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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.fatcat.FatCatRigid;
import org.biojava.nbio.structure.align.model.AFPChain;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.align.util.HTTPConnectionTools;
import org.biojava.nbio.structure.align.util.ResourceManager;
import org.biojava.nbio.structure.align.xml.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.URL;
import java.net.URLEncoder;
import java.util.Random;
import java.util.SortedSet;
import java.util.TreeSet;
public class JFatCatClient {
private final static Logger logger = LoggerFactory.getLogger(JFatCatClient.class);
private static ResourceManager resourceManager = ResourceManager.getResourceManager("jfatcat");
private static final String serverAPPEND = "show?name1=%s&name2=%s";
private static final String sendAPPEND = "submit?name1=%s&name2=%s&version=%s";
private static final String multiSendAPPEND = "jobSubmit?username=%s&version=%s";
private static final String representAPPEND = "representatives?cluster=%s";
private static final String serverHasResult = "hasResult?method=%s&name1=%s&name2=%s";
private static final int DEFAULT_TIMEOUT = 5000;
private static final String serverPositionInQueue = "queuePosition?method=%s&name1=%s&name2=%s";
private static Random generator;
private static String newline = System.getProperty("line.separator");
private static String KILL_JOB = "KILL_JOB";
private static String COME_BACK_LATER = "COME_BACK_LATER";
static {
generator = new Random();
}
public static void main(String[] args) throws Exception {
//System.out.println(hasPrecalculatedResult("http://source.rcsb.org/jfatcatserver/align/", "jCE Circular Permutation", "1CDG.A", "1TIM.A"));
AtomCache cache = new AtomCache();
String name1= "2W72.A";
String name2= "1D2Z.D";
Atom[] ca1 = cache.getAtoms(name1);
Atom[] ca2 = cache.getAtoms(name2);
int timeout = 10000;
String testServer = "http://source.rcsb.org/jfatcatserver/align/";
System.out.println(getAFPChainFromServer(testServer, FatCatRigid.algorithmName, name1, name2, ca1, ca2, timeout));
PdbPairsMessage msg = getPdbPairs(testServer, 1, "test");
System.out.println(msg);
System.out.println(getRepresentatives(FarmJobParameters.DEFAULT_SERVER_URL, 40));
}
public static boolean hasPrecalculatedResult(String serverLocation, String method, String name1, String name2 ){
return hasPrecalculatedResult(serverLocation, method, name1, name2, DEFAULT_TIMEOUT );
}
public static boolean hasPrecalculatedResult(String serverLocation, String method, String name1, String name2, int timeout){
String serverURL = serverLocation + serverHasResult;
boolean hasResults = false;
try {
String u = String.format(serverURL,URLEncoder.encode(method,"UTF-8"),name1,name2) ;
URL url = new URL(u);
//System.out.println("has result ? ..." + url);
InputStream stream = HTTPConnectionTools.getInputStream(url,timeout);
String xml = null;
if ( stream != null) {
xml = convertStreamToString(stream);
logger.info(" has PrecalcResults got XML from server: " + xml);
HasResultXMLConverter conv = new HasResultXMLConverter();
hasResults = conv.fromXML(xml);
}
} catch (IOException e){
// log error and return false
logger.error("error in JFatCatClient: getAFPChainFromServer",e);
}
return hasResults;
}
public int getPositionInQueue(String serverLocation, String method, String name1, String name2){
return getPositionInQueue(serverLocation, method, name1, name2, DEFAULT_TIMEOUT);
}
public int getPositionInQueue(String serverLocation, String method, String name1, String name2, int timeout){
String serverURL = serverLocation + serverPositionInQueue;
int position = Integer.MIN_VALUE;
try {
String u = String.format(serverURL,URLEncoder.encode(method,"UTF-8"),name1,name2) ;
URL url = new URL(u);
InputStream stream = HTTPConnectionTools.getInputStream(url,timeout);
String xml = null;
if ( stream != null) {
xml = convertStreamToString(stream);
//System.out.println("got XML from server: " + xml);
PositionInQueueXMLConverter conv = new PositionInQueueXMLConverter();
position = conv.fromXML(xml);
}
} catch (IOException e){
logger.error("error in JFatCatClient: getAFPChainFromServer",e); // TODO dmyersturnbull: method should throw; we shouldn't catch here
}
return position;
}
public static AFPChain getAFPChainFromServer(String serverLocation , String name1, String name2, Atom[] ca1, Atom[] ca2) {
String method = FatCatRigid.algorithmName;
return getAFPChainFromServer(serverLocation, method, name1, name2, ca1, ca2,DEFAULT_TIMEOUT);
}
public static AFPChain getAFPChainFromServer(String serverLocation , String method, String name1, String name2, Atom[] ca1, Atom[] ca2, int timeout)
{
String serverURL = serverLocation + serverAPPEND;
try {
String u = String.format(serverURL,name1,name2) ;
if ( method != null)
u+= "&method=" + URLEncoder.encode(method,"UTF-8");
URL url = new URL(u);
logger.info("requesting alignment from server..." + url);
// have a short timeout for this...
