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The protein structure modules of BioJava.
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.structure.align.client;
import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.align.StructureAlignment;
import org.biojava.nbio.structure.align.StructureAlignmentFactory;
import org.biojava.nbio.structure.align.ce.CeCPMain;
import org.biojava.nbio.structure.align.ce.CeMain;
import org.biojava.nbio.structure.align.events.AlignmentProgressListener;
import org.biojava.nbio.structure.align.fatcat.FatCatFlexible;
import org.biojava.nbio.structure.align.fatcat.FatCatRigid;
import org.biojava.nbio.structure.align.model.AFPChain;
import org.biojava.nbio.structure.align.util.AFPChainScorer;
import org.biojava.nbio.structure.align.util.AlignmentTools;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.align.util.ResourceManager;
import org.biojava.nbio.structure.align.xml.AFPChainXMLConverter;
import org.biojava.nbio.structure.align.xml.PdbPairsMessage;
import org.biojava.nbio.structure.domain.RemotePDPProvider;
import org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior;
import org.biojava.nbio.structure.scop.RemoteScopInstallation;
import org.biojava.nbio.structure.scop.ScopFactory;
import org.biojava.nbio.core.util.FlatFileCache;
import org.biojava.nbio.core.util.PrettyXMLWriter;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.net.InetAddress;
import java.net.UnknownHostException;
import java.util.*;
/** Contains the single thread for a job that can run multiple alignments.
*
* @author Andreas Prlic
*
*/
public class FarmJobRunnable implements Runnable {
private static final Logger logger = LoggerFactory.getLogger(FarmJobRunnable.class);
//private static final int DEFAULT_PAIR_FETCH_DELAY = 30000;
//private static final String CONNECTION_PAIR_DELAY = "connection.pair.delay";
private static final String JFATCAT_NAME = "jfatcat.name";
private static final String JFATCAT_VERSION = "jfatcat.version";
private static ResourceManager resourceManager = ResourceManager.getResourceManager("jfatcat");
//private static DateFormat dateFormat = new SimpleDateFormat("MMMM dd, yyyy h:mm a",Locale.US);
FarmJobParameters params;
String prevName1;
Atom[] ca1 ;
long startTime;
long maxTime;
int maxNrAlignments;
int alignmentsCalculated;
boolean waitForAlignments;
private static final String randomUsername = getRandomUsername();
boolean terminated ;
List progressListeners;
CountProgressListener counter ;
String userName = null;
protected AtomCache cache;
boolean verbose = false; // TODO dmyersturnbull: we should probably remove this in favor of SLF4J
String version = null;
private static final String alignURL = "/align/";
public FarmJobRunnable(FarmJobParameters params){
terminated = false;
this.params = params;
verbose = false;
// multiple farm jobs share the same SoftHashMap for caching coordinates
cache = new AtomCache( params.getPdbFilePath(), params.getCacheFilePath());
if ( params.getServer()!= null && (!params.getServer().equals("") ) ) {
RemotePDPProvider pdpprovider = new RemotePDPProvider();
String serverURL = params.getServer();
if ( ! serverURL.endsWith("/"))
serverURL += "/";
if ( serverURL.endsWith(alignURL)) {
serverURL = serverURL.substring(0,serverURL.length()-alignURL.length());
}
pdpprovider.setServer(serverURL+"/domains/");
cache.setPdpprovider(pdpprovider);
RemoteScopInstallation scop = new RemoteScopInstallation();
scop.setServer(serverURL+"/domains/");
ScopFactory.setScopDatabase(scop);
}
cache.setFetchBehavior(FetchBehavior.FETCH_FILES);
maxNrAlignments = params.getNrAlignments();
progressListeners = null;
if (params.getUsername() == null) {
userName = randomUsername;
} else {
userName = params.getUsername();
}
counter = new CountProgressListener();
addAlignmentProgressListener(counter);
waitForAlignments = true;
if ( params.isVerbose()){
verbose = true;
}
}
public void addAlignmentProgressListener(AlignmentProgressListener listener){
if (progressListeners == null)
progressListeners = new ArrayList();
progressListeners.add(listener);
}
public void clearListeners(){
if ( progressListeners == null)
return;
progressListeners.clear();
progressListeners = null;
}
protected static String getRandomUsername(){
String name = "";
try {
InetAddress i = InetAddress.getLocalHost();
name += i.getHostAddress();
name += "_";
} catch (UnknownHostException e){
throw new RuntimeException(e);
}
name += UUID.randomUUID();
return name;
}
@Override
public void run() {
// Retrieve resource
String appVersion = resourceManager.getString(JFATCAT_VERSION);
String appName = resourceManager.getString(JFATCAT_NAME);
logger.info("{} version: {}", appName, appVersion);
startTime = System.currentTimeMillis();
// -t ime is in seconds.
