/*
* 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.illumina;
import com.eaglegenomics.simlims.core.SecurityProfile;
import com.eaglegenomics.simlims.core.User;
import org.w3c.dom.Document;
import uk.ac.bbsrc.tgac.miso.core.data.*;
import uk.ac.bbsrc.tgac.miso.core.data.impl.RunImpl;
import uk.ac.bbsrc.tgac.miso.core.data.impl.StatusImpl;
import uk.ac.bbsrc.tgac.miso.core.data.type.PlatformType;
import uk.ac.bbsrc.tgac.miso.core.util.SubmissionUtils;
import uk.ac.bbsrc.tgac.miso.core.util.UnicodeReader;
import javax.persistence.*;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.TransformerException;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
/**
* uk.ac.bbsrc.tgac.miso.core.data.impl.illumina
* <p/>
* TODO Info
*
* @author Rob Davey
* @since 0.0.2
*/
@Entity
@DiscriminatorValue("Illumina")
public class IlluminaRun extends RunImpl {
public IlluminaRun() {
setPlatformType(PlatformType.ILLUMINA);
setStatus(new StatusImpl());
setSecurityProfile(new SecurityProfile());
}
public IlluminaRun(String statusXml) {
this(statusXml, null);
}
public IlluminaRun(String statusXml, User user) {
try {
Document statusDoc = SubmissionUtils.emptyDocument();
if (statusXml != null && !"".equals(statusXml)) {
SubmissionUtils.transform(new UnicodeReader(statusXml), statusDoc);
String runName = (statusDoc.getElementsByTagName("RunName").item(0).getTextContent());
setPairedEnd(false);
if (!statusDoc.getDocumentElement().getTagName().equals("error")) {
if (statusDoc.getElementsByTagName("IsPairedEndRun").getLength() > 0) {
boolean paired = Boolean.parseBoolean(statusDoc.getElementsByTagName("IsPairedEndRun").item(0).getTextContent().toLowerCase());
setPairedEnd(paired);
}
}
String runDirRegex = "[\\d]+_([A-z0-9\\-])+_([\\d])+_([A-z0-9_\\+\\-]*)";
Matcher m = Pattern.compile(runDirRegex).matcher(runName);
if (m.matches()) {
setPlatformRunId(Integer.parseInt(m.group(2)));
}
setAlias(runName);
setFilePath(runName);
setDescription(m.group(3));
setPlatformType(PlatformType.ILLUMINA);
setStatus(new IlluminaStatus(statusXml));
if (user != null) {
setSecurityProfile(new SecurityProfile(user));
}
else {
setSecurityProfile(new SecurityProfile());
}
}
else {
log.error("No status XML for this run");
}
}
catch (ParserConfigurationException e) {
e.printStackTrace();
}
catch (TransformerException e) {
log.error("Cannot parse status: " + statusXml);
e.printStackTrace();
}
}
public IlluminaRun(User user) {
setPlatformType(PlatformType.ILLUMINA);
setStatus(new StatusImpl());
setSecurityProfile(new SecurityProfile(user));
}
public void buildSubmission() {
/*
try {
DocumentBuilder docBuilder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
submissionDocument = docBuilder.newDocument();
}
catch (ParserConfigurationException e) {
e.printStackTrace();
}
ERASubmissionFactory.generateFullRunSubmissionXML(submissionDocument, this);
*/
}
@Override
public String toString() {
StringBuffer sb = new StringBuffer();
sb.append(super.toString());
/*
if (getFlowcells() != null) {
sb.append(" : ");
for(Flowcell f: getFlowcells()) {
sb.append(f.toString());
}
}
*/
if (getSequencerPartitionContainers() != null) {
sb.append(" : ");
for(SequencerPartitionContainer f: getSequencerPartitionContainers()) {
sb.append(f.toString());
}
}
return sb.toString();
}
/**
* Method buildReport ...
*/
public void buildReport() {
}
}