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.io.Writer;
  13 import java.io.OutputStreamWriter;
  14 import java.net.ConnectException;
  15 import java.util.ArrayList;
  16 import java.util.List;
  17
  18 import javax.xml.ws.WebServiceException;
  19
  20 import org.testng.annotations.BeforeTest;
  21 import org.testng.annotations.Test;
  22
  23 import compbio.data.msa.FoldWS;
  24 import compbio.data.msa.JABAService;
  25 import compbio.data.msa.SequenceAnnotation;
  26 import compbio.data.sequence.Alignment;
  27 import compbio.data.sequence.ClustalAlignmentUtil;
  28 import compbio.data.sequence.ConservationMethod;
  29 import compbio.data.sequence.FastaSequence;
  30 import compbio.data.sequence.RNAStructScoreManager;
  31 import compbio.data.sequence.ScoreManager;
  32 import compbio.data.sequence.SequenceUtil;
  33 import compbio.data.sequence.UnknownFileFormatException;
  34 import compbio.metadata.AllTestSuit;
  35 import compbio.metadata.JobSubmissionException;
  36 import compbio.metadata.LimitExceededException;
  37 import compbio.metadata.Option;
  38 import compbio.metadata.PresetManager;
  39 import compbio.metadata.ResultNotAvailableException;
  40 import compbio.metadata.RunnerConfig;
  41 import compbio.metadata.UnsupportedRuntimeException;
  42 import compbio.metadata.WrongParameterException;
  43 import compbio.runner.conservation.AACon;
  44 import compbio.runner.structure.RNAalifold;
  45 import compbio.util.SysPrefs;
  46 import compbio.ws.server.RNAalifoldWS;
  47
  48
  49 public class TestRNAalifoldWS {
  50
  51         SequenceAnnotation<RNAalifoldWS> foldws;
  52 //      RNAalifoldWS foldws;
  53
  54         @BeforeTest(groups = {AllTestSuit.test_group_webservices})
  55         void initConnection() {
  56
  57                 try {
  58                         JABAService client = Jws2Client.connect(
  59                                         "http://localhost:8080/jabaws", Services.RNAalifoldWS);
  60 //                      foldws = (RNAalifoldWS) client;
  61                         foldws = (SequenceAnnotation<RNAalifoldWS>) client;
  62                 } catch (ConnectException e) {
  63                         e.printStackTrace();
  64                         fail(e.getMessage());
  65                 } catch (WebServiceException e) {
  66                         e.printStackTrace();
  67                         fail(e.getMessage());
  68                 }
  69         }
  70
  71
  72         @Test(groups = {AllTestSuit.test_group_webservices})
  73         public void testFold() throws FileNotFoundException, IOException,
  74                         UnknownFileFormatException {
  75
  76
  77 //              String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
  78 //                              + File.separator;
  79
  80                 Alignment aln = ClustalAlignmentUtil.readClustalFile(new FileInputStream(
  81                                 AllTestSuit.test_input_aln));
  82
  83                 List<FastaSequence> fsl = aln.getSequences();
  84
  85                 try {
  86                         List<Option<RNAalifoldWS>> options  = new ArrayList<Option<RNAalifoldWS>>();
  87                         options.add(foldws.getRunnerOptions().getArgumentByOptionName("--mis"));
  88                         options.add(foldws.getRunnerOptions().getArgumentByOptionName("-p"));
  89                         options.add(foldws.getRunnerOptions().getArgumentByOptionName("--MEA"));
  90
  91                         System.out.println("TestRNAalifoldWS: print options: " + options.toString());
  92
  93                         String jobId = foldws.customAnalize(fsl, options);
  94                         System.out.println("J: " + jobId);
  95                         RNAStructScoreManager result = (RNAStructScoreManager)foldws.getAnnotation(jobId);
  96
  97
  98                         // standard and RNAStruct specific ways of formatting scoremanager
  99                         System.out.println("fold results: \n" + result.toString());
 100
 101                         Writer writer = new OutputStreamWriter(System.out);
 102                         result.writeOut(writer);
 103
 104                         assertNotNull(result);
 105
 106                 } catch (UnsupportedRuntimeException e) {
 107                         e.printStackTrace();
 108                         fail(e.getMessage());
 109                 } catch (LimitExceededException e) {
 110                         e.printStackTrace();
 111                         fail(e.getMessage());
 112                 } catch (JobSubmissionException e) {
 113                         e.printStackTrace();
 114                         fail(e.getMessage());
 115                 } catch (ResultNotAvailableException e) {
 116                         e.printStackTrace();
 117                         fail(e.getMessage());
 118                 } catch (WrongParameterException e) {
 119                         e.printStackTrace();
 120                         fail(e.getMessage());
 121                 }
 122         }
 123 }
 124
 125
 126