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.getFirstSequenceScores().getNumberOfScores(), 1);\r
  81 \r
  82                         assertEquals(result.getFirstSequenceScores().getFirstScore()\r
  83                                         .getMethod(), ConservationMethod.SHENKIN);\r
  84                         List<Float> scores = result.getFirstSequenceScores()\r
  85                                         .getFirstScore().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.getFirstSequenceScores().getNumberOfScores(),\r
  96                                         13);\r
  97 \r
  98                         jobId = msaws.presetAnalize(fsl,\r
  99                                         presets.getPresetByName("Slow conservation"));\r
 100                         result = msaws.getAnnotation(jobId);\r
 101                         assertNotNull(result);\r
 102                         assertEquals(result.getFirstSequenceScores().getNumberOfScores(), 5);\r
 103 \r
 104                         jobId = msaws.presetAnalize(fsl,\r
 105                                         presets.getPresetByName("Complete conservation"));\r
 106                         result = msaws.getAnnotation(jobId);\r
 107                         assertNotNull(result);\r
 108                         assertEquals(result.getFirstSequenceScores().getNumberOfScores(),\r
 109                                         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         @Test\r
 130         public void testPresetAnalize() throws FileNotFoundException, IOException {\r
 131 \r
 132                 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()\r
 133                                 + File.separator;\r
 134 \r
 135                 List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(\r
 136                                 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"\r
 137                                                 + File.separator + "TO1381.fasta.aln"));\r
 138 \r
 139                 try {\r
 140                         System.out.println("Pres: " + msaws.getPresets().getPresets());\r
 141 \r
 142                         // Using presets\r
 143                         PresetManager<AACon> presets = msaws.getPresets();\r
 144                         String jobId = msaws.presetAnalize(fsl,\r
 145                                         presets.getPresetByName("Quick conservation"));\r
 146                         ScoreManager result = msaws.getAnnotation(jobId);\r
 147                         assertNotNull(result);\r
 148                         assertEquals(result.getFirstSequenceScores().getNumberOfScores(),\r
 149                                         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.getFirstSequenceScores().getNumberOfScores(), 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.getFirstSequenceScores().getNumberOfScores(),\r
 162                                         18);\r
 163 \r
 164                 } catch (UnsupportedRuntimeException e) {\r
 165                         e.printStackTrace();\r
 166                         fail(e.getMessage());\r
 167                 } catch (LimitExceededException e) {\r
 168                         e.printStackTrace();\r
 169                         fail(e.getMessage());\r
 170                 } catch (JobSubmissionException e) {\r
 171                         e.printStackTrace();\r
 172                         fail(e.getMessage());\r
 173                 } catch (ResultNotAvailableException e) {\r
 174                         e.printStackTrace();\r
 175                         fail(e.getMessage());\r
 176                 } catch (WrongParameterException e) {\r
 177                         e.printStackTrace();\r
 178                         fail(e.getMessage());\r
 179                 }\r
 180 \r
 181         }\r
 182 \r
 183         @Test\r
 184         public void testCustomAnalize() throws FileNotFoundException, IOException {\r
 185 \r
 186                 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()\r
 187                                 + File.separator;\r
 188 \r
 189                 List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(\r
 190                                 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"\r
 191                                                 + File.separator + "TO1381.fasta.aln"));\r
 192 \r
 193                 // Using options\r
 194                 RunnerConfig<AACon> options = msaws.getRunnerOptions();\r
 195                 // System.out.println(options.getArguments());\r
 196 \r
 197                 try {\r
 198                         options.getArgument("Calculation method").setDefaultValue("SMERFS");\r
 199                         // options.getArgument("SMERFS Column Scoring Method")\r
 200                         // .setDefaultValue("MAX_SCORE");\r
 201                         // options.getArgument("SMERFS Gap Threshhold").setDefaultValue("1");\r
 202                         String jobId = msaws.customAnalize(fsl, options.getArguments());\r
 203                         ScoreManager result = msaws.getAnnotation(jobId);\r
 204                         assertNotNull(result);\r
 205                         assertEquals(result.getFirstSequenceScores().getNumberOfScores(), 1);\r
 206                         assertEquals(result.getFirstSequenceScores().getFirstScore()\r
 207                                         .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.getFirstSequenceScores().getNumberOfScores(), 1);\r
 216                         assertEquals(result.getFirstSequenceScores().getFirstScore()\r
 217                                         .getScores().get(0), 0.401f);\r
 218 \r
 219                 } catch (WrongParameterException e) {\r
 220                         e.printStackTrace();\r
 221                         fail(e.getMessage());\r
 222                 } catch (UnsupportedRuntimeException e) {\r
 223                         e.printStackTrace();\r
 224                         fail(e.getMessage());\r
 225                 } catch (LimitExceededException e) {\r
 226                         e.printStackTrace();\r
 227                         fail(e.getMessage());\r
 228                 } catch (JobSubmissionException e) {\r
 229                         e.printStackTrace();\r
 230                         fail(e.getMessage());\r
 231                 } catch (ResultNotAvailableException e) {\r
 232                         e.printStackTrace();\r
 233                         fail(e.getMessage());\r
 234                 }\r
 235         }\r
 236 }\r