synapseclient 4.1.0__tar.gz → 4.2.0__tar.gz

{synapseclient-4.1.0/synapseclient.egg-info → synapseclient-4.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: synapseclient
-Version: 4.1.0
+Version: 4.2.0
 Summary: A client for Synapse, a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate.
 Home-page: https://www.synapse.org
 Author: The Synapse Engineering Team
@@ -36,6 +36,12 @@ Requires-Dist: opentelemetry-api~=1.21.0
 Requires-Dist: opentelemetry-sdk~=1.21.0
 Requires-Dist: opentelemetry-exporter-otlp-proto-http~=1.21.0
 Requires-Dist: nest-asyncio~=1.6.0
+Requires-Dist: asyncio-atexit~=1.0.1
+Requires-Dist: httpx~=0.27.0
+Requires-Dist: tqdm<5.0,>=4.66.2
+Requires-Dist: loky~=3.0.0
+Requires-Dist: async-lru~=2.0.4
+Requires-Dist: psutil~=5.9.8
 Provides-Extra: dev
 Requires-Dist: pytest<7.0,>=6.0.0; extra == "dev"
 Requires-Dist: pytest-mock<4.0,>=3.0; extra == "dev"

{synapseclient-4.1.0 → synapseclient-4.2.0}/setup.cfg

@@ -45,6 +45,12 @@ install_requires =
 	opentelemetry-sdk~=1.21.0
 	opentelemetry-exporter-otlp-proto-http~=1.21.0
 	nest-asyncio~=1.6.0
+	asyncio-atexit~=1.0.1
+	httpx~=0.27.0
+	tqdm>=4.66.2,<5.0
+	loky~=3.0.0
+	async-lru~=2.0.4
+	psutil~=5.9.8
 tests_require = 
 	pytest>=6.0.0,<7.0
 	pytest-mock>=3.0,<4.0

{synapseclient-4.1.0 → synapseclient-4.2.0}/synapseclient/__main__.py

@@ -4,6 +4,7 @@ The Synapse command line client.
 For a description of its usage and parameters, see its documentation:
 https://python-docs.synapse.org/build/html/CommandLineClient.html
 """
+
 import argparse
 import collections.abc
 import logging
@@ -221,9 +222,11 @@ def store(args, syn):
     else:
         entity = {
             "concreteType": "org.sagebionetworks.repo.model.%s" % args.type,
-            "name": utils.guess_file_name(args.file)
-            if args.file and not args.name
-            else None,
+            "name": (
+                utils.guess_file_name(args.file)
+                if args.file and not args.name
+                else None
+            ),
             "parentId": None,
         }
     # Overide setting for parameters included in args
@@ -644,7 +647,7 @@ def submit(args, syn):
     )
 
 
-def get_download_list(args, syn):
+def get_download_list(args, syn: synapseclient.Synapse) -> None:
     """Download files from the Synapse download cart"""
     manifest_path = syn.get_download_list(downloadLocation=args.downloadLocation)
     syn.logger.info(f"Manifest file: {manifest_path}")
@@ -676,9 +679,11 @@ def test_encoding() -> None:
     print("python version =               ", platform.python_version())
     print(
         "sys.stdout.encoding =          ",
-        sys.stdout.encoding
-        if hasattr(sys.stdout, "encoding")
-        else "no encoding attribute",
+        (
+            sys.stdout.encoding
+            if hasattr(sys.stdout, "encoding")
+            else "no encoding attribute"
+        ),
     )
     print("sys.stdout.isatty() =          ", sys.stdout.isatty())
     print("locale.getpreferredencoding() =", locale.getpreferredencoding())

