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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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.util.ArrayList;
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12 import java.util.HashSet;
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13 import java.util.List;
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14 import java.util.Map;
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16 import org.testng.annotations.BeforeTest;
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17 import org.testng.annotations.Test;
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19 import compbio.data.msa.JABAService;
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20 import compbio.data.msa.SequenceAnnotation;
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21 import compbio.data.sequence.ConservationMethod;
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22 import compbio.data.sequence.FastaSequence;
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23 import compbio.data.sequence.Score;
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24 import compbio.data.sequence.SequenceUtil;
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25 import compbio.metadata.JobSubmissionException;
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26 import compbio.metadata.LimitExceededException;
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27 import compbio.metadata.PresetManager;
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28 import compbio.metadata.ResultNotAvailableException;
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29 import compbio.metadata.RunnerConfig;
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30 import compbio.metadata.UnsupportedRuntimeException;
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31 import compbio.metadata.WrongParameterException;
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32 import compbio.runner.conservation.AACon;
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33 import compbio.util.SysPrefs;
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35 public class TestAAConWS {
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37 SequenceAnnotation<AACon> msaws;
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40 void initConnection() {
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42 * URL url = null; try { url = new
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43 * URL("http://localhost:8080/jabaws/AAConWS?wsdl"); } catch
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44 * (MalformedURLException e) { e.printStackTrace();
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45 * fail(e.getLocalizedMessage()); } String namespace =
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46 * "http://msa.data.compbio/01/12/2010/"; QName qname = new
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47 * QName(namespace, "AAConWS"); Service serv = Service.create(url,
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48 * qname); msaws = serv.getPort(new QName(namespace, "AAConWSPort"),
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49 * Annotation.class);
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51 JABAService client = Jws2Client.connect("http://localhost:8080/jabaws",
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53 msaws = (SequenceAnnotation<AACon>) client;
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57 public void testAnalize() throws FileNotFoundException, IOException {
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60 * MsaWS msaws = serv.getPort(new QName(
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61 * "http://msa.data.compbio/01/01/2010/", "ClustalWSPort"),
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64 // Annotation<AACon> msaws = serv.getPort(new QName(namespace,
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65 // "ClustalWSPort"), Annotation.class);
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67 // List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
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68 // AAConTester.test_alignment_input));
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70 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
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73 List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
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74 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
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75 + File.separator + "TO1381.fasta.aln"));
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78 System.out.println("Pres: " + msaws.getPresets().getPresets());
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79 String jobId = msaws.analize(fsl);
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80 System.out.println("J: " + jobId);
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81 Map<String, HashSet<Score>> result = msaws.getAnnotation(jobId);
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82 assertNotNull(result);
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83 assertEquals(result.size(), 1);
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84 assertEquals(result.values().iterator().next().iterator().next()
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85 .getMethod(), ConservationMethod.SHENKIN);
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86 List<Float> scores = result.values().iterator().next().iterator()
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87 .next().getScores();
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88 assertNotNull(scores);
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89 assertEquals(scores.size(), 568);
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92 PresetManager<AACon> presets = msaws.getPresets();
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93 jobId = msaws.presetAnalize(fsl,
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94 presets.getPresetByName("Quick conservation"));
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95 result = msaws.getAnnotation(jobId);
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96 assertNotNull(result);
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97 assertEquals(result.size(), 13);
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99 jobId = msaws.presetAnalize(fsl,
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100 presets.getPresetByName("Slow conservation"));
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101 result = msaws.getAnnotation(jobId);
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102 assertNotNull(result);
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103 assertEquals(result.size(), 5);
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105 jobId = msaws.presetAnalize(fsl,
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106 presets.getPresetByName("Complete conservation"));
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107 result = msaws.getAnnotation(jobId);
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108 assertNotNull(result);
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109 assertEquals(result.size(), 18);
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111 } catch (UnsupportedRuntimeException e) {
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112 e.printStackTrace();
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113 fail(e.getMessage());
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114 } catch (LimitExceededException e) {
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115 e.printStackTrace();
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116 fail(e.getMessage());
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117 } catch (JobSubmissionException e) {
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118 e.printStackTrace();
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119 fail(e.getMessage());
