Skip to content

Instantly share code, notes, and snippets.

Embed
What would you like to do?
Java class to export Protege 3 database backend.
package ncbo.proto;
import java.io.FileInputStream;
import java.net.URI;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Properties;
import edu.stanford.smi.protegex.owl.database.creator.OwlDatabaseCreator;
import edu.stanford.smi.protegex.owl.model.OWLModel;
import edu.stanford.smi.protegex.owl.writer.rdfxml.rdfwriter.OWLModelAllTripleStoresWriter;
/**
*
* @author manuelso@stanford.edu
*
* Sample code to export a protege 3 database backend programatically.
* References:
* http://protegewiki.stanford.edu/wiki/LoadOWLOntologyFromDB (method 2)
* http://smi-protege.stanford.edu/svn/owl/trunk/src/edu/stanford/smi/protegex/owl/jena/export/JenaExportPlugin.java?view=markup
*
*/
public class MetadataExport {
public static void main(String[] args) throws Exception {
if (args.length < 1) {
System.out.println("use: java ncbo.proto.MetadataExport <file_to_export>");
System.out.println("make sure that MetadataExport.properties contains the database configuration");
return;
}
URI fileURI = new URI("file://"+(new File(args[0])).getAbsolutePath());
Properties properties = new Properties();
properties.load(new FileInputStream("MetadataExport.properties"));
Collection<String> errors = new ArrayList<String>();
//the "false" argument means that it won't overide the existing table <--- IMPORTANT otherwise will destroy existing database.
OwlDatabaseCreator creator = new OwlDatabaseCreator(false);
creator.setDriver(properties.getProperty("jdbcDriver"));
creator.setURL(properties.getProperty("protegeJdbcUrl"));
creator.setUsername(properties.getProperty("protegeJdbcUsername"));
creator.setPassword(properties.getProperty("protegeJdbcPassword"));
creator.setTable(properties.getProperty("tableName"));
creator.create(errors);
if (errors.size() > 0) {
System.out.println("Errors opening database ...\n" + StringUtils.join(errors,"\n"));
}
OWLModel owlModel = creator.getOwlModel();
try {
OWLModelAllTripleStoresWriter writer = new OWLModelAllTripleStoresWriter(owlModel, fileURI, true);
writer.write();
}
catch (Exception ex) {
String message = "Failed to save file " + fileURI;
System.out.println(message);
throw ex;
}
}
}
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
You can’t perform that action at this time.