1 package compbio.ws.client;
3 import static org.testng.Assert.assertEquals;
4 import static org.testng.Assert.assertNotNull;
5 import static org.testng.Assert.fail;
8 import java.io.FileInputStream;
9 import java.io.FileNotFoundException;
10 import java.io.IOException;
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.structure.FoldWS;
24 import compbio.data.sequence.RNAstruct;
25 import compbio.data.sequence.ClustalAlignmentUtil;
26 import compbio.data.sequence.ConservationMethod;
27 import compbio.data.sequence.FastaSequence;
28 import compbio.data.sequence.ScoreManager;
29 import compbio.data.sequence.SequenceUtil;
30 import compbio.data.sequence.UnknownFileFormatException;
31 import compbio.metadata.AllTestSuit;
32 import compbio.metadata.JobSubmissionException;
33 import compbio.metadata.LimitExceededException;
34 import compbio.metadata.Option;
35 import compbio.metadata.PresetManager;
36 import compbio.metadata.ResultNotAvailableException;
37 import compbio.metadata.RunnerConfig;
38 import compbio.metadata.UnsupportedRuntimeException;
39 import compbio.metadata.WrongParameterException;
41 import compbio.runner.conservation.AACon;
42 import compbio.util.SysPrefs;
43 import compbio.ws.server.RNAalifoldWS;
45 public class TestRNAalifoldWS {
47 FoldWS<RNAalifoldWS> foldws;
49 // @BeforeTest(groups = {AllTestSuit.test_group_webservices})
50 // void initConnection() {
53 // JABAService client = Jws2Client.connect(
54 // "http://localhost:8080/jabaws", Services.RNAalifoldWS);
55 // foldws = (FoldWS<RNAalifoldWS>) client;
56 // } catch (ConnectException e) {
57 // e.printStackTrace();
58 // fail(e.getMessage());
59 // } catch (WebServiceException e) {
60 // e.printStackTrace();
61 // fail(e.getMessage());
66 @Test(groups = {AllTestSuit.test_group_webservices})
67 public void testFold() throws FileNotFoundException, IOException,
68 UnknownFileFormatException {
70 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
73 Alignment aln = ClustalAlignmentUtil.readClustalFile(new FileInputStream(
74 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
75 + File.separator + "unfolded_RF00031.aln"));
78 String jobId = foldws.fold(aln);
79 System.out.println("J: " + jobId);
80 RNAstruct result = foldws.getResult(jobId);
81 assertNotNull(result);
83 } catch (UnsupportedRuntimeException e) {
86 } catch (LimitExceededException e) {
89 } catch (JobSubmissionException e) {
92 } catch (ResultNotAvailableException e) {