1 /* Copyright (c) 2009 Peter Troshin
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3 * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0
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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.util.Arrays;
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29 import java.util.List;
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31 import javax.xml.ws.WebServiceException;
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33 import compbio.data.msa.MsaWS;
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34 import compbio.data.sequence.Alignment;
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35 import compbio.data.sequence.FastaSequence;
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36 import compbio.data.sequence.SequenceUtil;
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37 import compbio.metadata.JobStatus;
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38 import compbio.metadata.JobSubmissionException;
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39 import compbio.metadata.Limit;
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40 import compbio.metadata.LimitsManager;
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41 import compbio.metadata.Preset;
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42 import compbio.metadata.PresetManager;
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43 import compbio.metadata.ResultNotAvailableException;
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44 import compbio.metadata.RunnerConfig;
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45 import compbio.metadata.UnsupportedRuntimeException;
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46 import compbio.metadata.WrongParameterException;
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49 * Class for testing web services
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53 * @version 1.0 February 2010
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55 public class WSTester {
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58 * Sequences to be used as input for all WS
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60 static final String fastaInput = ">Foobar\n"
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61 + "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQGVGAVEPFAFLSEDASAAEQLACARTRAQAIAASVRPLAPTRVRSKGPLRVGFVSNGFGAHPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHGIDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVLRLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLLSGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKA"
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63 + "ASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVAQGVGAVEPFAFLSEDASAAESVRPLAPTRVRSKGPLRVGFVSNGFGAHPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHGIDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVLRLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLLSGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRESGVFEMDGFADDFGALLQALARRHGWLGI"
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65 + "MTADGPRELLQLRAAVRHRPQDVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDHQLLPEEPYITAQLDVLSAQVRAAVAQGVGAVEPFAFLSEDASAAEQLACARTRAQAIAASVRPLAPTRVRSKGPLRVGFVSNGFGAHPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHGIDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVLRLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLLSGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRESI\n";
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67 static final List<FastaSequence> seqs = loadSeqs();
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69 private static final String FAILED = "FAILED";
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70 private static final String OK = "OK";
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73 * Converting input to a form accepted by WS
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75 * @return List of FastaSequence records
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77 static List<FastaSequence> loadSeqs() {
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79 return SequenceUtil.readFasta(new ByteArrayInputStream(fastaInput
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81 } catch (IOException ignored) {
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82 // Should not happen as a source is not a external stream
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83 ignored.printStackTrace();
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91 static void printUsage() {
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92 System.out.println("Usage: <Class or Jar file name> " + hostkey
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93 + pseparator + "host_and_context " + "<" + servicekey
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94 + pseparator + "serviceName>");
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95 System.out.println();
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99 + "<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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101 .println(servicekey
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103 + "<ServiceName> - optional if unspecified all services are tested otherwise one of "
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104 + Arrays.toString(Services.values()));
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105 System.out.println();
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110 * Calls alignment with preset
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115 * list of the Preset
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116 * @throws UnsupportedRuntimeException
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118 static <T> boolean presetAlign(MsaWS<T> msaws, List<Preset<T>> presets)
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119 throws UnsupportedRuntimeException {
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120 boolean succeed = false;
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121 for (Preset<T> preset : presets) {
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122 System.out.print("Aligning with preset '" + preset.getName()
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124 Alignment al = null;
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126 String taskId = msaws.presetAlign(seqs, preset);
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127 al = msaws.getResult(taskId);
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129 System.out.println(OK);
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132 } catch (UnsupportedRuntimeException e) {
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133 System.out.println(FAILED);
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134 // If executable is not supported than none of the presets are
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136 throw new UnsupportedRuntimeException(e);
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137 } catch (JobSubmissionException e) {
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138 // TODO custom message
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139 System.out.println(FAILED);
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140 System.out.println();
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141 e.printStackTrace();
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143 } catch (WrongParameterException e) {
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144 // TODO custom message
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145 System.out.println(FAILED);
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146 System.out.println();
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147 e.printStackTrace();
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149 } catch (ResultNotAvailableException e) {
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150 // TODO custom message
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151 System.out.println(FAILED);
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152 System.out.println();
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153 e.printStackTrace();
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161 * Call most of web services functions and check the output
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166 * @throws UnsupportedRuntimeException
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167 * is thrown if the connection to a web service was made, but
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168 * the web service is not functional. e.g. when native
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169 * executable does not exists for a server platform
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171 static <T> boolean checkService(MsaWS<T> msaws)
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172 throws UnsupportedRuntimeException {
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174 boolean succeed = testDefaultAlignment(msaws);
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176 // If exception above is thrown than the tests below is not run
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178 PresetManager<T> pmanager = msaws.getPresets();
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179 if (pmanager != null && pmanager.getPresets().size() > 0) {
