client.py

"""
The `Synapse` object encapsulates a connection to the Synapse service and is used for building projects, uploading and
retrieving data, and recording provenance of data analysis.
"""
import asyncio
import collections
import collections.abc
import configparser
import csv
import errno
import functools
import getpass
import hashlib
import json
import logging
import mimetypes
import numbers
import os
import re
import shutil
import sys
import tempfile
import threading
import time
import typing
import urllib.parse as urllib_urlparse
import urllib.request as urllib_request
import warnings
import webbrowser
import zipfile
from concurrent.futures import ThreadPoolExecutor
from http.client import HTTPResponse
from typing import Any, Dict, List, Optional, Tuple, Union

import asyncio_atexit
import httpx
import requests
from deprecated import deprecated
from opentelemetry import trace
from opentelemetry.instrumentation.httpx import HTTPXClientInstrumentor
from opentelemetry.instrumentation.requests import RequestsInstrumentor
from opentelemetry.instrumentation.threading import ThreadingInstrumentor
from opentelemetry.instrumentation.urllib import URLLibInstrumentor
from opentelemetry.trace import Span

import synapseclient
import synapseclient.core.multithread_download as multithread_download
from synapseclient.api import (
    get_client_authenticated_s3_profile,
    get_config_file,
    get_config_section_dict,
    get_file_handle_for_download,
    get_transfer_config,
)
from synapseclient.core import (
    cache,
    cumulative_transfer_progress,
    exceptions,
    sts_transfer,
    utils,
)
from synapseclient.core.async_utils import wrap_async_to_sync
from synapseclient.core.constants import concrete_types, config_file_constants
from synapseclient.core.credentials import UserLoginArgs, get_default_credential_chain
from synapseclient.core.download import (
    download_by_file_handle,
    download_file_entity,
    ensure_download_location_is_directory,
)
from synapseclient.core.dozer import doze
from synapseclient.core.exceptions import (
    SynapseAuthenticationError,
    SynapseError,
    SynapseFileNotFoundError,
    SynapseHTTPError,
    SynapseMalformedEntityError,
    SynapseMd5MismatchError,
    SynapseNoCredentialsError,
    SynapseProvenanceError,
    SynapseTimeoutError,
    SynapseUnmetAccessRestrictions,
)
from synapseclient.core.logging_setup import (
    DEBUG_LOGGER_NAME,
    DEFAULT_LOGGER_NAME,
    SILENT_LOGGER_NAME,
)
from synapseclient.core.models.dict_object import DictObject
from synapseclient.core.models.permission import Permissions
from synapseclient.core.pool_provider import DEFAULT_NUM_THREADS, get_executor
from synapseclient.core.remote_file_storage_wrappers import S3ClientWrapper, SFTPWrapper
from synapseclient.core.retry import (
    DEFAULT_RETRY_STATUS_CODES,
    RETRYABLE_CONNECTION_ERRORS,
    RETRYABLE_CONNECTION_EXCEPTIONS,
    with_retry,
    with_retry_time_based_async,
)
from synapseclient.core.upload.multipart_upload_async import (
    multipart_upload_file_async,
    multipart_upload_string_async,
)
from synapseclient.core.upload.upload_functions_async import (
    upload_file_handle as upload_file_handle_async,
)
from synapseclient.core.upload.upload_functions_async import upload_synapse_s3
from synapseclient.core.utils import (
    MB,
    extract_synapse_id_from_query,
    extract_zip_file_to_directory,
    find_data_file_handle,
    get_properties,
    id_of,
    is_integer,
    is_json,
    require_param,
    validate_submission_id,
)
from synapseclient.core.version_check import version_check

from .activity import Activity
from .annotations import (
    Annotations,
    check_annotations_changed,
    convert_old_annotation_json,
    from_synapse_annotations,
    to_synapse_annotations,
)
from .entity import (
    Entity,
    File,
    Folder,
    Versionable,
    is_container,
    is_synapse_entity,
    is_versionable,
    split_entity_namespaces,
)
from .evaluation import Evaluation, Submission, SubmissionStatus
from .table import (
    Column,
    CsvFileTable,
    Dataset,
    EntityViewSchema,
    Schema,
    SchemaBase,
    SubmissionViewSchema,
    TableQueryResult,
)
from .team import Team, TeamMember, UserGroupHeader, UserProfile
from .wiki import Wiki, WikiAttachment

tracer = trace.get_tracer("synapseclient")

PRODUCTION_ENDPOINTS = {
    "repoEndpoint": "https://repo-prod.prod.sagebase.org/repo/v1",
    "authEndpoint": "https://auth-prod.prod.sagebase.org/auth/v1",
    "fileHandleEndpoint": "https://file-prod.prod.sagebase.org/file/v1",
    "portalEndpoint": "https://www.synapse.org/",
}

STAGING_ENDPOINTS = {
    "repoEndpoint": "https://repo-staging.prod.sagebase.org/repo/v1",
    "authEndpoint": "https://auth-staging.prod.sagebase.org/auth/v1",
    "fileHandleEndpoint": "https://file-staging.prod.sagebase.org/file/v1",
    "portalEndpoint": "https://staging.synapse.org/",
}

CONFIG_FILE = os.path.join(os.path.expanduser("~"), ".synapseConfig")
SESSION_FILENAME = ".session"
FILE_BUFFER_SIZE = 2 * MB
CHUNK_SIZE = 5 * MB
QUERY_LIMIT = 1000
CHUNK_UPLOAD_POLL_INTERVAL = 1  # second
ROOT_ENTITY = "syn4489"
PUBLIC = 273949  # PrincipalId of public "user"
AUTHENTICATED_USERS = 273948
DEBUG_DEFAULT = False
REDIRECT_LIMIT = 5
MAX_THREADS_CAP = 128

# Defines the standard retry policy applied to the rest methods
# The retry period needs to span a minute because sending messages is limited to 10 per 60 seconds.
STANDARD_RETRY_PARAMS = {
    "retry_status_codes": DEFAULT_RETRY_STATUS_CODES,
    "retry_errors": RETRYABLE_CONNECTION_ERRORS,
    "retry_exceptions": RETRYABLE_CONNECTION_EXCEPTIONS,
    "retries": 60,  # Retries for up to about 30 minutes
    "wait": 1,
    "max_wait": 30,
    "back_off": 2,
}

STANDARD_RETRY_ASYNC_PARAMS = {
    "retry_status_codes": DEFAULT_RETRY_STATUS_CODES,
    "retry_errors": RETRYABLE_CONNECTION_ERRORS,
    "retry_exceptions": RETRYABLE_CONNECTION_EXCEPTIONS,
}

# Add additional mimetypes
mimetypes.add_type("text/x-r", ".R", strict=False)
mimetypes.add_type("text/x-r", ".r", strict=False)
mimetypes.add_type("text/tab-separated-values", ".maf", strict=False)
mimetypes.add_type("text/tab-separated-values", ".bed5", strict=False)
mimetypes.add_type("text/tab-separated-values", ".bed", strict=False)
mimetypes.add_type("text/tab-separated-values", ".vcf", strict=False)
mimetypes.add_type("text/tab-separated-values", ".sam", strict=False)
mimetypes.add_type("text/yaml", ".yaml", strict=False)
mimetypes.add_type("text/x-markdown", ".md", strict=False)
mimetypes.add_type("text/x-markdown", ".markdown", strict=False)

DEFAULT_STORAGE_LOCATION_ID = 1


def login(*args, **kwargs):
    """
    Convenience method to create a Synapse object and login.

    See `synapseclient.Synapse.login` for arguments and usage.

    Example: Getting started
        Logging in to Synapse using an authToken

            import synapseclient
            syn = synapseclient.login(authToken="authtoken")

        Using environment variable or `.synapseConfig`

            import synapseclient
            syn = synapseclient.login()
    """

    syn = Synapse()
    syn.login(*args, **kwargs)
    return syn


class Synapse(object):
    """
    Constructs a Python client object for the Synapse repository service

    Attributes:
        repoEndpoint:          Location of Synapse repository
        authEndpoint:          Location of authentication service
        fileHandleEndpoint:    Location of file service
        portalEndpoint:        Location of the website
        serviceTimeoutSeconds: Wait time before timeout (currently unused)
        debug:                 Print debugging messages if True
        skip_checks:           Skip version and endpoint checks
        configPath:            Path to config File with setting for Synapse. Defaults to ~/.synapseConfig
        requests_session:      A custom [requests.Session object](https://requests.readthedocs.io/en/latest/user/advanced/) that this Synapse instance will use
                               when making http requests.
        cache_root_dir:        Root directory for storing cache data
        silent:                Defaults to False.

    Example: Getting started
        Logging in to Synapse using an authToken

            import synapseclient
            syn = synapseclient.login(authToken="authtoken")

        Using environment variable or `.synapseConfig`

            import synapseclient
            syn = synapseclient.login()

    """

    _synapse_client = None
    _allow_client_caching = True
    _enable_open_telemetry = False

    # TODO: add additional boolean for write to disk?
    def __init__(
        self,
        repoEndpoint: str = None,
        authEndpoint: str = None,
        fileHandleEndpoint: str = None,
        portalEndpoint: str = None,
        debug: bool = None,
        skip_checks: bool = False,
        configPath: str = CONFIG_FILE,
        requests_session: requests.Session = None,
        cache_root_dir: str = None,
        silent: bool = None,
        requests_session_async_synapse: httpx.AsyncClient = None,
        requests_session_storage: httpx.Client = None,
        asyncio_event_loop: asyncio.AbstractEventLoop = None,
        cache_client: bool = True,
    ) -> "Synapse":
        """
        Initialize Synapse object

        Arguments:
            repoEndpoint:       Location of Synapse repository.
            authEndpoint:       Location of authentication service.
            fileHandleEndpoint: Location of file service.
            portalEndpoint:     Location of the website.
            debug:              Print debugging messages if True.
            skip_checks:        Skip version and endpoint checks.
            configPath:         Path to config File with setting for Synapse.
            requests_session:   A custom [requests.Session object](https://requests.readthedocs.io/en/latest/user/advanced/) that this Synapse instance will use
                                when making http requests.
            cache_root_dir:     Root directory for storing cache data.
            silent:             Suppresses message.
            requests_session_async_synapse: The HTTPX Async client for interacting with
                Synapse services.
            requests_session_storage: The HTTPX client for interacting with
                storage providers like AWS S3 and Google Cloud.
            asyncio_event_loop: The event loop that is going to be used while executing
                this code. This is optional and only used when you are manually
                specifying an async HTTPX client.
            cache_client: Whether to cache the Synapse client object in the Synapse module. Defaults to True.
                             When set to True anywhere a `Synapse` object is optional you do not need to pass an
                             instance of `Synapse` to that function, method, or class.
                             When working in a multi-user environment it is
                             recommended to set this to False, or use
                             `Synapse.allow_client_caching(False)`.

        Raises:
            ValueError: Warn for non-boolean debug value.
        """
        self._requests_session = requests_session or requests.Session()

        # `requests_session_async_synapse` and the thread pools are being stored in
        # a dict based on the current running event loop. This is to ensure that the
        # connection pooling is maintained within the same event loop. This is to
        # prevent the connection pooling from being shared across different event loops.
        if requests_session_async_synapse and asyncio_event_loop:
            self._requests_session_async_synapse = {
                asyncio_event_loop: requests_session_async_synapse
            }
        else:
            self._requests_session_async_synapse = {}

        httpx_timeout = httpx.Timeout(70, pool=None)
        self._requests_session_storage = requests_session_storage or httpx.Client(
            timeout=httpx_timeout
        )

        cache_root_dir = (
            cache.CACHE_ROOT_DIR if cache_root_dir is None else cache_root_dir
        )

        config_debug = None
        # Check for a config file
        self.configPath = configPath
        if os.path.isfile(configPath):
            config = get_config_file(configPath)
            if config.has_option("cache", "location"):
                cache_root_dir = config.get("cache", "location")
            if config.has_section("debug"):
                config_debug = True

        if debug is None:
            debug = config_debug if config_debug is not None else DEBUG_DEFAULT

        if not isinstance(debug, bool):
            raise ValueError("debug must be set to a bool (either True or False)")
        self.debug = debug

        self.cache = cache.Cache(cache_root_dir)
        self._sts_token_store = sts_transfer.StsTokenStore()

        self.setEndpoints(
            repoEndpoint, authEndpoint, fileHandleEndpoint, portalEndpoint, skip_checks
        )

        self.default_headers = {
            "content-type": "application/json; charset=UTF-8",
            "Accept": "application/json; charset=UTF-8",
        }
        self.credentials = None

        self.silent = silent
        self._init_logger()  # initializes self.logger

        self.skip_checks = skip_checks

        self.table_query_sleep = 0.2  # Sleep for 200ms between table query retries
        self.table_query_backoff = 1.1
        self.table_query_max_sleep = 20
        self.table_query_timeout = 600  # in seconds
        self.multi_threaded = True  # if set to True, multi threaded download will be used for http and https URLs

        transfer_config = get_transfer_config(config_path=self.configPath)
        self.max_threads = transfer_config["max_threads"]
        self._thread_executor = {}
        self._process_executor = {}
        self._parallel_file_transfer_semaphore = {}
        self.use_boto_sts_transfers = transfer_config["use_boto_sts"]
        self._parts_transfered_counter = 0
        if cache_client and Synapse._allow_client_caching:
            Synapse.set_client(synapse_client=self)

    def _get_requests_session_async_synapse(
        self, asyncio_event_loop: asyncio.AbstractEventLoop
    ) -> httpx.AsyncClient:
        """
        httpx.AsyncClient can only use connection pooling within the same event loop.
        As a result an `atexit` handler is used to close the connection when the event
        loop is closed. It will also delete the attribute from the object to prevent
        it from being reused in the future.

        Further documentation can be found here:
        <https://github.com/encode/httpx/discussions/2959>


        As a result of this issue: It is recommended to use the same event loop for all
        requests. This means to enter into an event loop before making any requests.

        This is expected to be called from within an AsyncIO loop.
        """
        if (
            hasattr(self, "_requests_session_async_synapse")
            and asyncio_event_loop in self._requests_session_async_synapse
            and self._requests_session_async_synapse[asyncio_event_loop] is not None
        ):
            return self._requests_session_async_synapse[asyncio_event_loop]

        async def close_connection() -> None:
            """Close connection when event loop exits"""
            await self._requests_session_async_synapse[asyncio_event_loop].aclose()
            del self._requests_session_async_synapse[asyncio_event_loop]

        httpx_timeout = httpx.Timeout(70, pool=None)
        self._requests_session_async_synapse.update(
            {
                asyncio_event_loop: httpx.AsyncClient(
                    limits=httpx.Limits(max_connections=25),
                    timeout=httpx_timeout,
                )
            }
        )

        asyncio_atexit.register(close_connection)
        return self._requests_session_async_synapse[asyncio_event_loop]

    def _get_thread_pool_executor(
        self, asyncio_event_loop: asyncio.AbstractEventLoop
    ) -> ThreadPoolExecutor:
        """
        Retrieve the thread pool executor for the Synapse client. Or create a new one if
        it does not exist. This executor is used for concurrent uploads of data to
        storage providers like AWS S3 and Google Cloud Storage.

        This is expected to be called from within an AsyncIO loop.
        """
        if (
            hasattr(self, "_thread_executor")
            and asyncio_event_loop in self._thread_executor
            and self._thread_executor[asyncio_event_loop] is not None
        ):
            return self._thread_executor[asyncio_event_loop]

        def close_pool() -> None:
            """Close pool when event loop exits"""
            self._thread_executor[asyncio_event_loop].shutdown(wait=True)
            del self._thread_executor[asyncio_event_loop]

        self._thread_executor.update(
            {asyncio_event_loop: get_executor(thread_count=self.max_threads)}
        )

        asyncio_atexit.register(close_pool)
        return self._thread_executor[asyncio_event_loop]

    def _get_parallel_file_transfer_semaphore(
        self, asyncio_event_loop: asyncio.AbstractEventLoop
    ) -> asyncio.Semaphore:
        """
        Retrieve the semaphore for the Synapse client. Or create a new one if it does
        not exist. This semaphore is used to limit the number of files that can actively
        enter the uploading/downloading process.

        This is expected to be called from within an AsyncIO loop.

        By default the number of files that can enter the "uploading" state will be
        limited to 2 * max_threads. This is to ensure that the files that are entering
        into the "uploading" state will have priority to finish. Additionally, it means
        that there should be a good spread of files getting up to the "uploading"
        state, entering the "uploading" state, and finishing the "uploading" state.

        If we break these states down into large components they would look like:
        - Before "uploading" state: HTTP rest calls to retrieve what data Synapse has
        - Entering "uploading" state: MD5 calculation and HTTP rest calls to determine
          how/where to upload a file to.
        - During "uploading" state: Uploading the file to a storage provider.
        - After "uploading" state: HTTP rest calls to finalize the upload.

        This has not yet been applied to parallel file downloads. That will take place
        later on.
        """
        if (
            hasattr(self, "_parallel_file_transfer_semaphore")
            and asyncio_event_loop in self._parallel_file_transfer_semaphore
            and self._parallel_file_transfer_semaphore[asyncio_event_loop] is not None
        ):
            return self._parallel_file_transfer_semaphore[asyncio_event_loop]

        self._parallel_file_transfer_semaphore.update(
            {asyncio_event_loop: asyncio.Semaphore(max(self.max_threads * 2, 1))}
        )

        return self._parallel_file_transfer_semaphore[asyncio_event_loop]

    # initialize logging
    def _init_logger(self):
        """
        Initialize logging
        """
        logger_name = (
            SILENT_LOGGER_NAME
            if self.silent
            else DEBUG_LOGGER_NAME
            if self.debug
            else DEFAULT_LOGGER_NAME
        )
        self.logger = logging.getLogger(logger_name)
        logging.getLogger("py.warnings").handlers = self.logger.handlers

    @classmethod
    def get_client(cls, synapse_client: typing.Union[None, "Synapse"]) -> "Synapse":
        """
        Convience function to get an instance of 'Synapse'. The latest instance created
        by 'login()' or set via `set_client` will be returned.

        When 'logout()' is called it will delete the instance.

        Arguments:
            synapse_client: An instance of 'Synapse' or None. This is used to simplify logical checks
                    in cases where synapse is passed into them.

        Returns:
            An instance of 'Synapse'.

        Raises:
            SynapseError: No Synapse client instance was provided, and no cached
                instance is available. Ensure that either an instance is passed as the
                `synapse_client` kwarg, or a cached instance is available.
        """
        if synapse_client:
            return synapse_client

        if not cls._synapse_client:
            raise SynapseError(
                "No Synapse client instance was provided, and no cached instance is available. Ensure that either an instance is passed as the `synapse_client` kwarg, or a cached instance is available."
            )
        return cls._synapse_client

    @staticmethod
    def allow_client_caching(allow_client_caching: bool) -> None:
        """Allows for a global setting to enable or disable caching of the Synapse
        client object. **If you are working in a multi-user environment you should set
        this to False to prevent any possibility of picking up another user session.**


        As a consequence of setting this to false you must pass a Synapse class instance
        to any function, method, or class that requires it - If if it is marked as
        `Optional`.
        """
        Synapse._allow_client_caching = allow_client_caching

    @staticmethod
    def enable_open_telemetry(enable_open_telemetry: bool) -> None:
        """Determines whether OpenTelemetry is enabled for the Synapse client. This is
        used to know whether or not this library will automatically kick off the
        instruementation of several dependent libraries including:

            - threading
            - urllib
            - requests
            - httpx

        When OpenTelemetry is enabled it will automatically start the instrumentation
        of these libraries. When it is disabled it will automatically stop the
        instrumentation of these libraries.
        """
        if enable_open_telemetry and not Synapse._enable_open_telemetry:
            set_up_tracing(enabled=True)
        elif not enable_open_telemetry and Synapse._enable_open_telemetry:
            set_up_tracing(enabled=False)
        Synapse._enable_open_telemetry = enable_open_telemetry

    @classmethod
    def set_client(cls, synapse_client) -> None:
        cls._synapse_client = synapse_client

    @property
    def max_threads(self) -> int:
        return self._max_threads

    @max_threads.setter
    def max_threads(self, value: int):
        self._max_threads = min(max(value, 1), MAX_THREADS_CAP)

    @property
    def username(self) -> Union[str, None]:
        # for backwards compatability when username was a part of the Synapse object and not in credentials
        return self.credentials.username if self.credentials is not None else None

    @deprecated(
        version="4.4.0",
        reason="To be removed in 5.0.0. "
        "Moved to synapseclient/api/configuration_services.py::get_config_file",
    )
    @functools.lru_cache()
    def getConfigFile(self, configPath: str) -> configparser.RawConfigParser:
        """
        Retrieves the client configuration information.

        Arguments:
            configPath:  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(configPath)  # Does not fail if the file does not exist
            return config
        except configparser.Error as ex:
            raise ValueError(
                "Error parsing Synapse config file: {}".format(configPath)
            ) from ex

    def setEndpoints(
        self,
        repoEndpoint: str = None,
        authEndpoint: str = None,
        fileHandleEndpoint: str = None,
        portalEndpoint: str = None,
        skip_checks: bool = False,
    ) -> None:
        """
        Sets the locations for each of the Synapse services (mostly useful for testing).

        Arguments:
            repoEndpoint:          Location of synapse repository
            authEndpoint:          Location of authentication service
            fileHandleEndpoint:    Location of file service
            portalEndpoint:        Location of the website
            skip_checks:           Skip version and endpoint checks

        Example: Switching endpoints
            To switch between staging and production endpoints

                syn.setEndpoints(**synapseclient.client.STAGING_ENDPOINTS)
                syn.setEndpoints(**synapseclient.client.PRODUCTION_ENDPOINTS)

        """

        endpoints = {
            "repoEndpoint": repoEndpoint,
            "authEndpoint": authEndpoint,
            "fileHandleEndpoint": fileHandleEndpoint,
            "portalEndpoint": portalEndpoint,
        }

        # For unspecified endpoints, first look in the config file
        config = get_config_file(self.configPath)
        for point in endpoints.keys():
            if endpoints[point] is None and config.has_option("endpoints", point):
                endpoints[point] = config.get("endpoints", point)

        # Endpoints default to production
        for point in endpoints.keys():
            if endpoints[point] is None:
                endpoints[point] = PRODUCTION_ENDPOINTS[point]

            # Update endpoints if we get redirected
            if not skip_checks:
                response = with_retry(
                    lambda point=point: self._requests_session.get(
                        endpoints[point],
                        allow_redirects=False,
                        headers=synapseclient.USER_AGENT,
                    ),
                    verbose=self.debug,
                    **STANDARD_RETRY_PARAMS,
                )
                if response.status_code == 301:
                    endpoints[point] = response.headers["location"]

        self.repoEndpoint = endpoints["repoEndpoint"]
        self.authEndpoint = endpoints["authEndpoint"]
        self.fileHandleEndpoint = endpoints["fileHandleEndpoint"]
        self.portalEndpoint = endpoints["portalEndpoint"]

    def login(
        self,
        email: str = None,
        silent: bool = False,
        authToken: str = None,
    ) -> None:
        """
        Valid combinations of login() arguments:

        - authToken

        If no login arguments are provided or only username is provided, login() will attempt to log in using
         information from these sources (in order of preference):

        1. .synapseConfig file (in user home folder unless configured otherwise)
        2. User defined arguments during a CLI session
        3. User's Personal Access Token (aka: Synapse Auth Token)
            from the environment variable: SYNAPSE_AUTH_TOKEN
        4. Retrieves user's authentication token from AWS SSM Parameter store (if configured)

        Arguments:
            email:        Synapse user name (or an email address associated with a Synapse account)
            authToken:    A bearer authorization token, e.g. a
                [personal access token](https://python-docs.synapse.org/tutorials/authentication/).
            silent:       Defaults to False.  Suppresses the "Welcome ...!" message.

        Example: Logging in
            Using an auth token:

                syn.login(authToken="authtoken")
                > Welcome, Me!

            Using an auth token and username. The username is optional but verified
            against the username in the auth token:

                syn.login(email="my-username", authToken="authtoken")
                > Welcome, Me!

        """
        # Note: the order of the logic below reflects the ordering in the docstring above.

