synapseclient 4.7.0__tar.gz → 4.8.0__tar.gz

{synapseclient-4.7.0/synapseclient.egg-info → synapseclient-4.8.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: synapseclient
-Version: 4.7.0
+Version: 4.8.0
 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
@@ -9,7 +9,7 @@ License: Apache-2.0
 Project-URL: Source, https://github.com/Sage-Bionetworks/synapsePythonClient
 Project-URL: Tracker, https://github.com/Sage-Bionetworks/synapsePythonClient/issues
 Project-URL: Documentation, https://python-docs.synapse.org
-Project-URL: Changelog, https://python-docs.synapse.org/build/html/index.html#release-notes
+Project-URL: Changelog, https://python-docs.synapse.org/en/stable/news/
 Platform: any
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Programming Language :: Python
@@ -17,6 +17,7 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Operating System :: MacOS
 Classifier: Operating System :: Microsoft :: Windows
 Classifier: Operating System :: Unix
@@ -27,7 +28,7 @@ Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Topic :: Software Development :: Libraries
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Requires-Python: <3.13,>=3.9
+Requires-Python: <3.14,>=3.9
 Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
 Requires-Dist: requests<3.0,>=2.22.0
 Requires-Dist: urllib3<2,>=1.26.18
@@ -41,15 +42,16 @@ Requires-Dist: opentelemetry-instrumentation-threading>=0.48b0
 Requires-Dist: opentelemetry-instrumentation-urllib>=0.48b0
 Requires-Dist: nest-asyncio~=1.6.0
 Requires-Dist: asyncio-atexit~=1.0.1
-Requires-Dist: httpx~=0.27.0
+Requires-Dist: httpx>=0.27.0
+Requires-Dist: httpcore>=1.0.9
 Requires-Dist: tqdm<5.0,>=4.66.2
 Requires-Dist: async-lru~=2.0.4
 Requires-Dist: psutil~=5.9.8
 Provides-Extra: dev
-Requires-Dist: pytest<8.0,>=7.0.0; extra == "dev"
+Requires-Dist: pytest~=8.2.0; extra == "dev"
 Requires-Dist: pytest-mock<4.0,>=3.0; extra == "dev"
 Requires-Dist: pytest-socket~=0.6.0; extra == "dev"
-Requires-Dist: pytest-asyncio<1.0,>=0.23.6; extra == "dev"
+Requires-Dist: pytest-asyncio<1.0,>=0.25.0; extra == "dev"
 Requires-Dist: flake8<4.0,>=3.7.0; extra == "dev"
 Requires-Dist: pytest-xdist[psutil]<3.0.0,>=2.2; extra == "dev"
 Requires-Dist: pytest-rerunfailures~=12.0; extra == "dev"
@@ -59,10 +61,10 @@ Requires-Dist: black; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
 Requires-Dist: pandas<3.0,>=1.5; extra == "dev"
 Provides-Extra: tests
-Requires-Dist: pytest<8.0,>=7.0.0; extra == "tests"
+Requires-Dist: pytest~=8.2.0; extra == "tests"
 Requires-Dist: pytest-mock<4.0,>=3.0; extra == "tests"
 Requires-Dist: pytest-socket~=0.6.0; extra == "tests"
-Requires-Dist: pytest-asyncio<1.0,>=0.23.6; extra == "tests"
+Requires-Dist: pytest-asyncio<1.0,>=0.25.0; extra == "tests"
 Requires-Dist: flake8<4.0,>=3.7.0; extra == "tests"
 Requires-Dist: pytest-xdist[psutil]<3.0.0,>=2.2; extra == "tests"
 Requires-Dist: pytest-rerunfailures~=12.0; extra == "tests"
@@ -88,7 +90,7 @@ Python Synapse Client
 =====================
 
