Midway through disaster of changing table names.
This commit is contained in:
Landon Wark
@@ -12,7 +12,6 @@ from typing import List
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from pandas import ExcelFile
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from pathlib import Path
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from . import Base, BaseClass, Organization
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from tools import Settings
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logger = logging.getLogger(f'submissions.{__name__}')
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@@ -32,11 +31,19 @@ equipmentroles_equipment = Table(
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extend_existing=True
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)
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equipment_processes = Table(
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"_equipment_processes",
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Base.metadata,
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Column("process_id", INTEGER, ForeignKey("_process.id")),
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Column("equipment_id", INTEGER, ForeignKey("_equipment.id")),
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extend_existing=True
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)
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equipmentroles_processes = Table(
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"_equipmentroles_processes",
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Base.metadata,
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Column("process_id", INTEGER, ForeignKey("_process.id")),
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Column("equipmentroles_id", INTEGER, ForeignKey("_equipment_roles.id")),
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Column("equipmentrole_id", INTEGER, ForeignKey("_equipment_roles.id")),
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extend_existing=True
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)
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@@ -48,16 +55,24 @@ submissiontypes_processes = Table(
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extend_existing=True
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)
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kittypes_processes = Table(
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"_kittypes_processes",
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Base.metadata,
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Column("process_id", INTEGER, ForeignKey("_process.id")),
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Column("kit_id", INTEGER, ForeignKey("_kits.id")),
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extend_existing=True
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)
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class KitType(BaseClass):
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"""
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Base of kits used in submission processing
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"""
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__tablename__ = "_kits"
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# __table_args__ = {'extend_existing': True}
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# __tablename__ = "_kits"
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id = Column(INTEGER, primary_key=True) #: primary key
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name = Column(String(64), unique=True) #: name of kit
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submissions = relationship("BasicSubmission", back_populates="extraction_kit") #: submissions this kit was used for
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processes = relationship("Process", back_populates="kit_types", secondary=kittypes_processes)
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kit_reagenttype_associations = relationship(
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"KitTypeReagentTypeAssociation",
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@@ -87,7 +102,7 @@ class KitType(BaseClass):
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Args:
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required (bool, optional): If true only return required types. Defaults to False.
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submission_type (str | None, optional): Submission type to narrow results. Defaults to None.
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submission_type (str | Submissiontype | None, optional): Submission type to narrow results. Defaults to None.
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Returns:
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list: List of reagent types
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@@ -109,12 +124,13 @@ class KitType(BaseClass):
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Creates map of locations in excel workbook for a SubmissionType
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Args:
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use (str): Submissiontype.name
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use (str | SubmissionType): Submissiontype.name
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Returns:
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dict: Dictionary containing information locations.
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"""
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map = {}
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# Account for submission_type variable type.
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match submission_type:
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case str():
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assocs = [item for item in self.kit_reagenttype_associations if item.submission_type.name==submission_type]
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@@ -125,7 +141,6 @@ class KitType(BaseClass):
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case _:
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raise ValueError(f"Wrong variable type: {type(submission_type)} used!")
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# Get all KitTypeReagentTypeAssociation for SubmissionType
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# assocs = [item for item in self.kit_reagenttype_associations if item.submission_type==submission_type]
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for assoc in assocs:
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try:
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map[assoc.reagent_type.name] = assoc.uses
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@@ -133,7 +148,6 @@ class KitType(BaseClass):
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continue
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# Get SubmissionType info map
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try:
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# st_assoc = [item for item in self.used_for if use == item.name][0]
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map['info'] = st_assoc.info_map
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except IndexError as e:
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map['info'] = {}
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@@ -152,7 +166,7 @@ class KitType(BaseClass):
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Args:
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name (str, optional): Name of desired kit (returns single instance). Defaults to None.
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used_for (str | models.Submissiontype | None, optional): Submission type the kit is used for. Defaults to None.
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used_for (str | Submissiontype | None, optional): Submission type the kit is used for. Defaults to None.