synapseclient-4.2.0/synapseclient/api/__init__.py

@@ -0,0 +1,54 @@
+# These are all of the models that are used by the Synapse client.
+from .annotations import set_annotations
+from .entity_bundle_services_v2 import (
+    get_entity_id_bundle2,
+    get_entity_id_version_bundle2,
+    post_entity_bundle2_create,
+    put_entity_id_bundle2,
+)
+from .entity_services import (
+    get_entity,
+    get_upload_destination,
+    get_upload_destination_location,
+    post_entity,
+    put_entity,
+    create_access_requirements_if_none,
+)
+from .file_services import (
+    get_file_handle,
+    post_external_filehandle,
+    post_external_object_store_filehandle,
+    post_external_s3_file_handle,
+    post_file_multipart,
+    put_file_multipart_complete,
+    post_file_multipart_presigned_urls,
+    put_file_multipart_add,
+    AddPartResponse,
+)
+
+__all__ = [
+    # annotations
+    "set_annotations",
+    "get_entity_id_bundle2",
+    "get_entity_id_version_bundle2",
+    "post_entity_bundle2_create",
+    "put_entity_id_bundle2",
+    # file_services
+    "post_file_multipart",
+    "put_file_multipart_add",
+    "put_file_multipart_complete",
+    "post_external_object_store_filehandle",
+    "post_external_s3_file_handle",
+    "get_file_handle",
+    "post_external_filehandle",
+    "post_file_multipart_presigned_urls",
+    "put_file_multipart_add",
+    "AddPartResponse",
+    # entity_services
+    "get_entity",
+    "put_entity",
+    "post_entity",
+    "get_upload_destination",
+    "get_upload_destination_location",
+    "create_access_requirements_if_none",
+]

{synapseclient-4.1.0 → synapseclient-4.2.0}/synapseclient/api/annotations.py

@@ -2,33 +2,40 @@
 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.
 """
+
 import json
 
 from dataclasses import asdict
 
 from typing import TYPE_CHECKING, Optional
-from synapseclient import Synapse
+
 from synapseclient.annotations import _convert_to_annotations_list
 
 if TYPE_CHECKING:
     from synapseclient.models import Annotations
+    from synapseclient import Synapse
 
 
 def set_annotations(
     annotations: "Annotations",
-    synapse_client: Optional[Synapse] = None,
+    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 or None this will use the last client from the `.login()` method.
+        annotations: The annotations to set. This is expected to have the id, etag,
+            and annotations filled in.
+        synapse_client: If not passed in or None this will use the last client from
+            the `.login()` method.
 
     Returns: The annotations set in Synapse.
     """
     annotations_dict = asdict(annotations)
 
-    synapse_annotations = _convert_to_annotations_list(annotations_dict["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",

synapseclient-4.2.0/synapseclient/api/entity_bundle_services_v2.py

@@ -0,0 +1,146 @@
+"""This module is responsible for exposing the services defined at:
+<https://rest-docs.synapse.org/rest/#org.sagebionetworks.repo.web.controller.EntityBundleV2Controller>
+"""
+
+import json
+from typing import Any, Dict, Optional, TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from synapseclient import Synapse
+
+
+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 or None this will use the last client from
+            the `.login()` method.
+
+    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),
+    )
+
+
+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 or None this will use the last client from
+            the `.login()` method.
+
+    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),
+    )
+
+
+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 or None this will use the last client from
+            the `.login()` method.
+
+    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),
+    )
+
+
+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 or None this will use the last client from
+            the `.login()` method.
+
+    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-4.2.0/synapseclient/api/entity_services.py

