Manage Synapse Credentials

There are multiple ways one can login to Synapse. We recommend users to choose the method that fits their workflow.

Use username and password to login as follows:

library("synapser")
synLogin("username", "password")

Alternately you can login using a personal access token obtained from synapse.org under your Settings. Note that a token must minimally have the view scope to be used with synapser.

library(synapser)
synLogin(authToken="authtoken")

Use `.synapseConfig`

For writing code using the synapser client, that is easy to share with others, please do not include your credentials in the code. Instead, please use .synapseConfig file. You can refer your collaborators to the following documentation on how to set up a .synapseConfig file.

First, create a .synapseConfig file in your home directory with the following content:

[authentication]

# either authtoken OR username and password
authtoken = <authtoken>

username = <username>
password = <password>

You can choose to specify either username and password or authtoken. For security purposes, we recommend that you use authtoken instead of your password. A personal access token generated from your synapse.org Settings can be used as your .synapseConfig authtoken.

Then login without specifying your username and password:

library("synapser")
synLogin()

For legacy compatibility, the .synapseConfig [authentication] section also supports apikey, which can be used instead of username + password pair, or authtoken, however apikey support in the .synapseConfig is considered deprecated in favor of personal access tokens (authtoken) which can be scoped to certain functions and are revocable. If needed, your legacy apikey can also be obtained from your synapse.org Settings.

Letting the Operating System Manage Your Synapse Credentials

For users who would like to save their credentials and let other OS configured applications (like keychain in Mac) manage credentials for them, when logging in for the first time, use:

library("synapser")
synLogin("username", "password", rememberMe=True)

The application (keychain in Mac) will then prompt you to allow other applications including Python and R to access these credentials. Please choose “Yes” or “OK”.

The second time you login, you will not have to enter your username or password:

library("synapser")
synLogin()

Manage Synapse Credentials

KimYen Ladia

2023-09-09