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id (int | None, optional): Kit id in the database. 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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@@ -190,17 +204,13 @@ class KitType(BaseClass):
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@check_authorization
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def save(self, ctx:Settings):
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"""
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Add this instance to database and commit
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"""
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self.__database_session__.add(self)
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self.__database_session__.commit()
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super().save()
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class ReagentType(BaseClass):
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"""
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Base of reagent type abstract
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"""
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__tablename__ = "_reagent_types"
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# __tablename__ = "_reagent_types"
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id = Column(INTEGER, primary_key=True) #: primary key
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name = Column(String(64)) #: name of reagent type
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@@ -281,130 +291,16 @@ class ReagentType(BaseClass):
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def to_pydantic(self):
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from backend.validators.pydant import PydReagent
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return PydReagent(lot=None, type=self.name, name=self.name, expiry=date.today())
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# class KitTypeReagentTypeAssociation(BaseClass):
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# """
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# table containing reagenttype/kittype associations
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# DOC: https://docs.sqlalchemy.org/en/14/orm/extensions/associationproxy.html
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# """
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# __tablename__ = "_reagenttypes_kittypes"
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# reagent_types_id = Column(INTEGER, ForeignKey("_reagent_types.id"), primary_key=True) #: id of associated reagent type
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# kits_id = Column(INTEGER, ForeignKey("_kits.id"), primary_key=True) #: id of associated reagent type
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# submission_type_id = (Column(INTEGER), ForeignKey("_submission_types.id"), primary_key=True)
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# uses = Column(JSON) #: map to location on excel sheets of different submission types
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# required = Column(INTEGER) #: whether the reagent type is required for the kit (Boolean 1 or 0)
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# last_used = Column(String(32)) #: last used lot number of this type of reagent
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# kit_type = relationship(KitType, back_populates="kit_reagenttype_associations") #: relationship to associated kit
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# # reference to the "ReagentType" object
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# reagent_type = relationship(ReagentType, back_populates="reagenttype_kit_associations") #: relationship to associated reagent type
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# submission_type = relationship(SubmissionType, back_populates="submissiontype_kit_rt_associations")
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# def __init__(self, kit_type=None, reagent_type=None, uses=None, required=1):
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# # logger.debug(f"Parameters: Kit={kit_type}, RT={reagent_type}, Uses={uses}, Required={required}")
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# self.kit_type = kit_type
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# self.reagent_type = reagent_type
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# self.uses = uses
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# self.required = required
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# def __repr__(self) -> str:
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# return f"<KitTypeReagentTypeAssociation({self.kit_type} & {self.reagent_type})>"
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# @validates('required')
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# def validate_age(self, key, value):
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# """
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# Ensures only 1 & 0 used in 'required'
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# Args:
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# key (str): name of attribute
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# value (_type_): value of attribute
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# Raises:
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# ValueError: Raised if bad value given
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# Returns:
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# _type_: value
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# """
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# if not 0 <= value < 2:
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# raise ValueError(f'Invalid required value {value}. Must be 0 or 1.')
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# return value
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# @validates('reagenttype')
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# def validate_reagenttype(self, key, value):
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# """
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# Ensures reagenttype is an actual ReagentType
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# Args:
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# key (str)): name of attribute
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# value (_type_): value of attribute
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# Raises:
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# ValueError: raised if reagenttype is not a ReagentType
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# Returns:
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# _type_: ReagentType
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# """
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# if not isinstance(value, ReagentType):
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# raise ValueError(f'{value} is not a reagenttype')
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# return value
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# @classmethod
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# @setup_lookup
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# def query(cls,
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# kit_type:KitType|str|None=None,
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# reagent_type:ReagentType|str|None=None,
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# limit:int=0
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# ) -> KitTypeReagentTypeAssociation|List[KitTypeReagentTypeAssociation]:
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# """
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# Lookup junction of ReagentType and KitType
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# Args:
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# kit_type (models.KitType | str | None): KitType of interest.
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# reagent_type (models.ReagentType | str | None): ReagentType of interest.
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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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# models.KitTypeReagentTypeAssociation|List[models.KitTypeReagentTypeAssociation]: Junction of interest.
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# """
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# query: Query = cls.__database_session__.query(cls)
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# match kit_type:
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# case KitType():
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# query = query.filter(cls.kit_type==kit_type)
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# case str():
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# query = query.join(KitType).filter(KitType.name==kit_type)
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# case _:
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# pass
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# match reagent_type:
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# case ReagentType():
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# query = query.filter(cls.reagent_type==reagent_type)
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# case str():
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# query = query.join(ReagentType).filter(ReagentType.name==reagent_type)
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# case _:
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# pass
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# if kit_type != None and reagent_type != None:
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# limit = 1
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# return query_return(query=query, limit=limit)
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# def save(self) -> Report:
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# """
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# Adds this instance to the database and commits.
