ubic.gemma.core.loader.util.ParserAndLoaderTools.java Source code

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Here is the source code for ubic.gemma.core.loader.util.ParserAndLoaderTools.java

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/*
 * The Gemma project
 * 
 * Copyright (c) 2006 University of British Columbia
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *       http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 *
 */
package ubic.gemma.core.loader.util;

import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.time.StopWatch;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import ubic.gemma.persistence.persister.Persister;

import java.lang.reflect.Method;
import java.util.Collection;
import java.util.Map;

/**
 * Utilities to be used by parsers and loaders.
 *
 * @author keshav
 */
@SuppressWarnings("unused") // Possible external use
public class ParserAndLoaderTools {
    protected static final Log log = LogFactory.getLog(ParserAndLoaderTools.class);

    /**
     * User the loader to persist the collection.
     *
     * @param loader loader
     * @param col    collection
     */
    public static void loadDatabase(Persister loader, Collection<?> col) {
        assert (loader != null);
        assert (col != null);
        if (col.size() == 0)
            return;

        StopWatch stopWatch = new StopWatch();
        stopWatch.start();

        loader.persist(col);

        stopWatch.stop();

        long time = stopWatch.getTime();
        if (time < 1000)
            log.info("Time taken: " + time + " ms.");
        else {
            log.info("Time taken: " + time / 1000 + " s.");
        }
    }

    public static void objectsPersistedUpdate(int count, int modulus, String objectName) {
        if (count % modulus == 0)
            log.info(count + " " + objectName + " persisted");

    }

    public static Method findParseLineMethod(Object obj, String fileName) throws NoSuchMethodException {
        String[] f = StringUtils.split(fileName, System.getProperty("file.separator"));
        String suffixOfFilename = f[f.length - 1];
        assert obj != null;
        Method[] methods = obj.getClass().getMethods();
        for (Method m : methods) {
            if (m.getName().toLowerCase().contains((suffixOfFilename).toLowerCase())
                    && m.getName().startsWith("mapFrom")) {
                return m;
            }
        }
        throw new NoSuchMethodException();
    }

    /**
     * Print content of map if debug is set to true.
     *
     * @param map map
     */
    public static void debugMap(Map<?, ?> map) {
        if (log.isDebugEnabled()) {
            log.info("Map contains: ");

            for (Object obj : map.keySet()) {
                log.info(obj);
            }

            log.info("map size: " + map.keySet().size());
        }
    }

}