I'm looking to run arbitrary XQuery code from Java. Oracle gives this example:
    OXQDataSource ds = new OXQDataSource();
    XQConnection con = ds.getConnection();
    String query = "<hello-world>{1 + 1}</hello-world>";
    XQPreparedExpression expr = con.prepareExpression(query);
    XQSequence result = expr.executeQuery();
Should that not also be possible through BaseX?  To my understanding, BaseX is quite compliant with XQuery.
From the CLI arbitrary XQuery code:
thufir@dur:~/basex$ 
thufir@dur:~/basex$ basex fetch.books.html.xq 
[warning] /usr/bin/basex: Unable to locate /usr/share/java/jing.jar in /usr/share/java
<html xmlns="http://www.w3.org/1999/xhtml" class="no-js" lang="en-us">
  <head>
    <title>
    All products | Books to Scrape - Sandbox
</title>
..        
    </body>
</html>thufir@dur:~/basex$ 
thufir@dur:~/basex$ 
thufir@dur:~/basex$ cat fetch.books.html.xq 
fetch:xml(
  'http://books.toscrape.com/',
  map {
    'parser': 'html',
    'htmlparser': map { 'nons': false() }
  }
)
thufir@dur:~/basex$ 
Other, non-proprietary XQuery code runs through BaseX as expected.
While this will populate the database:
package org.basex.examples.local;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.Iterator;
import java.util.Properties;
import java.util.logging.Logger;
import org.basex.core.BaseXException;
import org.basex.core.Context;
import org.basex.core.Databases;
import org.basex.core.cmd.CreateDB;
import org.basex.core.cmd.List;
import org.basex.core.cmd.Set;
import org.basex.util.list.StringList;
public class Scraper {
    private static final Logger LOG = Logger.getLogger(App.class.getName());
    private Properties properties = new Properties();
    private URL url = null;
    private String databaseName = null;
    private Context context = null;
    private String parserType = null;
    private Scraper() {
    }
    public Scraper(Properties properties) {
        this.properties = properties;
        LOG.fine(properties.toString());
    }
    public void init() throws MalformedURLException {
        parserType = properties.getProperty("parserType");
        url = new URL(properties.getProperty(parserType + "URL"));
        databaseName = properties.getProperty("databaseName");
        context = new Context();
    }
    private void list() throws BaseXException {
        LOG.info(new List().execute(context));
    }
    private void drop() throws BaseXException {
        list();
        new Set("parser", parserType).execute(context);
        new CreateDB(databaseName, url.toString()).execute(context);
        list();
    }
    private void create() throws BaseXException {
        list();
        new Set("parser", parserType).execute(context);
        new CreateDB(databaseName, url.toString()).execute(context);
        LOG.info(new List().execute(context));
        list();
    }
    private void infoOnDatabases() {
        Databases databases = context.databases();
        StringList stringListOfDatabases = databases.listDBs();
        String currentDatabaseName = null;
        Iterator<String> databaseIterator = stringListOfDatabases.iterator();
        while (databaseIterator.hasNext()) {
            currentDatabaseName = databaseIterator.next();
            LOG.info(currentDatabaseName);
            //xQuery here..
        }
    }
    public void fetch() throws BaseXException, MalformedURLException {
        drop();
        create();
        infoOnDatabases();
        list();
        context.close();
    }
}
it's rather limited.
reference:
http://docs.basex.org/wiki/Java_Examples
https://stackoverflow.com/a/44638635/262852
https://docs.oracle.com/database/121/ADXDK/adx_j_xqj.htm#ADXDK115