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# Returns:
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# Report: Result of save action
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# """
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# report = Report()
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# self.__database_session__.add(self)
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# self.__database_session__.commit()
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# return report
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@check_authorization
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def save(self, ctx:Settings):
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super().save()
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class Reagent(BaseClass):
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"""
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Concrete reagent instance
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"""
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__tablename__ = "_reagents"
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# __tablename__ = "_reagents"
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id = Column(INTEGER, primary_key=True) #: primary key
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type = relationship("ReagentType", back_populates="instances", secondary=reagenttypes_reagents) #: joined parent reagent type
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@@ -412,7 +308,6 @@ class Reagent(BaseClass):
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name = Column(String(64)) #: reagent name
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lot = Column(String(64)) #: lot number of reagent
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expiry = Column(TIMESTAMP) #: expiry date - extended by eol_ext of parent programmatically
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# submissions = relationship("BasicSubmission", back_populates="reagents", uselist=True) #: submissions this reagent is used in
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reagent_submission_associations = relationship(
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"SubmissionReagentAssociation",
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@@ -497,6 +392,7 @@ class Reagent(BaseClass):
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def query(cls,
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reagent_type:str|ReagentType|None=None,
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lot_number:str|None=None,
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name:str|None=None,
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limit:int=0
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) -> Reagent|List[Reagent]:
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"""
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@@ -505,6 +401,7 @@ class Reagent(BaseClass):
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Args:
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reagent_type (str | models.ReagentType | None, optional): Reagent type. Defaults to None.
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lot_number (str | None, optional): Reagent lot number. Defaults to None.
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name (str | None, optional): Reagent name. Defaults to None.
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limit (int, optional): limit of results returned. Defaults to 0.
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Returns:
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@@ -521,6 +418,12 @@ class Reagent(BaseClass):
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query = query.filter(cls.type.contains(reagent_type))
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case _:
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pass
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match name:
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case str():
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logger.debug(f"Looking up reagent by name: {name}")
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query = query.filter(cls.name==name)
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case _:
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pass
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match lot_number:
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case str():
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logger.debug(f"Looking up reagent by lot number: {lot_number}")
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@@ -530,19 +433,12 @@ class Reagent(BaseClass):
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case _:
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pass
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return query_return(query=query, limit=limit)
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def save(self):
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"""
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Add this instance to the database and commit
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"""
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self.__database_session__.add(self)
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self.__database_session__.commit()
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class Discount(BaseClass):
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"""
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Relationship table for client labs for certain kits.
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"""
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__tablename__ = "_discounts"
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# __tablename__ = "_discounts"
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id = Column(INTEGER, primary_key=True) #: primary key
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kit = relationship("KitType") #: joined parent reagent type
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@@ -604,17 +500,20 @@ class Discount(BaseClass):
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pass
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return query.all()
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@check_authorization
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def save(self, ctx:Settings):
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super().save()
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class SubmissionType(BaseClass):
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"""
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Abstract of types of submissions.
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"""
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__tablename__ = "_submission_types"
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# __tablename__ = "_submission_types"
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id = Column(INTEGER, primary_key=True) #: primary key
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name = Column(String(128), unique=True) #: name of submission type
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info_map = Column(JSON) #: Where basic information is found in the excel workbook corresponding to this type.
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instances = relationship("BasicSubmission", backref="submission_type") #: Concrete instances of this type.
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# regex = Column(String(512))
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template_file = Column(BLOB) #: Blank form for this type stored as binary.
