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