gov.nih.nci.cabig.caaers.web.admin.StudyImporter.java Source code

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Here is the source code for gov.nih.nci.cabig.caaers.web.admin.StudyImporter.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.web.admin;

import gov.nih.nci.cabig.caaers.CaaersSystemException;
import gov.nih.nci.cabig.caaers.api.impl.StudyProcessorImpl;
import gov.nih.nci.cabig.caaers.domain.LocalStudy;
import gov.nih.nci.cabig.caaers.domain.Study;
import gov.nih.nci.cabig.caaers.domain.repository.StudyRepository;
import gov.nih.nci.cabig.caaers.integration.schema.study.Studies;
import gov.nih.nci.cabig.caaers.service.DomainObjectImportOutcome;
import gov.nih.nci.cabig.caaers.service.DomainObjectImportOutcome.Severity;
import gov.nih.nci.cabig.caaers.validation.validator.DomainObjectValidator;

import java.io.File;
import java.util.ArrayList;
import java.util.List;

import javax.servlet.http.HttpServletRequest;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Unmarshaller;

import org.apache.commons.collections.CollectionUtils;
import org.apache.log4j.Logger;

/**
 * @author Sameer Sawant
 * @author Ion C. Olaru
 * 
 */
public class StudyImporter extends Importer {

    private static Logger logger = Logger.getLogger(StudyImporter.class);
    private DomainObjectValidator domainObjectValidator;
    private StudyProcessorImpl studyProcessorImpl;
    private StudyRepository studyRepository;

    public void processEntities(File xmlFile, ImportCommand command) {
        boolean valid = validateAgainstSchema(xmlFile, command, getXSDLocation(STUDY_IMPORT));
        if (!valid) {
            return;
        }

        Studies studies;

        try {
            JAXBContext jaxbContext = JAXBContext.newInstance("gov.nih.nci.cabig.caaers.integration.schema.study");
            Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();

            Object importObject = unmarshaller.unmarshal(xmlFile);
            if (!validRootElement(importObject, STUDY_IMPORT, command))
                return;

            studies = (Studies) importObject;
            if (studies != null) {
                for (gov.nih.nci.cabig.caaers.integration.schema.study.Study studyDto : studies.getStudy()) {
                    DomainObjectImportOutcome<Study> studyImportOutcome = studyProcessorImpl.importStudy(studyDto);
                    List<String> errors = domainObjectValidator
                            .validate(studyImportOutcome.getImportedDomainObject());
                    if (studyImportOutcome.isSavable() && errors.size() == 0) {
                        command.addImportableStudy(studyImportOutcome);
                    } else {
                        for (String errMsg : errors) {
                            studyImportOutcome.addErrorMessage(errMsg, Severity.ERROR);
                        }
                        command.addNonImportableStudy(studyImportOutcome);
                    }
                }

                //Remove Duplicate Studies in the List.
                List<DomainObjectImportOutcome<Study>> dupList = new ArrayList<DomainObjectImportOutcome<Study>>();
                for (int i = 0; i < command.getImportableStudies().size() - 1; i++) {
                    Study study1 = command.getImportableStudies().get(i).getImportedDomainObject();
                    for (int j = i + 1; j < command.getImportableStudies().size(); j++) {
                        Study study2 = command.getImportableStudies().get(j).getImportedDomainObject();
                        if (study1.equals(study2)) {
                            command.getImportableStudies().get(j).addErrorMessage(
                                    "Study Identifier already used in a different Study", Severity.ERROR);
                            command.addNonImportableStudy(command.getImportableStudies().get(j));
                            dupList.add(command.getImportableStudies().get(j));
                            logger.debug("Duplicate Study :: " + study2.getShortTitle());
                            break;
                        }
                    }
                }
                for (DomainObjectImportOutcome<Study> obj : dupList) {
                    command.getImportableStudies().remove(obj);
                }
            }
        } catch (JAXBException e) {
            throw new CaaersSystemException(
                    "There was an error converting study data transfer object to study domain object", e);
        }
    }

    public void save(ImportCommand command, HttpServletRequest request) {
        for (DomainObjectImportOutcome<Study> importOutcome : command.getImportableStudies()) {
            studyRepository.synchronizeStudyPersonnel(importOutcome.getImportedDomainObject());
            studyRepository.save(importOutcome.getImportedDomainObject());
        }
        //   CAAERS-4461
        if (CollectionUtils.isNotEmpty(command.getImportableStudies())) {
            getEventFactory().publishEntityModifiedEvent(new LocalStudy(), true);
        }
    }

    public void setStudyRepository(StudyRepository studyRepository) {
        this.studyRepository = studyRepository;
    }

    public DomainObjectValidator getDomainObjectValidator() {
        return domainObjectValidator;
    }

    public void setDomainObjectValidator(DomainObjectValidator domainObjectValidator) {
        this.domainObjectValidator = domainObjectValidator;
    }

    public StudyProcessorImpl getStudyProcessorImpl() {
        return studyProcessorImpl;
    }

    public void setStudyProcessorImpl(StudyProcessorImpl studyProcessorImpl) {
        this.studyProcessorImpl = studyProcessorImpl;
    }

}