Rest APIs

This section is for super users / developers only. These functions are subject to change as they are internal development functions. Use at your own risk.

The functions provided in these documents are generally direct representations of the Synapse REST API. They're used within the Synapse Python Client to interact with the Synapse servers. These will eventually be removed from the Synapse Python Client in favor of an auto-generated client derived from the Synapse Open API Spec.

synapseclient.api.entity_bundle_services_v2

This module is responsible for exposing the services defined at: https://rest-docs.synapse.org/rest/#org.sagebionetworks.repo.web.controller.EntityBundleV2Controller

Classes

Functions

get_entity_id_bundle2(entity_id, request=None, *, synapse_client=None) async

PARAMETER	DESCRIPTION
entity_id	The ID of the entity to which the bundle belongs TYPE: str
request	The request for the bundle matching https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/entitybundle/v2/EntityBundleRequest.html. If not passed in or None, the default request will be used: includeEntity: True includeAnnotations: True includeFileHandles: True includeRestrictionInformation: True TYPE: Optional[Dict[str, bool]] DEFAULT: None
synapse_client	If not passed in and caching was not disabled by Synapse.allow_client_caching(False) this will use the last created instance from the Synapse class constructor. TYPE: Optional[Synapse] DEFAULT: None

RETURNS	DESCRIPTION
Dict[str, Any]	The requested entity bundle matching https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/entitybundle/v2/EntityBundle.html

Source code in synapseclient/api/entity_bundle_services_v2.py

async def get_entity_id_bundle2(
    entity_id: str,
    request: Optional[Dict[str, bool]] = None,
    *,
    synapse_client: Optional["Synapse"] = None,
) -> Dict[str, Any]:
    """
    Arguments:
        entity_id: The ID of the entity to which the bundle belongs
        request: The request for the bundle matching
            <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/entitybundle/v2/EntityBundleRequest.html>.
            If not passed in or None, the default request will be used:

            - includeEntity: True
            - includeAnnotations: True
            - includeFileHandles: True
            - includeRestrictionInformation: True
        synapse_client: If not passed in and caching was not disabled by
                `Synapse.allow_client_caching(False)` this will use the last created
                instance from the Synapse class constructor.

    Returns:
        The requested entity bundle matching
            <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/entitybundle/v2/EntityBundle.html>
    """
    from synapseclient import Synapse

    if not request:
        request = {
            "includeEntity": True,
            "includeAnnotations": True,
            "includeFileHandles": True,
            "includeRestrictionInformation": True,
        }

    client = Synapse.get_client(synapse_client=synapse_client)
    return await client.rest_post_async(
        uri=f"/entity/{entity_id}/bundle2",
        body=json.dumps(request),
    )

get_entity_id_version_bundle2(entity_id, version, request=None, *, synapse_client=None) async

PARAMETER	DESCRIPTION
entity_id	The ID of the entity to which the bundle belongs TYPE: str
version	The version of the entity to which the bundle belongs TYPE: int
request	The request for the bundle matching https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/entitybundle/v2/EntityBundleRequest.html. If not passed in or None, the default request will be used: includeEntity: True includeAnnotations: True includeFileHandles: True includeRestrictionInformation: True TYPE: Optional[Dict[str, bool]] DEFAULT: None
synapse_client	If not passed in and caching was not disabled by Synapse.allow_client_caching(False) this will use the last created instance from the Synapse class constructor. TYPE: Optional[Synapse] DEFAULT: None

RETURNS	DESCRIPTION
Dict[str, Any]	The requested entity bundle matching https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/entitybundle/v2/EntityBundle.html

Source code in synapseclient/api/entity_bundle_services_v2.py

async def get_entity_id_version_bundle2(
    entity_id: str,
    version: int,
    request: Optional[Dict[str, bool]] = None,
    *,
    synapse_client: Optional["Synapse"] = None,
) -> Dict[str, Any]:
    """
    Arguments:
        entity_id: The ID of the entity to which the bundle belongs
        version: The version of the entity to which the bundle belongs
        request: The request for the bundle matching
            <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/entitybundle/v2/EntityBundleRequest.html>.
            If not passed in or None, the default request will be used:

            - includeEntity: True
            - includeAnnotations: True
            - includeFileHandles: True
            - includeRestrictionInformation: True
        synapse_client: If not passed in and caching was not disabled by
                `Synapse.allow_client_caching(False)` this will use the last created
                instance from the Synapse class constructor.

