/*
* 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.List;
import net.sf.beanlib.hibernate3.Hibernate3DtoCopier;
import net.sourceforge.seqware.common.business.LaneService;
import net.sourceforge.seqware.common.business.LibrarySelectionService;
import net.sourceforge.seqware.common.business.LibrarySourceService;
import net.sourceforge.seqware.common.business.LibraryStrategyService;
import net.sourceforge.seqware.common.business.SequencerRunService;
import net.sourceforge.seqware.common.factory.BeanFactory;
import net.sourceforge.seqware.common.model.Lane;
import net.sourceforge.seqware.common.model.LibrarySelection;
import net.sourceforge.seqware.common.model.LibrarySource;
import net.sourceforge.seqware.common.model.LibraryStrategy;
import net.sourceforge.seqware.common.model.Registration;
import net.sourceforge.seqware.common.model.SequencerRun;
import net.sourceforge.seqware.common.model.lists.LaneList;
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>
* LaneResource class.
* </p>
*
* @author mtaschuk
* @version $Id: $Id
*/
public class LaneResource extends DatabaseResource {
private Logger logger;
/**
* <p>
* Constructor for LaneResource.
* </p>
*/
public LaneResource() {
super("lane");
logger = Logger.getLogger(Lane.class);
}
/**
* <p>
* getXml.
* </p>
*
* @throws java.io.IOException
* if any.
*/
@Get
public void getXml() throws IOException {
authenticate();
LaneService ss = BeanFactory.getLaneServiceBean();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
Document line;
if (queryValues.get("id") != null) {
JaxbObject<Lane> jaxbTool = new JaxbObject<>();
Lane p = (Lane) testIfNull(ss.findByID(parseClientInt(queryValues.get("id"))));
Lane dto = copier.hibernate2dto(Lane.class, p);
line = XmlTools.marshalToDocument(jaxbTool, dto);
} else {
JaxbObject<LaneList> jaxbTool = new JaxbObject<>();
LaneList list = new LaneList();
List<Lane> lanes = (List<Lane>) testIfNull(ss.list());
for (Lane l : lanes) {
list.add(copier.hibernate2dto(Lane.class, l));
}
line = XmlTools.marshalToDocument(jaxbTool, list);
}
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<Lane> jo = new JaxbObject<>();
String text = entity.getText();
Lane o = null;
try {
o = (Lane) XmlTools.unMarshal(jo, new Lane(), 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.getSequencerRun() != null) {
SequencerRunService ps = BeanFactory.getSequencerRunServiceBean();
SequencerRun sequencerRun = (SequencerRun) testIfNull(ps.findByID(o.getSequencerRun().getSequencerRunId()));
o.setSequencerRun(sequencerRun);
}
if (o.getLibraryStrategy() != null) {
LibraryStrategyService ps = BeanFactory.getLibraryStrategyServiceBean();
LibraryStrategy obj = (LibraryStrategy) testIfNull(ps.findByID(o.getLibraryStrategy().getLibraryStrategyId()));
o.setLibraryStrategy(obj);
}
if (o.getLibrarySelection() != null) {
LibrarySelectionService ps = BeanFactory.getLibrarySelectionServiceBean();
LibrarySelection obj = (LibrarySelection) testIfNull(ps.findByID(o.getLibrarySelection().getLibrarySelectionId()));
o.setLibrarySelection(obj);
}
if (o.getLibrarySource() != null) {
LibrarySourceService ps = BeanFactory.getLibrarySourceServiceBean();
LibrarySource obj = (LibrarySource) testIfNull(ps.findByID(o.getLibrarySource().getLibrarySourceId()));
o.setLibrarySource(obj);
}
// persist object
LaneService service = BeanFactory.getLaneServiceBean();
Integer swAccession = service.insert(registration, o);
Lane obj = (Lane) testIfNull(service.findBySWAccession(swAccession));
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
Lane detachedLane = copier.hibernate2dto(Lane.class, obj);
Document line = XmlTools.marshalToDocument(jo, detachedLane);
getResponse().setEntity(XmlTools.getRepresentation(line));
getResponse().setLocationRef(getRequest().getRootRef() + "/lanes/" + detachedLane.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());
}
}
}