// 5 sec
InputStream stream = HTTPConnectionTools.getInputStream(url,timeout);
String xml = null;
if ( stream != null) {
xml = convertStreamToString(stream);
}
if (xml != null) {
return AFPChainXMLParser.fromXML (xml, name1, name2, ca1, ca2);
} else {
return null;
}
// TODO dmyersturnbull: method should throw; we shouldn't catch here
} catch (IOException e){
logger.error("error in JFatCatClient: getAFPChainFromServer",e);
} catch (StructureException e) {
logger.error("error in JFatCatClient: getAFPChainFromServer",e);
}
return null;
}
public static String convertStreamToString(InputStream stream){
BufferedReader reader = new BufferedReader(new InputStreamReader(stream));
StringBuilder sb = new StringBuilder();
String line = null;
try {
while ((line = reader.readLine()) != null) {
sb.append(line).append(newline);
}
} catch (IOException e) {
logger.error("Couldn't convert stream to string", e); // TODO dmyersturnbull: method should throw; we shouldn't catch here
} finally {
try {
stream.close();
} catch (IOException e) {
logger.warn("Can't close stream", e);
}
}
return sb.toString();
}
public static String sendMultiAFPChainToServer(String serverLocation, String multiXML, String username) throws JobKillException{
String version = resourceManager.getString("jfatcat.version");
return sendMultiAFPChainToServer(serverLocation, multiXML, username, version);
}
public static String sendMultiAFPChainToServer(String serverLocation, String multiXML, String username, String version) throws JobKillException{
String multiSendURL = serverLocation + multiSendAPPEND;
String responseS = "";
String u = String.format(multiSendURL,username,version);
int timeout = getTimeout();
boolean submitted = false;
while (! submitted ){
try {
URL url = new URL(u);
InputStream response = HTTPConnectionTools.doPOST(url, multiXML,timeout);
responseS = convertStreamToString(response);
submitted = true;
if (! responseS.contains("OK"))
logger.error("server returned " + responseS);
// server is busy... wait a bit and try again
if ( responseS.startsWith(COME_BACK_LATER)){
submitted = false;
}
} catch (Exception e){
logger.error("Error in JFatCatClient: while sending results back to server",e);
try {
int randomSleep = getRandomSleepTime();
logger.warn("sleeping " + (randomSleep/1000) + " sec.");
Thread.sleep(randomSleep);
} catch (InterruptedException ex){
logger.warn("Interrupted while sleeping", ex);
}
}
}
if ( responseS.startsWith(KILL_JOB)){
throw new JobKillException("Server responded with KILL message.");
}
return responseS;
}
public static int getRandomSleepTime() {
// now wait between 7 and 13 min.
int minTime = 560000;
int maxTime = 7800000 - minTime;
int nextId = generator.nextInt(maxTime);
return minTime + nextId;
}
public static final void sendAFPChainToServer(String serverLocation, AFPChain afpChain,Atom[] ca1, Atom[] ca2) throws JobKillException
{
String sendURL = serverLocation + sendAPPEND;
String version = resourceManager.getString("jfatcat.version");
int timeout = getTimeout();
try {
// just to make sure that similarity has been calculated!
afpChain.getSimilarity();
String xml = AFPChainXMLConverter.toXML(afpChain, ca1, ca2);
String u = String.format(sendURL,afpChain.getName1() , afpChain.getName2(),version);
URL url = new URL(u);
InputStream response = HTTPConnectionTools.doPOST(url, xml,timeout);
logger.debug("got response: {}", convertStreamToString(response));
if ( xml.startsWith("KILL_JOB")){
throw new JobKillException("Server responded with KILL message.");
}
} catch (IOException e){
logger.error("error in JFatCatClient: sendAFPChainToServer",e);
}
}
public static final int getTimeout(){
String timeoutS = resourceManager.getString("connection.timeout");
int timeout = 60000;
try {
timeout = Integer.parseInt(timeoutS);
} catch (NumberFormatException ex ){
logger.error("Bad connection.timeout parameter",ex);
}
return timeout;
}
public static final PdbPairsMessage getPdbPairs(String url,int nrPair, String username) throws IOException, JobKillException {
String urlS= url + "getPairs?" + "nrPairs=" + nrPair + "&username=" + URLEncoder.encode(username, "UTF-8");
int timeout = getTimeout();
PdbPairsMessage msg = null;
logger.info("requesting {}", urlS);
URL serverUrl = new URL(urlS);
// we are very tolerant with requesting a set of pairs, since we probably depend on getting it to get work started...
// 1 min...
InputStream stream = HTTPConnectionTools.getInputStream(serverUrl,timeout);
String xml = null;
if ( stream != null) {
xml = convertStreamToString(stream);
if (xml != null) {
if ( xml.startsWith("KILL_JOB")){
// we got the KILL signal from the server...
throw new JobKillException("Server responded with KILL message.");
}
msg = PdbPairXMLConverter.convertXMLtoPairs(xml);
}
}
return msg;
}
public static final SortedSet getRepresentatives(String serverLocation, int cutoff){
SortedSet representatives = new TreeSet();
String representURL = serverLocation + representAPPEND;
if ( cutoff < 20)
cutoff = 40;
int timeout = getTimeout();
String u = String.format(representURL,cutoff);
logger.info("Fetching representatives from "+u);
try {
URL url = new URL(u);
InputStream stream = HTTPConnectionTools.getInputStream(url,timeout);
String xml = null;
if ( stream != null) {
xml = convertStreamToString(stream);
}
if (xml != null) {
representatives = RepresentativeXMLConverter.fromXML(xml);
}
} catch (IOException e){ // TODO dmyersturnbull: method should throw; we shouldn't catch here
logger.error("Error fetching representatives",e);
}
return representatives;
}
}
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