Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
DesktopUrlProviderFactoryTest	36	26	3	0.9642857396.4%	Show methods

Class DesktopUrlProviderFactoryTest

Class DesktopUrlProviderFactoryTest	Line # 36	Total Statements 26	Complexity 3	TOTAL Coverage 0.9642857396.4%
setup() : void   setup() : void	4848	9.09	2.02	0.8888889 0.888888988.9%
testCreateUrlProvider() : void   testCreateUrlProvider() : void	7171	17.017	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.64285713	jalview.urls.DesktopUrlProviderFactoryTest.testCreateUrlProviderjalview.urls.DesktopUrlProviderFactoryTest.testCreateUrlProvider	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
26		import java.io.BufferedWriter;
27		import java.io.File;
28		import java.io.FileWriter;
29		import java.io.IOException;
30		import java.util.List;
31
32		import org.testng.Assert;
33		import org.testng.annotations.BeforeMethod;
34		import org.testng.annotations.Test;
35
		96.4% Uncovered Elements: 1 (28) Complexity: 3 Complexity Density: 0.12
36		public class DesktopUrlProviderFactoryTest
37		{
38		private static final String testIdOrgString = "{\"Local\": [{\"id\":\"MIR:00000002\",\"name\":\"ChEBI\",\"pattern\":\"^CHEBI:\\d+$\","
39		+ "\"definition\":\"Chemical Entities of Biological Interest (ChEBI)\",\"prefix\":\"chebi\","
40		+ "\"url\":\"http://identifiers.org/chebi\"},{\"id\":\"MIR:00000005\",\"name\":\"UniProt Knowledgebase\","
41		+ "\"pattern\":\"^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$\","
42		+ "\"definition\":\"The UniProt Knowledgebase (UniProtKB)\",\"prefix\":\"uniprot\",\"url\":\"http://identifiers.org/uniprot\"},"
43		+ "{\"id\":\"MIR:00000011\",\"name\":\"InterPro\",\"pattern\":\"^IPR\\d{6}$\",\"definition\":\"InterPro\",\"prefix\":\"interpro\","
44		+ "\"url\":\"http://identifiers.org/interpro\"},"
45		+ "{\"id\":\"MIR:00000372\",\"name\":\"ENA\",\"pattern\":\"^[A-Z]+[0-9]+(\\.\\d+)?$\",\"definition\":\"The European Nucleotide Archive (ENA),\""
46		+ "\"prefix\":\"ena.embl\",\"url\":\"http://identifiers.org/ena.embl\"}]}";
47
		88.9% Uncovered Elements: 1 (9) Complexity: 2 Complexity Density: 0.22
48	1	@BeforeMethod(alwaysRun = true)...
49		public void setup()
50		{
51		// make a dummy identifiers.org download file
52	1	File temp = null;
53
54	1	try
55		{
56	1	temp = File.createTempFile("tempfile", ".tmp");
57	1	temp.deleteOnExit();
58	1	BufferedWriter bw = new BufferedWriter(new FileWriter(temp));
59	1	bw.write(testIdOrgString);
60	1	bw.close();
61		} catch (IOException e)
62		{
63	0	System.out.println(
64		"Error initialising DesktopUrlProviderFactoryTest test: "
65		+ e.getMessage());
66		}
67
68	1	IdOrgSettings.setDownloadLocation(temp.getPath());
69		}
70
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06 1PASS
71	1	@Test(groups = { "Functional" })...
72		public void testCreateUrlProvider()
73		{
74	1	String defaultUrlString = "Test1";
75	1	String defaultUrl = "http://blah.blah/$SEQUENCE_ID$";
76	1	String cachedUrlList = "MIR:00000005|MIR:00000011|Test1|http://blah.blah/$SEQUENCE_ID$|"
77		+ "Test2|http://test2/$DB_ACCESSION$|Test3|http://test3/$SEQUENCE_ID$";
78	1	String userUrlList = "MIR:00000372|Test4|httpL//another.url/$SEQUENCE_ID$";
79
80	1	DesktopUrlProviderFactory factory = new DesktopUrlProviderFactory(
81		defaultUrlString, cachedUrlList, userUrlList);
82	1	UrlProviderI prov = factory.createUrlProvider();
83
84		// default url correctly set
85	1	Assert.assertEquals(prov.getPrimaryUrlId(), "Test1");
86	1	Assert.assertEquals(prov.getPrimaryUrl("FER_CAPAN"),
87		defaultUrl.replace("$SEQUENCE_ID$", "FER_CAPAN"));
88
89	1	List<String> menulinks = prov.getLinksForMenu();
90	1	List<UrlLinkDisplay> allLinks = prov.getLinksForTable();
91
92		// 8 links in provider - 4 from id file, 4 custom links
93	1	Assert.assertEquals(allLinks.size(), 8);
94
95		// 5 links in menu (cachedUrlList)
96	1	Assert.assertEquals(menulinks.size(), 5);
97
98	1	Assert.assertTrue(
99		menulinks.contains("Test1|http://blah.blah/$SEQUENCE_ID$"));
100	1	Assert.assertTrue(
101		menulinks.contains("Test2|http://test2/$DB_ACCESSION$"));
102	1	Assert.assertTrue(
103		menulinks.contains("Test3|http://test3/$SEQUENCE_ID$"));
104	1	Assert.assertTrue(menulinks.contains(
105		"UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$|uniprot"));
106	1	Assert.assertTrue(menulinks.contains(
107		"InterPro|http://identifiers.org/interpro/$DB_ACCESSION$|interpro"));
108		}
109		}