        # Check version before logging in
        if not self.skip_checks:
            version_check()

        # Make sure to invalidate the existing session
        self.logout()

        credential_provider_chain = get_default_credential_chain()

        self.credentials = credential_provider_chain.get_credentials(
            syn=self,
            user_login_args=UserLoginArgs(
                email,
                authToken,
            ),
        )

        # Final check on login success
        if not self.credentials:
            raise SynapseNoCredentialsError("No credentials provided.")

        if not silent:
            display_name = self.credentials.displayname or self.credentials.username
            self.logger.info(f"Welcome, {display_name}!\n")

    @deprecated(
        version="4.4.0",
        reason="To be removed in 5.0.0. "
        "Moved to synapseclient/api/configuration_services.py::get_config_section_dict",
    )
    def _get_config_section_dict(self, section_name: 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

        Returns:
            A dictionary containing the configuration profile section content
        """
        config = get_config_file(self.configPath)
        try:
            return dict(config.items(section_name))
        except configparser.NoSectionError:
            # section not present
            return {}

    @deprecated(
        version="4.4.0",
        reason="To be removed in 5.0.0. "
        "Moved to synapseclient/api/configuration_services.py::get_config_authentication",
    )
    def _get_config_authentication(self) -> Dict[str, str]:
        """
        Get the authentication section of the configuration file.

        Returns:
            The authentication section of the configuration file
        """
        return get_config_section_dict(
            section_name=config_file_constants.AUTHENTICATION_SECTION_NAME,
            config_path=self.configPath,
        )

    @deprecated(
        version="4.4.0",
        reason="To be removed in 5.0.0. "
        "Moved to synapseclient/api/configuration_services.py::get_client_authenticated_s3_profile",
    )
    def _get_client_authenticated_s3_profile(
        self, endpoint: str, bucket: 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

        Returns:
            The authenticated S3 profile
        """
        config_section = endpoint + "/" + bucket
        return get_config_section_dict(
            section_name=config_section, config_path=self.configPath
        ).get("profile_name", "default")

    @deprecated(
        version="4.4.0",
        reason="To be removed in 5.0.0. "
        "Moved to synapseclient/api/configuration_services.py::get_transfer_config",
    )
    def _get_transfer_config(self) -> Dict[str, str]:
        """
        Get the transfer profile from the configuration file.

        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=self.configPath
        ).items():
            if v:
                if k == "max_threads" and v:
                    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

    def _is_logged_in(self) -> bool:
        """
        Test whether the user is logged in to Synapse.

        Returns:
            Boolean value indicating current user's login status
        """
        # This is a quick sanity check to see if credentials have been
        # configured on the client
        if self.credentials is None:
            return False
        # The public can query this command so there is no need to try catch.
        user = self.restGET("/userProfile")
        if user.get("userName") == "anonymous":
            return False
        return True

    def logout(self) -> None:
        """
        Removes authentication information from the Synapse client.

        Returns:
            None
        """
        self.credentials = None

    @deprecated(
        version="4.0.0",
        reason="deprecated with no replacement. The client does not support API keys for "
        "authentication. Please use a personal access token instead. This method will "
        "be removed in a future release.",
    )
    def invalidateAPIKey(self):
        """
        **Deprecated with no replacement.** The client does not support API keys for
        authentication. Please use a
        [personal access token](https://python-docs.synapse.org/tutorials/authentication/)
        instead. This method will be removed in a future release.


        Invalidates authentication across all clients.

        Returns:
            None
        """

        # Logout globally
        if self._is_logged_in():
            self.restDELETE("/secretKey", endpoint=self.authEndpoint)

    @functools.lru_cache()
    def get_user_profile_by_username(
        self,
        username: str = None,
        sessionToken: str = None,
    ) -> UserProfile:
        """
        Get the details about a Synapse user.
        Retrieves information on the current user if 'id' is omitted or is empty string.

        Arguments:
            username:     The userName of a user
            sessionToken: The session token to use to find the user profile

        Returns:
            The user profile for the user of interest.

        Example: Using this function
            Getting your own profile

                my_profile = syn.get_user_profile_by_username()

            Getting another user's profile

                freds_profile = syn.get_user_profile_by_username('fredcommo')
        """
        is_none = username is None
        is_str = isinstance(username, str)
        if not is_str and not is_none:
            raise TypeError("username must be string or None")
        if is_str:
            principals = self._findPrincipals(username)
            for principal in principals:
                if principal.get("userName", None).lower() == username.lower():
                    id = principal["ownerId"]
                    break
            else:
                raise ValueError(f"Can't find user '{username}'")
        else:
            id = ""
        uri = f"/userProfile/{id}"
        return UserProfile(
            **self.restGET(
                uri, headers={"sessionToken": sessionToken} if sessionToken else None
            )
        )

    @functools.lru_cache()
    def get_user_profile_by_id(
        self,
        id: int = None,
        sessionToken: str = None,
    ) -> UserProfile:
        """
        Get the details about a Synapse user.
        Retrieves information on the current user if 'id' is omitted.

        Arguments:
            id:           The ownerId of a user
            sessionToken: The session token to use to find the user profile

        Returns:
            The user profile for the user of interest.


        Example: Using this function
            Getting your own profile

                my_profile = syn.get_user_profile_by_id()

            Getting another user's profile

                freds_profile = syn.get_user_profile_by_id(1234567)
        """
        if id:
            if not isinstance(id, int):
                raise TypeError("id must be an 'ownerId' integer")
        else:
            id = ""
        uri = f"/userProfile/{id}"
        return UserProfile(
            **self.restGET(
                uri, headers={"sessionToken": sessionToken} if sessionToken else None
            )
        )

    @functools.lru_cache()
    def getUserProfile(
        self,
        id: Union[str, int, UserProfile, TeamMember] = None,
        sessionToken: str = None,
    ) -> UserProfile:
        """
        Get the details about a Synapse user.
        Retrieves information on the current user if 'id' is omitted.

        Arguments:
            id:           The 'userId' (aka 'ownerId') of a user or the userName
            sessionToken: The session token to use to find the user profile

        Returns:
            The user profile for the user of interest.

        Example: Using this function
            Getting your own profile

                my_profile = syn.getUserProfile()

            Getting another user's profile

                freds_profile = syn.getUserProfile('fredcommo')
        """
        try:
            # if id is unset or a userID, this will succeed
            id = "" if id is None else int(id)
        except (TypeError, ValueError):
            if isinstance(id, collections.abc.Mapping) and "ownerId" in id:
                id = id.ownerId
            elif isinstance(id, TeamMember):
                id = id.member.ownerId
            else:
                principals = self._findPrincipals(id)
                if len(principals) == 1:
                    id = principals[0]["ownerId"]
                else:
                    for principal in principals:
                        if principal.get("userName", None).lower() == id.lower():
                            id = principal["ownerId"]
                            break
                    else:  # no break
                        raise ValueError('Can\'t find user "%s": ' % id)
        uri = "/userProfile/%s" % id
        return UserProfile(
            **self.restGET(
                uri, headers={"sessionToken": sessionToken} if sessionToken else None
            )
        )

    def _findPrincipals(self, query_string: str) -> List[UserGroupHeader]:
        """
        Find users or groups by name or email.

        Returns:
            A list of userGroupHeader objects with fields displayName, email, firstName, lastName, isIndividual, ownerId


        Example: Using this function
            Find userGroupHeader objects for test user

                syn._findPrincipals('test')

                [{u'displayName': u'Synapse Test',
                u'email': u'syn...t@sagebase.org',
                u'firstName': u'Synapse',
                u'isIndividual': True,
                u'lastName': u'Test',
                u'ownerId': u'1560002'},
                {u'displayName': ... }]
        """
        uri = "/userGroupHeaders?prefix=%s" % urllib_urlparse.quote(query_string)
        return [UserGroupHeader(**result) for result in self._GET_paginated(uri)]

    def _get_certified_passing_record(
        self, userid: int
    ) -> Dict[str, Union[str, int, bool, list]]:
        """
        Retrieve the Passing Record on the User Certification test for the given user.

        Arguments:
            userid: Synapse user Id

        Returns:
            Synapse Passing Record. A record of whether a given user passed a given test.
            <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/quiz/PassingRecord.html>
        """
        response = self.restGET(f"/user/{userid}/certifiedUserPassingRecord")
        return response

    def _get_user_bundle(self, userid: int, mask: int) -> Dict[str, Union[str, dict]]:
        """
        Retrieve the user bundle for the given user.

        Arguments:
            userid: Synapse user Id
            mask:   Bit field indicating which components to include in the bundle.

        Returns:
            [Synapse User Bundle](https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/UserBundle.html)
        """
        try:
            response = self.restGET(f"/user/{userid}/bundle?mask={mask}")
        except SynapseHTTPError as ex:
            if ex.response.status_code == 404:
                return None
        return response

    def is_certified(self, user: typing.Union[str, int]) -> bool:
        """Determines whether a Synapse user is a certified user.

        Arguments:
            user: Synapse username or Id

        Returns:
            True if the Synapse user is certified
        """
        # Check if userid or username exists
        syn_user = self.getUserProfile(user)
        # Get passing record

        try:
            certification_status = self._get_certified_passing_record(
                syn_user["ownerId"]
            )
            return certification_status["passed"]
        except SynapseHTTPError as ex:
            if ex.response.status_code == 404:
                # user hasn't taken the quiz
                return False
            raise

    def is_synapse_id(self, syn_id: str) -> bool:
        """Checks if given synID is valid (attached to actual entity?)

        Arguments:
            syn_id: A Synapse ID

        Returns:
            True if the Synapse ID is valid
        """
        if isinstance(syn_id, str):
            try:
                self.get(syn_id, downloadFile=False)
            except SynapseFileNotFoundError:
                return False
            except (
                SynapseHTTPError,
                SynapseAuthenticationError,
            ) as err:
                status = (
                    err.__context__.response.status_code or err.response.status_code
                )
                if status in (400, 404):
                    return False
                # Valid ID but user lacks permission or is not logged in
                elif status == 403:
                    return True
            return True
        self.logger.warning("synID must be a string")
        return False

    def onweb(self, entity, subpageId=None):
        """Opens up a browser window to the entity page or wiki-subpage.

        Arguments:
            entity:    Either an Entity or a Synapse ID
            subpageId: (Optional) ID of one of the wiki's sub-pages

        Returns:
            None
        """
        if isinstance(entity, str) and os.path.isfile(entity):
            entity = self.get(entity, downloadFile=False)
        synId = id_of(entity)
        if subpageId is None:
            webbrowser.open("%s#!Synapse:%s" % (self.portalEndpoint, synId))
        else:
            webbrowser.open(
                "%s#!Wiki:%s/ENTITY/%s" % (self.portalEndpoint, synId, subpageId)
            )

    def printEntity(self, entity, ensure_ascii=True) -> None:
        """
        Pretty prints an Entity.

        Arguments:
            entity: The entity to be printed.
            ensure_ascii: If True, escapes all non-ASCII characters

        Returns:
            None
        """

        if utils.is_synapse_id_str(entity):
            synid, version = utils.get_synid_and_version(entity)
            entity = self._getEntity(synid, version)
        try:
            self.logger.info(
                json.dumps(entity, sort_keys=True, indent=2, ensure_ascii=ensure_ascii)
            )
        except TypeError:
            self.logger.info(str(entity))

    def _print_transfer_progress(self, *args, **kwargs) -> None:
        """
        Checking synapse if the mode is silent mode.
        If self.silent is True, no need to print out transfer progress.
        """
        if self.silent is not True:
            cumulative_transfer_progress.printTransferProgress(*args, **kwargs)

    ############################################################
    #                      Service methods                     #
    ############################################################

    _services = {
        "json_schema": "JsonSchemaService",
    }

    def get_available_services(self) -> typing.List[str]:
        """Get available Synapse services
        This is a beta feature and is subject to change

        Returns:
            List of available services
        """
        services = self._services.keys()
        return list(services)

    def service(self, service_name: str):
        """Get available Synapse services
        This is a beta feature and is subject to change

        Arguments:
            service_name: name of the service
        """
        # This is to avoid circular imports
        # TODO: revisit the import order and method https://stackoverflow.com/a/37126790
        # To move this to the top
        import synapseclient.services

        assert isinstance(service_name, str)
        service_name = service_name.lower().replace(" ", "_")
        assert service_name in self._services, (
            f"Unrecognized service ({service_name}). Run the 'get_available_"
            "services()' method to get a list of available services."
        )
        service_attr = self._services[service_name]
        service_cls = getattr(synapseclient.services, service_attr)
        service = service_cls(self)
        return service

    ############################################################
    #                   Get / Store methods                    #
    ############################################################

    def get(self, entity, **kwargs):
        """
        Gets a Synapse entity from the repository service.

        Arguments:
            entity:           A Synapse ID (e.g. syn123 or syn123.1, with .1 denoting version), a Synapse Entity object,
                              a plain dictionary in which 'id' maps to a Synapse ID or a local file that is stored in
                              Synapse (found by the file MD5)
            version:          The specific version to get.
                                Defaults to the most recent version. If not denoted in the entity input.
            downloadFile:     Whether associated files(s) should be downloaded.
                                Defaults to True.
            downloadLocation: Directory where to download the Synapse File Entity.
                                Defaults to the local cache.
            followLink:       Whether the link returns the target Entity.
                                Defaults to False.
            ifcollision:      Determines how to handle file collisions.
                                May be "overwrite.local", "keep.local", or "keep.both".
                                Defaults to "keep.both".
            limitSearch:      A Synanpse ID used to limit the search in Synapse if entity is specified as a local
                                file.  That is, if the file is stored in multiple locations in Synapse only the ones
                                in the specified folder/project will be returned.
            md5: The MD5 checksum for the file, if known. Otherwise if the file is a
                local file, it will be calculated automatically.

        Returns:
            A new Synapse Entity object of the appropriate type.

        Example: Using this function
            Download file into cache

                entity = syn.get('syn1906479')
                print(entity.name)
                print(entity.path)

            Download file into current working directory

                entity = syn.get('syn1906479', downloadLocation='.')
                print(entity.name)
                print(entity.path)

            Determine the provenance of a locally stored file as indicated in Synapse

                entity = syn.get('/path/to/file.txt', limitSearch='syn12312')
                print(syn.getProvenance(entity))
        """
        # If entity is a local file determine the corresponding synapse entity
        if isinstance(entity, str) and os.path.isfile(entity):
            bundle = self._getFromFile(
                entity, kwargs.pop("limitSearch", None), md5=kwargs.get("md5", None)
            )
            kwargs["downloadFile"] = False
            kwargs["path"] = entity

        elif isinstance(entity, str) and not utils.is_synapse_id_str(entity):
            raise SynapseFileNotFoundError(
                (
                    "The parameter %s is neither a local file path "
                    " or a valid entity id" % entity
                )
            )
        # have not been saved entities
        elif isinstance(entity, Entity) and not entity.get("id"):
            raise ValueError(
                "Cannot retrieve entity that has not been saved."
                " Please use syn.store() to save your entity and try again."
            )
        else:
            input_version = kwargs.get("version", None)
            synid_and_version = utils.get_synid_and_version(entity)
            version = (
                input_version if input_version is not None else synid_and_version[1]
            )
            # If ``version`` is None, the arg will be ignored
            bundle = self._getEntityBundle(synid_and_version[0], version)

        # Check and warn for unmet access requirements
        self._check_entity_restrictions(
            bundle, entity, kwargs.get("downloadFile", True)
        )

        return_data = self._getWithEntityBundle(
            entityBundle=bundle, entity=entity, **kwargs
        )
        trace.get_current_span().set_attributes(
            {
                "synapse.id": return_data.get("id", ""),
                "synapse.concrete_type": return_data.get("concreteType", ""),
            }
        )
        return return_data

    def _check_entity_restrictions(
        self, bundle: dict, entity: Union[str, Entity, dict], downloadFile: bool
    ) -> None:
        """
        Check and warn for unmet access requirements.

        Arguments:
            bundle: A Synapse entityBundle
            entity: A Synapse ID, a Synapse Entity object, a plain dictionary in which 'id' maps to a
                    Synapse ID or a local file that is stored in Synapse (found by the file MD5)
            downloadFile: Whether associated files(s) should be downloaded.

        Raises:
            SynapseUnmetAccessRestrictions: Warning for unmet access requirements.
        """
        restrictionInformation = bundle["restrictionInformation"]
        if restrictionInformation["hasUnmetAccessRequirement"]:
            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)

    def _getFromFile(
        self, filepath: str, limitSearch: str = None, md5: str = None
    ) -> Dict[str, dict]:
        """
        Gets a Synapse entityBundle based on the md5 of a local file.
        See [get][synapseclient.Synapse.get].

        Arguments:
            filepath:    The path to local file
            limitSearch: Limits the places in Synapse where the file is searched for.
            md5: The MD5 checksum for the file, if known. Otherwise if the file is a
                local file, it will be calculated automatically.


        Raises:
            SynapseFileNotFoundError: If the file is not in Synapse.

        Returns:
            A Synapse entityBundle
        """
        results = self.restGET(
            "/entity/md5/%s" % (md5 or utils.md5_for_file(filepath).hexdigest())
        )["results"]
        if limitSearch is not None:
            # Go through and find the path of every entity found
            paths = [self.restGET("/entity/%s/path" % ent["id"]) for ent in results]
            # Filter out all entities whose path does not contain limitSearch
            results = [
                ent
                for ent, path in zip(results, paths)
                if utils.is_in_path(limitSearch, path)
            ]
        if len(results) == 0:  # None found
            raise SynapseFileNotFoundError("File %s not found in Synapse" % (filepath,))
        elif len(results) > 1:
            id_txts = "\n".join(
                ["%s.%i" % (r["id"], r["versionNumber"]) for r in results]
            )
            self.logger.warning(
                "\nThe file %s is associated with many files in Synapse:\n%s\n"
                "You can limit to files in specific project or folder by setting the limitSearch to the"
                " synapse Id of the project or folder.\n"
                "Will use the first one returned: \n"
                "%s version %i\n"
                % (filepath, id_txts, results[0]["id"], results[0]["versionNumber"])
            )
        entity = results[0]

        bundle = self._getEntityBundle(entity, version=entity["versionNumber"])
        self.cache.add(bundle["entity"]["dataFileHandleId"], filepath)

        return bundle

    def move(self, entity, new_parent):
        """
        Move a Synapse entity to a new container.

        Arguments:
            entity:     A Synapse ID, a Synapse Entity object, or a local file that is stored in Synapse
            new_parent: The new parent container (Folder or Project) to which the entity should be moved.

        Returns:
            The Synapse Entity object that has been moved.

        Example: Using this function
            Move a Synapse Entity object to a new parent container

                entity = syn.move('syn456', 'syn123')
        """

        entity = self.get(entity, downloadFile=False)
        entity.parentId = id_of(new_parent)
        entity = self.store(entity, forceVersion=False)
        trace.get_current_span().set_attributes(
            {
                "synapse.id": entity.get("id", ""),
                "synapse.parent_id": entity.get("parentId", ""),
            }
        )

        return entity

    def _getWithEntityBundle(
        self, entityBundle: dict, entity: Entity = None, **kwargs
    ) -> Entity:
        """
        Creates a [Entity][synapseclient.Entity] from an entity bundle returned by Synapse.
        An existing Entity can be supplied in case we want to refresh a stale Entity.

        Arguments:
            entityBundle: Uses the given dictionary as the meta information of the Entity to get
            entity:       Optional, entity whose local state will be copied into the returned entity
            submission:   Optional, access associated files through a submission rather than through an entity.

        Returns:
            A new Synapse Entity

        Also see:
        - See [get][synapseclient.Synapse.get].
        - See [_getEntityBundle][synapseclient.Synapse._getEntityBundle].
        - See [Entity][synapseclient.Entity].
        """
        # Note: This version overrides the version of 'entity' (if the object is Mappable)
        kwargs.pop("version", None)
        downloadFile = kwargs.pop("downloadFile", True)
        downloadLocation = kwargs.pop("downloadLocation", None)
        ifcollision = kwargs.pop("ifcollision", None)
        submission = kwargs.pop("submission", None)
        followLink = kwargs.pop("followLink", False)
        path = kwargs.pop("path", None)

        # If Link, get target ID entity bundle
        if (
            entityBundle["entity"]["concreteType"]
            == "org.sagebionetworks.repo.model.Link"
            and followLink
        ):
            targetId = entityBundle["entity"]["linksTo"]["targetId"]
            targetVersion = entityBundle["entity"]["linksTo"].get("targetVersionNumber")
            entityBundle = self._getEntityBundle(targetId, targetVersion)

        # TODO is it an error to specify both downloadFile=False and downloadLocation?
        # TODO this matters if we want to return already cached files when downloadFile=False

        # Make a fresh copy of the Entity
        local_state = (
            entity.local_state() if entity and isinstance(entity, Entity) else {}
        )
        if path is not None:
            local_state["path"] = path
        properties = entityBundle["entity"]
        annotations = from_synapse_annotations(entityBundle["annotations"])
        entity = Entity.create(properties, annotations, local_state)

        # Handle download of fileEntities
        if isinstance(entity, File):
            # update the entity with FileHandle metadata
            file_handle = next(
                (
                    handle
                    for handle in entityBundle["fileHandles"]
                    if handle["id"] == entity.dataFileHandleId
                ),
                None,
            )
            entity._update_file_handle(file_handle)

            if downloadFile:
                if file_handle:
                    wrap_async_to_sync(
                        coroutine=download_file_entity(
                            download_location=downloadLocation,
                            entity=entity,
                            if_collision=ifcollision,
                            submission=submission,
                            synapse_client=self,
                        ),
                        syn=self,
                    )
                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."
                    )
                    self.logger.warning(
                        "\n"
                        + "!" * len(warning_message)
                        + "\n"
                        + warning_message
                        + "\n"
                        + "!" * len(warning_message)
                        + "\n"
                    )
        return entity

    @deprecated(
        version="4.4.0",
        reason="To be removed in 5.0.0. "
        "Moved to synapseclient/core/download/download_functions.py::ensure_download_location_is_directory",
    )
    def _ensure_download_location_is_directory(self, downloadLocation: str) -> str:
        """
        Check if the download location is a directory

        Arguments:
            downloadLocation: The download location

        Raises:
            ValueError: If the downloadLocation is not a directory

        Returns:
            The download location
        """
        download_dir = os.path.expandvars(os.path.expanduser(downloadLocation))
        if os.path.isfile(download_dir):
            raise ValueError(
                "Parameter 'downloadLocation' should be a directory, not a file."
            )
        return download_dir

    @deprecated(
        version="4.4.0",
        reason="To be removed in 5.0.0. "
        "Moved to synapseclient/core/download/download_functions.py::download_file_entity",
    )
    def _download_file_entity(
        self,
        downloadLocation: str,
        entity: Entity,
        ifcollision: str,
        submission: str,
    ) -> None:
        """
        Download file entity

        Arguments:
            downloadLocation: The download location
            entity:           The Synapse Entity object
            ifcollision:      Determines how to handle file collisions.
                              May be

                - `overwrite.local`
                - `keep.local`
                - `keep.both`

            submission:       Access associated files through a submission rather than through an entity.
        """
        # set the initial local state
        entity.path = None
        entity.files = []
        entity.cacheDir = None

        # check to see if an UNMODIFIED version of the file (since it was last downloaded) already exists
        # this location could be either in .synapseCache or a user specified location to which the user previously
        # downloaded the file
        cached_file_path = self.cache.get(entity.dataFileHandleId, downloadLocation)

        # location in .synapseCache where the file would be corresponding to its FileHandleId
        synapseCache_location = self.cache.get_cache_dir(entity.dataFileHandleId)

        file_name = (
            entity._file_handle.fileName
            if cached_file_path is None
            else os.path.basename(cached_file_path)
        )

        # Decide the best download location for the file
        if downloadLocation is not None:
            # Make sure the specified download location is a fully resolved directory
            downloadLocation = self._ensure_download_location_is_directory(
                downloadLocation
            )
        elif cached_file_path is not None:
            # file already cached so use that as the download location
            downloadLocation = os.path.dirname(cached_file_path)
        else:
            # file not cached and no user-specified location so default to .synapseCache
            downloadLocation = synapseCache_location

        # resolve file path collisions by either overwriting, renaming, or not downloading, depending on the
        # ifcollision value
        downloadPath = self._resolve_download_path_collisions(
            downloadLocation,
            file_name,
            ifcollision,
            synapseCache_location,
            cached_file_path,
        )
        if downloadPath is None:
            return

        if cached_file_path is not None:  # copy from cache
            if downloadPath != cached_file_path:
                # create the foider if it does not exist already
                if not os.path.exists(downloadLocation):
                    os.makedirs(downloadLocation)
                shutil.copy(cached_file_path, downloadPath)

        else:  # download the file from URL (could be a local file)
            objectType = "FileEntity" if submission is None else "SubmissionAttachment"
            objectId = entity["id"] if submission is None else submission

            # reassign downloadPath because if url points to local file (e.g. file://~/someLocalFile.txt)
            # it won't be "downloaded" and, instead, downloadPath will just point to '~/someLocalFile.txt'
            # _downloadFileHandle may also return None to indicate that the download failed
            downloadPath = self._downloadFileHandle(
                entity.dataFileHandleId, objectId, objectType, downloadPath
            )

            if downloadPath is None or not os.path.exists(downloadPath):
                return

        # converts the path format from forward slashes back to backward slashes on Windows
        entity.path = os.path.normpath(downloadPath)
        entity.files = [os.path.basename(downloadPath)]
        entity.cacheDir = os.path.dirname(downloadPath)

    @deprecated(
        version="4.4.0",
        reason="To be removed in 5.0.0. "
        "Moved to synapseclient/core/download/download_functions.py::resolve_download_path_collisions",
    )
    def _resolve_download_path_collisions(
        self,
        downloadLocation: str,
        file_name: str,
        ifcollision: str,
        synapseCache_location: str,
        cached_file_path: str,
    ) -> str:
        """
        Resolve file path collisions

        Arguments:
            downloadLocation:      The download location
            file_name:             The file name
            ifcollision:           Determines how to handle file collisions.
                                   May be "overwrite.local", "keep.local", or "keep.both".
            synapseCache_location: The location in .synapseCache where the file would be
                                   corresponding to its FileHandleId.
            cached_file_path:      The file path of the cached copy

        Raises:
            ValueError: Invalid ifcollision. Should be "overwrite.local", "keep.local", or "keep.both".

