onconova.core.models

BaseModel

Bases: UntrackedBaseModel

Abstract base model that provides annotated properties for tracking creation and update metadata.

Attributes:

Name	Type	Description
created_at	AnnotationProperty	The earliest creation timestamp from related events with label create.
updated_at	AnnotationProperty	The latest update timestamp from related events with label update.
created_by	AnnotationProperty	The username associated with the creation event.
updated_by	AnnotationProperty	A list of distinct usernames associated with update events.

Note

This model is abstract and should be inherited by other models to include audit fields.

created_at class-attribute instance-attribute

created_by class-attribute instance-attribute

events instance-attribute

updated_at class-attribute instance-attribute

updated_by class-attribute instance-attribute

Meta

abstract class-attribute instance-attribute

CanManageCasesProperty

Bases: AnnotationGetterMixin, QueryableProperty

A queryable property that determines whether a user can manage cases.

This property evaluates several conditions to grant case management permissions: - The user is a service account. - The user has an access level greater than or equal to 2. - The user is a superuser. - The user has a valid ProjectDataManagerGrant.

Returns:

Type	Description
bool	Boolean indicating if the user can manage cases.

get_annotation(cls)

Source code in onconova/core/auth/models.py

def get_annotation(self, cls):
    from onconova.research.models.project import ProjectDataManagerGrant

    return Case(
        When(is_service_account=True, then=True),
        When(
            Q(access_level__gte=2)
            | Q(is_superuser=True)
            | Exists(
                ProjectDataManagerGrant.objects.filter(
                    member=OuterRef("pk"), is_valid=True
                )[:1]
            ),
            then=True,
        ),
        default=False,
        output_field=models.BooleanField(),
    )

QueryablePropertiesUserManager

Bases: UserManager, QueryablePropertiesManager

Custom user manager that combines the functionality of UserManager and QueryablePropertiesManager.

This manager enables querying user properties using advanced queryable properties features, while retaining all standard user management capabilities.

Inherits

UserManager: Provides standard user management operations. QueryablePropertiesManager: Adds support for queryable properties on user models.

UntrackedBaseModel

Bases: Model

Abstract base model providing common fields and behaviors for models that are not tracked by Django's built-in mechanisms. This model uses a custom manager (QueryablePropertiesManager) and includes fields for external data source tracking.

Attributes:

Name	Type	Description
objects	QueryablePropertiesManager	The default manager for querying model instances with annotated properties.
id	UUIDField	Primary key, automatically generated UUID.
external_source	CharField	Optional. The digital source of the data, useful for automated data imports.
external_source_id	CharField	Optional. The identifier of the data at the external source.

description property

A human-readable description of the model instance.

Subclasses must implement this property to provide a string suitable for display to users.

Raises:

Type	Description
NotImplementedError	If the subclass does not implement the description property.

external_source class-attribute instance-attribute

external_source_id class-attribute instance-attribute

id class-attribute instance-attribute

objects class-attribute instance-attribute

Meta

abstract class-attribute instance-attribute

__str__()

Source code in onconova/core/models.py

def __str__(self):
    try:
        return self.description
    except NotImplementedError:
        return f"{self.__class__.__name__} instance (description not implemented)"

User

Bases: AbstractUser

Custom User model extending Django's AbstractUser, with additional fields and properties for access control and user metadata.

Attributes:

Name	Type	Description
id	UUIDField	Primary key, unique identifier for the user.
full_name	AnnotationProperty	Computed full name from first and last name, or username if missing.
is_service_account	BooleanField	Indicates if the user is a technical service account.
title	CharField	Personal title of the user.
organization	CharField	Organization to which the user belongs.
department	CharField	Department within the organization.
access_level	IntegerField	Numeric access level (0-4) representing user permissions.
role	MappingProperty	Maps access_level to a human-readable role.
is_provided	AnnotationProperty	Indicates if the user's identity is provided by an external provider.
provider	AnnotationProperty	Name of the external provider if applicable.
can_view_cases	AnnotationProperty	Indicates if the user can view cases (min_access_level=1).
can_view_projects	AnnotationProperty	Indicates if the user can view projects (min_access_level=1).
can_view_cohorts	AnnotationProperty	Indicates if the user can view cohorts (min_access_level=1).
can_view_users	AnnotationProperty	Indicates if the user can view users (min_access_level=1).
can_view_datasets	AnnotationProperty	Indicates if the user can view datasets (min_access_level=1).
can_export_data	AnnotationProperty	Indicates if the user can export data (min_access_level=2).
can_manage_projects	AnnotationProperty	Indicates if the user can manage projects (min_access_level=2).
can_delete_projects	AnnotationProperty	Indicates if the user can delete projects (min_access_level=3).
can_delete_cohorts	AnnotationProperty	Indicates if the user can delete cohorts (min_access_level=3).
can_delete_datasets	AnnotationProperty	Indicates if the user can delete datasets (min_access_level=3).
can_manage_users	AnnotationProperty	Indicates if the user can manage users (min_access_level=3).
is_system_admin	AnnotationProperty	Indicates if the user is a system administrator (min_access_level=4).
can_manage_cases	CanManageCasesProperty	Indicates if the user can manage patient data.

