synapseclient 2.6.0__tar.gz → 2.7.1__tar.gz

{synapseclient-2.6.0/synapseclient.egg-info → synapseclient-2.7.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: synapseclient
-Version: 2.6.0
+Version: 2.7.1
 Summary: A client for Synapse, a collaborative compute space  that allows scientists to share and analyze data together.
 Home-page: https://www.synapse.org
 Author: The Synapse Engineering Team
@@ -206,7 +206,7 @@ Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Topic :: Software Development :: Libraries
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Requires-Python: >=3.7.*
+Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 Provides-Extra: pandas
 Provides-Extra: pysftp

synapseclient-2.7.1/pyproject.toml

@@ -0,0 +1,14 @@
+[tool.black]
+line-length = 88
+target-version = ['py37']
+include = '\.pyi?$'
+extend-exclude = '''
+(
+    /docs
+    |/synapseclient
+    |/synapseclient/core
+    |/synapseutils
+    |/tests/integration
+    |/tests/unit
+)
+'''

{synapseclient-2.6.0 → synapseclient-2.7.1}/setup.py

@@ -9,23 +9,30 @@ import json
 # check Python version, before we do anything
 if sys.version_info.major < 3 and sys.version_info.minor < 7:
     sys.stderr.write("The Synapse Client for Python requires Python 3.7+\n")
-    sys.stderr.write("Your Python appears to be version %d.%d.%d\n" % sys.version_info[:3])
+    sys.stderr.write(
+        "Your Python appears to be version %d.%d.%d\n" % sys.version_info[:3]
+    )
     sys.exit(-1)
 
 # figure out the version
-__version__ = json.loads(open('synapseclient/synapsePythonClient').read())['latestVersion']
+__version__ = json.loads(open("synapseclient/synapsePythonClient").read())[
+    "latestVersion"
+]
 
 description = """A client for Synapse, a collaborative compute space
- that allows scientists to share and analyze data together.""".replace("\n", " ")
+ that allows scientists to share and analyze data together.""".replace(
+    "\n", " "
+)
 
 with open("README.md", "r") as fh:
     long_description = fh.read()
 
 # make sure not to overwrite existing .synapseConfig with our example one
-data_files =\
-    [(os.path.expanduser('~'), ['synapseclient/.synapseConfig'])]\
-    if not os.path.exists(os.path.expanduser('~/.synapseConfig'))\
+data_files = (
+    [(os.path.expanduser("~"), ["synapseclient/.synapseConfig"])]
+    if not os.path.exists(os.path.expanduser("~/.synapseConfig"))
     else []
+)
 
 test_deps = [
     "pytest>=5.0.0,<7.0",
@@ -35,9 +42,10 @@ test_deps = [
 ]
 
 install_requires = [
-    'requests>=2.22.0,<3.0',
-    'keyring>=15,<23.5',
-    'deprecated>=1.2.4,<2.0',
+    "requests>=2.22.0,<3.0",
+    "keyring>=15,<23.5",
+    "deprecated>=1.2.4,<2.0",
+    "importlib-metadata<5.0",
 ]
 
 # on Linux specify a cryptography dependency that will not
@@ -51,72 +59,67 @@ install_requires = [
 # if a newer version of cryptography is already installed that is
 # fine we don't want to trigger a downgrade, hence the conditional
 # addition of the versioned dependency.
-if platform.system() == 'Linux':
+if platform.system() == "Linux":
     try:
         import cryptography  # noqa
+
         # already installed, don't need to install (or downgrade)
     except ImportError:
-        install_requires.append('cryptography<3.4')
+        install_requires.append("cryptography<3.4")
 