        Returns:
            The download file path with collisions resolved
        """
        # always overwrite if we are downloading to .synapseCache
        if utils.normalize_path(downloadLocation) == synapseCache_location:
            if ifcollision is not None and ifcollision != "overwrite.local":
                self.logger.warning(
                    "\n"
                    + "!" * 50
                    + f"\nifcollision={ifcollision} "
                    + "is being IGNORED because the download destination is synapse's cache."
                    ' Instead, the behavior is "overwrite.local". \n' + "!" * 50 + "\n"
                )
            ifcollision = "overwrite.local"
        # if ifcollision not specified, keep.local
        ifcollision = ifcollision or "keep.both"

        downloadPath = utils.normalize_path(os.path.join(downloadLocation, file_name))
        # resolve collison
        if os.path.exists(downloadPath):
            if ifcollision == "overwrite.local":
                pass
            elif ifcollision == "keep.local":
                # Don't want to overwrite the local file.
                return None
            elif ifcollision == "keep.both":
                if downloadPath != cached_file_path:
                    return utils.unique_filename(downloadPath)
            else:
                raise ValueError(
                    'Invalid parameter: "%s" is not a valid value '
                    'for "ifcollision"' % ifcollision
                )
        return downloadPath

    def store(
        self,
        obj,
        *,
        createOrUpdate=True,
        forceVersion=True,
        versionLabel=None,
        isRestricted=False,
        activity=None,
        used=None,
        executed=None,
        activityName=None,
        activityDescription=None,
        set_annotations=True,
    ):
        """
        Creates a new Entity or updates an existing Entity, uploading any files in the process.

        Arguments:
            obj: A Synapse Entity, Evaluation, or Wiki
            used: The Entity, Synapse ID, or URL used to create the object (can also be a list of these)
            executed: The Entity, Synapse ID, or URL representing code executed to create the object
                        (can also be a list of these)
            activity: Activity object specifying the user's provenance.
            activityName: Activity name to be used in conjunction with *used* and *executed*.
            activityDescription: Activity description to be used in conjunction with *used* and *executed*.
            createOrUpdate: Indicates whether the method should automatically perform an update if the 'obj'
                            conflicts with an existing Synapse object.
            forceVersion: Indicates whether the method should increment the version of the object even if nothing
                            has changed.
            versionLabel: Arbitrary string used to label the version.
            isRestricted: If set to true, 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.
                            You will be contacted with regards to the specific data being restricted and the
                            requirements of access.
            set_annotations: If True, set the annotations on the entity. If False, do not set the annotations.

        Returns:
            A Synapse Entity, Evaluation, or Wiki

        Example: Using this function
            Creating a new Project:

                from synapseclient import Project

                project = Project('My uniquely named project')
                project = syn.store(project)

            Adding files with [provenance (aka: Activity)][synapseclient.Activity]:

                from synapseclient import File, Activity

            A synapse entity *syn1906480* contains data and an entity *syn1917825* contains code

                activity = Activity(
                    'Fancy Processing',
                    description='No seriously, really fancy processing',
                    used=['syn1906480', 'http://data_r_us.com/fancy/data.txt'],
                    executed='syn1917825')

                test_entity = File('/path/to/data/file.xyz', description='Fancy new data', parent=project)
                test_entity = syn.store(test_entity, activity=activity)

        """
        trace.get_current_span().set_attributes({"thread.id": threading.get_ident()})
        # 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"):
            obj._before_synapse_store(self)

        # _synapse_store hook
        # for objects that know how to store themselves
        if hasattr(obj, "_synapse_store"):
            return obj._synapse_store(self)

        # Handle all non-Entity objects
        if not (isinstance(obj, Entity) or type(obj) == dict):
            if isinstance(obj, Wiki):
                return self._storeWiki(obj, createOrUpdate)

            if "id" in obj:  # If ID is present, update
                trace.get_current_span().set_attributes({"synapse.id": obj["id"]})
                return type(obj)(**self.restPUT(obj.putURI(), obj.json()))

            try:  # If no ID is present, attempt to POST the object
                trace.get_current_span().set_attributes({"synapse.id": ""})
                return type(obj)(**self.restPOST(obj.postURI(), obj.json()))

            except SynapseHTTPError as err:
                # If already present and we want to update attempt to get the object content
                if createOrUpdate and err.response.status_code == 409:
                    newObj = self.restGET(obj.getByNameURI(obj.name))
                    newObj.update(obj)
                    obj = type(obj)(**newObj)
                    trace.get_current_span().set_attributes({"synapse.id": obj["id"]})
                    obj.update(self.restPUT(obj.putURI(), obj.json()))
                    return obj
                raise

        # If the input object is an Entity or a dictionary
        entity = obj
        properties, annotations, local_state = split_entity_namespaces(entity)
        bundle = None
        # Explicitly set an empty versionComment property if none is supplied,
        # otherwise an existing entity bundle's versionComment will be copied to the update.
        properties["versionComment"] = (
            properties["versionComment"] if "versionComment" in properties else None
        )

        # Anything with a path is treated as a cache-able item
        # Only Files are expected in the following logic
        if entity.get("path", False) and not isinstance(obj, Folder):
            local_file_md5_hex = None
            if "concreteType" not in properties:
                properties["concreteType"] = File._synapse_entity_type
            # Make sure the path is fully resolved
            entity["path"] = os.path.expanduser(entity["path"])

            # Check if the File already exists in Synapse by fetching metadata on it
            bundle = self._getEntityBundle(entity)

            if bundle:
                if createOrUpdate:
                    # update our properties from the existing bundle so that we have
                    # enough to process this as an entity update.
                    properties = {**bundle["entity"], **properties}

                # Check if the file should be uploaded
                fileHandle = find_data_file_handle(bundle)
                if (
                    fileHandle
                    and fileHandle["concreteType"]
                    == "org.sagebionetworks.repo.model.file.ExternalFileHandle"
                ):
                    # switching away from ExternalFileHandle or the url was updated
                    needs_upload = entity["synapseStore"] or (
                        fileHandle["externalURL"] != entity["externalURL"]
                    )
                else:
                    synapse_store_flag = entity["synapseStore"] or local_state.get(
                        "synapseStore"
                    )
                    # Check if we need to upload a new version of an existing
                    # file. If the file referred to by entity['path'] has been
                    # modified, we want to upload the new version.
                    # If synapeStore is false then we must upload a ExternalFileHandle
                    needs_upload = not synapse_store_flag or not self.cache.contains(
                        bundle["entity"]["dataFileHandleId"], entity["path"]
                    )

                    md5_stored_in_synapse = local_state.get("_file_handle", {}).get(
                        "contentMd5", None
                    ) or (fileHandle or {}).get("contentMd5", None)

                    # Check if we got an MD5 checksum from Synapse and compare it to the local file
                    if (
                        synapse_store_flag
                        and needs_upload
                        and os.path.isfile(entity["path"])
                        and md5_stored_in_synapse
                        and md5_stored_in_synapse
                        == (
                            local_file_md5_hex := utils.md5_for_file(
                                entity["path"]
                            ).hexdigest()
                        )
                    ):
                        needs_upload = False
            elif entity.get("dataFileHandleId", None) is not None:
                needs_upload = False
            else:
                needs_upload = True

            if needs_upload:
                local_state_fh = local_state.get("_file_handle", {})
                synapseStore = local_state.get("synapseStore", True)

                # parent_id_for_upload is allowing `store` to be called on files that have
                # already been stored to Synapse, but did not specify a parentId in the
                # FileEntity. This is useful as it prevents the need to specify the
                # parentId every time a file is stored to Synapse when the ID is
                # already known.
                parent_id_for_upload = entity.get("parentId", None)
                if not parent_id_for_upload and bundle and bundle.get("entity", None):
                    parent_id_for_upload = bundle["entity"]["parentId"]

                if not parent_id_for_upload:
                    raise SynapseMalformedEntityError(
                        "Entities of type File must have a parentId."
                    )

                fileHandle = wrap_async_to_sync(
                    upload_file_handle_async(
                        self,
                        parent_id_for_upload,
                        local_state["path"]
                        if (synapseStore or local_state_fh.get("externalURL") is None)
                        else local_state_fh.get("externalURL"),
                        synapse_store=synapseStore,
                        md5=local_file_md5_hex or local_state_fh.get("contentMd5"),
                        file_size=local_state_fh.get("contentSize"),
                        mimetype=local_state_fh.get("contentType"),
                    ),
                    self,
                )
                properties["dataFileHandleId"] = fileHandle["id"]
                local_state["_file_handle"] = fileHandle

            elif "dataFileHandleId" not in properties:
                # Handle the case where the Entity lacks an ID
                # But becomes an update() due to conflict
                properties["dataFileHandleId"] = bundle["entity"]["dataFileHandleId"]

            # update the file_handle metadata if the FileEntity's FileHandle id has changed
            local_state_fh_id = local_state.get("_file_handle", {}).get("id")
            if (
                local_state_fh_id
                and properties["dataFileHandleId"] != local_state_fh_id
            ):
                local_state["_file_handle"] = find_data_file_handle(
                    self._getEntityBundle(
                        properties["id"],
                        requestedObjects={
                            "includeEntity": True,
                            "includeFileHandles": True,
                        },
                    )
                )

                # check if we already have the filehandleid cached somewhere
                cached_path = self.cache.get(properties["dataFileHandleId"])
                if cached_path is None:
                    local_state["path"] = None
                    local_state["cacheDir"] = None
                    local_state["files"] = []
                else:
                    local_state["path"] = cached_path
                    local_state["cacheDir"] = os.path.dirname(cached_path)
                    local_state["files"] = [os.path.basename(cached_path)]

        # Create or update Entity in Synapse
        if "id" in properties:
            trace.get_current_span().set_attributes({"synapse.id": properties["id"]})
            properties = self._updateEntity(properties, forceVersion, versionLabel)
        else:
            # If Link, get the target name, version number and concrete type and store in link properties
            if properties["concreteType"] == "org.sagebionetworks.repo.model.Link":
                target_properties = self._getEntity(
                    properties["linksTo"]["targetId"],
                    version=properties["linksTo"].get("targetVersionNumber"),
                )
                if target_properties["parentId"] == properties["parentId"]:
                    raise ValueError(
                        "Cannot create a Link to an entity under the same parent."
                    )
                properties["linksToClassName"] = target_properties["concreteType"]
                if (
                    target_properties.get("versionNumber") is not None
                    and properties["linksTo"].get("targetVersionNumber") is not None
                ):
                    properties["linksTo"]["targetVersionNumber"] = target_properties[
                        "versionNumber"
                    ]
                properties["name"] = target_properties["name"]
            try:
                properties = self._createEntity(properties)
            except SynapseHTTPError as ex:
                if createOrUpdate and ex.response.status_code == 409:
                    # Get the existing Entity's ID via the name and parent
                    existing_entity_id = self.findEntityId(
                        properties["name"], properties.get("parentId", None)
                    )
                    if existing_entity_id is None:
                        raise

                    # get existing properties and annotations
                    if not bundle:
                        bundle = self._getEntityBundle(
                            existing_entity_id,
                            requestedObjects={
                                "includeEntity": True,
                                "includeAnnotations": True,
                            },
                        )

                    properties = {**bundle["entity"], **properties}

                    # we additionally merge the annotations under the assumption that a missing annotation
                    # from a resolved conflict represents an newer annotation that should be preserved
                    # rather than an intentionally deleted annotation.
                    annotations = {
                        **from_synapse_annotations(bundle["annotations"]),
                        **annotations,
                    }

                    properties = self._updateEntity(
                        properties, forceVersion, versionLabel
                    )

                else:
                    raise

        # Deal with access restrictions
        if isRestricted:
            self._createAccessRequirementIfNone(properties)

        # Update annotations
        if set_annotations and (
            (not bundle and annotations)
            or (
                bundle and check_annotations_changed(bundle["annotations"], annotations)
            )
        ):
            annotations = self.set_annotations(
                Annotations(properties["id"], properties["etag"], annotations)
            )
            properties["etag"] = annotations.etag

        # If the parameters 'used' or 'executed' are given, create an Activity object
        if used or executed:
            if activity is not None:
                raise SynapseProvenanceError(
                    "Provenance can be specified as an Activity object or as used/executed"
                    " item(s), but not both."
                )
            activity = Activity(
                name=activityName,
                description=activityDescription,
                used=used,
                executed=executed,
            )

        # If we have an Activity, set it as the Entity's provenance record
        if activity:
            self.setProvenance(properties, activity)

            # 'etag' has changed, so get the new Entity
            properties = self._getEntity(properties)

        # Return the updated Entity object
        entity = Entity.create(properties, annotations, local_state)
        return_data = self.get(entity, downloadFile=False)

        trace.get_current_span().set_attributes(
            {
                "synapse.id": return_data.get("id", ""),
                "synapse.concrete_type": entity.get("concreteType", ""),
            }
        )
        return return_data

    def _createAccessRequirementIfNone(self, entity: Union[Entity, str]) -> None:
        """
        Checks to see if the given entity has access requirements. If not, then one is added

        Arguments:
            entity: A Synapse ID or a Synapse Entity object
        """
        existingRestrictions = self.restGET(
            "/entity/%s/accessRequirement?offset=0&limit=1" % id_of(entity)
        )
        if len(existingRestrictions["results"]) <= 0:
            self.restPOST("/entity/%s/lockAccessRequirement" % id_of(entity), body="")

    def _getEntityBundle(
        self,
        entity: Union[Entity, str],
        version: int = None,
        requestedObjects: Dict[str, bool] = None,
    ) -> Dict[str, Union[dict, str, int, bool]]:
        """
        Gets some information about the Entity.

        Arguments:
            entity:           A Synapse Entity or Synapse ID
            version:          The entity's version. Defaults to None meaning most recent version.
            requestedObjects: A dictionary indicating settings for what to include.

        Default value for requestedObjects is:

            requestedObjects = {'includeEntity': True,
                                'includeAnnotations': True,
                                'includeFileHandles': True,
                                'includeRestrictionInformation': True}

        Keys available for requestedObjects:

            includeEntity
            includeAnnotations
            includePermissions
            includeEntityPath
            includeHasChildren
            includeAccessControlList
            includeFileHandles
            includeTableBundle
            includeRootWikiId
            includeBenefactorACL
            includeDOIAssociation
            includeFileName
            includeThreadCount
            includeRestrictionInformation


        Keys with values set to False may simply be omitted.
        For example, we might ask for an entity bundle containing file handles, annotations, and properties:
            requested_objects = {'includeEntity':True
                                 'includeAnnotations':True,
                                 'includeFileHandles':True}
            bundle = syn._getEntityBundle('syn111111', )

        Returns:
            An EntityBundle with the requested fields or by default Entity header, annotations, unmet access
            requirements, and file handles
        """
        # If 'entity' is given without an ID, try to find it by 'parentId' and 'name'.
        # Use case:
        #     If the user forgets to catch the return value of a syn.store(e)
        #     this allows them to recover by doing: e = syn.get(e)
        if requestedObjects is None:
            requestedObjects = {
                "includeEntity": True,
                "includeAnnotations": True,
                "includeFileHandles": True,
                "includeRestrictionInformation": True,
            }
        if (
            isinstance(entity, collections.abc.Mapping)
            and "id" not in entity
            and "name" in entity
        ):
            entity = self.findEntityId(entity["name"], entity.get("parentId", None))

        # Avoid an exception from finding an ID from a NoneType
        try:
            id_of(entity)
        except ValueError:
            return None

        if version is not None:
            uri = f"/entity/{id_of(entity)}/version/{int(version):d}/bundle2"
        else:
            uri = f"/entity/{id_of(entity)}/bundle2"
        bundle = self.restPOST(uri, body=json.dumps(requestedObjects))

        return bundle

    def delete(
        self,
        obj,
        version=None,
    ):
        """
        Removes an object from Synapse.

        Arguments:
            obj: An existing object stored on Synapse such as Evaluation, File, Project, or Wiki
            version: For entities, specify a particular version to delete.
        """
        # Handle all strings as the Entity ID for backward compatibility
        if isinstance(obj, str):
            entity_id = id_of(obj)
            trace.get_current_span().set_attributes({"synapse.id": entity_id})
            if version:
                self.restDELETE(uri=f"/entity/{entity_id}/version/{version}")
            else:
                self.restDELETE(uri=f"/entity/{entity_id}")
        elif hasattr(obj, "_synapse_delete"):
            return obj._synapse_delete(self)
        else:
            try:
                if isinstance(obj, Versionable):
                    self.restDELETE(obj.deleteURI(versionNumber=version))
                else:
                    self.restDELETE(obj.deleteURI())
            except AttributeError:
                raise SynapseError(
                    f"Can't delete a {type(obj)}. Please specify a Synapse object or id"
                )

    _user_name_cache = {}

    def _get_user_name(self, user_id: str) -> str:
        """
        Get username with ownerId

        Arguments:
            user_id: The ownerId of a user

        Returns:
            A username
        """
        if user_id not in self._user_name_cache:
            self._user_name_cache[user_id] = utils.extract_user_name(
                self.getUserProfile(user_id)
            )
        return self._user_name_cache[user_id]

    def _list(
        self,
        parent: str,
        recursive: bool = False,
        long_format: bool = False,
        show_modified: bool = False,
        indent: float = 0,
        out=sys.stdout,
    ) -> None:
        """
        List child objects of the given parent, recursively if requested.

        Arguments:
            parent:        A Synapse ID for folder or project that you want to list child objects for
            recursive:     Whether to show subfolder
            long_format:   Whether to show createdOn, createdBy and version
            show_modified: Whether to show modifiedOn and modifiedBy
            indent:        The left padding of the file tree structure
            out:           The location to write the output.
        """
        fields = ["id", "name", "nodeType"]
        if long_format:
            fields.extend(["createdByPrincipalId", "createdOn", "versionNumber"])
        if show_modified:
            fields.extend(["modifiedByPrincipalId", "modifiedOn"])
        results = self.getChildren(parent)

        results_found = False
        for result in results:
            results_found = True

            fmt_fields = {
                "name": result["name"],
                "id": result["id"],
                "padding": " " * indent,
                "slash_or_not": "/" if is_container(result) else "",
            }
            fmt_string = "{id}"

            if long_format:
                fmt_fields["createdOn"] = utils.iso_to_datetime(
                    result["createdOn"]
                ).strftime("%Y-%m-%d %H:%M")
                fmt_fields["createdBy"] = self._get_user_name(result["createdBy"])[:18]
                fmt_fields["version"] = result["versionNumber"]
                fmt_string += " {version:3}  {createdBy:>18} {createdOn}"
            if show_modified:
                fmt_fields["modifiedOn"] = utils.iso_to_datetime(
                    result["modifiedOn"]
                ).strftime("%Y-%m-%d %H:%M")
                fmt_fields["modifiedBy"] = self._get_user_name(result["modifiedBy"])[
                    :18
                ]
                fmt_string += "  {modifiedBy:>18} {modifiedOn}"

            fmt_string += "  {padding}{name}{slash_or_not}\n"
            out.write(fmt_string.format(**fmt_fields))

            if (indent == 0 or recursive) and is_container(result):
                self._list(
                    result["id"],
                    recursive=recursive,
                    long_format=long_format,
                    show_modified=show_modified,
                    indent=indent + 2,
                    out=out,
                )

        if indent == 0 and not results_found:
            out.write(
                "No results visible to {username} found for id {id}\n".format(
                    username=self.credentials.username, id=id_of(parent)
                )
            )

    def uploadFileHandle(
        self, path, parent, synapseStore=True, mimetype=None, md5=None, file_size=None
    ):
        """Uploads the file in the provided path (if necessary) to a storage location based on project settings.
        Returns a new FileHandle as a dict to represent the stored file.

        Arguments:
            parent: Parent of the entity to which we upload.
            path:   File path to the file being uploaded
            synapseStore: If False, will not upload the file, but instead create an ExternalFileHandle that references
                            the file on the local machine.
                            If True, will upload the file based on StorageLocation determined by the entity_parent_id
            mimetype: The MIME type metadata for the uploaded file
            md5: The MD5 checksum for the file, if known. Otherwise if the file is a local file, it will be calculated
                    automatically.
            file_size: The size the file, if known. Otherwise if the file is a local file, it will be calculated
                        automatically.
            file_type: The MIME type the file, if known. Otherwise if the file is a local file, it will be calculated
                        automatically.

        Returns:
            A dict of a new FileHandle as a dict that represents the uploaded file
        """
        return wrap_async_to_sync(
            upload_file_handle_async(
                self, parent, path, synapseStore, md5, file_size, mimetype
            ),
            self,
        )

    ############################################################
    #                  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

        Arguments:
            list_of_files: 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

        Arguments:
            quoteCharacter:  The character to be used for quoted elements in the resulting file.
            escapeCharacter: The escape character to be used for escaping a separator or quote in the resulting file.
            lineEnd:         The line feed terminator to be used for the resulting file.
            separator:       The delimiter to be used for separating entries in the resulting file.
            header:          Is the first line a header?

        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 = get_file_handle_for_download(
            file_handle_id=manifest["resultFileHandleId"],
            synapse_id=manifest["resultFileHandleId"],
            entity_type="FileEntity",
            synapse_client=self,
        )
        # 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"),
        )
        trace.get_current_span().set_attributes(
            {"synapse.file_handle_id": file_result["fileHandleId"]}
        )
        return downloaded_path

    def get_download_list(self, downloadLocation: str = None) -> str:
        """Download all files from your Synapse download list

        Arguments:
            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.exception("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
        if downloaded_files:
            # Only want to invoke this if there is a list of files to remove
            # or the API call will error
            self.remove_from_download_list(list_of_files=downloaded_files)
        else:
            self.logger.warning("A manifest was created, but no files were downloaded")

        # Always remove original manifest file
        os.remove(dl_list_path)

        return new_manifest_path

    ############################################################
    #                  Get / Set Annotations                   #
    ############################################################

    def _getRawAnnotations(
        self, entity: Union[Entity, str], version: int = None
    ) -> Dict[str, Union[str, dict]]:
        """
        Retrieve annotations for an Entity returning them in the native Synapse format.

        Arguments:
            entity:  A Synapse Entity or Synapse ID
            version: The entity's version. Defaults to None meaning most recent version.

        Returns:
            An annotation dictionary
        """
        # Note: Specifying the version results in a zero-ed out etag,
        # even if the version is the most recent.
        # See [PLFM-1874](https://sagebionetworks.jira.com/browse/PLFM-1874) for more details.
        if version:
            uri = f"/entity/{id_of(entity)}/version/{str(version)}/annotations2"
        else:
            uri = f"/entity/{id_of(entity)}/annotations2"
        return self.restGET(uri)

    def get_annotations(
        self, entity: typing.Union[str, Entity], version: typing.Union[str, int] = None
    ) -> Annotations:
        """
        Retrieve annotations for an Entity from the Synapse Repository as a Python dict.

        Note that collapsing annotations from the native Synapse format to a Python dict may involve some loss of
        information. See `_getRawAnnotations` to get annotations in the native format.

        Arguments:
            entity: An Entity or Synapse ID to lookup
            version: The version of the Entity to retrieve.

        Returns:
            A [synapseclient.annotations.Annotations][] object, a dict that also has id and etag attributes
        """
        return from_synapse_annotations(self._getRawAnnotations(entity, version))

    def set_annotations(self, annotations: Annotations):
        """
        Store annotations for an Entity in the Synapse Repository.

