--- /dev/null
+package compbio.ws.client;\r
+\r
+import static org.testng.Assert.assertEquals;\r
+import static org.testng.Assert.assertNotNull;\r
+import static org.testng.Assert.fail;\r
+import static org.testng.Assert.assertTrue;\r
+import java.io.File;\r
+import java.io.FileInputStream;\r
+import java.io.FileNotFoundException;\r
+import java.io.IOException;\r
+import java.net.ConnectException;\r
+import java.util.ArrayList;\r
+import java.util.List;\r
+\r
+import javax.xml.ws.WebServiceException;\r
+\r
+import org.testng.annotations.BeforeTest;\r
+import org.testng.annotations.Test;\r
+\r
+import compbio.data.msa.JABAService;\r
+import compbio.data.msa.SequenceAnnotation;\r
+import compbio.data.sequence.ConservationMethod;\r
+import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.ScoreManager;\r
+import compbio.data.sequence.SequenceUtil;\r
+import compbio.metadata.AllTestSuit;\r
+import compbio.metadata.JobSubmissionException;\r
+import compbio.metadata.LimitExceededException;\r
+import compbio.metadata.Option;\r
+import compbio.metadata.Preset;\r
+import compbio.metadata.PresetManager;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.metadata.RunnerConfig;\r
+import compbio.metadata.UnsupportedRuntimeException;\r
+import compbio.metadata.WrongParameterException;\r
+import compbio.runner.conservation.AACon;\r
+import compbio.util.SysPrefs;\r
+\r
+public class TestAAConWS {\r
+\r
+ SequenceAnnotation<AACon> msaws;\r
+\r
+ @BeforeTest(groups = {AllTestSuit.test_group_webservices})\r
+ void initConnection() {\r
+ /*\r
+ * URL url = null; try { url = new\r
+ * URL("http://localhost:8080/jabaws/AAConWS?wsdl"); } catch\r
+ * (MalformedURLException e) { e.printStackTrace();\r
+ * fail(e.getLocalizedMessage()); } String namespace =\r
+ * "http://msa.data.compbio/01/12/2010/"; QName qname = new\r
+ * QName(namespace, "AAConWS"); Service serv = Service.create(url,\r
+ * qname); msaws = serv.getPort(new QName(namespace, "AAConWSPort"),\r
+ * Annotation.class);\r
+ */try {\r
+ JABAService client = Jws2Client.connect(\r
+ "http://localhost:8080/jabaws", Services.AAConWS);\r
+ msaws = (SequenceAnnotation<AACon>) client;\r
+ } catch (ConnectException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (WebServiceException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ }\r
+\r
+ @Test(groups = {AllTestSuit.test_group_webservices})\r
+ public void testAnalize() throws FileNotFoundException, IOException {\r
+\r
+ /*\r
+ * MsaWS msaws = serv.getPort(new QName(\r
+ * "http://msa.data.compbio/01/01/2010/", "ClustalWSPort"),\r
+ * MsaWS.class);\r
+ */\r
+ // Annotation<AACon> msaws = serv.getPort(new QName(namespace,\r
+ // "ClustalWSPort"), Annotation.class);\r
+\r
+ // List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(\r
+ // AAConTester.test_alignment_input));\r
+\r
+ String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()\r
+ + File.separator;\r
+\r
+ List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(\r
+ CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"\r
+ + File.separator + "TO1381.fasta.aln"));\r
+\r
+ try {\r
+ System.out.println("Pres: " + msaws.getPresets().getPresets());\r
+ String jobId = msaws.analize(fsl);\r
+ System.out.println("J: " + jobId);\r
+ ScoreManager result = msaws.getAnnotation(jobId);\r
+ assertNotNull(result);\r
+ assertEquals(result.asSet().size(), 1);\r
+\r
+ assertEquals(result.asSet().iterator().next().getMethod(),\r
+ ConservationMethod.SHENKIN.toString());\r
+ List<Float> scores = result.asSet().iterator().next().getScores();\r
+ assertNotNull(scores);\r
+ assertEquals(scores.size(), 568);\r
+\r
+ // Using presets\r
+ PresetManager<AACon> presets = msaws.getPresets();\r
+ jobId = msaws.presetAnalize(fsl,\r
+ presets.getPresetByName("Quick conservation"));\r
+ result = msaws.getAnnotation(jobId);\r
+ assertNotNull(result);\r
+ assertEquals(result.asSet().size(), 13);\r
+\r
+ jobId = msaws.presetAnalize(fsl,\r
+ presets.getPresetByName("Slow conservation"));\r
+ result = msaws.getAnnotation(jobId);\r
+ assertNotNull(result);\r
+ assertEquals(result.asSet().size(), 5);\r
+\r
+ jobId = msaws.presetAnalize(fsl,\r
+ presets.getPresetByName("Complete conservation"));\r
