/*
* 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 java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import net.sf.beanlib.CollectionPropertyName;
import net.sf.beanlib.hibernate3.Hibernate3DtoCopier;
import net.sourceforge.seqware.common.business.PlatformService;
import net.sourceforge.seqware.common.business.SequencerRunService;
import net.sourceforge.seqware.common.factory.BeanFactory;
import net.sourceforge.seqware.common.model.Platform;
import net.sourceforge.seqware.common.model.Registration;
import net.sourceforge.seqware.common.model.SequencerRun;
import net.sourceforge.seqware.common.model.lists.SequencerRunList;
import net.sourceforge.seqware.common.util.xmltools.JaxbObject;
import net.sourceforge.seqware.common.util.xmltools.XmlTools;
import org.apache.log4j.Logger;
import org.restlet.data.Status;
import org.restlet.representation.Representation;
import org.restlet.resource.Get;
import org.restlet.resource.Post;
import org.restlet.resource.ResourceException;
import org.w3c.dom.Document;
import org.xml.sax.SAXException;
/**
* <p>
* SequencerRunResource class.
* </p>
*
* @author mtaschuk
* @version $Id: $Id
*/
public class SequencerRunResource extends DatabaseResource {
private Logger logger;
/**
* <p>
* Constructor for SequencerRunResource.
* </p>
*/
public SequencerRunResource() {
super("sequencer_run");
logger = Logger.getLogger(SequencerRun.class);
}
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
authenticate();
SequencerRunService ss = BeanFactory.getSequencerRunServiceBean();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
CollectionPropertyName<SequencerRun>[] createCollectionPropertyNames = CollectionPropertyName.createCollectionPropertyNames(
SequencerRun.class, new String[] { "sequencerRunAttributes" });
if (queryValues.get("name") != null) {
String name = queryValues.get("name");
SequencerRun study = testIfNull(ss.findByName(name));
JaxbObject<SequencerRun> jaxbTool = new JaxbObject<>();
SequencerRun dto = copier.hibernate2dto(SequencerRun.class, study, new Class<?>[] {}, createCollectionPropertyNames);
Document line = XmlTools.marshalToDocument(jaxbTool, dto);
getResponse().setEntity(XmlTools.getRepresentation(line));
} else {
JaxbObject<SequencerRunList> jaxbTool = new JaxbObject<>();
List<SequencerRun> runs = testIfNull(ss.list());
SequencerRunList eList = new SequencerRunList();
eList.setList(new ArrayList());
for (SequencerRun sequencerRun : runs) {
SequencerRun dto = copier.hibernate2dto(SequencerRun.class, sequencerRun, new Class<?>[] {}, createCollectionPropertyNames);
eList.add(dto);
}
Document line = XmlTools.marshalToDocument(jaxbTool, eList);
getResponse().setEntity(XmlTools.getRepresentation(line));
}
}
/**
* <p>
* postJaxb.
* </p>
*
* @param entity
* a {@link org.restlet.representation.Representation} object.
* @throws org.restlet.resource.ResourceException
* if any.
*/
@Post("xml")
public void postJaxb(Representation entity) throws ResourceException {
authenticate();
try {
JaxbObject<SequencerRun> jo = new JaxbObject<>();
String text = entity.getText();
SequencerRun o = null;
try {
o = (SequencerRun) XmlTools.unMarshal(jo, new SequencerRun(), text);
} catch (SAXException ex) {
throw new ResourceException(Status.CLIENT_ERROR_UNPROCESSABLE_ENTITY, ex);
}
if (o.getOwner() == null) {
o.setOwner(registration);
} else {
Registration reg = BeanFactory.getRegistrationServiceBean().findByEmailAddress(o.getOwner().getEmailAddress());
if (reg != null) {
o.setOwner(reg);
} else {
logger.info("Could not be found: " + o.getOwner());
}
}
// attempt to save foreign keys, I guess this is replacing an empty object with a fully populated one?
if (o.getPlatform() != null) {
PlatformService ps = BeanFactory.getPlatformServiceBean();
Platform platform = testIfNull(ps.findByID(o.getPlatform().getPlatformId()));
o.setPlatform(platform);
}
// persist object
SequencerRunService service = BeanFactory.getSequencerRunServiceBean();
Integer swAccession = service.insert(registration, o);
SequencerRun obj = testIfNull(service.findBySWAccession(swAccession));
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
SequencerRun detachedSequencerRun = copier.hibernate2dto(SequencerRun.class, obj);
Document line = XmlTools.marshalToDocument(jo, detachedSequencerRun);
getResponse().setEntity(XmlTools.getRepresentation(line));
getResponse().setLocationRef(getRequest().getRootRef() + "/sequencerruns/" + detachedSequencerRun.getSwAccession());
getResponse().setStatus(Status.SUCCESS_CREATED);
} catch (SecurityException e) {
getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, e.getMessage());
} catch (IOException e) {
e.printStackTrace();
getResponse().setStatus(Status.CLIENT_ERROR_BAD_REQUEST);
} catch (Exception e) {
e.printStackTrace();
getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, e.getMessage());
}
}
}