AAConWS is working

[jabaws.git] / testsrc / compbio / ws / client / TestWSClient.java

diff --git a/testsrc/compbio/ws/client/TestWSClient.java b/testsrc/compbio/ws/client/TestWSClient.java
index 3928549..3eda42b 100644 (file)
--- a/testsrc/compbio/ws/client/TestWSClient.java
+++ b/testsrc/compbio/ws/client/TestWSClient.java
@@ -1,5 +1,6 @@
 package compbio.ws.client;\r
 \r
+import static org.testng.Assert.assertEquals;\r
 import static org.testng.Assert.assertNotNull;\r
 import static org.testng.Assert.fail;\r
 \r
@@ -8,6 +9,7 @@ import java.io.FileInputStream;
 import java.io.FileNotFoundException;\r
 import java.io.IOException;\r
 import java.net.URL;\r
+import java.util.HashSet;\r
 import java.util.List;\r
 \r
 import javax.xml.namespace.QName;\r
@@ -15,25 +17,26 @@ import javax.xml.ws.Service;
 \r
 import org.testng.annotations.Test;\r
 \r
-import compbio.data.msa.MsaWS;\r
-import compbio.data.sequence.Alignment;\r
+import compbio.conservation.Method;\r
+import compbio.data.msa.Annotation;\r
 import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.Score;\r
 import compbio.data.sequence.SequenceUtil;\r
 import compbio.metadata.JobSubmissionException;\r
 import compbio.metadata.LimitExceededException;\r
 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.metadata.UnsupportedRuntimeException;\r
 import compbio.util.SysPrefs;\r
-import compbio.ws.server.ClustalWS;\r
+import compbio.ws.server.AAConWS;\r
 \r
 public class TestWSClient {\r
 \r
        @Test\r
        public void test() throws FileNotFoundException, IOException {\r
 \r
-               URL url = new URL("http://localhost:8080/jaba/ClustalWS?wsdl");\r
-               String namespace = "http://msa.data.compbio/01/01/2010/";\r
-               QName qname = new QName(namespace, "ClustalWS");\r
+               URL url = new URL("http://localhost:8080/jabaws/AAConWS?wsdl");\r
+               String namespace = "http://msa.data.compbio/01/12/2010/";\r
+               QName qname = new QName(namespace, "AAConWS");\r
                Service serv = Service.create(url, qname);\r
                /*\r
                 * MsaWS msaws = serv.getPort(new QName(\r
@@ -43,8 +46,8 @@ public class TestWSClient {
                // Annotation<AACon> msaws = serv.getPort(new QName(namespace,\r
                // "ClustalWSPort"), Annotation.class);\r
 \r
-               MsaWS<ClustalWS> msaws = serv.getPort(new QName(namespace,\r
-                               "ClustalWSPort"), MsaWS.class);\r
+               Annotation<AAConWS> msaws = serv.getPort(new QName(namespace,\r
+                               "AAConWSPort"), Annotation.class);\r
 \r
                // List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(\r
                // AAConTester.test_alignment_input));\r
@@ -54,13 +57,21 @@ public class TestWSClient {
 \r
                List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(\r
                                CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"\r
-                                               + File.separator + "testlimit.in"));\r
+                                               + File.separator + "TO1381.fasta.aln"));\r
 \r
                try {\r
-                       String jobId = msaws.align(fsl);\r
-                       Alignment result = msaws.getResult(jobId);\r
+                       System.out.println("Pres: "\r
+                                       + msaws.getPresets().getPresets().get(0));\r
+                       String jobId = msaws.analize(fsl);\r
+                       System.out.println("J: " + jobId);\r
+                       HashSet<Score> result = msaws.getConservation(jobId);\r
                        assertNotNull(result);\r
-                       System.out.println(result);\r
+                       assertEquals(result.size(), 1);\r
+                       assertEquals(result.iterator().next().getMethod(), Method.SHENKIN);\r
+                       List<Float> scores = result.iterator().next().getScores();\r
+                       assertNotNull(scores);\r
+                       assertEquals(scores.size(), 568);\r
+\r
                } catch (UnsupportedRuntimeException e) {\r
                        e.printStackTrace();\r
                        fail(e.getMessage());\r
@@ -74,6 +85,6 @@ public class TestWSClient {
                        e.printStackTrace();\r
                        fail(e.getMessage());\r
                }\r
-               System.out.println("Pres: " + msaws.getPresets());\r
+\r
        }\r
 }\r