 setuptools.setup(
     # basic
-    name='synapseclient',
+    name="synapseclient",
     version=__version__,
     packages=setuptools.find_packages(exclude=["tests", "tests.*"]),
-
     # requirements
-    python_requires='>=3.7.*',
+    python_requires=">=3.7",
     install_requires=install_requires,
     extras_require={
-        'pandas': ["pandas>=0.25.0,<2.0"],
-        'pysftp': ["pysftp>=0.2.8,<0.3"],
-        'boto3': ["boto3>=1.7.0,<2.0"],
-        'docs': ["sphinx>=3.0,<4.0", "sphinx-argparse>=0.2,<0.3"],
-        'tests': test_deps,
-        ':sys_platform=="linux"': ['keyrings.alt==3.1'],
+        "pandas": ["pandas>=0.25.0,<1.5"],
+        "pysftp": ["pysftp>=0.2.8,<0.3"],
+        "boto3": ["boto3>=1.7.0,<2.0"],
+        "docs": ["sphinx>=3.0,<4.0", "sphinx-argparse>=0.2,<0.3"],
+        "tests": test_deps,
+        ':sys_platform=="linux"': ["keyrings.alt==3.1"],
     },
-
     # command line
-    entry_points={
-        'console_scripts': ['synapse = synapseclient.__main__:main']
-    },
-
+    entry_points={"console_scripts": ["synapse = synapseclient.__main__:main"]},
     # data
-    package_data={'synapseclient': ['synapsePythonClient', '.synapseConfig']},
+    package_data={"synapseclient": ["synapsePythonClient", ".synapseConfig"]},
     data_files=data_files,
     zip_safe=False,
-
     # test
     tests_require=test_deps,
-
     # metadata to display on PyPI
     description=description,
     long_description=long_description,
     long_description_content_type="text/markdown",
-    url='https://www.synapse.org',
-    author='The Synapse Engineering Team',
-    author_email='platform@sagebase.org',
-    license='Apache',
+    url="https://www.synapse.org",
+    author="The Synapse Engineering Team",
+    author_email="platform@sagebase.org",
+    license="Apache",
     project_urls={
         "Documentation": "https://python-docs.synapse.org",
         "Source Code": "https://github.com/Sage-Bionetworks/synapsePythonClient",
         "Bug Tracker": "https://github.com/Sage-Bionetworks/synapsePythonClient/issues",
     },
     classifiers=[
-        'Development Status :: 5 - Production/Stable',
-        'Programming Language :: Python',
-        'Programming Language :: Python :: 3.7',
-        'Programming Language :: Python :: 3.8',
-        'Programming Language :: Python :: 3.9',
-        'Programming Language :: Python :: 3.10',
-        'Operating System :: MacOS',
-        'Operating System :: Microsoft :: Windows',
-        'Operating System :: Unix',
-        'Operating System :: POSIX :: Linux',
-        'Intended Audience :: Developers',
-        'Intended Audience :: Science/Research',
-        'License :: OSI Approved :: Apache Software License',
-        'Topic :: Software Development :: Libraries',
-        'Topic :: Scientific/Engineering',
-        'Topic :: Scientific/Engineering :: Bio-Informatics'],
+        "Development Status :: 5 - Production/Stable",
+        "Programming Language :: Python",
+        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+        "Operating System :: MacOS",
+        "Operating System :: Microsoft :: Windows",
+        "Operating System :: Unix",
+        "Operating System :: POSIX :: Linux",
+        "Intended Audience :: Developers",
+        "Intended Audience :: Science/Research",
+        "License :: OSI Approved :: Apache Software License",
+        "Topic :: Software Development :: Libraries",
+        "Topic :: Scientific/Engineering",
+        "Topic :: Scientific/Engineering :: Bio-Informatics",
+    ],
 )

{synapseclient-2.6.0 → synapseclient-2.7.1}/synapseclient/__init__.py

@@ -21,6 +21,20 @@ the `web <https://www.synapse.org/>`_. The Python client can also be used from t
 If you're just getting started with Synapse, have a look at the Getting Started guides for
 `Synapse <https://docs.synapse.org/articles/getting_started.html>`_.
 
+
+Next Major Release (3.0.0)
+==========================
+- Support only pandas `>=` 1.5
+- Remove support for Python 3.7 due to its end of life.
+- Remove support for login via passwords for best security practices.
+- There will be major cosmetic changes to the cli such as
+  removing all camel case or non-standard single dash long command line interface (cli)
+  parameters.
+  Example: command line arguments like `-parent` will become
+  `--parent`.  Commands that support camel case like `--parentId`
+  will be changed to `--parent-id`.
+
+
 Installation
 ============
 
@@ -56,11 +70,6 @@ Next, either install the package in the site-packages directory ``python setup.p
     python setup.py <install or develop>
 
 
-Python 2 Support
-----------------
-
-synapseclient versions 2.0 and above require Python 3.6 or greater. Python 2.7 is no longer supported.
-
 Connecting to Synapse
 =====================
 
