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