synapseclient 4.2.0__tar.gz → 4.3.1__tar.gz

{synapseclient-4.2.0/synapseclient.egg-info → synapseclient-4.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: synapseclient
-Version: 4.2.0
+Version: 4.3.1
 Summary: A client for Synapse, a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate.
 Home-page: https://www.synapse.org
 Author: The Synapse Engineering Team
@@ -39,14 +39,13 @@ Requires-Dist: nest-asyncio~=1.6.0
 Requires-Dist: asyncio-atexit~=1.0.1
 Requires-Dist: httpx~=0.27.0
 Requires-Dist: tqdm<5.0,>=4.66.2
-Requires-Dist: loky~=3.0.0
 Requires-Dist: async-lru~=2.0.4
 Requires-Dist: psutil~=5.9.8
 Provides-Extra: dev
-Requires-Dist: pytest<7.0,>=6.0.0; extra == "dev"
+Requires-Dist: pytest<8.0,>=7.0.0; extra == "dev"
 Requires-Dist: pytest-mock<4.0,>=3.0; extra == "dev"
 Requires-Dist: pytest-socket~=0.6.0; extra == "dev"
-Requires-Dist: pytest-asyncio~=0.19; extra == "dev"
+Requires-Dist: pytest-asyncio<1.0,>=0.23.6; extra == "dev"
 Requires-Dist: flake8<4.0,>=3.7.0; extra == "dev"
 Requires-Dist: pytest-xdist[psutil]<3.0.0,>=2.2; extra == "dev"
 Requires-Dist: pytest-rerunfailures~=12.0; extra == "dev"
@@ -54,16 +53,18 @@ Requires-Dist: func-timeout~=4.3; extra == "dev"
 Requires-Dist: pytest-cov~=4.1.0; extra == "dev"
 Requires-Dist: black; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: pandas<3.0,>=1.5; extra == "dev"
 Provides-Extra: tests
-Requires-Dist: pytest<7.0,>=6.0.0; extra == "tests"
+Requires-Dist: pytest<8.0,>=7.0.0; extra == "tests"
 Requires-Dist: pytest-mock<4.0,>=3.0; extra == "tests"
 Requires-Dist: pytest-socket~=0.6.0; extra == "tests"
-Requires-Dist: pytest-asyncio~=0.19; extra == "tests"
+Requires-Dist: pytest-asyncio<1.0,>=0.23.6; extra == "tests"
 Requires-Dist: flake8<4.0,>=3.7.0; extra == "tests"
 Requires-Dist: pytest-xdist[psutil]<3.0.0,>=2.2; extra == "tests"
 Requires-Dist: pytest-rerunfailures~=12.0; extra == "tests"
 Requires-Dist: func-timeout~=4.3; extra == "tests"
 Requires-Dist: pytest-cov~=4.1.0; extra == "tests"
+Requires-Dist: pandas<3.0,>=1.5; extra == "tests"
 Provides-Extra: pandas
 Requires-Dist: pandas<3.0,>=1.5; extra == "pandas"
 Provides-Extra: pysftp
@@ -125,16 +126,24 @@ The Python Synapse client has been tested on 3.8, 3.9, 3.10 and 3.11 on Mac OS X
 
 The [Python Synapse Client is on PyPI](https://pypi.python.org/pypi/synapseclient) and can be installed with pip:
 
-    (sudo) pip install synapseclient[pandas,pysftp]
+    # Here are a few ways to install the client. Choose the one that fits your use-case
+    # sudo may optionally be needed depending on your setup
+
+    pip install --upgrade synapseclient
+    pip install --upgrade "synapseclient[pandas]"
+    pip install --upgrade "synapseclient[pandas, pysftp, boto3]"
 
 ...or to upgrade an existing installation of the Synapse client:
 
-    (sudo) pip install --upgrade synapseclient
+    # sudo may optionally be needed depending on your setup
+    pip install --upgrade synapseclient
 
-The dependencies on `pandas` and `pysftp` are optional. Synapse [Tables](https://python-docs.synapse.org/reference/tables/) integrate
+The dependencies on `pandas`, `pysftp`, and `boto3` are optional. Synapse
+[Tables](https://python-docs.synapse.org/reference/tables/) integrate
 with [Pandas](http://pandas.pydata.org/). The library `pysftp` is required for users of
-[SFTP](https://python-docs.synapse.org/guides/data_storage/#sftp) file storage. Both libraries require native code
-to be compiled or installed separately from prebuilt binaries.
+[SFTP](https://python-docs.synapse.org/guides/data_storage/#sftp) file storage. All
+libraries require native code to be compiled or installed separately from prebuilt
+binaries.
 
