testsrc/compbio/ws/client/TestAAConWS.java

   1 package compbio.ws.client;\r
   2 \r
   3 import static org.testng.Assert.assertEquals;\r
   4 import static org.testng.Assert.assertNotNull;\r
   5 import static org.testng.Assert.fail;\r
   6 \r
   7 import java.io.File;\r
   8 import java.io.FileInputStream;\r
   9 import java.io.FileNotFoundException;\r
  10 import java.io.IOException;\r
  11 import java.net.ConnectException;\r
  12 import java.util.List;\r
  13 \r
  14 import javax.xml.ws.WebServiceException;\r
  15 \r
  16 import org.testng.annotations.BeforeTest;\r
  17 import org.testng.annotations.Test;\r
  18 \r
  19 import compbio.data.msa.JABAService;\r
  20 import compbio.data.msa.SequenceAnnotation;\r
  21 import compbio.data.sequence.ConservationMethod;\r
  22 import compbio.data.sequence.FastaSequence;\r
  23 import compbio.data.sequence.ScoreManager;\r
  24 import compbio.data.sequence.SequenceUtil;\r
  25 import compbio.metadata.AllTestSuit;\r
  26 import compbio.metadata.JobSubmissionException;\r
  27 import compbio.metadata.LimitExceededException;\r
  28 import compbio.metadata.PresetManager;\r
  29 import compbio.metadata.ResultNotAvailableException;\r
  30 import compbio.metadata.RunnerConfig;\r
  31 import compbio.metadata.UnsupportedRuntimeException;\r
  32 import compbio.metadata.WrongParameterException;\r
  33 import compbio.runner.conservation.AACon;\r
  34 import compbio.util.SysPrefs;\r
  35 \r
  36 public class TestAAConWS {\r
  37 \r
  38         SequenceAnnotation<AACon> msaws;\r
  39 \r
  40         @BeforeTest(groups = {AllTestSuit.test_group_webservices})\r
  41         void initConnection() {\r
  42                 /*\r
  43                  * URL url = null; try { url = new\r
  44                  * URL("http://localhost:8080/jabaws/AAConWS?wsdl"); } catch\r
  45                  * (MalformedURLException e) { e.printStackTrace();\r
  46                  * fail(e.getLocalizedMessage()); } String namespace =\r
  47                  * "http://msa.data.compbio/01/12/2010/"; QName qname = new\r
  48                  * QName(namespace, "AAConWS"); Service serv = Service.create(url,\r
  49                  * qname); msaws = serv.getPort(new QName(namespace, "AAConWSPort"),\r
  50                  * Annotation.class);\r
  51                  */try {\r
  52                         JABAService client = Jws2Client.connect(\r
  53                                         "http://localhost:8080/jabaws", Services.AAConWS);\r
  54                         msaws = (SequenceAnnotation<AACon>) client;\r
  55                 } catch (ConnectException e) {\r
  56                         e.printStackTrace();\r
  57                         fail(e.getMessage());\r
  58                 } catch (WebServiceException e) {\r
  59                         e.printStackTrace();\r
  60                         fail(e.getMessage());\r
  61                 }\r
  62         }\r
  63 \r
  64         @Test(groups = {AllTestSuit.test_group_webservices})\r
  65         public void testAnalize() throws FileNotFoundException, IOException {\r
  66 \r
  67                 /*\r
  68                  * MsaWS msaws = serv.getPort(new QName(\r
  69                  * "http://msa.data.compbio/01/01/2010/", "ClustalWSPort"),\r
  70                  * MsaWS.class);\r
  71                  */\r
  72                 // Annotation<AACon> msaws = serv.getPort(new QName(namespace,\r
  73                 // "ClustalWSPort"), Annotation.class);\r
  74 \r
  75                 // List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(\r
  76                 // AAConTester.test_alignment_input));\r
  77 \r
  78                 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()\r
  79                                 + File.separator;\r
  80 \r
  81                 List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(\r
  82                                 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"\r
  83                                                 + File.separator + "TO1381.fasta.aln"));\r
  84 \r
  85                 try {\r
  86                         System.out.println("Pres: " + msaws.getPresets().getPresets());\r
  87                         String jobId = msaws.analize(fsl);\r
  88                         System.out.println("J: " + jobId);\r
  89                         ScoreManager result = msaws.getAnnotation(jobId);\r
  90                         assertNotNull(result);\r
  91                         assertEquals(result.asSet().size(), 1);\r
  92 \r
  93                         assertEquals(result.asSet().iterator().next().getMethod(),\r
  94                                         ConservationMethod.SHENKIN.toString());\r
  95                         List<Float> scores = result.asSet().iterator().next().getScores();\r
  96                         assertNotNull(scores);\r
  97                         assertEquals(scores.size(), 568);\r
  98 \r
  99                         // Using presets\r
 100                         PresetManager<AACon> presets = msaws.getPresets();\r
 101                         jobId = msaws.presetAnalize(fsl,\r
 102                                         presets.getPresetByName("Quick conservation"));\r
 103                         result = msaws.getAnnotation(jobId);\r
 104                         assertNotNull(result);\r
 105                         assertEquals(result.asSet().size(), 13);\r
 106 \r
 107                         jobId = msaws.presetAnalize(fsl,\r
 108                                         presets.getPresetByName("Slow conservation"));\r
 109                         result = msaws.getAnnotation(jobId);\r
 110                         assertNotNull(result);\r
 111                         assertEquals(result.asSet().size(), 5);\r
 112 \r
 113                         jobId = msaws.presetAnalize(fsl,\r
 114                                         presets.getPresetByName("Complete conservation"));\r
 115                         result = msaws.getAnnotation(jobId);\r
 116                         assertNotNull(result);\r
 117                         assertEquals(result.asSet().size(), 18);\r
 118 \r
 119                 } catch (UnsupportedRuntimeException e) {\r
 120                         e.printStackTrace();\r
 121                         fail(e.getMessage());\r
 122                 } catch (LimitExceededException e) {\r
 123                         e.printStackTrace();\r
 124                         fail(e.getMessage());\r
 125                 } catch (JobSubmissionException e) {\r
