edu.harvard.i2b2.basex.XQueryUtil.java Source code

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Here is the source code for edu.harvard.i2b2.basex.XQueryUtil.java

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/*
 * Copyright (c) 2006-2007 Massachusetts General Hospital 
 * All rights reserved. This program and the accompanying materials 
 * are made available under the terms of the i2b2 Software License v1.0 
 * which accompanies this distribution. 
 * 
 * Contributors:
 *       Kavishwar Wagholikar (kavi)
 *       July 4, 2015
 */

/*
 * Copyright (c) 2006-2007 Massachusetts General Hospital 
 * All rights reserved. This program and the accompanying materials 
 * are made available under the terms of the i2b2 Software License v1.0 
 * which accompanies this distribution. 
 * 
 * Contributors:
 *       Kavishwar Wagholikar (kavi)
 *       July 4, 2015
 */

/*
 * Copyright (c) 2006-2007 Massachusetts General Hospital 
 * All rights reserved. This program and the accompanying materials 
 * are made available under the terms of the i2b2 Software License v1.0 
 * which accompanies this distribution. 
 * 
 * Contributors:
 *       Kavishwar Wagholikar (kavi)
 *       July 4, 2015
 */
package edu.harvard.i2b2.basex;

import java.io.IOException;
import java.util.ArrayList;
import java.util.UUID;

import org.apache.commons.io.IOUtils;
import org.basex.core.*;
import org.basex.core.cmd.*;
import org.basex.data.Result;
import org.basex.query.QueryException;
import org.basex.query.QueryIOException;
import org.basex.query.QueryProcessor;
import org.basex.query.iter.Iter;
import org.basex.query.value.item.Item;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

public final class XQueryUtil {
    static Logger logger = LoggerFactory.getLogger(XQueryUtil.class);

    /**
     * Runs the example code.
     * 
     * @param args
     *            (ignored) command-line arguments
     * @throws XQueryUtilException
     * @throws BaseXException
     *             if a database command fails
     */

    public static ArrayList<String> getStringSequence(String query, String input) throws XQueryUtilException {
        ArrayList<String> resList = new ArrayList<String>();
        // Database context.
        Context context = new Context();

        // Create a database from a remote XML document
        // System.out.println("\n* Create a database from a file via http.");

        // Use internal parser to skip DTD parsing
        try {
            new Set("intparse", true).execute(context);
            String dbName = UUID.randomUUID().toString();
            new org.basex.core.cmd.CreateDB(dbName, input).execute(context);

            try (QueryProcessor proc = new QueryProcessor(query, context)) {
                // Store the pointer to the result in an iterator:
                Iter iter = proc.iter();

                // Iterate through all items and serialize
                int count = 0;
                for (Item item; (item = iter.next()) != null;) {
                    String r = item.serialize().toString();
                    resList.add(r);
                }
            } catch (QueryException | QueryIOException e) {
                //e.printStackTrace();
                logger.error(e.getMessage(), e);
                throw new XQueryUtilException(e);
            }

            // System.out.println("\n* Drop the database.");

            new DropIndex("text").execute(context);
            new DropIndex("attribute").execute(context);
            new DropIndex("fulltext").execute(context);

            new DropDB(dbName).execute(context);
        } catch (BaseXException e1) {
            //e1.printStackTrace();
            logger.error("", e1);
            throw new XQueryUtilException(e1);
        }
        context.close();
        return resList;
    }

    public static String processXQuery(String query, String input) throws XQueryUtilException {
        String result = null;
        try {

            Context context = new Context();
            if (query == null)
                throw new XQueryUtilException("query is null");
            if (input == null)
                throw new XQueryUtilException("input is null");

            // Create a database from a remote XML document
            // System.out.println("\n* Create a database from a file via
            // http.");

            // Use internal parser to skip DTD parsing
            String dbName = UUID.randomUUID().toString();
            try {
                if (input != null) {
                    new Set("intparse", true).execute(context);

                    new org.basex.core.cmd.CreateDB(dbName, input).execute(context);
                }
                try (QueryProcessor proc = new QueryProcessor(query, context)) {
                    // Store the pointer to the result in an iterator:
                    result = proc.execute().serialize();
                } catch (QueryException | IOException e) {
                    //e.printStackTrace();
                    throw new XQueryUtilException(e);

                }

                // System.out.println("\n* Drop the database.");
                if (input != null) {
                    new DropIndex("text").execute(context);
                    new DropIndex("attribute").execute(context);
                    new DropIndex("fulltext").execute(context);

                    new DropDB(dbName).execute(context);
                }
            } catch (BaseXException e1) {

                logger.error(e1.getMessage(), e1);
                throw new XQueryUtilException(e1);

            }
            context.close();

        } catch (java.nio.file.FileSystemNotFoundException e) {
            logger.error(">>>>>>>>caught exception");
        }
        return result;
    }

}