gov.nih.nci.ncicb.tcga.dcc.qclive.live.service.BiospecimenMetadataPlatformsJob.java Source code

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Here is the source code for gov.nih.nci.ncicb.tcga.dcc.qclive.live.service.BiospecimenMetadataPlatformsJob.java

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/*
 * Software License, Version 1.0 Copyright 2011 SRA International, Inc.
 * Copyright Notice.  The software subject to this notice and license includes both human
 * readable source code form and machine readable, binary, object code form (the "caBIG
 * Software").
 *
 * Please refer to the complete License text for full details at the root of the project.
 */
package gov.nih.nci.ncicb.tcga.dcc.qclive.live.service;

import gov.nih.nci.ncicb.tcga.dcc.ConstantValues;
import gov.nih.nci.ncicb.tcga.dcc.common.dao.UUIDHierarchyQueries;
import gov.nih.nci.ncicb.tcga.dcc.common.framework.SpringApplicationContext;
import gov.nih.nci.ncicb.tcga.dcc.common.mail.MailErrorHelper;
import gov.nih.nci.ncicb.tcga.dcc.common.util.StringUtil;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.quartz.Job;
import org.quartz.JobExecutionContext;
import org.quartz.JobExecutionException;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.DefaultTransactionDefinition;

/**
 * BiospecimenMetadataPlatforms job is used to populate platforms in 
 * uuid_hierarchy table. The job queries the database for platform/uuid associations
 * and updates uuid metadata table with these platforms.
 *
 * @author Stanley Girshik Last updated by: $Author$
 * @version $Rev$
 */
public class BiospecimenMetadataPlatformsJob implements Job {

    private final Log logger = LogFactory.getLog(getClass());
    // since Quartz and Spring don't share a lifecycle, lookup the bean manually
    UUIDHierarchyQueries uuidHierarchyQueries = (UUIDHierarchyQueries) SpringApplicationContext
            .getObject(ConstantValues.UUID_HIERARCHY_QUERIES);
    PlatformTransactionManager transactionManager = (PlatformTransactionManager) SpringApplicationContext
            .getObject("transactionManager");

    @Override
    public void execute(JobExecutionContext context) throws JobExecutionException {
        logger.debug(" Updating platforms in uuid_hierarchy ");

        // start TX
        DefaultTransactionDefinition transactionDefinition = new DefaultTransactionDefinition();
        transactionDefinition.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
        TransactionStatus status = transactionManager.getTransaction(transactionDefinition);
        try {
            uuidHierarchyQueries.deletePlatforms();
            uuidHierarchyQueries.updateAllUUIDHierarchyPlatforms();
            uuidHierarchyQueries.deduplicatePlatforms();
            transactionManager.commit(status);
        } catch (Exception e) {
            transactionManager.rollback(status);
            String errorMessage = "Unable to update platforms for uuid_hierarchy table due to an unexpected condition";
            // email full stack trace                
            sendErrorEmail(e, errorMessage);
            throw new JobExecutionException(errorMessage, e);
        }
    }

    protected MailErrorHelper getErrorMailSender() {
        return (MailErrorHelper) SpringApplicationContext
                .getObject(ConstantValues.MAIL_ERROR_HELPER_SPRING_BEAN_NAME);
    }

    private void sendErrorEmail(final Exception exception, final String message) {
        getErrorMailSender().send(message, StringUtil.stackTraceAsString(exception));
    }

    public void setUuidHierarchyQueries(UUIDHierarchyQueries uuidHierarchyQueries) {
        this.uuidHierarchyQueries = uuidHierarchyQueries;
    }
}