testsrc/compbio/ws/client/TestRNAalifoldWS.java

   1         package compbio.ws.client;
   2
   3 import compbio.metadata.AllTestSuit;
   4 import static org.testng.Assert.assertEquals;
   5 import static org.testng.Assert.assertNotNull;
   6 import static org.testng.Assert.fail;
   7
   8 import java.io.File;
   9 import java.io.FileInputStream;
  10 import java.io.FileNotFoundException;
  11 import java.io.IOException;
  12 import java.net.ConnectException;
  13 import java.util.ArrayList;
  14 import java.util.List;
  15
  16 import javax.xml.ws.WebServiceException;
  17
  18 import org.testng.annotations.BeforeTest;
  19 import org.testng.annotations.Test;
  20
  21 import compbio.data.msa.FoldWS;
  22 import compbio.data.msa.JABAService;
  23 import compbio.data.msa.SequenceAnnotation;
  24 import compbio.data.sequence.Alignment;
  25 import compbio.data.sequence.RNAStruct;
  26 import compbio.data.sequence.ClustalAlignmentUtil;
  27 import compbio.data.sequence.ConservationMethod;
  28 import compbio.data.sequence.FastaSequence;
  29 import compbio.data.sequence.ScoreManager;
  30 import compbio.data.sequence.SequenceUtil;
  31 import compbio.data.sequence.UnknownFileFormatException;
  32 import compbio.metadata.AllTestSuit;
  33 import compbio.metadata.JobSubmissionException;
  34 import compbio.metadata.LimitExceededException;
  35 import compbio.metadata.Option;
  36 import compbio.metadata.PresetManager;
  37 import compbio.metadata.ResultNotAvailableException;
  38 import compbio.metadata.RunnerConfig;
  39 import compbio.metadata.UnsupportedRuntimeException;
  40 import compbio.metadata.WrongParameterException;
  41 import compbio.runner.conservation.AACon;
  42 import compbio.util.SysPrefs;
  43 import compbio.ws.server.RNAalifoldWS;
  44
  45
  46 public class TestRNAalifoldWS {
  47
  48         SequenceAnnotation<RNAalifoldWS> foldws;
  49
  50         @BeforeTest(groups = {AllTestSuit.test_group_webservices})
  51         void initConnection() {
  52
  53                 try {
  54                         JABAService client = Jws2Client.connect(
  55                                         "http://localhost:8080/jabaws", Services.RNAalifoldWS);
  56                         foldws = (SequenceAnnotation<RNAalifoldWS>) client;
  57                 } catch (ConnectException e) {
  58                         e.printStackTrace();
  59                         fail(e.getMessage());
  60                 } catch (WebServiceException e) {
  61                         e.printStackTrace();
  62                         fail(e.getMessage());
  63                 }
  64         }
  65
  66
  67         @Test(groups = {AllTestSuit.test_group_webservices})
  68         public void testFold() throws FileNotFoundException, IOException,
  69                         UnknownFileFormatException {
  70
  71 //              String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
  72 //                              + File.separator;
  73
  74                 Alignment aln = ClustalAlignmentUtil.readClustalFile(new FileInputStream(
  75                                 AllTestSuit.test_input_aln));
  76
  77                 List<FastaSequence> fsl = aln.getSequences();
  78
  79                 try {
  80                         List<Option<RNAalifoldWS>> options  = new ArrayList<Option<RNAalifoldWS>>();
  81                         options.add(foldws.getRunnerOptions().getArgumentByOptionName("--mis"));
  82                         options.add(foldws.getRunnerOptions().getArgumentByOptionName("-p"));
  83                         options.add(foldws.getRunnerOptions().getArgumentByOptionName("--MEA"));
  84
  85                         System.out.println("TestRNAalifoldWS: print options: " + options.toString());
  86
  87                         String jobId = foldws.customAnalize(fsl, options);
  88                         System.out.println("J: " + jobId);
  89                         ScoreManager result = foldws.getAnnotation(jobId);
  90                         System.out.println("fold results: \n" + result.asRNAStruct().toString());
  91                         assertNotNull(result);
  92
  93                 } catch (UnsupportedRuntimeException e) {
  94                         e.printStackTrace();
  95                         fail(e.getMessage());
  96                 } catch (LimitExceededException e) {
  97                         e.printStackTrace();
  98                         fail(e.getMessage());
  99                 } catch (JobSubmissionException e) {
 100                         e.printStackTrace();
 101                         fail(e.getMessage());
 102                 } catch (ResultNotAvailableException e) {
 103                         e.printStackTrace();
 104                         fail(e.getMessage());
 105                 } catch (WrongParameterException e) {
 106                         e.printStackTrace();
 107                         fail(e.getMessage());
 108                 }
 109         }
 110 }
 111
 112
 113