Hello,
I tried to download sample data from Synapse demo project (Simple matrix example Python).
So, I logined into synapse on python, and tried to get demo files.
```
Iimport synapseclient
import synapseutils
syn = synapseclient.Synapse()
syn.login('synapse_username','password')
files = synapseutils.syncFromSynapse(syn, 'syn1901030')
```
and the result was as below
```
Welcome, My name!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
WARNING: ifcollision=overwrite.localis being IGNORED because the download destination is synapse's cache. Instead, the behavior is "overwrite.local".
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Traceback (most recent call last):
File "getSynapse.py", line 11, in
files = synapseutils.syncFromSynapse(syn, 'syn1901030')
File "/usr/local/lib/python2.7/dist-packages/synapseutils/sync.py", line 84, in syncFromSynapse
ent = syn.get(result['entity.id'], downloadLocation = path, ifcollision = ifcollision, followLink=followLink)
File "/usr/local/lib/python2.7/dist-packages/synapseclient/client.py", line 695, in get
return self._getWithEntityBundle(entityBundle=bundle, entity=entity, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/synapseclient/client.py", line 784, in _getWithEntityBundle
self._download_file_entity(downloadLocation, entity, ifcollision, submission)
File "/usr/local/lib/python2.7/dist-packages/synapseclient/client.py", line 841, in _download_file_entity
downloadPath)
File "/usr/local/lib/python2.7/dist-packages/synapseclient/client.py", line 1847, in _downloadFileHandle
raise exc_info[0](exc_info[1])
**io.UnsupportedOperation: seek**
```
Could you check why this error occurs? and How can I solve this problem?
Created by Seunghwan Shin dolph04 Hello
I got the error as shown below
```
Traceback (most recent call last):
File "getSynapse.py", line 25, in
aFile = syn.get('syn1901031')
File "/usr/local/lib/python2.7/dist-packages/synapseclient/client.py", line 695, in get
return self._getWithEntityBundle(entityBundle=bundle, entity=entity, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/synapseclient/client.py", line 784, in _getWithEntityBundle
self._download_file_entity(downloadLocation, entity, ifcollision, submission)
File "/usr/local/lib/python2.7/dist-packages/synapseclient/client.py", line 841, in _download_file_entity
downloadPath)
File "/usr/local/lib/python2.7/dist-packages/synapseclient/client.py", line 1847, in _downloadFileHandle
raise exc_info[0](exc_info[1])
io.UnsupportedOperation: seek
```
and synapseclient.__version__ is '1.7.2'
Thank you!
Could you try to use `syn.get` to get a single file? In your example syn1901030 is a Folder. The `syn.get` function does not fetch the whole contents of a Folder. You could try this ID, which is a File in the Folder you tried:
```
aFile = syn.get('syn1901031')
```
Let's see if you get the same error.
Could you also let me know what version of the Synapse Python client you have?
```
import synapseclient
synapseclient.__version__
```
Thanks! 1. ubuntu 14.04
2. Python 2.7.6
3. Company network
I tried to use syn.get('syn1901030') instead of synapseutils.syncFromSynapse(syn, 'syn1901030'), then I got entity information as below
```
Folder: Simple matrix example Python (syn1901030)
path=.
properties:
accessControlList=/repo/v1/entity/syn1901030/acl
annotations=/repo/v1/entity/syn1901030/annotations
concreteType=org.sagebionetworks.repo.model.Folder
createdBy=377358
createdOn=2013-06-01T18:29:24.698Z
entityType=org.sagebionetworks.repo.model.Folder
etag=44bb5acd-311f-4d8d-8964-1ad3358645ce
id=syn1901030
modifiedBy=377358
modifiedOn=2013-06-01T18:29:24.698Z
name=Simple matrix example Python
parentId=syn1899339
uri=/repo/v1/entity/syn1901030
annotations:
```
However, when I try to download files by using syncFromSynapse, the upper error occurs.
My system is connected to our corporate networks. Therefore, some security settings may be a problem.
To download files from synapse by using Python/R, what additional security settings should I change?
Thanks for the report, @dolph04!
There are two things going on there: The `WARNING` is explainable, and I have filed a bug report for that (it can safely be ignored):
https://sagebionetworks.jira.com/browse/SYNPY-570
The error you're getting I'm not sure about. I have filed a separate bug report for that as well:
https://sagebionetworks.jira.com/browse/SYNPY-571
1. What operating system are you using?
1. What Python version?
1. Anything else about your operating environment (shared HPC system, AWS, etc).
Thanks!
Drop files to upload
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