JAL-4119 use split_xml directories rather than the single path
[jalview.git] / test / jalview / ws / jabaws / MinJabawsClientTests.java
1 /*
2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
4  * 
5  * This file is part of Jalview.
6  * 
7  * Jalview is free software: you can redistribute it and/or
8  * modify it under the terms of the GNU General Public License 
9  * as published by the Free Software Foundation, either version 3
10  * of the License, or (at your option) any later version.
11  *  
12  * Jalview is distributed in the hope that it will be useful, but 
13  * WITHOUT ANY WARRANTY; without even the implied warranty 
14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
15  * PURPOSE.  See the GNU General Public License for more details.
16  * 
17  * You should have received a copy of the GNU General Public License
18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
19  * The Jalview Authors are detailed in the 'AUTHORS' file.
20  */
21 package jalview.ws.jabaws;
22
23 import static org.testng.AssertJUnit.assertEquals;
24
25 import jalview.gui.JvOptionPane;
26
27 import java.util.ArrayList;
28 import java.util.List;
29
30 import org.testng.Assert;
31 import org.testng.annotations.BeforeClass;
32 import org.testng.annotations.Test;
33
34 import compbio.data.msa.MsaWS;
35 import compbio.data.msa.RegistryWS;
36 import compbio.data.sequence.FastaSequence;
37 import compbio.metadata.JobStatus;
38 import compbio.ws.client.Jws2Client;
39 import compbio.ws.client.Services;
40
41 public class MinJabawsClientTests
42 {
43
44   @BeforeClass(alwaysRun = true)
45   public void setUpJvOptionPane()
46   {
47     JvOptionPane.setInteractiveMode(false);
48     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
49   }
50
51   /**
52    * simple test for the benefit of JAL-1338
53    * 
54    * @throws Exception
55    */
56   @SuppressWarnings("rawtypes")
57   @Test(groups = { "Network" })
58   public void msaTest() throws Exception
59   {
60     String url;
61     RegistryWS registry = Jws2Client.connectToRegistry(
62             url = "http://www.compbio.dundee.ac.uk/jabaws");
63     if (registry != null)
64     {
65
66       MsaWS msaservice = null;
67       for (Services service : registry.getSupportedServices())
68       {
69         if (service == null)
70         {
71           // the 'unsupported service'
72           continue;
73         }
74         if (service.equals(Services.ClustalOWS))
75         {
76           msaservice = (MsaWS) Jws2Client.connect(url, service);
77           if (msaservice != null)
78           {
79             break;
80           }
81         }
82       }
83       if (msaservice == null)
84       {
85         Assert.fail(
86                 "couldn't find a clustalO service on the public registry");
87       }
88       FastaSequence fsq = new FastaSequence("seqA",
89               "SESESESESESESESSESESSESESESESESESESESESEEEEEESSESESESESSSSESESESESESESE");
90       List<FastaSequence> iseqs = new ArrayList<FastaSequence>();
91       for (int i = 0; i < 9; i++)
92       {
93         iseqs.add(new FastaSequence(fsq.getId() + i, fsq.getSequence()
94                 + fsq.getSequence().substring(i + 3, i + 3 + i)));
95       }
96
97       String jobid = msaservice.align(iseqs);
98       if (jobid != null)
99       {
100         JobStatus js = null;
101         do
102         {
103           try
104           {
105             Thread.sleep(500);
106           } catch (InterruptedException q)
107           {
108           }
109           ;
110           js = msaservice.getJobStatus(jobid);
111         } while (!js.equals(JobStatus.FAILED)
112                 && !js.equals(JobStatus.CANCELLED)
113                 && !js.equals(JobStatus.FINISHED));
114         assertEquals("Trial alignment failed. State was " + js.name(), js,
115                 JobStatus.FINISHED);
116         assertEquals(
117                 "Mismatch in number of input and result sequences - assume alignment service wasn't interacted with correctly",
118                 msaservice.getResult(jobid).getSequences().size(),
119                 iseqs.size());
120         for (FastaSequence t : msaservice.getResult(jobid).getSequences())
121         {
122           System.out.println(">" + t.getId());
123           System.out.println(t.getFormattedFasta());
124         }
125         // .forEach(new Consumer<FastaSequence>() {
126         // @Override
127         // public void accept(FastaSequence t) {
128         // System.out.println(">"+t.getId());
129         // System.out.println(t.getFormattedFasta());
130         // }
131         // });
132       }
133
134     }
135   }
136 }