/*
* 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.Date;
import java.util.SortedSet;
import java.util.TreeSet;
import net.sf.beanlib.CollectionPropertyName;
import net.sf.beanlib.hibernate3.Hibernate3DtoCopier;
import net.sourceforge.seqware.common.business.RegistrationService;
import net.sourceforge.seqware.common.business.WorkflowService;
import net.sourceforge.seqware.common.factory.BeanFactory;
import net.sourceforge.seqware.common.model.Registration;
import net.sourceforge.seqware.common.model.Workflow;
import net.sourceforge.seqware.common.model.WorkflowParam;
import net.sourceforge.seqware.common.util.Log;
import net.sourceforge.seqware.common.util.xmltools.JaxbObject;
import net.sourceforge.seqware.common.util.xmltools.XmlTools;
import net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication;
import org.restlet.data.Status;
import org.restlet.representation.Representation;
import org.restlet.resource.Get;
import org.restlet.resource.ResourceException;
import org.w3c.dom.Document;
import org.xml.sax.SAXException;
/**
* <p>
* WorkflowIDResource class.
* </p>
*
* @author mtaschuk
* @version $Id: $Id
*/
public class WorkflowIDResource extends DatabaseIDResource {
/**
* <p>
* Constructor for WorkflowIDResource.
* </p>
*/
public WorkflowIDResource() {
super("workflowId");
}
/**
* {@inheritDoc}
*
* @return
*/
@Override
public SeqWareWebServiceApplication getApplication() {
return (SeqWareWebServiceApplication) super.getApplication();
}
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
authenticate();
WorkflowService ss = BeanFactory.getWorkflowServiceBean();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<Workflow> jaxbTool = new JaxbObject<>();
Workflow workflow = testIfNull(ss.findBySWAccession(getId()));
CollectionPropertyName<Workflow>[] createCollectionPropertyNames = CollectionPropertyName.createCollectionPropertyNames(
Workflow.class, new String[] { "workflowAttributes" });
Workflow dto = copier.hibernate2dto(Workflow.class, workflow, new Class<?>[] {}, createCollectionPropertyNames);
if (fields.contains("params")) {
SortedSet<WorkflowParam> wps = workflow.getWorkflowParams();
if (wps != null) {
SortedSet<WorkflowParam> copiedParams = new TreeSet<>();
for (WorkflowParam param : workflow.getWorkflowParams()) {
copiedParams.add(copier.hibernate2dto(WorkflowParam.class, param));
}
dto.setWorkflowParams(copiedParams);
} else {
Log.info("Could not be found: workflow params");
}
}
Document line = XmlTools.marshalToDocument(jaxbTool, dto);
getResponse().setEntity(XmlTools.getRepresentation(line));
}
/**
* {@inheritDoc}
*
* @return
*/
@Override
public Representation put(Representation entity) {
authenticate();
Representation representation = null;
Workflow newWorkflow = null;
JaxbObject<Workflow> jo = new JaxbObject<>();
try {
String text = entity.getText();
newWorkflow = (Workflow) XmlTools.unMarshal(jo, new Workflow(), text);
} catch (SAXException ex) {
ex.printStackTrace();
throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, ex.getMessage());
} catch (IOException e) {
e.printStackTrace();
throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, e.getMessage());
}
try {
WorkflowService fs = BeanFactory.getWorkflowServiceBean();
Workflow workflow = testIfNull(fs.findByID(newWorkflow.getWorkflowId()));
workflow.givesPermission(registration);
// simple types
String name = newWorkflow.getName();
String desc = newWorkflow.getDescription();
String baseIniFile = newWorkflow.getBaseIniFile();
String command = newWorkflow.getCommand();
String cwd = newWorkflow.getCwd();
String host = newWorkflow.getHost();
String inputAlgorithm = newWorkflow.getInputAlgorithm();
String permanentBundleLocation = newWorkflow.getPermanentBundleLocation();
String seqwareVersion = newWorkflow.getSeqwareVersion();
String template = newWorkflow.getTemplate();
String username = newWorkflow.getUsername();
String version = newWorkflow.getVersion();
// foreign keys
Registration owner = newWorkflow.getOwner();
workflow.setName(name);
workflow.setDescription(desc);
workflow.setBaseIniFile(baseIniFile);
workflow.setCommand(command);
workflow.setCwd(cwd);
workflow.setHost(host);
workflow.setInputAlgorithm(inputAlgorithm);
workflow.setPermanentBundleLocation(permanentBundleLocation);
workflow.setSeqwareVersion(seqwareVersion);
workflow.setTemplate(template);
workflow.setUsername(username);
workflow.setVersion(version);
workflow.setUpdateTimestamp(new Date());
workflow.setWorkflowClass(newWorkflow.getWorkflowClass());
workflow.setWorkflowType(newWorkflow.getWorkflowType());
workflow.setWorkflowEngine(newWorkflow.getWorkflowEngine());
if (owner != null) {
RegistrationService rs = BeanFactory.getRegistrationServiceBean();
Registration newReg = rs.findByEmailAddress(owner.getEmailAddress());
if (newReg != null) {
workflow.setOwner(newReg);
} else {
Log.info("Could not be found: " + owner);
}
} else if (workflow.getOwner() == null) {
workflow.setOwner(registration);
}
if (newWorkflow.getWorkflowAttributes() != null) {
// SEQWARE-1577 - AttributeAnnotator cascades deletes when annotating
WorkflowIDResource.mergeAttributes(workflow.getWorkflowAttributes(), newWorkflow.getWorkflowAttributes(), workflow);
}
fs.update(registration, workflow);
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
Workflow detachedWorkflow = copier.hibernate2dto(Workflow.class, workflow);
Document line = XmlTools.marshalToDocument(jo, detachedWorkflow);
representation = XmlTools.getRepresentation(line);
getResponse().setEntity(representation);
getResponse().setLocationRef(getRequest().getRootRef() + "/workflows/" + detachedWorkflow.getSwAccession());
getResponse().setStatus(Status.SUCCESS_CREATED);
} catch (SecurityException e) {
getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, e.getMessage());
} catch (Exception e) {
e.printStackTrace();
getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, e.getMessage());
}
return representation;
}
}