Methods:

Name	Description
construct_permission_field_from_access_level	Static method to construct permission annotation properties based on access level.
__str__	Returns the username as string representation.
save	Ensures superusers have the highest access level before saving.

Constraints

access_level must be between 0 and 4 (inclusive).

access_level class-attribute instance-attribute

can_delete_cohorts class-attribute instance-attribute

can_delete_datasets class-attribute instance-attribute

can_delete_projects class-attribute instance-attribute

can_export_data class-attribute instance-attribute

can_manage_cases class-attribute instance-attribute

can_manage_projects class-attribute instance-attribute

can_manage_users class-attribute instance-attribute

can_view_cases class-attribute instance-attribute

can_view_cohorts class-attribute instance-attribute

can_view_datasets class-attribute instance-attribute

can_view_projects class-attribute instance-attribute

can_view_users class-attribute instance-attribute

department class-attribute instance-attribute

external_source class-attribute instance-attribute

external_source_id class-attribute instance-attribute

full_name class-attribute instance-attribute

id class-attribute instance-attribute

is_provided class-attribute instance-attribute

is_service_account class-attribute instance-attribute

is_system_admin class-attribute instance-attribute

objects class-attribute instance-attribute

organization class-attribute instance-attribute

provider class-attribute instance-attribute

role class-attribute instance-attribute

shareable class-attribute instance-attribute

title class-attribute instance-attribute

AccessRoles

Bases: TextChoices

Enumeration of access roles within the system.

Attributes:

Name	Type	Description
EXTERNAL		Represents an external user with limited access.
MEMBER		Represents a standard member with regular access.
PROJECT_MANAGER		Represents a user with project management privileges.
PLATFORM_MANAGER		Represents a user with platform management privileges.
SYSTEM_ADMIN		Represents a system administrator with full access.

EXTERNAL class-attribute instance-attribute

MEMBER class-attribute instance-attribute

PLATFORM_MANAGER class-attribute instance-attribute

PROJECT_MANAGER class-attribute instance-attribute

SYSTEM_ADMIN class-attribute instance-attribute

Meta

constraints class-attribute instance-attribute

__str__()

Source code in onconova/core/auth/models.py

def __str__(self):
    return self.username

construct_permission_field_from_access_level(min_access_level, action) staticmethod

Constructs an annotation property representing a permission field based on the minimum access level and action.

Parameters:

Name	Type	Description	Default
min_access_level	int	The minimum required access level for the permission.	required
action	str	The action for which the permission is being checked (e.g., 'edit', 'delete').	required

Returns:

Type	Description
AnnotationProperty	An annotation property that evaluates to True if the user's access level is greater than or equal to the specified minimum or if the user is a superuser; otherwise, False. The property is annotated with a verbose name describing the action.

Source code in onconova/core/auth/models.py

@staticmethod
def construct_permission_field_from_access_level(min_access_level, action):
    """
    Constructs an annotation property representing a permission field based on the minimum access level and action.

    Args:
        min_access_level (int): The minimum required access level for the permission.
        action (str): The action for which the permission is being checked (e.g., 'edit', 'delete').

    Returns:
        (AnnotationProperty): An annotation property that evaluates to True if the user's access level is greater than or equal to the specified minimum or if the user is a superuser; otherwise, False. The property is annotated with a verbose name describing the action.
    """
    return AnnotationProperty(
        verbose_name=_(f"Can {action}"),
        annotation=Case(
            When(
                Q(access_level__gte=min_access_level) | Q(is_superuser=True),
                then=True,
            ),
            default=False,
            output_field=models.BooleanField(),
        ),
    )

save(*args, **kwargs)

Saves the current instance to the database.

If the user is a superuser, sets the access_level to 4 before saving. Calls the parent class's save method to perform the actual save operation.

Parameters:

Name	Type	Description	Default
args	tuple	Variable length argument list.	()
kwargs	dict	Arbitrary keyword arguments.	{}

Source code in onconova/core/auth/models.py

def save(self, *args, **kwargs):
    """
    Saves the current instance to the database.

    If the user is a superuser, sets the access_level to 4 before saving.
    Calls the parent class's save method to perform the actual save operation.

    Args:
        args (tuple): Variable length argument list.
        kwargs (dict): Arbitrary keyword arguments.
    """
    if self.is_superuser:
        self.access_level = 4
    super().save(*args, **kwargs)

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