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