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GBrowse Configuration/Authentication

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This article describes user authentication and how to configure it to work with GBrowse.

For the main GBrowse2 configuration article, see GBrowse 2.0 HOWTO.

Authentication & Authorization, Introduction

You can restrict who has access to gbrowse by IP address, host name, domain, username and password, by OpenID, or, via the authentication plugin mechanism, by site-specific restrictions such as possession of a crypto card. Restriction can apply to the database as a whole, or to particular annotation tracks. You can also make a datasource visible only to authorized users.

Authentication Systems

As of version 2.20, GBrowse has three distinct authentication mechanisms:

  1. Authentication via Apache's built-in authentication modules (present in all versions of GBrowse).
  2. Authentication via a built-in user accounts database (GBrowse versions 2.16 and higher).
  3. Authentication via a plugin architecture (GBrowse 2.20 and higher).

The first mechanism uses Apache's standard authentication and authorization modules. This provides you with a large number of authentication backends, but users will not be able to examine and change their credentials unless you install a third-party application for managing Apache authentication.

The second mechanism provides an "accounts database" that is accessible to the server that is running GBrowse. The database is either a local SQLite database, or a local/remote MySQL database. This mechanism provides a way for users to register themselves (if registration is enabled), and allows users to associate OpenIDs with their accounts for one-click login. Users can change their passwords and other information such as their full name and email address.

The third mechanism uses authentication plugins that are similar in spirit to other GBrowse Plugins. Plugins can be written to implement a variety of authentication mechanisms, and are intended to be used by organizations to allow users to use the same authentication mechanism for GBrowse as they use for other organizational assets. This mechanism does not allow users to inspect or change their credentials, but one can easily add a link to the login dialogue that directs them to the organization's web site to help them with this. Authentication plugins do, however, provide the ability to restrict access to role-based groups, something that neither of the other two mechanisms allows. Currently there is are two GBrowse authentication plugins defined, the PamAuthenticate plugin, which authenticates users via the Pluggable Authentication Module (PAM) system, and fetches groups from whatever group database is defined in /etc/nsswitch.conf, and the LDAP authentication plugin, LDAPAuthenticate.pm. The PAM module is the most flexible, so we describe it in detail later in this article.

GBrowse Authentication via Apache's Built-in Authentication Modules

To use Apache's standard authentication and authorization system, we take advantage of the fact that GBrowse uses a URL of this form to select which data source is active:

     http://your.host/cgi-bin/gb2/gbrowse/your_datasource

where "your_datasource" is the name of the currently selected datasource. For example, the yeast datasource is http://your.host/cgi-bin/gbrowse/yeast.

Apache's access control mechanism is based on URLs. To control access to an entire datasource, create a <Location> section in httpd.conf. The <Location> section should look like this:

 
 <Location /cgi-bin/gb2/gbrowse/your_datasource>
        Order deny,allow
        deny from all
        allow from localhost .oicr.on.ca .cshl.edu .ebi.ac.uk
  </Location>

This denies access to everybody except for "localhost" and browsers from the domains .oirc.on.ca, .cshl.edu and .ebi.ac.uk. You can also limit by IP address, by username and password or by combinations of these techniques. See Apache Authentication for the full details. Note that the datasource will still be visible in the pop-up menu of datasources in the GBrowse navigation panel, unless you specify "hide=1" in the GBrowse.conf stanza that defines the datasource.

You can limit individual tracks to certain individuals or organizations. Unless the stated requirements are met, the track will not appear on the main screen or any of the configuration screens. To set this up, add a "restrict" option to the track you wish to make off-limits:

 
       [PROPRIETARY]
        feature = etc
        glyph   = etc
        restrict = Order deny,allow
                   deny from all
                   allow from localhost .oicr.on.ca .cshl.edu .ebi.ac.uk

The value of the restrict option is identical to the Apache authorization directives and can include any of the directives "Order," "Satisfy," "deny from," "allow from," "require valid-user" or "require user." The only difference is that the "require group" directive is not supported, since the location of Apache's group file is not passed to CGI scripts.

As with other gbrowse options, restrict can be a code subroutine. The subroutine will be called with three arguments consisting of the host, ip address and authenticated user. It should return a true value to allow access to the track, or a false value to forbid it. This can be used to implement group-based authorization or more complex schemes.

