Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
MinJabawsClientTests	41	32	13	0.00%	Show methods

Class MinJabawsClientTests

Class MinJabawsClientTests	Line # 41	Total Statements 32	Complexity 13	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4444	2.02	1.01	0.0 0.00%
msaTest() : void   msaTest() : void	5656	30.030	12.012	0.0 0.00%

 

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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
		0% Uncovered Elements: 50 (50) Complexity: 13 Complexity Density: 0.41
41		public class MinJabawsClientTests
42		{
43
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
44	0	@BeforeClass(alwaysRun = true)...
45		public void setUpJvOptionPane()
46		{
47	0	JvOptionPane.setInteractiveMode(false);
48	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
49		}
50
51		/**
52		* simple test for the benefit of JAL-1338
53		*
54		* @throws Exception
55		*/
		0% Uncovered Elements: 46 (46) Complexity: 12 Complexity Density: 0.4 4-
56	0	@SuppressWarnings("rawtypes")...
57		@Test(groups = { "Network" })
58		public void msaTest() throws Exception
59		{
60	0	String url;
61	0	RegistryWS registry = Jws2Client.connectToRegistry(
62		url = "http://www.compbio.dundee.ac.uk/jabaws");
63	0	if (registry != null)
64		{
65
66	0	MsaWS msaservice = null;
67	0	for (Services service : registry.getSupportedServices())
68		{
69	0	if (service == null)
70		{
71		// the 'unsupported service'
72	0	continue;
73		}
74	0	if (service.equals(Services.ClustalOWS))
75		{
76	0	msaservice = (MsaWS) Jws2Client.connect(url, service);
77	0	if (msaservice != null)
78		{
79	0	break;
80		}
81		}
82		}
83	0	if (msaservice == null)
84		{
85	0	Assert.fail(
86		"couldn't find a clustalO service on the public registry");
87		}
88	0	FastaSequence fsq = new FastaSequence("seqA",
89		"SESESESESESESESSESESSESESESESESESESESESEEEEEESSESESESESSSSESESESESESESE");
90	0	List<FastaSequence> iseqs = new ArrayList<FastaSequence>();
91	0	for (int i = 0; i < 9; i++)
92		{
93	0	iseqs.add(new FastaSequence(fsq.getId() + i, fsq.getSequence()
94		+ fsq.getSequence().substring(i + 3, i + 3 + i)));
95		}
96
97	0	String jobid = msaservice.align(iseqs);
98	0	if (jobid != null)
99		{
100	0	JobStatus js = null;
101	0	do
102		{
103	0	try
104		{
105	0	Thread.sleep(500);
106		} catch (InterruptedException q)
107		{
108		}
109	0	;
110	0	js = msaservice.getJobStatus(jobid);
111	0	} while (!js.equals(JobStatus.FAILED)
112		&& !js.equals(JobStatus.CANCELLED)
113		&& !js.equals(JobStatus.FINISHED));
114	0	assertEquals("Trial alignment failed. State was " + js.name(), js,
115		JobStatus.FINISHED);
116	0	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	0	for (FastaSequence t : msaservice.getResult(jobid).getSequences())
121		{
122	0	System.out.println(">" + t.getId());
123	0	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		}