 Branch  | Build Status
---------|-------------
+--------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 develop | [![Build Status develop branch](https://github.com/Sage-Bionetworks/synapsePythonClient/workflows/build/badge.svg?branch=develop)](https://github.com/Sage-Bionetworks/synapsePythonClient/actions?query=branch%3Adevelop)
 master  | [![Build Status master branch](https://github.com/Sage-Bionetworks/synapsePythonClient/workflows/build/badge.svg?branch=master)](https://github.com/Sage-Bionetworks/synapsePythonClient/actions?query=branch%3Amaster)
 
@@ -122,7 +124,7 @@ or by sending an email to [python-announce+subscribe@sagebase.org](mailto:python
 Installation
 ------------
 
-The Python Synapse client has been tested on versions 3.9, 3.10, 3.11 and 3.12 on Mac OS X, Ubuntu Linux and Windows.
+The Python Synapse client has been tested on versions 3.9, 3.10, 3.11, 3.12 and 3.13 on Mac OS X, Ubuntu Linux and Windows.
 
 **Starting from Synapse Python client version 3.0, Synapse Python client requires Python >= 3.9**
 

{synapseclient-4.7.0 → synapseclient-4.8.0}/README.md

@@ -2,7 +2,7 @@ Python Synapse Client
 =====================
 
 Branch  | Build Status
---------|-------------
+--------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 develop | [![Build Status develop branch](https://github.com/Sage-Bionetworks/synapsePythonClient/workflows/build/badge.svg?branch=develop)](https://github.com/Sage-Bionetworks/synapsePythonClient/actions?query=branch%3Adevelop)
 master  | [![Build Status master branch](https://github.com/Sage-Bionetworks/synapsePythonClient/workflows/build/badge.svg?branch=master)](https://github.com/Sage-Bionetworks/synapsePythonClient/actions?query=branch%3Amaster)
 
@@ -36,7 +36,7 @@ or by sending an email to [python-announce+subscribe@sagebase.org](mailto:python
 Installation
 ------------
 
-The Python Synapse client has been tested on versions 3.9, 3.10, 3.11 and 3.12 on Mac OS X, Ubuntu Linux and Windows.
+The Python Synapse client has been tested on versions 3.9, 3.10, 3.11, 3.12 and 3.13 on Mac OS X, Ubuntu Linux and Windows.
 
 **Starting from Synapse Python client version 3.0, Synapse Python client requires Python >= 3.9**
 

{synapseclient-4.7.0 → synapseclient-4.8.0}/setup.cfg

@@ -12,7 +12,7 @@ project_urls =
 	Source = https://github.com/Sage-Bionetworks/synapsePythonClient
 	Tracker = https://github.com/Sage-Bionetworks/synapsePythonClient/issues
 	Documentation = https://python-docs.synapse.org
-	Changelog = https://python-docs.synapse.org/build/html/index.html#release-notes
+	Changelog = https://python-docs.synapse.org/en/stable/news/
 platforms = any
 classifiers = 
 	Development Status :: 5 - Production/Stable
@@ -21,6 +21,7 @@ classifiers =
 	Programming Language :: Python :: 3.10
 	Programming Language :: Python :: 3.11
 	Programming Language :: Python :: 3.12
+	Programming Language :: Python :: 3.13
 	Operating System :: MacOS
 	Operating System :: Microsoft :: Windows
 	Operating System :: Unix
@@ -36,7 +37,7 @@ classifiers =
 zip_safe = False
 include_package_data = True
 packages = find:
-python_requires = >=3.9, <3.13
+python_requires = >=3.9, <3.14
 install_requires = 
 	requests>=2.22.0,<3.0
 	urllib3>=1.26.18,<2
@@ -50,15 +51,16 @@ install_requires =
 	opentelemetry-instrumentation-urllib>=0.48b0
 	nest-asyncio~=1.6.0
 	asyncio-atexit~=1.0.1
-	httpx~=0.27.0
+	httpx>=0.27.0
+	httpcore>=1.0.9
 	tqdm>=4.66.2,<5.0
 	async-lru~=2.0.4
 	psutil~=5.9.8
 tests_require = 
-	pytest>=7.0.0,<8.0
+	pytest~=8.2.0
 	pytest-mock>=3.0,<4.0
 	pytest-socket~=0.6.0
-	pytest-asyncio>=0.23.6,<1.0
+	pytest-asyncio>=0.25.0,<1.0
 	flake8>=3.7.0,<4.0
 	pytest-xdist[psutil]>=2.2,<3.0.0
 	pytest-rerunfailures~=12.0
@@ -68,10 +70,10 @@ tests_require =
 
