/*
* 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.service.integration.strategy.interrogator;
import net.sf.json.JSON;
import net.sf.json.JSONArray;
import net.sf.json.JSONObject;
import net.sf.json.xml.XMLSerializer;
import net.sourceforge.fluxion.spi.ServiceProvider;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import uk.ac.bbsrc.tgac.miso.core.data.SequencerReference;
import uk.ac.bbsrc.tgac.miso.core.data.Status;
import uk.ac.bbsrc.tgac.miso.core.data.impl.StatusImpl;
import uk.ac.bbsrc.tgac.miso.core.data.type.HealthType;
import uk.ac.bbsrc.tgac.miso.core.data.type.PlatformType;
import uk.ac.bbsrc.tgac.miso.core.service.integration.mechanism.interrogator.MisoPerlDaemonInterrogationMechanism;
import uk.ac.bbsrc.tgac.miso.core.util.SubmissionUtils;
import uk.ac.bbsrc.tgac.miso.core.exception.InterrogationException;
import uk.ac.bbsrc.tgac.miso.core.service.integration.contract.InterrogationResult;
import uk.ac.bbsrc.tgac.miso.core.service.integration.contract.impl.MisoPerlDaemonQuery;
import uk.ac.bbsrc.tgac.miso.core.service.integration.mechanism.InterrogationMechanism;
import uk.ac.bbsrc.tgac.miso.core.service.integration.strategy.SequencerInterrogationStrategy;
import uk.ac.bbsrc.tgac.miso.core.util.UnicodeReader;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.TransformerException;
import java.io.StringReader;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
/**
* A concrete implementation of a SequencerInterrogationStrategy that can make queries and parse results, supported by a MisoPerlDaemonInterrogationMechanism, to a 454 sequencer.
* <p/>
* Methods in this class are not usually called explicitly, but via a {@link SequencerInterrogator} that has wrapped up this strategy to a SequencerReference.
*
* @author Rob Davey
* @since 0.0.2
*/
@ServiceProvider
public class LS454SequencerInterrogationStrategy implements SequencerInterrogationStrategy {
protected static final Logger log = LoggerFactory.getLogger(LS454SequencerInterrogationStrategy.class);
private static final MisoPerlDaemonQuery statusQuery = new MisoPerlDaemonQuery("454", "status");
private static final MisoPerlDaemonQuery completeRunsQuery = new MisoPerlDaemonQuery("454", "complete");
private static final MisoPerlDaemonQuery incompleteRunsQuery = new MisoPerlDaemonQuery("454", "running");
public boolean isStrategyFor(SequencerReference sr) {
return (sr.getPlatform().getPlatformType().equals(PlatformType.LS454));
}
public List<Status> listAllStatus(SequencerReference sr) throws InterrogationException {
List<Status> s = new ArrayList<Status>();
JSONObject response = JSONObject.fromObject(doQuery(sr, new MisoPerlDaemonInterrogationMechanism(), statusQuery).parseResult());
if (response != null && response.has("response")) {
JSONArray a = response.getJSONArray("response");
for (JSONObject j : (Iterable<JSONObject>) a) {
if (j.has("file") && j.has("xml")) {
try {
StatusImpl status = new StatusImpl();
if (j.has("complete") && j.getString("complete").equals("true")) {
status.setHealth(HealthType.Completed);
}
else {
status.setHealth(HealthType.Running);
}
Document statusDoc = DocumentBuilderFactory.newInstance().newDocumentBuilder().newDocument();
SubmissionUtils.transform(new UnicodeReader(j.getString("xml")), statusDoc);
String runStarted = statusDoc.getElementsByTagName("date").item(0).getTextContent();
status.setStartDate(new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss'Z'").parse(runStarted));
status.setInstrumentName(statusDoc.getElementsByTagName("serialNumber").item(0).getTextContent());
Node n = statusDoc.getElementsByTagName("run").item(0);
for (int i = 0; i < n.getChildNodes().getLength(); i++) {
Node child = n.getChildNodes().item(i);
if(child instanceof Element && ((Element) child).getTagName().equals("id")) {
status.setRunName(child.getTextContent());
}
}
s.add(status);
}
catch (ParserConfigurationException e) {
e.printStackTrace();
throw new InterrogationException(e.getMessage());
}
catch (ParseException e) {
e.printStackTrace();
throw new InterrogationException(e.getMessage());
}
catch (TransformerException e) {
e.printStackTrace();
throw new InterrogationException(e.getMessage());
}
}
}
}
return s;
}
public List<Status> listAllStatusBySequencerName(SequencerReference sr, String name) throws InterrogationException {
return null;
}
@Override
public List<String> listRunsByHealthType(SequencerReference sr, HealthType healthType) throws InterrogationException {
String response = doQuery(sr, new MisoPerlDaemonInterrogationMechanism(), new MisoPerlDaemonQuery("454", healthType.getKey().toLowerCase())).parseResult();