 ### Install from source
 
@@ -144,6 +153,13 @@ Clone the [source code repository](https://github.com/Sage-Bionetworks/synapsePy
     cd synapsePythonClient
     pip install .
 
+Alternatively, you can use pip to install a particular branch, commit, or other git reference:
+
+    pip install git+https://github.com/Sage-Bionetworks/synapsePythonClient@master
+
+or
+
+    pip install git+https://github.com/Sage-Bionetworks/synapsePythonClient@my-commit-hash
 
 Command line usage
 ------------------

{synapseclient-4.2.0 → synapseclient-4.3.1}/README.md

@@ -44,16 +44,24 @@ The Python Synapse client has been tested on 3.8, 3.9, 3.10 and 3.11 on Mac OS X
 
 The [Python Synapse Client is on PyPI](https://pypi.python.org/pypi/synapseclient) and can be installed with pip:
 
-    (sudo) pip install synapseclient[pandas,pysftp]
+    # Here are a few ways to install the client. Choose the one that fits your use-case
+    # sudo may optionally be needed depending on your setup
+
+    pip install --upgrade synapseclient
+    pip install --upgrade "synapseclient[pandas]"
+    pip install --upgrade "synapseclient[pandas, pysftp, boto3]"
 
 ...or to upgrade an existing installation of the Synapse client:
 
-    (sudo) pip install --upgrade synapseclient
+    # sudo may optionally be needed depending on your setup
+    pip install --upgrade synapseclient
 
-The dependencies on `pandas` and `pysftp` are optional. Synapse [Tables](https://python-docs.synapse.org/reference/tables/) integrate
+The dependencies on `pandas`, `pysftp`, and `boto3` are optional. Synapse
+[Tables](https://python-docs.synapse.org/reference/tables/) integrate
 with [Pandas](http://pandas.pydata.org/). The library `pysftp` is required for users of
-[SFTP](https://python-docs.synapse.org/guides/data_storage/#sftp) file storage. Both libraries require native code
-to be compiled or installed separately from prebuilt binaries.
+[SFTP](https://python-docs.synapse.org/guides/data_storage/#sftp) file storage. All
+libraries require native code to be compiled or installed separately from prebuilt
+binaries.
 
 ### Install from source
 
@@ -63,6 +71,13 @@ Clone the [source code repository](https://github.com/Sage-Bionetworks/synapsePy
     cd synapsePythonClient
     pip install .
 
+Alternatively, you can use pip to install a particular branch, commit, or other git reference:
+
+    pip install git+https://github.com/Sage-Bionetworks/synapsePythonClient@master
+
+or
+
+    pip install git+https://github.com/Sage-Bionetworks/synapsePythonClient@my-commit-hash
 
 Command line usage
 ------------------

{synapseclient-4.2.0 → synapseclient-4.3.1}/setup.cfg

@@ -48,26 +48,26 @@ install_requires =
 	asyncio-atexit~=1.0.1
 	httpx~=0.27.0
 	tqdm>=4.66.2,<5.0
-	loky~=3.0.0
 	async-lru~=2.0.4
 	psutil~=5.9.8
 tests_require = 
-	pytest>=6.0.0,<7.0
+	pytest>=7.0.0,<8.0
 	pytest-mock>=3.0,<4.0
 	pytest-socket~=0.6.0
-	pytest-asyncio~=0.19
+	pytest-asyncio>=0.23.6,<1.0
 	flake8>=3.7.0,<4.0
 	pytest-xdist[psutil]>=2.2,<3.0.0
 	pytest-rerunfailures~=12.0
 	func-timeout~=4.3
 	pytest-cov~=4.1.0
+	pandas>=1.5,<3.0
 
