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
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