I need help with some issues I'm facing when trying to download data from the _CTSP-DLBCL-AWG_ project hosted on here in Synapse.
My Synapse account seems to work fine see below.
I also have check that my configuration file (/home/.synapseConfig.) has the right user and token,
But when I try to download the files, I get the following errors. It seems that the issues are related to AWS, but I am not aware of the need for AWS credentials for this project. If I do need them, I don't know how to proceed with those credentials. Can you help me figure out what I am missing?
**Testing my account login **
```
synapse login -p $MY_SYNAPSE_TOKEN
UPGRADE AVAILABLE
A more recent version of the Synapse Client (4.6.0) is available. Your version (4.5.1) can be upgraded by typing:
pip install --upgrade synapseclient
Python Synapse Client version 4.6.0 release notes
https://python-docs.synapse.org/news/
Welcome, Alexander Martinez-Fundichely!
Logged in as: Alexander (3336115)
Use `synapse config` to create or modify a Synapse configuration file. This will allow all commands to authenticate without passing in an Auth Token.
`synapse login` is only used to verify your credentials are valid to login.
```
**Trying to download the files**
```
synapse get -r syn25925371
UPGRADE AVAILABLE
A more recent version of the Synapse Client (4.6.0) is available. Your version (4.5.1) can be upgraded by typing:
pip install --upgrade synapseclient
Python Synapse Client version 4.6.0 release notes
https://python-docs.synapse.org/news/
Syncing Folder (syn25925371:DLBCL_enhancers) from Synapse.
Syncing Folder (syn25925372:Bunting_et_al_2016) from Synapse.
Syncing Folder (syn50694641:Bradner and Payton Super-enhancer Lists) from Synapse.
Provided region_name 'us-east-1 # or your preferred AWS region' doesn't match a supported format.
Traceback (most recent call last):
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/models/services/storable_entity_components.py", line 39, in wrap_coroutine
return await task
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/async_utils.py", line 56, in otel_trace_method_wrapper
return await func(self, *arg, **kwargs)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/models/file.py", line 1013, in get_async
await get_from_entity_factory(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/api/entity_factory.py", line 137, in get_from_entity_factory
return_data = await _cast_into_class_type(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/api/entity_factory.py", line 331, in _cast_into_class_type
await download_file_entity_model(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/download/download_functions.py", line 283, in download_file_entity_model
download_path = await download_by_file_handle(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/download/download_functions.py", line 435, in download_by_file_handle
downloaded_path = await loop.run_in_executor(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/concurrent/futures/thread.py", line 57, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/download/download_functions.py", line 437, in
lambda: S3ClientWrapper.download_file(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/remote_file_storage_wrappers.py", line 119, in download_file
s3 = boto_session.resource("s3", endpoint_url=endpoint_url)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/boto3/session.py", line 444, in resource
client = self.client(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/boto3/session.py", line 297, in client
return self._session.create_client(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/botocore/session.py", line 924, in create_client
region_name = self._resolve_region_name(region_name, config)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/botocore/session.py", line 1023, in _resolve_region_name
validate_region_name(region_name)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/botocore/utils.py", line 1318, in validate_region_name
raise InvalidRegionError(region_name=region_name)
botocore.exceptions.InvalidRegionError: Provided region_name 'us-east-1 # or your preferred AWS region' doesn't match a supported format.
Provided region_name 'us-east-1 # or your preferred AWS region' doesn't match a supported format.
Traceback (most recent call last):
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/models/services/storable_entity_components.py", line 39, in wrap_coroutine
return await task
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/async_utils.py", line 56, in otel_trace_method_wrapper
return await func(self, *arg, **kwargs)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/models/file.py", line 1013, in get_async
await get_from_entity_factory(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/api/entity_factory.py", line 137, in get_from_entity_factory
return_data = await _cast_into_class_type(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/api/entity_factory.py", line 331, in _cast_into_class_type
await download_file_entity_model(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/download/download_functions.py", line 283, in download_file_entity_model
download_path = await download_by_file_handle(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/download/download_functions.py", line 435, in download_by_file_handle
downloaded_path = await loop.run_in_executor(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/concurrent/futures/thread.py", line 57, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/download/download_functions.py", line 437, in
lambda: S3ClientWrapper.download_file(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/remote_file_storage_wrappers.py", line 119, in download_file
s3 = boto_session.resource("s3", endpoint_url=endpoint_url)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/boto3/session.py", line 444, in resource
client = self.client(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/boto3/session.py", line 297, in client
return self._session.create_client(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/botocore/session.py", line 924, in create_client
region_name = self._resolve_region_name(region_name, config)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/botocore/session.py", line 1023, in _resolve_region_name
validate_region_name(region_name)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/botocore/utils.py", line 1318, in validate_region_name
raise InvalidRegionError(region_name=region_name)
botocore.exceptions.InvalidRegionError: Provided region_name 'us-east-1 # or your preferred AWS region' doesn't match a supported format.