 126                         e.printStackTrace();\r
 127                         fail(e.getMessage());\r
 128                 } catch (ResultNotAvailableException e) {\r
 129                         e.printStackTrace();\r
 130                         fail(e.getMessage());\r
 131                 } catch (WrongParameterException e) {\r
 132                         e.printStackTrace();\r
 133                         fail(e.getMessage());\r
 134                 }\r
 135 \r
 136         }\r
 137         @Test(groups = {AllTestSuit.test_group_webservices})\r
 138         public void testPresetAnalize() throws FileNotFoundException, IOException {\r
 139 \r
 140                 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()\r
 141                                 + File.separator;\r
 142 \r
 143                 List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(\r
 144                                 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"\r
 145                                                 + File.separator + "TO1381.fasta.aln"));\r
 146 \r
 147                 try {\r
 148                         System.out.println("Pres: " + msaws.getPresets().getPresets());\r
 149 \r
 150                         // Using presets\r
 151                         PresetManager<AACon> presets = msaws.getPresets();\r
 152                         String jobId = msaws.presetAnalize(fsl,\r
 153                                         presets.getPresetByName("Quick conservation"));\r
 154                         ScoreManager result = msaws.getAnnotation(jobId);\r
 155                         assertNotNull(result);\r
 156                         assertEquals(result.asSet().size(), 13);\r
 157 \r
 158                         jobId = msaws.presetAnalize(fsl,\r
 159                                         presets.getPresetByName("Slow conservation"));\r
 160                         result = msaws.getAnnotation(jobId);\r
 161                         assertNotNull(result);\r
 162                         assertEquals(result.asSet().size(), 5);\r
 163 \r
 164                         jobId = msaws.presetAnalize(fsl,\r
 165                                         presets.getPresetByName("Complete conservation"));\r
 166                         result = msaws.getAnnotation(jobId);\r
 167                         assertNotNull(result);\r
 168                         assertEquals(result.asSet().size(), 18);\r
 169 \r
 170                 } catch (UnsupportedRuntimeException e) {\r
 171                         e.printStackTrace();\r
 172                         fail(e.getMessage());\r
 173                 } catch (LimitExceededException e) {\r
 174                         e.printStackTrace();\r
 175                         fail(e.getMessage());\r
 176                 } catch (JobSubmissionException e) {\r
 177                         e.printStackTrace();\r
 178                         fail(e.getMessage());\r
 179                 } catch (ResultNotAvailableException e) {\r
 180                         e.printStackTrace();\r
 181                         fail(e.getMessage());\r
 182                 } catch (WrongParameterException e) {\r
 183                         e.printStackTrace();\r
 184                         fail(e.getMessage());\r
 185                 }\r
 186 \r
 187         }\r
 188 \r
 189         @Test(groups = {AllTestSuit.test_group_webservices})\r
 190         public void testCustomAnalize() throws FileNotFoundException, IOException {\r
 191 \r
 192                 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()\r
 193                                 + File.separator;\r
 194 \r
 195                 List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(\r
 196                                 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"\r
 197                                                 + File.separator + "TO1381.fasta.aln"));\r
 198 \r
 199                 // Using options\r
 200                 RunnerConfig<AACon> options = msaws.getRunnerOptions();\r
 201                 // System.out.println(options.getArguments());\r
 202 \r
 203                 try {\r
 204                         options.getArgument("Calculation method").setDefaultValue("SMERFS");\r
 205                         // options.getArgument("SMERFS Column Scoring Method")\r
 206                         // .setDefaultValue("MAX_SCORE");\r
 207                         // options.getArgument("SMERFS Gap Threshhold").setDefaultValue("1");\r
 208                         String jobId = msaws.customAnalize(fsl, options.getArguments());\r
 209                         ScoreManager result = msaws.getAnnotation(jobId);\r
 210                         assertNotNull(result);\r
 211                         assertEquals(result.asSet().size(), 1);\r
 212                         assertEquals(result.asSet().iterator().next().getScores().get(0),\r
 213                                         0.698f);\r
 214 \r
 215                         options.getArgument("Calculation method").setDefaultValue("SMERFS");\r
 216                         options.removeArgument("Normalize");\r
 217                         System.out.println(options);\r
 218                         jobId = msaws.customAnalize(fsl, options.getArguments());\r
 219                         result = msaws.getAnnotation(jobId);\r
 220                         assertNotNull(result);\r
 221                         assertEquals(result.asSet().size(), 1);\r
 222                         assertEquals(result.asSet().iterator().next().getScores().get(0),\r
 223                                         0.401f);\r
 224 \r
 225                 } catch (WrongParameterException e) {\r
 226                         e.printStackTrace();\r
 227                         fail(e.getMessage());\r
 228                 } catch (UnsupportedRuntimeException e) {\r
 229                         e.printStackTrace();\r
 230                         fail(e.getMessage());\r
 231                 } catch (LimitExceededException e) {\r
 232                         e.printStackTrace();\r
 233                         fail(e.getMessage());\r
 234                 } catch (JobSubmissionException e) {\r
 235                         e.printStackTrace();\r
 236                         fail(e.getMessage());\r
 237                 } catch (ResultNotAvailableException e) {\r
 238                         e.printStackTrace();\r
 239                         fail(e.getMessage());\r
 240                 }\r
 241         }\r
 242 }\r