@@ -281,7 +290,7 @@ from .core.version_check import check_for_updates, release_notes
 from .entity import Entity, Project, Folder, File, Link, DockerRepository
 from .evaluation import Evaluation, Submission, SubmissionStatus
 from .table import Schema, EntityViewSchema, Column, RowSet, Row, as_table_columns, Table, PartialRowset, \
-    EntityViewType, build_table, SubmissionViewSchema, MaterializedViewSchema
+    EntityViewType, build_table, SubmissionViewSchema, MaterializedViewSchema, Dataset
 from .team import Team, UserProfile, UserGroupHeader, TeamMember
 from .wiki import Wiki
 
@@ -297,7 +306,7 @@ __all__ = [
     'Synapse', 'Activity', 'Entity', 'Project', 'Folder', 'File', 'Link', 'DockerRepository', 'Evaluation',
     'Submission', 'SubmissionStatus', 'Schema', 'EntityViewSchema', 'Column', 'Row', 'RowSet', 'Table', 'PartialRowset',
     'Team', 'UserProfile', 'UserGroupHeader', 'TeamMember', 'Wiki', 'Annotations', 'SubmissionViewSchema',
-    'MaterializedViewSchema',
+    'MaterializedViewSchema', 'Dataset',
     # functions
     'login', 'build_table', 'as_table_columns', 'check_for_updates', 'release_notes',
     # enum

{synapseclient-2.6.0 → synapseclient-2.7.1}/synapseclient/__main__.py

@@ -525,6 +525,12 @@ def submit(args, syn):
                      % (submission['id'], submission['entityId'], submission['name'], submission['evaluationId']))
 
 
+def get_download_list(args, syn):
+    """Download files from the Synapse download cart"""
+    manifest_path = syn.get_download_list(downloadLocation=args.downloadLocation)
+    syn.logger.info(f"Manifest file: {manifest_path}")
+
+
 def login(args, syn):
     """Log in to Synapse, optionally caching credentials"""
     login_with_prompt(syn, args.synapseUser, args.synapsePassword, rememberMe=args.rememberMe, forced=True)
@@ -711,8 +717,14 @@ def build_parser():
                              help='Send notifications via Synapse messaging (email) at specific intervals, '
                                   'on errors and on completion.')
     parser_sync.add_argument('--retries', metavar='INT', type=int, default=4)
-    parser_sync.add_argument('manifestFile', metavar='FILE', type=argparse.FileType("r"),
-                             help='A tsv file with file locations and metadata to be pushed to Synapse.')
+    parser_sync.add_argument(
+        'manifestFile', metavar='FILE', type=argparse.FileType("r"),
+        help=(
+            'A tsv file with file locations and metadata to be pushed to Synapse. '
+            'See https://python-docs.synapse.org/build/html/synapseutils.html#synapseutils.sync.syncToSynapse '
+            'for details on the format of a manifest.'
+        )
+    )
     parser_sync.set_defaults(func=sync)
 
     parser_store = subparsers.add_parser('store',  # Python 3.2+ would support alias=['store']
@@ -834,6 +846,12 @@ def build_parser():
                            help='Do not copy the wiki pages')
     parser_cp.set_defaults(func=copy)
 
+    parser_get_dl_list = subparsers.add_parser('get-download-list',
+                                               help='Download files from the Synapse download cart')
+    parser_get_dl_list.add_argument('--downloadLocation', metavar='path', type=str, default="./",
+                                    help='Directory to download file to [default: %(default)s].')
+    parser_get_dl_list.set_defaults(func=get_download_list)
+
     parser_associate = subparsers.add_parser('associate',
                                              help=(
                                                  'Associate local files with the files stored in Synapse so that calls'
@@ -1032,7 +1050,7 @@ See https://docs.synapse.org/rest/org/sagebionetworks/repo/web/controller/TableE
     parser_login.add_argument('-u', '--username', dest='synapseUser',
                               help='Username used to connect to Synapse')
     parser_login.add_argument('-p', '--password', dest='synapsePassword',
-                              help='Password or api key used to connect to Synapse')
+                              help='This will be deprecated. Password or api key used to connect to Synapse.')
     parser_login.add_argument('--rememberMe', '--remember-me', dest='rememberMe', action='store_true', default=False,
                               help='Cache credentials for automatic authentication on future interactions with Synapse')
     parser_login.set_defaults(func=login)