        Arguments:
            annotations: A [synapseclient.annotations.Annotations][] of annotation names and values,
                            with the id and etag attribute set

        Returns:
            The updated [synapseclient.annotations.Annotations][] for the entity

        Example: Using this function
            Getting annotations, adding a new annotation, and updating the annotations:

                annos = syn.get_annotations('syn123')

            `annos` will contain the id and etag associated with the entity upon retrieval

                print(annos.id)
                > syn123
                print(annos.etag)
                > 7bdb83e9-a50a-46e4-987a-4962559f090f   (Usually some UUID in the form of a string)

            Returned `annos` object from `get_annotations()` can be used as if it were a dict.
            Set key 'foo' to have value of 'bar' and 'baz'

                annos['foo'] = ['bar', 'baz']

            Single values will automatically be wrapped in a list once stored

                annos['qwerty'] = 'asdf'

            Store the annotations

                annos = syn.set_annotations(annos)

                print(annos)
                > {'foo':['bar','baz], 'qwerty':['asdf']}
        """

        if not isinstance(annotations, Annotations):
            raise TypeError("Expected a synapseclient.Annotations object")

        synapseAnnos = to_synapse_annotations(annotations)

        entity_id = id_of(annotations)
        trace.get_current_span().set_attributes({"synapse.id": entity_id})

        return from_synapse_annotations(
            self.restPUT(
                f"/entity/{entity_id}/annotations2",
                body=json.dumps(synapseAnnos),
            )
        )

    ############################################################
    #                         Querying                         #
    ############################################################

    def getChildren(
        self,
        parent,
        includeTypes=[
            "folder",
            "file",
            "table",
            "link",
            "entityview",
            "dockerrepo",
            "submissionview",
            "dataset",
            "materializedview",
        ],
        sortBy="NAME",
        sortDirection="ASC",
    ):
        """
        Retrieves all of the entities stored within a parent such as folder or project.

        Arguments:
            parent: An id or an object of a Synapse container or None to retrieve all projects
            includeTypes: Must be a list of entity types (ie. ["folder","file"]) which can be found [here](http://docs.synapse.org/rest/org/sagebionetworks/repo/model/EntityType.html)
            sortBy: How results should be sorted. Can be NAME, or CREATED_ON
            sortDirection: The direction of the result sort. Can be ASC, or DESC

        Yields:
            An iterator that shows all the children of the container.

        Also see:

        - [synapseutils.walk][]
        """
        parentId = id_of(parent) if parent is not None else None

        trace.get_current_span().set_attributes({"synapse.parent_id": parentId})
        entityChildrenRequest = {
            "parentId": parentId,
            "includeTypes": includeTypes,
            "sortBy": sortBy,
            "sortDirection": sortDirection,
            "nextPageToken": None,
        }
        entityChildrenResponse = {"nextPageToken": "first"}
        while entityChildrenResponse.get("nextPageToken") is not None:
            entityChildrenResponse = self.restPOST(
                "/entity/children", body=json.dumps(entityChildrenRequest)
            )
            for child in entityChildrenResponse["page"]:
                yield child
            if entityChildrenResponse.get("nextPageToken") is not None:
                entityChildrenRequest["nextPageToken"] = entityChildrenResponse[
                    "nextPageToken"
                ]

    def md5Query(self, md5):
        """
        Find the Entities which have attached file(s) which have the given MD5 hash.

        Arguments:
            md5: The MD5 to query for (hexadecimal string)

        Returns:
            A list of Entity headers
        """

        return self.restGET("/entity/md5/%s" % md5)["results"]

    ############################################################
    #                     ACL manipulation                     #
    ############################################################

    def _getBenefactor(
        self, entity: Union[Entity, str]
    ) -> Dict[str, Union[str, int, bool]]:
        """
        Get an Entity's benefactor.
        An Entity gets its ACL from its benefactor.

        Arguments:
            entity: A Synapse Entity or Synapse ID

        Returns:
            A dictionary of the Entity's benefactor

        """
        if utils.is_synapse_id_str(entity) or is_synapse_entity(entity):
            synid, _ = utils.get_synid_and_version(entity)
            return self.restGET("/entity/%s/benefactor" % synid)

        return entity

    def _getACL(self, entity: Union[Entity, str]) -> Dict[str, Union[str, list]]:
        """
        Get the effective Access Control Lists (ACL) for a Synapse Entity.

        Arguments:
            entity: A Synapse Entity or Synapse ID

        Returns:
            A dictionary of the Entity's ACL
        """
        if hasattr(entity, "getACLURI"):
            uri = entity.getACLURI()
        else:
            # Get the ACL from the benefactor (which may be the entity itself)
            benefactor = self._getBenefactor(entity)
            trace.get_current_span().set_attributes({"synapse.id": benefactor["id"]})
            uri = "/entity/%s/acl" % (benefactor["id"])
        return self.restGET(uri)

    def _storeACL(
        self, entity: Union[Entity, str], acl: Dict[str, Union[str, list]]
    ) -> Dict[str, Union[str, list]]:
        """
        Create or update the ACL for a Synapse Entity.

        Arguments:
            entity:  A Synapse Entity or Synapse ID
            acl:     An ACl as a dictionary

        The format of acl:

            {'resourceAccess': [
                {'accessType': ['READ'],
                 'principalId': 222222}
            ]}

        Returns:
            The new or updated ACL
        """
        if hasattr(entity, "putACLURI"):
            return self.restPUT(entity.putACLURI(), json.dumps(acl))
        else:
            # Get benefactor. (An entity gets its ACL from its benefactor.)
            entity_id = id_of(entity)
            uri = "/entity/%s/benefactor" % entity_id
            benefactor = self.restGET(uri)

            # Update or create new ACL
            uri = "/entity/%s/acl" % entity_id
            if benefactor["id"] == entity_id:
                return self.restPUT(uri, json.dumps(acl))
            else:
                return self.restPOST(uri, json.dumps(acl))

    def _getUserbyPrincipalIdOrName(self, principalId: str = None) -> int:
        """
        Given either a string, int or None finds the corresponding user where None implies PUBLIC

        Arguments:
            principalId: Identifier of a user or group

        Raises:
            SynapseError: Warn for unknown user principalId

        Returns:
            The integer ID of the user
        """
        if principalId is None or principalId == "PUBLIC":
            return PUBLIC
        try:
            return int(principalId)

        # If principalId is not a number assume it is a name or email
        except ValueError:
            userProfiles = self.restGET("/userGroupHeaders?prefix=%s" % principalId)
            totalResults = len(userProfiles["children"])
            if totalResults == 1:
                return int(userProfiles["children"][0]["ownerId"])
            elif totalResults > 1:
                for profile in userProfiles["children"]:
                    if profile["userName"] == principalId:
                        return int(profile["ownerId"])

            supplementalMessage = (
                "Please be more specific" if totalResults > 1 else "No matches"
            )
            raise SynapseError(
                "Unknown Synapse user (%s).  %s." % (principalId, supplementalMessage)
            )

    def get_acl(
        self,
        entity: Union[Entity, Evaluation, str, collections.abc.Mapping],
        principal_id: str = None,
    ) -> typing.List[str]:
        """
        Get the [ACL](https://rest-docs.synapse.org/rest/org/
        sagebionetworks/repo/model/ACCESS_TYPE.html)
        that a user or group has on an Entity.

        Arguments:
            entity:      An Entity or Synapse ID to lookup
            principal_id: Identifier of a user or group (defaults to PUBLIC users)

        Returns:
            An array containing some combination of
                ['READ', 'UPDATE', 'CREATE', 'DELETE', 'DOWNLOAD', 'MODERATE',
                'CHANGE_PERMISSIONS', 'CHANGE_SETTINGS']
                or an empty array
        """

        principal_id = self._getUserbyPrincipalIdOrName(principal_id)

        trace.get_current_span().set_attributes(
            {"synapse.id": id_of(entity), "synapse.principal_id": principal_id}
        )

        acl = self._getACL(entity)

        team_list = self._find_teams_for_principal(principal_id)
        team_ids = [int(team.id) for team in team_list]
        effective_permission_set = set()

        # This user_profile_bundle is being used to verify that the principal_id
        #  is a registered user of the system
        user_profile_bundle = self._get_user_bundle(principal_id, 1)

        # Loop over all permissions in the returned ACL and add it to the effective_permission_set
        # if the principalId in the ACL matches
        # 1) the one we are looking for,
        # 2) a team the entity is a member of,
        # 3) PUBLIC
        # 4) A user_profile_bundle exists for the principal_id
        for permissions in acl["resourceAccess"]:
            if "principalId" in permissions and (
                permissions["principalId"] == principal_id
                or permissions["principalId"] in team_ids
                or permissions["principalId"] == PUBLIC
                or (
                    permissions["principalId"] == AUTHENTICATED_USERS
                    and user_profile_bundle is not None
                )
            ):
                effective_permission_set = effective_permission_set.union(
                    permissions["accessType"]
                )
        return list(effective_permission_set)

    @deprecated(
        version="4.0.0",
        reason="deprecated and replaced with synapseclient.Synapse.get_acl",
    )
    def getPermissions(
        self,
        entity: Union[Entity, Evaluation, str, collections.abc.Mapping],
        principal_id: str = None,
    ) -> typing.List[str]:
        """
        **Deprecated** and replaced with [get_acl][synapseclient.Synapse.get_acl].


        Get the permissions that a user or group has on an Entity.

        Arguments:
            entity:      An Entity or Synapse ID to lookup
            principal_id: Identifier of a user or group (defaults to PUBLIC users)

        Returns:
            An array containing some combination of
                ['READ', 'UPDATE', 'CREATE', 'DELETE', 'DOWNLOAD', 'MODERATE',
                'CHANGE_PERMISSIONS', 'CHANGE_SETTINGS']
                or an empty array
        """

        return self.get_acl(entity=entity, principal_id=principal_id)

    def get_permissions(
        self, entity: Union[Entity, Evaluation, str, collections.abc.Mapping]
    ) -> Permissions:
        """
        Get the [permissions](https://rest-docs.synapse.org/rest/org/
        sagebionetworks/repo/model/auth/UserEntityPermissions.html)
        that the caller has on an Entity.

        Arguments:
            entity: An Entity or Synapse ID to lookup

        Returns:
            An Permissions object


        Example: Using this function:
            Getting permissions for a Synapse Entity

                permissions = syn.get_permissions(Entity)

            Getting permissions for a Synapse ID

                permissions = syn.get_permissions("syn12345")

            Getting access types list from the Permissions object

                permissions.access_types
        """

        entity_id = id_of(entity)

        trace.get_current_span().set_attributes({"synapse.id": entity_id})

        url = f"/entity/{entity_id}/permissions"
        data = self.restGET(url)
        return Permissions.from_dict(data)

    def setPermissions(
        self,
        entity,
        principalId=None,
        accessType=["READ", "DOWNLOAD"],
        modify_benefactor=False,
        warn_if_inherits=True,
        overwrite=True,
    ):
        """
        Sets permission that a user or group has on an Entity.
        An Entity may have its own ACL or inherit its ACL from a benefactor.

        Arguments:
            entity: An Entity or Synapse ID to modify
            principalId: Identifier of a user or group. '273948' is for all registered Synapse users
                            and '273949' is for public access. None implies public access.
            accessType: Type of permission to be granted. One or more of CREATE, READ, DOWNLOAD, UPDATE,
                            DELETE, CHANGE_PERMISSIONS
            modify_benefactor: Set as True when modifying a benefactor's ACL
            warn_if_inherits: Set as False, when creating a new ACL.
                                Trying to modify the ACL of an Entity that inherits its ACL will result in a warning
            overwrite: By default this function overwrites existing permissions for the specified user.
                        Set this flag to False to add new permissions non-destructively.

        Returns:
            An Access Control List object

        Example: Setting permissions
            Grant all registered users download access

                syn.setPermissions('syn1234','273948',['READ','DOWNLOAD'])

            Grant the public view access

                syn.setPermissions('syn1234','273949',['READ'])
        """
        entity_id = id_of(entity)
        trace.get_current_span().set_attributes({"synapse.id": entity_id})

        benefactor = self._getBenefactor(entity)
        if benefactor["id"] != entity_id:
            if modify_benefactor:
                entity = benefactor
            elif warn_if_inherits:
                self.logger.warning(
                    "Creating an ACL for entity %s, which formerly inherited access control from a"
                    ' benefactor entity, "%s" (%s).\n'
                    % (entity_id, benefactor["name"], benefactor["id"])
                )

        acl = self._getACL(entity)

        principalId = self._getUserbyPrincipalIdOrName(principalId)

        # Find existing permissions
        permissions_to_update = None
        for permissions in acl["resourceAccess"]:
            if (
                "principalId" in permissions
                and permissions["principalId"] == principalId
            ):
                permissions_to_update = permissions
                break

        if accessType is None or accessType == []:
            # remove permissions
            if permissions_to_update and overwrite:
                acl["resourceAccess"].remove(permissions_to_update)
        else:
            # add a 'resourceAccess' entry, if necessary
            if not permissions_to_update:
                permissions_to_update = {"accessType": [], "principalId": principalId}
                acl["resourceAccess"].append(permissions_to_update)
            if overwrite:
                permissions_to_update["accessType"] = accessType
            else:
                permissions_to_update["accessType"] = list(
                    set(permissions_to_update["accessType"]) | set(accessType)
                )
        return self._storeACL(entity, acl)

    ############################################################
    #                        Provenance                        #
    ############################################################

    # TODO: rename these to Activity
    def getProvenance(
        self,
        entity: typing.Union[str, collections.abc.Mapping, numbers.Number],
        version: int = None,
    ) -> Activity:
        """
        Retrieve provenance information for a Synapse Entity.

        Arguments:
            entity:  An Entity or Synapse ID to lookup
            version: The version of the Entity to retrieve. Gets the most recent version if omitted

        Returns:
            An Activity object or raises exception if no provenance record exists

        Raises:
            SynapseHTTPError: if no provenance record exists
        """
        # Get versionNumber from Entity
        if version is None and "versionNumber" in entity:
            version = entity["versionNumber"]
        entity_id = id_of(entity)
        if version:
            uri = "/entity/%s/version/%d/generatedBy" % (entity_id, version)
        else:
            uri = "/entity/%s/generatedBy" % entity_id

        trace.get_current_span().set_attributes({"synapse.id": entity_id})
        return Activity(data=self.restGET(uri))

    def setProvenance(
        self,
        entity: typing.Union[str, collections.abc.Mapping, numbers.Number],
        activity: Activity,
    ) -> Activity:
        """
        Stores a record of the code and data used to derive a Synapse entity.

        Arguments:
            entity:   An Entity or Synapse ID to modify
            activity: A [synapseclient.activity.Activity][]

        Returns:
            An updated [synapseclient.activity.Activity][] object
        """
        # Assert that the entity was generated by a given Activity.
        activity = self._saveActivity(activity)

        entity_id = id_of(entity)
        # assert that an entity is generated by an activity
        uri = "/entity/%s/generatedBy?generatedBy=%s" % (entity_id, activity["id"])
        activity = Activity(data=self.restPUT(uri))

        trace.get_current_span().set_attributes({"synapse.id": entity_id})
        return activity

    def deleteProvenance(
        self,
        entity: typing.Union[str, collections.abc.Mapping, numbers.Number],
    ) -> None:
        """
        Removes provenance information from an Entity and deletes the associated Activity.

        Arguments:
            entity: An Entity or Synapse ID to modify
        """
        activity = self.getProvenance(entity)
        if not activity:
            return
        entity_id = id_of(entity)
        trace.get_current_span().set_attributes({"synapse.id": entity_id})

        uri = "/entity/%s/generatedBy" % entity_id
        self.restDELETE(uri)

        # If the activity is shared by more than one entity you recieve an HTTP 400 error:
        # "If you wish to delete this activity, please first delete all Entities generated by this Activity.""
        uri = "/activity/%s" % activity["id"]
        self.restDELETE(uri)

    def _saveActivity(self, activity: Activity) -> Activity:
        """
        Save the Activity

        Arguments:
            activity: The Activity to be saved

        Returns:
            An Activity object
        """
        if "id" in activity:
            # We're updating provenance
            uri = "/activity/%s" % activity["id"]
            activity = Activity(data=self.restPUT(uri, json.dumps(activity)))
        else:
            activity = self.restPOST("/activity", body=json.dumps(activity))
        return activity

    def updateActivity(self, activity) -> Activity:
        """
        Modifies an existing Activity.

        Arguments:
            activity: The Activity to be updated.

        Returns:
            An updated Activity object
        """
        if "id" not in activity:
            raise ValueError("The activity you want to update must exist on Synapse")
        trace.get_current_span().set_attributes({"synapse.id": activity["id"]})
        return self._saveActivity(activity)

    def _convertProvenanceList(self, usedList: list, limitSearch: str = None) -> list:
        """
        Convert a list of Synapse IDs, URLs and local files by replacing local files with Synapse IDs

        Arguments:
            usedList:    A list of Synapse IDs, URLs and local files
            limitSearch: Limits the places in Synapse where the file is searched for.

        Returns:
            A converted list with local files being replaced with Synapse IDs
        """
        if usedList is None:
            return None
        usedList = [
            self.get(target, limitSearch=limitSearch)
            if (os.path.isfile(target) if isinstance(target, str) else False)
            else target
            for target in usedList
        ]
        return usedList

    ############################################################
    #                File handle service calls                 #
    ############################################################

    @deprecated(
        version="4.4.0",
        reason="To be removed in 5.0.0. "
        "Moved to synapseclient/api/file_services.py::get_file_handle_for_download",
    )
    def _getFileHandleDownload(
        self, fileHandleId: str, objectId: str, objectType: str = None
    ) -> Dict[str, str]:
        """
        Gets the URL and the metadata as filehandle object for a filehandle or fileHandleId

        Arguments:
            fileHandleId:   ID of fileHandle to download
            objectId:       The ID of the object associated with the file e.g. syn234
            objectType:     Type of object associated with a file e.g. FileEntity, TableEntity

        Raises:
            SynapseFileNotFoundError: If the fileHandleId is not found in Synapse.
            SynapseError:             If the user does not have the permission to access the fileHandleId.

        Returns:
            A dictionary with keys: fileHandle, fileHandleId and preSignedURL
        """
        body = {
            "includeFileHandles": True,
            "includePreSignedURLs": True,
            "requestedFiles": [
                {
                    "fileHandleId": fileHandleId,
                    "associateObjectId": objectId,
                    "associateObjectType": objectType or "FileEntity",
                }
            ],
        }
        response = self.restPOST(
            "/fileHandle/batch", body=json.dumps(body), endpoint=self.fileHandleEndpoint
        )
        result = response["requestedFiles"][0]
        failure = result.get("failureCode")
        if failure == "NOT_FOUND":
            raise SynapseFileNotFoundError(
                "The fileHandleId %s could not be found" % fileHandleId
            )
        elif failure == "UNAUTHORIZED":
            raise SynapseError(
                "You are not authorized to access fileHandleId %s associated with the Synapse"
                " %s: %s" % (fileHandleId, objectType, objectId)
            )
        return result

    @staticmethod
    @deprecated(
        version="4.4.0",
        reason="To be removed in 5.0.0. "
        "Moved to synapseclient/core/download/download_functions.py::is_retryable_download_error",
    )
    def _is_retryable_download_error(ex: Exception) -> bool:
        """
        Check if the download error is retryable

        Arguments:
            ex: An exception

        Returns:
            Boolean value indicating whether the download error is retryable
        """
        # some exceptions caught during download indicate non-recoverable situations that
        # will not be remedied by a repeated download attempt.
        return not (
            (isinstance(ex, OSError) and ex.errno == errno.ENOSPC)
            or isinstance(ex, SynapseMd5MismatchError)  # out of disk space
        )

    @deprecated(
        version="4.4.0",
        reason="To be removed in 5.0.0. "
        "Moved to synapseclient/core/download/download_functions.py::download_by_file_handle",
    )
    def _downloadFileHandle(
        self,
        fileHandleId: str,
        objectId: str,
        objectType: str,
        destination: str,
        retries: int = 5,
    ) -> str:
        """
        Download a file from the given URL to the local file system.

        Arguments:
            fileHandleId: The id of the FileHandle to download
            objectId:     The id of the Synapse object that uses the FileHandle e.g. "syn123"
            objectType:   The type of the Synapse object that uses the FileHandle e.g. "FileEntity"
            destination:  The destination on local file system
            retries:      The Number of download retries attempted before throwing an exception.

        Returns:
            The path to downloaded file
        """
        os.makedirs(os.path.dirname(destination), exist_ok=True)

        while retries > 0:
            try:
                fileResult = self._getFileHandleDownload(
                    fileHandleId, objectId, objectType
                )
                fileHandle = fileResult["fileHandle"]
                concreteType = fileHandle["concreteType"]
                storageLocationId = fileHandle.get("storageLocationId")

                if concreteType == concrete_types.EXTERNAL_OBJECT_STORE_FILE_HANDLE:
                    profile = get_client_authenticated_s3_profile(
                        endpoint=fileHandle["endpointUrl"],
                        bucket=fileHandle["bucket"],
                        config_path=self.configPath,
                    )
                    downloaded_path = S3ClientWrapper.download_file(
                        fileHandle["bucket"],
                        fileHandle["endpointUrl"],
                        fileHandle["fileKey"],
                        destination,
                        profile_name=profile,
                        show_progress=not self.silent,
                    )

                elif (
                    sts_transfer.is_boto_sts_transfer_enabled(self)
                    and sts_transfer.is_storage_location_sts_enabled(
                        self, objectId, storageLocationId
                    )
                    and concreteType == concrete_types.S3_FILE_HANDLE
                ):

                    def download_fn(credentials):
                        return S3ClientWrapper.download_file(
                            fileHandle["bucketName"],
                            None,
                            fileHandle["key"],
                            destination,
                            credentials=credentials,
                            show_progress=not self.silent,
                            # pass through our synapse threading config to boto s3
                            transfer_config_kwargs={
                                "max_concurrency": self.max_threads
                            },
                        )

                    downloaded_path = sts_transfer.with_boto_sts_credentials(
                        download_fn,
                        self,
                        objectId,
                        "read_only",
                    )

                elif (
                    self.multi_threaded
                    and concreteType == concrete_types.S3_FILE_HANDLE
                    and fileHandle.get("contentSize", 0)
                    > multithread_download.SYNAPSE_DEFAULT_DOWNLOAD_PART_SIZE
                ):
                    # run the download multi threaded if the file supports it, we're configured to do so,
                    # and the file is large enough that it would be broken into parts to take advantage of
                    # multiple downloading threads. otherwise it's more efficient to run the download as a simple
                    # single threaded URL download.
                    downloaded_path = self._download_from_url_multi_threaded(
                        fileHandleId,
                        objectId,
                        objectType,
                        destination,
                        expected_md5=fileHandle.get("contentMd5"),
                    )

                else:
                    downloaded_path = self._download_from_URL(
                        fileResult["preSignedURL"],
                        destination,
                        fileHandle["id"],
                        expected_md5=fileHandle.get("contentMd5"),
                    )
                self.cache.add(fileHandle["id"], downloaded_path)
                return downloaded_path

            except Exception as ex:
                if not self._is_retryable_download_error(ex):
                    raise

                exc_info = sys.exc_info()
                ex.progress = 0 if not hasattr(ex, "progress") else ex.progress
                self.logger.debug(
                    "\nRetrying download on error: [%s] after progressing %i bytes"
                    % (exc_info[0], ex.progress),
                    exc_info=True,
                )  # this will include stack trace
                if ex.progress == 0:  # No progress was made reduce remaining retries.
                    retries -= 1
                if retries <= 0:
                    # Re-raise exception
                    raise

        raise Exception("should not reach this line")

    @deprecated(
        version="4.4.0",
        reason="To be removed in 5.0.0. "
        "Moved to synapseclient/core/download/download_functions.py::download_from_url_multi_threaded",
    )
    def _download_from_url_multi_threaded(
        self,
        file_handle_id: str,
        object_id: str,
        object_type: str,
        destination: str,
        *,
        expected_md5: str = None,
    ) -> str:
        """
        Download a file from the given URL using multiple threads.

        Arguments:
            file_handle_id: The id of the FileHandle to download
            object_id:      The id of the Synapse object that uses the FileHandle e.g. "syn123"
            object_type:    The type of the Synapse object that uses the FileHandle e.g. "FileEntity"
            destination:    The destination on local file system
            expected_md5:   The expected MD5
        Raises:
            SynapseMd5MismatchError: If the actual MD5 does not match expected MD5.