Provided region_name 'us-east-1 # or your preferred AWS region' doesn't match a supported format.
Traceback (most recent call last):
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/models/services/storable_entity_components.py", line 39, in wrap_coroutine
return await task
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/async_utils.py", line 56, in otel_trace_method_wrapper
return await func(self, *arg, **kwargs)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/models/file.py", line 1013, in get_async
await get_from_entity_factory(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/api/entity_factory.py", line 137, in get_from_entity_factory
return_data = await _cast_into_class_type(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/api/entity_factory.py", line 331, in _cast_into_class_type
await download_file_entity_model(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/download/download_functions.py", line 283, in download_file_entity_model
download_path = await download_by_file_handle(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/download/download_functions.py", line 435, in download_by_file_handle
downloaded_path = await loop.run_in_executor(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/concurrent/futures/thread.py", line 57, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/download/download_functions.py", line 437, in
lambda: S3ClientWrapper.download_file(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/remote_file_storage_wrappers.py", line 119, in download_file
s3 = boto_session.resource("s3", endpoint_url=endpoint_url)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/boto3/session.py", line 444, in resource
client = self.client(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/boto3/session.py", line 297, in client
return self._session.create_client(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/botocore/session.py", line 924, in create_client
region_name = self._resolve_region_name(region_name, config)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/botocore/session.py", line 1023, in _resolve_region_name
validate_region_name(region_name)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/botocore/utils.py", line 1318, in validate_region_name
raise InvalidRegionError(region_name=region_name)
botocore.exceptions.InvalidRegionError: Provided region_name 'us-east-1 # or your preferred AWS region' doesn't match a supported format.
Provided region_name 'us-east-1 # or your preferred AWS region' doesn't match a supported format.
Traceback (most recent call last):
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/models/services/storable_entity_components.py", line 39, in wrap_coroutine
return await task
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/async_utils.py", line 56, in otel_trace_method_wrapper
return await func(self, *arg, **kwargs)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/models/file.py", line 1013, in get_async
await get_from_entity_factory(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/api/entity_factory.py", line 137, in get_from_entity_factory
return_data = await _cast_into_class_type(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/api/entity_factory.py", line 331, in _cast_into_class_type
await download_file_entity_model(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/download/download_functions.py", line 283, in download_file_entity_model
download_path = await download_by_file_handle(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/download/download_functions.py", line 435, in download_by_file_handle
downloaded_path = await loop.run_in_executor(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/concurrent/futures/thread.py", line 57, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/download/download_functions.py", line 437, in
lambda: S3ClientWrapper.download_file(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/remote_file_storage_wrappers.py", line 119, in download_file
s3 = boto_session.resource("s3", endpoint_url=endpoint_url)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/boto3/session.py", line 444, in resource
client = self.client(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/boto3/session.py", line 297, in client
return self._session.create_client(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/botocore/session.py", line 924, in create_client
region_name = self._resolve_region_name(region_name, config)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/botocore/session.py", line 1023, in _resolve_region_name
validate_region_name(region_name)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/botocore/utils.py", line 1318, in validate_region_name
raise InvalidRegionError(region_name=region_name)
botocore.exceptions.InvalidRegionError: Provided region_name 'us-east-1 # or your preferred AWS region' doesn't match a supported format.
Provided region_name 'us-east-1 # or your preferred AWS region' doesn't match a supported format.
