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

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Here is the source code for uk.ac.ebi.fg.jobs.PubMedDataMinerWrapperJob.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.JobDetail;
import org.quartz.JobExecutionContext;
import org.quartz.SchedulerException;
import uk.ac.ebi.arrayexpress.utils.controller.IJobsController;
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.concurrent.ConcurrentHashMap;
import java.util.concurrent.atomic.AtomicInteger;

import static org.quartz.JobBuilder.newJob;

/**
 * Separates PubMed id list into smaller lists and creates concurrent jobs for gathering similar PubMed ids
 */
public class PubMedDataMinerWrapperJob extends ApplicationJob {
    public PubMedDataMinerWrapperJob() {
    }

    public void doExecute(JobExecutionContext jobExecutionContext) throws SchedulerException, 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");
        PubMedRetriever pubMedRetriever = (PubMedRetriever) dataMap.get("pubMedRetriever");
        IJobsController jobsController = (IJobsController) dataMap.get("jobsController");
        String jobGroup = properties.getString("quartz_job_group_name");
        int maxPubMedDist = properties.getInt("max_pubmed_distance");

        AtomicInteger pubMedCounter = new AtomicInteger();
        int i = 0;

        if (!pubMedNewIds.isEmpty() && maxPubMedDist >= 0) {
            for (String entry : pubMedNewIds) {
                ++i;

                JobDetail pubMedJobDetail = newJob(PubMedDataMinerJob.class)
                        .withIdentity("pubMedDataMinerJob" + i, jobGroup).storeDurably(true).requestRecovery(false)
                        .build();

                pubMedJobDetail.getJobDataMap().put("pubMedNewIds", pubMedNewIds);
                pubMedJobDetail.getJobDataMap().put("pubMedIdRelationMap", pubMedIdRelationMap);
                pubMedJobDetail.getJobDataMap().put("properties", properties);
                pubMedJobDetail.getJobDataMap().put("pubMedCounter", pubMedCounter);
                pubMedJobDetail.getJobDataMap().put("pubMedRetriever", pubMedRetriever);
                pubMedJobDetail.getJobDataMap().put("entry", entry);

                jobsController.addJob("pubMedDataMinerJob" + i, PubMedDataMinerJob.class, pubMedJobDetail);

                Thread.currentThread().wait(1);
            }

            // start first 3 jobs
            jobsController.executeJob("pubMedDataMinerJob" + 1, jobGroup);
            if (i > 1) {
                jobsController.executeJob("pubMedDataMinerJob" + 2, jobGroup);
                if (i > 2)
                    jobsController.executeJob("pubMedDataMinerJob" + 3, jobGroup);
            }
        }
    }
}