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