1 package compbio.ws.client;
3 import static org.testng.Assert.assertNotNull;
4 import static org.testng.Assert.fail;
6 import java.io.FileInputStream;
7 import java.io.FileNotFoundException;
8 import java.io.IOException;
9 import java.io.OutputStreamWriter;
10 import java.io.Writer;
11 import java.net.ConnectException;
12 import java.util.ArrayList;
13 import java.util.List;
15 import javax.xml.ws.WebServiceException;
17 import org.testng.annotations.BeforeTest;
18 import org.testng.annotations.Test;
20 import compbio.data.msa.JABAService;
21 import compbio.data.msa.SequenceAnnotation;
22 import compbio.data.sequence.Alignment;
23 import compbio.data.sequence.ClustalAlignmentUtil;
24 import compbio.data.sequence.FastaSequence;
25 import compbio.data.sequence.RNAStructScoreManager;
26 import compbio.data.sequence.UnknownFileFormatException;
27 import compbio.metadata.AllTestSuit;
28 import compbio.metadata.JobSubmissionException;
29 import compbio.metadata.LimitExceededException;
30 import compbio.metadata.Option;
31 import compbio.metadata.ResultNotAvailableException;
32 import compbio.metadata.UnsupportedRuntimeException;
33 import compbio.metadata.WrongParameterException;
34 import compbio.ws.server.RNAalifoldWS;
37 public class TestRNAalifoldWS {
39 SequenceAnnotation<RNAalifoldWS> foldws;
40 // RNAalifoldWS foldws;
42 @BeforeTest(groups = {AllTestSuit.test_group_webservices})
43 void initConnection() {
46 JABAService client = Jws2Client.connect(
47 "http://localhost:8080/jabaws", Services.RNAalifoldWS);
48 // foldws = (RNAalifoldWS) client;
49 foldws = (SequenceAnnotation<RNAalifoldWS>) client;
50 } catch (ConnectException e) {
53 } catch (WebServiceException e) {
60 @Test(groups = {AllTestSuit.test_group_webservices})
61 public void testFold() throws FileNotFoundException, IOException,
62 UnknownFileFormatException {
64 Alignment aln = ClustalAlignmentUtil.readClustalFile(new FileInputStream(
65 AllTestSuit.test_input_aln));
67 List<FastaSequence> fsl = aln.getSequences();
70 List<Option<RNAalifoldWS>> options = new ArrayList<Option<RNAalifoldWS>>();
71 options.add(foldws.getRunnerOptions().getArgumentByOptionName("--mis"));
72 options.add(foldws.getRunnerOptions().getArgumentByOptionName("-p"));
73 options.add(foldws.getRunnerOptions().getArgumentByOptionName("--MEA"));
75 System.out.println("TestRNAalifoldWS: print options: " + options.toString());
77 String jobId = foldws.customAnalize(fsl, options);
78 System.out.println("J: " + jobId);
79 RNAStructScoreManager result = (RNAStructScoreManager)foldws.getAnnotation(jobId);
81 Writer writer = new OutputStreamWriter(System.out);
82 result.writeOut(writer);
84 assertNotNull(result);
86 } catch (UnsupportedRuntimeException e) {
89 } catch (LimitExceededException e) {
92 } catch (JobSubmissionException e) {
95 } catch (ResultNotAvailableException e) {
98 } catch (WrongParameterException e) {
100 fail(e.getMessage());