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processes = relationship("Process", back_populates="submission_types", secondary=submissiontypes_processes)
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@@ -664,20 +563,25 @@ class SubmissionType(BaseClass):
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output = []
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for item in self.submissiontype_equipmentrole_associations:
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map = item.uses
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map['role'] = item.equipment_role.name
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if map == None:
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map = {}
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try:
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map['role'] = item.equipment_role.name
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except TypeError:
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pass
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output.append(map)
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return output
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# return [item.uses for item in self.submissiontype_equipmentrole_associations]
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def get_equipment(self) -> List['PydEquipmentRole']:
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return [item.to_pydantic(submission_type=self) for item in self.equipment]
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def get_equipment(self, extraction_kit:str|KitType|None=None) -> List['PydEquipmentRole']:
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return [item.to_pydantic(submission_type=self, extraction_kit=extraction_kit) for item in self.equipment]
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def get_processes_for_role(self, equipment_role:str|EquipmentRole):
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def get_processes_for_role(self, equipment_role:str|EquipmentRole, kit:str|KitType|None=None):
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match equipment_role:
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case str():
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relevant = [item.get_all_processes() for item in self.submissiontype_equipmentrole_associations if item.equipment_role.name==equipment_role]
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relevant = [item.get_all_processes(kit) for item in self.submissiontype_equipmentrole_associations if item.equipment_role.name==equipment_role]
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case EquipmentRole():
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relevant = [item.get_all_processes() for item in self.submissiontype_equipmentrole_associations if item.equipment_role==equipment_role]
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relevant = [item.get_all_processes(kit) for item in self.submissiontype_equipmentrole_associations if item.equipment_role==equipment_role]
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case _:
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raise TypeError(f"Type {type(equipment_role)} is not allowed")
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return list(set([item for items in relevant for item in items if item != None ]))
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@@ -728,7 +632,7 @@ class SubmissionTypeKitTypeAssociation(BaseClass):
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"""
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Abstract of relationship between kits and their submission type.
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"""
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__tablename__ = "_submissiontypes_kittypes"
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# __tablename__ = "_submissiontypes_kittypes"
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submission_types_id = Column(INTEGER, ForeignKey("_submission_types.id"), primary_key=True) #: id of joined submission type
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kits_id = Column(INTEGER, ForeignKey("_kits.id"), primary_key=True) #: id of joined kit
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@@ -801,7 +705,7 @@ class KitTypeReagentTypeAssociation(BaseClass):
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table containing reagenttype/kittype associations
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DOC: https://docs.sqlalchemy.org/en/14/orm/extensions/associationproxy.html
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"""
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__tablename__ = "_reagenttypes_kittypes"
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# __tablename__ = "_reagenttypes_kittypes"
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reagent_types_id = Column(INTEGER, ForeignKey("_reagent_types.id"), primary_key=True) #: id of associated reagent type
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kits_id = Column(INTEGER, ForeignKey("_kits.id"), primary_key=True) #: id of associated reagent type
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@@ -902,22 +806,9 @@ class KitTypeReagentTypeAssociation(BaseClass):
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limit = 1
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return query_return(query=query, limit=limit)
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def save(self) -> Report:
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"""
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Adds this instance to the database and commits.
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Returns:
