Synapse provides physical storage for files using Amazon S3, however, you can configure your own custom storage locations as well. For example, data files can physically reside in your own S3 bucket, SFTP servers, or a local file server using a proxy servers. Creating a custom storage location allows you greater ownership and control of your files, especially when you have a large amount of data or when additional restrictions need to be set on the data.
...
| Code Block |
|---|
{
"Statement": [
{
"Action": [ "s3:ListBucket*", "s3:GetBucketLocation" ],
"Effect": "Allow",
"Resource": "arn:aws:s3:::synapse-share.yourcompany.com",
"Principal": { "AWS": "325565585839" }
},
{
"Action": [ "s3:GetObject*", "s3:*MultipartUpload*" ],
"Effect": "Allow",
"Resource": "arn:aws:s3:::synapse-share.yourcompany.com/*",
"Principal": { "AWS": "325565585839" }
}
]
}
|
...
Instructions:
Download the CF template.
Use the AWS Command Line or AWS Console to execute the template which will automatically provision the bucket.
...
Navigate to your project or folder of interest, then select Tools, and Change Storage Location. In the resulting pop-up, select the Amazon S3 Bucket option and fill in the relevant information, where Bucket is the name of your external bucket, the optional Base Key is the name of the folder in your bucket to upload to, and Banner is a short description such as who owns the storage location:
...
Select the newly created bucket and click the Permissions tab.
Select the Add members button and enter the member
synapse-svc-prod@uplifted-crow-246820.iam.gserviceaccount.com. This is Synapse’s service account. Give the account the permissions Storage Legacy Bucket Reader and Storage Object Viewer for read permission. To allow Synapse to upload files, additionally grant the Storage Legacy Bucket Writer permission.
For read-write permissionsTo register the bucket with Synapse, you also need to create an object that proves to the Synapse service that you own this bucket. This can be done by creating a file named owner.txt that contains a line or comma separated list of user identifiers that are allowed to register the bucket and uploading it to your bucket. Valid user identifiers are: a Synapse user ID or the ID of a team that you are a member of.
...
The ID of the user or the team can be obtained by navigating to the user profile or to the team page, the ID is the numeric value shown in the browser URL bar after the Profile: or Team: prefixes:
...
You can upload the file with the Google Cloud Platform Console, or using the command line gsutil application.
...
| Info |
|---|
Note: Files in an external bucket will not be automatically added to Synapse. |
...
Please see the REST docs for more information on setting external storage location settings using our REST API.
Using SFTP
To setup an SFTP as a storage location, the settings on the project need to be changed, specifically the storageLocation needs to be set. This is best done using either R or Python but has alpha support in the web browser. Customize the code below to set the storage location as your SFTP server:
Python
| Code Block |
|---|
import synapseclient
import json
syn = synapseclient.login()
destination = { "uploadType":"SFTP",
"concreteType":"org.sagebionetworks.repo.model.project.ExternalStorageLocationSetting",
"description":"My SFTP upload location",
"supportsSubfolders":True,
"url":"sftp://your-sftp-server.com",
"banner":"A descriptive banner, tada!"}
destination = syn.restPOST('/storageLocation', body=json.dumps(destination))
project_destination = {"concreteType":"org.sagebionetworks.repo.model.project.UploadDestinationListSetting",
"settingsType":"upload"}
project_destination['projectId'] = PROJECT
project_destination['locations'] = [destination['storageLocationId']]
project_destination = syn.restPOST('/projectSettings', body = json.dumps(project_destination))
|
R
| Code Block |
|---|
library(synapseClient)
synapseLogin()
projectId <- 'syn12345'
destination <- list(uploadType='SFTP',
concreteType='org.sagebionetworks.repo.model.project.ExternalStorageLocationSetting',
description='My SFTP upload location',
supportsSubfolders=TRUE,
url='https://your-sftp-server.com',
banner='A descriptive banner, tada!')
destination <- synRestPOST('/storageLocation', body=destination)
projectDestination <- list(concreteType='org.sagebionetworks.repo.model.project.UploadDestinationListSetting',
settingsType='upload')
projectDestination$locations <- list(destination$storageLocationId)
projectDestination$projectId <- projectId
projectDestination <- synRestPOST('/projectSettings', body = projectDestination)
|
Using a Proxy to Access a Local File Server or SFTP Server
For files stored outside of Amazon, an additional proxy is needed to validate the pre-signed URL and then proxy the requested file contents. View more information here about the process as well as about creating a local proxy or a SFTP proxy.
Set Project Settings for a Local Proxy
You must have a key (“your_secret_key”) to allow Synapse to interact with the file system.
Python
| Code Block | ||
|---|---|---|
| ||
import synapseclient
import json
syn = synapseclient.login()
PROJECT = 'syn12345'
destination = {"uploadType":"PROXYLOCAL",
"secretKey":"your_secret_key",
"proxyUrl":"https://your-proxy.prod.sagebase.org",
"concreteType":"org.sagebionetworks.repo.model.project.ProxyStorageLocationSettings"}
destination = syn.restPOST('/storageLocation', body=json.dumps(destination))
project_destination ={"concreteType": "org.sagebionetworks.repo.model.project.UploadDestinationListSetting",
"settingsType": "upload"}
project_destination['locations'] = [destination['storageLocationId']]
project_destination['projectId'] = PROJECT
project_destination = syn.restPOST('/projectSettings', body = json.dumps(project_destination))
|
R
| Code Block | ||
|---|---|---|
| ||
library(synapser)
synLogin()
projectId <- 'syn12345'
destination <- list(uploadType='PROXYLOCAL',
secretKey='your_secret_key',
proxyUrl='https://your-proxy.prod.sagebase.org',
concreteType='org.sagebionetworks.repo.model.project.ProxyStorageLocationSettings')
destination <- synRestPOST('/storageLocation', body=toJSON(destination))
projectDestination <- list(concreteType='org.sagebionetworks.repo.model.project.UploadDestinationListSetting',
settingsType='upload')
projectDestination$locations <- list(destination$storageLocationId)
projectDestination$projectId <- projectId
projectDestination <- synRestPOST('/projectSettings', body=toJSON(projectDestination))
|
Set Project Settings for a SFTP Proxy
You must have a key (“your_secret_key”) to allow Synapse to interact with the file system.
Python
| Code Block |
|---|
import synapseclient
import json
syn = synapseclient.login()
PROJECT = 'syn12345'
destination = {"uploadType":"SFTP",
"secretKey":"your_secret_key",
"proxyUrl":"https://your-proxy.prod.sagebase.org",
"concreteType":"org.sagebionetworks.repo.model.project.ProxyStorageLocationSettings"}
destination = syn.restPOST('/storageLocation', body=json.dumps(destination))
project_destination ={"concreteType": "org.sagebionetworks.repo.model.project.UploadDestinationListSetting",
"settingsType": "upload"}
project_destination['locations'] = [destination['storageLocationId']]
project_destination['projectId'] = PROJECT
project_destination = syn.restPOST('/projectSettings', body = json.dumps(project_destination))
|
R
...
See also: