1 /* Copyright (c) 2011 Peter Troshin
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3 * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0
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5 * This library is free software; you can redistribute it and/or modify it under the terms of the
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6 * Apache License version 2 as published by the Apache Software Foundation
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8 * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
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9 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
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10 * License for more details.
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12 * A copy of the license is in apache_license.txt. It is also available here:
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13 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
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15 * Any republication or derived work distributed in source code form
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16 * must include this copyright and license notice.
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19 package compbio.ws.client;
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21 import static compbio.ws.client.Constraints.hostkey;
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22 import static compbio.ws.client.Constraints.pseparator;
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23 import static compbio.ws.client.Constraints.servicekey;
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25 import java.io.ByteArrayInputStream;
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26 import java.io.Closeable;
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27 import java.io.IOException;
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28 import java.io.PrintWriter;
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29 import java.net.ConnectException;
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30 import java.util.Arrays;
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31 import java.util.List;
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33 import javax.xml.ws.WebServiceException;
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35 import compbio.data.msa.JABAService;
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36 import compbio.data.msa.Metadata;
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37 import compbio.data.msa.MsaWS;
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38 import compbio.data.msa.SequenceAnnotation;
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39 import compbio.data.sequence.Alignment;
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40 import compbio.data.sequence.FastaSequence;
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41 import compbio.data.sequence.ScoreManager;
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42 import compbio.data.sequence.SequenceUtil;
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43 import compbio.metadata.JobStatus;
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44 import compbio.metadata.Limit;
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45 import compbio.metadata.LimitsManager;
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46 import compbio.metadata.Option;
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47 import compbio.metadata.Preset;
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48 import compbio.metadata.PresetManager;
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49 import compbio.metadata.RunnerConfig;
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50 import compbio.metadata.UnsupportedRuntimeException;
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51 import compbio.util.FileUtil;
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52 import compbio.util.Util;
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55 * Class for testing web services
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59 * @version 1.0 February 2010
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61 public class WSTester {
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64 * Sequences to be used as input for all WS
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66 public static final String fastaInput2records = ">Foo\n"
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67 + "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV"
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69 + "ASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n";
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70 public static final String fastaInput1record = ">Foo\n"
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71 + "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV"
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74 public static final String fastaAlignment = ">Foo\n"
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75 + "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n"
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77 + "ASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n"
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80 static final List<FastaSequence> seqs = loadSeqs(2);
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82 private static final String FAILED = "FAILED";
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83 private static final String OK = "OK";
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85 private static final String UNSUPPORTED = "UNSUPPORTED";
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88 * Converting input to a form accepted by WS
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90 * @return List of FastaSequence records
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92 private static List<FastaSequence> loadSeqs(int nLines) {
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95 return SequenceUtil.readFasta(new ByteArrayInputStream(fastaInput1record.getBytes()));
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97 return SequenceUtil.readFasta(new ByteArrayInputStream(fastaInput2records.getBytes()));
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98 } catch (IOException ignored) {
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99 // Should not happen as a source is not a external stream
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100 ignored.printStackTrace();
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106 * Converting input to a form accepted by WS
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108 * @return List of FastaSequence records
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110 private static List<FastaSequence> loadAlignment() {
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112 return SequenceUtil.readFasta(new ByteArrayInputStream(
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113 fastaAlignment.getBytes()));
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114 } catch (IOException ignored) {
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115 // Should not happen as a source is not a external stream
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116 ignored.printStackTrace();
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121 private final PrintWriter writer;
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122 private final String hostname;
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125 * Construct an instance of JABAWS tester
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128 * - fully qualified host and context name of JABAWS e.g.
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129 * http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba
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131 * a PrintWriter instance to writer test log to.