        Returns:
            The path to downloaded file
        """
        destination = os.path.abspath(destination)
        temp_destination = utils.temp_download_filename(destination, file_handle_id)

        request = multithread_download.DownloadRequest(
            file_handle_id=int(file_handle_id),
            object_id=object_id,
            object_type=object_type,
            path=temp_destination,
            debug=self.debug,
        )

        multithread_download.download_file(self, request)

        if (
            expected_md5
        ):  # if md5 not set (should be the case for all except http download)
            actual_md5 = utils.md5_for_file(temp_destination).hexdigest()
            # check md5 if given
            if actual_md5 != expected_md5:
                try:
                    os.remove(temp_destination)
                except FileNotFoundError:
                    # file already does not exist. nothing to do
                    pass
                raise SynapseMd5MismatchError(
                    "Downloaded file {filename}'s md5 {md5} does not match expected MD5 of"
                    " {expected_md5}".format(
                        filename=temp_destination,
                        md5=actual_md5,
                        expected_md5=expected_md5,
                    )
                )
        # once download completed, rename to desired destination
        shutil.move(temp_destination, destination)

        return destination

    @deprecated(
        version="4.4.0",
        reason="To be removed in 5.0.0. "
        "Moved to synapseclient/core/download/download_functions.py::is_synapse_uri",
    )
    def _is_synapse_uri(self, uri: str) -> bool:
        """
        Check whether the given uri is hosted at the configured Synapse repo endpoint

        Arguments:
            uri: A given uri

        Returns:
            A boolean value indicating whether the given uri is hosted at the configured Synapse repo endpoint
        """
        uri_domain = urllib_urlparse.urlparse(uri).netloc
        synapse_repo_domain = urllib_urlparse.urlparse(self.repoEndpoint).netloc
        return uri_domain.lower() == synapse_repo_domain.lower()

    @deprecated(
        version="4.4.0",
        reason="To be removed in 5.0.0. "
        "Moved to synapseclient/core/download/download_functions.py::download_from_url",
    )
    def _download_from_URL(
        self,
        url: str,
        destination: str,
        fileHandleId: Optional[str] = None,
        expected_md5: Optional[str] = None,
    ) -> str:
        """
        Download a file from the given URL to the local file system.

        Arguments:
            url:           The source of download
            destination:   The destination on local file system
            fileHandleId:  Optional. If given, the file will be given a temporary name that includes the file
                                    handle id which allows resuming partial downloads of the same file from previous
                                    sessions
            expected_md5:  Optional. If given, check that the MD5 of the downloaded file matches the expected MD5

        Raises:
            IOError:                 If the local file does not exist.
            SynapseError:            If fail to download the file.
            SynapseHTTPError:        If there are too many redirects.
            SynapseMd5MismatchError: If the actual MD5 does not match expected MD5.

        Returns:
            The path to downloaded file
        """
        destination = os.path.abspath(destination)
        actual_md5 = None
        redirect_count = 0
        delete_on_md5_mismatch = True
        self.logger.debug(f"Downloading from {url} to {destination}")
        while redirect_count < REDIRECT_LIMIT:
            redirect_count += 1
            scheme = urllib_urlparse.urlparse(url).scheme
            if scheme == "file":
                delete_on_md5_mismatch = False
                destination = utils.file_url_to_path(url, verify_exists=True)
                if destination is None:
                    raise IOError("Local file (%s) does not exist." % url)
                break
            elif scheme == "sftp":
                username, password = self._getUserCredentials(url)
                destination = SFTPWrapper.download_file(
                    url, destination, username, password, show_progress=not self.silent
                )
                break
            elif scheme == "ftp":
                transfer_start_time = time.time()

                def _ftp_report_hook(
                    block_number: int, read_size: int, total_size: int
                ) -> None:
                    show_progress = not self.silent
                    if show_progress:
                        self._print_transfer_progress(
                            transferred=block_number * read_size,
                            toBeTransferred=total_size,
                            prefix="Downloading ",
                            postfix=os.path.basename(destination),
                            dt=time.time() - transfer_start_time,
                        )

                urllib_request.urlretrieve(
                    url=url, filename=destination, reporthook=_ftp_report_hook
                )
                break
            elif scheme == "http" or scheme == "https":
                # if a partial download exists with the temporary name,
                temp_destination = utils.temp_download_filename(
                    destination, fileHandleId
                )
                range_header = (
                    {
                        "Range": "bytes={start}-".format(
                            start=os.path.getsize(temp_destination)
                        )
                    }
                    if os.path.exists(temp_destination)
                    else {}
                )

                # pass along synapse auth credentials only if downloading directly from synapse
                auth = self.credentials if self._is_synapse_uri(url) else None
                response = with_retry(
                    lambda: self._requests_session.get(
                        url,
                        headers=self._generate_headers(range_header),
                        stream=True,
                        allow_redirects=False,
                        auth=auth,
                    ),
                    verbose=self.debug,
                    **STANDARD_RETRY_PARAMS,
                )
                try:
                    exceptions._raise_for_status(response, verbose=self.debug)
                except SynapseHTTPError as err:
                    if err.response.status_code == 404:
                        raise SynapseError("Could not download the file at %s" % url)
                    elif (
                        err.response.status_code == 416
                    ):  # Requested Range Not Statisfiable
                        # this is a weird error when the client already finished downloading but the loop continues
                        # When this exception occurs, the range we request is guaranteed to be >= file size so we
                        # assume that the file has been fully downloaded, rename it to destination file
                        # and break out of the loop to perform the MD5 check.
                        # If it fails the user can retry with another download.
                        shutil.move(temp_destination, destination)
                        break
                    raise

                # handle redirects
                if response.status_code in [301, 302, 303, 307, 308]:
                    url = response.headers["location"]
                    # don't break, loop again
                else:
                    # get filename from content-disposition, if we don't have it already
                    if os.path.isdir(destination):
                        filename = utils.extract_filename(
                            content_disposition_header=response.headers.get(
                                "content-disposition", None
                            ),
                            default_filename=utils.guess_file_name(url),
                        )
                        destination = os.path.join(destination, filename)
                    # Stream the file to disk
                    if "content-length" in response.headers:
                        toBeTransferred = float(response.headers["content-length"])
                    else:
                        toBeTransferred = -1
                    transferred = 0

                    # Servers that respect the Range header return 206 Partial Content
                    if response.status_code == 206:
                        mode = "ab"
                        previouslyTransferred = os.path.getsize(temp_destination)
                        toBeTransferred += previouslyTransferred
                        transferred += previouslyTransferred
                        sig = utils.md5_for_file(temp_destination)
                    else:
                        mode = "wb"
                        previouslyTransferred = 0
                        sig = hashlib.new("md5", usedforsecurity=False)  # nosec

                    try:
                        with open(temp_destination, mode) as fd:
                            t0 = time.time()
                            for nChunks, chunk in enumerate(
                                response.iter_content(FILE_BUFFER_SIZE)
                            ):
                                fd.write(chunk)
                                sig.update(chunk)

                                # the 'content-length' header gives the total number of bytes that will be transferred
                                # to us len(chunk) cannot be used to track progress because iter_content automatically
                                # decodes the chunks if the response body is encoded so the len(chunk) could be
                                # different from the total number of bytes we've read read from the response body
                                # response.raw.tell() is the total number of response body bytes transferred over the
                                # wire so far
                                transferred = (
                                    response.raw.tell() + previouslyTransferred
                                )
                                self._print_transfer_progress(
                                    transferred,
                                    toBeTransferred,
                                    "Downloading ",
                                    os.path.basename(destination),
                                    dt=time.time() - t0,
                                )
                    except (
                        Exception
                    ) as ex:  # We will add a progress parameter then push it back to retry.
                        ex.progress = transferred - previouslyTransferred
                        raise

                    # verify that the file was completely downloaded and retry if it is not complete
                    if toBeTransferred > 0 and transferred < toBeTransferred:
                        self.logger.warning(
                            "\nRetrying download because the connection ended early.\n"
                        )
                        continue

                    actual_md5 = sig.hexdigest()
                    # rename to final destination
                    shutil.move(temp_destination, destination)
                    break
            else:
                self.logger.error("Unable to download URLs of type %s" % scheme)
                return None

        else:  # didn't break out of loop
            raise SynapseHTTPError("Too many redirects")

        if (
            actual_md5 is None
        ):  # if md5 not set (should be the case for all except http download)
            actual_md5 = utils.md5_for_file(destination).hexdigest()

        # check md5 if given
        if expected_md5 and actual_md5 != expected_md5:
            if delete_on_md5_mismatch and os.path.exists(destination):
                os.remove(destination)
            raise SynapseMd5MismatchError(
                "Downloaded file {filename}'s md5 {md5} does not match expected MD5 of"
                " {expected_md5}".format(
                    filename=destination, md5=actual_md5, expected_md5=expected_md5
                )
            )

        return destination

    def _createExternalFileHandle(
        self,
        externalURL: str,
        mimetype: str = None,
        md5: str = None,
        fileSize: int = None,
    ) -> Dict[str, Union[str, int]]:
        """
        Create a new FileHandle representing an external URL.

        Arguments:
            externalURL: An external URL
            mimetype:    The Mimetype of the file, if known.
            md5:         The file's content MD5.
            fileSize:    The size of the file in bytes.

        Returns:
            A FileHandle for files that are stored externally.
        """
        fileName = externalURL.split("/")[-1]
        externalURL = utils.as_url(externalURL)
        fileHandle = {
            "concreteType": concrete_types.EXTERNAL_FILE_HANDLE,
            "fileName": fileName,
            "externalURL": externalURL,
            "contentMd5": md5,
            "contentSize": fileSize,
        }
        if mimetype is None:
            (mimetype, enc) = mimetypes.guess_type(externalURL, strict=False)
        if mimetype is not None:
            fileHandle["contentType"] = mimetype
        return self.restPOST(
            "/externalFileHandle", json.dumps(fileHandle), self.fileHandleEndpoint
        )

    def _createExternalObjectStoreFileHandle(
        self,
        s3_file_key,
        file_path: str,
        storage_location_id: int,
        mimetype: str = None,
        md5: str = None,
    ) -> Dict[str, Union[str, int]]:
        """
        Create a new FileHandle representing an external object.

        Arguments:
            s3_file_key:         S3 key of the uploaded object
            file_path:           The local path of the uploaded file
            storage_location_id: The optional storage location descriptor
            mimetype:            The Mimetype of the file, if known.
            md5:                 The file's content MD5, if known.

        Returns:
            A FileHandle for objects that are stored externally.
        """
        if mimetype is None:
            mimetype, _ = mimetypes.guess_type(file_path, strict=False)
        file_handle = {
            "concreteType": concrete_types.EXTERNAL_OBJECT_STORE_FILE_HANDLE,
            "fileKey": s3_file_key,
            "fileName": os.path.basename(file_path),
            "contentMd5": md5 or utils.md5_for_file(file_path).hexdigest(),
            "contentSize": os.stat(file_path).st_size,
            "storageLocationId": storage_location_id,
            "contentType": mimetype,
        }

        return self.restPOST(
            "/externalFileHandle", json.dumps(file_handle), self.fileHandleEndpoint
        )

    def create_external_s3_file_handle(
        self,
        bucket_name,
        s3_file_key,
        file_path,
        *,
        parent=None,
        storage_location_id=None,
        mimetype=None,
        md5: str = None,
    ):
        """
        Create an external S3 file handle for e.g. a file that has been uploaded directly to
        an external S3 storage location.

        Arguments:
            bucket_name: Name of the S3 bucket
            s3_file_key: S3 key of the uploaded object
            file_path: Local path of the uploaded file
            parent: Parent entity to create the file handle in, the file handle will be created
                    in the default storage location of the parent. Mutually exclusive with
                    storage_location_id
            storage_location_id: Explicit storage location id to create the file handle in, mutually exclusive
                    with parent
            mimetype: Mimetype of the file, if known
            md5: MD5 of the file, if known

        Raises:
            ValueError: If neither parent nor storage_location_id is specified, or if both are specified.
        """

        if storage_location_id:
            if parent:
                raise ValueError("Pass parent or storage_location_id, not both")
        elif not parent:
            raise ValueError("One of parent or storage_location_id is required")
        else:
            upload_destination = self._getDefaultUploadDestination(parent)
            storage_location_id = upload_destination["storageLocationId"]

        if mimetype is None:
            mimetype, _ = mimetypes.guess_type(file_path, strict=False)

        file_handle = {
            "concreteType": concrete_types.S3_FILE_HANDLE,
            "key": s3_file_key,
            "bucketName": bucket_name,
            "fileName": os.path.basename(file_path),
            "contentMd5": md5 or utils.md5_for_file(file_path).hexdigest(),
            "contentSize": os.stat(file_path).st_size,
            "storageLocationId": storage_location_id,
            "contentType": mimetype,
        }

        return self.restPOST(
            "/externalFileHandle/s3",
            json.dumps(file_handle),
            endpoint=self.fileHandleEndpoint,
        )

    def _get_file_handle_as_creator(
        self, fileHandle: Dict[str, Union[str, int]]
    ) -> Dict[str, Union[str, int]]:
        """
        Retrieve a fileHandle from the fileHandle service.
        Note: You must be the creator of the filehandle to use this method. Otherwise, an 403-Forbidden error will be raised.

        Arguments:
            fileHandle: A fileHandle

        Returns:
            A fileHandle retrieved from the fileHandle service.
        """
        uri = "/fileHandle/%s" % (id_of(fileHandle),)
        return self.restGET(uri, endpoint=self.fileHandleEndpoint)

    def _deleteFileHandle(self, fileHandle: Dict[str, Union[str, int]]) -> None:
        """
        Delete the given file handle.

        Note: Only the user that created the FileHandle can delete it. Also, a FileHandle cannot be deleted if it is
        associated with a FileEntity or WikiPage.

        Arguments:
            fileHandle: A fileHandle
        """
        uri = "/fileHandle/%s" % (id_of(fileHandle),)
        self.restDELETE(uri, endpoint=self.fileHandleEndpoint)
        return fileHandle

    ############################################################
    #                    SFTP                                  #
    ############################################################

    def _getDefaultUploadDestination(self, parent_entity):
        return self.restGET(
            "/entity/%s/uploadDestination" % id_of(parent_entity),
            endpoint=self.fileHandleEndpoint,
        )

    def _getUserCredentials(
        self, url: str, username: str = None, password: str = None
    ) -> Tuple[str, str]:
        """
        Get user credentials for a specified URL by either looking in the configFile or querying the user.

        Arguments:
            username: The username on server (optionally specified).
            password: The password for authentication on the server (optionally specified).

        Returns:
            A tuple of username, password.
        """
        # Get authentication information from configFile
        parsedURL = urllib_urlparse.urlparse(url)
        baseURL = parsedURL.scheme + "://" + parsedURL.hostname

        config = get_config_file(self.configPath)
        if username is None and config.has_option(baseURL, "username"):
            username = config.get(baseURL, "username")
        if password is None and config.has_option(baseURL, "password"):
            password = config.get(baseURL, "password")
        # If I still don't have a username and password prompt for it
        if username is None:
            username = getpass.getuser()  # Default to login name
            # Note that if we hit the following line from within nosetests in
            # Python 3, we get "TypeError: bad argument type for built-in operation".
            # Luckily, this case isn't covered in our test suite!
            user = input("Username for %s (%s):" % (baseURL, username))
            username = username if user == "" else user
        if password is None:
            password = getpass.getpass("Password for %s:" % baseURL)
        return username, password

    ############################################
    # Project/Folder storage location settings #
    ############################################

    def createStorageLocationSetting(self, storage_type, **kwargs):
        """
        Creates an IMMUTABLE storage location based on the specified type.

        For each storage_type, the following kwargs should be specified:

        **ExternalObjectStorage**: (S3-like (e.g. AWS S3 or Openstack) bucket not accessed by Synapse)

        - `endpointUrl`: endpoint URL of the S3 service (for example: 'https://s3.amazonaws.com')
        - `bucket`: the name of the bucket to use

        **ExternalS3Storage**: (Amazon S3 bucket accessed by Synapse)

        - `bucket`: the name of the bucket to use

        **ExternalStorage**: (SFTP or FTP storage location not accessed by Synapse)

        - `url`: the base URL for uploading to the external destination
        - `supportsSubfolders(optional)`: does the destination support creating subfolders under the base url
            (default: false)

        **ProxyStorage**: (a proxy server that controls access to a storage)

        - `secretKey`: The encryption key used to sign all pre-signed URLs used to communicate with the proxy.
        - `proxyUrl`: The HTTPS URL of the proxy used for upload and download.

        Arguments:
            storage_type: The type of the StorageLocationSetting to create
            banner: (Optional) The optional banner to show every time a file is uploaded
            description: (Optional) The description to show the user when the user has to choose which upload destination to use
            kwargs: fields necessary for creation of the specified storage_type

        Returns:
            A dict of the created StorageLocationSetting
        """
        upload_type_dict = {
            "ExternalObjectStorage": "S3",
            "ExternalS3Storage": "S3",
            "ExternalStorage": "SFTP",
            "ProxyStorage": "PROXYLOCAL",
        }

        if storage_type not in upload_type_dict:
            raise ValueError("Unknown storage_type: %s", storage_type)

        # ProxyStorageLocationSettings has an extra 's' at the end >:(
        kwargs["concreteType"] = (
            "org.sagebionetworks.repo.model.project."
            + storage_type
            + "LocationSetting"
            + ("s" if storage_type == "ProxyStorage" else "")
        )
        kwargs["uploadType"] = upload_type_dict[storage_type]

        return self.restPOST("/storageLocation", body=json.dumps(kwargs))

    def getMyStorageLocationSetting(self, storage_location_id):
        """
        Get a StorageLocationSetting by its id.

        Arguments:
            storage_location_id: id of the StorageLocationSetting to retrieve.
                                    The corresponding StorageLocationSetting must have been created by this user.

        Returns:
            A dict describing the StorageLocationSetting retrieved by its id
        """
        return self.restGET("/storageLocation/%s" % storage_location_id)

    def setStorageLocation(self, entity, storage_location_id):
        """
        Sets the storage location for a Project or Folder

        Arguments:
            entity: A Project or Folder to which the StorageLocationSetting is set
            storage_location_id: A StorageLocation id or a list of StorageLocation ids. Pass in None for the default
                                    Synapse storage.

        Returns:
            The created or updated settings as a dict.
        """
        if storage_location_id is None:
            storage_location_id = DEFAULT_STORAGE_LOCATION_ID
        locations = (
            storage_location_id
            if isinstance(storage_location_id, list)
            else [storage_location_id]
        )

        existing_setting = self.getProjectSetting(entity, "upload")
        if existing_setting is not None:
            existing_setting["locations"] = locations
            self.restPUT("/projectSettings", body=json.dumps(existing_setting))
            return self.getProjectSetting(entity, "upload")
        else:
            project_destination = {
                "concreteType": "org.sagebionetworks.repo.model.project.UploadDestinationListSetting",
                "settingsType": "upload",
                "locations": locations,
                "projectId": id_of(entity),
            }

            return self.restPOST(
                "/projectSettings", body=json.dumps(project_destination)
            )

    def getProjectSetting(self, project, setting_type):
        """
        Gets the ProjectSetting for a project.

        Arguments:
            project: Project entity or its id as a string
            setting_type: Type of setting. Choose from:

                - `upload`
                - `external_sync`
                - `requester_pays`

        Returns:
            The ProjectSetting as a dict or None if no settings of the specified type exist.
        """
        if setting_type not in {"upload", "external_sync", "requester_pays"}:
            raise ValueError("Invalid project_type: %s" % setting_type)

        response = self.restGET(
            "/projectSettings/{projectId}/type/{type}".format(
                projectId=id_of(project), type=setting_type
            )
        )
        return (
            response if response else None
        )  # if no project setting, a empty string is returned as the response

    def get_sts_storage_token(
        self, entity, permission, *, output_format="json", min_remaining_life=None
    ):
        """Get STS credentials for the given entity_id and permission, outputting it in the given format

        Arguments:
            entity: The entity or entity id whose credentials are being returned
            permission: One of:

                - `read_only`
                - `read_write`

            output_format: One of:

                - `json`: the dictionary returned from the Synapse STS API including expiration
                - `boto`: a dictionary compatible with a boto session (aws_access_key_id, etc)
                - `shell`: output commands for exporting credentials appropriate for the detected shell
                - `bash`: output commands for exporting credentials into a bash shell
                - `cmd`: output commands for exporting credentials into a windows cmd shell
                - `powershell`: output commands for exporting credentials into a windows powershell

            min_remaining_life: The minimum allowable remaining life on a cached token to return. If a cached token
                                has left than this amount of time left a fresh token will be fetched
        """
        return sts_transfer.get_sts_credentials(
            self,
            id_of(entity),
            permission,
            output_format=output_format,
            min_remaining_life=min_remaining_life,
        )

    def create_s3_storage_location(
        self,
        *,
        parent=None,
        folder_name=None,
        folder=None,
        bucket_name=None,
        base_key=None,
        sts_enabled=False,
    ) -> Tuple[Folder, Dict[str, str], Dict[str, str]]:
        """
        Create a storage location in the given parent, either in the given folder or by creating a new
        folder in that parent with the given name. This will both create a StorageLocationSetting,
        and a ProjectSetting together, optionally creating a new folder in which to locate it,
        and optionally enabling this storage location for access via STS. If enabling an existing folder for STS,
        it must be empty.

        Arguments:
            parent: The parent in which to locate the storage location (mutually exclusive with folder)
            folder_name: The name of a new folder to create (mutually exclusive with folder)
            folder: The existing folder in which to create the storage location (mutually exclusive with folder_name)
            bucket_name: The name of an S3 bucket, if this is an external storage location,
                            if None will use Synapse S3 storage
            base_key: The base key of within the bucket, None to use the bucket root,
                            only applicable if bucket_name is passed
            sts_enabled: Whether this storage location should be STS enabled

        Returns:
            A 3-tuple of the synapse Folder, a the storage location setting, and the project setting dictionaries.
        """
        if folder_name and parent:
            if folder:
                raise ValueError(
                    "folder and  folder_name are mutually exclusive, only one should be passed"
                )

            folder = self.store(Folder(name=folder_name, parent=parent))

        elif not folder:
            raise ValueError("either folder or folder_name should be required")

        storage_location_kwargs = {
            "uploadType": "S3",
            "stsEnabled": sts_enabled,
        }

        if bucket_name:
            storage_location_kwargs[
                "concreteType"
            ] = concrete_types.EXTERNAL_S3_STORAGE_LOCATION_SETTING
            storage_location_kwargs["bucket"] = bucket_name
            if base_key:
                storage_location_kwargs["baseKey"] = base_key
        else:
            storage_location_kwargs[
                "concreteType"
            ] = concrete_types.SYNAPSE_S3_STORAGE_LOCATION_SETTING

        storage_location_setting = self.restPOST(
            "/storageLocation", json.dumps(storage_location_kwargs)
        )

        storage_location_id = storage_location_setting["storageLocationId"]
        project_setting = self.setStorageLocation(
            folder,
            storage_location_id,
        )

        return folder, storage_location_setting, project_setting

    ############################################################
    #                   CRUD for Evaluations                   #
    ############################################################

    def getEvaluation(self, id):
        """
        Gets an Evaluation object from Synapse.

        Arguments:
            id: The ID of the [synapseclient.evaluation.Evaluation][] to return.

        Returns:
            An [synapseclient.evaluation.Evaluation][] object

        Example: Using this function
            Creating an Evaluation instance

                evaluation = syn.getEvaluation(2005090)
        """

        evaluation_id = id_of(id)
        uri = Evaluation.getURI(evaluation_id)
        return Evaluation(**self.restGET(uri))

    # TODO: Should this be combined with getEvaluation?
    def getEvaluationByName(self, name):
        """
        Gets an Evaluation object from Synapse.

        Arguments:
            Name: The name of the [synapseclient.evaluation.Evaluation][] to return.

        Returns:
            An [synapseclient.evaluation.Evaluation][] object
        """
        uri = Evaluation.getByNameURI(name)
        return Evaluation(**self.restGET(uri))

    def getEvaluationByContentSource(self, entity):
        """
        Returns a generator over evaluations that derive their content from the given entity

        Arguments:
            entity: The [synapseclient.entity.Project][] whose Evaluations are to be fetched.

