repositories

oxytcmri.domain.ports.repositories

This module defines repositories for the application, storing and retrieving entities.

Classes:

Name	Description
EntityNotFoundException	Exception raised when an entity is not found in the repository.
Repository	Abstract base class for repositories.
SubjectRepository
MRIExamRepository	Abstract base class for MRI repository.
AtlasRepository	Abstract base class for Atlas repository.
CenterRepository	Abstract base class for Center repository.
RepositoriesRegistry	Abstract base class for a registry responsible for managing the repositories in the application.

Attributes:

Name	Type	Description
Entity
EntityIdentifier

Entity = TypeVar('Entity') module-attribute

EntityIdentifier = TypeVar('EntityIdentifier') module-attribute

EntityNotFoundException(entity_id, repository)

Bases: Exception

Exception raised when an entity is not found in the repository.

Source code in oxytcmri/domain/ports/repositories.py

def __init__(self, entity_id: EntityIdentifier, repository: Repository):
    super().__init__(f"Entity id {entity_id} not found in repository {repository}")

Repository

Bases: ABC, Generic[Entity, EntityIdentifier]

Abstract base class for repositories. Defines the interface for all repositories in the application.

Methods:

Name	Description
find_by_id	Retrieve an entity by its ID.
get_by_id	Retrieve an entity by its ID.
list_all	List all entities in the repository.
save	Save an entity to the repository.
save_list	Save a list of entities to the repository.
delete	Delete an entity from the repository.

find_by_id(entity_id) abstractmethod

Retrieve an entity by its ID.

Parameters:

Name	Type	Description	Default
entity_id	EntityIdentifier	The ID of the entity	required

Returns:

Type	Description
Entity	The entity object if found, otherwise None

Source code in oxytcmri/domain/ports/repositories.py

@abstractmethod
def find_by_id(self, entity_id: EntityIdentifier) -> Optional[Entity]:
    """
    Retrieve an entity by its ID.

    Parameters
    ----------
    entity_id : EntityIdentifier
        The ID of the entity

    Returns
    -------
    Entity
        The entity object if found, otherwise None
    """

get_by_id(entity_id)

Retrieve an entity by its ID.

Parameters:

Name	Type	Description	Default
entity_id	EntityIdentifier	The ID of the entity	required

Returns:

Type	Description
Entity	The entity object

Raises:

Type	Description
EntityNotFoundException	If the entity with the given ID does not exist

Source code in oxytcmri/domain/ports/repositories.py

def get_by_id(self, entity_id: EntityIdentifier) -> Entity:
    """
    Retrieve an entity by its ID.

    Parameters
    ----------
    entity_id : EntityIdentifier
        The ID of the entity

    Returns
    -------
    Entity
        The entity object

    Raises
    -------
    EntityNotFoundException
        If the entity with the given ID does not exist
    """
    entity = self.find_by_id(entity_id)
    if entity is None:
        raise EntityNotFoundException(entity_id, self)
    return entity

list_all() abstractmethod

List all entities in the repository.

Returns:

Type	Description
List[Entity]	List of all entities

Source code in oxytcmri/domain/ports/repositories.py

@abstractmethod
def list_all(self) -> List[Entity]:
    """
    List all entities in the repository.

    Returns
    -------
    List[Entity]
        List of all entities
    """

save(entity) abstractmethod

Save an entity to the repository.

Parameters:

Name	Type	Description	Default
entity	Entity	The entity to save	required

Source code in oxytcmri/domain/ports/repositories.py

@abstractmethod
def save(self, entity: Entity) -> None:
    """
    Save an entity to the repository.

    Parameters
    ----------
    entity : Entity
        The entity to save
    """

save_list(entity_list)

Save a list of entities to the repository.

Parameters:

Name	Type	Description	Default
entity_list	List[Entity]	The list of entities to save	required

Source code in oxytcmri/domain/ports/repositories.py

def save_list(self, entity_list: List[Entity]) -> None:
    """
    Save a list of entities to the repository.

    Parameters
    ----------
    entity_list : List[Entity]
        The list of entities to save
    """
    for entity in entity_list:
        self.save(entity)

delete(entity) abstractmethod

Delete an entity from the repository.

Parameters:

Name	Type	Description	Default
entity	Entity	The entity to delete	required

Source code in oxytcmri/domain/ports/repositories.py

@abstractmethod
def delete(self, entity: Entity) -> None:
    """
    Delete an entity from the repository.

    Parameters
    ----------
    entity : Entity
        The entity to delete
    """

SubjectRepository

Bases: Repository[Subject, SubjectId]

Methods:

Name	Description
find_subjects_by_center	Find subjects for a given center, optionally filtered by type.

find_subjects_by_center(center, subject_type=None) abstractmethod

Find subjects for a given center, optionally filtered by type.

Parameters:

Name	Type	Description	Default
center	Center	The center to find subjects for	required
subject_type	Optional[SubjectType]	If provided, only return subjects of this type	None

Returns:

Type	Description
List[Subject]	List of matching subjects

Source code in oxytcmri/domain/ports/repositories.py

@abstractmethod
def find_subjects_by_center(
        self, center: Center, subject_type: Optional[SubjectType] = None
) -> List[Subject]:
    """
    Find subjects for a given center, optionally filtered by type.

    Parameters
    ----------
    center : Center
        The center to find subjects for
    subject_type : Optional[SubjectType], default=None
        If provided, only return subjects of this type

    Returns
    -------
    List[Subject]
        List of matching subjects
    """

MRIExamRepository

Bases: Repository[MRIExam, MRIExamId]

Abstract base class for MRI repository. Defines the interface for retrieving MRI exam data.

Methods:

Name	Description
get_exam_for_subject	Retrieve the MRI exam for a specific subject.

get_exam_for_subject(subject_id) abstractmethod

Retrieve the MRI exam for a specific subject.

Parameters:

Name	Type	Description	Default
subject_id	SubjectId	The identifier of the subject	required

Returns:

Type	Description
MRIExam	The MRI exam for the subject

Source code in oxytcmri/domain/ports/repositories.py

@abstractmethod
def get_exam_for_subject(self, subject_id: SubjectId) -> MRIExam:
    """
    Retrieve the MRI exam for a specific subject.

    Parameters
    ----------
    subject_id : SubjectId
        The identifier of the subject

    Returns
    -------
    MRIExam
        The MRI exam for the subject
    """

AtlasRepository

Bases: Repository[Atlas, int], ABC

Abstract base class for Atlas repository. Defines the interface for retrieving atlas data.

CenterRepository

Bases: Repository[Center, int], ABC

Abstract base class for Center repository.

RepositoriesRegistry

Bases: ABC

Abstract base class for a registry responsible for managing the repositories in the application.

Methods:

Name	Description
get_repository	Return the repository corresponding to the given entity type.
list_all_repositories	Return a list of all repositories in the registry.

get_repository(entity_type) abstractmethod

Return the repository corresponding to the given entity type.

Source code in oxytcmri/domain/ports/repositories.py

@abstractmethod
def get_repository(self, entity_type: Type[Entity]) -> Repository[Entity, EntityIdentifier]:
    """Return the repository corresponding to the given entity type."""

list_all_repositories() abstractmethod

Return a list of all repositories in the registry.

Source code in oxytcmri/domain/ports/repositories.py

@abstractmethod
def list_all_repositories(self) -> List[Repository[Entity, EntityIdentifier]]:
    """Return a list of all repositories in the registry."""