Integration of Freemarker API to the Jalview help system to aid self-documentation...

[jalview.git] / test / jalview / ws / jabaws / MinJabawsClientTests.java

diff --git a/test/jalview/ws/jabaws/MinJabawsClientTests.java b/test/jalview/ws/jabaws/MinJabawsClientTests.java
index 5c9a192..145cddf 100644 (file)
--- a/test/jalview/ws/jabaws/MinJabawsClientTests.java
+++ b/test/jalview/ws/jabaws/MinJabawsClientTests.java
@@ -1,18 +1,13 @@
 package jalview.ws.jabaws;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
 
 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;
@@ -22,63 +17,87 @@ 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) {
+  /**
+   * simple test for the benefit of JAL-1338
+   * @throws Exception
+   */
+  @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)));
+      }
 
-                       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());
 
-                       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());
-                                                       }
-                                               });
-                       }
+        List<FastaSequence> fastaSequences = msaservice.getResult(jobid).getSequences();
+        for(FastaSequence fastaSequence : fastaSequences){
+          System.out.println(">" + fastaSequence.getId());
+          System.out.println(fastaSequence.getFormattedFasta());
+        }
+      }
 
-               }
-       }
+      //        msaservice.getResult(jobid).getSequences()
+      //        .forEach(new Consumer<FastaSequence>()
+      //                {
+      //                  @Override
+      //                  public void accept(FastaSequence t)
+      //                  {
+      //                    System.out.println(">" + t.getId());
+      //                    System.out.println(t.getFormattedFasta());
+      //                  }
+      //                });
+    }
+
+  }
 }
+