au.org.theark.phenotypic.job.PhenoDataUploadExecutor.java Source code

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Here is the source code for au.org.theark.phenotypic.job.PhenoDataUploadExecutor.java

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/*******************************************************************************
 * Copyright (c) 2011  University of Western Australia. All rights reserved.
 * 
 * This file is part of The Ark.
 * 
 * The Ark is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 3
 * of the License, or (at your option) any later version.
 * 
 * The Ark is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 ******************************************************************************/
package au.org.theark.phenotypic.job;

import static org.quartz.DateBuilder.nextGivenSecondDate;
import static org.quartz.JobBuilder.newJob;
import static org.quartz.SimpleScheduleBuilder.simpleSchedule;
import static org.quartz.TriggerBuilder.newTrigger;

import java.io.InputStream;
import java.util.Date;
import java.util.List;

import org.apache.shiro.SecurityUtils;
import org.jfree.util.Log;
import org.quartz.JobDetail;
import org.quartz.Scheduler;
import org.quartz.SchedulerFactory;
import org.quartz.SimpleTrigger;
import org.quartz.impl.StdSchedulerFactory;

import au.org.theark.core.Constants;
import au.org.theark.core.model.pheno.entity.PhenoDataSetCollection;
import au.org.theark.core.model.pheno.entity.PhenoDataSetGroup;
import au.org.theark.core.service.IArkCommonService;
import au.org.theark.phenotypic.service.IPhenotypicService;

public class PhenoDataUploadExecutor {
    //private static final Logger   log   = LoggerFactory.getLogger(CustomDataUploadExecutor.class);

    private IArkCommonService<Void> iArkCommonService = null;
    private IPhenotypicService iPhenoService = null;
    private Long uploadId;
    private Long studyId;
    private String fileFormat;
    private InputStream inputStream;
    private char delimiter = Constants.IMPORT_DELIM_CHAR_COMMA;
    private long size;
    private String report;
    private List<String> uidsToUpload;
    private PhenoDataSetCollection phenoCollection;
    private PhenoDataSetGroup phenoDataSetGroup;
    private boolean overwriteExisting;

    /**
     * StudyDataUploadExecutor constructor
     * @param iArkCommonService
     * @param iPhenoService
     * @param uploadId
     * @param currentUser
     * @param study
     * @param phenoCollection
     * @param file
     * @param delimiter
     * @param report 
     * @param uidsToUpload 
     */
    public PhenoDataUploadExecutor(IArkCommonService iArkCommonService, IPhenotypicService iPhenoService,
            InputStream inputStream, Long uploadId, Long studyId, String fileFormat, char delimiter, long size,
            String report, List<String> uidsToUpload, PhenoDataSetCollection phenoCollection,
            PhenoDataSetGroup phenoDataSetGroup, boolean overwriteExisting) {
        this.iArkCommonService = iArkCommonService;
        this.iPhenoService = iPhenoService;
        this.inputStream = inputStream;
        this.uploadId = uploadId;
        this.studyId = studyId;
        this.fileFormat = fileFormat;
        this.delimiter = delimiter;
        this.size = size;
        this.report = report;
        this.uidsToUpload = uidsToUpload;
        this.phenoCollection = phenoCollection;
        this.phenoDataSetGroup = phenoDataSetGroup;
        this.overwriteExisting = overwriteExisting;
    }

    public void run() throws Exception {

        SchedulerFactory sf = new StdSchedulerFactory();
        Scheduler sched = sf.getScheduler();
        Log.warn("executor " + uidsToUpload.size());
        JobDetail phenoDataUploadJob = newJob(PhenoDataUploadJob.class).withIdentity("PhenoDataUploadJob", "group2")
                .build();
        // pass initialization parameters into the job
        phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.IARKCOMMONSERVICE, iArkCommonService);
        phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.IPHENOSERVICE, iPhenoService);
        phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.UPLOADID, uploadId);
        phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.STUDY_ID, studyId);
        phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.REPORT, report);
        phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.FILE_FORMAT, fileFormat);
        phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.INPUT_STREAM, inputStream);
        phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.DELIMITER, delimiter);
        phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.SIZE, size);
        phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.LIST_OF_UIDS_TO_UPDATE, uidsToUpload);
        phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.PHENO_COLLECTION, phenoCollection);
        phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.PHENO_FIELD_GROUP, phenoDataSetGroup);
        phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.OVERWRITE_EXISTING, overwriteExisting);
        phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.USERNAME,
                SecurityUtils.getSubject().getPrincipal().toString());
        Date startTime = nextGivenSecondDate(null, 1);
        SimpleTrigger trigger1 = newTrigger().withIdentity("PhenoDataUploadJobTrigger", "group1").startAt(startTime)
                .withSchedule(simpleSchedule()).build();
        sched.scheduleJob(phenoDataUploadJob, trigger1);
        //      log.warn(studyUploadJob.getKey() + " will run at: " + scheduleTime1 + " and repeat: " + trigger1.getRepeatCount() + " times, every " + trigger1.getRepeatInterval() / 1000 + " seconds");
        // All of the jobs have been added to the scheduler, but none of the jobs will run until the scheduler has been started
        sched.start();
        //sched.triggerJob(phenoDataUploadJob.getKey());
    }

}