List<String> s = new ArrayList<String>();
if (response != null) {
String[] ss = response.split(",");
for (String sss : ss) {
String regex = ".*/([\\d]+_[A-z0-9]+_[\\d]+_[A-z0-9_]*)/.*";
Pattern p = Pattern.compile(regex);
Matcher m = p.matcher(sss);
if (m.matches()) {
s.add(m.group(1));
}
}
}
Collections.sort(s);
return s;
}
public List<String> listAllCompleteRuns(SequencerReference sr) throws InterrogationException {
String response = doQuery(sr, new MisoPerlDaemonInterrogationMechanism(), completeRunsQuery).parseResult();
List<String> s = new ArrayList<String>();
if (response != null) {
String[] ss = response.split(",");
for (String sss : ss) {
String regex = ".*\\/(R_\\d{4}_\\d{2}_\\d{2}_\\d{2}_\\d{2}_\\d{2}_[A-z0-9]+_[A-z0-9]+_[A-z0-9_\\-]+)\\/.*";
Pattern p = Pattern.compile(regex);
Matcher m = p.matcher(sss);
if (m.matches()) {
s.add(m.group(1));
}
}
}
Collections.sort(s);
return s;
}
public List<String> listAllIncompleteRuns(SequencerReference sr) throws InterrogationException {
String response = doQuery(sr, new MisoPerlDaemonInterrogationMechanism(), incompleteRunsQuery).parseResult();
List<String> s = new ArrayList<String>();
if (response != null) {
String[] ss = response.split(",");
for (String sss : ss) {
String regex = ".*\\/(R_\\d{4}_\\d{2}_\\d{2}_\\d{2}_\\d{2}_\\d{2}_[A-z0-9]+_[A-z0-9]+_[A-z0-9_\\-]+)\\/.*";
Pattern p = Pattern.compile(regex);
Matcher m = p.matcher(sss);
if (m.matches()) {
s.add(m.group(1));
}
}
}
Collections.sort(s);
return s;
}
public Status getRunStatus(SequencerReference sr, String runName) throws InterrogationException {
MisoPerlDaemonQuery runStatusQuery = new MisoPerlDaemonQuery("454", runName, "status");
try {
JSONObject response = JSONObject.fromObject(doQuery(sr, new MisoPerlDaemonInterrogationMechanism(), runStatusQuery).parseResult());
if (response != null && response.has("response")) {
JSONArray a = response.getJSONArray("response");
if (a.iterator().hasNext()) {
JSONObject j = (JSONObject) a.iterator().next();
if (j.has("file") && j.has("xml")) {
StatusImpl status = new StatusImpl();
if (j.has("complete") && j.getString("complete").equals("true")) {
status.setHealth(HealthType.Completed);
}
else {
status.setHealth(HealthType.Running);
}
Document statusDoc = DocumentBuilderFactory.newInstance().newDocumentBuilder().newDocument();
SubmissionUtils.transform(new UnicodeReader(j.getString("xml")), statusDoc);
String runStarted = statusDoc.getElementsByTagName("date").item(0).getTextContent();
status.setStartDate(new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss'Z'").parse(runStarted));
status.setInstrumentName(statusDoc.getElementsByTagName("serialNumber").item(0).getTextContent());
Node n = statusDoc.getElementsByTagName("run").item(0);
for (int i = 0; i < n.getChildNodes().getLength(); i++) {
Node child = n.getChildNodes().item(i);
if(child instanceof Element && ((Element) child).getTagName().equals("id")) {
status.setRunName(child.getTextContent());
}
}
return status;
}
}
}
}
catch (ParserConfigurationException e) {
e.printStackTrace();
throw new InterrogationException(e.getMessage());
}
catch (ParseException e) {
e.printStackTrace();
throw new InterrogationException(e.getMessage());
}
catch (TransformerException e) {
e.printStackTrace();
throw new InterrogationException(e.getMessage());
}
return null;
}
public JSONObject getRunInformation(SequencerReference sr, String runName) throws InterrogationException {
MisoPerlDaemonQuery runInfoQuery = new MisoPerlDaemonQuery("454", runName, "status");
JSONObject json = new JSONObject();
try {
JSONObject response = JSONObject.fromObject(doQuery(sr, new MisoPerlDaemonInterrogationMechanism(), runInfoQuery).parseResult());
if (response != null && response.has("response")) {
JSONArray a = response.getJSONArray("response");
if (a.iterator().hasNext()) {
JSONObject j = (JSONObject) a.iterator().next();
if (j.has("file") && j.has("xml")) {
XMLSerializer xmls = new XMLSerializer();
JSON info = xmls.read(j.getString("xml"));
if (!info.isEmpty()) {
if (info.isArray()) {
json.put("response", info);
}
else {
return (JSONObject)info;
}
}
}
}
}
}
catch (InterrogationException ie) {
ie.printStackTrace();
}
return json;
}
private InterrogationResult<String> doQuery(SequencerReference sr, InterrogationMechanism mechanism, MisoPerlDaemonQuery query) throws InterrogationException {
log.info("Pushing query: " + query.generateQuery());
InterrogationResult<String> result = mechanism.doQuery(sr, query);
log.info("Consuming result: " + result.parseResult());
return result;
}
}