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ENA Sequence Search

Introduction

ENA sequence search is search service against all nucleotide sequences available in the European Nucleotide Archive (ENA), Ensembl and Ensembl Genomes databases.

Programmatic access

A SOAP service is available for programmatic users:

http://www.ebi.ac.uk/ena/web-service/search/services/SearchService?wsdl

The rest of the document describes how to use this service with Java.

Requirements :

  1. Java JDK1.5 or above
  2. AXIS2 (currently on version 1.6.1)
  3. CVS Client

Building java stubs from the WDSL

The following instructions explain how to build the Java stubs from the WDSL. It assumes that you have installed a working JDK and a copy of AXIS2.

axis_home/bin/wsdl2java.sh -uri http://www.ebi.ac.uk/ena/web-service/search/services/SearchService?wsdl -o . -p uk.ac.ebi.ena.searchservice

This will generate a Java skeleton in the src directory along with an associated ant build file. The following code fragment will instantiate a connection to the web service using a Java stub:

String serviceEPR = "http://www.ebi.ac.uk/ena/web-service/search/services/SearchService?wsdl";

SearchServiceStub searchServiceStub = new SearchServiceStub(serviceEPR);

searchServiceStub._getServiceClient().getOptions().setManageSession(true); Options options = searchServiceStub._getServiceClient().getOptions(); searchServiceStub._getServiceClient().getOptions().setTimeOutInMilliSeconds(0);

Checking out and building sample applications 

The following instructions will check out the search-service-web-client from CVS and build the sample applications:

export CVSROOT=:pserver:userid@cvsebi.ebi.ac.uk:2401/ebi/cvs/new-webin

cd search-service-web-api
./scripts/generate_java_stubs.sh
ant