{synapseclient-2.6.0 → synapseclient-2.7.1}/synapseclient/client.py

@@ -30,6 +30,7 @@ See also the `Synapse API documentation <https://docs.synapse.org/rest/>`_.
 import collections
 import collections.abc
 import configparser
+import csv
 import deprecated
 import errno
 import functools
@@ -65,7 +66,8 @@ from .entity import Entity, File, Folder, Versionable,\
     split_entity_namespaces, is_versionable, is_container, is_synapse_entity
 from synapseclient.core.models.dict_object import DictObject
 from .evaluation import Evaluation, Submission, SubmissionStatus
-from .table import Schema, SchemaBase, Column, TableQueryResult, CsvFileTable, EntityViewSchema, SubmissionViewSchema
+from .table import Schema, SchemaBase, Column, TableQueryResult, CsvFileTable, \
+    EntityViewSchema, SubmissionViewSchema, Dataset
 from .team import UserProfile, Team, TeamMember, UserGroupHeader
 from .wiki import Wiki, WikiAttachment
 from synapseclient.core import cache, exceptions, utils
@@ -335,9 +337,9 @@ class Synapse(object):
         """
         Valid combinations of login() arguments:
 
-        - email/username and password
+        - email/username and password (**WILL BE DEPRECATED**)
 
-        - email/username and apiKey (Base64 encoded string)
+        - email/username and apiKey (Base64 encoded string) (**WILL BE DEPRECATED**)
 
         - authToken
 
@@ -353,14 +355,14 @@ class Synapse(object):
         #. cached credentials from previous `login()` where `rememberMe=True` was passed as a parameter
 
         :param email:        Synapse user name (or an email address associated with a Synapse account)
-        :param password:     password
-        :param apiKey:       Base64 encoded Synapse API key
+        :param password:     **!!WILL BE DEPRECATED!!** password. Please use authToken (Synapse personal access token)
+        :param apiKey:       **!!WILL BE DEPRECATED!!** Base64 encoded Synapse API key
         :param sessionToken: **!!DEPRECATED FIELD!!** User's current session token. Using this field will ignore the
                              following fields: email, password, apiKey
         :param rememberMe:   Whether the authentication information should be cached in your operating system's
                              credential storage.
         :param authToken:    A bearer authorization token, e.g. a personal access token, can be used in lieu of a
-                                password or apiKey
+                             password or apiKey
 
         **GNOME Keyring** (recommended) or **KWallet** is recommended to be installed for credential storage on
         **Linux** systems.
@@ -731,9 +733,12 @@ class Synapse(object):
     def _check_entity_restrictions(self, bundle, entity, downloadFile):
         restrictionInformation = bundle['restrictionInformation']
         if restrictionInformation['hasUnmetAccessRequirement']:
-            warning_message = ("\nThis entity has access restrictions. Please visit the web page for this entity "
-                               "(syn.onweb(\"%s\")). Click the downward pointing arrow next to the file's name to "
-                               "review and fulfill its download requirement(s).\n" % id_of(entity))
+            warning_message = (
+                '\nThis entity has access restrictions. Please visit the web page for this entity '
+                f'(syn.onweb(\"{id_of(entity)}\")). 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 downloadFile and bundle.get('entityType') not in ('project', 'folder'):
                 raise SynapseUnmetAccessRestrictions(warning_message)
             warnings.warn(warning_message)
@@ -991,7 +996,10 @@ class Synapse(object):
             test_entity = syn.store(test_entity, activity=activity)
 
         """
-
+        # SYNPY-1031: activity must be Activity object or code will fail later
+        if activity:
+            if not isinstance(activity, synapseclient.Activity):
+                raise ValueError("activity should be synapseclient.Activity object")
         # _before_store hook
         # give objects a chance to do something before being stored
         if hasattr(obj, '_before_synapse_store'):
@@ -1059,7 +1067,7 @@ class Synapse(object):
                     # modified, we want to upload the new version.
                     # If synapeStore is false then we must upload a ExternalFileHandle
                     needs_upload = not entity['synapseStore'] \
-                                   or not self.cache.contains(bundle['entity']['dataFileHandleId'], entity['path'])
+                        or not self.cache.contains(bundle['entity']['dataFileHandleId'], entity['path'])
             elif entity.get('dataFileHandleId', None) is not None:
                 needs_upload = False
             else:
@@ -1355,6 +1363,130 @@ class Synapse(object):
         """
         return upload_file_handle(self, parent, path, synapseStore, md5, file_size, mimetype)
 
