Can now calculate turnaround time including holidays.
This commit is contained in:
@@ -142,97 +142,97 @@ class Control(BaseClass):
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def __repr__(self) -> str:
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return f"<{self.controltype_name}({self.name})>"
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# @classmethod
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# @setup_lookup
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# def query(cls,
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# submission_type: str | None = None,
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# subtype: str | None = None,
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# start_date: date | str | int | None = None,
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# end_date: date | str | int | None = None,
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# control_name: str | None = None,
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# limit: int = 0, **kwargs
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# ) -> Control | List[Control]:
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# """
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# Lookup control objects in the database based on a number of parameters.
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#
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# Args:
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# submission_type (str | None, optional): Control archetype. Defaults to None.
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# start_date (date | str | int | None, optional): Beginning date to search by. Defaults to 2023-01-01 if end_date not None.
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# end_date (date | str | int | None, optional): End date to search by. Defaults to today if start_date not None.
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# control_name (str | None, optional): Name of control. Defaults to None.
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# limit (int, optional): Maximum number of results to return (0 = all). Defaults to 0.
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#
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# Returns:
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# PCRControl|List[PCRControl]: Control object of interest.
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# """
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# from backend.db import SubmissionType
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# query: Query = cls.__database_session__.query(cls)
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# match submission_type:
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# case str():
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# from backend import BasicSubmission, SubmissionType
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# # logger.debug(f"Lookup controls by SubmissionType str: {submission_type}")
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# query = query.join(BasicSubmission).join(SubmissionType).filter(SubmissionType.name == submission_type)
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# case SubmissionType():
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# from backend import BasicSubmission
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# # logger.debug(f"Lookup controls by SubmissionType: {submission_type}")
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# query = query.join(BasicSubmission).filter(BasicSubmission.submission_type_name == submission_type.name)
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# case _:
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# pass
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# # NOTE: by control type
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# match subtype:
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# case str():
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# if cls.__name__ == "Control":
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# raise ValueError(f"Cannot query base class Control with subtype.")
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# elif cls.__name__ == "IridaControl":
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# query = query.filter(cls.subtype == subtype)
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# else:
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# try:
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# query = query.filter(cls.subtype == subtype)
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# except AttributeError as e:
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# logger.error(e)
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# case _:
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# pass
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# # NOTE: by date range
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# if start_date is not None and end_date is None:
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# logger.warning(f"Start date with no end date, using today.")
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# end_date = date.today()
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# if end_date is not None and start_date is None:
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# logger.warning(f"End date with no start date, using 90 days ago.")
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# # start_date = date(2023, 1, 1)
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# start_date = date.today() - timedelta(days=90)
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# if start_date is not None:
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# match start_date:
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# case date():
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# # logger.debug(f"Lookup control by start date({start_date})")
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# start_date = start_date.strftime("%Y-%m-%d")
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# case int():
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# # logger.debug(f"Lookup control by ordinal start date {start_date}")
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# start_date = datetime.fromordinal(
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# datetime(1900, 1, 1).toordinal() + start_date - 2).date().strftime("%Y-%m-%d")
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# case _:
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# # logger.debug(f"Lookup control with parsed start date {start_date}")
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# start_date = parse(start_date).strftime("%Y-%m-%d")
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# match end_date:
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# case date():
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# # logger.debug(f"Lookup control by end date({end_date})")
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# end_date = end_date.strftime("%Y-%m-%d")
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# case int():
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# # logger.debug(f"Lookup control by ordinal end date {end_date}")
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# end_date = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + end_date - 2).date().strftime(
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# "%Y-%m-%d")
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# case _:
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# # logger.debug(f"Lookup control with parsed end date {end_date}")
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# end_date = parse(end_date).strftime("%Y-%m-%d")
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# # logger.debug(f"Looking up BasicSubmissions from start date: {start_date} and end date: {end_date}")
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# query = query.filter(cls.submitted_date.between(start_date, end_date))
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# match control_name:
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# case str():
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# # logger.debug(f"Lookup control by name {control_name}")
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# query = query.filter(cls.name.startswith(control_name))
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# limit = 1
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# case _:
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# pass
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# return cls.execute_query(query=query, limit=limit)
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@classmethod
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@setup_lookup
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def query(cls,
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submission_type: str | None = None,
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subtype: str | None = None,
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start_date: date | str | int | None = None,
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end_date: date | str | int | None = None,
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name: str | None = None,
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limit: int = 0, **kwargs
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) -> Control | List[Control]:
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"""
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Lookup control objects in the database based on a number of parameters.
