/*
* 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.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import net.sf.beanlib.hibernate3.Hibernate3DtoCopier;
import net.sourceforge.seqware.common.business.ExperimentService;
import net.sourceforge.seqware.common.business.SampleService;
import net.sourceforge.seqware.common.factory.BeanFactory;
import net.sourceforge.seqware.common.model.Experiment;
import net.sourceforge.seqware.common.model.Sample;
import net.sourceforge.seqware.common.model.lists.SampleList;
import net.sourceforge.seqware.common.util.Log;
import net.sourceforge.seqware.common.util.xmltools.JaxbObject;
import net.sourceforge.seqware.common.util.xmltools.XmlTools;
import org.hibernate.Query;
import org.hibernate.classic.Session;
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>
* SampleResource class.
* </p>
*
* @author mtaschuk
* @version $Id: $Id
*/
public class SampleResource extends DatabaseResource {
/**
* <p>
* Constructor for SampleResource.
* </p>
*/
public SampleResource() {
super("sample");
}
/**
* {@inheritDoc}
*/
@Override
protected void doInit() throws ResourceException {
super.doInit();
}
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
authenticate();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject jaxbTool;
for (String key : queryValues.keySet()) {
Log.debug("key: " + key + " -> " + queryValues.get(key));
}
SampleService ss = BeanFactory.getSampleServiceBean();
if (queryValues.get("title") != null) {
jaxbTool = new JaxbObject<>();
Sample sample = (Sample) testIfNull(ss.findByTitle(queryValues.get("title")));
Sample dto = copier.hibernate2dto(Sample.class, sample);
Document line = XmlTools.marshalToDocument(jaxbTool, dto);
getResponse().setEntity(XmlTools.getRepresentation(line));
} else if (queryValues.get("name") != null) {
jaxbTool = new JaxbObject<>();
Sample sample = (Sample) testIfNull(ss.findByName(queryValues.get("name")));
Sample dto = copier.hibernate2dto(Sample.class, sample);
Document line = XmlTools.marshalToDocument(jaxbTool, dto);
getResponse().setEntity(XmlTools.getRepresentation(line));
} else if (queryValues.get("matches") != null) {
jaxbTool = new JaxbObject<>();
String name = queryValues.get("matches");
List<Sample> samples = (List<Sample>) testIfNull(ss.matchName(name));
SampleList eList = new SampleList();
eList.setList(new ArrayList());
for (Sample sample : samples) {
Sample dto = copier.hibernate2dto(Sample.class, sample);
eList.add(dto);
}
Document line = XmlTools.marshalToDocument(jaxbTool, eList);
getResponse().setEntity(XmlTools.getRepresentation(line));
} else {
jaxbTool = new JaxbObject<>();
List<Sample> samples = (List<Sample>) testIfNull(ss.list());
SampleList eList = new SampleList();
eList.setList(new ArrayList());
for (Sample sample : samples) {
Sample dto = copier.hibernate2dto(Sample.class, sample);
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 {
try {
authenticate();
JaxbObject<Sample> jo = new JaxbObject<>();
String text = entity.getText();
Sample o = null;
try {
o = (Sample) XmlTools.unMarshal(jo, new Sample(), text);
} catch (SAXException ex) {
throw new ResourceException(Status.CLIENT_ERROR_UNPROCESSABLE_ENTITY, ex);
}
if (o.getOwner() == null) {
o.setOwner(registration);
}
if (o.getExperiment() != null) {
ExperimentService es = BeanFactory.getExperimentServiceBean();
Experiment newExp = es.findBySWAccession(o.getExperiment().getSwAccession());
if (newExp != null) {
o.setExperiment(newExp);
} else {
Log.info("Could not be found " + o.getExperiment());
}
}
boolean createExplicitRootSample = false;
// SEQWARE-1576, 1724 In this bug, attempting to force a root sample by adding an explicit null
// leads to a weird sample with a null sample id,
// this seems to be the cause for the two duplicates, ignoring them and triggering an SQL update below
// we're changing this behaviour to use a empty or null parent set instead
if (o.getParents() == null || o.getParents().isEmpty()) {
createExplicitRootSample = true;
} else {
SampleService ss = BeanFactory.getSampleServiceBean();
HashSet<Sample> parents = new HashSet<>();
for (Sample s : o.getParents()) {
// leaving in this guard against these strange sample objects will all null fields
if (s.getSampleId() != null) {
parents.add(ss.findByID(s.getSampleId()));
}
}
o.setParents(parents);
}
if (null != o.getChildren()) {
SampleService ss = BeanFactory.getSampleServiceBean();
HashSet<Sample> children = new HashSet<>();
for (Sample s : o.getChildren()) {
children.add(ss.findByID(s.getSampleId()));
}
o.setChildren(children);
}
// persist object
SampleService service = BeanFactory.getSampleServiceBean();
Integer swAccession = service.insert(registration, o);
Sample sample = (Sample) testIfNull(service.findBySWAccession(swAccession));
// explicitly create root sample if needed
if (createExplicitRootSample) {
Log.info("Found null parent in sample object, creating explicit root sample in sample_hierarchy");
Session openSession = BeanFactory.getSessionFactoryBean().openSession();
try {
Query query = openSession.createSQLQuery("INSERT INTO sample_hierarchy(sample_id, parent_id) VALUES ("
+ sample.getSampleId() + ",null)");
query.executeUpdate();
} catch (Exception e) {
getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, e);
return;
} finally {
openSession.close();
}
}
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
Sample detachedSample = copier.hibernate2dto(Sample.class, sample);
if (null != o.getParents()) {
for (Sample s : sample.getParents()) {
detachedSample.getParents().add(copier.hibernate2dto(Sample.class, s));
}
}
Document line = XmlTools.marshalToDocument(jo, detachedSample);
getResponse().setEntity(XmlTools.getRepresentation(line));
getResponse().setLocationRef(getRequest().getRootRef() + "/samples/" + detachedSample.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);
}
}
}