 [options.extras_require]
 dev = 
-	pytest>=6.0.0,<7.0
+	pytest>=7.0.0,<8.0
 	pytest-mock>=3.0,<4.0
 	pytest-socket~=0.6.0
-	pytest-asyncio~=0.19
+	pytest-asyncio>=0.23.6,<1.0
 	flake8>=3.7.0,<4.0
 	pytest-xdist[psutil]>=2.2,<3.0.0
 	pytest-rerunfailures~=12.0
@@ -75,16 +75,18 @@ dev =
 	pytest-cov~=4.1.0
 	black
 	pre-commit
+	pandas>=1.5,<3.0
 tests = 
-	pytest>=6.0.0,<7.0
+	pytest>=7.0.0,<8.0
 	pytest-mock>=3.0,<4.0
 	pytest-socket~=0.6.0
-	pytest-asyncio~=0.19
+	pytest-asyncio>=0.23.6,<1.0
 	flake8>=3.7.0,<4.0
 	pytest-xdist[psutil]>=2.2,<3.0.0
 	pytest-rerunfailures~=12.0
 	func-timeout~=4.3
 	pytest-cov~=4.1.0
+	pandas>=1.5,<3.0
 pandas = 
 	pandas>=1.5,<3.0
 pysftp = 

{synapseclient-4.2.0 → synapseclient-4.3.1}/synapseclient/__init__.py

@@ -88,6 +88,11 @@ USER_AGENT = {
     % (__version__, requests.utils.default_user_agent())
 }
 
+USER_AGENT_COMMAND_LINE = {
+    "User-Agent": "synapsecommandlineclient/%s %s"
+    % (__version__, requests.utils.default_user_agent())
+}
+
 # patch json
 from .core.models import custom_json  # noqa
 

{synapseclient-4.2.0 → synapseclient-4.3.1}/synapseclient/__main__.py

@@ -1871,9 +1871,7 @@ def _authenticate_login(
 
 def main():
     args = build_parser().parse_args()
-    synapseclient.USER_AGENT["User-Agent"] = (
-        "synapsecommandlineclient " + synapseclient.USER_AGENT["User-Agent"]
-    )
+    synapseclient.USER_AGENT = synapseclient.USER_AGENT_COMMAND_LINE
     if args.otel:
         trace.set_tracer_provider(
             TracerProvider(

{synapseclient-4.2.0 → synapseclient-4.3.1}/synapseclient/api/__init__.py

@@ -13,6 +13,7 @@ from .entity_services import (
     post_entity,
     put_entity,
     create_access_requirements_if_none,
+    delete_entity_generated_by,
 )
 from .file_services import (
     get_file_handle,
@@ -51,4 +52,5 @@ __all__ = [
     "get_upload_destination",
     "get_upload_destination_location",
     "create_access_requirements_if_none",
+    "delete_entity_generated_by",
 ]

{synapseclient-4.2.0 → synapseclient-4.3.1}/synapseclient/api/entity_services.py

@@ -175,3 +175,23 @@ async def create_access_requirements_if_none(
             "the Synapse access control team to start the process of adding "
             "terms-of-use or review board approval for this entity."
         )
+
+
+async def delete_entity_generated_by(
+    entity_id: str,
+    synapse_client: Optional["Synapse"] = None,
+) -> None:
+    """
+    Arguments:
+        entity_id: The ID of the entity.
+        synapse_client: If not passed in or None this will use the last client from
+            the `.login()` method.
+
+    Returns: None
+    """
+    from synapseclient import Synapse
+
+    client = Synapse.get_client(synapse_client=synapse_client)
+    return await client.rest_delete_async(
+        uri=f"/entity/{entity_id}/generatedBy",
+    )

{synapseclient-4.2.0 → synapseclient-4.3.1}/synapseclient/client.py

@@ -34,7 +34,6 @@ import httpx
 from deprecated import deprecated
 
 from concurrent.futures import ThreadPoolExecutor
-from loky import get_reusable_executor
 
 import synapseclient
 from .annotations import (
@@ -121,9 +120,6 @@ from synapseclient.core.upload.multipart_upload_async import (
     multipart_upload_string_async,
 )
 from synapseclient.core.remote_file_storage_wrappers import S3ClientWrapper, SFTPWrapper
-from synapseclient.core.upload.upload_functions import (
-    upload_file_handle,
-)
 from synapseclient.core.upload.upload_functions_async import (
     upload_file_handle as upload_file_handle_async,
     upload_synapse_s3,
@@ -136,7 +132,6 @@ from synapseclient.core.models.permission import Permissions
 from opentelemetry import trace
 from opentelemetry.trace import SpanKind
 