    Returns:
        The requested entity bundle matching
            <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/entitybundle/v2/EntityBundle.html>
    """
    from synapseclient import Synapse

    if not request:
        request = {
            "includeEntity": True,
            "includeAnnotations": True,
            "includeFileHandles": True,
            "includeRestrictionInformation": True,
        }
    client = Synapse.get_client(synapse_client=synapse_client)
    return await client.rest_post_async(
        uri=f"/entity/{entity_id}/version/{version}/bundle2",
        body=json.dumps(request),
    )

post_entity_bundle2_create(request, generated_by=None, *, synapse_client=None) async

PARAMETER	DESCRIPTION
request	The request for the bundle matching https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/entitybundle/v2/EntityBundleCreate.html TYPE: Dict[str, Any]
generated_by	The ID of the activity to associate with the entity. TYPE: Optional[str] DEFAULT: None
synapse_client	If not passed in and caching was not disabled by Synapse.allow_client_caching(False) this will use the last created instance from the Synapse class constructor. TYPE: Optional[Synapse] DEFAULT: None

RETURNS	DESCRIPTION
Dict[str, Any]	The requested entity bundle matching https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/entitybundle/v2/EntityBundle.html

Source code in synapseclient/api/entity_bundle_services_v2.py

async def post_entity_bundle2_create(
    request: Dict[str, Any],
    generated_by: Optional[str] = None,
    *,
    synapse_client: Optional["Synapse"] = None,
) -> Dict[str, Any]:
    """
    Arguments:
        request: The request for the bundle matching
            <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/entitybundle/v2/EntityBundleCreate.html>
        generated_by: The ID of the activity to associate with the entity.
        synapse_client: If not passed in and caching was not disabled by
                `Synapse.allow_client_caching(False)` this will use the last created
                instance from the Synapse class constructor.

    Returns:
        The requested entity bundle matching
            <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/entitybundle/v2/EntityBundle.html>
    """
    from synapseclient import Synapse

    client = Synapse.get_client(synapse_client=synapse_client)
    return await client.rest_post_async(
        uri="/entity/bundle2/create"
        + (f"?generatedBy={generated_by}" if generated_by else ""),
        body=json.dumps(request),
    )

put_entity_id_bundle2(entity_id, request, generated_by=None, *, synapse_client=None) async

PARAMETER	DESCRIPTION
entity_id	The ID of the entity to which the bundle belongs. TYPE: str
request	The request for the bundle matching https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/entitybundle/v2/EntityBundleCreate.html TYPE: Dict[str, Any]
generated_by	The ID of the activity to associate with the entity. TYPE: Optional[str] DEFAULT: None
synapse_client	If not passed in and caching was not disabled by Synapse.allow_client_caching(False) this will use the last created instance from the Synapse class constructor. TYPE: Optional[Synapse] DEFAULT: None

RETURNS	DESCRIPTION
Dict[str, Any]	The requested entity bundle matching https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/entitybundle/v2/EntityBundle.html

Source code in synapseclient/api/entity_bundle_services_v2.py

async def put_entity_id_bundle2(
    entity_id: str,
    request: Dict[str, Any],
    generated_by: Optional[str] = None,
    *,
    synapse_client: Optional["Synapse"] = None,
) -> Dict[str, Any]:
    """
    Arguments:
        entity_id: The ID of the entity to which the bundle belongs.
        request: The request for the bundle matching
            <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/entitybundle/v2/EntityBundleCreate.html>
        generated_by: The ID of the activity to associate with the entity.
        synapse_client: If not passed in and caching was not disabled by
                `Synapse.allow_client_caching(False)` this will use the last created
                instance from the Synapse class constructor.