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Report: Result of save action
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"""
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report = Report()
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self.__database_session__.add(self)
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self.__database_session__.commit()
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return report
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class SubmissionReagentAssociation(BaseClass):
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__tablename__ = "_reagents_submissions"
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# __tablename__ = "_reagents_submissions"
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reagent_id = Column(INTEGER, ForeignKey("_reagents.id"), primary_key=True) #: id of associated sample
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submission_id = Column(INTEGER, ForeignKey("_submissions.id"), primary_key=True)
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@@ -961,8 +852,6 @@ class SubmissionReagentAssociation(BaseClass):
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# logger.debug(f"Filtering query with reagent: {reagent}")
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reagent = Reagent.query(lot_number=reagent)
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query = query.filter(cls.reagent==reagent)
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# logger.debug([item.reagent.lot for item in query.all()])
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# query = query.join(Reagent).filter(Reagent.lot==reagent)
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case _:
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pass
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# logger.debug(f"Result of query after reagent: {query.all()}")
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@@ -976,7 +865,6 @@ class SubmissionReagentAssociation(BaseClass):
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case _:
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pass
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# logger.debug(f"Result of query after submission: {query.all()}")
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# limit = query.count()
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return query_return(query=query, limit=limit)
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def to_sub_dict(self, extraction_kit):
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@@ -989,13 +877,14 @@ class Equipment(BaseClass):
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# Currently abstract until ready to implement
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# __abstract__ = True
|
||||
|
||||
__tablename__ = "_equipment"
|
||||
# __tablename__ = "_equipment"
|
||||
|
||||
id = Column(INTEGER, primary_key=True)
|
||||
name = Column(String(64))
|
||||
nickname = Column(String(64))
|
||||
asset_number = Column(String(16))
|
||||
roles = relationship("EquipmentRole", back_populates="instances", secondary=equipmentroles_equipment)
|
||||
processes = relationship("Process", back_populates="equipment", secondary=equipment_processes)
|
||||
|
||||
equipment_submission_associations = relationship(
|
||||
"SubmissionEquipmentAssociation",
|
||||
@@ -1008,10 +897,30 @@ class Equipment(BaseClass):
|
||||
def __repr__(self):
|
||||
return f"<Equipment({self.name})>"
|
||||
|
||||
def get_processes(self, submission_type:SubmissionType):
|
||||
processes = [assoc.process for assoc in self.equipment_submission_associations if assoc.submission.submission_type_name==submission_type.name]
|
||||
def to_dict(self, processes:bool=False):
|
||||
if not processes:
|
||||
return {k:v for k,v in self.__dict__.items() if k != 'processes'}
|
||||
else:
|
||||
return {k:v for k,v in self.__dict__.items()}
|
||||
|
||||
def get_processes(self, submission_type:SubmissionType, extraction_kit:str|KitType|None=None):
|
||||
processes = [process for process in self.processes if submission_type in process.submission_types]
|
||||
match extraction_kit:
|
||||
case str():
|
||||
processes = [process for process in processes if extraction_kit in [kit.name for kit in process.kit_types]]
|
||||
case KitType():
|
||||
processes = [process for process in processes if extraction_kit in process.kit_types]
|
||||
case _:
|
||||
pass
|
||||
processes = [process.name for process in processes]
|
||||
# try:
|
||||
assert all([isinstance(process, str) for process in processes])
|
||||
# except AssertionError as e:
|
||||
# logger.error(processes)
|
||||
# raise e
|
||||
if len(processes) == 0:
|
||||
processes = ['']
|
||||
# logger.debug(f"Processes: {processes}")
|
||||
return processes
|
||||
|
||||
@classmethod
|
||||
@@ -1043,10 +952,10 @@ class Equipment(BaseClass):
|
||||
pass
|
||||
return query_return(query=query, limit=limit)
|
||||
|
||||
def to_pydantic(self, submission_type:SubmissionType):
|
||||
def to_pydantic(self, submission_type:SubmissionType, extraction_kit:str|KitType|None=None):
|
||||
from backend.validators.pydant import PydEquipment
|
||||
# return PydEquipment(process=self.get_processes(submission_type=submission_type), role=None, **self.__dict__)
|
||||
return PydEquipment(process=None, role=None, **self.__dict__)
|
||||
return PydEquipment(processes=self.get_processes(submission_type=submission_type, extraction_kit=extraction_kit), role=None, **self.to_dict(processes=False))
|
||||
# return PydEquipment(process=None, role=None, **self.__dict__)
|
||||
|
||||
def save(self):
|
||||
self.__database_session__.add(self)
|
||||
@@ -1064,12 +973,12 @@ class Equipment(BaseClass):
|
||||
|
||||
class EquipmentRole(BaseClass):