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120 } catch (ResultNotAvailableException e) {
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121 e.printStackTrace();
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122 fail(e.getMessage());
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123 } catch (WrongParameterException e) {
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124 e.printStackTrace();
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125 fail(e.getMessage());
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131 public void testPresetAnalize() throws FileNotFoundException, IOException {
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133 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
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136 List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
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137 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
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138 + File.separator + "TO1381.fasta.aln"));
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141 System.out.println("Pres: " + msaws.getPresets().getPresets());
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144 PresetManager<AACon> presets = msaws.getPresets();
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145 String jobId = msaws.presetAnalize(fsl,
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146 presets.getPresetByName("Quick conservation"));
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147 Map<String, HashSet<Score>> result = msaws.getAnnotation(jobId);
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148 assertNotNull(result);
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149 assertEquals(result.size(), 13);
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151 jobId = msaws.presetAnalize(fsl,
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152 presets.getPresetByName("Slow conservation"));
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153 result = msaws.getAnnotation(jobId);
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154 assertNotNull(result);
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155 assertEquals(result.size(), 5);
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157 jobId = msaws.presetAnalize(fsl,
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158 presets.getPresetByName("Complete conservation"));
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159 result = msaws.getAnnotation(jobId);
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160 assertNotNull(result);
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161 assertEquals(result.size(), 18);
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163 } catch (UnsupportedRuntimeException e) {
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164 e.printStackTrace();
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165 fail(e.getMessage());
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166 } catch (LimitExceededException e) {
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167 e.printStackTrace();
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168 fail(e.getMessage());
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169 } catch (JobSubmissionException e) {
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170 e.printStackTrace();
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171 fail(e.getMessage());
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172 } catch (ResultNotAvailableException e) {
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173 e.printStackTrace();
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174 fail(e.getMessage());
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175 } catch (WrongParameterException e) {
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176 e.printStackTrace();
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177 fail(e.getMessage());
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183 public void testCustomAnalize() throws FileNotFoundException, IOException {
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185 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
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188 List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
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189 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
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190 + File.separator + "TO1381.fasta.aln"));
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193 RunnerConfig<AACon> options = msaws.getRunnerOptions();
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194 // System.out.println(options.getArguments());
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197 options.getArgument("Calculation method").setDefaultValue("SMERFS");
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198 // options.getArgument("SMERFS Column Scoring Method")
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199 // .setDefaultValue("MAX_SCORE");
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200 // options.getArgument("SMERFS Gap Threshhold").setDefaultValue("1");
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201 String jobId = msaws.customAnalize(fsl, options.getArguments());
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202 Map<String, HashSet<Score>> result = msaws.getAnnotation(jobId);
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203 assertNotNull(result);
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204 assertEquals(result.size(), 1);
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206 new ArrayList<Score>(result.values().iterator().next())
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207 .get(0).getScores().get(0), 0.698f);
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209 options.getArgument("Calculation method").setDefaultValue("SMERFS");
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210 options.removeArgument("Normalize");
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211 System.out.println(options);
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212 jobId = msaws.customAnalize(fsl, options.getArguments());
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213 result = msaws.getAnnotation(jobId);
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214 assertNotNull(result);
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215 assertEquals(result.size(), 1);
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217 new ArrayList<Score>(result.values().iterator().next())
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218 .get(0).getScores().get(0), 0.401f);
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220 } catch (WrongParameterException e) {
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221 e.printStackTrace();
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222 fail(e.getMessage());
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223 } catch (UnsupportedRuntimeException e) {
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224 e.printStackTrace();
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225 fail(e.getMessage());
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226 } catch (LimitExceededException e) {
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227 e.printStackTrace();
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228 fail(e.getMessage());
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229 } catch (JobSubmissionException e) {
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230 e.printStackTrace();
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231 fail(e.getMessage());
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232 } catch (ResultNotAvailableException e) {
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233 e.printStackTrace();
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234 fail(e.getMessage());
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