Hi Andrea, there is a simple example on page 75 of our manual http://www.biomart.org/other/rc6_documentation.pdf
For downloading and installing BioMart software see sections 1-3 page 5 a On Thu, Feb 9, 2012 at 7:21 AM, Andrea Gangi <[email protected]> wrote: > Hi, i want to use our service for my Java application. > I need to access PRIDE data. The query XML automatically generated by > central.biomart.org is: > > <!DOCTYPE Query> > <Query client="true" processor="TSV" limit="-1" header="1"> > <Dataset name="pride" config="pride_config"> > <Attribute name="experiment_ac"/> > <Attribute name="experiment_title"/> > <Attribute name="pubmed_id"/> > <Attribute name="uniprot_id"/> > <Attribute name="submitted_accession"/> > </Dataset > </Query> > > How can I use this query from my Java application? > > Alternatively: I have generated this Java code too. But where can I find > the BiomartAPI for Java? I need to install anything or is there a .jar file > that include Biomart JAVA api? > > import org.biomart.api.factory.*; >> import org.biomart.api.Portal; >> import org.biomart.api.Query; >> >> /* >> * This is a runnable Java class that executes the query. >> * Please adapt this code as needed, and DON'T forget to change the >> xmlPath. >> */ >> >> public class QueryTest { >> public static void main(String[] args) throws Exception { >> String xmlPath = "/path/to/registry_xml"; // Needs to be changed >> >> MartRegistryFactory factory = new XmlMartRegistryFactory(xmlPath, >> null); >> Portal portal = new Portal(factory, null); >> >> Query query = new Query(portal); >> query.setProcessor("TSV"); >> query.setClient("biomartclient"); >> query.setLimit(-1); >> query.setHeader(true); >> >> Query.Dataset ds = query.addDataset("pride", "pride_config"); >> ds.addAttribute("experiment_ac"); >> ds.addAttribute("experiment_title"); >> ds.addAttribute("pubmed_id"); >> ds.addAttribute("uniprot_id"); >> ds.addAttribute("submitted_accession"); >> >> // Print to System.out, but you can pass in any >> java.io.OutputStream >> query.getResults(System.out); >> >> System.exit(0); >> } >> } >> > > How can I easily access this information by my application? > > Thank you > > Bye > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users > > -- Arek Kasprzyk, MD, MSc, PhD BioMart Project Lead
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