 [options.extras_require]
 dev = 
-	pytest>=7.0.0,<8.0
+	pytest~=8.2.0
 	pytest-mock>=3.0,<4.0
 	pytest-socket~=0.6.0
-	pytest-asyncio>=0.23.6,<1.0
+	pytest-asyncio>=0.25.0,<1.0
 	flake8>=3.7.0,<4.0
 	pytest-xdist[psutil]>=2.2,<3.0.0
 	pytest-rerunfailures~=12.0
@@ -81,10 +83,10 @@ dev =
 	pre-commit
 	pandas>=1.5,<3.0
 tests = 
-	pytest>=7.0.0,<8.0
+	pytest~=8.2.0
 	pytest-mock>=3.0,<4.0
 	pytest-socket~=0.6.0
-	pytest-asyncio>=0.23.6,<1.0
+	pytest-asyncio>=0.25.0,<1.0
 	flake8>=3.7.0,<4.0
 	pytest-xdist[psutil]>=2.2,<3.0.0
 	pytest-rerunfailures~=12.0

{synapseclient-4.7.0 → synapseclient-4.8.0}/synapseclient/__main__.py

@@ -359,12 +359,12 @@ def show(args, syn):
 
     ent = syn.get(args.id, downloadFile=False)
     syn.printEntity(ent)
-    sys.stdout.write("Provenance:\n")
+    syn.logger.info("Provenance:")
     try:
         prov = syn.getProvenance(ent)
         syn.logger.info(prov)
     except SynapseHTTPError:
-        syn.logger.error("  No Activity specified.\n")
+        syn.logger.exception("No Activity specified.")
 
 
 def delete(args, syn):
@@ -1785,11 +1785,11 @@ def perform_main(args, syn):
             )
         try:
             args.func(args, syn)
-        except Exception as ex:
+        except Exception:
             if args.debug:
                 raise
             else:
-                sys.stderr.write(utils._synapse_error_msg(ex))
+                syn.logger.exception(f"Failed to perform command: {args.func}")
                 sys.exit(1)
     else:
         # if no command provided print out help and quit

{synapseclient-4.7.0 → synapseclient-4.8.0}/synapseclient/api/__init__.py

@@ -24,6 +24,7 @@ from .entity_bundle_services_v2 import (
 from .entity_factory import get_from_entity_factory
 from .entity_services import (
     create_access_requirements_if_none,
+    delete_entity,
     delete_entity_generated_by,
     get_entities_by_md5,
     get_entity,
@@ -46,6 +47,13 @@ from .file_services import (
     put_file_multipart_add,
     put_file_multipart_complete,
 )
+from .table_services import (
+    ViewEntityType,
+    ViewTypeMask,
+    get_columns,
+    get_default_columns,
+    post_columns,
+)
 
 __all__ = [
     # annotations
@@ -72,6 +80,7 @@ __all__ = [
     "get_entity",
     "put_entity",
     "post_entity",
+    "delete_entity",
     "get_upload_destination",
     "get_upload_destination_location",
     "create_access_requirements_if_none",
@@ -93,4 +102,10 @@ __all__ = [
     "get_session",
     "update_session",
     "get_trace",
+    # columns
+    "get_columns",
+    "post_columns",
+    "get_default_columns",
+    "ViewTypeMask",
+    "ViewEntityType",
 ]

