Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
UrlProviderTest	18	32	5	1	0.972222297.2%	Show methods

Class UrlProviderTest

Class UrlProviderTest	Line # 18	Total Statements 32	Complexity 5	Uncovered Elements 1	TOTAL Coverage 0.972222297.2%
setup() : void   setup() : void	3333	14.014	2.02	1.01	0.9285714 0.928571492.9%
testInitUrlProvider() : void   testInitUrlProvider() : void	6464	13.013	1.01	0.00	1.0 1.0100%
testSetDefaultUrl() : void   testSetDefaultUrl() : void	100100	4.04	1.01	0.00	1.0 1.0100%
testSetDefaultUrlWrongly() : void   testSetDefaultUrlWrongly() : void	112112	1.01	1.01	0.00	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

 

Source view

1		package jalview.urls;
2
3		import jalview.urls.api.UrlProviderI;
4		import jalview.urls.desktop.DesktopUrlProviderFactory;
5		import jalview.util.UrlConstants;
6
7		import java.io.BufferedWriter;
8		import java.io.File;
9		import java.io.FileWriter;
10		import java.io.IOException;
11		import java.util.List;
12
13		import org.testng.Assert;
14		import org.testng.annotations.BeforeMethod;
15		import org.testng.annotations.Test;
16
17
		97.2% Uncovered Elements: 1 (36) Complexity: 5 Complexity Density: 0.16
18		public class UrlProviderTest {
19
20		// Test identifiers.org download file
21		private static final String testIdOrgString = "{\"Local\": [{\"id\":\"MIR:00000002\",\"name\":\"ChEBI\",\"pattern\":\"^CHEBI:\\d+$\","
22		+ "\"definition\":\"Chemical Entities of Biological Interest (ChEBI)\",\"prefix\":\"chebi\","
23		+ "\"url\":\"http://identifiers.org/chebi\"},{\"id\":\"MIR:00000005\",\"name\":\"UniProt Knowledgebase\","
24		+ "\"pattern\":\"^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$\","
25		+ "\"definition\":\"The UniProt Knowledgebase (UniProtKB)\",\"prefix\":\"uniprot\",\"url\":\"http://identifiers.org/uniprot\"},"
26		+ "{\"id\":\"MIR:00000011\",\"name\":\"InterPro\",\"pattern\":\"^IPR\\d{6}$\",\"definition\":\"InterPro\",\"prefix\":\"interpro\","
27		+ "\"url\":\"http://identifiers.org/interpro\"},"
28		+ "{\"id\":\"MIR:00000372\",\"name\":\"ENA\",\"pattern\":\"^[A-Z]+[0-9]+(\\.\\d+)?$\",\"definition\":\"The European Nucleotide Archive (ENA),\""
29		+ "\"prefix\":\"ena.embl\",\"url\":\"http://identifiers.org/ena.embl\"}]}";
30
31		private UrlProviderI prov;
32
		92.9% Uncovered Elements: 1 (14) Complexity: 2 Complexity Density: 0.14
33	3	@BeforeMethod(alwaysRun = true)...
34		public void setup()
35		{
36		// make a dummy identifiers.org download file
37	3	File temp = null;
38
39	3	try
40		{
41	3	temp = File.createTempFile("tempfile", ".tmp");
42	3	temp.deleteOnExit();
43	3	BufferedWriter bw = new BufferedWriter(new FileWriter(temp));
44	3	bw.write(testIdOrgString);
45	3	bw.close();
46		} catch (IOException e)
47		{
48	0	System.out.println("Error initialising UrlProviderTest test: "
49		+ e.getMessage());
50		}
51
52	3	IdOrgSettings.setDownloadLocation(temp.getPath());
53
54	3	String defaultUrlString = "No default";
55	3	String cachedUrlList = "MIR:00000005|MIR:00000011|Test1|http://blah.blah/$SEQUENCE_ID$|"
56		+ "Test2|http://test2/$DB_ACCESSION$|Test3|http://test3/$SEQUENCE_ID$";
57	3	String userUrlList = "MIR:00000372|Test4|httpL//another.url/$SEQUENCE_ID$";
58
59	3	DesktopUrlProviderFactory factory = new DesktopUrlProviderFactory(
60		defaultUrlString, cachedUrlList, userUrlList);
61	3	prov = factory.createUrlProvider();
62		}
63
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
64	1	@Test(groups = { "Functional" })...
65		public void testInitUrlProvider()
66		{
67	1	String emblUrl = UrlConstants.DEFAULT_STRING.substring(
68		UrlConstants.DEFAULT_STRING.indexOf(UrlConstants.SEP) + 1,
69		UrlConstants.DEFAULT_STRING.length());
70
71		// chooses EMBL url when default Url id does not exist in provided url lists
72	1	Assert.assertEquals(prov.getPrimaryUrlId(), UrlConstants.DEFAULT_LABEL);
73	1	Assert.assertEquals(prov.getPrimaryUrl("FER_CAPAN"),
74		emblUrl.replace("$SEQUENCE_ID$", "FER_CAPAN"));
75
76	1	List<String> menulinks = prov.getLinksForMenu();
77	1	List<UrlLinkDisplay> allLinks = prov.getLinksForTable();
78
79		// 9 links in provider - 4 from id file, 4 custom links, 1 additional
80		// default
81	1	Assert.assertEquals(allLinks.size(), 9);
82
83		// 6 links in menu (cachedUrlList) + new default
84	1	Assert.assertEquals(menulinks.size(), 6);
85
86	1	Assert.assertTrue(menulinks
87		.contains("Test1|http://blah.blah/$SEQUENCE_ID$"));
88	1	Assert.assertTrue(menulinks
89		.contains("Test2|http://test2/$DB_ACCESSION$"));
90	1	Assert.assertTrue(menulinks
91		.contains("Test3|http://test3/$SEQUENCE_ID$"));
92	1	Assert.assertTrue(menulinks
93		.contains("UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$|uniprot"));
94	1	Assert.assertTrue(menulinks
95		.contains("InterPro|http://identifiers.org/interpro/$DB_ACCESSION$|interpro"));
96	1	Assert.assertTrue(menulinks.contains(UrlConstants.DEFAULT_LABEL
97		+ UrlConstants.SEP + emblUrl));
98		}
99
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25 1PASS
100	1	@Test(groups = { "Functional" })...
101		public void testSetDefaultUrl()
102		{
103		// set custom url as default
104	1	Assert.assertTrue(prov.setPrimaryUrl("Test1"));
105	1	Assert.assertEquals(prov.getPrimaryUrlId(), "Test1");
106
107		// set identifiers url as default
108	1	Assert.assertTrue(prov.setPrimaryUrl("MIR:00000011"));
109	1	Assert.assertEquals(prov.getPrimaryUrlId(), "MIR:00000011");
110		}
111
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1 1PASS
112	1	@Test(...
113		groups = { "Functional" },
114		expectedExceptions = { IllegalArgumentException.class })
115		public void testSetDefaultUrlWrongly()
116		{
117		// don't allow default to be a non-key
118	1	prov.setPrimaryUrl("not-a-key");
119		}
120		}