/*
* Copyright (c) 2012. The Genome Analysis Centre, Norwich, UK
* MISO project contacts: Robert Davey, Mario Caccamo @ TGAC
* *********************************************************************
*
* This file is part of MISO.
*
* MISO 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.
*
* MISO 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 MISO. If not, see <http://www.gnu.org/licenses/>.
*
* *********************************************************************
*/
package uk.ac.bbsrc.tgac.miso.core.data.impl;
import com.eaglegenomics.simlims.core.SecurityProfile;
import com.eaglegenomics.simlims.core.User;
import net.sourceforge.fluxion.spi.ServiceProvider;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import uk.ac.bbsrc.tgac.miso.core.data.*;
import uk.ac.bbsrc.tgac.miso.core.factory.submission.ERASubmissionFactory;
import javax.persistence.*;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import java.io.Serializable;
import java.util.Collection;
import java.util.LinkedList;
import java.util.Set;
/**
* uk.ac.bbsrc.tgac.miso.core.data.impl
* <p/>
* TODO Info
*
* @author Rob Davey
* @since 0.0.2
*/
@Entity
public class SampleImpl extends AbstractSample implements Serializable {
/**
* Construct a new Sample with a default empty SecurityProfile
*/
public SampleImpl() {
setSecurityProfile(new SecurityProfile());
}
/**
* Construct a new Sample with a SecurityProfile owned by the given User
*
* @param user of type User
*/
public SampleImpl(User user) {
setSecurityProfile(new SecurityProfile(user));
}
/**
* If the given User can read the parent Project, construct a new Sample with a SecurityProfile inherited from the parent Project.
* If not, construct a new Sample with a SecurityProfile owned by the given User
*
* @param project of type Project
* @param user of type User
*/
public SampleImpl(Project project, User user) {
if (project.userCanRead(user)) {
setProject(project);
setSecurityProfile(project.getSecurityProfile());
}
else {
setSecurityProfile(new SecurityProfile(user));
}
}
public void buildSubmission() {
/*
try {
DocumentBuilder docBuilder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
submissionDocument = docBuilder.newDocument();
}
catch (ParserConfigurationException e) {
e.printStackTrace();
}
ERASubmissionFactory.generateSampleSubmissionXML(submissionDocument, this);
*/
}
/**
* Method buildReport ...
*/
public void buildReport() {
}
}