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180 System.out.println("Testing alignment with presets:");
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181 List<Preset<T>> plist = pmanager.getPresets();
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182 succeed = !succeed ? presetAlign(msaws, plist) : succeed;
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185 System.out.print("Querying presets...");
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187 if (pmanager != null && pmanager.getPresets().size() > 0) {
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188 System.out.println(OK);
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190 System.out.println("UNSUPPORTED");
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193 System.out.print("Querying Parameters...");
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194 RunnerConfig<T> options = msaws.getRunnerOptions();
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195 if (options != null && options.getArguments().size() > 0) {
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196 System.out.println(OK);
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198 System.out.println(FAILED);
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202 System.out.print("Querying Limits...");
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203 LimitsManager<T> limits = msaws.getLimits();
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204 if (limits != null && limits.getLimits().size() > 0) {
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205 System.out.println(OK);
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207 System.out.println("UNSUPPORTED");
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210 System.out.print("Querying Local Engine Limits...");
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211 Limit<T> localLimit = msaws
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212 .getLimit(PresetManager.LOCAL_ENGINE_LIMIT_PRESET);
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213 if (localLimit != null) {
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214 System.out.println(OK);
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216 System.out.println("UNSUPPORTED");
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222 * Align using default settings
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226 * @throws UnsupportedRuntimeException
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228 static <T> boolean testDefaultAlignment(MsaWS<T> msaws)
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229 throws UnsupportedRuntimeException {
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230 System.out.print("Testing alignment with default parameters:");
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231 Alignment al = null;
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232 boolean succeed = false;
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234 String taskId = msaws.align(seqs);
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235 System.out.print("\nQuerying job status...");
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236 JobStatus status = msaws.getJobStatus(taskId);
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237 while (status != JobStatus.FINISHED) {
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238 Thread.sleep(1000);
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239 status = msaws.getJobStatus(taskId);
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241 System.out.println(OK);
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242 System.out.print("Retrieving results...");
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243 al = msaws.getResult(taskId);
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245 } catch (ResultNotAvailableException e) {
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246 System.out.println(FAILED);
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247 e.printStackTrace();
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248 } catch (JobSubmissionException e) {
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249 System.out.println(FAILED);
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250 System.out.println();
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251 e.printStackTrace();
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252 } catch (InterruptedException e) {
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253 System.out.println(FAILED);
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254 System.out.println();
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255 e.printStackTrace();
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258 System.out.println(OK);
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264 * Connect to a WS using the host and the service name
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271 static <T> MsaWS<T> connect(String host, Services service) {
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272 MsaWS<T> msaws = null;
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274 System.out.print("Connecting to service " + service + " on " + host
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276 msaws = (MsaWS<T>) Jws2Client.connect(host, service);
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277 System.out.println(OK);
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278 } catch (WebServiceException e) {
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279 System.out.println(FAILED);
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285 * Test JWS2 web services
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290 * -h=<Your web application server host name, port and JWS2
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293 * -s=<ServiceName> which is optional. If service name is not
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294 * provided then all known JWS2 web services are tested
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295 * @throws IOException
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297 public static <T> void main(String[] args) throws IOException {
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299 if (args == null || args.length < 1) {
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303 String host = CmdHelper.getHost(args);
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304 String serviceName = CmdHelper.getServiceName(args);
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305 if (!Jws2Client.validURL(host)) {
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307 .println("<host_and_context> parameter is not provided or is incorrect!");
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310 boolean succeed = false;
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311 MsaWS<T> msaws = null;
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312 if (serviceName != null) {
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313 Services service = Services.getService(serviceName);
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314 if (service == null) {
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315 System.out.println("Service '" + serviceName
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316 + "' is not supported. Valid values are: "
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317 + Arrays.toString(Services.values()));
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318 System.out.println();
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323 msaws = connect(host, service);
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324 if (msaws == null) {
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328 succeed = checkService(msaws);
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329 } catch (UnsupportedRuntimeException ignored) {
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332 ((Closeable) msaws).close();
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334 reportResults(service, succeed);
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339 .println("<ServiceName> is not provided checking all known services...");
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341 for (Services serv : Services.values()) {
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342 System.out.println();
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343 msaws = connect(host, serv);
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344 if (msaws == null) {
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348 succeed = checkService(msaws);
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349 } catch (UnsupportedRuntimeException ignored) {
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350 System.out.println("Service " + serv + " IS NOT FUNCTIONAL");
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353 ((Closeable) msaws).close();
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355 reportResults(serv, succeed);
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360 private static void reportResults(Services serv, boolean succeed) {
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362 System.out.println("Check is completed. The Service " + serv
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365 System.out.println("Check is completed. The Service " + serv
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366 + " HAS SOME PROBLEMS");
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