|
||||
|
||||
__tablename__ = "_equipment_roles"
|
||||
# __tablename__ = "_equipment_roles"
|
||||
|
||||
id = Column(INTEGER, primary_key=True)
|
||||
name = Column(String(32))
|
||||
instances = relationship("Equipment", back_populates="roles", secondary=equipmentroles_equipment)
|
||||
processes = relationship("Process", back_populates="equipment_roles", secondary=equipmentroles_processes)
|
||||
processes = relationship("Process", back_populates='equipment_roles', secondary=equipmentroles_processes)
|
||||
|
||||
equipmentrole_submissiontype_associations = relationship(
|
||||
"SubmissionTypeEquipmentRoleAssociation",
|
||||
@@ -1081,12 +990,24 @@ class EquipmentRole(BaseClass):
|
||||
|
||||
def __repr__(self):
|
||||
return f"<EquipmentRole({self.name})>"
|
||||
|
||||
def to_dict(self):
|
||||
output = {}
|
||||
for key, value in self.__dict__.items():
|
||||
match key:
|
||||
case "processes":
|
||||
pass
|
||||
case _:
|
||||
value = value
|
||||
output[key] = value
|
||||
return output
|
||||
|
||||
def to_pydantic(self, submission_type:SubmissionType):
|
||||
def to_pydantic(self, submission_type:SubmissionType, extraction_kit:str|KitType|None=None):
|
||||
from backend.validators.pydant import PydEquipmentRole
|
||||
equipment = [item.to_pydantic(submission_type=submission_type) for item in self.instances]
|
||||
pyd_dict = self.__dict__
|
||||
pyd_dict['processes'] = self.get_processes(submission_type=submission_type)
|
||||
equipment = [item.to_pydantic(submission_type=submission_type, extraction_kit=extraction_kit) for item in self.instances]
|
||||
# processes = [item.name for item in self.processes]
|
||||
pyd_dict = self.to_dict()
|
||||
pyd_dict['processes'] = self.get_processes(submission_type=submission_type, extraction_kit=extraction_kit)
|
||||
return PydEquipmentRole(equipment=equipment, **pyd_dict)
|
||||
|
||||
@classmethod
|
||||
@@ -1107,31 +1028,36 @@ class EquipmentRole(BaseClass):
|
||||
pass
|
||||
return query_return(query=query, limit=limit)
|
||||
|
||||
def get_processes(self, submission_type:str|SubmissionType|None) -> List[Process]:
|
||||
def get_processes(self, submission_type:str|SubmissionType|None, extraction_kit:str|KitType|None=None) -> List[Process]:
|
||||
if isinstance(submission_type, str):
|
||||
submission_type = SubmissionType.query(name=submission_type)
|
||||
# assert all([isinstance(process, Process) for process in self.processes])
|
||||
# logger.debug(self.processes)
|
||||
if submission_type != None:
|
||||
output = [process.name for process in self.processes if submission_type in process.submission_types]
|
||||
# for process in self.processes:
|
||||
# logger.debug(f"Process: {type(process)}: {process}")
|
||||
processes = [process for process in self.processes if submission_type in process.submission_types]
|
||||
else:
|
||||
output = [process.name for process in self.processes]
|
||||
processes = self.processes
|
||||
match extraction_kit:
|
||||
case str():
|
||||
processes = [item for item in processes if extraction_kit in [kit.name for kit in item.kit_type]]
|
||||
case KitType():
|
||||
processes = [item for item in processes if extraction_kit in [kit for kit in item.kit_type]]
|
||||
case _:
|
||||
pass
|
||||
output = [item.name for item in processes]
|
||||
if len(output) == 0:
|
||||
return ['']
|
||||
else:
|
||||
return output
|
||||
|
||||
def save(self):
|
||||
try:
|
||||
self.__database_session__.add(self)
|
||||
self.__database_session__.commit()
|
||||
except:
|
||||
self.__database_session__.rollback()
|
||||
|
||||
class SubmissionEquipmentAssociation(BaseClass):
|
||||
|
||||
# Currently abstract until ready to implement
|
||||
# __abstract__ = True
|
||||
|
||||
__tablename__ = "_equipment_submissions"
|
||||
# __tablename__ = "_equipment_submissions"
|
||||
|
||||
equipment_id = Column(INTEGER, ForeignKey("_equipment.id"), primary_key=True) #: id of associated equipment
|
||||
submission_id = Column(INTEGER, ForeignKey("_submissions.id"), primary_key=True) #: id of associated submission
|
||||
@@ -1144,14 +1070,14 @@ class SubmissionEquipmentAssociation(BaseClass):
|
||||
|
||||
submission = relationship("BasicSubmission", back_populates="submission_equipment_associations") #: associated submission
|
||||
|
||||
equipment = relationship(Equipment, back_populates="equipment_submission_associations") #: associated submission
|
||||
equipment = relationship(Equipment, back_populates="equipment_submission_associations") #: associated equipment
|
||||
|
||||
def __init__(self, submission, equipment):
|
||||
self.submission = submission
|
||||
self.equipment = equipment
|
||||
|
||||
def to_sub_dict(self) -> dict:
|
||||
output = dict(name=self.equipment.name, asset_number=self.equipment.asset_number, comment=self.comments, process=self.process.name, role=self.role, nickname=self.equipment.nickname)
|
||||
output = dict(name=self.equipment.name, asset_number=self.equipment.asset_number, comment=self.comments, processes=[self.process.name], role=self.role, nickname=self.equipment.nickname)
|
||||
return output
|
||||
|
||||
def save(self):
|
||||
@@ -1162,7 +1088,7 @@ class SubmissionTypeEquipmentRoleAssociation(BaseClass):
|
||||
|
||||
# __abstract__ = True
|
||||
|
||||
__tablename__ = "_submissiontype_equipmentrole"
|
||||
# __tablename__ = "_submissiontype_equipmentrole"
|
||||
|
||||
equipmentrole_id = Column(INTEGER, ForeignKey("_equipment_roles.id"), primary_key=True) #: id of associated equipment
|
||||
submissiontype_id = Column(INTEGER, ForeignKey("_submission_types.id"), primary_key=True) #: id of associated submission
|
||||
@@ -1192,25 +1118,38 @@ class SubmissionTypeEquipmentRoleAssociation(BaseClass):
|
||||
raise ValueError(f'Invalid required value {value}. Must be 0 or 1.')