long maxSec = params.getTime();
if ( maxSec < 5 )
maxTime = Long.MAX_VALUE;
else
maxTime = startTime + params.getTime() * 1000;
terminated = false;
alignmentsCalculated = 0;
maxNrAlignments = params.getNrAlignments();
if ( maxNrAlignments < 0 ){
maxNrAlignments = Integer.MAX_VALUE;
}
logger.info("running job for max {} alignments", maxNrAlignments);
while (! terminated){
// talk to server
// get list of alignments to run
// if maxNrAlignments > 100 we split up the calculations in chunks of 100.
// otherwise we request all of them at once.
// we request
PdbPairsMessage msg = getAlignmentPairsFromServer();
if ( msg == null) {
logger.error("Got null instead of alignment pairs from server.");
randomSleep();
continue;
}
SortedSet alignmentPairs = msg.getPairs();
logger.debug("{}: Server responded with {} pairs.", userName, alignmentPairs.size());
List results = new ArrayList();
String algorithmName = msg.getMethod();
if ( version == null) {
setVersion(algorithmName);
}
for(PdbPair pair : alignmentPairs){
if ( terminated)
break;
long now = System.currentTimeMillis();
if ( now >= maxTime) {
terminated = true;
break;
}
if ( alignmentsCalculated >= maxNrAlignments) {
terminated = true;
break;
}
String name1 = pair.getName1();
String name2 = pair.getName2();
if ( progressListeners != null)
notifyStartAlignment(name1,name2);
try {
String resultXML = alignPair(name1, name2,algorithmName);
if ( progressListeners != null)
notifyEndAlignment();
results.add(resultXML);
} catch (Exception e){
logger.error("Problem aligning {} with {}", name1, name2, e);
StringWriter sw = new StringWriter();
PrettyXMLWriter xml = new PrettyXMLWriter(new PrintWriter(sw));
try {
xml.openTag("AFPChain");
xml.attribute("name1", name1);
xml.attribute("name2", name2);
xml.attribute("error", e.getMessage());
xml.closeTag("AFPChain");
} catch(IOException ex){
logger.error("Error occured converting alignment for {} and {} to XML", name1, name2, ex);
}
if ( progressListeners != null)
notifyEndAlignment();
results.add(sw.toString());
}
alignmentsCalculated++;
}
// send results back to server
sendResultsToServer(results);
long end = System.currentTimeMillis();
if ( end >= maxTime) {
logger.info("OK end of job: reached maxTime {}", maxTime);
terminated = true;
}
if ( alignmentsCalculated >= maxNrAlignments) {
logger.info("OK end of job: reached maxNrAlignments", maxNrAlignments);
terminated = true;
}
long tdiff = (end - startTime);
if ( tdiff != 0) {
logger.info(userName + String.format(": job has run for : %.2f", (tdiff) / 1000.0 / 60) + " min.");
logger.info("{}: total nr of alignments calculated: {}", userName, alignmentsCalculated);
if ( alignmentsCalculated > 0)
logger.info(userName + String.format(": average time / alignment: %.2f", (tdiff / alignmentsCalculated / 1000.0)) + " sec.");
}
}
logger.info(userName + ": jFATCAT job result: " + counter);
// clean up in the end...
