package compbio.ws.client;
+import compbio.metadata.AllTestSuit;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.fail;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
+import compbio.data.msa.FoldWS;
import compbio.data.msa.JABAService;
import compbio.data.msa.SequenceAnnotation;
import compbio.data.sequence.Alignment;
-import compbio.data.structure.FoldWS;
import compbio.data.sequence.RNAstruct;
import compbio.data.sequence.ClustalAlignmentUtil;
import compbio.data.sequence.ConservationMethod;
import compbio.metadata.RunnerConfig;
import compbio.metadata.UnsupportedRuntimeException;
import compbio.metadata.WrongParameterException;
-
import compbio.runner.conservation.AACon;
import compbio.util.SysPrefs;
import compbio.ws.server.RNAalifoldWS;
+
public class TestRNAalifoldWS {
FoldWS<RNAalifoldWS> foldws;
-// @BeforeTest(groups = {AllTestSuit.test_group_webservices})
-// void initConnection() {
-//
-// try {
-// JABAService client = Jws2Client.connect(
-// "http://localhost:8080/jabaws", Services.RNAalifoldWS);
-// foldws = (FoldWS<RNAalifoldWS>) client;
-// } catch (ConnectException e) {
-// e.printStackTrace();
-// fail(e.getMessage());
-// } catch (WebServiceException e) {
-// e.printStackTrace();
-// fail(e.getMessage());
-// }
-// }
+ @BeforeTest(groups = {AllTestSuit.test_group_webservices})
+ void initConnection() {
+
+ try {
+ JABAService client = Jws2Client.connect(
+ "http://localhost:8080/jabaws", Services.RNAalifoldWS);
+ foldws = (FoldWS<RNAalifoldWS>) client;
+ } catch (ConnectException e) {
+ e.printStackTrace();
+ fail(e.getMessage());
+ } catch (WebServiceException e) {
+ e.printStackTrace();
+ fail(e.getMessage());
+ }
+ }
@Test(groups = {AllTestSuit.test_group_webservices})
public void testFold() throws FileNotFoundException, IOException,
UnknownFileFormatException {
- String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
- + File.separator;
+// String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
+// + File.separator;
Alignment aln = ClustalAlignmentUtil.readClustalFile(new FileInputStream(
- CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
- + File.separator + "unfolded_RF00031.aln"));
+ AllTestSuit.test_input_aln));
try {
- String jobId = foldws.fold(aln);
+ List<Option<RNAalifoldWS>> options = new ArrayList<Option<RNAalifoldWS>>();
+ options.add(foldws.getRunnerOptions().getArgumentByOptionName("--mis"));
+ System.out.println("TestRNAalifoldWS: print options: " + options.toString());
+ String jobId = foldws.customFold(aln, options);
System.out.println("J: " + jobId);
- RNAstruct result = foldws.getResult(jobId);
+ String result = foldws.getResult(jobId);
+ System.out.println("fold results: \n" + result);
assertNotNull(result);
} catch (UnsupportedRuntimeException e) {
} catch (ResultNotAvailableException e) {
e.printStackTrace();
fail(e.getMessage());
- }
+ } catch (WrongParameterException e) {
+ e.printStackTrace();
+ fail(e.getMessage());
+ }
}
}