|
||||
# match start_date:
|
||||
# case date():
|
||||
# # logger.debug(f"Lookup control by start date({start_date})")
|
||||
# start_date = start_date.strftime("%Y-%m-%d")
|
||||
# case int():
|
||||
# # logger.debug(f"Lookup control by ordinal start date {start_date}")
|
||||
# start_date = datetime.fromordinal(
|
||||
# datetime(1900, 1, 1).toordinal() + start_date - 2).date().strftime("%Y-%m-%d")
|
||||
# case _:
|
||||
# # logger.debug(f"Lookup control with parsed start date {start_date}")
|
||||
# start_date = parse(start_date).strftime("%Y-%m-%d")
|
||||
# match end_date:
|
||||
# case date():
|
||||
# # logger.debug(f"Lookup control by end date({end_date})")
|
||||
# end_date = end_date.strftime("%Y-%m-%d")
|
||||
# case int():
|
||||
# # logger.debug(f"Lookup control by ordinal end date {end_date}")
|
||||
# end_date = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + end_date - 2).date().strftime(
|
||||
# "%Y-%m-%d")
|
||||
# case _:
|
||||
# # logger.debug(f"Lookup control with parsed end date {end_date}")
|
||||
# end_date = parse(end_date).strftime("%Y-%m-%d")
|
||||
# # logger.debug(f"Looking up BasicSubmissions from start date: {start_date} and end date: {end_date}")
|
||||
# query = query.filter(cls.submitted_date.between(start_date, end_date))
|
||||
# match control_name:
|
||||
# case str():
|
||||
# # logger.debug(f"Lookup control by name {control_name}")
|
||||
# query = query.filter(cls.name.startswith(control_name))
|
||||
# limit = 1
|
||||
# case _:
|
||||
# pass
|
||||
# return cls.execute_query(query=query, limit=limit)
|
||||
|
||||
@classmethod
|
||||
def make_parent_buttons(cls, parent: QWidget) -> None:
|
||||
"""
|
||||
@@ -650,7 +500,7 @@ class IridaControl(Control):
|
||||
"""
|
||||
super().make_parent_buttons(parent=parent)
|
||||
rows = parent.layout.rowCount()
|
||||
logger.debug(f"Parent rows: {rows}")
|
||||
# logger.debug(f"Parent rows: {rows}")
|
||||
checker = QCheckBox(parent)
|
||||
checker.setChecked(True)
|
||||
checker.setObjectName("irida_check")
|
||||
|
||||
Reference in New Issue
Block a user