-
 tracer = trace.get_tracer("synapseclient")
 
 PRODUCTION_ENDPOINTS = {
@@ -348,7 +343,7 @@ class Synapse(object):
                 span.end()
 
         event_hooks = {"request": [log_request], "response": [log_response]}
-        httpx_timeout = httpx.Timeout(70)
+        httpx_timeout = httpx.Timeout(70, pool=None)
         self._requests_session_storage = requests_session_storage or httpx.Client(
             timeout=httpx_timeout, event_hooks=event_hooks
         )
@@ -402,7 +397,7 @@ class Synapse(object):
         self.max_threads = transfer_config["max_threads"]
         self._thread_executor = {}
         self._process_executor = {}
-        self._md5_semaphore = {}
+        self._parallel_file_transfer_semaphore = {}
         self.use_boto_sts_transfers = transfer_config["use_boto_sts"]
 
     def _get_requests_session_async_synapse(
@@ -435,7 +430,7 @@ class Synapse(object):
             await self._requests_session_async_synapse[asyncio_event_loop].aclose()
             del self._requests_session_async_synapse[asyncio_event_loop]
 
-        httpx_timeout = httpx.Timeout(70)
+        httpx_timeout = httpx.Timeout(70, pool=None)
         span_dict: Dict[httpx.Request, trace.Span] = {}
 
         async def log_request(request: httpx.Request) -> None:
@@ -513,54 +508,44 @@ class Synapse(object):
         asyncio_atexit.register(close_pool)
         return self._thread_executor[asyncio_event_loop]
 
-    def _get_process_pool_executor(self, asyncio_event_loop: asyncio.AbstractEventLoop):
+    def _get_parallel_file_transfer_semaphore(
+        self, asyncio_event_loop: asyncio.AbstractEventLoop
+    ) -> asyncio.Semaphore:
         """
-        Retrieve the process pool executor for the Synapse client. Or create a new one
-        if it does not exist. This executor is used for parallel processing of data.
+        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.
 
-        Note: Within Windows a ProcessPoolExecutor requires that the initial entry point
-        into the code be within a `if __name__ == "__main__":` block. This is not
-        possible within the current codebase as it would require everyone using this
-        library to have this as their entry point. As a result, the ProcessPoolExecutor
-        will not work within Windows.
-
-        To get around this Windows limitation this is using this package:
-        https://github.com/joblib/loky
-        """
-        if (
-            hasattr(self, "_process_executor")
-            and asyncio_event_loop in self._process_executor
-            and self._process_executor[asyncio_event_loop] is not None
-        ):
-            return self._process_executor[asyncio_event_loop]
-
-        self._process_executor.update({asyncio_event_loop: get_reusable_executor(1)})
+        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.
 
-        return self._process_executor[asyncio_event_loop]
-
-    def _get_md5_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 ensure that only one process is calculating the
-        MD5 hash at a time. This is to prevent the custom process pool executor from
-        thrashing or handling the waiting. We should let asyncio handle the waiting.
+        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 is expected to be called from within an AsyncIO loop.
+        This has not yet been applied to parallel file downloads. That will take place
+        later on.
         """
         if (
-            hasattr(self, "_md5_semaphore")
-            and asyncio_event_loop in self._md5_semaphore
-            and self._md5_semaphore[asyncio_event_loop] is not None
+            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._md5_semaphore[asyncio_event_loop]
+            return self._parallel_file_transfer_semaphore[asyncio_event_loop]
 
-        self._md5_semaphore.update({asyncio_event_loop: asyncio.Semaphore(1)})
+        self._parallel_file_transfer_semaphore.update(
+            {asyncio_event_loop: asyncio.Semaphore(max(self.max_threads * 2, 1))}
+        )
 
-        return self._md5_semaphore[asyncio_event_loop]
+        return self._parallel_file_transfer_semaphore[asyncio_event_loop]
 
     # initialize logging
     def _init_logger(self):
@@ -716,10 +701,10 @@ class Synapse(object):
         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. User defined arguments during a CLI session
-        2. User's Personal Access Token (aka: Synapse Auth Token)
+        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
-        3. .synapseConfig file (in user home folder unless configured otherwise)
         4. Retrieves user's authentication token from AWS SSM Parameter store (if configured)
 
         Arguments:
@@ -1729,7 +1714,6 @@ class Synapse(object):
         activityName=None,
         activityDescription=None,
         set_annotations=True,
-        async_file_handle_upload: bool = True,
     ):
         """
         Creates a new Entity or updates an existing Entity, uploading any files in the process.
@@ -1752,11 +1736,6 @@ class Synapse(object):
                             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.
-            async_file_handle_upload: Temporary feature flag that will be removed at an
-                unannounced later date. This is used during the Synapse Utils
-                syncToSynapse to disable the async file handle upload. The is because
-                the multi-threaded logic in the syncToSynapse is not compatible with
-                the async file handle upload.
 