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133 public WSTester(String hostname, PrintWriter writer) {
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134 if (Util.isEmpty(hostname)) {
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135 throw new NullPointerException("Hostname must be provided!");
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137 this.hostname = hostname;
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138 this.writer = writer;
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144 static void printUsage() {
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145 System.out.println("Usage: <Class or Jar file name> " + hostkey
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146 + pseparator + "host_and_context " + "<" + servicekey
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147 + pseparator + "serviceName>");
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148 System.out.println();
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149 System.out.println(hostkey
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151 + "<host_and_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.1.159:8080/ws");
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152 System.out.println(servicekey
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154 + "<ServiceName> - optional if unspecified all services are tested otherwise one of "
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155 + Arrays.toString(Services.values()));
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156 System.out.println();
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161 * Calls alignment with preset
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166 * list of the Preset
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167 * @throws UnsupportedRuntimeException
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169 private <T> boolean presetAlign(MsaWS<T> msaws, List<Preset<T>> presets)
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170 throws UnsupportedRuntimeException {
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171 boolean succeed = false;
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172 for (Preset<T> preset : presets) {
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173 writer.print("Aligning with preset '" + preset.getName() + "'... ");
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174 Alignment al = null;
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176 String taskId = msaws.presetAlign(seqs, preset);
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177 al = msaws.getResult(taskId);
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179 writer.println(OK);
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182 } catch (Exception e) {
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183 if (e instanceof UnsupportedRuntimeException) {
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184 // If executable is not supported than none of the presets
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187 throw (UnsupportedRuntimeException) e;
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189 reportException(e);
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197 private <T> boolean testMsaWS(MsaWS<T> msaws) throws Exception {
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198 assert msaws != null;
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200 boolean succeed = testDefaultAlignment(msaws);
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201 // If exception above is thrown than the tests below is not run
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203 PresetManager<T> pmanager = msaws.getPresets();
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204 if (pmanager != null && pmanager.getPresets().size() > 0) {
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205 writer.println("Testing alignment with presets:");
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206 List<Preset<T>> plist = pmanager.getPresets();
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207 succeed = !succeed ? presetAlign(msaws, plist) : succeed;
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209 testMetadata(msaws);
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213 * Call most of web services functions and check the output
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218 * @throws UnsupportedRuntimeException
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219 * is thrown if the connection to a web service was made, but
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220 * the web service is not functional. e.g. when native
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221 * executable does not exists for a server platform
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223 @SuppressWarnings("unchecked")
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224 private <T> boolean checkService(JABAService wservice, Services service) {
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226 if (wservice == null) {
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227 throw new NullPointerException("JABAService instance must be provided!");
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230 if (wservice instanceof MsaWS) {
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231 return testMsaWS((MsaWS<T>) wservice);
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232 } else if (wservice instanceof SequenceAnnotation) {
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233 return testSequenceAnnotationWS(
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234 (SequenceAnnotation<T>) wservice, service);
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236 throw new UnsupportedOperationException("The service: " + wservice.getClass() + " is not supported! ");
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238 } catch (Exception e) {
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239 reportException(e);
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244 private <T> boolean testSequenceAnnotationWS(
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245 SequenceAnnotation<T> wservice, Services service) throws Exception {
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246 writer.print("Calling analyse.........");
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248 List<FastaSequence> input = loadSeqs(2);
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249 if (service == Services.AAConWS) {
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250 input = loadAlignment();
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252 if (service == Services.JpredWS) {
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253 input = loadSeqs(1);
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255 boolean success = testDefaultAnalyse(input, wservice, null, null);
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257 PresetManager<T> presetman = wservice.getPresets();
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258 if (presetman != null) {
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259 List<Preset<T>> presets = presetman.getPresets();
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260 if (presets != null && !presets.isEmpty()) {
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261 Preset<T> preset = presets.get(0);
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262 writer.print("Calling analyse with Preset.........");
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263 success = testDefaultAnalyse(input, wservice, preset, null);
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266 testMetadata(wservice);
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270 private <T> boolean testDefaultAnalyse(List<FastaSequence> fastalist,
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271 SequenceAnnotation<T> wsproxy, Preset<T> preset,
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272 List<Option<T>> customOptions) throws Exception {
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274 ScoreManager scores = null;
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276 String jobId = null;
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277 if (customOptions != null) {
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278 jobId = wsproxy.customAnalize(fastalist, customOptions);
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279 } else if (preset != null) {
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280 jobId = wsproxy.presetAnalize(fastalist, preset);
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282 jobId = wsproxy.analize(fastalist);
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284 Thread.sleep(1000);
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285 scores = wsproxy.getAnnotation(jobId);
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286 if (scores != null) {
