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.List;
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13 import org.testng.annotations.BeforeTest;
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14 import org.testng.annotations.Test;
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16 import compbio.data.msa.JABAService;
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17 import compbio.data.msa.SequenceAnnotation;
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18 import compbio.data.sequence.ConservationMethod;
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19 import compbio.data.sequence.FastaSequence;
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20 import compbio.data.sequence.ScoreManager;
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21 import compbio.data.sequence.SequenceUtil;
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22 import compbio.metadata.JobSubmissionException;
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23 import compbio.metadata.LimitExceededException;
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24 import compbio.metadata.PresetManager;
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25 import compbio.metadata.ResultNotAvailableException;
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26 import compbio.metadata.RunnerConfig;
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27 import compbio.metadata.UnsupportedRuntimeException;
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28 import compbio.metadata.WrongParameterException;
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29 import compbio.runner.conservation.AACon;
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30 import compbio.util.SysPrefs;
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32 public class TestAAConWS {
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34 SequenceAnnotation<AACon> msaws;
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37 void initConnection() {
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39 * URL url = null; try { url = new
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40 * URL("http://localhost:8080/jabaws/AAConWS?wsdl"); } catch
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41 * (MalformedURLException e) { e.printStackTrace();
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42 * fail(e.getLocalizedMessage()); } String namespace =
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43 * "http://msa.data.compbio/01/12/2010/"; QName qname = new
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44 * QName(namespace, "AAConWS"); Service serv = Service.create(url,
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45 * qname); msaws = serv.getPort(new QName(namespace, "AAConWSPort"),
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46 * Annotation.class);
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48 JABAService client = Jws2Client.connect("http://localhost:8080/jabaws",
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50 msaws = (SequenceAnnotation<AACon>) client;
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54 public void testAnalize() throws FileNotFoundException, IOException {
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57 * MsaWS msaws = serv.getPort(new QName(
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58 * "http://msa.data.compbio/01/01/2010/", "ClustalWSPort"),
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61 // Annotation<AACon> msaws = serv.getPort(new QName(namespace,
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62 // "ClustalWSPort"), Annotation.class);
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64 // List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
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65 // AAConTester.test_alignment_input));
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67 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
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70 List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
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71 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
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72 + File.separator + "TO1381.fasta.aln"));
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75 System.out.println("Pres: " + msaws.getPresets().getPresets());
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76 String jobId = msaws.analize(fsl);
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77 System.out.println("J: " + jobId);
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78 ScoreManager result = msaws.getAnnotation(jobId);
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79 assertNotNull(result);
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80 assertEquals(result.asSet().size(), 1);
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82 assertEquals(result.asSet().iterator().next().getMethod(),
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83 ConservationMethod.SHENKIN.toString());
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84 List<Float> scores = result.asSet().iterator().next().getScores();
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85 assertNotNull(scores);
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86 assertEquals(scores.size(), 568);
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89 PresetManager<AACon> presets = msaws.getPresets();
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90 jobId = msaws.presetAnalize(fsl,
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91 presets.getPresetByName("Quick conservation"));
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92 result = msaws.getAnnotation(jobId);
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93 assertNotNull(result);
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94 assertEquals(result.asSet().size(), 13);
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96 jobId = msaws.presetAnalize(fsl,
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97 presets.getPresetByName("Slow conservation"));
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98 result = msaws.getAnnotation(jobId);
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99 assertNotNull(result);
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100 assertEquals(result.asSet().size(), 5);
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102 jobId = msaws.presetAnalize(fsl,
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103 presets.getPresetByName("Complete conservation"));
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104 result = msaws.getAnnotation(jobId);
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105 assertNotNull(result);
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106 assertEquals(result.asSet().size(), 18);
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108 } catch (UnsupportedRuntimeException e) {
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109 e.printStackTrace();
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110 fail(e.getMessage());
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111 } catch (LimitExceededException e) {
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112 e.printStackTrace();
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113 fail(e.getMessage());
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114 } catch (JobSubmissionException e) {
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115 e.printStackTrace();
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116 fail(e.getMessage());
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117 } catch (ResultNotAvailableException e) {