|
||||
return value
|
||||
|
||||
def get_all_processes(self):
|
||||
def get_all_processes(self, extraction_kit:KitType|str|None=None):
|
||||
processes = [equipment.get_processes(self.submission_type) for equipment in self.equipment_role.instances]
|
||||
# flatten list
|
||||
processes = [item for items in processes for item in items if item != None ]
|
||||
match extraction_kit:
|
||||
case str():
|
||||
processes = [item for item in processes if extraction_kit in [kit.name for kit in item.kit_type]]
|
||||
case KitType():
|
||||
processes = [item for item in processes if extraction_kit in [kit for kit in item.kit_type]]
|
||||
case _:
|
||||
pass
|
||||
return processes
|
||||
|
||||
@check_authorization
|
||||
def save(self, ctx:Settings):
|
||||
self.__database_session__.add(self)
|
||||
self.__database_session__.commit()
|
||||
# self.__database_session__.add(self)
|
||||
# self.__database_session__.commit()
|
||||
super().save()
|
||||
|
||||
class Process(BaseClass):
|
||||
|
||||
__tablename__ = "_process"
|
||||
"""
|
||||
A Process is a method used by a piece of equipment.
|
||||
"""
|
||||
# __tablename__ = "_process"
|
||||
|
||||
id = Column(INTEGER, primary_key=True)
|
||||
name = Column(String(64))
|
||||
submission_types = relationship("SubmissionType", back_populates='processes', secondary=submissiontypes_processes)
|
||||
equipment = relationship("Equipment", back_populates='processes', secondary=equipment_processes)
|
||||
equipment_roles = relationship("EquipmentRole", back_populates='processes', secondary=equipmentroles_processes)
|
||||
submissions = relationship("SubmissionEquipmentAssociation", backref='process')
|
||||
kit_types = relationship("KitType", back_populates='processes', secondary=kittypes_processes)
|
||||
|
||||
def __repr__(self):
|
||||
return f"<Process({self.name})"
|
||||
@@ -1227,124 +1166,3 @@ class Process(BaseClass):
|
||||
pass
|
||||
return query_return(query=query, limit=limit)
|
||||
|
||||
def save(self):
|
||||
try:
|
||||
self.__database_session__.add(self)
|
||||
self.__database_session__.commit()
|
||||
except:
|
||||
self.__database_session__.rollback()
|
||||
|
||||
# class KitTypeReagentTypeAssociation(BaseClass):
|
||||
# """
|
||||
# table containing reagenttype/kittype associations
|
||||
# DOC: https://docs.sqlalchemy.org/en/14/orm/extensions/associationproxy.html
|
||||
# """
|
||||
# __tablename__ = "_reagenttypes_kittypes"
|
||||
|
||||
# reagent_types_id = Column(INTEGER, ForeignKey("_reagent_types.id"), primary_key=True) #: id of associated reagent type
|
||||
# kits_id = Column(INTEGER, ForeignKey("_kits.id"), primary_key=True) #: id of associated reagent type
|
||||
# uses = Column(JSON) #: map to location on excel sheets of different submission types
|
||||
# required = Column(INTEGER) #: whether the reagent type is required for the kit (Boolean 1 or 0)
|
||||
# last_used = Column(String(32)) #: last used lot number of this type of reagent
|
||||
|
||||
# kit_type = relationship(KitType, back_populates="kit_reagenttype_associations") #: relationship to associated kit
|
||||
|
||||
# # reference to the "ReagentType" object
|
||||
# reagent_type = relationship(ReagentType, back_populates="reagenttype_kit_associations") #: relationship to associated reagent type
|
||||
|
||||
