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.net.URL;\r
  12 import java.util.HashSet;\r
  13 import java.util.List;\r
  14 \r
  15 import javax.xml.namespace.QName;\r
  16 import javax.xml.ws.Service;\r
  17 \r
  18 import org.testng.annotations.Test;\r
  19 \r
  20 import compbio.conservation.Method;\r
  21 import compbio.data.msa.Annotation;\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.ResultNotAvailableException;\r
  28 import compbio.metadata.UnsupportedRuntimeException;\r
  29 import compbio.util.SysPrefs;\r
  30 import compbio.ws.server.AAConWS;\r
  31 \r
  32 public class TestAAConWS {\r
  33 \r
  34         @Test\r
  35         public void test() throws FileNotFoundException, IOException {\r
  36 \r
  37                 URL url = new URL("http://localhost:8080/jabaws/AAConWS?wsdl");\r
  38                 String namespace = "http://msa.data.compbio/01/12/2010/";\r
  39                 QName qname = new QName(namespace, "AAConWS");\r
  40                 Service serv = Service.create(url, qname);\r
  41                 /*\r
  42                  * MsaWS msaws = serv.getPort(new QName(\r
  43                  * "http://msa.data.compbio/01/01/2010/", "ClustalWSPort"),\r
  44                  * MsaWS.class);\r
  45                  */\r
  46                 // Annotation<AACon> msaws = serv.getPort(new QName(namespace,\r
  47                 // "ClustalWSPort"), Annotation.class);\r
  48 \r
  49                 Annotation<AAConWS> msaws = serv.getPort(new QName(namespace,\r
  50                                 "AAConWSPort"), Annotation.class);\r
  51 \r
  52                 // List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(\r
  53                 // AAConTester.test_alignment_input));\r
  54 \r
  55                 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()\r
  56                                 + File.separator;\r
  57 \r
  58                 List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(\r
  59                                 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"\r
  60                                                 + File.separator + "TO1381.fasta.aln"));\r
  61 \r
  62                 try {\r
  63                         System.out.println("Pres: "\r
  64                                         + msaws.getPresets().getPresets().get(0));\r
  65                         String jobId = msaws.analize(fsl);\r
  66                         System.out.println("J: " + jobId);\r
  67                         HashSet<Score> result = msaws.getConservation(jobId);\r
  68                         assertNotNull(result);\r
  69                         assertEquals(result.size(), 1);\r
  70                         assertEquals(result.iterator().next().getMethod(), Method.SHENKIN);\r
  71                         List<Float> scores = result.iterator().next().getScores();\r
  72                         assertNotNull(scores);\r
  73                         assertEquals(scores.size(), 568);\r
  74 \r
  75                 } catch (UnsupportedRuntimeException e) {\r
  76                         e.printStackTrace();\r
  77                         fail(e.getMessage());\r
  78                 } catch (LimitExceededException e) {\r
  79                         e.printStackTrace();\r
  80                         fail(e.getMessage());\r
  81                 } catch (JobSubmissionException e) {\r
  82                         e.printStackTrace();\r
  83                         fail(e.getMessage());\r
  84                 } catch (ResultNotAvailableException e) {\r
  85                         e.printStackTrace();\r
  86                         fail(e.getMessage());\r
  87                 }\r
  88 \r
  89         }\r
  90 }\r