External web applications can log in to Synapse and access users’ identity and resources with their consent and with a select, limited scope. This is accomplished using a secure and industry-standard protocol called OpenID Connect (OIDC), which is an extension of OAuth 2.0.

Registering and Linking an OAuth 2.0 Client

The details of the Synapse Open ID Connect implementation are published on the web in a standard Open ID Configuration document (aka the “discovery document”). The document includes the web endpoints for registration, authorization, and token generation, as well as the scope of resources that can be requested, and the formats in which Synapse will return information.

All the OAuth clients in Synapse need to be verified after creation and before usage. If an unverified client is used to perform requests, Synapse will prevent their execution replying with a HTTP 403 Forbidden response.

In order to verify an OAuth client, contact synapseinfo@sagebase.org detailing:

  • Your name

  • The ID of the client to be verified (see below on how to obtain the client ID)

  • A description of your application

Create an OAuth 2.0 Client

An external application can be registered with Synapse as a “client” application by following the steps below. The API reference documents are here, and the following instructions show how to invoke them from the Python and R clients:

Python

import synapseclient
import json
syn = synapseclient.login()

client_meta_data = {
  'client_name': 'Your client name',
  'redirect_uris': [
    'https://yourhost.com/user/login'
  ],
  'client_uri': 'https://yourhost.com/index.html',
  'policy_uri': 'https://yourhost.com/policy',
  'tos_uri': 'https://yourhost.com/terms_of_service',
  'userinfo_signed_response_alg': 'RS256'
}

# Create the client:
client_meta_data = syn.restPOST(uri='/oauth2/client', 
	endpoint=syn.authEndpoint, body=json.dumps(client_meta_data))

client_id = client_meta_data['client_id']

# Generate and retrieve the client secret:
client_id_and_secret = syn.restPOST(uri='/oauth2/client/secret/'+client_id, 
	endpoint=syn.authEndpoint, body='')

print(client_id_and_secret)
PY

R

library(synapser)
library(rjson)
synLogin()

client_meta_data <- list(
  client_name='Your client name',
  redirect_uris= list(
    'https://yourhost.com/user/login'
  ),
  client_uri='https://yourhost.com/index.html',
  policy_uri='https://yourhost.com/policy',
  tos_uri='https://yourhost.com/terms_of_service',
  userinfo_signed_response_alg='RS256'
)

# Create the client:
client_meta_data<-synRestPOST('/oauth2/client', toJSON(client_meta_data), 
  'https://repo-prod.prod.sagebase.org/auth/v1')

client_id <-  client_meta_data$client_id

# Generate and retrieve the client secret:
client_id_and_secret<-synRestPOST(paste0('/oauth2/client/secret/',client_id), 
  '', 'https://repo-prod.prod.sagebase.org/auth/v1')

print(client_id_and_secret)
R

The client URI, policy URI, and terms of service URI are optional, as is the userinfo_signed_response_al parameter. You can optionally include a sector_identifier_uri parameter, an advanced feature described here, relevant if the client uses multiple hosts since Synapse only returns pairwise subject values to its OAuth clients.

The returned client_id and client_secret will be needed later when getting an access token. The secret is only returned once, and it is not stored in Synapse. If lost, you can generate a new secret but the previous one will be invalidated.

You can retrieve, update, and delete your client programmatically using the following commands:

Python

# Retrieve a client using its ID:
client_meta_data = syn.restGET(uri='/oauth2/client/'+client_id, 
	endpoint=syn.authEndpoint)

client_meta_data['policy_uri'] = 'https://yourhost.com/updated_policy'

# Update a client's metadata:
client_meta_data = syn.restPUT(uri='/oauth2/client/'+client_id, 
	endpoint=syn.authEndpoint, body=json.dumps(client_meta_data))

# Delete a client:
syn.restDELETE(uri='/oauth2/client/'+client_id, endpoint=syn.authEndpoint)

PY

R

# Retrieve a client using its ID:
client_meta_data <- synRestGET(paste0('/oauth2/client/',client_id), 
	'https://repo-prod.prod.sagebase.org/auth/v1')

client_meta_data$policy_uri <- 'https://yourhost.com/updated_policy'

# Update a client's metadata:
client_meta_data <- synRestPUT(paste0('/oauth2/client/',client_id), 
	toJSON(client_meta_data), 'https://repo-prod.prod.sagebase.org/auth/v1')

# Delete a client:
synRestDELETE(paste0('/oauth2/client/',client_id), 
	'https://repo-prod.prod.sagebase.org/auth/v1')

R

Authenticating with Synapse

To log in via Synapse your client application should redirect the browser from your application to https://signin.synapse.org, with the standard OAuth 2.0 request parameters:

  • client_id=<your client id>

  • scope=<space-separated list of scopes>

  • redirect_uri=<the redirect uri registered with your client>

  • response_type=code

  • state=<any state you want returned>

  • nonce=<some string to be returned in the ID token>

  • claims=<a JSON object>

As per the OpenID Connect specification, scope is a space-separated list of scopes, and it must include the scope openid in order for the client to receive user identity information. To receive a refresh token the scope offline_access must be included. The complete list of available scopes is given here.