        Yields:
            A generator over [synapseclient.evaluation.Evaluation][] objects for the given [synapseclient.entity.Project][].
        """

        entityId = id_of(entity)
        url = "/entity/%s/evaluation" % entityId

        for result in self._GET_paginated(url):
            yield Evaluation(**result)

    def _findTeam(self, name: str) -> typing.Iterator[Team]:
        """
        Retrieve a Teams matching the supplied name fragment

        Arguments:
            name: A team name

        Yields:
            A generator that yields objects of type [Team][synapseclient.team.Team]
        """
        for result in self._GET_paginated("/teams?fragment=%s" % name):
            yield Team(**result)

    def _find_teams_for_principal(self, principal_id: str) -> typing.Iterator[Team]:
        """
        Retrieve a list of teams for the matching principal ID. If the principalId that is passed in is a team itself,
        or not found, this will return a generator that yields no results.

        Arguments:
            principal_id: Identifier of a user or group.

        Yields:
            A generator that yields objects of type [Team][synapseclient.team.Team]
        """
        for result in self._GET_paginated(f"/user/{principal_id}/team"):
            yield Team(**result)

    def create_team(
        self,
        name: str,
        description: str = None,
        icon: str = None,
        can_public_join: bool = False,
        can_request_membership: bool = True,
    ) -> Team:
        """
        Creates a new team.

        Arguments:
            name: The name of the team to create.
            description: A description of the team.
            icon: The FileHandleID of the icon to be used for the team.
            canPublicJoin: Whether the team can be joined by anyone. Defaults to False.
            canRequestMembership: Whether the team can request membership. Defaults to True.

        Returns:
            An object of type [synapseclient.team.Team][]
        """
        request_body = {
            "name": name,
            "description": description,
            "icon": icon,
            "canPublicJoin": can_public_join,
            "canRequestMembership": can_request_membership,
        }
        return Team(
            **self.restPOST(
                "/team",
                json.dumps(request_body),
            )
        )

    def delete_team(self, id: int) -> None:
        """
        Deletes a team.

        Arguments:
            id: The ID of the team to delete.

        """
        return self.restDELETE(f"/team/{id}")

    def getTeam(self, id: Union[int, str]) -> Team:
        """
        Finds a team with a given ID or name.

        Arguments:
            id: The ID or name of the team or a Team object to retrieve.

        Returns:
            An object of type [synapseclient.team.Team][]
        """
        # Retrieves team id
        teamid = id_of(id)
        try:
            int(teamid)
        except (TypeError, ValueError):
            if isinstance(id, str):
                for team in self._findTeam(id):
                    if team.name == id:
                        teamid = team.id
                        break
                else:
                    raise ValueError('Can\'t find team "{}"'.format(teamid))
            else:
                raise ValueError('Can\'t find team "{}"'.format(teamid))
        return Team(**self.restGET("/team/%s" % teamid))

    def getTeamMembers(
        self, team: Union[Team, int, str]
    ) -> typing.Generator[TeamMember, None, None]:
        """
        Lists the members of the given team.

        Arguments:
            team: A [synapseclient.team.Team][] object or a team's ID.

        Yields:
            A generator over [synapseclient.team.TeamMember][] objects.

        """
        for result in self._GET_paginated("/teamMembers/{id}".format(id=id_of(team))):
            yield TeamMember(**result)

    def _get_docker_digest(
        self, entity: Union[Entity, str], docker_tag: str = "latest"
    ) -> str:
        """
        Get matching Docker sha-digest of a DockerRepository given a Docker tag

        Arguments:
            entity:      Synapse ID or Entity of Docker repository
            docker_tag:  Docker tag

        Returns:
            Docker digest matching Docker tag
        """
        entityid = id_of(entity)
        uri = "/entity/{entityId}/dockerTag".format(entityId=entityid)

        docker_commits = self._GET_paginated(uri)
        docker_digest = None
        for commit in docker_commits:
            if docker_tag == commit["tag"]:
                docker_digest = commit["digest"]
        if docker_digest is None:
            raise ValueError(
                "Docker tag {docker_tag} not found.  Please specify a "
                "docker tag that exists. 'latest' is used as "
                "default.".format(docker_tag=docker_tag)
            )
        return docker_digest

    def get_team_open_invitations(
        self, team: Union[Team, int, str]
    ) -> typing.Generator[dict, None, None]:
        """Retrieve the open requests submitted to a Team
        <https://rest-docs.synapse.org/rest/GET/team/id/openInvitation.html>

        Arguments:
            team: A [synapseclient.team.Team][] object or a team's ID.

        Yields:
            Generator of MembershipRequest dictionaries
        """
        teamid = id_of(team)
        request = "/team/{team}/openInvitation".format(team=teamid)
        open_requests = self._GET_paginated(request)
        return open_requests

    def get_membership_status(self, userid, team):
        """Retrieve a user's Team Membership Status bundle.
        <https://rest-docs.synapse.org/rest/GET/team/id/member/principalId/membershipStatus.html>

        Arguments:
            user: Synapse user ID
            team: A [synapseclient.team.Team][] object or a team's ID.

        Returns:
            dict of TeamMembershipStatus
        """
        teamid = id_of(team)
        request = "/team/{team}/member/{user}/membershipStatus".format(
            team=teamid, user=userid
        )
        membership_status = self.restGET(request)
        return membership_status

    def _delete_membership_invitation(self, invitationid: str) -> None:
        """
        Delete an invitation Note: The client must be an administrator of the
        Team referenced by the invitation or the invitee to make this request.

        Arguments:
            invitationid: Open invitation id
        """
        self.restDELETE("/membershipInvitation/{id}".format(id=invitationid))

    def send_membership_invitation(
        self, teamId, inviteeId=None, inviteeEmail=None, message=None
    ):
        """Create a membership invitation and send an email notification
        to the invitee.

        Arguments:
            teamId: Synapse teamId
            inviteeId: Synapse username or profile id of user
            inviteeEmail: Email of user
            message: Additional message for the user getting invited to the
                     team.

        Returns:
            MembershipInvitation
        """

        invite_request = {"teamId": str(teamId), "message": message}
        if inviteeEmail is not None:
            invite_request["inviteeEmail"] = str(inviteeEmail)
        if inviteeId is not None:
            invite_request["inviteeId"] = str(inviteeId)

        response = self.restPOST(
            "/membershipInvitation", body=json.dumps(invite_request)
        )
        return response

    def invite_to_team(
        self,
        team: Union[Team, int, str],
        user: str = None,
        inviteeEmail: str = None,
        message: str = None,
        force: bool = False,
    ):
        """Invite user to a Synapse team via Synapse username or email
        (choose one or the other)

        Arguments:
            syn: Synapse object
            team: A [synapseclient.team.Team][] object or a team's ID.
            user: Synapse username or profile id of user
            inviteeEmail: Email of user
            message: Additional message for the user getting invited to the team.
            force: If an open invitation exists for the invitee, the old invite will be cancelled.

        Returns:
            MembershipInvitation or None if user is already a member
        """
        # Throw error if both user and email is specified and if both not
        # specified
        id_email_specified = inviteeEmail is not None and user is not None
        id_email_notspecified = inviteeEmail is None and user is None
        if id_email_specified or id_email_notspecified:
            raise ValueError("Must specify either 'user' or 'inviteeEmail'")

        teamid = id_of(team)
        is_member = False
        open_invitations = self.get_team_open_invitations(teamid)

        if user is not None:
            inviteeId = self.getUserProfile(user)["ownerId"]
            membership_status = self.get_membership_status(inviteeId, teamid)
            is_member = membership_status["isMember"]
            open_invites_to_user = [
                invitation
                for invitation in open_invitations
                if invitation.get("inviteeId") == inviteeId
            ]
        else:
            inviteeId = None
            open_invites_to_user = [
                invitation
                for invitation in open_invitations
                if invitation.get("inviteeEmail") == inviteeEmail
            ]
        # Only invite if the invitee is not a member and
        # if invitee doesn't have an open invitation unless force=True
        if not is_member and (not open_invites_to_user or force):
            # Delete all old invitations
            for invite in open_invites_to_user:
                self._delete_membership_invitation(invite["id"])
            return self.send_membership_invitation(
                teamid,
                inviteeId=inviteeId,
                inviteeEmail=inviteeEmail,
                message=message,
            )
        if is_member:
            not_sent_reason = "invitee is already a member"
        else:
            not_sent_reason = (
                "invitee already has an open invitation "
                "Set force=True to send new invite."
            )

        self.logger.warning("No invitation sent: {}".format(not_sent_reason))
        # Return None if no invite is sent.
        return None

    def submit(
        self,
        evaluation,
        entity,
        name=None,
        team=None,
        silent=False,
        submitterAlias=None,
        teamName=None,
        dockerTag="latest",
    ):
        """
        Submit an Entity for [evaluation][synapseclient.evaluation.Evaluation].

        Arguments:
            evalation: Evaluation queue to submit to
            entity: The Entity containing the Submissions
            name: A name for this submission. In the absent of this parameter, the entity name will be used.
                    (Optional) A [synapseclient.team.Team][] object, ID or name of a Team that is registered for the challenge
            team: (optional) A [synapseclient.team.Team][] object, ID or name of a Team that is registered for the challenge
            silent: Set to True to suppress output.
            submitterAlias: (optional) A nickname, possibly for display in leaderboards in place of the submitter's name
            teamName: (deprecated) A synonym for submitterAlias
            dockerTag: (optional) The Docker tag must be specified if the entity is a DockerRepository.

        Returns:
            A [synapseclient.evaluation.Submission][] object


        In the case of challenges, a team can optionally be provided to give credit to members of the team that
        contributed to the submission. The team must be registered for the challenge with which the given evaluation is
        associated. The caller must be a member of the submitting team.

        Example: Using this function
            Getting and submitting an evaluation

                evaluation = syn.getEvaluation(123)
                entity = syn.get('syn456')
                submission = syn.submit(evaluation, entity, name='Our Final Answer', team='Blue Team')
        """

        require_param(evaluation, "evaluation")
        require_param(entity, "entity")

        evaluation_id = id_of(evaluation)

        entity_id = id_of(entity)
        if isinstance(entity, synapseclient.DockerRepository):
            # Edge case if dockerTag is specified as None
            if dockerTag is None:
                raise ValueError(
                    "A dockerTag is required to submit a DockerEntity. Cannot be None"
                )
            docker_repository = entity["repositoryName"]
        else:
            docker_repository = None

        if "versionNumber" not in entity:
            entity = self.get(entity, downloadFile=False)
        # version defaults to 1 to hack around required version field and allow submission of files/folders
        entity_version = entity.get("versionNumber", 1)

        # default name of submission to name of entity
        if name is None and "name" in entity:
            name = entity["name"]

        team_id = None
        if team:
            team = self.getTeam(team)
            team_id = id_of(team)

        contributors, eligibility_hash = self._get_contributors(evaluation_id, team)

        # for backward compatible until we remove supports for teamName
        if not submitterAlias:
            if teamName:
                submitterAlias = teamName
            elif team and "name" in team:
                submitterAlias = team["name"]

        if isinstance(entity, synapseclient.DockerRepository):
            docker_digest = self._get_docker_digest(entity, dockerTag)
        else:
            docker_digest = None

        submission = {
            "evaluationId": evaluation_id,
            "name": name,
            "entityId": entity_id,
            "versionNumber": entity_version,
            "dockerDigest": docker_digest,
            "dockerRepositoryName": docker_repository,
            "teamId": team_id,
            "contributors": contributors,
            "submitterAlias": submitterAlias,
        }

        submitted = self._submit(submission, entity["etag"], eligibility_hash)

        # if we want to display the receipt message, we need the full object
        if not silent:
            if not (isinstance(evaluation, Evaluation)):
                evaluation = self.getEvaluation(evaluation_id)
            if "submissionReceiptMessage" in evaluation:
                self.logger.info(evaluation["submissionReceiptMessage"])

        return Submission(**submitted)

    def _submit(self, submission, entity_etag, eligibility_hash):
        require_param(submission, "submission")
        require_param(entity_etag, "entity_etag")
        # URI requires the etag of the entity and, in the case of a team submission, requires an eligibilityStateHash
        uri = "/evaluation/submission?etag=%s" % entity_etag
        if eligibility_hash:
            uri += "&submissionEligibilityHash={0}".format(eligibility_hash)
        submitted = self.restPOST(uri, json.dumps(submission))
        return submitted

    def _get_contributors(self, evaluation_id, team):
        if not evaluation_id or not team:
            return None, None

        team_id = id_of(team)
        # see <https://rest-docs.synapse.org/rest/GET/evaluation/evalId/team/id/submissionEligibility.html>
        eligibility = self.restGET(
            "/evaluation/{evalId}/team/{id}/submissionEligibility".format(
                evalId=evaluation_id, id=team_id
            )
        )

        if not eligibility["teamEligibility"]["isEligible"]:
            # Check team eligibility and raise an exception if not eligible
            if not eligibility["teamEligibility"]["isRegistered"]:
                raise SynapseError(
                    'Team "{team}" is not registered.'.format(team=team.name)
                )
            if eligibility["teamEligibility"]["isQuotaFilled"]:
                raise SynapseError(
                    'Team "{team}" has already submitted the full quota of submissions.'.format(
                        team=team.name
                    )
                )
            raise SynapseError('Team "{team}" is not eligible.'.format(team=team.name))

        # Include all team members who are eligible.
        contributors = [
            {"principalId": member["principalId"]}
            for member in eligibility["membersEligibility"]
            if member["isEligible"] and not member["hasConflictingSubmission"]
        ]
        return contributors, eligibility["eligibilityStateHash"]

    def _allowParticipation(
        self,
        evaluation: Union[Evaluation, str],
        user: str,
        rights: list = ["READ", "PARTICIPATE", "SUBMIT", "UPDATE_SUBMISSION"],
    ) -> Dict[str, Union[str, list]]:
        """
        Grants the given user the minimal access rights to join and submit to an Evaluation.
        Note: The specification of this method has not been decided yet, so the method is likely to change in future.

        Arguments:
            evaluation: An Evaluation object or Evaluation ID
            user:       Either a user group or the principal ID of a user to grant rights to.

                - To allow all users, use "PUBLIC".
                - To allow authenticated users, use "AUTHENTICATED_USERS".

            rights:     The access rights to give to the users.

                - `READ`
                - `PARTICIPATE`
                - `SUBMIT`
                - `UPDATE_SUBMISSION`

        Raises:
            SynapseError: If the user does not exist

        Returns:
            The new or updated ACL
        """
        # Check to see if the user is an ID or group
        userId = -1
        try:
            # TODO: is there a better way to differentiate between a userID and a group name?
            # What if a group is named with just numbers?
            userId = int(user)

            # Verify that the user exists
            try:
                self.getUserProfile(userId)
            except SynapseHTTPError as err:
                if err.response.status_code == 404:
                    raise SynapseError("The user (%s) does not exist" % str(userId))
                raise

        except ValueError:
            # Fetch the ID of the user group
            userId = self._getUserbyPrincipalIdOrName(user)

        if not isinstance(evaluation, Evaluation):
            evaluation = self.getEvaluation(id_of(evaluation))

        self.setPermissions(evaluation, userId, accessType=rights, overwrite=False)

    def getSubmissions(self, evaluation, status=None, myOwn=False, limit=20, offset=0):
        """
        Arguments:
            evaluation: Evaluation to get submissions from.
            status: Optionally filter submissions for a specific status.
                    One of:

                - `OPEN`
                - `CLOSED`
                - `SCORED`
                - `INVALID`
                - `VALIDATED`
                - `EVALUATION_IN_PROGRESS`
                - `RECEIVED`
                - `REJECTED`
                - `ACCEPTED`

            myOwn: Determines if only your Submissions should be fetched.
                     Defaults to False (all Submissions)
            limit: Limits the number of submissions in a single response.
                        Because this method returns a generator and repeatedly
                        fetches submissions, this argument is limiting the
                        size of a single request and NOT the number of sub-
                        missions returned in total.
            offset: Start iterating at a submission offset from the first submission.

        Yields:
            A generator over [synapseclient.evaluation.Submission][] objects for an Evaluation

        Example: Using this function
            Print submissions

                for submission in syn.getSubmissions(1234567):
                    print(submission['entityId'])

        See:

        - [synapseclient.evaluation][]
        """

        evaluation_id = id_of(evaluation)
        uri = "/evaluation/%s/submission%s" % (evaluation_id, "" if myOwn else "/all")

        if status is not None:
            uri += "?status=%s" % status

        for result in self._GET_paginated(uri, limit=limit, offset=offset):
            yield Submission(**result)

    def _getSubmissionBundles(
        self,
        evaluation: Union[Evaluation, str],
        status: str = None,
        myOwn: bool = False,
        limit: int = 20,
        offset: int = 0,
    ) -> typing.Iterator[Dict[str, Union[Submission, dict]]]:
        """
        Gets the requesting user's bundled Submissions and SubmissionStatuses to a specified Evaluation.

        Arguments:
            evaluation: Evaluation to get submissions from.
            status:     Optionally filter submissions for a specific status.
                        One of {OPEN, CLOSED, SCORED, INVALID}
            myOwn:      Determines if only your Submissions should be fetched.
                        Defaults to False (all Submissions)
            limit:      Limits the number of submissions coming back from the
                        service in a single response.
            offset:     Start iterating at a submission offset from the first
                        submission.

        Returns:
            A generator over dictionaries with keys 'submission' and 'submissionStatus'.

        Example:

            for sb in syn._getSubmissionBundles(1234567):
                print(sb['submission']['name'],
                      sb['submission']['submitterAlias'],
                      sb['submissionStatus']['status'],
                      sb['submissionStatus']['score'])

        This may later be changed to return objects, pending some thought on how submissions along with related status
        and annotations should be represented in the clients.

        See: [synapseclient.evaluation][]
        """

        evaluation_id = id_of(evaluation)
        url = "/evaluation/%s/submission/bundle%s" % (
            evaluation_id,
            "" if myOwn else "/all",
        )
        if status is not None:
            url += "?status=%s" % status

        return self._GET_paginated(url, limit=limit, offset=offset)

    def getSubmissionBundles(
        self, evaluation, status=None, myOwn=False, limit=20, offset=0
    ):
        """
        Retrieve submission bundles (submission and submissions status) for an evaluation queue, optionally filtered by
        submission status and/or owner.

        Arguments:
            evaluation: Evaluation to get submissions from.
            status:     Optionally filter submissions for a specific status.
                        One of:

                - `OPEN`
                - `CLOSED`
                - `SCORED`
                - `INVALID`

            myOwn:      Determines if only your Submissions should be fetched.
                        Defaults to False (all Submissions)
            limit:      Limits the number of submissions coming back from the
                        service in a single response.
            offset:     Start iterating at a submission offset from the first submission.

        Yields:
            A generator over tuples containing a [synapseclient.evaluation.Submission][] and a [synapseclient.evaluation.SubmissionStatus][].

        Example: Using this function
            Loop over submissions

                for submission, status in syn.getSubmissionBundles(evaluation):
                    print(submission.name,
                          submission.submitterAlias,
                          status.status,
                          status.score)

        This may later be changed to return objects, pending some thought on how submissions along with related status
        and annotations should be represented in the clients.

        See:
        - [synapseclient.evaluation][]
        """
        for bundle in self._getSubmissionBundles(
            evaluation, status=status, myOwn=myOwn, limit=limit, offset=offset
        ):
            yield (
                Submission(**bundle["submission"]),
                SubmissionStatus(**bundle["submissionStatus"]),
            )

    def _GET_paginated(self, uri: str, limit: int = 20, offset: int = 0):
        """
        Get paginated results

        Arguments:
            uri:     A URI that returns paginated results
            limit:   How many records should be returned per request
            offset:  At what record offset from the first should iteration start

        Returns:
            A generator over some paginated results

        The limit parameter is set at 20 by default. Using a larger limit results in fewer calls to the service, but if
        responses are large enough to be a burden on the service they may be truncated.
        """
        prev_num_results = sys.maxsize
        while prev_num_results > 0:
            uri = utils._limit_and_offset(uri, limit=limit, offset=offset)
            page = self.restGET(uri)
            results = page["results"] if "results" in page else page["children"]
            prev_num_results = len(results)

            for result in results:
                offset += 1
                yield result

    def _POST_paginated(self, uri: str, body, **kwargs):
        """
        Get paginated results

        Arguments:
            uri:     A URI that returns paginated results
            body:    POST request payload

        Returns:
            A generator over some paginated results
        """

        next_page_token = None
        while True:
            body["nextPageToken"] = next_page_token
            response = self.restPOST(uri, body=json.dumps(body), **kwargs)
            next_page_token = response.get("nextPageToken")
            for item in response["page"]:
                yield item
            if next_page_token is None:
                break

    def getSubmission(
        self, id: typing.Union[str, int, collections.abc.Mapping], **kwargs
    ) -> Submission:
        """
        Gets a [synapseclient.evaluation.Submission][] object based on a given ID
        or previous [synapseclient.evaluation.Submission][] object.

        Arguments:
            id: The ID of the submission to retrieve or a [synapseclient.evaluation.Submission][] object

        Returns:
            A [synapseclient.evaluation.Submission][] object

        See:

        - [synapseclient.Synapse.get][] for information
             on the *downloadFile*, *downloadLocation*, and *ifcollision* parameters
        """

        submission_id = validate_submission_id(id)
        uri = Submission.getURI(submission_id)
        submission = Submission(**self.restGET(uri))

        # Pre-fetch the Entity tied to the Submission, if there is one
        if "entityId" in submission and submission["entityId"] is not None:
            entityBundleJSON = json.loads(submission["entityBundleJSON"])

            # getWithEntityBundle expects a bundle services v2 style
            # annotations dict, but the evaluations API may return
            # an older format annotations object in the encoded JSON
            # depending on when the original submission was made.
            annotations = entityBundleJSON.get("annotations")
            if annotations:
                entityBundleJSON["annotations"] = convert_old_annotation_json(
                    annotations
                )

            related = self._getWithEntityBundle(
                entityBundle=entityBundleJSON,
                entity=submission["entityId"],
                submission=submission_id,
                **kwargs,
            )
            submission.entity = related
            submission.filePath = related.get("path", None)

        return submission

    def getSubmissionStatus(
        self, submission: typing.Union[str, int, collections.abc.Mapping]
    ) -> SubmissionStatus:
        """
        Downloads the status of a Submission given its ID or previous [synapseclient.evaluation.Submission][] object.

        Arguments:
            submission: The submission to lookup (ID or [synapseclient.evaluation.Submission][] object)

        Returns:
            A [synapseclient.evaluation.SubmissionStatus][] object
        """

        submission_id = validate_submission_id(submission)
        uri = SubmissionStatus.getURI(submission_id)
        val = self.restGET(uri)
        return SubmissionStatus(**val)

    ############################################################
    #                      CRUD for Wikis                      #
    ############################################################

    def getWiki(self, owner, subpageId=None, version=None):
        """
        Get a [synapseclient.wiki.Wiki][] object from Synapse. Uses wiki2 API which supports versioning.

        Arguments:
            owner: The entity to which the Wiki is attached
            subpageId: The id of the specific sub-page or None to get the root Wiki page
            version: The version of the page to retrieve or None to retrieve the latest

        Returns:
            A [synapseclient.wiki.Wiki][] object
        """
        uri = "/entity/{ownerId}/wiki2".format(ownerId=id_of(owner))
        if subpageId is not None:
            uri += "/{wikiId}".format(wikiId=subpageId)
        if version is not None:
            uri += "?wikiVersion={version}".format(version=version)

        wiki = self.restGET(uri)
        wiki["owner"] = owner
        wiki = Wiki(**wiki)

        path = self.cache.get(wiki.markdownFileHandleId)
        if not path:
            cache_dir = self.cache.get_cache_dir(wiki.markdownFileHandleId)
            if not os.path.exists(cache_dir):
                os.makedirs(cache_dir)
            path = wrap_async_to_sync(
                coroutine=download_by_file_handle(
                    file_handle_id=wiki["markdownFileHandleId"],
                    synapse_id=wiki["id"],
                    entity_type="WikiMarkdown",
                    destination=os.path.join(
                        cache_dir, str(wiki.markdownFileHandleId) + ".md"
                    ),
                    synapse_client=self,
                ),
                syn=self,
            )
        try:
            import gzip

            with gzip.open(path) as f:
                markdown = f.read().decode("utf-8")
        except IOError:
            with open(path) as f:
                markdown = f.read().decode("utf-8")

        wiki.markdown = markdown
        wiki.markdown_path = path

        return wiki

    def getWikiHeaders(self, owner):
        """
        Retrieves the headers of all Wikis belonging to the owner (the entity to which the Wiki is attached).

        Arguments:
            owner: An Entity

        Returns:
            A list of Objects with three fields: id, title and parentId.
        """

        uri = "/entity/%s/wikiheadertree" % id_of(owner)
        return [DictObject(**header) for header in self._GET_paginated(uri)]

    def _storeWiki(self, wiki: Wiki, createOrUpdate: bool) -> Wiki:
        """
        Stores or updates the given Wiki.

        Arguments:
            wiki:           A Wiki object
            createOrUpdate: Indicates whether the method should automatically perform an update if the 'obj'
                            conflicts with an existing Synapse object.

        Returns:
            An updated Wiki object
        """
        # Make sure the file handle field is a list
        if "attachmentFileHandleIds" not in wiki:
            wiki["attachmentFileHandleIds"] = []

        # Convert all attachments into file handles
        if wiki.get("attachments") is not None:
            for attachment in wiki["attachments"]:
                fileHandle = wrap_async_to_sync(
                    upload_synapse_s3(self, attachment), self
                )
                wiki["attachmentFileHandleIds"].append(fileHandle["id"])
            del wiki["attachments"]

        # Perform an update if the Wiki has an ID
        if "id" in wiki:
            updated_wiki = Wiki(
                owner=wiki.ownerId, **self.restPUT(wiki.putURI(), wiki.json())
            )

        # Perform a create if the Wiki has no ID
        else:
            try:
                updated_wiki = Wiki(
                    owner=wiki.ownerId, **self.restPOST(wiki.postURI(), wiki.json())
                )
            except SynapseHTTPError as err:
                # If already present we get an unhelpful SQL error
                if createOrUpdate and (
                    (
                        err.response.status_code == 400
                        and "DuplicateKeyException" in err.message
                    )
                    or err.response.status_code == 409
                ):
                    existing_wiki = self.getWiki(wiki.ownerId)

                    # overwrite everything except for the etag (this will keep unmodified fields in the existing wiki)
                    etag = existing_wiki["etag"]
                    existing_wiki.update(wiki)
                    existing_wiki.etag = etag

                    updated_wiki = Wiki(
                        owner=wiki.ownerId,
                        **self.restPUT(existing_wiki.putURI(), existing_wiki.json()),
                    )
                else:
                    raise
        return updated_wiki

    def getWikiAttachments(self, wiki):
        """
        Retrieve the attachments to a wiki page.

        Arguments:
            wiki: The Wiki object for which the attachments are to be returned.

        Returns:
            A list of file handles for the files attached to the Wiki.
        """
        uri = "/entity/%s/wiki/%s/attachmenthandles" % (wiki.ownerId, wiki.id)
        results = self.restGET(uri)
        file_handles = list(WikiAttachment(**fh) for fh in results["list"])
        return file_handles

    ############################################################
    #                      Tables                              #
    ############################################################

    @tracer.start_as_current_span("Synapse::_waitForAsync")
    def _waitForAsync(self, uri, request, endpoint=None):
        if endpoint is None:
            endpoint = self.repoEndpoint
        async_job_id = self.restPOST(
            uri + "/start", body=json.dumps(request), endpoint=endpoint
        )

        # https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/asynch/AsynchronousJobStatus.html
        sleep = self.table_query_sleep
        start_time = time.time()
        lastMessage, lastProgress, lastTotal, progressed = "", 0, 1, False
        while time.time() - start_time < self.table_query_timeout:
            result = self.restGET(
                uri + "/get/%s" % async_job_id["token"], endpoint=endpoint
            )
            if result.get("jobState", None) == "PROCESSING":
                progressed = True
                message = result.get("progressMessage", lastMessage)
                progress = result.get("progressCurrent", lastProgress)
                total = result.get("progressTotal", lastTotal)
                if message != "":
                    self._print_transfer_progress(
                        progress, total, message, isBytes=False
                    )
                # Reset the time if we made progress (fix SYNPY-214)
                if message != lastMessage or lastProgress != progress:
                    start_time = time.time()
                    lastMessage, lastProgress, lastTotal = message, progress, total
                sleep = min(
                    self.table_query_max_sleep, sleep * self.table_query_backoff
                )
                doze(sleep, trace_span_name="Synapse::doze_for_async")
            else:
                break
        else:
            raise SynapseTimeoutError(
                "Timeout waiting for query results: %0.1f seconds "
                % (time.time() - start_time)
            )
        if result.get("jobState", None) == "FAILED":
            raise SynapseError(
                result.get("errorMessage", None)
                + "\n"
                + result.get("errorDetails", None),
                asynchronousJobStatus=result,
            )
        if progressed:
            self._print_transfer_progress(total, total, message, isBytes=False)
        return result

    def getColumn(self, id):
        """
        Gets a Column object from Synapse by ID.

        See: [synapseclient.table.Column][]

        Arguments:
            id: The ID of the column to retrieve

        Returns:
            An object of type [synapseclient.table.Column][]


        Example: Using this function
            Getting a column

                column = syn.getColumn(123)
        """
        return Column(**self.restGET(Column.getURI(id)))

    def getColumns(self, x, limit=100, offset=0):
        """
        Get the columns defined in Synapse either (1) corresponding to a set of column headers, (2) those for a given
        schema, or (3) those whose names start with a given prefix.

        Arguments:
            x: A list of column headers, a Table Entity object (Schema/EntityViewSchema), a Table's Synapse ID, or a
                string prefix
            limit: maximum number of columns to return (pagination parameter)
            offset: the index of the first column to return (pagination parameter)

        Yields:
            A generator over [synapseclient.table.Column][] objects
        """
        if x is None:
            uri = "/column"
            for result in self._GET_paginated(uri, limit=limit, offset=offset):
                yield Column(**result)
        elif isinstance(x, (list, tuple)):
            for header in x:
                try:
                    # if header is an integer, it's a columnID, otherwise it's an aggregate column, like "AVG(Foo)"
                    int(header)
                    yield self.getColumn(header)
                except ValueError:
                    # ignore aggregate column
                    pass
        elif isinstance(x, SchemaBase) or utils.is_synapse_id_str(x):
            for col in self.getTableColumns(x):
                yield col
        elif isinstance(x, str):
            uri = "/column?prefix=" + x
            for result in self._GET_paginated(uri, limit=limit, offset=offset):
                yield Column(**result)
        else:
            ValueError("Can't get columns for a %s" % type(x))

    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, new View version, or new Dataset version.

        Arguments:
            table: The schema of the Table/View, or its ID.
            comment: Optional snapshot comment.
            label: Optional snapshot label.
            activity: Optional activity ID applied to snapshot version.
            wait: True if this method should return the snapshot version after waiting for any necessary
                    asynchronous table updates to complete. If False this method will return
                    as soon as any updates are initiated.

        Returns:
            The snapshot version number if wait=True, None if wait=False
        """
        ent = self.get(id_of(table), downloadFile=False)
        if isinstance(ent, (EntityViewSchema, SubmissionViewSchema, Dataset)):
            result = self._async_table_update(
                table,
                create_snapshot=True,
                comment=comment,
                label=label,
                activity=activity,
                wait=wait,
            )
        elif isinstance(ent, Schema):
            result = self._create_table_snapshot(
                table,
                comment=comment,
                label=label,
                activity=activity,
            )
        else:
            raise ValueError(
                "This function only accepts Synapse ids of Tables or Views"
            )

        # for consistency we return nothing if wait=False since we can't
        # supply the snapshot version on an async table update without waiting
        return result["snapshotVersionNumber"] if wait else None

    def _create_table_snapshot(
        self,
        table: typing.Union[Schema, str],
        comment: str = None,
        label: str = None,
        activity: typing.Union[Activity, str] = None,
    ) -> dict:
        """
        Creates Table snapshot

        Arguments:
            table:  The schema of the Table
            comment:  Optional snapshot comment.
            label:  Optional snapshot label.
            activity:  Optional activity ID or activity instance applied to snapshot version.

        Returns:
            Snapshot Response
        """

        # check the activity id or object is provided
        activity_id = None
        if isinstance(activity, collections.abc.Mapping):
            if "id" not in activity:
                activity = self._saveActivity(activity)
            activity_id = activity["id"]
        elif activity is not None:
            activity_id = str(activity)

        snapshot_body = {
            "snapshotComment": comment,
            "snapshotLabel": label,
            "snapshotActivityId": activity_id,
        }
        new_body = {
            key: value for key, value in snapshot_body.items() if value is not None
        }
        snapshot = self.restPOST(
            "/entity/{}/table/snapshot".format(id_of(table)), body=json.dumps(new_body)
        )
        return snapshot

    def _async_table_update(
        self,
        table: typing.Union[EntityViewSchema, Schema, str, SubmissionViewSchema],
        changes: typing.List[dict] = [],
        create_snapshot: bool = False,
        comment: str = None,
        label: str = None,
        activity: str = None,
        wait: bool = True,
    ) -> dict:
        """
        Creates view updates and snapshots

        Arguments:
            table:           The schema of the EntityView or its ID.
            changes:         Array of Table changes
            create_snapshot: Create snapshot
            comment:         Optional snapshot comment.
            label:           Optional snapshot label.
            activity:        Optional activity ID applied to snapshot version.
            wait:            True to wait for async table update to complete

        Returns:
            A Snapshot Response
        """
        snapshot_options = {
            "snapshotComment": comment,
            "snapshotLabel": label,
            "snapshotActivityId": activity,
        }
        new_snapshot = {
            key: value for key, value in snapshot_options.items() if value is not None
        }
        table_update_body = {
            "changes": changes,
            "createSnapshot": create_snapshot,
            "snapshotOptions": new_snapshot,
        }

        uri = "/entity/{}/table/transaction/async".format(id_of(table))

        if wait:
            result = self._waitForAsync(uri, table_update_body)

        else:
            result = self.restPOST(
                "{}/start".format(uri), body=json.dumps(table_update_body)
            )

        return result

    def getTableColumns(self, table):
        """
        Retrieve the column models used in the given table schema.

        Arguments:
            table: The schema of the Table whose columns are to be retrieved

        Yields:
            A Generator over the Table's [columns][synapseclient.table.Column]
        """
        uri = "/entity/{id}/column".format(id=id_of(table))
        # The returned object type for this service, PaginatedColumnModels, is a misnomer.
        # This service always returns the full list of results so the pagination does not not actually matter.
        for result in self.restGET(uri)["results"]:
            yield Column(**result)

    def tableQuery(self, query: str, resultsAs: str = "csv", **kwargs):
        """
        Query a Synapse Table.

        You can receive query results either as a generator over rows or as a CSV file. For smallish tables, either
        method will work equally well. Use of a "rowset" generator allows rows to be processed one at a time and
        processing may be stopped before downloading the entire table.

        Optional keyword arguments differ for the two return types of `rowset` or `csv`

        Arguments:
            query: Query string in a [SQL-like syntax](https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/web/controller/TableExamples.html), for example: `"SELECT * from syn12345"`
            resultsAs: select whether results are returned as a CSV file ("csv") or incrementally downloaded as sets of rows ("rowset")
            limit: (rowset only) Specify the maximum number of rows to be returned, defaults to None
            offset: (rowset only) Don't return the first n rows, defaults to None
            quoteCharacter: (csv only) default double quote
            escapeCharacter: (csv only) default backslash
            lineEnd: (csv only) defaults to os.linesep
            separator: (csv only) defaults to comma
            header: (csv only) True by default
            includeRowIdAndRowVersion: (csv only) True by default
            downloadLocation: (csv only) directory path to download the CSV file to

        Returns:
            A [TableQueryResult][synapseclient.table.TableQueryResult] or [CsvFileTable][synapseclient.table.CsvFileTable] object

        NOTE:
            When performing queries on frequently updated tables, the table can be inaccessible for a period leading
              to a timeout of the query.  Since the results are guaranteed to eventually be returned you can change the
              max timeout by setting the table_query_timeout variable of the Synapse object:

                  # Sets the max timeout to 5 minutes.
                  syn.table_query_timeout = 300

        """
        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)
            )

    def _queryTable(
        self,
        query: str,
        limit: int = None,
        offset: int = None,
        isConsistent: bool = True,
        partMask=None,
    ) -> TableQueryResult:
        """
        Query a table and return the first page of results as a [QueryResultBundle](https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/table/QueryResultBundle.html).
        If the result contains a *nextPageToken*, following pages a retrieved by calling [_queryTableNext][].

        Arguments:
            query:        A sql query
            limit:        The optional limit to the results
            offset:       The optional offset into the results
            isConsistent: Whether the index is inconsistent with the true state of the table
            partMask:     Optional, default all. The 'partsMask' is a bit field for requesting
                          different elements in the resulting JSON bundle.
                          Query Results (queryResults) = 0x1
                          Query Count (queryCount) = 0x2
                          Select Columns (selectColumns) = 0x4
                          Max Rows Per Page (maxRowsPerPage) = 0x8

        Returns:
            The first page of results as a QueryResultBundle
        """
        # See: <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/table/QueryBundleRequest.html>
        query_bundle_request = {
            "concreteType": "org.sagebionetworks.repo.model.table.QueryBundleRequest",
            "query": {
                "sql": query,
                "isConsistent": isConsistent,
                "includeEntityEtag": True,
            },
        }

        if partMask:
            query_bundle_request["partMask"] = partMask
        if limit is not None:
            query_bundle_request["query"]["limit"] = limit
        if offset is not None:
            query_bundle_request["query"]["offset"] = offset
        query_bundle_request["query"]["isConsistent"] = isConsistent

        uri = "/entity/{id}/table/query/async".format(
            id=extract_synapse_id_from_query(query)
        )

        return self._waitForAsync(uri=uri, request=query_bundle_request)

    def _queryTableNext(self, nextPageToken: str, tableId: str) -> TableQueryResult:
        """
        Retrieve following pages if the result contains a *nextPageToken*

        Arguments:
            nextPageToken: Forward this token to get the next page of results.
            tableId:       The Synapse ID of the table

        Returns:
            The following page of results as a QueryResultBundle
        """
        uri = "/entity/{id}/table/query/nextPage/async".format(id=tableId)
        return self._waitForAsync(uri=uri, request=nextPageToken)

    def _uploadCsv(
        self,
        filepath: str,
        schema: Union[Entity, str],
        updateEtag: str = None,
        quoteCharacter: str = '"',
        escapeCharacter: str = "\\",
        lineEnd: str = os.linesep,
        separator: str = ",",
        header: bool = True,
        linesToSkip: int = 0,
    ) -> dict:
        """
        Send an [UploadToTableRequest](https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/table/UploadToTableRequest.html) to Synapse.

        Arguments:
            filepath:        Path of a [CSV](https://en.wikipedia.org/wiki/Comma-separated_values) file.
            schema:          A table entity or its Synapse ID.
            updateEtag:      Any RowSet returned from Synapse will contain the current etag of the change set.
                             To update any rows from a RowSet the etag must be provided with the POST.
            quoteCharacter:  Quotation character
            escapeCharacter: Escape character
            lineEnd:         The string used to separate lines
            separator:       Separator character
            header:          Whether to set the first line as header.
            linesToSkip:     The number of lines to skip from the start of the file.
                             The default value of 0 will be used if this is not provided by the caller.

        Returns:
            [UploadToTableResult](https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/table/UploadToTableResult.html)
        """

        fileHandleId = wrap_async_to_sync(
            multipart_upload_file_async(self, filepath, content_type="text/csv"), self
        )

        uploadRequest = {
            "concreteType": "org.sagebionetworks.repo.model.table.UploadToTableRequest",
            "csvTableDescriptor": {
                "isFirstLineHeader": header,
                "quoteCharacter": quoteCharacter,
                "escapeCharacter": escapeCharacter,
                "lineEnd": lineEnd,
                "separator": separator,
            },
            "linesToSkip": linesToSkip,
            "tableId": id_of(schema),
            "uploadFileHandleId": fileHandleId,
        }

        if updateEtag:
            uploadRequest["updateEtag"] = updateEtag

        response = self._async_table_update(schema, changes=[uploadRequest], wait=True)
        self._check_table_transaction_response(response)

        return response

    def _check_table_transaction_response(self, response):
        for result in response["results"]:
            result_type = result["concreteType"]

            if result_type in {
                concrete_types.ROW_REFERENCE_SET_RESULTS,
                concrete_types.TABLE_SCHEMA_CHANGE_RESPONSE,
                concrete_types.UPLOAD_TO_TABLE_RESULT,
            }:
                # if these fail, it we would have gotten an HttpError before the results came back
                pass
            elif result_type == concrete_types.ENTITY_UPDATE_RESULTS:
                # TODO: output full response to error file when the logging JIRA issue gets pulled in
                successful_updates = []
                failed_updates = []
                for update_result in result["updateResults"]:
                    failure_code = update_result.get("failureCode")
                    failure_message = update_result.get("failureMessage")
                    entity_id = update_result.get("entityId")
                    if failure_code or failure_message:
                        failed_updates.append(update_result)
                    else:
                        successful_updates.append(entity_id)

                if failed_updates:
                    raise SynapseError(
                        "Not all of the entities were updated."
                        " Successful updates: %s.  Failed updates: %s"
                        % (successful_updates, failed_updates)
                    )

            else:
                warnings.warn(
                    "Unexpected result from a table transaction of type [%s]."
                    " Please check the result to make sure it is correct. %s"
                    % (result_type, result)
                )

    def _queryTableCsv(
        self,
        query: str,
        quoteCharacter: str = '"',
        escapeCharacter: str = "\\",
        lineEnd: str = os.linesep,
        separator: str = ",",
        header: bool = True,
        includeRowIdAndRowVersion: bool = True,
        downloadLocation: str = None,
    ) -> Tuple:
        """
        Query a Synapse Table and download a CSV file containing the results.

        Sends a [DownloadFromTableRequest](https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/table/DownloadFromTableRequest.html) to Synapse.

        Arguments:
            query:                     A sql query
            quoteCharacter:            Quotation character
            escapeCharacter:           Escape character
            lineEnd:                   The string used to separate lines
            separator:                 Separator character
            header:                    Whether to set the first line as header.
            includeRowIdAndRowVersion: Whether to set the first two columns contains the row ID and row version.
            downloadLocation:          The download location

        Returns:
            A tuple containing a [DownloadFromTableResult](https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/table/DownloadFromTableResult.html)

        The DownloadFromTableResult object contains these fields:
         * headers:             ARRAY<STRING>, The list of ColumnModel IDs that describes the rows of this set.
         * resultsFileHandleId: STRING, The resulting file handle ID can be used to download the CSV file created by
                                this query.
         * concreteType:        STRING
         * etag:                STRING, Any RowSet returned from Synapse will contain the current etag of the change
                                set.
                                To update any rows from a RowSet the etag must be provided with the POST.
         * tableId:             STRING, The ID of the table identified in the from clause of the table query.
        """
        download_from_table_request = {
            "concreteType": "org.sagebionetworks.repo.model.table.DownloadFromTableRequest",
            "csvTableDescriptor": {
                "isFirstLineHeader": header,
                "quoteCharacter": quoteCharacter,
                "escapeCharacter": escapeCharacter,
                "lineEnd": lineEnd,
                "separator": separator,
            },
            "sql": query,
            "writeHeader": header,
            "includeRowIdAndRowVersion": includeRowIdAndRowVersion,
            "includeEntityEtag": True,
        }

        uri = "/entity/{id}/table/download/csv/async".format(
            id=extract_synapse_id_from_query(query)
        )
        download_from_table_result = self._waitForAsync(
            uri=uri, request=download_from_table_request
        )
        file_handle_id = download_from_table_result["resultsFileHandleId"]
        cached_file_path = self.cache.get(
            file_handle_id=file_handle_id, path=downloadLocation
        )
        if cached_file_path is not None:
            return download_from_table_result, cached_file_path

        if downloadLocation:
            download_dir = ensure_download_location_is_directory(
                download_location=downloadLocation
            )
        else:
            download_dir = self.cache.get_cache_dir(file_handle_id=file_handle_id)

        os.makedirs(download_dir, exist_ok=True)
        filename = f"SYNAPSE_TABLE_QUERY_{file_handle_id}.csv"
        path = wrap_async_to_sync(
            coroutine=download_by_file_handle(
                file_handle_id=file_handle_id,
                synapse_id=extract_synapse_id_from_query(query),
                entity_type="TableEntity",
                destination=os.path.join(download_dir, filename),
                synapse_client=self,
            ),
            syn=self,
        )

        return download_from_table_result, path

    # This is redundant with syn.store(Column(...)) and will be removed unless people prefer this method.
    def createColumn(
        self,
        name,
        columnType,
        maximumSize=None,
        defaultValue=None,
        enumValues=None,
    ):
        columnModel = Column(
            name=name,
            columnType=columnType,
            maximumSize=maximumSize,
            defaultValue=defaultValue,
            enumValue=enumValues,
        )
        return Column(**self.restPOST("/column", json.dumps(columnModel)))

    def createColumns(self, columns: typing.List[Column]) -> typing.List[Column]:
        """
        Creates a batch of [synapseclient.table.Column][]'s within a single request.

        Arguments:
            columns: A list of [synapseclient.table.Column][]'s

        Returns:
            A list of [synapseclient.table.Column][]'s that have been created in Synapse
        """
        request_body = {
            "concreteType": "org.sagebionetworks.repo.model.ListWrapper",
            "list": list(columns),
        }
        response = self.restPOST("/column/batch", json.dumps(request_body))
        return [Column(**col) for col in response["list"]]

    def _getColumnByName(self, schema: Schema, column_name: str) -> Column:
        """
        Given a schema and a column name, get the corresponding [Column][synapseclient.table.Column] object.

        Arguments:
            schema: The Schema is an [Entity][synapseclient.entity.Entity] that defines a set of columns in a table.
            column_name: The column name

        Returns:
            A Column object
        """
        for column in self.getColumns(schema):
            if column.name == column_name:
                return column
        return None

    def downloadTableColumns(self, table, columns, downloadLocation=None, **kwargs):
        """
        Bulk download of table-associated files.

        Arguments:
            table: Table query result
            columns: A list of column names as strings
            downloadLocation: Directory into which to download the files

        Returns:
            A dictionary from file handle ID to path in the local file system.

