synapseclient 4.3.0__tar.gz → 4.4.0__tar.gz

{synapseclient-4.3.0/synapseclient.egg-info → synapseclient-4.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: synapseclient
-Version: 4.3.0
+Version: 4.4.0
 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
@@ -39,7 +39,6 @@ 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

{synapseclient-4.3.0 → synapseclient-4.4.0}/pyproject.toml

@@ -13,3 +13,6 @@ exclude = [
 [tool.bandit]
 exclude_dirs = ["tests"]
 skips = ["B101", "B303", "B608", "B311", "B113", "B310", "B110"]
+
+[tool.isort]
+profile = "black"

{synapseclient-4.3.0 → synapseclient-4.4.0}/setup.cfg

@@ -48,7 +48,6 @@ install_requires =
 	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 = 

{synapseclient-4.3.0 → synapseclient-4.4.0}/synapseclient/__init__.py

@@ -1,36 +1,35 @@
 import importlib.resources
-
 import json
+
 import requests  # ensure user-agent is set to track Synapse Python client usage
 
 from .activity import Activity
 from .annotations import Annotations
-from .client import PUBLIC, AUTHENTICATED_USERS
 
 # public APIs
-from .client import Synapse, login
+from .client import AUTHENTICATED_USERS, PUBLIC, Synapse, login
+from .core.models.permission import Permissions
 from .core.version_check import check_for_updates, release_notes
-from .entity import Entity, Project, Folder, File, Link, DockerRepository
+from .entity import DockerRepository, Entity, File, Folder, Link, Project
 from .evaluation import Evaluation, Submission, SubmissionStatus
 from .table import (
-    Schema,
-    EntityViewSchema,
     Column,
-    RowSet,
+    Dataset,
+    EntityViewSchema,
+    EntityViewType,
+    MaterializedViewSchema,
+    PartialRowset,
     Row,
-    as_table_columns,
+    RowSet,
+    Schema,
+    SubmissionViewSchema,
     Table,
-    PartialRowset,
-    EntityViewType,
+    as_table_columns,
     build_table,
-    SubmissionViewSchema,
-    MaterializedViewSchema,
-    Dataset,
     delete_rows,
 )
-from .team import Team, UserProfile, UserGroupHeader, TeamMember
+from .team import Team, TeamMember, UserGroupHeader, UserProfile
 from .wiki import Wiki
-from .core.models.permission import Permissions
 
 # ref = importlib.resources.files(__name__).joinpath("synapsePythonClient")
 # with ref.open("r") as fp:
@@ -93,8 +92,8 @@ USER_AGENT_COMMAND_LINE = {
     % (__version__, requests.utils.default_user_agent())
 }
 
-# patch json
-from .core.models import custom_json  # noqa
-
 # patch logging
 from .core import logging_setup  # noqa
+
+# patch json
+from .core.models import custom_json  # noqa

{synapseclient-4.3.0 → synapseclient-4.4.0}/synapseclient/__main__.py

@@ -7,35 +7,35 @@ https://python-docs.synapse.org/build/html/CommandLineClient.html
 
 import argparse
 import collections.abc
+import csv
+import getpass
+import json
 import logging
 import os
-import sys
-import signal
-import json
-import getpass
-import csv
 import re
 import shutil
+import signal
+import sys
+
+from opentelemetry import trace
+from opentelemetry.exporter.otlp.proto.http.trace_exporter import OTLPSpanExporter
+from opentelemetry.sdk.resources import SERVICE_NAME, Resource
+from opentelemetry.sdk.trace import TracerProvider
+from opentelemetry.sdk.trace.export import BatchSpanProcessor, ConsoleSpanExporter
+from opentelemetry.sdk.trace.sampling import ALWAYS_OFF, ALWAYS_ON, ParentBased
 
 import synapseclient
 import synapseutils
-
 from synapseclient import Activity
-from synapseclient.wiki import Wiki
 from synapseclient.annotations import Annotations
 from synapseclient.core import utils
 from synapseclient.core.exceptions import (
     SynapseAuthenticationError,
-    SynapseHTTPError,
     SynapseFileNotFoundError,
+    SynapseHTTPError,
     SynapseNoCredentialsError,
 )
-from opentelemetry import trace
-from opentelemetry.sdk.trace import TracerProvider
-from opentelemetry.sdk.trace.export import BatchSpanProcessor, ConsoleSpanExporter
-from opentelemetry.sdk.resources import SERVICE_NAME, Resource
-from opentelemetry.exporter.otlp.proto.http.trace_exporter import OTLPSpanExporter
-from opentelemetry.sdk.trace.sampling import ALWAYS_OFF, ALWAYS_ON, ParentBased
+from synapseclient.wiki import Wiki
 
 tracer = trace.get_tracer("synapseclient")
 
