From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 3 Oct 2014 09:55:18 +0000 (+0100)
Subject: Merge branch 'bugs/JAL-1138_osgi' into Release_2_8_2_Branch
X-Git-Tag: Release_2_8_2b1^2~52
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c761d32b1a115a1f200fe280e7c546ad37e9957d;hp=55fc8f004dac252b5b89ac91cf506e4844a6b1da;p=jalview.git

Merge branch 'bugs/JAL-1138_osgi' into Release_2_8_2_Branch
---

diff --git a/test/jalview/ws/jabaws/MinJabawsClientTests.java b/test/jalview/ws/jabaws/MinJabawsClientTests.java
new file mode 100644
index 0000000..5c9a192
--- /dev/null
+++ b/test/jalview/ws/jabaws/MinJabawsClientTests.java
@@ -0,0 +1,84 @@
+package jalview.ws.jabaws;
+
+import static org.junit.Assert.*;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.function.Consumer;
+
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.jws2.jabaws2.Jws2InstanceFactory;
+
+import org.junit.Test;
+
+import compbio.data.msa.Category;
+import compbio.data.msa.JABAService;
+import compbio.data.msa.MsaWS;
+import compbio.data.msa.RegistryWS;
+import compbio.data.sequence.FastaSequence;
+import compbio.metadata.JobStatus;
+import compbio.ws.client.Jws2Client;
+import compbio.ws.client.Services;
+
+public class MinJabawsClientTests {
+
+	@SuppressWarnings("rawtypes")
+	@Test
+	public void msaTest() throws Exception {
+		String url;
+		RegistryWS registry = Jws2Client
+				.connectToRegistry(url = "http://www.compbio.dundee.ac.uk/jabaws");
+		if (registry != null) {
+
+			MsaWS msaservice = null;
+			for (Services service : registry.getSupportedServices()) {
+				if (service.equals(Services.ClustalOWS)) {
+					msaservice = (MsaWS) Jws2Client.connect(url, service);
+					if (msaservice != null) {
+						break;
+					}
+				}
+			}
+			if (msaservice == null) {
+				fail("couldn't find a clustalO service on the public registry");
+			}
+			FastaSequence fsq = new FastaSequence("seqA",
+					"SESESESESESESESSESESSESESESESESESESESESEEEEEESSESESESESSSSESESESESESESE");
+			List<FastaSequence> iseqs = new ArrayList<FastaSequence>();
+			for (int i = 0; i < 9; i++) {
+				iseqs.add(new FastaSequence(fsq.getId() + i, fsq.getSequence()
+						+ fsq.getSequence().substring(i + 3, i + 3 + i)));
+			}
+
+			String jobid = msaservice.align(iseqs);
+			if (jobid != null) {
+				JobStatus js = null;
+				do {
+					try {
+						Thread.sleep(500);
+					} catch (InterruptedException q) {
+					}
+					;
+					js = msaservice.getJobStatus(jobid);
+				} while (!js.equals(JobStatus.FAILED)
+						&& !js.equals(JobStatus.CANCELLED)
+						&& !js.equals(JobStatus.FINISHED));
+				assertEquals("Trial alignment failed. State was " + js.name(),
+						js, JobStatus.FINISHED);
+				assertEquals(
+						"Mismatch in number of input and result sequences - assume alignment service wasn't interacted with correctly",
+						msaservice.getResult(jobid).getSequences().size(),
+						iseqs.size());
+				msaservice.getResult(jobid).getSequences()
+						.forEach(new Consumer<FastaSequence>() {
+							@Override
+							public void accept(FastaSequence t) {
+								System.out.println(">"+t.getId());
+								System.out.println(t.getFormattedFasta());
+							}
+						});
+			}
+
+		}
+	}
+}