+    ############################################################
+    #                  Download List                           #
+    ############################################################
+    def clear_download_list(self):
+        """Clear all files from download list"""
+        self.restDELETE("/download/list")
+
+    def remove_from_download_list(self, list_of_files: typing.List[typing.Dict]) -> int:
+        """Remove a batch of files from download list
+
+        :param: array of files in the format of a mapping
+                {fileEntityId: synid, versionNumber: version}
+
+        :returns: Number of files removed from download list
+        """
+        request_body = {"batchToRemove": list_of_files}
+        num_files_removed = self.restPOST(
+            "/download/list/remove",
+            body=json.dumps(request_body)
+        )
+        return num_files_removed
+
+    def _generate_manifest_from_download_list(
+        self, quoteCharacter: str = '"',
+        escapeCharacter: str = "\\",
+        lineEnd: str = os.linesep,
+        separator: str = ",",
+        header: bool = True
+    ):
+        """Creates a download list manifest generation request
+
+        :param quoteCharacter:  The character to be used for quoted elements in the resulting file.
+                                Defaults to '"'.
+        :param escapeCharacter: The escape character to be used for escaping a separator or quote in the resulting
+                                file. Defaults to "\".
+        :param lineEnd:         The line feed terminator to be used for the resulting file. Defaults to os.linesep.
+        :param separator:       The delimiter to be used for separating entries in the resulting file. Defaults to ",".
+        :param header:          Is the first line a header? Defaults to True.
+
+        :returns: Filehandle of download list manifest
+        """
+        request_body = {
+            "concreteType": "org.sagebionetworks.repo.model.download.DownloadListManifestRequest",
+            "csvTableDescriptor": {
+                "separator": separator,
+                "quoteCharacter": quoteCharacter,
+                "escapeCharacter": escapeCharacter,
+                "lineEnd": lineEnd,
+                "isFirstLineHeader": header
+            }
+        }
+        return self._waitForAsync(uri="/download/list/manifest/async", request=request_body)
+
+    def get_download_list_manifest(self):
+        """Get the path of the download list manifest file
+
+        :returns: path of download list manifest file
+        """
+        manifest = self._generate_manifest_from_download_list()
+        # Get file handle download link
+        file_result = self._getFileHandleDownload(
+            fileHandleId=manifest['resultFileHandleId'],
+            objectId=manifest['resultFileHandleId'],
+            objectType="FileEntity"
+        )
+        # Download the manifest
+        downloaded_path = self._download_from_URL(
+            url=file_result['preSignedURL'],
+            destination="./",
+            fileHandleId=file_result['fileHandleId'],
+            expected_md5=file_result['fileHandle'].get('contentMd5')
+        )
+        return downloaded_path
+
+    def get_download_list(self, downloadLocation: str = None) -> str:
+        """Download all files from your Synapse download list
+
+        :param downloadLocation: Directory to download files to.
+
+        :returns: manifest file with file paths
+        """
+        dl_list_path = self.get_download_list_manifest()
+        downloaded_files = []
+        new_manifest_path = f'manifest_{time.time_ns()}.csv'
+        with open(dl_list_path) as manifest_f, \
+             open(new_manifest_path, 'w') as write_obj:
+
+            reader = csv.DictReader(manifest_f)
+            columns = reader.fieldnames
+            columns.extend(["path", "error"])
+            # Write the downloaded paths to a new manifest file
+            writer = csv.DictWriter(write_obj, fieldnames=columns)
+            writer.writeheader()
+
+            for row in reader:
+                # You can add things to the download list that you don't have access to
+                # So there must be a try catch here
+                try:
+                    entity = self.get(row['ID'], downloadLocation=downloadLocation)
+                    # Must include version number because you can have multiple versions of a
+                    # file in the download list
+                    downloaded_files.append(
+                        {"fileEntityId": row['ID'], "versionNumber": row['versionNumber']}
+                    )
+                    row['path'] = entity.path
+                    row['error'] = ''
+                except Exception:
+                    row['path'] = ''
+                    row['error'] = 'DOWNLOAD FAILED'
+                    self.logger.error("Unable to download file")
+                writer.writerow(row)
+
+        # Don't want to clear all the download list because you can add things
+        # to the download list after initiating this command.
+        # Files that failed to download should not be removed from download list
+        # Remove all files from download list after the entire download is complete.
+        # This is because if download fails midway, we want to return the full manifest
+        self.remove_from_download_list(list_of_files=downloaded_files)
+
+        # Always remove original manifest file
+        os.remove(dl_list_path)
+
+        return new_manifest_path
+
     ############################################################
     #                  Get / Set Annotations                   #
     ############################################################
@@ -2963,9 +3095,9 @@ class Synapse(object):
                 entityBundleJSON['annotations'] = convert_old_annotation_json(annotations)
 
             related = self._getWithEntityBundle(
-                                entityBundle=entityBundleJSON,
-                                entity=submission['entityId'],
-                                submission=submission_id, **kwargs)
+                entityBundle=entityBundleJSON,
+                entity=submission['entityId'],
+                submission=submission_id, **kwargs)
             submission.entity = related
             submission.filePath = related.get('path', None)
 