@@ -109,6 +109,7 @@ def _getIdsFromQuery(queryString, syn, downloadLocation):
 @tracer.start_as_current_span("main::get")
 def get(args, syn):
     syn.multi_threaded = args.multiThreaded
+    printed_download_message = False
     if args.recursive:
         if args.version is not None:
             raise ValueError(
@@ -161,13 +162,14 @@ def get(args, syn):
                 and entity.path is not None
                 and os.path.exists(entity.path)
             ):
-                syn.logger.info("Downloaded file: %s", os.path.basename(entity.path))
+                # The core download functionality of syn.get will print out the message
+                printed_download_message = True
             else:
                 syn.logger.info(
                     "WARNING: No files associated with entity %s\n", entity.id
                 )
                 syn.logger.info(entity)
-        if "path" in entity:
+        if "path" in entity and not printed_download_message:
             syn.logger.info("Creating %s", entity.path)
 
 

{synapseclient-4.3.0 → synapseclient-4.4.0}/synapseclient/activity.py

@@ -55,7 +55,7 @@ For example, when storing a data entity, it's a good idea to record its source:
 import collections.abc
 
 from synapseclient.core.exceptions import SynapseError, SynapseMalformedEntityError
-from synapseclient.core.utils import is_url, is_synapse_id_str, get_synid_and_version
+from synapseclient.core.utils import get_synid_and_version, is_synapse_id_str, is_url
 from synapseclient.entity import is_synapse_entity
 
 

{synapseclient-4.3.0 → synapseclient-4.4.0}/synapseclient/annotations.py

@@ -71,17 +71,18 @@ See also:
 """
 
 import collections
+import datetime
+import typing
 
-from .entity import Entity
 from synapseclient.core.utils import (
-    to_unix_epoch_time,
     from_unix_epoch_time,
+    id_of,
     is_date,
     to_list,
-    id_of,
+    to_unix_epoch_time,
 )
-import typing
-import datetime
+
+from .entity import Entity
 
 
 def _identity(x):

{synapseclient-4.3.0 → synapseclient-4.4.0}/synapseclient/api/__init__.py

@@ -1,35 +1,48 @@
 # These are all of the models that are used by the Synapse client.
-from .annotations import set_annotations
+from .annotations import set_annotations, set_annotations_async
+from .configuration_services import (
+    get_client_authenticated_s3_profile,
+    get_config_authentication,
+    get_config_file,
+    get_config_section_dict,
+    get_transfer_config,
+)
 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_factory import get_from_entity_factory
 from .entity_services import (
+    create_access_requirements_if_none,
+    delete_entity_generated_by,
+    get_entities_by_md5,
     get_entity,
+    get_entity_path,
     get_upload_destination,
     get_upload_destination_location,
     post_entity,
     put_entity,
-    create_access_requirements_if_none,
-    delete_entity_generated_by,
 )
 from .file_services import (
+    AddPartResponse,
     get_file_handle,
+    get_file_handle_for_download,
+    get_file_handle_for_download_async,
     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,
+    put_file_multipart_complete,
 )
 
 __all__ = [
     # annotations
     "set_annotations",
+    "set_annotations_async",
     "get_entity_id_bundle2",
     "get_entity_id_version_bundle2",
     "post_entity_bundle2_create",
@@ -45,6 +58,8 @@ __all__ = [
     "post_file_multipart_presigned_urls",
     "put_file_multipart_add",
     "AddPartResponse",
+    "get_file_handle_for_download_async",
+    "get_file_handle_for_download",
     # entity_services
     "get_entity",
     "put_entity",
@@ -53,4 +68,14 @@ __all__ = [
     "get_upload_destination_location",
     "create_access_requirements_if_none",
     "delete_entity_generated_by",
+    "get_entity_path",
+    "get_entities_by_md5",
+    # configuration_services
+    "get_config_file",
+    "get_config_section_dict",
+    "get_config_authentication",
+    "get_client_authenticated_s3_profile",
+    "get_transfer_config",
+    # entity_factory
+    "get_from_entity_factory",
 ]

{synapseclient-4.3.0 → synapseclient-4.4.0}/synapseclient/api/annotations.py

@@ -4,20 +4,19 @@ annotations that are not cleanly provided by the synapseclient library.
 """
 
 import json
-
 from dataclasses import asdict
-
 from typing import TYPE_CHECKING, Optional
 
 from synapseclient.annotations import _convert_to_annotations_list
 
 if TYPE_CHECKING:
-    from synapseclient.models import Annotations
     from synapseclient import Synapse
+    from synapseclient.models import Annotations
 
 
 def set_annotations(
     annotations: "Annotations",
+    *,
     synapse_client: Optional["Synapse"] = None,
 ):
     """Call to synapse and set the annotations for the given input.
@@ -47,3 +46,37 @@ def set_annotations(
             }
         ),
     )
+
+
+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 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"] 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,
+            }
+        ),
+    )

