1 package compbio.ws.client;
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3 import static org.testng.Assert.assertEquals;
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4 import static org.testng.Assert.assertNotNull;
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5 import static org.testng.Assert.fail;
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6 import static org.testng.Assert.assertTrue;
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8 import java.io.FileInputStream;
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9 import java.io.FileNotFoundException;
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10 import java.io.IOException;
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11 import java.net.ConnectException;
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12 import java.util.ArrayList;
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13 import java.util.List;
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15 import javax.xml.ws.WebServiceException;
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17 import org.testng.annotations.BeforeTest;
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18 import org.testng.annotations.Test;
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20 import compbio.data.msa.JABAService;
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21 import compbio.data.msa.SequenceAnnotation;
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22 import compbio.data.sequence.ConservationMethod;
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23 import compbio.data.sequence.FastaSequence;
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24 import compbio.data.sequence.ScoreManager;
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25 import compbio.data.sequence.SequenceUtil;
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26 import compbio.metadata.AllTestSuit;
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27 import compbio.metadata.JobSubmissionException;
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28 import compbio.metadata.LimitExceededException;
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29 import compbio.metadata.Option;
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30 import compbio.metadata.Preset;
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31 import compbio.metadata.PresetManager;
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32 import compbio.metadata.ResultNotAvailableException;
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33 import compbio.metadata.RunnerConfig;
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34 import compbio.metadata.UnsupportedRuntimeException;
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35 import compbio.metadata.WrongParameterException;
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36 import compbio.runner.conservation.AACon;
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37 import compbio.util.SysPrefs;
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39 public class TestAAConWS {
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41 SequenceAnnotation<AACon> msaws;
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43 @BeforeTest(groups = {AllTestSuit.test_group_webservices})
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44 void initConnection() {
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46 * URL url = null; try { url = new
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47 * URL("http://localhost:8080/jabaws/AAConWS?wsdl"); } catch
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48 * (MalformedURLException e) { e.printStackTrace();
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49 * fail(e.getLocalizedMessage()); } String namespace =
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50 * "http://msa.data.compbio/01/12/2010/"; QName qname = new
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51 * QName(namespace, "AAConWS"); Service serv = Service.create(url,
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52 * qname); msaws = serv.getPort(new QName(namespace, "AAConWSPort"),
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53 * Annotation.class);
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55 JABAService client = Jws2Client.connect(
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56 "http://localhost:8080/jabaws", Services.AAConWS);
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57 msaws = (SequenceAnnotation<AACon>) client;
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58 } catch (ConnectException e) {
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59 e.printStackTrace();
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60 fail(e.getMessage());
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61 } catch (WebServiceException e) {
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62 e.printStackTrace();
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63 fail(e.getMessage());
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67 @Test(groups = {AllTestSuit.test_group_webservices})
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68 public void testAnalize() throws FileNotFoundException, IOException {
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71 * MsaWS msaws = serv.getPort(new QName(
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72 * "http://msa.data.compbio/01/01/2010/", "ClustalWSPort"),
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75 // Annotation<AACon> msaws = serv.getPort(new QName(namespace,
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76 // "ClustalWSPort"), Annotation.class);
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78 // List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
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79 // AAConTester.test_alignment_input));
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81 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
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84 List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
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85 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
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86 + File.separator + "TO1381.fasta.aln"));
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89 System.out.println("Pres: " + msaws.getPresets().getPresets());
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90 String jobId = msaws.analize(fsl);
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91 System.out.println("J: " + jobId);
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92 ScoreManager result = msaws.getAnnotation(jobId);
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93 assertNotNull(result);
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94 assertEquals(result.asSet().size(), 1);
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96 assertEquals(result.asSet().iterator().next().getMethod(),
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97 ConservationMethod.SHENKIN.toString());
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98 List<Float> scores = result.asSet().iterator().next().getScores();
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99 assertNotNull(scores);
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100 assertEquals(scores.size(), 568);
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103 PresetManager<AACon> presets = msaws.getPresets();
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104 jobId = msaws.presetAnalize(fsl,
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105 presets.getPresetByName("Quick conservation"));
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106 result = msaws.getAnnotation(jobId);
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107 assertNotNull(result);
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108 assertEquals(result.asSet().size(), 13);
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110 jobId = msaws.presetAnalize(fsl,
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111 presets.getPresetByName("Slow conservation"));
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112 result = msaws.getAnnotation(jobId);
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113 assertNotNull(result);
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114 assertEquals(result.asSet().size(), 5);
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116 jobId = msaws.presetAnalize(fsl,
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117 presets.getPresetByName("Complete conservation"));
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118 result = msaws.getAnnotation(jobId);
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119 assertNotNull(result);
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120 assertEquals(result.asSet().size(), 18);
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122 } catch (UnsupportedRuntimeException e) {
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123 e.printStackTrace();
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124 fail(e.getMessage());
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125 } catch (LimitExceededException e) {
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126 e.printStackTrace();
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127 fail(e.getMessage());
