uk.ac.ebi.fg.jobs.PubMedDataMinerJob.java Source code

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Here is the source code for uk.ac.ebi.fg.jobs.PubMedDataMinerJob.java

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package uk.ac.ebi.fg.jobs;

/*
 * Copyright 2009-2014 European Molecular Biology Laboratory
 *
 * 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.
 *
 */

import org.apache.commons.configuration.Configuration;
import org.quartz.JobDataMap;
import org.quartz.JobExecutionContext;
import org.quartz.JobExecutionException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import uk.ac.ebi.fg.utils.ApplicationJob;
import uk.ac.ebi.fg.utils.PubMedRetriever;
import uk.ac.ebi.fg.utils.objects.PubMedId;

import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.atomic.AtomicInteger;

/**
 * Adds records to PubMed id relation map. Record contains id and set of ids with distances
 */
public class PubMedDataMinerJob extends ApplicationJob {
    private final Logger logger = LoggerFactory.getLogger(getClass());

    public PubMedDataMinerJob() {
    }

    public void doExecute(JobExecutionContext jobExecutionContext)
            throws JobExecutionException, InterruptedException {
        JobDataMap dataMap = jobExecutionContext.getMergedJobDataMap();

        Set<String> pubMedNewIds = (Set<String>) dataMap.get("pubMedNewIds");
        ConcurrentHashMap<String, SortedSet<PubMedId>> pubMedIdRelationMap = (ConcurrentHashMap<String, SortedSet<PubMedId>>) dataMap
                .get("pubMedIdRelationMap");
        Configuration properties = (Configuration) dataMap.get("properties");
        AtomicInteger pubMedCounter = (AtomicInteger) dataMap.get("pubMedCounter");
        PubMedRetriever pubMedRetriever = (PubMedRetriever) dataMap.get("pubMedRetriever");
        String entry = (String) dataMap.get("entry");

        String pubMedURL = properties.getString("pub_med_url");
        int maxPubMedDist = properties.getInt("max_pubmed_distance");
        SortedSet<PubMedId> similarPublications = new TreeSet<PubMedId>();

        // add publication with distance 0
        similarPublications.add(new PubMedId(entry, 0));

        // get similar publications (distance 1)
        if (maxPubMedDist >= 1)
            similarPublications.addAll(getPubMedIdSet(pubMedRetriever.getSimilars(pubMedURL, entry), 1));

        // get publications with distance 2
        if (null != similarPublications && maxPubMedDist == 2) {
            SortedSet<PubMedId> iterationSet = new TreeSet<PubMedId>(similarPublications);

            for (PubMedId publication : iterationSet)
                similarPublications.addAll(
                        getPubMedIdSet(pubMedRetriever.getSimilars(pubMedURL, publication.getPublicationId()), 2));
        }

        if (!similarPublications.isEmpty())
            pubMedIdRelationMap.putIfAbsent(entry, similarPublications);

        // delay job to run for 1 second
        Thread.currentThread().wait(1000);

        logger.debug("Finished " + pubMedCounter.incrementAndGet() + " of " + pubMedNewIds.size()
                + " PubMedDataMinerJobs");
    }

    /**
     * Creates PubMed publications with set distance
     *
     * @param set      publications
     * @param distance distance
     * @return
     */
    private SortedSet<PubMedId> getPubMedIdSet(SortedSet<String> set, int distance) {
        SortedSet<PubMedId> result = new TreeSet<PubMedId>();

        if (null != set) {
            for (String pubMedId : set) {
                result.add(new PubMedId(pubMedId, distance));
            }
        }

        return result;
    }
}