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Args:
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submission_type (str | None, optional): Control archetype. Defaults to None.
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start_date (date | str | int | None, optional): Beginning date to search by. Defaults to 2023-01-01 if end_date not None.
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end_date (date | str | int | None, optional): End date to search by. Defaults to today if start_date not None.
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name (str | None, optional): Name of control. Defaults to None.
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limit (int, optional): Maximum number of results to return (0 = all). Defaults to 0.
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Returns:
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Control|List[Control]: Control object of interest.
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"""
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from backend.db import SubmissionType
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query: Query = cls.__database_session__.query(cls)
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match submission_type:
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case str():
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from backend import BasicSubmission, SubmissionType
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# logger.debug(f"Lookup controls by SubmissionType str: {submission_type}")
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query = query.join(BasicSubmission).join(SubmissionType).filter(SubmissionType.name == submission_type)
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case SubmissionType():
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from backend import BasicSubmission
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# logger.debug(f"Lookup controls by SubmissionType: {submission_type}")
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query = query.join(BasicSubmission).filter(BasicSubmission.submission_type_name == submission_type.name)
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case _:
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pass
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# NOTE: by control type
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match subtype:
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case str():
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if cls.__name__ == "Control":
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raise ValueError(f"Cannot query base class Control with subtype.")
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elif cls.__name__ == "IridaControl":
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query = query.filter(cls.subtype == subtype)
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else:
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try:
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query = query.filter(cls.subtype == subtype)
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except AttributeError as e:
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logger.error(e)
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case _:
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pass
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# NOTE: by date range
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if start_date is not None and end_date is None:
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logger.warning(f"Start date with no end date, using today.")
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end_date = date.today()
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if end_date is not None and start_date is None:
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logger.warning(f"End date with no start date, using 90 days ago.")
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# start_date = date(2023, 1, 1)
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start_date = date.today() - timedelta(days=90)
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if start_date is not None:
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match start_date:
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case date():
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# logger.debug(f"Lookup control by start date({start_date})")
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start_date = start_date.strftime("%Y-%m-%d")
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case int():
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# logger.debug(f"Lookup control by ordinal start date {start_date}")
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start_date = datetime.fromordinal(
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datetime(1900, 1, 1).toordinal() + start_date - 2).date().strftime("%Y-%m-%d")
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case _:
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# logger.debug(f"Lookup control with parsed start date {start_date}")
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start_date = parse(start_date).strftime("%Y-%m-%d")
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match end_date:
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case date():
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# logger.debug(f"Lookup control by end date({end_date})")
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end_date = end_date.strftime("%Y-%m-%d")
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case int():
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# logger.debug(f"Lookup control by ordinal end date {end_date}")
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end_date = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + end_date - 2).date().strftime(
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"%Y-%m-%d")
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case _:
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# logger.debug(f"Lookup control with parsed end date {end_date}")
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end_date = parse(end_date).strftime("%Y-%m-%d")
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# logger.debug(f"Looking up BasicSubmissions from start date: {start_date} and end date: {end_date}")
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query = query.filter(cls.submitted_date.between(start_date, end_date))
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match name:
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case str():
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# logger.debug(f"Lookup control by name {control_name}")
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query = query.filter(cls.name.startswith(name))
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limit = 1
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case _:
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pass
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return cls.execute_query(query=query, limit=limit)
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@classmethod
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def find_polymorphic_subclass(cls, polymorphic_identity: str | ControlType | None = None,
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@@ -323,82 +323,82 @@ class PCRControl(Control):
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return dict(name=self.name, ct=self.ct, subtype=self.subtype, target=self.target, reagent_lot=self.reagent_lot,
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submitted_date=self.submitted_date.date())
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@classmethod
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@setup_lookup
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def query(cls,
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submission_type: str | None = None,
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start_date: date | str | int | None = None,
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end_date: date | str | int | None = None,
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control_name: str | None = None,
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limit: int = 0
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) -> Control | List[Control]:
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"""
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Lookup control objects in the database based on a number of parameters.
