Installation

The Arvados Java SDK v2 provides a high level API for working with Arvados resources.

Using the SDK

The SDK is packaged as a JAR named arvados-java-<version>.jar, which is published to Maven Central and can be included using Maven, Gradle, or by hand.

Here is an example build.gradle file that uses the Arados java sdk:

apply plugin: 'application'
apply plugin: 'java-library'
apply plugin: 'maven'

repositories {
    mavenCentral()
}

application {
    mainClassName = "org.arvados.example.CollectionExample"
}

dependencies {
    api 'org.arvados:arvados-java-sdk:0.1.0'
}

See Java SDK Examples to get started using the SDK.

Logging

The SDK uses the SLF4J facade library for logging. A concrete logging binding (and configuration, if required) must be provided by a client. For small applications, you can use the Simple implementation by adding slf4j-simple-1.8.0-beta4.jar to your classpath.

Configuration

TypeSafe Configuration is used for configuring this library.

Please review src/main/resources/reference.conf for default values provided with this library.

• keepweb-host – host of your Keep-Web server (default: localhost)
• keepweb-port – port of your Keep-Web server (default: 8000)
• host – host of your Arvados API server
• port – port of your Arvados API server
• token – Arvados token to authenticate registered user, one must provide token obtained from Arvados Workbench
• protocol – don’t change to unless really needed (default: https)
• host-insecure – ignores SSL certificate verification if true (default: false Don’t change to true unless really needed)
• split-size – size of chunk files in megabytes (default: 64)
• temp-dir – temporary chunk files storage
• copies – amount of chunk files duplicates per Keep server
• retries – UNIMPLEMENTED

In order to override default settings one can create an application.conf file in an application. Example: src/test/resources/application.conf.

Alternatively ExternalConfigProvider class can be used to pass configuration via code. ExternalConfigProvider comes with a builder and all of the above values must be provided in order for it to work properly.

ArvadosFacade has two constructors, one without arguments that uses values from application.conf and second one taking ExternalConfigProvider as an argument.

API clients

All API clients inherit from BaseStandardApiClient. This class contains implementation of all common methods as described in Arvados Common Resource Methods.

Parameters provided to common or specific methods are String UUID or fields wrapped in Java objects. For example:

String uuid = "ardev-4zz18-rxcql7qwyakg1r1";

Collection actual = client.get(uuid);

ListArgument listArgument = ListArgument.builder()
        .filters(Arrays.asList(
                Filter.of("owner_uuid", Operator.LIKE, "ardev%"),
                Filter.of("name", Operator.LIKE, "Super%"),
                Filter.of("portable_data_hash", Operator.IN, Lists.newArrayList("54f6d9f59065d3c009d4306660989379+65")
            )))
        .build();

CollectionList actual = client.list(listArgument);

Non-standard API clients must inherit from BaseApiClient. For example: KeepServerApiClient communicates directly with Keep servers using exclusively non-common methods.

Business logic

More advanced API data handling could be implemented as Facade classes. In current version functionalities provided by SDK are handled by ArvadosFacade. They include:

• downloading single file from collection – using Keep-Web
• downloading whole collection – using Keep-Web or Keep Server API
• listing file info from certain collection – information is returned as list of FileTokens providing file details
• uploading single file – to either new or existing collection
• uploading list of files – to either new or existing collection
• creating an empty collection
• getting current user info
• listing current user’s collections
• creating new project
• deleting certain collection

Note regarding Keep-Web

The Java SDK requires Keep Web (which is part of the standard configuration) as well as the API server and Keep server(s).

Integration tests

In order to run the integration tests, all fields within following configuration file must be provided: src/test/resources/integration-test-appliation.conf

The parameter integration-tests.project-uuid should contain UUID of one project available to user who’s token was provided within configuration file.

Integration tests require connection to a real Arvados server.

Note regarding file naming

When uploading via the current implementation of the Java SDK all uploaded files within single collection must have different names. This applies also to uploading files to already existing collection. Renaming files with duplicate names is not currently implemented.

Javadoc

See Javadoc

Building the Arvados SDK

Dependencies:

• JDK for Java 8 or later https://www.oracle.com/technetwork/java/javase/downloads/index.html
• Gradle https://gradle.org/install/

$ git clone https://github.com/curoverse/arvados.git
$ cd arvados/sdk/java-v2
$ gradle test
$ gradle jar