gov.nih.nci.cabig.caaers.service.synchronizer.StudyAgentsSynchronizer.java Source code

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Here is the source code for gov.nih.nci.cabig.caaers.service.synchronizer.StudyAgentsSynchronizer.java

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/*******************************************************************************
 * Copyright SemanticBits, Northwestern University and Akaza Research
 * 
 * Distributed under the OSI-approved BSD 3-Clause License.
 * See http://ncip.github.com/caaers/LICENSE.txt for details.
 ******************************************************************************/
package gov.nih.nci.cabig.caaers.service.synchronizer;

import edu.nwu.bioinformatics.commons.CollectionUtils;
import gov.nih.nci.cabig.caaers.domain.AbstractMutableRetireableDomainObject;
import gov.nih.nci.cabig.caaers.domain.Study;
import gov.nih.nci.cabig.caaers.domain.StudyAgent;
import gov.nih.nci.cabig.caaers.domain.StudyAgentINDAssociation;
import gov.nih.nci.cabig.caaers.service.DomainObjectImportOutcome;
import gov.nih.nci.cabig.caaers.service.migrator.Migrator;

import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;

import org.apache.commons.collections.map.HashedMap;

/**
 * @author Monish Domla
 * @author Biju Joseph (refactored)
 *
 */
public class StudyAgentsSynchronizer implements Migrator<gov.nih.nci.cabig.caaers.domain.Study> {

    public void migrate(Study dbStudy, Study xmlStudy, DomainObjectImportOutcome<Study> outcome) {

        //Ignore if the section is empty- Update- This is no longer true since CTEP sync should remove and override the agents
        //      if(CollectionUtils.isEmpty(xmlStudy.getStudyAgents())){
        //         return;
        //      }

        //create an index of existing agents in the dbStudy.
        HashMap<String, StudyAgent> dbStudyAgentIndexMap = new HashMap<String, StudyAgent>();
        for (StudyAgent sa : dbStudy.getActiveStudyAgents()) {
            dbStudyAgentIndexMap.put(sa.getAgentName(), sa);
        }

        //identify new study agents, also update existing ones.
        for (StudyAgent xmlStudyAgent : xmlStudy.getStudyAgents()) {
            StudyAgent sa = dbStudyAgentIndexMap.remove(xmlStudyAgent.getAgentName());
            if (sa == null) {
                //newly added one, so add it to study
                dbStudy.addStudyAgent(xmlStudyAgent);
                continue;
            }

            //existing one - so update if necessary
            //BJ : the original code did not do anything, so nothing to update. 
            //Update the StudyAgents as it can change between Adders Sync
            sa.setIndType(xmlStudyAgent.getIndType());
            sa.setPartOfLeadIND(xmlStudyAgent.getPartOfLeadIND());
            sa.getStudyAgentINDAssociations().clear();
            for (StudyAgentINDAssociation ass : xmlStudyAgent.getStudyAgentINDAssociations()) {
                sa.addStudyAgentINDAssociation(ass);
            }
        }

        //now soft delete, all the ones not present in XML Study
        AbstractMutableRetireableDomainObject.retire(dbStudyAgentIndexMap.values());
    }
}