synapseclient-4.4.0/synapseclient/api/configuration_services.py

@@ -0,0 +1,138 @@
+"""This module is responsible for exposing access to any configuration either through
+file, environment variables, or other means.
+"""
+
+import configparser
+import functools
+import urllib.parse
+from typing import Dict
+
+from synapseclient.core.constants import config_file_constants
+from synapseclient.core.pool_provider import DEFAULT_NUM_THREADS
+
+
+@functools.lru_cache()
+def get_config_file(config_path: str) -> configparser.RawConfigParser:
+    """
+    Retrieves the client configuration information.
+
+    Arguments:
+        config_path:  Path to configuration file on local file system
+
+    Returns:
+        A RawConfigParser populated with properties from the user's configuration file.
+    """
+
+    try:
+        config = configparser.RawConfigParser()
+        config.read(config_path)  # Does not fail if the file does not exist
+        return config
+    except configparser.Error as ex:
+        raise ValueError(f"Error parsing Synapse config file: {config_path}") from ex
+
+
+def get_config_section_dict(
+    section_name: str,
+    config_path: str,
+) -> Dict[str, str]:
+    """
+    Get a profile section in the configuration file with the section name.
+
+    Arguments:
+        section_name: The name of the profile section in the configuration file
+        config_path:  Path to configuration file on local file system
+
+    Returns:
+        A dictionary containing the configuration profile section content. If the
+        section does not exist, an empty dictionary is returned.
+    """
+    config = get_config_file(config_path)
+    try:
+        return dict(config.items(section_name))
+    except configparser.NoSectionError:
+        # section not present
+        return {}
+
+
+def get_client_authenticated_s3_profile(
+    endpoint: str,
+    bucket: str,
+    config_path: str,
+) -> Dict[str, str]:
+    """
+    Get the authenticated S3 profile from the configuration file.
+
+    Arguments:
+        endpoint: The location of the target service
+        bucket:   AWS S3 bucket name
+        config_path:  Path to configuration file on local file system
+
+    Returns:
+        The authenticated S3 profile
+    """
+
+    config_section = urllib.parse.urljoin(base=endpoint, url=bucket)
+    return get_config_section_dict(
+        section_name=config_section, config_path=config_path
+    ).get("profile_name", "default")
+
+
+def get_config_authentication(
+    config_path: str,
+) -> Dict[str, str]:
+    """
+    Get the authentication section of the configuration file.
+
+    Arguments:
+        config_path:  Path to configuration file on local file system
+
+    Returns:
+        The authentication section of the configuration file
+    """
+    return get_config_section_dict(
+        section_name=config_file_constants.AUTHENTICATION_SECTION_NAME,
+        config_path=config_path,
+    )
+
+
+def get_transfer_config(
+    config_path: str,
+) -> Dict[str, str]:
+    """
+    Get the transfer profile from the configuration file.
+
+    Arguments:
+        config_path:  Path to configuration file on local file system
+
+    Raises:
+        ValueError: Invalid max_threads value. Should be equal or less than 16.
+        ValueError: Invalid use_boto_sts value. Should be true or false.
+
+    Returns:
+        The transfer profile
+    """
+    # defaults
+    transfer_config = {"max_threads": DEFAULT_NUM_THREADS, "use_boto_sts": False}
+
+    for k, v in get_config_section_dict(
+        section_name="transfer", config_path=config_path
+    ).items():
+        if v:
+            if k == "max_threads":
+                try:
+                    transfer_config["max_threads"] = int(v)
+                except ValueError as cause:
+                    raise ValueError(
+                        f"Invalid transfer.max_threads config setting {v}"
+                    ) from cause
+
+            elif k == "use_boto_sts":
+                lower_v = v.lower()
+                if lower_v not in ("true", "false"):
+                    raise ValueError(
+                        f"Invalid transfer.use_boto_sts config setting {v}"
+                    )
+
+                transfer_config["use_boto_sts"] = "true" == lower_v
+
+    return transfer_config

{synapseclient-4.3.0 → synapseclient-4.4.0}/synapseclient/api/entity_bundle_services_v2.py

@@ -3,7 +3,7 @@
 """
 
 import json
-from typing import Any, Dict, Optional, TYPE_CHECKING
+from typing import TYPE_CHECKING, Any, Dict, Optional
 
 if TYPE_CHECKING:
     from synapseclient import Synapse
@@ -12,6 +12,7 @@ if TYPE_CHECKING:
 async def get_entity_id_bundle2(
     entity_id: str,
     request: Optional[Dict[str, bool]] = None,
+    *,
     synapse_client: Optional["Synapse"] = None,
 ) -> Dict[str, Any]:
     """
@@ -53,6 +54,7 @@ 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]:
     """
@@ -93,6 +95,7 @@ async def get_entity_id_version_bundle2(
 async def post_entity_bundle2_create(
     request: Dict[str, Any],
     generated_by: Optional[str] = None,
+    *,
     synapse_client: Optional["Synapse"] = None,
 ) -> Dict[str, Any]:
     """
@@ -121,6 +124,7 @@ 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]:
     """