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