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 `async` ¶

get_entity_id_bundle2(entity_id: str, request: Optional[Dict[str, bool]] = None, *, synapse_client: Optional[Synapse] = None) -> Dict[str, Any]

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 `async` ¶

get_entity_id_version_bundle2(entity_id: str, version: int, request: Optional[Dict[str, bool]] = None, *, synapse_client: Optional[Synapse] = None) -> Dict[str, Any]

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 `async` ¶

post_entity_bundle2_create(request: Dict[str, Any], generated_by: Optional[str] = None, *, synapse_client: Optional[Synapse] = None) -> Dict[str, Any]

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 `async` ¶

put_entity_id_bundle2(entity_id: str, request: Dict[str, Any], generated_by: Optional[str] = None, *, synapse_client: Optional[Synapse] = None) -> Dict[str, Any]

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 ¶

set_annotations(annotations: Annotations, *, synapse_client: Optional[Synapse] = 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 `async` ¶

set_annotations_async(annotations: Annotations, *, synapse_client: Optional[Synapse] = 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

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,
            }
        ),
    )

Rest APIs¶

synapseclient.api.entity_bundle_services_v2 ¶

Classes¶

Functions¶

get_entity_id_bundle2 async ¶

get_entity_id_version_bundle2 async ¶

post_entity_bundle2_create async ¶

put_entity_id_bundle2 async ¶

synapseclient.api.annotations ¶

Classes¶

Functions¶

set_annotations ¶

set_annotations_async async ¶

get_entity_id_bundle2 `async` ¶

get_entity_id_version_bundle2 `async` ¶

post_entity_bundle2_create `async` ¶

put_entity_id_bundle2 `async` ¶

set_annotations_async `async` ¶