clearListeners();
cache.notifyShutdown();
}
private void setVersion(String algorithmName) {
StructureAlignment algorithm;
try {
algorithm = StructureAlignmentFactory.getAlgorithm(algorithmName);
version = algorithm.getVersion();
} catch (StructureException e) {
throw new RuntimeException("Couldn't set version for algorithm \"" + algorithmName + "\"", e);
// version = resourceManager.getString(JFATCAT_VERSION); // dmyersturnbull: was this
}
}
private void notifyStartAlignment(String name1, String name2) {
if ( progressListeners != null){
for (AlignmentProgressListener li : progressListeners){
li.alignmentStarted(name1, name2);
}
}
}
private void notifyEndAlignment(){
if ( progressListeners != null){
for (AlignmentProgressListener li : progressListeners){
li.alignmentEnded();
}
}
}
private void notifyRequestingAlignments(int nrAlignments){
if ( progressListeners != null){
for (AlignmentProgressListener li : progressListeners){
li.requestingAlignmentsFromServer(nrAlignments);
}
}
}
private void notifySubmittingAlignments(int nrAlignments, String message){
if ( progressListeners != null){
for (AlignmentProgressListener li : progressListeners){
li.sentResultsToServer(nrAlignments,message);
}
}
}
public String alignPair(String name1, String name2)
throws StructureException, IOException {
return alignPair(name1, name2, FatCatRigid.algorithmName);
}
public String alignPair(String name1, String name2, String algorithmName)
throws StructureException, IOException {
// make sure each thread has an independent instance of the algorithm object ...
StructureAlignment algorithm = getAlgorithm(algorithmName);
// we are running with default parameters
if ( verbose ) {
logger.debug("aligning {} against {}", name1, name2);
}
long startTime = System.currentTimeMillis();
if ( prevName1 == null)
initMaster(name1);
if ( ! prevName1.equals(name1) ) {
// we need to reload the master
initMaster(name1);
}
// get a copy of the atoms, but clone them, since they will be rotated...
Atom[] ca2 = cache.getAtoms(name2);
AFPChain afpChain = algorithm.align(ca1, ca2);
afpChain.setName1(name1);
afpChain.setName2(name2);
try {
// add tmScore
double tmScore = AFPChainScorer.getTMScore(afpChain, ca1, ca2);
afpChain.setTMScore(tmScore);
} catch (RuntimeException e){
logger.error("ca1 size: {} ca2 length: {} {} {}", ca1.length, ca2.length, afpChain.getName1(), afpChain.getName2(), e);
}
long endTime = System.currentTimeMillis();
long calcTime = (endTime-startTime);
if ( verbose ){
boolean isCP = !AlignmentTools.isSequentialAlignment(afpChain, false);
String msg = "finished alignment: " + name1 + " vs. " + name2 + " in " + (calcTime) / 1000.0 + " sec.";
msg += " algo: " + algorithmName + " v:" + version + " " + afpChain;
if ( isCP ) msg += "HAS A CIRCULAR PERMUTATION!!!";
logger.debug(msg);
}
if (verbose){
printMemory();
}
afpChain.setCalculationTime(calcTime);
return AFPChainXMLConverter.toXML(afpChain, ca1, ca2);
}
private void printMemory() {
int size = 1048576;
long heapSize = Runtime.getRuntime().totalMemory() / size;
// Get maximum size of heap in bytes. The heap cannot grow beyond this size.
