-```
-Copyright (C) The Arvados Authors. All rights reserved.
-
-SPDX-License-Identifier: CC-BY-SA-3.0
-```
+[comment]: # (Copyright © The Arvados Authors. All rights reserved.)
+[comment]: # ()
+[comment]: # (SPDX-License-Identifier: CC-BY-SA-3.0)
-# Arvados Java SDK
+[](https://gitter.im/arvados/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) | [Installing Arvados](https://doc.arvados.org/install/index.html) | [Installing Client SDKs](https://doc.arvados.org/sdk/index.html) | [Report a bug](https://dev.arvados.org/projects/arvados/issues/new) | [Development and Contributing](CONTRIBUTING.md)
-##### About
-Arvados Java Client allows to access Arvados servers and uses two APIs:
-* lower level [Keep Server API](https://doc.arvados.org/api/index.html)
-* higher level [Keep-Web API](https://godoc.org/github.com/curoverse/arvados/services/keep-web) (when needed)
+<img align="right" src="doc/images/dax.png" height="240px">
-##### Required Java version
-This SDK requires Java 8+
+[Arvados](https://arvados.org) is an open source platform for
+managing, processing, and sharing genomic and other large scientific
+and biomedical data. With Arvados, bioinformaticians run and scale
+compute-intensive workflows, developers create biomedical
+applications, and IT administrators manage large compute and storage
+resources.
-##### Logging
+The key components of Arvados are:
-SLF4J is used for logging. Concrete logging framework and configuration must be provided by a client.
+* *Keep*: Keep is the Arvados storage system for managing and storing large
+collections of files. Keep combines content addressing and a
+distributed storage architecture resulting in both high reliability
+and high throughput. Every file stored in Keep can be accurately
+verified every time it is retrieved. Keep supports the creation of
+collections as a flexible way to define data sets without having to
+re-organize or needlessly copy data. Keep works on a wide range of
+underlying filesystems and object stores.
-##### Configuration
+* *Crunch*: Crunch is the orchestration system for running [Common Workflow Language](https://www.commonwl.org) workflows. It is
+designed to maintain data provenance and workflow
+reproducibility. Crunch automatically tracks data inputs and outputs
+through Keep and executes workflow processes in Docker containers. In
+a cloud environment, Crunch optimizes costs by scaling compute on demand.
-[TypeSafe Configuration](https://github.com/lightbend/config) is used for configuring this library.
+* *Workbench*: The Workbench web application allows users to interactively access
+Arvados functionality. It is especially helpful for querying and
+browsing data, visualizing provenance, and tracking the progress of
+workflows.
-Please, have a look at java/resources/reference.conf for default values provided with this library.
+* *Command Line tools*: The command line interface (CLI) provides convenient access to Arvados
+functionality in the Arvados platform from the command line.
-* **keepweb-host** - change to host of your Keep-Web installation
-* **keepweb-port** - change to port of your Keep-Web installation
-* **host** - change to host of your Arvados installation
-* **port** - change to port of your Arvados installation
-* **token** - authenticates registered user, one must provide
- [token obtained from Arvados Workbench](https://doc.arvados.org/user/reference/api-tokens.html)
-* **protocol** - don't change to unless really needed
-* **host-insecure** - insecure communication with Arvados (ignores SSL certificate verification),
- don't change to *true* unless really needed
-* **split-size** - size of chunk files in megabytes
-* **temp-dir** - temporary chunk files storage
-* **copies** - amount of chunk files duplicates per Keep server
-* **retries** - in case of chunk files send failure this should allow to repeat send
- (*NOTE*: this parameter is not used at the moment but was left for future improvements)
+* *API and SDKs*: Arvados is designed to be integrated with existing infrastructure. All
+the services in Arvados are accessed through a RESTful API. SDKs are
+available for Python, Go, R, Perl, Ruby, and Java.
-In order to override default settings one can create application.conf file in an application.
-Example: src/test/resources/application.conf.
+# Quick start
-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.
+To try out Arvados on your local workstation, you can use Arvbox, which
+provides Arvados components pre-installed in a Docker container (requires
+Docker 1.9+). After cloning the Arvados git repository:
-ArvadosFacade has two constructors, one without arguments that uses values from reference.conf and second one
-taking ExternalConfigProvider as an argument.
-
-##### API clients
+```
+$ cd arvados/tools/arvbox/bin
+$ ./arvbox start localdemo
+```
-All API clients inherit from BaseStandardApiClient. This class contains implementation of all
-common methods as described in http://doc.arvados.org/api/methods.html.
+In this mode you will only be able to connect to Arvbox from the same host. To
+configure Arvbox to be accessible over a network and for other options see
+http://doc.arvados.org/install/arvbox.html for details.
-Parameters provided to common or specific methods are String UUID or fields wrapped in Java objects. For example:
+# Documentation
-```java
-String uuid = "ardev-4zz18-rxcql7qwyakg1r1";
+Complete documentation, including the [User Guide](https://doc.arvados.org/user/index.html), [Installation documentation](https://doc.arvados.org/install/index.html), [Administrator documentation](https://doc.arvados.org/admin/index.html) and
+[API documentation](https://doc.arvados.org/api/index.html) is available at http://doc.arvados.org/
-Collection actual = client.get(uuid);
-```
+If you wish to build the Arvados documentation from a local git clone, see
+[doc/README.textile](doc/README.textile) for instructions.
-```java
-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();
+# Community
-CollectionList actual = client.list(listArgument);
-```
+[](https://gitter.im/arvados/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
-Non-standard API clients must inherit from BaseApiClient.
-For example: KeepServerApiClient communicates directly with Keep servers using exclusively non-common methods.
+The [Arvados community channel](https://gitter.im/arvados/community)
+channel at [gitter.im](https://gitter.im) is available for live
+discussion and support.
-##### Business logic
+The [Arvados developement channel](https://gitter.im/arvados/development)
+channel at [gitter.im](https://gitter.im) is used to coordinate development.
-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**
+The [Arvados user mailing list](http://lists.arvados.org/mailman/listinfo/arvados)
+is used to announce new versions and other news.
-##### Note regarding Keep-Web
+All participants are expected to abide by the [Arvados Code of Conduct](CODE_OF_CONDUCT.md).
-Current version requires both Keep Web and standard Keep Server API configured in order to use Keep-Web functionalities.
+# Reporting bugs
-##### Integration tests
+[Report a bug](https://dev.arvados.org/projects/arvados/issues/new) on [dev.arvados.org](https://dev.arvados.org).
-In order to run integration tests all fields within following configuration file must be provided:
-```java
-src/test/resources/integration-test-appliation.conf
-```
-Parameter **integration-tests.project-uuid** should contain UUID of one project available to user,
-whose token was provided within configuration file.
+# Development and Contributing
-Integration tests require connection to real Arvados server.
+See [CONTRIBUTING](CONTRIBUTING.md) for information about Arvados development and how to contribute to the Arvados project.
-##### Note regarding file naming
+The [development road map](https://dev.arvados.org/issues/gantt?utf8=%E2%9C%93&set_filter=1&gantt=1&f%5B%5D=project_id&op%5Bproject_id%5D=%3D&v%5Bproject_id%5D%5B%5D=49&f%5B%5D=&zoom=1) outlines some of the project priorities over the next twelve months.
-While uploading via this 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 implemented in current version.
+# Licensing
+Arvados is Free Software. See [COPYING](COPYING) for information about the open source licenses used in Arvados.
projects / arvados.git / blobdiff