My Profile

Every user in Opal has a profile. This page is accessible by clicking on the user name on the top right corner of the web interface.

Account Settings

This section gives information about the user account: groups and how to change the password. As Opal is able to delegate the user authentication to tier systems (such as Agate or Identity Providers), Opal may have no control on the user’s password. Unless the user has been defined in Opal (the opal-user-realm), the password update may be delegated to the original realm of the user.

Two-factor Authentication

Two-factor authentication (2FA) is an extra step added to the log-in process: in addition to your username and password, a temporary code is requested. This temporary code is to be provided by an “authenticator” app installed on your mobile phone. The technology used is the time-based one-time password (TOTP), that consists of generating synchronized temporary codes both in the mobile app and the Opal server. There are several authenticator apps available in app stores; we recommend installing either Microsoft Authenticator (free, fully featured and robust solution, available on Android and Apple app stores) or FreeOTP+ (open source solution, available on Android app store only).

Note that the 2FA feature is not available for users that identify from an external ID provider (i.e. through the OpenID Connect protocol, or in Agate). It is assumed that any 2FA/multi-factor auth process would be part of the external authentication flow.

The process of enabling 2FA is the following:

  • Login with your username and password,
  • Go to your profile page,
  • Install an Authenticator app on your mobile phone (see above for recommended ones),
  • Press “Enable 2FA”: a QR code appears (shown only once!), to be scanned by your Authenticator app to register your account’s 2FA settings.

To verify:

  • Logout and login again with your username and password,
  • Press “Sign In” and enter the requested temporary PIN code provided by the Authenticator app and “Validate”.

In case the Authenticator app settings are lost, you can contact the system’s administrator to disable your 2FA setting: as an administrator, go to Administration > Profiles pages and in the list of user profiles, press “Disable 2FA” for the considered user.

When 2FA is enabled, it affects the client libraries:

  • R, when using opal.login() function with username and password you will be prompted to enter the PIN code.
  • Python, the Opal Python commands accept the argument --otp (stands for “one-time password”) to capture the PIN code from the prompt.
  • Java, the PIN code cannot be provided.

Note that the 2FA mechanism does not apply when authenticating with a Personal Access Token. This “API key” is the recommended authentication process.

Personal Access Tokens

Personal access tokens can be created for use in scripts and on the command line (using R or Python client API). Be careful, these tokens are like passwords so you should guard them carefully. The advantage to using a token over putting your password into a script is that a token can be revoked, and you can generate lots of them. See also this Personal Access Token page.

In addition to that, the scope of the access granted to the token can be restricted by projects, data access and operations that can be performed on these projects and system services. Note that the personal access token does not grant new permissions but rather alter the ones you have.

The personal access token is also the only way to authenticate in a script for users defined in delegated Identity Providers, as the process of authentication for such realms implies the redirect of the user to a web page for manual login. The token is guaranteed to be safe for the Opal server as it is created by the user itself.

For these reasons, the personal API access token is the recommended way for authenticating within a Opal server (since Opal 2.15).

Settings

Projects

The projects that are accessible using the token can be limited. When none is enumerated, all the projects accessible by the user will be accessible using the token.

Project Data

The read/write operations can be controlled:

  • Default, the user permissions apply,
  • Read only, no data can be imported, nor modified/deleted. Individual-level data are still accessible.
  • Read only, without individual-level data, no data can imported/exported, nor modified/deleted/extracted. Only reporting, analysis or DataSHIELD actions can be performed.

Project Tasks

This scope is for controlling which tasks can be launched on project:

  • Import, import data (not available when project’s data are read-only),
  • Export, export data (not available when project’s data are read-only without access to individual-level data),
  • Copy, copy data (not available when project’s data are read-only)
  • Backup, backup project (not available when project’s data are read-only without access to individual-level data),
  • Restore, restore project (not available when project’s data are read-only),
  • Report, execute a report,
  • Analyse, execute an analysis,
  • Import VCF, import a VCF, when a VCF store plugin is installed (not available when project’s data are read-only),
  • Export VCF, export a VCF, when a VCF store plugin is installed (not available when project’s data are read-only without access to individual-level data).

Project Administration

This scope of operations is for managing projects:

  • Create, to create new projects, not available when project access is restricted to some enumerated ones (otherwise created project would not be accessible),
  • Update, to update a project settings (does not apply to project’s data),
  • Delete, to delete a project.

Services

Along with project data, some system services can be used:

  • R, which allows to create a plain R session in the R server backend, and assign some data (tables or resources), as soon as the user and token have permission to read individual-level data.
  • DataSHIELD, which allows to create a DataSHIELD’s R session in the R server backend, and assign some data (tables or resources), even when the user and token have not the permission to read individual-level data.
  • SQL, which allows to make SQL queries on tables, as soon as the user and token have permission to read individual-level data.
  • Administrate system, which allows to manage plugins, DataSHIELD configuration and much more (administrator users only).

Operations

Remove

You can permanently remove a token, effect is immediate.

Note that if the token has reached the end-of-life (system setting, by default there is no expiration timeout), it will be automatically removed, no action needed.

Renew

There is an inactivity timeout (system setting, 2 months by default) after which a token is not functional. When a token has been marked as being inactive, it can be renewed an unlimited number of times (until the token expires).

Examples

Example of usage in R (see section Using R):

o <- opal.login(token='dXvJKhk17RiO0TguRmR0EQlJxweCFyUX', url='https://opal-demo.obiba.org')
...

Example of usage in Python (see section Python Commands)

opal dict "CNSIM.*" --opal https://opal-demo.obiba.org --token 'dXvJKhk17RiO0TguRmR0EQlJxweCFyUX'

Example of usage with cURL command line;

curl -H "X-Opal-Auth: dXvJKhk17RiO0TguRmR0EQlJxweCFyUX" -H "Accept: application/json" -X GET https://opal-demo.obiba.org/ws/projects

Bookmarks

Bookmarks are shortcuts to specific pages (project, table, variable) that can be selected by clicking on the start icon on the right of the title.