{synapseclient-4.7.0 → synapseclient-4.8.0}/synapseclient/api/entity_factory.py

@@ -19,8 +19,10 @@ from synapseclient.core.exceptions import (
 )
 
 if TYPE_CHECKING:
+    from models.entityview import EntityView
+
     from synapseclient import Synapse
-    from synapseclient.models import File, Folder, Project
+    from synapseclient.models import Dataset, File, Folder, Project, Table
 
 
 async def get_from_entity_factory(
@@ -32,7 +34,9 @@ async def get_from_entity_factory(
     download_file: bool = True,
     download_location: str = None,
     follow_link: bool = False,
-    entity_to_update: Union["Project", "File", "Folder"] = None,
+    entity_to_update: Union[
+        "Project", "File", "Folder", "Table", "Dataset", "EntityView"
+    ] = None,
     *,
     synapse_client: Optional["Synapse"] = None,
 ) -> Union["Project", "File", "Folder"]:
@@ -228,6 +232,64 @@ async def _search_for_file_by_md5(
     return bundle
 
 
+async def _handle_file_entity(
+    entity_instance: "File",
+    entity_bundle: Dict[str, Any],
+    download_file: bool,
+    download_location: str,
+    if_collision: str,
+    submission: str,
+    synapse_client: "Synapse",
+) -> "File":
+    """Helper function to handle File entity specific logic."""
+    from synapseclient.models import FileHandle
+
+    entity_instance.fill_from_dict(
+        synapse_file=entity_bundle["entity"], set_annotations=False
+    )
+
+    # Update entity with FileHandle metadata
+    file_handle = next(
+        (
+            handle
+            for handle in entity_bundle.get("fileHandles", [])
+            if handle and handle["id"] == entity_instance.data_file_handle_id
+        ),
+        {},
+    )
+
+    entity_instance.file_handle = FileHandle().fill_from_dict(
+        synapse_instance=file_handle
+    )
+    entity_instance._fill_from_file_handle()
+
+    if download_file:
+        if file_handle:
+            await download_file_entity_model(
+                download_location=download_location,
+                file=entity_instance,
+                if_collision=if_collision,
+                submission=submission,
+                synapse_client=synapse_client,
+            )
+        else:
+            warning_message = (
+                "WARNING: You have READ permission on this file entity but not DOWNLOAD "
+                "permission. The file has NOT been downloaded."
+            )
+            synapse_client.logger.warning(
+                "\n"
+                + "!" * len(warning_message)
+                + "\n"
+                + warning_message
+                + "\n"
+                + "!" * len(warning_message)
+                + "\n"
+            )
+
+    return entity_instance
+
+
 async def _cast_into_class_type(
     entity_bundle: Dict[str, Any],
     download_file: bool = True,
@@ -238,7 +300,7 @@ async def _cast_into_class_type(
     entity_to_update: Union["Project", "File", "Folder"] = None,
     *,
     synapse_client: Optional["Synapse"] = None,
-) -> Union["Project", "File", "Folder"]:
+) -> Union["Project", "File", "Folder", "Table", "Dataset", "EntityView"]:
     """
     Take an entity_bundle returned from the Synapse API and cast it into the appropriate
     class type. This will also download the file if `download_file` is set to True.
@@ -271,6 +333,18 @@ async def _cast_into_class_type(
         ValueError: If the entity type is not supported.
     """
     from synapseclient import Synapse
+    from synapseclient.models import (
+        Annotations,
+        Dataset,
+        DatasetCollection,
+        EntityView,
+        File,
+        Folder,
+        MaterializedView,
+        Project,
+        SubmissionView,
+        Table,
+    )
 
     syn = Synapse.get_client(synapse_client=synapse_client)
 
@@ -284,79 +358,53 @@ async def _cast_into_class_type(
         entity_bundle = await get_entity_id_version_bundle2(
             entity_id=target_id, version=target_version, synapse_client=synapse_client
         )
-    entity = entity_bundle["entity"]
-
-    from synapseclient.models import Annotations
 