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287 writer.println(OK);
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290 return scores != null;
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293 private void reportException(Exception e) {
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294 writer.println(FAILED);
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295 writer.println("Exception while waiting for results. "
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296 + "Exception details are below:");
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297 writer.println(e.getLocalizedMessage());
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298 e.printStackTrace(writer);
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301 private <T> void testMetadata(Metadata<T> msaws)
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302 throws UnsupportedRuntimeException {
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304 writer.print("Querying presets...");
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305 PresetManager<T> pmanager = msaws.getPresets();
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306 if (pmanager != null && pmanager.getPresets().size() > 0) {
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307 writer.println(OK);
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309 writer.println(UNSUPPORTED);
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312 writer.print("Querying Parameters...");
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313 RunnerConfig<T> options = msaws.getRunnerOptions();
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314 if (options != null && options.getArguments().size() > 0) {
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315 writer.println(OK);
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317 writer.println(UNSUPPORTED);
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320 writer.print("Querying Limits...");
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321 LimitsManager<T> limits = msaws.getLimits();
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322 if (limits != null && limits.getLimits().size() > 0) {
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323 writer.println(OK);
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324 // writer.println("Limits details: \n" + limits.toString());
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326 writer.println(UNSUPPORTED);
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329 writer.print("Querying Local Engine Limits...");
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330 Limit<T> localLimit = msaws
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331 .getLimit(PresetManager.LOCAL_ENGINE_LIMIT_PRESET);
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332 if (localLimit != null) {
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333 writer.println(OK);
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335 writer.println(UNSUPPORTED);
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340 * Align using default settings
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344 * @throws UnsupportedRuntimeException
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346 private <T> boolean testDefaultAlignment(MsaWS<T> msaws) throws Exception {
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347 writer.print("Testing alignment with default parameters:");
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348 Alignment al = null;
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349 boolean succeed = false;
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351 String taskId = msaws.align(seqs);
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352 writer.print("\nQuerying job status...");
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353 JobStatus status = msaws.getJobStatus(taskId);
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354 while (status != JobStatus.FINISHED) {
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355 Thread.sleep(1000);
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356 status = msaws.getJobStatus(taskId);
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358 writer.println(OK);
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359 writer.print("Retrieving results...");
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360 al = msaws.getResult(taskId);
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363 writer.println(OK);
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368 * Test JWS2 web services
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373 * -h=<Your web application server host name, port and JWS2
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376 * -s=<ServiceName> which is optional. If service name is not
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377 * provided then all known JWS2 web services are tested
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378 * @throws IOException
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380 public static <T> void main(String[] args) throws IOException {
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382 if (args == null || args.length < 1) {
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383 WSTester.printUsage();
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386 String host = CmdHelper.getHost(args);
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387 String serviceName = CmdHelper.getServiceName(args);
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388 if (!Jws2Client.validURL(host)) {
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389 System.err.println("<host_and_context> parameter is not provided or is incorrect!");
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392 WSTester tester = new WSTester(host, new PrintWriter(System.out, true));
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394 if (serviceName != null) {
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395 Services service = Services.getService(serviceName);
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396 if (service == null) {
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397 tester.writer.println("Service '" + serviceName + "' is not supported. Valid values are: "
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398 + Arrays.toString(Services.values()));
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399 tester.writer.println();
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403 tester.checkService(service);
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407 tester.writer.println("<ServiceName> is not provided checking all known services...");
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409 for (Services serv : Services.values()) {
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410 tester.writer.println();
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411 tester.checkService(serv);
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417 * Test JABA web service
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420 * the service to test
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421 * @return true if the service works as expected, false otherwise
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422 * @throws WebServiceException
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423 * @throws ConnectException
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425 public boolean checkService(Services service) throws ConnectException,
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426 WebServiceException {
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427 JABAService ws = Jws2Client.connect(hostname, service);
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429 String line = "Cannot estabilish the connection to host " + hostname + " with service ";
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430 writer.println(line + service.toString());
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433 boolean succeed = false;
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435 writer.println("Checking service " + service.toString());
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436 succeed = checkService(ws, service);
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438 FileUtil.closeSilently(((Closeable) ws));
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440 reportResults(service, succeed);
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444 private void reportResults(Services serv, boolean succeed) {
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446 writer.println("Check is completed. The Service " + serv + " IS WORKING\n");
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448 writer.println("Check is aborted. The Service " + serv + " HAS SOME PROBLEMS\n");
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