        For example, consider a Synapse table whose ID is "syn12345" with two columns of type FILEHANDLEID named 'foo'
        and 'bar'. The associated files are JSON encoded, so we might retrieve the files from Synapse and load for the
        second 100 of those rows as shown here:

            import json

            results = syn.tableQuery('SELECT * FROM syn12345 LIMIT 100 OFFSET 100')
            file_map = syn.downloadTableColumns(results, ['foo', 'bar'])

            for file_handle_id, path in file_map.items():
                with open(path) as f:
                    data[file_handle_id] = f.read()

        """

        RETRIABLE_FAILURE_CODES = ["EXCEEDS_SIZE_LIMIT"]
        MAX_DOWNLOAD_TRIES = 100
        max_files_per_request = kwargs.get("max_files_per_request", 2500)
        # Rowset tableQuery result not allowed
        if isinstance(table, TableQueryResult):
            raise ValueError(
                "downloadTableColumn doesn't work with rowsets. Please use default tableQuery settings."
            )
        if isinstance(columns, str):
            columns = [columns]
        if not isinstance(columns, collections.abc.Iterable):
            raise TypeError("Columns parameter requires a list of column names")

        (
            file_handle_associations,
            file_handle_to_path_map,
        ) = self._build_table_download_file_handle_list(
            table,
            columns,
            downloadLocation,
        )

        self.logger.info(
            "Downloading %d files, %d cached locally"
            % (len(file_handle_associations), len(file_handle_to_path_map))
        )

        permanent_failures = collections.OrderedDict()

        attempts = 0
        while len(file_handle_associations) > 0 and attempts < MAX_DOWNLOAD_TRIES:
            attempts += 1

            file_handle_associations_batch = file_handle_associations[
                :max_files_per_request
            ]

            # ------------------------------------------------------------
            # call async service to build zip file
            # ------------------------------------------------------------

            # returns a BulkFileDownloadResponse:
            #   <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/file/BulkFileDownloadResponse.html>
            request = dict(
                concreteType="org.sagebionetworks.repo.model.file.BulkFileDownloadRequest",
                requestedFiles=file_handle_associations_batch,
            )
            response = self._waitForAsync(
                uri="/file/bulk/async",
                request=request,
                endpoint=self.fileHandleEndpoint,
            )

            # ------------------------------------------------------------
            # download zip file
            # ------------------------------------------------------------

            temp_dir = tempfile.mkdtemp()
            zipfilepath = os.path.join(temp_dir, "table_file_download.zip")
            try:
                zipfilepath = wrap_async_to_sync(
                    download_by_file_handle(
                        file_handle_id=response["resultZipFileHandleId"],
                        synapse_id=table.tableId,
                        entity_type="TableEntity",
                        destination=zipfilepath,
                    ),
                    syn=self,
                )
                # TODO handle case when no zip file is returned
                # TODO test case when we give it partial or all bad file handles
                # TODO test case with deleted fileHandleID
                # TODO return null for permanent failures

                # ------------------------------------------------------------
                # unzip into cache
                # ------------------------------------------------------------

                if downloadLocation:
                    download_dir = ensure_download_location_is_directory(
                        downloadLocation
                    )

                with zipfile.ZipFile(zipfilepath) as zf:
                    # the directory structure within the zip follows that of the cache:
                    # {fileHandleId modulo 1000}/{fileHandleId}/{fileName}
                    for summary in response["fileSummary"]:
                        if summary["status"] == "SUCCESS":
                            if not downloadLocation:
                                download_dir = self.cache.get_cache_dir(
                                    summary["fileHandleId"]
                                )

                            filepath = extract_zip_file_to_directory(
                                zf, summary["zipEntryName"], download_dir
                            )
                            self.cache.add(summary["fileHandleId"], filepath)
                            file_handle_to_path_map[summary["fileHandleId"]] = filepath
                        elif summary["failureCode"] not in RETRIABLE_FAILURE_CODES:
                            permanent_failures[summary["fileHandleId"]] = summary
            finally:
                if os.path.exists(zipfilepath):
                    os.remove(zipfilepath)

            # Do we have remaining files to download?
            file_handle_associations = [
                fha
                for fha in file_handle_associations
                if fha["fileHandleId"] not in file_handle_to_path_map
                and fha["fileHandleId"] not in permanent_failures.keys()
            ]

        # TODO if there are files we still haven't downloaded

        return file_handle_to_path_map

    def _build_table_download_file_handle_list(self, table, columns, downloadLocation):
        # ------------------------------------------------------------
        # build list of file handles to download
        # ------------------------------------------------------------
        cols_not_found = [
            c for c in columns if c not in [h.name for h in table.headers]
        ]
        if len(cols_not_found) > 0:
            raise ValueError(
                "Columns not found: "
                + ", ".join('"' + col + '"' for col in cols_not_found)
            )
        col_indices = [i for i, h in enumerate(table.headers) if h.name in columns]
        # see: <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/file/BulkFileDownloadRequest.html>
        file_handle_associations = []
        file_handle_to_path_map = collections.OrderedDict()
        seen_file_handle_ids = (
            set()
        )  # ensure not sending duplicate requests for the same FileHandle IDs
        for row in table:
            for col_index in col_indices:
                file_handle_id = row[col_index]
                if is_integer(file_handle_id):
                    path_to_cached_file = self.cache.get(
                        file_handle_id, path=downloadLocation
                    )
                    if path_to_cached_file:
                        file_handle_to_path_map[file_handle_id] = path_to_cached_file
                    elif file_handle_id not in seen_file_handle_ids:
                        file_handle_associations.append(
                            dict(
                                associateObjectType="TableEntity",
                                fileHandleId=file_handle_id,
                                associateObjectId=table.tableId,
                            )
                        )
                    seen_file_handle_ids.add(file_handle_id)
                else:
                    warnings.warn("Weird file handle: %s" % file_handle_id)
        return file_handle_associations, file_handle_to_path_map

    def _get_default_view_columns(self, view_type, view_type_mask=None):
        """Get default view columns"""
        uri = f"/column/tableview/defaults?viewEntityType={view_type}"
        if view_type_mask:
            uri += f"&viewTypeMask={view_type_mask}"
        return [Column(**col) for col in self.restGET(uri)["list"]]

    def _get_annotation_view_columns(
        self, scope_ids: list, view_type: str, view_type_mask: str = None
    ) -> list:
        """
        Get all the columns of a submission of entity view based on existing annotations

        Arguments:
            scope_ids:      List of Evaluation Queue or Project/Folder Ids
            view_type:      The submissionview or entityview
            view_type_mask: Bit mask representing the types to include in the view.

        Returns:
            The list of columns
        """
        columns = []
        next_page_token = None
        while True:
            view_scope = {
                "concreteType": "org.sagebionetworks.repo.model.table.ViewColumnModelRequest",
                "viewScope": {
                    "scope": scope_ids,
                    "viewEntityType": view_type,
                    "viewTypeMask": view_type_mask,
                },
            }
            if next_page_token:
                view_scope["nextPageToken"] = next_page_token
            response = self._waitForAsync(
                uri="/column/view/scope/async", request=view_scope
            )
            columns.extend(Column(**column) for column in response["results"])
            next_page_token = response.get("nextPageToken")
            if next_page_token is None:
                break
        return columns

    ############################################################
    #              CRUD for Entities (properties)              #
    ############################################################

    def _getEntity(
        self, entity: Union[str, dict, Entity], version: int = None
    ) -> Dict[str, Union[str, bool]]:
        """
        Get an entity from Synapse.

        Arguments:
            entity:  A Synapse ID, a dictionary representing an Entity, or a Synapse Entity object
            version: The version number to fetch

        Returns:
            A dictionary containing an Entity's properties
        """

        uri = "/entity/" + id_of(entity)
        if version:
            uri += "/version/%d" % version
        return self.restGET(uri)

    def _createEntity(self, entity: Union[dict, Entity]) -> Dict[str, Union[str, bool]]:
        """
        Create a new entity in Synapse.

        Arguments:
            entity: A dictionary representing an Entity or a Synapse Entity object

        Returns:
            A dictionary containing an Entity's properties
        """

        return self.restPOST(uri="/entity", body=json.dumps(get_properties(entity)))

    def _updateEntity(
        self,
        entity: Union[dict, Entity],
        incrementVersion: bool = True,
        versionLabel: str = None,
    ) -> Dict[str, Union[str, bool]]:
        """
        Update an existing entity in Synapse.

        Arguments:
            entity:           A dictionary representing an Entity or a Synapse Entity object
            incrementVersion: Whether to increment the entity version (if Versionable)
            versionLabel:     A label for the entity version (if Versionable)

        Returns:
            A dictionary containing an Entity's properties
        """

        uri = "/entity/%s" % id_of(entity)

        params = {}
        if is_versionable(entity):
            if versionLabel:
                # a versionLabel implicitly implies incrementing
                incrementVersion = True
            elif incrementVersion and "versionNumber" in entity:
                versionLabel = str(entity["versionNumber"] + 1)

            if incrementVersion:
                entity["versionLabel"] = versionLabel
                params["newVersion"] = "true"

        return self.restPUT(uri, body=json.dumps(get_properties(entity)), params=params)

    def findEntityId(self, name, parent=None):
        """
        Find an Entity given its name and parent.

        Arguments:
            name: Name of the entity to find
            parent: An Entity object or the Id of an entity as a string. Omit if searching for a Project by name

        Returns:
            The Entity ID or None if not found
        """
        # when we want to search for a project by name. set parentId as None instead of ROOT_ENTITY
        entity_lookup_request = {
            "parentId": id_of(parent) if parent else None,
            "entityName": name,
        }
        try:
            return self.restPOST(
                "/entity/child", body=json.dumps(entity_lookup_request)
            ).get("id")
        except SynapseHTTPError as e:
            if (
                e.response.status_code == 404
            ):  # a 404 error is raised if the entity does not exist
                return None
            raise

    ############################################################
    #                       Send Message                       #
    ############################################################
    def sendMessage(
        self, userIds, messageSubject, messageBody, contentType="text/plain"
    ):
        """
        send a message via Synapse.

        Arguments:
            userIds: A list of user IDs to which the message is to be sent
            messageSubject: The subject for the message
            messageBody: The body of the message
            contentType: optional contentType of message body (default="text/plain")
                            Should be one of "text/plain" or "text/html"

        Returns:
            The metadata of the created message
        """

        fileHandleId = wrap_async_to_sync(
            multipart_upload_string_async(self, messageBody, content_type=contentType),
            self,
        )
        message = dict(
            recipients=userIds, subject=messageSubject, fileHandleId=fileHandleId
        )
        return self.restPOST(uri="/message", body=json.dumps(message))

    ############################################################
    #                   Low level Rest calls                   #
    ############################################################

    def _generate_headers(self, headers: Dict[str, str] = None) -> Dict[str, str]:
        """
        Generate headers (auth headers produced separately by credentials object)

        """
        if headers is None:
            headers = dict(self.default_headers)
        headers.update(synapseclient.USER_AGENT)

        return headers

    def _handle_synapse_http_error(self, response):
        """Raise errors as appropriate for returned Synapse http status codes"""

        try:
            exceptions._raise_for_status(response, verbose=self.debug)
        except exceptions.SynapseHTTPError as ex:
            # if we get a unauthenticated or forbidden error and the user is not logged in
            # then we raise it as an authentication error.
            # we can't know for certain that logging in to their particular account will grant them
            # access to this resource but more than likely it's the cause of this error.
            if response.status_code in (401, 403) and not self.credentials:
                raise SynapseAuthenticationError(
                    "You are not logged in and do not have access to a requested resource."
                ) from ex

            raise

    def _handle_httpx_synapse_http_error(self, response: httpx.Response) -> None:
        """Raise errors as appropriate for the HTTPX library returned Synapse http
        status codes

        Arguments:
            response: The HTTPX response object
        """

        try:
            exceptions._raise_for_status_httpx(
                response=response, verbose=self.debug, logger=self.logger
            )
        except exceptions.SynapseHTTPError as ex:
            # if we get a unauthenticated or forbidden error and the user is not logged in
            # then we raise it as an authentication error.
            # we can't know for certain that logging in to their particular account will grant them
            # access to this resource but more than likely it's the cause of this error.
            if response.status_code in (401, 403) and not self.credentials:
                raise SynapseAuthenticationError(
                    "You are not logged in and do not have access to a requested resource."
                ) from ex

            raise

    def _rest_call(
        self,
        method,
        uri,
        data,
        endpoint,
        headers,
        retryPolicy,
        requests_session,
        **kwargs,
    ):
        """
        Sends an HTTP request to the Synapse server.

        Arguments:
            method:           The method to implement Create, Read, Update, Delete operations.
                              Should be post, get, put, delete.
            uri:              URI on which the method is performed
            endpoint:         Server endpoint, defaults to self.repoEndpoint
            headers:          Dictionary of headers to use rather than the API-key-signed default set of headers
            retryPolicy:      A retry policy
            requests_session: An external [requests.Session object](https://requests.readthedocs.io/en/latest/user/advanced/) to use when making this specific call
            kwargs:           Any other arguments taken by a
                              [request](http://docs.python-requests.org/en/latest/) method

        Returns:
            JSON encoding of response
        """
        self.logger.debug(f"Sending {method} request to {uri}")
        uri, headers = self._build_uri_and_headers(
            uri, endpoint=endpoint, headers=headers
        )

        retryPolicy = self._build_retry_policy(retryPolicy)
        requests_session = requests_session or self._requests_session

        auth = kwargs.pop("auth", self.credentials)
        requests_method_fn = getattr(requests_session, method)
        response = with_retry(
            lambda: requests_method_fn(
                uri,
                data=data,
                headers=headers,
                auth=auth,
                **kwargs,
            ),
            verbose=self.debug,
            **retryPolicy,
        )
        self._handle_synapse_http_error(response)
        return response

    def restGET(
        self,
        uri,
        endpoint=None,
        headers=None,
        retryPolicy={},
        requests_session=None,
        **kwargs,
    ):
        """
        Sends an HTTP GET request to the Synapse server.

        Arguments:
            uri: URI on which get is performed
            endpoint: Server endpoint, defaults to self.repoEndpoint
            headers: Dictionary of headers to use rather than the API-key-signed default set of headers
            requests_session: An external [requests.Session object](https://requests.readthedocs.io/en/latest/user/advanced/) to use when making this specific call
            kwargs: Any other arguments taken by a [request](http://docs.python-requests.org/en/latest/) method

        Returns:
            JSON encoding of response
        """
        response = self._rest_call(
            "get", uri, None, endpoint, headers, retryPolicy, requests_session, **kwargs
        )
        return self._return_rest_body(response)

    def restPOST(
        self,
        uri,
        body,
        endpoint=None,
        headers=None,
        retryPolicy={},
        requests_session=None,
        **kwargs,
    ):
        """
        Sends an HTTP POST request to the Synapse server.

        Arguments:
            uri: URI on which get is performed
            endpoint: Server endpoint, defaults to self.repoEndpoint
            body: The payload to be delivered
            headers: Dictionary of headers to use rather than the API-key-signed default set of headers
            requests_session: An external [requests.Session object](https://requests.readthedocs.io/en/latest/user/advanced/) to use when making this specific call
            kwargs: Any other arguments taken by a [request](http://docs.python-requests.org/en/latest/) method

        Returns:
            JSON encoding of response
        """
        response = self._rest_call(
            "post",
            uri,
            body,
            endpoint,
            headers,
            retryPolicy,
            requests_session,
            **kwargs,
        )
        return self._return_rest_body(response)

    def restPUT(
        self,
        uri,
        body=None,
        endpoint=None,
        headers=None,
        retryPolicy={},
        requests_session=None,
        **kwargs,
    ):
        """
        Sends an HTTP PUT request to the Synapse server.

        Arguments:
            uri: URI on which get is performed
            endpoint: Server endpoint, defaults to self.repoEndpoint
            body: The payload to be delivered
            headers: Dictionary of headers to use rather than the API-key-signed default set of headers
            requests_session: An external [requests.Session object](https://requests.readthedocs.io/en/latest/user/advanced/) to use when making this specific call
            kwargs: Any other arguments taken by a [request](http://docs.python-requests.org/en/latest/) method

        Returns
            JSON encoding of response
        """
        response = self._rest_call(
            "put",
            uri,
            body,
            endpoint,
            headers,
            retryPolicy,
            requests_session,
            **kwargs,
        )
        return self._return_rest_body(response)

    def restDELETE(
        self,
        uri,
        endpoint=None,
        headers=None,
        retryPolicy={},
        requests_session=None,
        **kwargs,
    ):
        """
        Sends an HTTP DELETE request to the Synapse server.

        Arguments:
            uri: URI of resource to be deleted
            endpoint: Server endpoint, defaults to self.repoEndpoint
            headers: Dictionary of headers to use rather than the API-key-signed default set of headers
            requests_session: An external [requests.Session object](https://requests.readthedocs.io/en/latest/user/advanced/) to use when making this specific call
            kwargs: Any other arguments taken by a [request](http://docs.python-requests.org/en/latest/) method

        """
        self._rest_call(
            "delete",
            uri,
            None,
            endpoint,
            headers,
            retryPolicy,
            requests_session,
            **kwargs,
        )

    def _build_uri_and_headers(
        self, uri: str, endpoint: str = None, headers: Dict[str, str] = None
    ) -> Tuple[str, Dict[str, str]]:
        """Returns a tuple of the URI and headers to request with."""

        if endpoint is None:
            endpoint = self.repoEndpoint

        trace.get_current_span().set_attributes({"server.address": endpoint})

        # Check to see if the URI is incomplete (i.e. a Synapse URL)
        # In that case, append a Synapse endpoint to the URI
        parsedURL = urllib_urlparse.urlparse(uri)
        if parsedURL.netloc == "":
            uri = endpoint + uri

        if headers is None:
            headers = self._generate_headers()
        return uri, headers

    def _build_retry_policy(self, retryPolicy={}):
        """Returns a retry policy to be passed onto _with_retry."""

        defaults = dict(STANDARD_RETRY_PARAMS)
        defaults.update(retryPolicy)
        return defaults

    def _build_retry_policy_async(
        self, retry_policy: Dict[str, Any] = {}
    ) -> Dict[str, Any]:
        """Returns a retry policy to be passed onto with_retry_time_based_async."""

        defaults = dict(STANDARD_RETRY_ASYNC_PARAMS)
        defaults.update(retry_policy)
        return defaults

    def _return_rest_body(self, response) -> Union[Dict[str, Any], str]:
        """Returns either a dictionary or a string depending on the 'content-type' of the response."""
        if is_json(response.headers.get("content-type", None)):
            return response.json()
        return response.text

    async def _rest_call_async(
        self,
        method: str,
        uri: str,
        data: Any,
        endpoint: str,
        headers: Dict[str, str],
        retry_policy: Dict[str, Any],
        requests_session_async_synapse: httpx.AsyncClient,
        **kwargs,
    ) -> Union[httpx.Response, None]:
        """
        Sends an HTTP request to the Synapse server.

        Arguments:
            method: The method to implement Create, Read, Update, Delete operations.
                Should be post, get, put, delete.
            uri: URI on which the method is performed.
            data: The payload to be delivered.
            endpoint: Server endpoint, defaults to self.repoEndpoint
            headers: Dictionary of headers to use.
            retry_policy: A retry policy that matches the arguments of
                [synapseclient.core.retry.with_retry_time_based_async][].
            requests_session_async_synapse: The async client to use when making this
                specific call.
            kwargs: Any other arguments taken by a
                [request](https://www.python-httpx.org/api/) method

        Returns:
            JSON encoding of response
        """
        uri, headers = self._build_uri_and_headers(
            uri, endpoint=endpoint, headers=headers
        )

        retry_policy = self._build_retry_policy_async(retry_policy)
        requests_session = (
            requests_session_async_synapse
            or self._get_requests_session_async_synapse(
                asyncio_event_loop=asyncio.get_running_loop()
            )
        )

        auth = kwargs.pop("auth", self.credentials)
        requests_method_fn = getattr(requests_session, method)
        if data:
            response = await with_retry_time_based_async(
                lambda: requests_method_fn(
                    uri,
                    content=data,
                    headers=headers,
                    auth=auth,
                    **kwargs,
                ),
                verbose=self.debug,
                **retry_policy,
            )
        else:
            response = await with_retry_time_based_async(
                lambda: requests_method_fn(
                    uri,
                    headers=headers,
                    auth=auth,
                    **kwargs,
                ),
                verbose=self.debug,
                **retry_policy,
            )

        self._handle_httpx_synapse_http_error(response)

        return response

    async def rest_get_async(
        self,
        uri: str,
        endpoint: str = None,
        headers: httpx.Headers = None,
        retry_policy: Dict[str, Any] = {},
        requests_session_async_synapse: httpx.AsyncClient = None,
        **kwargs,
    ) -> Union[Dict[str, Any], str, None]:
        """
        Sends an HTTP GET request to the Synapse server.

        Arguments:
            uri: URI on which get is performed
            endpoint: Server endpoint, defaults to self.repoEndpoint
            headers: Dictionary of headers to use.
            retry_policy: A retry policy that matches the arguments of
                [synapseclient.core.retry.with_retry_time_based_async][].
            requests_session_async_synapse: The async client to use when making this
                specific call.
            kwargs: Any other arguments taken by a
                [request](https://www.python-httpx.org/api/) method

        Returns:
            JSON encoding of response
        """
        try:
            response = await self._rest_call_async(
                "get",
                uri,
                None,
                endpoint,
                headers,
                retry_policy,
                requests_session_async_synapse,
                **kwargs,
            )
            return self._return_rest_body(response)
        except Exception:
            self.logger.exception("Error in rest_get_async")

    async def rest_post_async(
        self,
        uri: str,
        body: Any = None,
        endpoint: str = None,
        headers: httpx.Headers = None,
        retry_policy: Dict[str, Any] = {},
        requests_session_async_synapse: httpx.AsyncClient = None,
        **kwargs,
    ) -> Union[Dict[str, Any], str]:
        """
        Sends an HTTP POST request to the Synapse server.

        Arguments:
            uri: URI on which get is performed
            body: The payload to be delivered
            endpoint: Server endpoint, defaults to self.repoEndpoint
            headers: Dictionary of headers to use.
            retry_policy: A retry policy that matches the arguments of
                [synapseclient.core.retry.with_retry_time_based_async][].
            requests_session_async_synapse: The async client to use when making this
                specific call.
            kwargs: Any other arguments taken by a
                [request](https://www.python-httpx.org/api/) method

        Returns:
            JSON encoding of response
        """
        response = await self._rest_call_async(
            "post",
            uri,
            body,
            endpoint,
            headers,
            retry_policy,
            requests_session_async_synapse,
            **kwargs,
        )
        return self._return_rest_body(response)

    async def rest_put_async(
        self,
        uri: str,
        body: Any = None,
        endpoint: str = None,
        headers: httpx.Headers = None,
        retry_policy: Dict[str, Any] = {},
        requests_session_async_synapse: httpx.AsyncClient = None,
        **kwargs,
    ) -> Union[Dict[str, Any], str]:
        """
        Sends an HTTP PUT request to the Synapse server.

        Arguments:
            uri: URI on which get is performed
            body: The payload to be delivered.
            endpoint: Server endpoint, defaults to self.repoEndpoint
            headers: Dictionary of headers to use.
            retry_policy: A retry policy that matches the arguments of
                [synapseclient.core.retry.with_retry_time_based_async][].
            requests_session_async_synapse: The async client to use when making this
                specific call.
            kwargs: Any other arguments taken by a
                [request](https://www.python-httpx.org/api/) method

        Returns
            JSON encoding of response
        """
        response = await self._rest_call_async(
            "put",
            uri,
            body,
            endpoint,
            headers,
            retry_policy,
            requests_session_async_synapse,
            **kwargs,
        )
        return self._return_rest_body(response)

    async def rest_delete_async(
        self,
        uri: str,
        endpoint: str = None,
        headers: httpx.Headers = None,
        retry_policy: Dict[str, Any] = {},
        requests_session_async_synapse: httpx.AsyncClient = None,
        **kwargs,
    ) -> None:
        """
        Sends an HTTP DELETE request to the Synapse server.

        Arguments:
            uri: URI of resource to be deleted
            endpoint: Server endpoint, defaults to self.repoEndpoint
            headers: Dictionary of headers to use.
            retry_policy: A retry policy that matches the arguments of
                [synapseclient.core.retry.with_retry_time_based_async][].
            requests_session_async_synapse: The async client to use when making this
                specific call
            kwargs: Any other arguments taken by a [request](https://www.python-httpx.org/api/) method

        """
        await self._rest_call_async(
            "delete",
            uri,
            None,
            endpoint,
            headers,
            retry_policy,
            requests_session_async_synapse,
            **kwargs,
        )


async def async_request_hook_httpx(span: Span, request: httpx.Request) -> None:
    """Hook used to encapsulate a span for this library. The request hook is called
    shortly after entering the library. The response hook is called shortly before
    exiting the library."""
    try:
        syn_id = re.search(r"syn\d+", request.url).group()
        span.set_attribute("synapse.id", syn_id)
    except Exception:
        # Let this silently fail at this point. To revist later.
        pass


async def async_response_hook_httpx(
    span: Span, request: httpx.Request, response: httpx.Response
) -> None:
    """Hook used to encapsulate a span for this library. The request hook is called
    shortly after entering the library. The response hook is called shortly before
    exiting the library."""
    pass


def request_hook_requests(span: Span, request_obj: requests.PreparedRequest) -> None:
    """Hook used to encapsulate a span for this library. The request hook is called
    shortly after entering the library. The response hook is called shortly before
    exiting the library."""
    try:
        syn_id = re.search(r"syn\d+", request_obj.url).group()
        span.set_attribute("synapse.id", syn_id)
    except Exception:
        # Let this silently fail at this point. To revist later.
        pass


def response_hook_requests(
    span: Span, request_obj: requests.PreparedRequest, response: requests.Response
) -> None:
    """Hook used to encapsulate a span for this library. The request hook is called
    shortly after entering the library. The response hook is called shortly before
    exiting the library."""
    pass


def request_hook_urllib(span: Span, request_obj: urllib_request.Request) -> None:
    """Hook used to encapsulate a span for this library. The request hook is called
    shortly after entering the library. The response hook is called shortly before
    exiting the library."""
    try:
        syn_id = re.search(r"syn\d+", request_obj.full_url).group()
        span.set_attribute("synapse.id", syn_id)
    except Exception:
        # Let this silently fail at this point. To revist later.
        pass


def response_hook_urllib(
    span: Span, request_obj: urllib_request.Request, response: HTTPResponse
) -> None:
    """Hook used to encapsulate a span for this library. The request hook is called
    shortly after entering the library. The response hook is called shortly before
    exiting the library."""
    pass


# These libraries are used to automatically trace requests made by the Synapse client.
# As well as the ThreadingInstrumentor provides context propagation through threads.
def set_up_tracing(enabled: bool) -> None:
    if enabled:
        ThreadingInstrumentor().instrument()
        HTTPXClientInstrumentor().instrument(
            async_request_hook=async_request_hook_httpx,
            async_response_hook=async_response_hook_httpx,
        )
        RequestsInstrumentor().instrument(
            request_hook=request_hook_requests, response_hook=response_hook_requests
        )
        URLLibInstrumentor().instrument(
            request_hook=request_hook_urllib, response_hook=response_hook_urllib
        )
    else:
        ThreadingInstrumentor().uninstrument()
        HTTPXClientInstrumentor().uninstrument()
        RequestsInstrumentor().uninstrument()
        URLLibInstrumentor().uninstrument()