testsrc/compbio/ws/client/TestRNAalifoldWS.java

   1         package compbio.ws.client;\r
   2 \r
   3 import static org.testng.Assert.assertNotNull;\r
   4 import static org.testng.Assert.fail;\r
   5 \r
   6 import java.io.FileInputStream;\r
   7 import java.io.FileNotFoundException;\r
   8 import java.io.IOException;\r
   9 import java.io.OutputStreamWriter;\r
  10 import java.io.Writer;\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.Alignment;\r
  23 import compbio.data.sequence.ClustalAlignmentUtil;\r
  24 import compbio.data.sequence.FastaSequence;\r
  25 import compbio.data.sequence.RNAStructScoreManager;\r
  26 import compbio.data.sequence.ScoreManager;\r
  27 import compbio.data.sequence.UnknownFileFormatException;\r
  28 import compbio.metadata.AllTestSuit;\r
  29 import compbio.metadata.JobSubmissionException;\r
  30 import compbio.metadata.LimitExceededException;\r
  31 import compbio.metadata.Option;\r
  32 import compbio.metadata.ResultNotAvailableException;\r
  33 import compbio.metadata.UnsupportedRuntimeException;\r
  34 import compbio.metadata.WrongParameterException;\r
  35 import compbio.runner.structure.RNAalifold;\r
  36 import compbio.ws.server.RNAalifoldWS;\r
  37 \r
  38 \r
  39 public class TestRNAalifoldWS {\r
  40         \r
  41 //      SequenceAnnotation<RNAalifoldWS> foldws;\r
  42         RNAalifoldWS foldws;\r
  43         \r
  44         @BeforeTest(groups = {AllTestSuit.test_group_webservices})\r
  45         void initConnection() {\r
  46                 \r
  47                 try {\r
  48                         JABAService client = Jws2Client.connect(\r
  49                                         "http://localhost:8080/jabaws", Services.RNAalifoldWS);\r
  50                         foldws = (RNAalifoldWS) client;\r
  51                 } catch (ConnectException e) {\r
  52                         e.printStackTrace();\r
  53                         fail(e.getMessage());\r
  54                 } catch (WebServiceException e) {\r
  55                         e.printStackTrace();\r
  56                         fail(e.getMessage());\r
  57                 }\r
  58         }\r
  59 \r
  60         \r
  61         @Test(groups = {AllTestSuit.test_group_webservices})\r
  62         public void testFold() throws FileNotFoundException, IOException,\r
  63                         UnknownFileFormatException {\r
  64                 \r
  65 //              String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()\r
  66 //                              + File.separator;\r
  67                 \r
  68                 Alignment aln = ClustalAlignmentUtil.readClustalFile(new FileInputStream(\r
  69                                 AllTestSuit.test_input_aln));\r
  70                 \r
  71                 List<FastaSequence> fsl = aln.getSequences();\r
  72                 \r
  73                 try {\r
  74                         List<Option<RNAalifold>> options  = new ArrayList<Option<RNAalifold>>();\r
  75                         options.add(foldws.getRunnerOptions().getArgumentByOptionName("--mis"));\r
  76                         options.add(foldws.getRunnerOptions().getArgumentByOptionName("-p"));\r
  77                         options.add(foldws.getRunnerOptions().getArgumentByOptionName("--MEA"));\r
  78                         \r
  79 //                      System.out.println("TestRNAalifoldWS: print options: " + options.toString());\r
  80                         \r
  81                         String jobId = foldws.customAnalize(fsl, options);\r
  82                         System.out.println("J: " + jobId);\r
  83                         \r
  84                         Writer stdout = new OutputStreamWriter(System.out);\r
  85                         \r
  86                         System.out.println("results class: " + foldws.getAnnotation(jobId).getClass().getName());\r
  87                         RNAStructScoreManager result = (RNAStructScoreManager)foldws.getAnnotation(jobId);\r
  88                         \r
  89                         \r
  90                         result.writeOut(stdout);\r
  91                         System.out.println("fold results: \n" + result.toString());\r
  92                         assertNotNull(result);\r
  93                         \r
  94                 } catch (UnsupportedRuntimeException e) {\r
  95                         e.printStackTrace();\r
  96                         fail(e.getMessage());\r
  97                 } catch (LimitExceededException e) {\r
  98                         e.printStackTrace();\r
  99                         fail(e.getMessage());\r
 100                 } catch (JobSubmissionException e) {\r
 101                         e.printStackTrace();\r
 102                         fail(e.getMessage());\r
 103                 } catch (ResultNotAvailableException e) {\r
 104                         e.printStackTrace();\r
 105                         fail(e.getMessage());\r
 106                 } catch (WrongParameterException e) {\r
 107                         e.printStackTrace();\r
 108                         fail(e.getMessage());\r
 109                 }\r
 110         }\r
 111 }\r
 112         \r
 113 \r
 114 \r