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

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Here is the source code for gov.nih.nci.cabig.caaers.service.synchronizer.StudyDiseasesSynchronizer.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 gov.nih.nci.cabig.caaers.domain.*;
import gov.nih.nci.cabig.caaers.service.DomainObjectImportOutcome;
import gov.nih.nci.cabig.ctms.domain.DomainObject;
import org.apache.commons.collections.CollectionUtils;

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

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

    private List<String> context = new ArrayList<String>();

    @Override
    public List<String> contexts() {
        return context;
    }

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

        //ignore if disease section is empty in xmlstudy
        if (CollectionUtils.isEmpty(xmlStudy.getActiveStudyDiseases())) {
            return;
        }

        //create an Index of existing study diseases
        HashMap<AbstractStudyDisease<? extends DomainObject>, AbstractStudyDisease<? extends DomainObject>> dbDiseasesIndexMap = new HashMap<AbstractStudyDisease<? extends DomainObject>, AbstractStudyDisease<? extends DomainObject>>();

        for (AbstractStudyDisease<? extends DomainObject> studyDisease : dbStudy.getActiveStudyDiseases()) {
            dbDiseasesIndexMap.put(studyDisease, studyDisease);
        }

        //loop through the xml study, then add/update existing diseases
        for (AbstractStudyDisease<? extends DomainObject> xmlDisease : xmlStudy.getActiveStudyDiseases()) {
            AbstractStudyDisease<? extends DomainObject> disease = dbDiseasesIndexMap.remove(xmlDisease);
            if (disease == null) {
                //new disease, so add to dbstudy
                if (xmlDisease instanceof CtepStudyDisease)
                    dbStudy.addCtepStudyDisease((CtepStudyDisease) xmlDisease);
                if (xmlDisease instanceof MeddraStudyDisease)
                    dbStudy.addMeddraStudyDisease((MeddraStudyDisease) xmlDisease);
                if (xmlDisease instanceof StudyCondition)
                    dbStudy.addStudyCondition((StudyCondition) xmlDisease);
                continue;
            }

            //update the primary indicator (if CTEP Disease)
            if (disease instanceof CtepStudyDisease) {
                ((CtepStudyDisease) disease).setLeadDisease(((CtepStudyDisease) xmlDisease).getLeadDisease());
            }
        }

        //mark retired the diseases still in index
        AbstractMutableRetireableDomainObject.retire(dbDiseasesIndexMap.values());

    }

}