+    entity = entity_bundle["entity"]
     annotations = Annotations.from_dict(
         synapse_annotations=entity_bundle.get("annotations", None)
     )
 
-    from synapseclient.models import File, Folder, Project
-
-    if entity["concreteType"] == concrete_types.PROJECT_ENTITY:
-        if not entity_to_update:
-            entity_to_update = Project()
-        entity = entity_to_update.fill_from_dict(
-            synapse_project=entity_bundle["entity"], set_annotations=False
-        )
-    elif entity["concreteType"] == concrete_types.FOLDER_ENTITY:
-        if not entity_to_update:
-            entity_to_update = Folder()
-        entity = entity_to_update.fill_from_dict(
-            synapse_folder=entity_bundle["entity"], set_annotations=False
-        )
-    elif entity["concreteType"] == concrete_types.FILE_ENTITY:
-        if not entity_to_update:
-            entity_to_update = File()
-        entity = entity_to_update.fill_from_dict(
-            synapse_file=entity_bundle["entity"], set_annotations=False
-        )
-        # update the entity with FileHandle metadata
-        file_handle = next(
-            (
-                handle
-                for handle in entity_bundle.get("fileHandles", [])
-                if handle and handle["id"] == entity.data_file_handle_id
-            ),
-            {},
-        )
-        from synapseclient.models import FileHandle
-
-        entity.file_handle = FileHandle().fill_from_dict(synapse_instance=file_handle)
-        entity._fill_from_file_handle()
-
-        if download_file:
-            if file_handle:
-                await download_file_entity_model(
-                    download_location=download_location,
-                    file=entity,
-                    if_collision=if_collision,
-                    submission=submission,
-                    synapse_client=synapse_client,
-                )
-            else:  # no filehandle means that we do not have DOWNLOAD permission
-                warning_message = (
-                    "WARNING: You have READ permission on this file entity but not DOWNLOAD "
-                    "permission. The file has NOT been downloaded."
-                )
-                syn.logger.warning(
-                    "\n"
-                    + "!" * len(warning_message)
-                    + "\n"
-                    + warning_message
-                    + "\n"
-                    + "!" * len(warning_message)
-                    + "\n"
-                )
-    else:
+    # Map concrete types to their corresponding classes
+    ENTITY_TYPE_MAP = {
+        concrete_types.PROJECT_ENTITY: Project,
+        concrete_types.FOLDER_ENTITY: Folder,
+        concrete_types.FILE_ENTITY: File,
+        concrete_types.TABLE_ENTITY: Table,
+        concrete_types.DATASET_ENTITY: Dataset,
+        concrete_types.DATASET_COLLECTION_ENTITY: DatasetCollection,
+        concrete_types.ENTITY_VIEW: EntityView,
+        concrete_types.MATERIALIZED_VIEW: MaterializedView,
+        concrete_types.SUBMISSION_VIEW: SubmissionView,
+    }
+
+    entity_class = ENTITY_TYPE_MAP.get(entity["concreteType"], None)
+    if not entity_class:
         raise ValueError(
             f"Attempting to retrieve an unsupported entity type of {entity['concreteType']}."
         )
+
+    # Create or use existing entity instance
+    entity_instance = entity_to_update or entity_class()
+
+    # Handle special case for File entities
+    if entity["concreteType"] == concrete_types.FILE_ENTITY:
+        entity_instance = await _handle_file_entity(
+            entity_instance=entity_instance,
+            entity_bundle=entity_bundle,
+            download_file=download_file,
+            download_location=download_location,
+            if_collision=if_collision,
+            submission=submission,
+            synapse_client=syn,
+        )
+    else:
+        # Handle all other entity types
+        entity_instance.fill_from_dict(entity_bundle["entity"], set_annotations=False)
+
     if annotations:
-        entity.annotations = annotations
+        entity_instance.annotations = annotations
 