         Returns:
             A Synapse Entity, Evaluation, or Wiki
@@ -1916,37 +1895,20 @@ class Synapse(object):
                         "Entities of type File must have a parentId."
                     )
 
-                if async_file_handle_upload:
-                    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,
-                    )
-                else:
-                    fileHandle = upload_file_handle(
+                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"),
-                        synapseStore=synapseStore,
+                        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"),
-                        max_threads=self.max_threads,
-                    )
+                    ),
+                    self,
+                )
                 properties["dataFileHandleId"] = fileHandle["id"]
                 local_state["_file_handle"] = fileHandle
 
@@ -3521,7 +3483,7 @@ class Synapse(object):
                     else:
                         mode = "wb"
                         previouslyTransferred = 0
-                        sig = hashlib.new("md5", usedforsecurity=False)
+                        sig = hashlib.new("md5", usedforsecurity=False)  # nosec
 
                     try:
                         with open(temp_destination, mode) as fd:
@@ -6027,7 +5989,6 @@ class Synapse(object):
                 else:
                     return
                 data_dict = json.loads(data_to_parse)
-
                 if "parentId" in data_dict:
                     current_span.set_attribute(
                         "synapse.parent_id", data_dict["parentId"]

{synapseclient-4.2.0 → synapseclient-4.3.1}/synapseclient/core/cache.py

@@ -87,7 +87,7 @@ class Cache:
             value = os.path.expandvars(os.path.expanduser(value))
             # create the cache_root_dir if it does not already exist
             if not os.path.exists(value):
-                os.makedirs(value)
+                os.makedirs(value, exist_ok=True)
         self.__dict__[key] = value
 
     def __init__(self, cache_root_dir=CACHE_ROOT_DIR, fanout=1000):

{synapseclient-4.2.0 → synapseclient-4.3.1}/synapseclient/core/credentials/credential_provider.py

@@ -209,9 +209,9 @@ class SynapseCredentialsProviderChain(object):
 
     By default this class uses the following providers in this order:
 
-    1. [UserArgsCredentialsProvider][synapseclient.core.credentials.credential_provider.UserArgsCredentialsProvider]
-    2. [EnvironmentVariableCredentialsProvider][synapseclient.core.credentials.credential_provider.EnvironmentVariableCredentialsProvider]
-    3. [ConfigFileCredentialsProvider][synapseclient.core.credentials.credential_provider.ConfigFileCredentialsProvider]
+    1. [ConfigFileCredentialsProvider][synapseclient.core.credentials.credential_provider.ConfigFileCredentialsProvider]
+    2. [UserArgsCredentialsProvider][synapseclient.core.credentials.credential_provider.UserArgsCredentialsProvider]
+    3. [EnvironmentVariableCredentialsProvider][synapseclient.core.credentials.credential_provider.EnvironmentVariableCredentialsProvider]
     4. [AWSParameterStoreCredentialsProvider][synapseclient.core.credentials.credential_provider.AWSParameterStoreCredentialsProvider]
 
     Attributes:

{synapseclient-4.2.0 → synapseclient-4.3.1}/synapseclient/core/logging_setup.py

@@ -96,6 +96,16 @@ logging_config.dictConfig(
                 "propagate": True,
             },
             SILENT_LOGGER_NAME: {"handlers": [], "level": "INFO", "propagate": False},
+            # "httpx": {
+            #     "handlers": ["debug_stderr"],
+            #     "level": "DEBUG",
+            #     "propagate": True,
+            # },
+            # "httpcore": {
+            #     "handlers": ["debug_stderr"],
+            #     "level": "DEBUG",
+            #     "propagate": True,
+            # },
         },
     }
 )

