/*
* Copyright (C) 2011 SeqWare
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package net.sourceforge.seqware.webservice.resources.tables;
import net.sf.beanlib.CollectionPropertyName;
import net.sf.beanlib.hibernate3.Hibernate3DtoCopier;
import net.sourceforge.seqware.common.business.StudyService;
import net.sourceforge.seqware.common.factory.BeanFactory;
import net.sourceforge.seqware.common.model.Study;
import net.sourceforge.seqware.common.util.xmltools.JaxbObject;
import net.sourceforge.seqware.common.util.xmltools.XmlTools;
import org.restlet.data.Status;
import org.restlet.representation.Representation;
import org.restlet.resource.Get;
import org.restlet.resource.Put;
import org.restlet.resource.ResourceException;
import org.w3c.dom.Document;
import org.xml.sax.SAXException;
/**
* <p>
* StudyIDResource class.
* </p>
*
* @author mtaschuk
* @version $Id: $Id
*/
public class StudyIDResource extends DatabaseIDResource {
/**
* <p>
* Constructor for StudyIDResource.
* </p>
*/
public StudyIDResource() {
super("studyId");
}
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
authenticate();
StudyService ss = BeanFactory.getStudyServiceBean();
Study study = testIfNull(ss.findBySWAccession(getId()));
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<Study> jaxbTool = new JaxbObject<>();
CollectionPropertyName<Study>[] createCollectionPropertyNames = CollectionPropertyName.createCollectionPropertyNames(Study.class,
new String[] { "studyAttributes" });
Study dto = copier.hibernate2dto(Study.class, study, new Class<?>[] {}, createCollectionPropertyNames);
Document line = XmlTools.marshalToDocument(jaxbTool, dto);
getResponse().setEntity(XmlTools.getRepresentation(line));
}
/**
* {@inheritDoc}
*
* @return
*/
@Override
@Put
public Representation put(Representation entity) {
Representation representation = null;
try {
JaxbObject<Study> jo = new JaxbObject<>();
String text = entity.getText();
Study p = null;
try {
p = (Study) XmlTools.unMarshal(jo, new Study(), text);
} catch (SAXException ex) {
throw new ResourceException(Status.CLIENT_ERROR_UNPROCESSABLE_ENTITY, ex);
}
if (p.getOwner() == null) {
p.setOwner(registration);
}
// persist object
StudyService service = BeanFactory.getStudyServiceBean();
Study study = testIfNull(service.findByID(p.getStudyId()));
if (null != p.getStudyAttributes()) {
// SEQWARE-1577 - AttributeAnnotator cascades deletes when annotating
StudyIDResource.mergeAttributes(study.getStudyAttributes(), p.getStudyAttributes(), study);
}
String title = p.getTitle();
String description = p.getDescription();
String alias = p.getAlias();
String accession = p.getAccession();
String status = p.getStatus();
String abstractStr = p.getAbstractStr();
String newType = p.getNewType();
String centerName = p.getCenterName();
String centerProjectName = p.getCenterProjectName();
Integer projectId = p.getProjectId();
Boolean isSelected = p.getIsSelected();
Boolean isHasFile = p.getIsHasFile();
String html = p.getHtml();
Integer existingTypeInt = p.getExistingTypeInt();
if (null != title) {
study.setTitle(title);
}
if (null != description) {
study.setDescription(description);
}
if (null != alias) {
study.setAlias(alias);
}
if (null != accession) {
study.setAccession(accession);
}
if (null != status) {
study.setStatus(status);
}
if (null != abstractStr) {
study.setAbstractStr(abstractStr);
}
if (null != newType) {
study.setNewType(newType);
}
if (null != centerName) {
study.setCenterName(centerName);
}
if (null != centerProjectName) {
study.setCenterProjectName(centerProjectName);
}
if (null != projectId) {
study.setProjectId(projectId);
}
if (null != isSelected) {
study.setIsSelected(isSelected);
}
if (null != isHasFile) {
study.setIsHasFile(isHasFile);
}
if (null != html) {
study.setHtml(html);
}
if (null != existingTypeInt) {
study.setExistingTypeInt(existingTypeInt);
}
service.update(study);
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
Study detachedStudy = copier.hibernate2dto(Study.class, study);
Document line = XmlTools.marshalToDocument(jo, detachedStudy);
representation = XmlTools.getRepresentation(line);
getResponse().setEntity(representation);
getResponse().setLocationRef(getRequest().getRootRef() + "/studies/" + detachedStudy.getSwAccession());
getResponse().setStatus(Status.SUCCESS_CREATED);
} catch (SecurityException e) {
getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, e);
} catch (Exception e) {
e.printStackTrace();
getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, e);
}
return representation;
}
}