gov.nih.nci.cabig.caaers.service.migrator.adverseevent.SAEAdverseEventReportingPeriodConverter.java Source code

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Here is the source code for gov.nih.nci.cabig.caaers.service.migrator.adverseevent.SAEAdverseEventReportingPeriodConverter.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.migrator.adverseevent;

import gov.nih.nci.cabig.caaers.domain.*;
import gov.nih.nci.cabig.caaers.integration.schema.adverseevent.AdverseEventType;
import gov.nih.nci.cabig.caaers.integration.schema.adverseevent.CourseType;
import gov.nih.nci.cabig.caaers.integration.schema.saerules.AdverseEventResult;
import gov.nih.nci.cabig.caaers.integration.schema.saerules.SaveAndEvaluateAEsInputMessage;
import gov.nih.nci.cabig.caaers.integration.schema.saerules.Criteria;
import org.apache.commons.lang.StringUtils;

import java.util.ArrayList;
import java.util.Map;

/**
 * User: Vijendhar Meda
 * Date: 3/27/13
 */
public class SAEAdverseEventReportingPeriodConverter {

    private AdverseEventConverter aeConverter;

    public AdverseEventConverter getAeConverter() {
        return aeConverter;
    }

    public void setAeConverter(AdverseEventConverter aeConverter) {
        this.aeConverter = aeConverter;
    }

    /**
     * Will convert to domain object from AdverseEventInputMessage
     * @param aeiMsg
     * @return
     */
    public AdverseEventReportingPeriod convert(SaveAndEvaluateAEsInputMessage aeiMsg,
            Map<AdverseEvent, AdverseEventResult> mapAE2DTO) {
        Criteria criteria = aeiMsg.getCriteria();
        AdverseEventReportingPeriod rp = new AdverseEventReportingPeriod();
        Study study = new LocalStudy();
        StudySite studySite = new StudySite();
        study.addStudySite(studySite);

        Participant participant = new Participant();
        StudyParticipantAssignment assignment = new StudyParticipantAssignment();
        assignment.setReportingPeriods(new ArrayList<AdverseEventReportingPeriod>());
        participant.addAssignment(assignment);
        rp.setAssignment(assignment);
        assignment.getReportingPeriods().add(rp);
        assignment.setStudySite(studySite);

        //set SSI
        assignment.setStudySubjectIdentifier(criteria.getStudySubjectIdentifier());

        //set Study Protocol Identifier
        Identifier studyIdentifier = new OrganizationAssignedIdentifier();
        studyIdentifier.setType(OrganizationAssignedIdentifier.SPONSOR_IDENTIFIER_TYPE);
        studyIdentifier.setValue(criteria.getStudyIdentifier());
        study.addIdentifier(studyIdentifier);

        //set the course details
        CourseType course = criteria.getCourse();
        if (course.getCycleNumber() != null)
            rp.setCycleNumber(course.getCycleNumber().intValue());
        if (course.getExternalId() != null)
            rp.setExternalId(course.getExternalId());
        if (course.getTreatmentType() != null) {
            rp.setEpoch(new Epoch());
            rp.getEpoch().setName(course.getTreatmentType());
        }
        String desc = course.getOtherTreatmentAssignmentDescription();
        if (course.getTreatmentAssignmentCode() != null) {
            String code = course.getTreatmentAssignmentCode();

            //other TAC ?
            if (StringUtils.equalsIgnoreCase("other", code)) {
                if (StringUtils.isNotEmpty(desc) && !StringUtils.equalsIgnoreCase("n/a", desc)) {
                    rp.setTreatmentAssignmentDescription(desc);
                }
            } else {
                TreatmentAssignment ta = new TreatmentAssignment();
                ta.setCode(code);
                ta.setStudy(study);
                rp.setTreatmentAssignment(ta);
            }
        } else {
            rp.setTreatmentAssignmentDescription(desc);
        }

        if (course.getStartDateOfFirstCourse() != null) {
            rp.getAssignment()
                    .setStartDateOfFirstCourse(course.getStartDateOfFirstCourse().toGregorianCalendar().getTime());
        }

        if (course.getStartDateOfThisCourse() != null) {
            rp.setStartDate(course.getStartDateOfThisCourse().toGregorianCalendar().getTime());
        }

        if (course.getEndDateOfThisCourse() != null) {
            rp.setEndDate(course.getEndDateOfThisCourse().toGregorianCalendar().getTime());
        }

        if (aeiMsg.getAdverseEvents() != null && aeiMsg.getAdverseEvents().getAdverseEvent() != null) {
            for (AdverseEventType aeType : aeiMsg.getAdverseEvents().getAdverseEvent()) {
                AdverseEvent ae = aeConverter.convert(aeType);

                // Create a Map to convert given ae to result object.
                AdverseEventResult result = new AdverseEventResult();
                result.setAdverseEvent(aeType);
                result.setRequiresReporting(false);
                mapAE2DTO.put(ae, result);

                rp.addAdverseEvent(ae);
            }
        }

        return rp;
    }

}