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Args:
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submission_type (str | None, optional): Control archetype. Defaults to None.
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start_date (date | str | int | None, optional): Beginning date to search by. Defaults to 2023-01-01 if end_date not None.
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end_date (date | str | int | None, optional): End date to search by. Defaults to today if start_date not None.
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control_name (str | None, optional): Name of control. Defaults to None.
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limit (int, optional): Maximum number of results to return (0 = all). Defaults to 0.
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Returns:
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PCRControl|List[PCRControl]: Control object of interest.
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"""
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from backend.db import SubmissionType
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query: Query = cls.__database_session__.query(cls)
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# NOTE: by date range
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if start_date is not None and end_date is None:
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logger.warning(f"Start date with no end date, using today.")
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end_date = date.today()
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if end_date is not None and start_date is None:
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logger.warning(f"End date with no start date, using 90 days ago.")
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# start_date = date(2023, 1, 1)
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start_date = date.today() - timedelta(days=90)
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if start_date is not None:
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match start_date:
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case date():
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# logger.debug(f"Lookup control by start date({start_date})")
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start_date = start_date.strftime("%Y-%m-%d")
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case int():
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# logger.debug(f"Lookup control by ordinal start date {start_date}")
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start_date = datetime.fromordinal(
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datetime(1900, 1, 1).toordinal() + start_date - 2).date().strftime("%Y-%m-%d")
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case _:
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# logger.debug(f"Lookup control with parsed start date {start_date}")
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start_date = parse(start_date).strftime("%Y-%m-%d")
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match end_date:
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case date():
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# logger.debug(f"Lookup control by end date({end_date})")
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end_date = end_date.strftime("%Y-%m-%d")
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case int():
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# logger.debug(f"Lookup control by ordinal end date {end_date}")
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end_date = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + end_date - 2).date().strftime(
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"%Y-%m-%d")
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case _:
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# logger.debug(f"Lookup control with parsed end date {end_date}")
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end_date = parse(end_date).strftime("%Y-%m-%d")
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# logger.debug(f"Looking up BasicSubmissions from start date: {start_date} and end date: {end_date}")
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query = query.filter(cls.submitted_date.between(start_date, end_date))
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match submission_type:
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case str():
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from backend import BasicSubmission, SubmissionType
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# logger.debug(f"Lookup controls by SubmissionType str: {submission_type}")
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query = query.join(BasicSubmission).join(SubmissionType).filter(SubmissionType.name == submission_type)
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case SubmissionType():
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from backend import BasicSubmission
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# logger.debug(f"Lookup controls by SubmissionType: {submission_type}")
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query = query.join(BasicSubmission).filter(BasicSubmission.submission_type_name==submission_type.name)
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case _:
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pass
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match control_name:
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case str():
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# logger.debug(f"Lookup control by name {control_name}")
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query = query.filter(cls.name.startswith(control_name))
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limit = 1
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case _:
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pass
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return cls.execute_query(query=query, limit=limit)
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# @classmethod
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# @setup_lookup
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# def query(cls,
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# submission_type: str | None = None,
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# start_date: date | str | int | None = None,
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# end_date: date | str | int | None = None,
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# name: str | None = None,
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# limit: int = 0
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# ) -> Control | List[Control]:
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# """
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# Lookup control objects in the database based on a number of parameters.
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#
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# Args:
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# submission_type (str | None, optional): Control archetype. Defaults to None.