    Returns:
        The requested entity bundle matching
            <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/entitybundle/v2/EntityBundle.html>
    """
    from synapseclient import Synapse

    client = Synapse.get_client(synapse_client=synapse_client)
    return await client.rest_put_async(
        uri=f"/entity/{entity_id}/bundle2"
        + (f"?generatedBy={generated_by}" if generated_by else ""),
        body=json.dumps(request),
    )

synapseclient.api.annotations

The purpose of this module is to provide any functions that are needed to interact with annotations that are not cleanly provided by the synapseclient library.

Classes

Functions

set_annotations(annotations, *, synapse_client=None)

Call to synapse and set the annotations for the given input.

PARAMETER	DESCRIPTION
annotations	The annotations to set. This is expected to have the id, etag, and annotations filled in. TYPE: Annotations
synapse_client	If not passed in and caching was not disabled by Synapse.allow_client_caching(False) this will use the last created instance from the Synapse class constructor. TYPE: Optional[Synapse] DEFAULT: None

Returns: The annotations set in Synapse.

Source code in synapseclient/api/annotations.py

def set_annotations(
    annotations: "Annotations",
    *,
    synapse_client: Optional["Synapse"] = None,
):
    """Call to synapse and set the annotations for the given input.

    Arguments:
        annotations: The annotations to set. This is expected to have the id, etag,
            and annotations filled in.
        synapse_client: If not passed in and caching was not disabled by
                `Synapse.allow_client_caching(False)` this will use the last created
                instance from the Synapse class constructor.

    Returns: The annotations set in Synapse.
    """
    annotations_dict = asdict(annotations)

    synapse_annotations = _convert_to_annotations_list(
        annotations_dict["annotations"] or {}
    )
    from synapseclient import Synapse

    return Synapse.get_client(synapse_client=synapse_client).restPUT(
        f"/entity/{annotations.id}/annotations2",
        body=json.dumps(
            {
                "id": annotations.id,
                "etag": annotations.etag,
                "annotations": synapse_annotations,
            }
        ),
    )

set_annotations_async(annotations, *, synapse_client=None) async

Call to synapse and set the annotations for the given input.

PARAMETER	DESCRIPTION
annotations	The annotations to set. This is expected to have the id, etag, and annotations filled in. TYPE: Annotations
synapse_client	If not passed in and caching was not disabled by Synapse.allow_client_caching(False) this will use the last created instance from the Synapse class constructor. TYPE: Optional[Synapse] DEFAULT: None

Returns: The annotations set in Synapse.

Source code in synapseclient/api/annotations.py

async def set_annotations_async(
    annotations: "Annotations",
    *,
    synapse_client: Optional["Synapse"] = None,
):
    """Call to synapse and set the annotations for the given input.

    Arguments:
        annotations: The annotations to set. This is expected to have the id, etag,
            and annotations filled in.
        synapse_client: If not passed in and caching was not disabled by
                `Synapse.allow_client_caching(False)` this will use the last created
                instance from the Synapse class constructor.

    Returns: The annotations set in Synapse.
    """
    annotations_dict = asdict(annotations)

    synapse_annotations = _convert_to_annotations_list(
        annotations_dict["annotations"] or {}
    )
    from synapseclient import Synapse

    return await Synapse.get_client(synapse_client=synapse_client).rest_put_async(
        f"/entity/{annotations.id}/annotations2",
        body=json.dumps(
            {
                "id": annotations.id,
                "etag": annotations.etag,
                "annotations": synapse_annotations,
            }
        ),
    )