Update to add SQL Server support.
This commit is contained in:
lwark
@@ -66,18 +66,18 @@ class ControlType(BaseClass):
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Returns:
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List[str]: list of subtypes available
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"""
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# NOTE: Get first instance since all should have same subtypes
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# NOTE: Get mode of instance
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if not self.instances:
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return
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# NOTE: Get first instance since all should have same subtypes
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# NOTE: Get mode of instance
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jsoner = getattr(self.instances[0], mode)
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try:
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# NOTE: Pick genera (all should have same subtypes)
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genera = list(jsoner.keys())[0]
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except IndexError:
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return []
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# NOTE: remove items that don't have relevant data
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subtypes = [item for item in jsoner[genera] if "_hashes" not in item and "_ratio" not in item]
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# NOTE subtypes now created for all modes, but ignored for all but allowed_for_subtyping later in the ControlsChart
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subtypes = sorted(list(jsoner[genera].keys()), reverse=True)
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return subtypes
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def get_instance_class(self) -> Control:
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@@ -98,7 +98,7 @@ class ControlType(BaseClass):
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Generator[str, None, None]: Control types that have targets
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"""
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ct = cls.query(name=control_type).targets
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return (item for item in ct.keys() if ct[item])
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return (k for k, v in ct.items() if v)
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@classmethod
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def build_positive_regex(cls, control_type:str) -> Pattern:
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@@ -141,6 +141,98 @@ 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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def find_polymorphic_subclass(cls, polymorphic_identity: str | ControlType | None = None,
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attrs: dict | None = None) -> Control:
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@@ -155,10 +247,9 @@ class Control(BaseClass):
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Control: Subclass of interest.
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"""
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if isinstance(polymorphic_identity, dict):
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# logger.debug(f"Controlling for dict value")
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polymorphic_identity = polymorphic_identity['value']
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if isinstance(polymorphic_identity, ControlType):
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polymorphic_identity = polymorphic_identity.name
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# if isinstance(polymorphic_identity, ControlType):
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# polymorphic_identity = polymorphic_identity.name
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model = cls
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match polymorphic_identity:
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case str():
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@@ -167,6 +258,12 @@ class Control(BaseClass):
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except Exception as e:
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logger.error(
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f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}, falling back to BasicSubmission")
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case ControlType():
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try:
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model = cls.__mapper__.polymorphic_map[polymorphic_identity.name].class_
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except Exception as e:
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logger.error(
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f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}, falling back to BasicSubmission")
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case _:
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pass
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if attrs and any([not hasattr(cls, attr) for attr in attrs.keys()]):
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@@ -228,7 +325,7 @@ class PCRControl(Control):
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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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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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@@ -238,7 +335,7 @@ class PCRControl(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 (str | None, optional): Control archetype. Defaults to None.
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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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@@ -254,8 +351,9 @@ class PCRControl(Control):
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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 Jan 1, 2023")
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start_date = date(2023, 1, 1)
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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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@@ -281,15 +379,15 @@ class PCRControl(Control):
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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 sub_type:
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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: {sub_type}")
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query = query.join(BasicSubmission).join(SubmissionType).filter(SubmissionType.name == sub_type)
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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: {sub_type}")
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query = query.join(BasicSubmission).filter(BasicSubmission.submission_type_name==sub_type.name)
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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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@@ -319,7 +417,8 @@ class PCRControl(Control):
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parent.mode_typer.clear()
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parent.mode_typer.setEnabled(False)
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report = Report()
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controls = cls.query(sub_type=chart_settings['sub_type'], start_date=chart_settings['start_date'],
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logger.debug(f"Chart settings: {pformat(chart_settings)}")
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controls = cls.query(submission_type=chart_settings['sub_type'], start_date=chart_settings['start_date'],
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end_date=chart_settings['end_date'])
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data = [control.to_sub_dict() for control in controls]
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df = DataFrame.from_records(data)
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@@ -332,11 +431,14 @@ class PCRControl(Control):
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class IridaControl(Control):
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subtyping_allowed = ['kraken']
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id = Column(INTEGER, ForeignKey('_control.id'), primary_key=True)
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contains = Column(JSON) #: unstructured hashes in contains.tsv for each organism
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matches = Column(JSON) #: unstructured hashes in matches.tsv for each organism
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kraken = Column(JSON) #: unstructured output from kraken_report
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sub_type = Column(String(16), nullable=False) #: EN-NOS, MCS-NOS, etc
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subtype = Column(String(16), nullable=False) #: EN-NOS, MCS-NOS, etc
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refseq_version = Column(String(16)) #: version of refseq used in fastq parsing
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kraken2_version = Column(String(16)) #: version of kraken2 used in fastq parsing
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kraken2_db_version = Column(String(32)) #: folder name of kraken2 db
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@@ -488,16 +590,17 @@ class IridaControl(Control):
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# NOTE: by control type
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match sub_type:
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case str():
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query = query.filter(cls.sub_type == sub_type)
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query = query.filter(cls.subtype == sub_type)
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case _:
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pass
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# NOTE: by date range
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# NOTE: If one date exists, we need the other one to exist as well.
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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 Jan 1, 2023")
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start_date = date(2023, 1, 1)
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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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