Here is an example that uses the Text::GenderFromName to allow access if the user's name sounds female and forbids access if the name sounds male. (It might be useful for an X-chromosome annotation site.)

    restrict = sub {
        my ($host,$ip,$user) = @_;
        return unless defined $user;
        use Text::GenderFromName qw(gender);
        return gender($user) eq 'f';
    }

You should be aware that the username will only be defined if username authentication is turned on and the user has successfully authenticated himself against Apache's user database using the correct password. In addition, the hostname will only be defined if HostnameLookups have been turned on in httpd.conf. In the latter case, you can convert the IP address into a hostname using this piece of code:

    use Socket;
    $host = gethostbyaddr(inet_aton($addr),AF_INET);

Note that this may slow down the response time of gbrowse noticeably if you have a slow DNS name server.

Another thing to be aware of when restricting access to an entire database is that that even though the database itself will not be accessible to unauthorized users, the name of the database will still be available from the popup "Data Source" menu. There are two ways to suppress this display:

  1. Place "hide=1" in the GBrowse.conf stanza that defines the datasource. This will hide the source from all users, even those who are allowed to access it.
  2. Place a "restrict" option in the GBrowse.conf stanza that defines the datasource. In this way, only users who meet the requirements will be able to see and select the datasource. For example:
 
 [yeast]
 description = Yeast Chromosomes 1+2
 path        = yeast_simple.conf
 restrict    = require valid-user

Finally, you may place a "restrict" option in the [GENERAL] section of an individual datasource conf file, in which case the restrictions are applied on top of those defined by Apache. This might be useful if you prefer to modify the GBrowse conf file rather than Apache's conf file. For example, if Apache's config file contains this section:

 
    <Location /cgi-bin/gb2/gbrowse/yeast>
        Order deny,allow
        deny from all
        Satisfy all
        allow from .oicr.on.ca
        require valid-user
    </Location>

then any valid user (who can provide a recognized username and password) who accesses the site from a workstation in the .oicr.on.ca domain will be able to get in. You can further restrict access by adding the following to the [GENERAL] section of yeast_simple.conf:

 
  [GENERAL]
   # .... other stuff ...
   restrict  = require user fred joseph andrew vivian

This will return an unauthorized message for anyone except the four named users.

GBrowse Authentication via its Built-in User Account Database

The GBrowse user account system provides users with a link in the upper right corner of the screen that lets them login, register, and manage their account settings.

Gbrowse login.png

Configuration

The GBrowse user account system is activated when the following requirements are met:

  1. The Perl DBI module is installed, and one or both of DBD::mysql and DBD::SQLite.
  2. The "user accounts" option is set to a "1" (or any other true value) in GBrowse.conf's [GENERAL] section.
  3. No "authentication plugin" option is defined in GBrowse.conf's [GENERAL] section.

User accounts can be created and managed with the utilities gbrowse_create_account.pl and gbrowse_change_passwd.pl. Users can register themselves and manage their own account settings if:

  1. The Perl {[CPAN|Net::SMTP}} module is installed (required to validate users via email).
  2. The "user accounts registration" option is set to a true value in GBrowse.conf.
  3. The "user_account_db" option is set to a valid MySQL or SQLite path.
  4. The "smtp_gateway" is set to a working mail gateway that can forward mail to end users.

To enable users to log in using OpenIDs, these requirements must be met:

  1. The Perl Net::OpenID::Consumer module must be installed.
  2. The "user_accounts_openid" option in the [GENERAL] section of GBrowse.conf should be set to a true value.

The following is a GBrowse.conf configuration file with all the bells and whistles turned on:

 
 [GENERAL]
 # ...lots of stuff...
 
 # Login Settings
 user_accounts               = 1
 user_accounts_registration  = 1
 user_accounts_openid        = 1
 user_account_db             = DBI:SQLite:/var/www/gbrowse2/databases/users.sqlite
 smtp_gateway                = localhost
 application_name            = GBrowse
 application_name_long       = The Generic Genome Browser
 email_address               = noreply@gbrowse.com

This configuration should work on most servers provided that there is a properly-configured mail exchanger running on the server itself. You will need to replace this with an appropriate mail exchanger if this is not the case. The format of this option is described in more detail below. In the case of new installations of GBrowse2 (versions 2.20 and higher), the installer will detect if the prerequisites are present, and establish reasonable starting values.