Synapse supports the claims request parameter, a JSON document containing the details of the user identity information you would like returned, as described here. The list of supported claims is given here. For most claims the value to include in the JSON document is null. The exception is the team claim, for which you provide the IDs of one or more teams, the membership of which you wish to inquire about. Synapse will return the IDs of the subset of the given list of teams to which the user belongs. Here is an example of a claims parameter JSON object:

 {
   "id_token":
    {
     "given_name": null,
     "family_name": null,
     "is_certified": null,
     "team": {"values":["273957", "3385814"]}
    },
   "userinfo":
    {
     "given_name": null,
     "family_name": null,
     "is_certified": null,
     "team": {"values":["273957", "3385814"]}
    }
  }
CODE

Following the user’s consent, Synapse will redirect back to your specified redirect URI with an authorization code and your ‘state’ data. You can then exchange the authorization code for a ID token and access token in the standard way. Here is an example using curl:

curl -H "Authorization:Basic XXXXXXXXXXX" -X POST "https://repo-prod.prod.sagebase.org/auth/v1/oauth2/token?grant_type=authorization_code&redirect_uri=<redirect URI>&code=<authorization code>

CODE

where <redirect URI> is as before and <authorization code> is the value returned to your application by Synapse. The request is authorized using the client_id and client_secret provided by Synapse, encoded in the header in the standard way: joined with a ‘:’ separator and base 64 encoded. Synapse responds with an ID Token, an access token and (if offline_access was a specified scope) a refresh token:

{
  "id_token": ...,
  "access_token": ...,
  "refresh_token": ...
}
CODE

The ID token is a signed JSON Web Token. The public key(s) used to verify the token signatures are available at the JSON Web Key Set (jwks) URL listed in the OpenID Configuration document. The ID Token contains the requested user identity information. The access token can be used to authorize future requests.

Making Authorized Requests

Access tokens authorize requests to Synapse services. For example, to get an entity’s metadata:

curl -H "Authorization:Bearer <access token>" https://repo-prod.prod.sagebase.org/repo/v1/entity/syn123456

CODE

where is the value returned from the token endpoint and `syn123456` is replaced with the ID of the entity of interest. As with all available services, this service is defined in the Synapse REST documents. The page for each service requiring authorization lists the "Required OAuth Scopes" for the service, i.e., the scope(s) that the access token must have in order to access the service. In this example, the required scope is `view`.

One service specifically defined by OpenID Connect is the userinfo service. To get an updated ID Token using the access token as authorization, send a request to the userinfo endpoint:

curl -H "Authorization:Bearer <access token>" https://repo-prod.prod.sagebase.org/auth/v1/oauth2/userinfo

CODE

If the 'userinfo_signed_response_alg': 'RS256' option was included in the client registration, then the result will be returned as a signed JSON Web Token, otherwise a simple JSON object will be returned.

Refresh Tokens

Access tokens last for 24 hours, after which the client must either repeat the authorization process or use the refresh token to get a new access token. To do the latter, send a request to the refresh token endpoint:

curl -H "Authorization:Basic XXXXXXXXXXX" -X POST "https://repo-prod.prod.sagebase.org/auth/v1/oauth2/token?grant_type=refresh_token&refresh_token=<refresh_token>"

CODE

Synapse supports an optional scope parameter which is a down selected list of scopes, reducing the scope of the new access token. The response includes a new refresh token, the previous one being rendered obsolete. Refresh tokens expire 180 days after their last use. As long as a refresh token continues to be used, it will not expire. If a refresh token expires the client can get a new one by asking the user to login again.

The client may revoke a refresh token and the associated active access token (if any). This is a request to the revocation endpoint:

curl -H Content-Type:application/json -d "{\"token\":\"<refresh token>\",\"token_type_hint\":\"refresh_token\"}" -X POST "https://repo-prod.prod.sagebase.org/auth/v1/oauth2/revoke"

CODE

If using the access token in the aforementioned request, change token_type_hint to access_token.

The services described here allow an OAuth client to manage tokens. A separate set of services allow the user to review and revoke refresh tokens that they have granted to an OAuth client. The details are given here.


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