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128 } catch (JobSubmissionException e) {
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129 e.printStackTrace();
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130 fail(e.getMessage());
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131 } catch (ResultNotAvailableException e) {
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132 e.printStackTrace();
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133 fail(e.getMessage());
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134 } catch (WrongParameterException e) {
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135 e.printStackTrace();
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136 fail(e.getMessage());
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140 @Test(groups = {AllTestSuit.test_group_webservices})
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141 public void testRecoverArgsForPreset() throws Exception {
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142 PresetManager<AACon> presets = msaws.getPresets();
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143 for (Preset<AACon> preset:presets.getPresets())
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145 List<Option<AACon>> args = preset.getArguments(msaws.getRunnerOptions());
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146 List opts = preset.getOptions();
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147 assertTrue(args.size()>=opts.size(),"Couldn't recover all Option items for preset "+preset.getName());
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150 @Test(groups = {AllTestSuit.test_group_webservices})
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151 public void testPresetAnalize() throws FileNotFoundException, IOException {
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153 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
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156 List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
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157 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
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158 + File.separator + "TO1381.fasta.aln"));
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161 System.out.println("Pres: " + msaws.getPresets().getPresets());
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164 PresetManager<AACon> presets = msaws.getPresets();
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165 String jobId = msaws.presetAnalize(fsl,
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166 presets.getPresetByName("Quick conservation"));
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167 ScoreManager result = msaws.getAnnotation(jobId);
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168 assertNotNull(result);
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169 assertEquals(result.asSet().size(), 13);
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171 jobId = msaws.presetAnalize(fsl,
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172 presets.getPresetByName("Slow conservation"));
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173 result = msaws.getAnnotation(jobId);
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174 assertNotNull(result);
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175 assertEquals(result.asSet().size(), 5);
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177 jobId = msaws.presetAnalize(fsl,
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178 presets.getPresetByName("Complete conservation"));
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179 result = msaws.getAnnotation(jobId);
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180 assertNotNull(result);
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181 assertEquals(result.asSet().size(), 18);
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183 } catch (UnsupportedRuntimeException e) {
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184 e.printStackTrace();
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185 fail(e.getMessage());
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186 } catch (LimitExceededException e) {
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187 e.printStackTrace();
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188 fail(e.getMessage());
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189 } catch (JobSubmissionException e) {
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190 e.printStackTrace();
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191 fail(e.getMessage());
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192 } catch (ResultNotAvailableException e) {
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193 e.printStackTrace();
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194 fail(e.getMessage());
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195 } catch (WrongParameterException e) {
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196 e.printStackTrace();
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197 fail(e.getMessage());
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202 @Test(groups = {AllTestSuit.test_group_webservices})
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203 public void testCustomAnalize() throws FileNotFoundException, IOException {
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205 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
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208 List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
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209 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
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210 + File.separator + "TO1381.fasta.aln"));
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213 RunnerConfig<AACon> options = msaws.getRunnerOptions();
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214 // System.out.println(options.getArguments());
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217 List<Option<AACon>> args = new ArrayList<Option<AACon>>();
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218 Option<AACon> arg,normarg;
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219 args.add(arg=options.getArgument("SMERFS"));
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220 args.add(normarg=options.getArgument("Normalize"));
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221 arg.setValue(arg.getPossibleValues().get(0));
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222 // options.getArgument("SMERFS Column Scoring Method")
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223 // .setDefaultValue("MAX_SCORE");
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224 // options.getArgument("SMERFS Gap Threshhold").setDefaultValue("1");
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225 String jobId = msaws.customAnalize(fsl, args);
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226 ScoreManager result = msaws.getAnnotation(jobId);
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227 assertNotNull(result);
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228 assertEquals(result.asSet().size(), 1);
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229 assertEquals(result.asSet().iterator().next().getScores().get(0),
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231 args.remove(normarg); // remove normalization argument
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232 // System.out.println(options);
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233 jobId = msaws.customAnalize(fsl, args);
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234 result = msaws.getAnnotation(jobId);
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235 assertNotNull(result);
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236 assertEquals(result.asSet().size(), 1);
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237 assertEquals(result.asSet().iterator().next().getScores().get(0),
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240 } catch (WrongParameterException e) {
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241 e.printStackTrace();
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242 fail(e.getMessage());
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243 } catch (UnsupportedRuntimeException e) {
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244 e.printStackTrace();
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245 fail(e.getMessage());
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246 } catch (LimitExceededException e) {
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247 e.printStackTrace();
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248 fail(e.getMessage());
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249 } catch (JobSubmissionException e) {
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250 e.printStackTrace();
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251 fail(e.getMessage());
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252 } catch (ResultNotAvailableException e) {
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253 e.printStackTrace();
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254 fail(e.getMessage());
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