@@ -0,0 +1,177 @@
+"""This module is responsible for exposing the services defined at:
+<https://rest-docs.synapse.org/rest/#org.sagebionetworks.repo.web.controller.EntityController>
+"""
+
+import json
+from typing import Any, Dict, Optional, Union, TYPE_CHECKING
+from async_lru import alru_cache
+
+if TYPE_CHECKING:
+    from synapseclient import Synapse
+
+
+async def post_entity(
+    request: Dict[str, Any],
+    generated_by: Optional[str] = None,
+    synapse_client: Optional["Synapse"] = None,
+) -> Dict[str, Any]:
+    """
+    Arguments:
+        request: The request for the entity matching
+            <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/Entity.html>
+        generated_by: The ID of the activity to associate with the entity.
+        synapse_client: If not passed in or None this will use the last client from
+            the `.login()` method.
+
+    Returns:
+        The requested entity matching
+            <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/Entity.html>
+    """
+    from synapseclient import Synapse
+
+    client = Synapse.get_client(synapse_client=synapse_client)
+    params = {}
+    if generated_by:
+        params["generatedBy"] = generated_by
+    return await client.rest_post_async(
+        uri="/entity", body=json.dumps(request), params=params
+    )
+
+
+async def put_entity(
+    entity_id: str,
+    request: Dict[str, Any],
+    new_version: bool = False,
+    generated_by: Optional[str] = None,
+    synapse_client: Optional["Synapse"] = None,
+) -> Dict[str, Any]:
+    """
+    Arguments:
+        entity_id: The ID of the entity to update.
+        request: The request for the entity matching
+            <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/Entity.html>
+        new_version: If true, a new version of the entity will be created.
+        generated_by: The ID of the activity to associate with the entity.
+        synapse_client: If not passed in or None this will use the last client from
+            the `.login()` method.
+
+    Returns:
+        The requested entity bundle matching
+            <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/Entity.html>
+    """
+    from synapseclient import Synapse
+
+    client = Synapse.get_client(synapse_client=synapse_client)
+    params = {}
+    if generated_by:
+        params["generatedBy"] = generated_by
+    if new_version:
+        params["newVersion"] = "true"
+    return await client.rest_put_async(
+        uri=f"/entity/{entity_id}", body=json.dumps(request), params=params
+    )
+
+
+async def get_entity(
+    entity_id: str,
+    synapse_client: Optional["Synapse"] = None,
+) -> Dict[str, Any]:
+    """
+    Arguments:
+        entity_id: The ID of the entity.
+        synapse_client: If not passed in or None this will use the last client from
+            the `.login()` method.
+
+    Returns:
+        The requested entity bundle matching
+            <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/Entity.html>
+    """
+    from synapseclient import Synapse
+
+    client = Synapse.get_client(synapse_client=synapse_client)
+    return await client.rest_get_async(
+        uri=f"/entity/{entity_id}",
+    )
+
+
+@alru_cache(ttl=60)
+async def get_upload_destination(
+    entity_id: str, synapse_client: Optional["Synapse"] = None
+) -> Dict[str, Union[str, int]]:
+    """
+    <https://rest-docs.synapse.org/rest/GET/entity/id/uploadDestination.html>
+
+    Arguments:
+        entity_id: The ID of the entity.
+        synapse_client: If not passed in or None this will use the last client from
+            the `.login()` method.
+
+    Returns:
+        The upload destination.
+        <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/file/UploadDestination.html>
+    """
+    from synapseclient import Synapse
+
+    client = Synapse.get_client(synapse_client=synapse_client)
+    return await client.rest_get_async(
+        uri=f"/entity/{entity_id}/uploadDestination",
+        endpoint=client.fileHandleEndpoint,
+    )
+
+
+async def get_upload_destination_location(
+    entity_id: str, location: str, synapse_client: Optional["Synapse"] = None
+) -> Dict[str, Union[str, int]]:
+    """
+    <https://rest-docs.synapse.org/rest/GET/entity/id/uploadDestination/storageLocationId.html>
+
+    Arguments:
+        entity_id: The ID of the entity.
+        location: A storage location ID of the upload destination.
+        synapse_client: If not passed in or None this will use the last client from
+            the `.login()` method.
+
+    Returns:
+        The upload destination.
+        <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/file/UploadDestination.html>
+    """
+    from synapseclient import Synapse
+
+    client = Synapse.get_client(synapse_client=synapse_client)
+    return await client.rest_get_async(
+        uri=f"/entity/{entity_id}/uploadDestination/{location}",
+        endpoint=client.fileHandleEndpoint,
+    )
+
+
+async def create_access_requirements_if_none(
+    entity_id: str, synapse_client: Optional["Synapse"] = None
+) -> None:
+    """
+    Checks to see if the given entity has access requirements. If not, then one is added
+
+    Arguments:
+        entity_id: The ID of the entity.
+        synapse_client: If not passed in or None this will use the last client from
+            the `.login()` method.
+    """
+    from synapseclient import Synapse
+
+    client = Synapse.get_client(synapse_client=synapse_client)
+    existing_restrictions = await client.rest_get_async(
+        f"/entity/{entity_id}/accessRequirement?offset=0&limit=1"
+    )
+    if (
+        existing_restrictions is None
+        or not hasattr(existing_restrictions, "results")
+        or len(existing_restrictions["results"]) == 0
+    ):
+        access_requirements = await client.rest_post_async(
+            f"/entity/{entity_id}/lockAccessRequirement"
+        )
+        client.logger.info(
+            "Created an access requirements request for "
+            f"{entity_id}: {access_requirements['jiraKey']}. An email will be sent to "
+            "the Synapse access control team to start the process of adding "
+            "terms-of-use or review board approval for this entity."
+        )