Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblXrefTest	38	17	3	1.0100%	Show methods

Class EnsemblXrefTest

Class EnsemblXrefTest	Line # 38	Total Statements 17	Complexity 3	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4141	2.02	1.01	1.0 1.0100%
getJSON(URL,List<String>,int,int,String) : Object   getJSON(URL,List<String>,int,int,String) : Object	6464	1.01	1.01	1.0 1.0100%
testGetCrossReferences() : void   testGetCrossReferences() : void	5555	14.014	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.85	jalview.ext.ensembl.EnsemblXrefTest.testGetCrossReferencesjalview.ext.ensembl.EnsemblXrefTest.testGetCrossReferences	1PASS

 

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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.ext.ensembl;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertFalse;
25
26		import jalview.datamodel.DBRefEntry;
27		import jalview.gui.JvOptionPane;
28		import jalview.util.JSONUtils;
29
30		import java.io.IOException;
31		import java.net.URL;
32		import java.util.List;
33
34		import org.json.simple.parser.ParseException;
35		import org.testng.annotations.BeforeClass;
36		import org.testng.annotations.Test;
37
		100% Uncovered Elements: 0 (20) Complexity: 3 Complexity Density: 0.18
38		public class EnsemblXrefTest
39		{
40
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
41	1	@BeforeClass(alwaysRun = true)...
42		public void setUpJvOptionPane()
43		{
44	1	JvOptionPane.setInteractiveMode(false);
45	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
46		}
47
48		//@formatter:off
49		private static final String JSON =
50		"[{\"primary_id\":\"CCDS5863\",\"dbname\":\"CCDS\"}," +
51		"{\"primary_id\":\"P15056\",\"dbname\":\"Uniprot/SWISSPROT\",\"synonyms\":[\"C21\"]}," +
52		"{\"primary_id\":\"GO:0000165\",\"dbname\":\"GO\"}]";
53		//@formatter:on
54
		100% Uncovered Elements: 0 (14) Complexity: 1 Complexity Density: 0.07 1PASS
55	1	@Test(groups = "Functional")...
56		public void testGetCrossReferences()
57		{
58	1	String dbName = "ENSEMBL";
59	1	String dbVers = "0.6.2b1";
60	1	System.out.println(JSON);
61	1	EnsemblXref testee = new EnsemblXref("http://rest.ensembl.org", dbName,
62		dbVers)
63		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
64	1	@SuppressWarnings("unchecked")...
65		@Override
66		protected Object getJSON(URL url, List<String> ids, int msDelay,
67		int mode, String mapKey) throws IOException, ParseException
68		{
69	1	return ((List<Object>) JSONUtils.parse(JSON)).iterator();
70		}
71
72		};
73
74		// synonyms and GO terms are not returned
75	1	List<DBRefEntry> dbrefs = testee.getCrossReferences("ABCDE");
76	1	assertEquals(2, dbrefs.size());
77	1	assertEquals("CCDS", dbrefs.get(0).getSource());
78	1	assertEquals("CCDS5863", dbrefs.get(0).getAccessionId());
79	1	assertFalse(dbrefs.get(0).isPrimaryCandidate());
80	1	assertEquals(dbName + ":" + dbVers, dbrefs.get(0).getVersion());
81		// Uniprot name should get converted to Jalview canonical form
82	1	assertEquals("UNIPROT", dbrefs.get(1).getSource());
83	1	assertEquals("P15056", dbrefs.get(1).getAccessionId());
84	1	assertEquals(dbName + ":" + dbVers, dbrefs.get(1).getVersion());
85	1	assertFalse(dbrefs.get(1).isPrimaryCandidate());
86		}
87		}