+ result = msaws.getAnnotation(jobId);\r
+ assertNotNull(result);\r
+ assertEquals(result.asSet().size(), 18);\r
+\r
+ } catch (UnsupportedRuntimeException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (LimitExceededException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (WrongParameterException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+\r
+ }\r
+ @Test(groups = {AllTestSuit.test_group_webservices})\r
+ public void testRecoverArgsForPreset() throws Exception {\r
+ PresetManager<AACon> presets = msaws.getPresets();\r
+ for (Preset<AACon> preset:presets.getPresets())\r
+ {\r
+ List<Option<AACon>> args = preset.getArguments(msaws.getRunnerOptions());\r
+ List opts = preset.getOptions();\r
+ assertTrue(args.size()>=opts.size(),"Couldn't recover all Option items for preset "+preset.getName());\r
+ }\r
+ }\r
+ @Test(groups = {AllTestSuit.test_group_webservices})\r
+ public void testPresetAnalize() throws FileNotFoundException, IOException {\r
+\r
+ String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()\r
+ + File.separator;\r
+\r
+ List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(\r
+ CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"\r
+ + File.separator + "TO1381.fasta.aln"));\r
+\r
+ try {\r
+ System.out.println("Pres: " + msaws.getPresets().getPresets());\r
+\r
+ // Using presets\r
+ PresetManager<AACon> presets = msaws.getPresets();\r
+ String jobId = msaws.presetAnalize(fsl,\r
+ presets.getPresetByName("Quick conservation"));\r
+ ScoreManager result = msaws.getAnnotation(jobId);\r
+ assertNotNull(result);\r
+ assertEquals(result.asSet().size(), 13);\r
+\r
+ jobId = msaws.presetAnalize(fsl,\r
+ presets.getPresetByName("Slow conservation"));\r
+ result = msaws.getAnnotation(jobId);\r
+ assertNotNull(result);\r
+ assertEquals(result.asSet().size(), 5);\r
+\r
+ jobId = msaws.presetAnalize(fsl,\r
+ presets.getPresetByName("Complete conservation"));\r
+ result = msaws.getAnnotation(jobId);\r
+ assertNotNull(result);\r
+ assertEquals(result.asSet().size(), 18);\r
+\r
+ } catch (UnsupportedRuntimeException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (LimitExceededException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (WrongParameterException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+\r
+ }\r
+\r
+ @Test(groups = {AllTestSuit.test_group_webservices})\r
+ public void testCustomAnalize() throws FileNotFoundException, IOException {\r
+\r
+ String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()\r
+ + File.separator;\r
+\r
+ List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(\r
+ CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"\r
+ + File.separator + "TO1381.fasta.aln"));\r
+\r
+ // Using options\r
+ RunnerConfig<AACon> options = msaws.getRunnerOptions();\r
+ // System.out.println(options.getArguments());\r
+\r
+ try {\r
+ List<Option<AACon>> args = new ArrayList<Option<AACon>>();\r
+ Option<AACon> arg,normarg;\r
+ args.add(arg=options.getArgument("SMERFS"));\r
+ args.add(normarg=options.getArgument("Normalize"));\r
+ arg.setValue(arg.getPossibleValues().get(0));\r
+ // options.getArgument("SMERFS Column Scoring Method")\r
+ // .setDefaultValue("MAX_SCORE");\r
+ // options.getArgument("SMERFS Gap Threshhold").setDefaultValue("1");\r
+ String jobId = msaws.customAnalize(fsl, args);\r
+ ScoreManager result = msaws.getAnnotation(jobId);\r
+ assertNotNull(result);\r
+ assertEquals(result.asSet().size(), 1);\r
+ assertEquals(result.asSet().iterator().next().getScores().get(0),\r
+ 0.698f);\r
+ args.remove(normarg); // remove normalization argument\r
+ // System.out.println(options);\r
+ jobId = msaws.customAnalize(fsl, args);\r
+ result = msaws.getAnnotation(jobId);\r
+ assertNotNull(result);\r
+ assertEquals(result.asSet().size(), 1);\r
+ assertEquals(result.asSet().iterator().next().getScores().get(0),\r
+ 0.401f);\r
+\r
+ } catch (WrongParameterException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (UnsupportedRuntimeException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (LimitExceededException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ }\r
+}\r
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