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118 e.printStackTrace();
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119 fail(e.getMessage());
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120 } catch (WrongParameterException e) {
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121 e.printStackTrace();
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122 fail(e.getMessage());
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127 public void testPresetAnalize() throws FileNotFoundException, IOException {
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129 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
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132 List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
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133 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
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134 + File.separator + "TO1381.fasta.aln"));
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137 System.out.println("Pres: " + msaws.getPresets().getPresets());
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140 PresetManager<AACon> presets = msaws.getPresets();
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141 String jobId = msaws.presetAnalize(fsl,
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142 presets.getPresetByName("Quick conservation"));
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143 ScoreManager result = msaws.getAnnotation(jobId);
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144 assertNotNull(result);
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145 assertEquals(result.asSet().size(), 13);
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147 jobId = msaws.presetAnalize(fsl,
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148 presets.getPresetByName("Slow conservation"));
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149 result = msaws.getAnnotation(jobId);
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150 assertNotNull(result);
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151 assertEquals(result.asSet().size(), 5);
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153 jobId = msaws.presetAnalize(fsl,
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154 presets.getPresetByName("Complete conservation"));
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155 result = msaws.getAnnotation(jobId);
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156 assertNotNull(result);
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157 assertEquals(result.asSet().size(), 18);
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159 } catch (UnsupportedRuntimeException e) {
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160 e.printStackTrace();
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161 fail(e.getMessage());
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162 } catch (LimitExceededException e) {
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163 e.printStackTrace();
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164 fail(e.getMessage());
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165 } catch (JobSubmissionException e) {
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166 e.printStackTrace();
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167 fail(e.getMessage());
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168 } catch (ResultNotAvailableException e) {
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169 e.printStackTrace();
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170 fail(e.getMessage());
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171 } catch (WrongParameterException e) {
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172 e.printStackTrace();
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173 fail(e.getMessage());
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179 public void testCustomAnalize() throws FileNotFoundException, IOException {
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181 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
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184 List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
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185 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
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186 + File.separator + "TO1381.fasta.aln"));
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189 RunnerConfig<AACon> options = msaws.getRunnerOptions();
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190 // System.out.println(options.getArguments());
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193 options.getArgument("Calculation method").setDefaultValue("SMERFS");
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194 // options.getArgument("SMERFS Column Scoring Method")
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195 // .setDefaultValue("MAX_SCORE");
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196 // options.getArgument("SMERFS Gap Threshhold").setDefaultValue("1");
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197 String jobId = msaws.customAnalize(fsl, options.getArguments());
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198 ScoreManager result = msaws.getAnnotation(jobId);
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199 assertNotNull(result);
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200 assertEquals(result.asSet().size(), 1);
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201 assertEquals(result.asSet().iterator().next().getScores().get(0),
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204 options.getArgument("Calculation method").setDefaultValue("SMERFS");
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205 options.removeArgument("Normalize");
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206 System.out.println(options);
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207 jobId = msaws.customAnalize(fsl, options.getArguments());
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208 result = msaws.getAnnotation(jobId);
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209 assertNotNull(result);
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210 assertEquals(result.asSet().size(), 1);
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211 assertEquals(result.asSet().iterator().next().getScores().get(0),
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214 } catch (WrongParameterException e) {
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215 e.printStackTrace();
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216 fail(e.getMessage());
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217 } catch (UnsupportedRuntimeException e) {
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218 e.printStackTrace();
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219 fail(e.getMessage());
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220 } catch (LimitExceededException e) {
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221 e.printStackTrace();
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222 fail(e.getMessage());
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223 } catch (JobSubmissionException e) {
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224 e.printStackTrace();
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225 fail(e.getMessage());
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226 } catch (ResultNotAvailableException e) {
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227 e.printStackTrace();
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228 fail(e.getMessage());
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