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# start_date (date | str | int | None, optional): Beginning date to search by. Defaults to 2023-01-01 if end_date not None.
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# end_date (date | str | int | None, optional): End date to search by. Defaults to today if start_date not None.
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# control_name (str | None, optional): Name of control. Defaults to None.
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# limit (int, optional): Maximum number of results to return (0 = all). Defaults to 0.
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#
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# Returns:
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# PCRControl|List[PCRControl]: Control object of interest.
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# """
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# from backend.db import SubmissionType
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# query: Query = cls.__database_session__.query(cls)
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# # NOTE: by date range
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# if start_date is not None and end_date is None:
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# logger.warning(f"Start date with no end date, using today.")
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# end_date = date.today()
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# if end_date is not None and start_date is None:
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# logger.warning(f"End date with no start date, using 90 days ago.")
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# # start_date = date(2023, 1, 1)
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# start_date = date.today() - timedelta(days=90)
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# if start_date is not None:
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# match start_date:
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# case date():
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# # logger.debug(f"Lookup control by start date({start_date})")
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# start_date = start_date.strftime("%Y-%m-%d")
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# case int():
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# # logger.debug(f"Lookup control by ordinal start date {start_date}")
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# start_date = datetime.fromordinal(
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# datetime(1900, 1, 1).toordinal() + start_date - 2).date().strftime("%Y-%m-%d")
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# case _:
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# # logger.debug(f"Lookup control with parsed start date {start_date}")
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# start_date = parse(start_date).strftime("%Y-%m-%d")
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# match end_date:
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# case date():
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# # logger.debug(f"Lookup control by end date({end_date})")
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# end_date = end_date.strftime("%Y-%m-%d")
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# case int():
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# # logger.debug(f"Lookup control by ordinal end date {end_date}")
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# end_date = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + end_date - 2).date().strftime(
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# "%Y-%m-%d")
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# case _:
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# # logger.debug(f"Lookup control with parsed end date {end_date}")
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# end_date = parse(end_date).strftime("%Y-%m-%d")
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# # logger.debug(f"Looking up BasicSubmissions from start date: {start_date} and end date: {end_date}")
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# query = query.filter(cls.submitted_date.between(start_date, end_date))
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# match submission_type:
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# case str():
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# from backend import BasicSubmission, SubmissionType
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# # logger.debug(f"Lookup controls by SubmissionType str: {submission_type}")
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# query = query.join(BasicSubmission).join(SubmissionType).filter(SubmissionType.name == submission_type)
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# case SubmissionType():
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# from backend import BasicSubmission
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# # logger.debug(f"Lookup controls by SubmissionType: {submission_type}")
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# query = query.join(BasicSubmission).filter(BasicSubmission.submission_type_name==submission_type.name)
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# case _:
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# pass
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# match control_name:
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# case str():
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# # logger.debug(f"Lookup control by name {control_name}")
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# query = query.filter(cls.name.startswith(control_name))
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# limit = 1
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# case _:
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# pass
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# return cls.execute_query(query=query, limit=limit)
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@classmethod
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@report_result
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@@ -432,7 +432,7 @@ class PCRControl(Control):
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def to_pydantic(self):
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from backend.validators import PydPCRControl
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return PydPCRControl(**self.to_sub_dict())
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return PydPCRControl(**self.to_sub_dict(), controltype_name=self.controltype_name, submission_id=self.submission_id)
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class IridaControl(Control):
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@@ -569,76 +569,76 @@ class IridaControl(Control):
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cols = []
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return cols
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@classmethod
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@setup_lookup
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def query(cls,
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sub_type: str | None = None,
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start_date: date | str | int | None = None,
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end_date: date | str | int | None = None,
|
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control_name: str | None = None,
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limit: int = 0
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) -> Control | List[Control]:
|
||||
"""
|
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Lookup control objects in the database based on a number of parameters.
|
||||
|
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Args:
|
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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
|
||||
# @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:
|
||||
@@ -828,7 +828,7 @@ 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
|
||||
|
||||
|
||||
Reference in New Issue
Block a user