-    return entity
+    return entity_instance
 
 
 def _check_entity_restrictions(
@@ -386,12 +434,19 @@ def _check_entity_restrictions(
     if restriction_information and restriction_information.get(
         "hasUnmetAccessRequirement", None
     ):
-        warning_message = (
-            "\nThis entity has access restrictions. Please visit the web page for this entity "
-            f'(syn.onweb("{synapse_id}")). Look for the "Access" label and the lock icon underneath '
-            'the file name. Click "Request Access", and then review and fulfill the file '
-            "download requirement(s).\n"
-        )
+        if not syn.credentials or not syn.credentials._token:
+            warning_message = (
+                "You have not provided valid credentials for authentication with Synapse."
+                " Please provide an authentication token and use `synapseclient.login()` before your next attempt."
+                " See https://python-docs.synapse.org/tutorials/authentication/ for more information."
+            )
+        else:
+            warning_message = (
+                "\nThis entity has access restrictions. Please visit the web page for this entity "
+                f'(syn.onweb("{synapse_id}")). Look for the "Access" label and the lock icon underneath '
+                'the file name. Click "Request Access", and then review and fulfill the file '
+                "download requirement(s).\n"
+            )
         if download_file and bundle.get("entityType") not in ("project", "folder"):
             raise SynapseUnmetAccessRestrictions(warning_message)
-        syn.logger.warn(warning_message)
+        syn.logger.warning(warning_message)

{synapseclient-4.7.0 → synapseclient-4.8.0}/synapseclient/api/entity_services.py

@@ -7,6 +7,8 @@ from typing import TYPE_CHECKING, Any, Dict, List, Optional, Union
 
 from async_lru import alru_cache
 
+from synapseclient.core.utils import get_synid_and_version
+
 if TYPE_CHECKING:
     from synapseclient import Synapse
 
@@ -215,6 +217,80 @@ async def delete_entity_generated_by(
     )
 
 
+async def delete_entity(
+    entity_id: str,
+    version_number: int = None,
+    *,
+    synapse_client: Optional["Synapse"] = None,
+) -> None:
+    """
+    Deletes an entity from Synapse.
+
+    Arguments:
+        entity_id: The ID of the entity. This may include version `syn123.0` or `syn123`.
+            If the version is included in `entity_id` and `version_number` is also
+            passed in, then the version in `entity_id` will be used.
+        version_number: The version number of the entity to delete.
+        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.
+
+    Example: Delete the entity `syn123`:
+        This will delete all versions of the entity.
+
+        ```python
+        import asyncio
+        from synapseclient import Synapse
+        from synapseclient.api import delete_entity
+
+        syn = Synapse()
+        syn.login()
+
+
+        async def main():
+            await delete_entity(entity_id="syn123")
+
+        asyncio.run(main())
+        ```
+
+    Example: Delete a specific version of the entity `syn123`:
+        This will delete version `3` of the entity.
+
+        ```python
+        import asyncio
+        from synapseclient import Synapse
+        from synapseclient.api import delete_entity
+
+        syn = Synapse()
+        syn.login()
+
+
+        async def main():
+            await delete_entity(entity_id="syn123", version_number=3)
+
+        asyncio.run(main())
+        ```
+
+    Returns: None
+    """
+    from synapseclient import Synapse
+
+    client = Synapse.get_client(synapse_client=synapse_client)
+
+    syn_id, syn_version = get_synid_and_version(entity_id)
+    if not syn_version:
+        syn_version = version_number
+
+    if syn_version:
+        return await client.rest_delete_async(
+            uri=f"/entity/{syn_id}/version/{syn_version}",
+        )
+    else:
+        return await client.rest_delete_async(
+            uri=f"/entity/{syn_id}",
+        )
+
+
 async def get_entity_path(
     entity_id: str,
     *,