{synapseclient-4.2.0 → synapseclient-4.3.1}/synapseclient/core/retry.py

@@ -328,6 +328,8 @@ async def with_retry_time_based_async(
         caught_exception = None
         caught_exception_info = None
         response = None
+        current_span = trace.get_current_span()
+        current_span.set_attribute("synapse.retries", str(retries + 1))
 
         try:
             response = await function()
@@ -449,6 +451,8 @@ def with_retry_time_based(
         caught_exception = None
         caught_exception_info = None
         response = None
+        current_span = trace.get_current_span()
+        current_span.set_attribute("synapse.retries", str(retries + 1))
 
         try:
             response = function()

{synapseclient-4.2.0 → synapseclient-4.3.1}/synapseclient/core/upload/multipart_upload_async.py

@@ -64,6 +64,7 @@ flowchart  TD
 
 # pylint: disable=protected-access
 import asyncio
+from contextlib import contextmanager
 import gc
 import mimetypes
 import os
@@ -113,7 +114,7 @@ from synapseclient.core.upload.upload_utils import (
 )
 from synapseclient.core.utils import MB
 from synapseclient.core.utils import md5_fn as md5_fn_util
-from synapseclient.core.utils import md5_for_file_multiprocessing
+from synapseclient.core.utils import md5_for_file_hex
 
 if TYPE_CHECKING:
     from synapseclient import Synapse
@@ -126,6 +127,22 @@ MIN_PART_SIZE = 5 * MB
 DEFAULT_PART_SIZE = 8 * MB
 MAX_RETRIES = 7
 
+_thread_local = threading.local()
+
+
+@contextmanager
+def shared_progress_bar(progress_bar):
+    """An outside process that will eventually trigger an upload through this module
+    can configure a shared Progress Bar by running its code within this context manager.
+    """
+    _thread_local.progress_bar = progress_bar
+    try:
+        yield
+    finally:
+        _thread_local.progress_bar.close()
+        _thread_local.progress_bar.refresh()
+        del _thread_local.progress_bar
+
 
 @dataclass
 class HandlePartResult:
@@ -173,6 +190,7 @@ class UploadAttemptAsync:
         self._aborted = False
         self._storage_str = storage_str
 
+        self._close_progress_bar = getattr(_thread_local, "progress_bar", None) is None
         # populated later
         self._upload_id: Optional[str] = None
         self._pre_signed_part_urls: Optional[Mapping[int, str]] = None
@@ -329,7 +347,9 @@ class UploadAttemptAsync:
             if self._is_copy():
                 # we won't have bytes to measure during a copy so the byte oriented
                 # progress bar is not useful
-                self._progress_bar = tqdm(
+                self._progress_bar = getattr(
+                    _thread_local, "progress_bar", None
+                ) or tqdm(
                     total=part_count,
                     desc=self._storage_str or "Copying",
                     unit_scale=True,
@@ -343,7 +363,9 @@ class UploadAttemptAsync:
                     file_size,
                 )
 
-                self._progress_bar = tqdm(
+                self._progress_bar = getattr(
+                    _thread_local, "progress_bar", None
+                ) or tqdm(
                     total=file_size,
                     desc=self._storage_str or "Uploading",
                     unit="B",
@@ -448,7 +470,7 @@ class UploadAttemptAsync:
         Returns:
             The response from the server for the completed upload.
         """
-        if not self._syn.silent and self._progress_bar:
+        if not self._syn.silent and self._progress_bar and self._close_progress_bar:
             self._progress_bar.close()
         upload_status_response = await put_file_multipart_complete(
             upload_id=self._upload_id,
@@ -647,17 +669,7 @@ async def multipart_upload_file_async(
         mime_type, _ = mimetypes.guess_type(file_path, strict=False)
         content_type = mime_type or "application/octet-stream"
 
-    md5_hex = md5 or (
-        await md5_for_file_multiprocessing(
-            filename=file_path,
-            process_pool_executor=syn._get_process_pool_executor(
-                asyncio_event_loop=asyncio.get_running_loop()
-            ),
-            md5_semaphore=syn._get_md5_semaphore(
-                asyncio_event_loop=asyncio.get_running_loop()
-            ),
-        )
-    )
+    md5_hex = md5 or md5_for_file_hex(filename=file_path)
 
     part_size = get_part_size(
         part_size or DEFAULT_PART_SIZE,