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.ConservationMethod;
23 import compbio.data.sequence.FastaSequence;
24 import compbio.data.sequence.ScoreManager;
25 import compbio.data.sequence.SequenceUtil;
26 import compbio.metadata.AllTestSuit;
27 import compbio.metadata.JobSubmissionException;
28 import compbio.metadata.LimitExceededException;
29 import compbio.metadata.Option;
30 import compbio.metadata.PresetManager;
31 import compbio.metadata.ResultNotAvailableException;
32 import compbio.metadata.RunnerConfig;
33 import compbio.metadata.UnsupportedRuntimeException;
34 import compbio.metadata.WrongParameterException;
35 import compbio.runner.conservation.AACon;
36 import compbio.util.SysPrefs;
37 import compbio.ws.server.IUPredWS;
39 public class TestIUPredWS {
41 SequenceAnnotation<IUPredWS> msaws;
43 @BeforeTest(groups = {AllTestSuit.test_group_webservices})
44 void initConnection() {
46 * URL url = null; try { url = new
47 * URL("http://localhost:8080/jabaws/AAConWS?wsdl"); } catch
48 * (MalformedURLException e) { e.printStackTrace();
49 * fail(e.getLocalizedMessage()); } String namespace =
50 * "http://msa.data.compbio/01/12/2010/"; QName qname = new
51 * QName(namespace, "AAConWS"); Service serv = Service.create(url,
52 * qname); msaws = serv.getPort(new QName(namespace, "AAConWSPort"),
55 JABAService client = Jws2Client.connect(
56 "http://localhost:8080/jabaws", Services.IUPredWS);
57 msaws = (SequenceAnnotation<IUPredWS>) client;
58 } catch (ConnectException e) {
61 } catch (WebServiceException e) {
67 @Test(groups = {AllTestSuit.test_group_webservices})
68 public void testCustomAnalize() throws FileNotFoundException, IOException {
70 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
73 List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
74 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
75 + File.separator + "TO1381.fasta"));
78 List<Option<IUPredWS>> opts=new ArrayList<Option<IUPredWS>>();
79 opts.add(msaws.getRunnerOptions().getArgumentByOptionName("Long"));
80 String jobId = msaws.customAnalize(fsl,opts);
81 System.out.println("J: " + jobId);
82 ScoreManager result = msaws.getAnnotation(jobId);
83 assertNotNull(result);
84 // assertEquals(result.asSet().size(), 1);
86 } catch (UnsupportedRuntimeException e) {
89 } catch (LimitExceededException e) {
92 } catch (JobSubmissionException e) {
95 } catch (ResultNotAvailableException e) {
98 } catch (WrongParameterException e) {
100 fail(e.getMessage());