EMBL-EBI Web Services

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====== Java ======

===== Web Services Tool-kits =====

There are many tool-kits available for developing Web Services clients or servers available for Java ((Java - http://www.oracle.com/technetwork/java/)) ((Java.net - http://www.java.net/)). These fall into two broad categories:
  - General purpose libraries which implement Web Services technologies (i.e. REST or SOAP)
  - Service libraries which implement the client and/or server interface for a service type (e.g. OpenSearch ((OpenSearch - http://www.opensearch.org/))) or for a specific service.

A selection of libraries commonly used to access Web Services are listed below.

==== General Purpose ====

Java tool-kits which implement Web Services technologies:

^ Web Service Style ^ Java Tool-kit^
| REST | [[http://hc.apache.org/httpcomponents-client/index.html|HttpComponents HttpClient]] |
|      | [[http://www.innovation.ch/java/HTTPClient/|Innovation HTTPClient]] |
|      | [[http://hc.apache.org/httpclient-3.x/|Jakarta Commons HttpClient]] |
|      | java.net.HttpURLConnection and java.net.URL |
|      | [[http://jersey.java.net/|Jersey]] (JAX-RS) |
| SOAP | [[http://ws.apache.org/axis/|Apache Axis]] |
|      | [[http://ws.apache.org/axis2/|Apache Axis2/Java]] |
|      | [[http://cxf.apache.org/|Apache CXF]] |
|      | [[http://java.net/projects/jax-rpc/|JAX-RPC Reference Implementation]] |
|      | [[http://jax-ws.java.net/|JAX-WS Reference Implementation]] |
|      | [[http://ksoap.org/|kSOAP]] |
|      | [[http://wso2.org/projects/wsf/spring|WSO2 WSF/Spring]] |

**Note**: When building a SOAP client the choice of Java tool-kit is often driven by compatibility with the Web Service(s) being used (e.g. RPC/encoded vs. Document/literal support), see [[..:03_soap#soap_styles|SOAP Styles]] and the [[#tutorials]].

==== Client Libraries ====

Purpose built libraries for a type of service or a specific service, for example:

^ Web Service Type ^ Java Tool-kit ^
| [[http://www.opensearch.org/|OpenSearch]] | [[http://wiki.java.net/bin/view/Javawsxml/OpenSearch|OpenSearch plug-in]] for [[http://java.net/projects/rome/|ROME]] |

==== BioJava ====

[[http://www.biojava.org/|BioJava]] includes support for a number of bioinformatics Web Services, for example:

BioJava 1.8:
^ Web Service ^ BioJava ^
| [[http://biodas.org/|DAS]] | [[http://www.biojava.org/docs/api1.8/org/biojava/dasobert/das/package-summary.html|org.biojava.dasobert.das ]] |
| [[http://www.ebi.ac.uk/Tools/dbfetch/dbfetch|dbfetch]] | [[http://www.biojava.org/docs/api1.8/org/biojava/bio/seq/db/biofetch/package-summary.html|org.biojava.bio.seq.db.biofetch]] |
| [[http://eutils.ncbi.nlm.nih.gov/|NCBI E-Utilities]] | [[http://www.biojava.org/docs/api1.8/org/biojavax/bio/db/ncbi/package-summary.html|org.biojavax.bio.db.ncbi]] |
| [[http://www.ebi.ac.uk/~senger/openbqs/|OpenBQS]]    | [[http://www.biojava.org/docs/api1.8/org/biojava/bibliography/package-summary.html|org.biojava.bibliography]] |
| [[http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html|QBlAST URL API]] | [[http://www.biojava.org/docs/api1.8/org/biojavax/bio/alignment/blast/package-summary.html|org.biojavax.bio.alignment.blast.RemoteQBlastService]] |

BioJava 3:
^ Web Service ^ BioJava ^
| [[http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html|QBlAST URL API]] | [[http://www.biojava.org/docs/api/org/biojava3/ws/alignment/qblast/package-summary.html|org.biojava3.ws.alignment.qblast ]] |

===== Tutorials =====

==== Prerequisites ====

Knowledge of the following is required for these tutorials:
  * [[http://www.oracle.com/technetwork/java/|Java]]
  * Extensible Markup Language (XML) ((Extensible Markup Language (XML) - http://www.w3.org/XML/))
    * [[http://www.w3schools.com/xml/|XML Tutorial]] from w3schools.com
  * XML Schema ((XML Schema - http://www.w3.org/XML/Schema))
    * [[http://www.w3schools.com/schema/|XML Schema Tutorial]] from w3schools.com

==== Web Services Tutorials Examples and Solutions ====

The examples and solutions for the exercises are available: [[http://www.ebi.ac.uk/Tools/webservices/downloads/java_exercises.zip|java_exercises.zip]]

The download is based on the Eclipse project used to develop the tutorials. The files are explicitly referenced in the tutorials and links provided to the on-line versions. Eclipse is not required to work though the exercises, although you may find it useful, a text editor and a working Java installation are the only requirements.

To import the project into [[http://www.eclipse.org/|Eclipse]]:
  - Download and install [[http://www.eclipse.org/|Eclipse]]
  - If necessary install Java, see http://www.oracle.com/technetwork/java/index.html
  - Download the [[http://www.ebi.ac.uk/Tools/webservices/downloads/java_exercises.zip|project]]
  - Unpack the project into a working directory
  - Import the project into Eclipse using "File" -> "Import..."
    - For "import source" select "General" -> "Existing Projects into Workspace"
    - Specify the working directory containing the project
    - Select the project

Initially the project will contain errors due to some code generated as part of the exercises not being present. Additionally there may be some errors due to some of the Perl modules required by the scripts not being installed.

==== Web Services Tutorials ====

Tutorials on using a selection of popular Java modules to develop clients for Web Services:
  * REST
    * [[.:Java:REST:java.net]]
    * [[.:Java:REST:Jakarta Commons HttpClient 3.x]]
  * SOAP
    * [[.:Java:SOAP:Apache Axis]]
    * [[.:Java:SOAP:JAX-WS]]

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^ Up | [[..:06_Programming|Programming Web Services]] ^ Contents | [[..:00_Contents|Contents]] |
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