// Any attempt will result in an OutOfMemoryException.
long heapMaxSize = Runtime.getRuntime().maxMemory() / size;
// Get amount of free memory within the heap in bytes. This size will increase
// after garbage collection and decrease as new objects are created.
long heapFreeSize = Runtime.getRuntime().freeMemory() / size;
StringBuilder msg = new StringBuilder();
msg.append(" total: ").append(heapSize).append(" M");
msg.append(" max: "). append(heapMaxSize).append(" M");
msg.append(" free: ").append(heapFreeSize).append(" M");
logger.debug(msg.toString());
}
private StructureAlignment getAlgorithm(String algorithmName) throws StructureException {
StructureAlignment algorithm = null;
if ( algorithmName == null){
algorithm = new FatCatRigid();
} else if ( algorithmName.equalsIgnoreCase(FatCatRigid.algorithmName)){
algorithm = new FatCatRigid();
} else if ( algorithmName.equalsIgnoreCase(CeMain.algorithmName)){
algorithm = new CeMain();
} else if ( algorithmName.equalsIgnoreCase(CeCPMain.algorithmName)){
algorithm = new CeCPMain();
} else if ( algorithmName.equalsIgnoreCase(FatCatFlexible.algorithmName)){
algorithm = new FatCatFlexible();
} else {
algorithm = StructureAlignmentFactory.getAlgorithm(algorithmName);
}
if ( algorithm == null) {
algorithm = new FatCatRigid();
}
return algorithm;
}
private void initMaster(String name1) throws IOException, StructureException{
ca1 = cache.getAtoms(name1);
prevName1 = name1;
}
/** talk to centralized server and fetch all alignments to run.
*
* @return a list of pairs to align.
*/
protected PdbPairsMessage getAlignmentPairsFromServer() {
String url = params.getServer();
int nrPairs = params.getStepSize();
if ( maxNrAlignments < nrPairs )
nrPairs = maxNrAlignments;
SortedSet allPairs = new TreeSet();
PdbPairsMessage msg = null;
try {
if ( progressListeners != null)
notifyRequestingAlignments(nrPairs);
if ( ! waitForAlignments) {
msg = JFatCatClient.getPdbPairs(url, nrPairs, userName);
allPairs = msg.getPairs();
} else {
while (allPairs.isEmpty()) {
msg = JFatCatClient.getPdbPairs(url, nrPairs, userName);
allPairs = msg.getPairs();
if (allPairs.isEmpty()) {
randomSleep();
}
}
}
} catch ( JobKillException k ){
logger.debug("Terminating job", k);
terminate();
} catch (Exception e) {
logger.error("Error while requesting alignment pairs", e);
// an error has occured sleep 30 sec.
randomSleep();
}
return msg;
}
private void randomSleep() {
try {
int delay = JFatCatClient.getRandomSleepTime();
logger.debug("sleeping {} sec.", delay/1000);
Thread.sleep(delay);
} catch (InterruptedException ex){
logger.trace("InterruptedException occurred while sleeping", ex);
}
}
protected void sendResultsToServer(List results) {
String serverLocation = params.getServer();
if ( results.size() < 1)
return;
String fullXml = "";
for (String xml: results){
fullXml +=xml;
}
fullXml += " ";
String msg = "";
try {
msg = JFatCatClient.sendMultiAFPChainToServer(serverLocation,fullXml, userName, version );
} catch (JobKillException e){
logger.info("{} Got Job Kill message from server, terminating...", userName, e);
terminate();
}
if ( progressListeners != null)
notifySubmittingAlignments(results.size(), msg);
logger.info("{}: Sent {} results to server. job status: {}", userName, results.size(), counter);
logger.info("{}: fileCache size: {}", userName, FlatFileCache.getInstance().size());
}
/** Send signal to terminate calculations
*
*/
public synchronized void terminate(){
terminated = true;
}
public boolean isWaitForAlignments() {
return waitForAlignments;
}
public void setWaitForAlignments(boolean waitForAlignments) {
this.waitForAlignments = waitForAlignments;
}
}
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