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

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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.fhir.intake.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
     */
    static Context context = new Context();

    public static ArrayList<String> getStringSequence(String query, String input) throws XQueryUtilException {

        synchronized (context) {
            ArrayList<String> resList = new ArrayList<String>();
            // Database 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 {
        synchronized (context) {
            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;
        }
    }

}