Here is more information on these options:

user_account_db

This is a Perl DBI-style description of the database that will hold user accounts. Only SQLite and MySQL databases are usable at the current time. For MySQL databases, the full form of the option is:

 
  DBI:mysql:database=gbrowse_login;host=mysql.oicr.on.ca;user=gbrowse;password=gbrowse

This indicates that the account database is running on a MySQL server named "mysql.oicr.on.ca" and that the database is named "gbrowse_login". The GBrowse application will use the username "gbrowse" and the password "gbrowse" to access the database.

For SQLite databases, the format is:

 
  DBI:SQLite:/var/www/gbrowse2/databases/users.sqlite

The latter part of the description is a path to the database file.

user_accounts, user_accounts_registration, user_accounts_openid
These options turn on and off user accounts, new users' ability to register themselves and OpenID support, respectively. Pass a true value (usually "1" to turn the feature on). Pass a false value ("0" or just comment out the option) to turn the feature off.
smtp_gateway

This option sets the mail gateway that GBrowse uses to register new users and to communicate track sharing information one user to another. The full format is:

 
 <smtp.server.com>:<port>:<encryption>:<username>:<password>

There are up to five fields, each separated by colons. The first field, which is required, is the hostname or IP address of a mail server running the SMTP protocol (Simple Mail Transport Protocol, the standard email exchange language). The second field is the port on which SMTP is running. You can leave this empty to accept the defaults. The third field specifies the encryption system, if any. The two options are "plain", for no encryption, and "ssl", for encryption. The last two fields specify the username and password, if these are needed to establish a connection with the server.

An example of a server that requires encryption, username and password is Gmail. Here, for example, is how to route mail through a user account at GMail:

 
  smtp_gateway           = smtp.gmail.com:465:ssl:john.doe:open_sesame

Replace "john.doe" and "open_sesame" with the appropriate username and password for the service.

application_name, application_name_long, email_address
These options control the "From" address that users will see when they receive their account registration confirmations. The defaults should work fine, but you may want to customize them for your site (e.g. replace "The Generic Genome Browser" default with "The BeetleBase Genome Browser".) email_address controls the Reply-to field, and by default is set to a non-working email address. Note that when using some mail relayers, such as GMail, the gateway will force the Reply-to field to be the same as the user's email account, to avoid spam relaying.

Before you run an account-enabled GBrowse for the very first time, you should run the gbrowse_metadb_config.pl script, which is installed along with GBrowse. Ordinarily this script is run automatically for you during "./Build install" (or during automatic CPAN shell installation), but you will need to run this script again if you change the "user_account_db" setting in order to change the type or location of the accounts database. gbrowse_metadb_config.pl also does routine maintenance on the database, such as removing orphaned uploads, and so it is worth running it occasionally to see if any inconsistencies are corrected.

NOTE: Permissions: For GBrowse2 to be able to accept new user registrations and to allow users to change their account information, the web user (e.g. "www-data") must have write privileges on the user account database. In the case of a SQLite database, this means that the database file and the directory that contains it must be writable by the web user. For MySQL databases, the MySQL user ("gbrowse" in the example above) must have SELECT, INSERT, DELETE and UPDATE privileges. The gbrowse_metadb_config.pl script will check and fix the permissions for you.

Adding User Accounts

You can create a new user account using gbrowse_create_account.pl, which is installed with GBrowse. If user self-registration is turned off, then this is the only way to create and manage user accounts.

The command's syntax is:

 gbrowse_create_account.pl [-pass <password> -fullname <name> -email <email>] <username>

The username is required. All other fields will be prompted for if not provided on the command line. If you call gbrowse_create_account.pl with the name of an existing user, you can change the user's password and other information.

The gbrowse_change_passwd.pl command can be used for setting or resetting an existing user's password:

gbrowse_change_passwd.pl <username> [<password>]

If no password is provided on the command line, then a random password will be generated and printed out for your use.