# def __init__(self, kit_type=None, reagent_type=None, uses=None, required=1):
|
||||
# # logger.debug(f"Parameters: Kit={kit_type}, RT={reagent_type}, Uses={uses}, Required={required}")
|
||||
# self.kit_type = kit_type
|
||||
# self.reagent_type = reagent_type
|
||||
# self.uses = uses
|
||||
# self.required = required
|
||||
|
||||
# def __repr__(self) -> str:
|
||||
# return f"<KitTypeReagentTypeAssociation({self.kit_type} & {self.reagent_type})>"
|
||||
|
||||
# @validates('required')
|
||||
# def validate_age(self, key, value):
|
||||
# """
|
||||
# Ensures only 1 & 0 used in 'required'
|
||||
|
||||
# Args:
|
||||
# key (str): name of attribute
|
||||
# value (_type_): value of attribute
|
||||
|
||||
# Raises:
|
||||
# ValueError: Raised if bad value given
|
||||
|
||||
# Returns:
|
||||
# _type_: value
|
||||
# """
|
||||
# if not 0 <= value < 2:
|
||||
# raise ValueError(f'Invalid required value {value}. Must be 0 or 1.')
|
||||
# return value
|
||||
|
||||
# @validates('reagenttype')
|
||||
# def validate_reagenttype(self, key, value):
|
||||
# """
|
||||
# Ensures reagenttype is an actual ReagentType
|
||||
|
||||
# Args:
|
||||
# key (str)): name of attribute
|
||||
# value (_type_): value of attribute
|
||||
|
||||
# Raises:
|
||||
# ValueError: raised if reagenttype is not a ReagentType
|
||||
|
||||
# Returns:
|
||||
# _type_: ReagentType
|
||||
# """
|
||||
# if not isinstance(value, ReagentType):
|
||||
# raise ValueError(f'{value} is not a reagenttype')
|
||||
# return value
|
||||
|
||||
# @classmethod
|
||||
# @setup_lookup
|
||||
# def query(cls,
|
||||
# kit_type:KitType|str|None=None,
|
||||
# reagent_type:ReagentType|str|None=None,
|
||||
# limit:int=0
|
||||
# ) -> KitTypeReagentTypeAssociation|List[KitTypeReagentTypeAssociation]:
|
||||
# """
|
||||
# Lookup junction of ReagentType and KitType
|
||||
|
||||
# Args:
|
||||
# kit_type (models.KitType | str | None): KitType of interest.
|
||||
# reagent_type (models.ReagentType | str | None): ReagentType of interest.
|
||||
# limit (int, optional): Maximum number of results to return (0 = all). Defaults to 0.
|
||||
|
||||
# Returns:
|
||||
# models.KitTypeReagentTypeAssociation|List[models.KitTypeReagentTypeAssociation]: Junction of interest.
|
||||
# """
|
||||
# query: Query = cls.__database_session__.query(cls)
|
||||
# match kit_type:
|
||||
# case KitType():
|
||||
# query = query.filter(cls.kit_type==kit_type)
|
||||
# case str():
|
||||
# query = query.join(KitType).filter(KitType.name==kit_type)
|
||||
# case _:
|
||||
# pass
|
||||
# match reagent_type:
|
||||
# case ReagentType():
|
||||
# query = query.filter(cls.reagent_type==reagent_type)
|
||||
# case str():
|
||||
# query = query.join(ReagentType).filter(ReagentType.name==reagent_type)
|
||||
# case _:
|
||||
# pass
|
||||
# if kit_type != None and reagent_type != None:
|
||||
# limit = 1
|
||||
# return query_return(query=query, limit=limit)
|
||||
|
||||
# def save(self) -> Report:
|
||||
# """
|
||||
# Adds this instance to the database and commits.
|
||||
|
||||
# Returns:
|
||||
# Report: Result of save action
|
||||
# """
|
||||
# report = Report()
|
||||
# self.__database_session__.add(self)
|
||||
# self.__database_session__.commit()
|
||||
# return report
|
||||
|
||||
Reference in New Issue
Block a user