@@ -3189,10 +3321,10 @@ class Synapse(object):
         else:
             ValueError("Can't get columns for a %s" % type(x))
 
-    def create_snapshot_version(self, table: typing.Union[EntityViewSchema, Schema, str, SubmissionViewSchema],
+    def create_snapshot_version(self, table: typing.Union[EntityViewSchema, Schema, str, SubmissionViewSchema, Dataset],
                                 comment: str = None, label: str = None, activity: typing.Union[Activity, str] = None,
                                 wait: bool = True) -> int:
-        """Create a new Table Version or a new View version.
+        """Create a new Table Version, new View version, or new Dataset version.
 
         :param table:  The schema of the Table/View, or its ID.
         :param comment:  Optional snapshot comment.
@@ -3204,7 +3336,7 @@ class Synapse(object):
         :return: the snapshot version number if wait=True, None if wait=False
         """
         ent = self.get(id_of(table), downloadFile=False)
-        if isinstance(ent, (EntityViewSchema, SubmissionViewSchema)):
+        if isinstance(ent, (EntityViewSchema, SubmissionViewSchema, Dataset)):
             result = self._async_table_update(
                 table,
                 create_snapshot=True,
@@ -3323,9 +3455,7 @@ class Synapse(object):
 
         :param  limit:          specify the maximum number of rows to be returned, defaults to None
         :param offset:          don't return the first n rows, defaults to None
-        :param isConsistent:    defaults to True. If set to False, return results based on current state of the index
-                                without waiting for pending writes to complete.
-                                Only use this if you know what you're doing.
+        :param isConsistent:    (**DEPRECATED**)
 
         For CSV files, there are several parameters to control the format of the resulting file:
 
@@ -3351,6 +3481,10 @@ class Synapse(object):
         if resultsAs.lower() == "rowset":
             return TableQueryResult(self, query, **kwargs)
         elif resultsAs.lower() == "csv":
+            # TODO: remove isConsistent because it has now been deprecated
+            # from the backend
+            if kwargs.get("isConsistent") is not None:
+                kwargs.pop('isConsistent')
             return CsvFileTable.from_table_query(self, query, **kwargs)
         else:
             raise ValueError("Unknown return type requested from tableQuery: " + str(resultsAs))

{synapseclient-2.6.0 → synapseclient-2.7.1}/synapseclient/entity.py

@@ -240,6 +240,12 @@ class Entity(collections.abc.MutableMapping):
                 if 'annotations' in properties and isinstance(properties['annotations'], collections.abc.Mapping):
                     annotations.update(properties['annotations'])
                     del properties['annotations']
+
+                # Re-map `items` to `datasetItems` to avoid namespace conflicts
+                # between Dataset schema and the items() builtin method.
+                if 'items' in properties:
+                    properties['datasetItems'] = properties['items']
+                    del properties['items']
                 self.__dict__['properties'].update(properties)
             else:
                 raise SynapseMalformedEntityError(
@@ -731,7 +737,8 @@ ENTITY_TYPES = [
     'org.sagebionetworks.repo.model.Folder',
     'org.sagebionetworks.repo.model.Link',
     'org.sagebionetworks.repo.model.Project',
-    'org.sagebionetworks.repo.model.table.TableEntity'
+    'org.sagebionetworks.repo.model.table.TableEntity',
+    'org.sagebionetworks.repo.model.table.Dataset'
 ]
 
 

{synapseclient-2.6.0 → synapseclient-2.7.1}/synapseclient/synapsePythonClient

@@ -1,6 +1,6 @@
 {
   "client":"synapsePythonClient",
-  "latestVersion":"2.6.0",
+  "latestVersion":"2.7.1",
   "blacklist":["0.0.0", "0.4.1", "0.4.0", "0.3.0", "0.2.1", "0.2.0", "0.1.4"],
   "releaseNotes":"https://python-docs.synapse.org/build/html/news.html"
 }