Traceback (most recent call last):
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/models/services/storable_entity_components.py", line 39, in wrap_coroutine
return await task
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/async_utils.py", line 56, in otel_trace_method_wrapper
return await func(self, *arg, **kwargs)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/models/file.py", line 1013, in get_async
await get_from_entity_factory(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/api/entity_factory.py", line 137, in get_from_entity_factory
return_data = await _cast_into_class_type(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/api/entity_factory.py", line 331, in _cast_into_class_type
await download_file_entity_model(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/download/download_functions.py", line 283, in download_file_entity_model
download_path = await download_by_file_handle(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/download/download_functions.py", line 435, in download_by_file_handle
downloaded_path = await loop.run_in_executor(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/concurrent/futures/thread.py", line 57, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/download/download_functions.py", line 437, in
lambda: S3ClientWrapper.download_file(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/remote_file_storage_wrappers.py", line 119, in download_file
s3 = boto_session.resource("s3", endpoint_url=endpoint_url)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/boto3/session.py", line 444, in resource
client = self.client(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/boto3/session.py", line 297, in client
return self._session.create_client(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/botocore/session.py", line 924, in create_client
region_name = self._resolve_region_name(region_name, config)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/botocore/session.py", line 1023, in _resolve_region_name
validate_region_name(region_name)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/botocore/utils.py", line 1318, in validate_region_name
raise InvalidRegionError(region_name=region_name)
botocore.exceptions.InvalidRegionError: Provided region_name 'us-east-1 # or your preferred AWS region' doesn't match a supported format.
Provided region_name 'us-east-1 # or your preferred AWS region' doesn't match a supported format.
Traceback (most recent call last):
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/models/services/storable_entity_components.py", line 39, in wrap_coroutine
return await task
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/async_utils.py", line 56, in otel_trace_method_wrapper
return await func(self, *arg, **kwargs)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/models/file.py", line 1013, in get_async
await get_from_entity_factory(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/api/entity_factory.py", line 137, in get_from_entity_factory
return_data = await _cast_into_class_type(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/api/entity_factory.py", line 331, in _cast_into_class_type
await download_file_entity_model(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/download/download_functions.py", line 283, in download_file_entity_model
download_path = await download_by_file_handle(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/download/download_functions.py", line 435, in download_by_file_handle
downloaded_path = await loop.run_in_executor(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/concurrent/futures/thread.py", line 57, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/download/download_functions.py", line 437, in
lambda: S3ClientWrapper.download_file(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/synapseclient/core/remote_file_storage_wrappers.py", line 119, in download_file
s3 = boto_session.resource("s3", endpoint_url=endpoint_url)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/boto3/session.py", line 444, in resource
client = self.client(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/boto3/session.py", line 297, in client
return self._session.create_client(
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/botocore/session.py", line 924, in create_client
region_name = self._resolve_region_name(region_name, config)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/botocore/session.py", line 1023, in _resolve_region_name
validate_region_name(region_name)
File "/home/fs01/alm2069/.conda/envs/synapse-env/lib/python3.8/site-packages/botocore/utils.py", line 1318, in validate_region_name
raise InvalidRegionError(region_name=region_name)
botocore.exceptions.InvalidRegionError: Provided region_name 'us-east-1 # or your preferred AWS region' doesn't match a supported format.
Provided region_name 'us-east-1 # or your preferred AWS region' doesn't match a supported format.
NoneType: None
Provided region_name 'us-east-1 # or your preferred AWS region' doesn't match a supported format.
NoneType: None
Provided region_name 'us-east-1 # or your preferred AWS region' doesn't match a supported format.
NoneType: None
Provided region_name 'us-east-1 # or your preferred AWS region' doesn't match a supported format.
NoneType: None
Provided region_name 'us-east-1 # or your preferred AWS region' doesn't match a supported format.
NoneType: None
Provided region_name 'us-east-1 # or your preferred AWS region' doesn't match a supported format.
NoneType: None
Downloading files: 0%| | 0.00/1.00 [00:03Created by Alexander Martinez-Fundichely Alexander Hi @Alexander ,
Thanks - I think we corresponded in the service desk, what I meant was to post in the Discussion forum of the Project itself: syn25925371.
You can find a "Discussion" tab where the data contributors of the project could help you with data access. It appears that they have special setup of the project which I'm not knowledgable about.
It may also help to email the data contributors and managers of that project, as Sage does not manage the project.
Drop files to upload
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