From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 2 Aug 2012 11:46:51 +0000 (+0100)
Subject: JWS-47 new customAnalize test for IUPredWS - with several unaligned sequences of... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2ccf319191155419dc119567e5d4e5ac4c3dc84f;p=jabaws.git

JWS-47 new customAnalize test for IUPredWS - with several unaligned sequences of different lengths.
---

diff --git a/testsrc/compbio/ws/client/TestIUPredWS.java b/testsrc/compbio/ws/client/TestIUPredWS.java
new file mode 100644
index 0000000..56533fa
--- /dev/null
+++ b/testsrc/compbio/ws/client/TestIUPredWS.java
@@ -0,0 +1,105 @@
+package compbio.ws.client;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.fail;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.net.ConnectException;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.ws.WebServiceException;
+
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.Test;
+
+import compbio.data.msa.JABAService;
+import compbio.data.msa.SequenceAnnotation;
+import compbio.data.sequence.ConservationMethod;
+import compbio.data.sequence.FastaSequence;
+import compbio.data.sequence.ScoreManager;
+import compbio.data.sequence.SequenceUtil;
+import compbio.metadata.AllTestSuit;
+import compbio.metadata.JobSubmissionException;
+import compbio.metadata.LimitExceededException;
+import compbio.metadata.Option;
+import compbio.metadata.PresetManager;
+import compbio.metadata.ResultNotAvailableException;
+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.IUPredWS;
+
+public class TestIUPredWS {
+
+	SequenceAnnotation<IUPredWS> msaws;
+
+	@BeforeTest(groups = {AllTestSuit.test_group_webservices})
+	void initConnection() {
+		/*
+		 * URL url = null; try { url = new
+		 * URL("http://localhost:8080/jabaws/AAConWS?wsdl"); } catch
+		 * (MalformedURLException e) { e.printStackTrace();
+		 * fail(e.getLocalizedMessage()); } String namespace =
+		 * "http://msa.data.compbio/01/12/2010/"; QName qname = new
+		 * QName(namespace, "AAConWS"); Service serv = Service.create(url,
+		 * qname); msaws = serv.getPort(new QName(namespace, "AAConWSPort"),
+		 * Annotation.class);
+		 */try {
+			JABAService client = Jws2Client.connect(
+					"http://localhost:18080/jaba", Services.IUPredWS);
+			msaws = (SequenceAnnotation<IUPredWS>) 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 testCustomAnalize() throws FileNotFoundException, IOException {
+
+		String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
+				+ File.separator;
+
+		List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
+				CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
+						+ File.separator + "TO1381.fasta"));
+
+		try {
+			List<Option<IUPredWS>> opts=new ArrayList<Option<IUPredWS>>();
+			opts.add(msaws.getRunnerOptions().getArgumentByOptionName("Long"));
+			
+			String jobId = msaws.customAnalize(fsl,opts);
+			System.out.println("J: " + jobId);
+			ScoreManager result = msaws.getAnnotation(jobId);
+			assertNotNull(result);
+//			assertEquals(result.asSet().size(), 1);
+
+		} catch (UnsupportedRuntimeException e) {
+			e.printStackTrace();
+			fail(e.getMessage());
+		} catch (LimitExceededException e) {
+			e.printStackTrace();
+			fail(e.getMessage());
+		} catch (JobSubmissionException e) {
+			e.printStackTrace();
+			fail(e.getMessage());
+		} catch (ResultNotAvailableException e) {
+			e.printStackTrace();
+			fail(e.getMessage());
+		} catch (WrongParameterException e) {
+			e.printStackTrace();
+			fail(e.getMessage());
+		}
+
+	}
+}