Both of these scripts need to run as the web user (e.g. "www-data") in order to access and update the accounts database. If they are not run as this user, then the script will relaunch itself under sudo. Sudo may prompt you for your login password; do not get your password confused with the new user's password!

Restricting Access to Datasources with GBrowse Account Database

You can restrict access to datasources and individual tracks using exactly the same restrict syntax described in the previous section. For example in yeast_simple.conf, you could have:

 [GENERAL]
 # lots of other stuff...
 restrict = require valid-user
 ...
 
 [5_prime_RACE]
 glyph    = generic
 feature  = RACE:5_prime
 restrict = require user fred joseph andrea marta

The effect will be to require everyone to log in successfully in order to view the datasource at all. In addition, only the users logged in under one of the names "fred", "joseph", "andrea" and "marta" will have access to the "5_prime_RACE" track.

As in Apache-based authorization, you can shield the name of the datasource from view in the popup datasources menu by placing a "restrict" in the GBrowse.conf stanza that describes the datasource.

GBrowse Authentication via Authentication Plugins

GBrowse (versions 2.20 and higher) offers user authentication via a plug-in mechanism that lets organizations integrate the software with such enterprise authentication systems as LDAP, Kerberos, NIS, and UNIX password files. The Authentication Plugins are easy to write, but GBrowse comes with a very flexible default one that makes use of the PAM (Pluggable Authentication Modules) system that is installed on most if not all modern Linux distributions. Basically, you need only to define a PAM definition file for the GBrowse service, or reuse an existing one, and then activate the PAM plugin. The plugin will use whatever authentication mechanism is defined in the PAM definition file to authenticate users. In addition, the plugin will use the standard /etc/nsswitch.conf settings to map users onto groups for the purpose of group-based access control.

To get started using the PAM authentication module, create a PAM service definition file in /etc/pam.d named "gbrowse". It's usually easiest to start by copying an existing definition file such as login. (This will have the effect of using the same authentication database for GBrowse users as for regular logins on the GBrowse host machine.) A simple /etc/pam.d/gbrowse file that uses local UNIX password/shadow databases would look like this:

auth     requisite   pam_unix.so

an LDAP-based authentication would refer to pam_ldap.so instead.

Note that if you are going to use the UNIX shadow password system for authentication, the web user must belong to the "shadow" group on many systems. You can arrange this as follows:

usermod -G shadow -a www-data

Change "shadow" and "www-data" to the group that can read the /etc/shadow file and the Apache user respectively. Note that you will typically not want to give server login privileges to all individuals who have genome browser accounts. You can use PAM to forbid actual logins to members of certain groups (see the pam_group.so module for more information).

The PAM authentication plugin uses /etc/nsswitch.conf system configuration file to map users onto groups for group-based authentication. nsswitch.conf, in turn, provides connections to the traditional /etc/group file, the NIS database, or LDAP databases, depending on how it is configured. For example, to fetch user and group information from the local filesystem first, and then to look in LDAP, nsswitch.conf should have lines that looks like this:

passwd: compat ldap
group:  compat ldap

Once these steps are taken, you'll configure GBrowse to use the PAM authentication plugin. Edit /etc/gbrowse2/GBrowse.conf and add or uncomment the following line in the [GENERAL] section:

authentication plugin = PamAuthenticate

When you reload GBrowse, you will see a simple "Login" link in the upper right hand corner of the screen. Clicking on this link will bring up a dialog that prompts you for your login username and password. If all is configured correctly, then you'll be able to log in using your Unix username and password. See PamAuthenticate for more information on customizing the plugin, including how to add site-specific messages to the login dialog.

Group-based Authorization

The PamAuthenticate plugin allows you to authorize users via their group membership. The syntax is similar to the "require user" directive described earlier:

[MySecretTrack]
restrict = require group Principal_Investigators Postdocs

The track "MySecretTrack" will now only be visible to users who are members of either the "Principal_Investigators" or "Postdocs" groups. "require group" lines can be mixed with "require user", and host-based "allow" and "deny" directives. As before, the "restrict" statement can be placed in a datasource configuration file's track stanza, in its [GENERAL] section, or in the stanza in GBrowse.conf that refers to the datasource.