Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
UrlProviderTest	37	32	5	0.972222297.2%	Show methods

Class UrlProviderTest

Class UrlProviderTest	Line # 37	Total Statements 32	Complexity 5	TOTAL Coverage 0.972222297.2%
setup() : void   setup() : void	5353	14.014	2.02	0.9285714 0.928571492.9%
testInitUrlProvider() : void   testInitUrlProvider() : void	8484	13.013	1.01	1.0 1.0100%
testSetDefaultUrl() : void   testSetDefaultUrl() : void	120120	4.04	1.01	1.0 1.0100%
testSetDefaultUrlWrongly() : void   testSetDefaultUrlWrongly() : void	132132	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.3888889	jalview.urls.UrlProviderTest.testInitUrlProviderjalview.urls.UrlProviderTest.testInitUrlProvider	1PASS
	0.1388889	jalview.urls.UrlProviderTest.testSetDefaultUrljalview.urls.UrlProviderTest.testSetDefaultUrl	1PASS
	0.055555556	jalview.urls.UrlProviderTest.testSetDefaultUrlWronglyjalview.urls.UrlProviderTest.testSetDefaultUrlWrongly	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.urls;
22
23		import jalview.urls.api.UrlProviderI;
24		import jalview.urls.desktop.DesktopUrlProviderFactory;
25		import jalview.util.UrlConstants;
26
27		import java.io.BufferedWriter;
28		import java.io.File;
29		import java.io.FileWriter;
30		import java.io.IOException;
31		import java.util.List;
32
33		import org.testng.Assert;
34		import org.testng.annotations.BeforeMethod;
35		import org.testng.annotations.Test;
36
		97.2% Uncovered Elements: 1 (36) Complexity: 5 Complexity Density: 0.16
37		public class UrlProviderTest
38		{
39
40		// Test identifiers.org download file
41		private static final String testIdOrgString = "{\"Local\": [{\"id\":\"MIR:00000002\",\"name\":\"ChEBI\",\"pattern\":\"^CHEBI:\\d+$\","
42		+ "\"definition\":\"Chemical Entities of Biological Interest (ChEBI)\",\"prefix\":\"chebi\","
43		+ "\"url\":\"http://identifiers.org/chebi\"},{\"id\":\"MIR:00000005\",\"name\":\"UniProt Knowledgebase\","
44		+ "\"pattern\":\"^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$\","
45		+ "\"definition\":\"The UniProt Knowledgebase (UniProtKB)\",\"prefix\":\"uniprot\",\"url\":\"http://identifiers.org/uniprot\"},"
46		+ "{\"id\":\"MIR:00000011\",\"name\":\"InterPro\",\"pattern\":\"^IPR\\d{6}$\",\"definition\":\"InterPro\",\"prefix\":\"interpro\","
47		+ "\"url\":\"http://identifiers.org/interpro\"},"
48		+ "{\"id\":\"MIR:00000372\",\"name\":\"ENA\",\"pattern\":\"^[A-Z]+[0-9]+(\\.\\d+)?$\",\"definition\":\"The European Nucleotide Archive (ENA),\""
49		+ "\"prefix\":\"ena.embl\",\"url\":\"http://identifiers.org/ena.embl\"}]}";
50
51		private UrlProviderI prov;
52
		92.9% Uncovered Elements: 1 (14) Complexity: 2 Complexity Density: 0.14
53	3	@BeforeMethod(alwaysRun = true)...
54		public void setup()
55		{
56		// make a dummy identifiers.org download file
57	3	File temp = null;
58
59	3	try
60		{
61	3	temp = File.createTempFile("tempfile", ".tmp");
62	3	temp.deleteOnExit();
63	3	BufferedWriter bw = new BufferedWriter(new FileWriter(temp));
64	3	bw.write(testIdOrgString);
65	3	bw.close();
66		} catch (IOException e)
67		{
68	0	System.out.println(
69		"Error initialising UrlProviderTest test: " + e.getMessage());
70		}
71
72	3	IdOrgSettings.setDownloadLocation(temp.getPath());
73
74	3	String defaultUrlString = "No default";
75	3	String cachedUrlList = "MIR:00000005|MIR:00000011|Test1|http://blah.blah/$SEQUENCE_ID$|"
76		+ "Test2|http://test2/$DB_ACCESSION$|Test3|http://test3/$SEQUENCE_ID$";
77	3	String userUrlList = "MIR:00000372|Test4|httpL//another.url/$SEQUENCE_ID$";
78
79	3	DesktopUrlProviderFactory factory = new DesktopUrlProviderFactory(
80		defaultUrlString, cachedUrlList, userUrlList);
81	3	prov = factory.createUrlProvider();
82		}
83
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
84	1	@Test(groups = { "Functional" })...
85		public void testInitUrlProvider()
86		{
87	1	String emblUrl = UrlConstants.DEFAULT_STRING.substring(
88		UrlConstants.DEFAULT_STRING.indexOf(UrlConstants.SEP) + 1,
89		UrlConstants.DEFAULT_STRING.length());
90
91		// chooses EMBL url when default Url id does not exist in provided url lists
92	1	Assert.assertEquals(prov.getPrimaryUrlId(), UrlConstants.DEFAULT_LABEL);
93	1	Assert.assertEquals(prov.getPrimaryUrl("FER_CAPAN"),
94		emblUrl.replace("$SEQUENCE_ID$", "FER_CAPAN"));
95
96	1	List<String> menulinks = prov.getLinksForMenu();
97	1	List<UrlLinkDisplay> allLinks = prov.getLinksForTable();
98
99		// 9 links in provider - 4 from id file, 4 custom links, 1 additional
100		// default
101	1	Assert.assertEquals(allLinks.size(), 9);
102
103		// 6 links in menu (cachedUrlList) + new default
104	1	Assert.assertEquals(menulinks.size(), 6);
105
106	1	Assert.assertTrue(
107		menulinks.contains("Test1|http://blah.blah/$SEQUENCE_ID$"));
108	1	Assert.assertTrue(
109		menulinks.contains("Test2|http://test2/$DB_ACCESSION$"));
110	1	Assert.assertTrue(
111		menulinks.contains("Test3|http://test3/$SEQUENCE_ID$"));
112	1	Assert.assertTrue(menulinks.contains(
113		"UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$|uniprot"));
114	1	Assert.assertTrue(menulinks.contains(
115		"InterPro|http://identifiers.org/interpro/$DB_ACCESSION$|interpro"));
116	1	Assert.assertTrue(menulinks.contains(
117		UrlConstants.DEFAULT_LABEL + UrlConstants.SEP + emblUrl));
118		}
119
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25 1PASS
120	1	@Test(groups = { "Functional" })...
121		public void testSetDefaultUrl()
122		{
123		// set custom url as default
124	1	Assert.assertTrue(prov.setPrimaryUrl("Test1"));
125	1	Assert.assertEquals(prov.getPrimaryUrlId(), "Test1");
126
127		// set identifiers url as default
128	1	Assert.assertTrue(prov.setPrimaryUrl("MIR:00000011"));
129	1	Assert.assertEquals(prov.getPrimaryUrlId(), "MIR:00000011");
130		}
131
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1 1PASS
132	1	@Test(...
133		groups =
134		{ "Functional" },
135		expectedExceptions =
136		{ IllegalArgumentException.class })
137		public void testSetDefaultUrlWrongly()
138		{
139		// don't allow default to be a non-key
140	1	prov.setPrimaryUrl("not-a-key");
141		}
142		}