Usage

Command line usage

General way to run VDJdb server would be the following:

$ ./vdjdb-server -Darg1=value1 -Darg2=value2 ...etc

Note

If you want to change JRE arguments use -J- prefix. For example, to change memory heap size for Java Virtual Machine run the following command in your console:

$ ./vdjdb-server -J-Xmx16G

If insufficient amount memory is allocated, the Java Virtual Machine could drop with a Java Heap Space Out of Memory error.

Advanced configuration

VDJdb server configuration can be performed by passing additional arguments to vdjdb-server script with -D prefix in console or by manually editing application.conf file in the conf/ directory.

List of all available arguments can be found in conf/application.conf file.

Play framework uses the HOCON syntax for configuration.

More about HOCON syntax, data types and other features can be found here.

You can also specify another local configuration file not packaged into the application artifacts:

$ ./vdjdb-server -Dconfig.file=/path/to/application.conf

VDJdb Database configuration

Argument Type Default Description
application.database.useLocal Boolean true Specify if use local vdjdb-database or try to download latest release from github repository
application.database.path String database/ Specify path to local vdjdb-database relative to vdjdb-server binary executable

Example:

// For local database
$ ./vdjdb-server -Dapplication.database.useLocal=true -Dapplication.database.path=path/to/local/database/

// Automatic download latest release from github repository
$ ./vdjdb-server -Dapplication.database.useLocal=false

Temporary files configuration

VDJdb server can create some temporary files during execution.

Argument Type Default Description
application.temporary.path String /tmp/vdjdb-temporary Path to store temporary files
application.temporary.keep Duration 12 hours Specify the time during which the file is guaranteed to exist
application.temporary.interval Duration 12 hours Specify an interval for deleting expired temporary files

Example:

$ ./vdjdb-server -Dapplication.temporary.path=/tmp -Dapplication.temporary.interval=30minutes -Dapplication.temporary.keep=1hour

Autorization configuration

Common configuration:

Argument Type Default Description
application.auth.common.uploadLocation Boolean /tmp/vdjdb/ Is verification required or not
application.auth.common.createUsers User Array 
[{
   "login": "test",
   "email": "test@mail.com",
   "password": "123456",
   "permissionsID": "1",
}]
Create default users with application startup
Note: This field can’t be passed as command
line argument. Use application.conf file
instead.
application.auth.common.enableDefaultUsers Boolean true Enable default users feature
application.auth.common.clearDefaultUsers Boolean false Clear default users if exists

Demo user configuration:

Argument Type Default Description
application.auth.demo.enabled Boolean true Is demo user enabled or not
application.auth.demo.filesLocation String /tmp/vdjdb/demo Demo account sample files location
application.auth.demo.login String vdjdb@vdjdb-demo.com Demo account login and email
application.auth.demo.password String demo Demo account password

List of available permissions ID:

  • 0 - No-limits
  • 1 - Standart, max files count is equal to 10, max file size is equal to 16MB
  • 2 - Demo account, uploading is not allowed

Verification token configuration:

Argument Type Default Description
application.auth.verification.required Boolean true Is verification required or not
application.auth.verification.method String console Verification method (console or email)
application.auth.verification.server String localhost Verification server location
application.auth.verification.keep Duration 24 hours Specify the time during which the token is guaranteed to be valid
application.auth.verification.interval Duration 24 hours Specify an interval for deleting expired tokens

Example

//Disable verfication
$ ./vdjdb-server -Dapplication.auth.verification.required=false

Session token configuration:

Argument Type Default Description
application.auth.session.keep Duration 30 days Specify the time during which the token is guaranteed to be valid
application.auth.session.interval Duration 1 day Specify an interval for deleting expired tokens

Reset token configuration:

Argument Type Default Description
application.auth.reset.keep Duration 24 hours Specify the time during which the token is guaranteed to be valid
application.auth.reset.interval Duration 24 hours Specify an interval for deleting expired tokens

Annotations page configuration

Annotations upload page configuration:

Argument Type Default Description
application.annotations.upload.maxFileSize Size 64MiB Max sample files size

Limits configuration

Argument Type Default Description
application.limits.maxRequestsCount Number 10 000 Max number of requests available to the user
application.limits.countClearInterval Duration 1 hour An interval for resetting number of request for user
application.limits.maxRequestsTime Number 900 000 Total request time available to the user (in milliseconds)
application.limits.timeClearInterval Duration 30 minutes An interval for resetting total request time for user

SQL Database configuration

VDJdb server uses Slick API for accessing and storing data in SQL database.

Important

Standalone version uses H2 Database for handling metadata by default, if you want to change H2 to another DBMS please see the corresponding Play documentation section. You can also use this database to manually modify user limits.

It is safe to change default database location with slick.dbs.default.db.url argument.

Example:

// Change '/path/to/sql/database'
$ ./vdjdb-server -Dslick.dbs.default.db.url=jdbc:h2:file:/path/to/sql/database;DB_CLOSE_DELAY=-1

The remaining slick.dbs.default.* arguments are best kept to the default settings.

More information about Slick API configuration arguments can be found here.