Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
IdentifiersUrlProviderTest	39	31	5	0.971428697.1%	Show methods

Class IdentifiersUrlProviderTest

Class IdentifiersUrlProviderTest	Line # 39	Total Statements 31	Complexity 5	TOTAL Coverage 0.971428697.1%
<init>, line 85()   <init>, line 85()	8585	3.03	1.01	1.0 1.0100%
setup() : void   setup() : void	9494	10.010	2.02	0.9 0.990%
testUrlLinks() : void   testUrlLinks() : void	121121	9.09	1.01	1.0 1.0100%
testDefaultUrl() : void   testDefaultUrl() : void	145145	9.09	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.2857143	jalview.urls.IdentifiersUrlProviderTest.testUrlLinksjalview.urls.IdentifiersUrlProviderTest.testUrlLinks	1PASS
	0.2857143	jalview.urls.IdentifiersUrlProviderTest.testDefaultUrljalview.urls.IdentifiersUrlProviderTest.testDefaultUrl	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
22		package jalview.urls;
23
24		import static org.testng.AssertJUnit.assertEquals;
25		import static org.testng.AssertJUnit.assertFalse;
26		import static org.testng.AssertJUnit.assertTrue;
27
28		import jalview.urls.api.UrlProviderI;
29
30		import java.io.File;
31		import java.io.FileWriter;
32		import java.util.Arrays;
33		import java.util.HashMap;
34		import java.util.Vector;
35
36		import org.testng.annotations.BeforeClass;
37		import org.testng.annotations.Test;
38
		97.1% Uncovered Elements: 1 (35) Complexity: 5 Complexity Density: 0.16
39		public class IdentifiersUrlProviderTest
40		{
41		private static final String testIdOrgFile = "{\"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 static final String[] dlinks = {
52		"UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$|uniprot",
53		"InterPro|http://identifiers.org/interpro/$DB_ACCESSION$|interpro",
54		"ENA|http://identifiers.org/ena.embl/$DB_ACCESSION$|ena.embl" };
55
56		private static final String[] dlinks1 = {
57		"MIR:00000011|http://identifiers.org/interpro/$DB_ACCESSION$",
58		"MIR:00000372|http://identifiers.org/ena.embl/$DB_ACCESSION$" };
59
60		private static final String[] dlinks2 = {
61		"MIR:00000005|http://identifiers.org/uniprot/$DB_ACCESSION$",
62		"MIR:00000011|http://identifiers.org/interpro/$DB_ACCESSION$" };
63
64		private static final String stringLinks = "MIR:00000005|http://identifiers.org/uniprot/$DB_ACCESSION$"
65		+ "MIR:00000011|http://identifiers.org/interpro/$DB_ACCESSION$"
66		+ "MIR:00000372|http://identifiers.org/ena.embl/$DB_ACCESSION$";
67
68		private static final String[] unselDlinks = {
69		"ChEBI|http://identifiers.org/chebi/$DB_ACCESSION$" };
70
71		private static final Vector<String> displayLinks = new Vector<String>(
72		Arrays.asList(dlinks));
73
74		private static final Vector<String> unselDisplayLinks = new Vector<String>(
75		Arrays.asList(unselDlinks));
76
77		private static final Vector<String> displayLinks1 = new Vector<String>(
78		Arrays.asList(dlinks1));
79
80		private static final Vector<String> displayLinks2 = new Vector<String>(
81		Arrays.asList(dlinks2));
82
83		private static final HashMap<String, String> urlMap = new HashMap<String, String>()
84		{
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
85	4	{...
86	4	put("MIR:00000005", "http://identifiers.org/uniprot/$DB_ACCESSION$");
87	4	put("MIR:00000011", "http://identifiers.org/interpro/$DB_ACCESSION$");
88	4	put("MIR:00000372", "http://identifiers.org/ena.embl/$DB_ACCESSION$");
89		}
90		};
91
92		private String testfile = "";
93
		90% Uncovered Elements: 1 (10) Complexity: 2 Complexity Density: 0.2
94	1	@BeforeClass(alwaysRun = true)...
95		public void setup()
96		{
97		// setup test ids in a file
98	1	File outFile = null;
99	1	try
100		{
101	1	outFile = File.createTempFile("testidsfile", "txt");
102	1	outFile.deleteOnExit();
103
104	1	FileWriter fw = new FileWriter(outFile);
105	1	fw.write(testIdOrgFile);
106	1	fw.close();
107
108	1	testfile = outFile.getAbsolutePath();
109
110		} catch (Exception ex)
111		{
112	0	System.err.println(ex);
113		}
114
115	1	IdOrgSettings.setDownloadLocation(testfile);
116		}
117
118		/*
119		* Test urls are set and returned correctly
120		*/
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
121	1	@Test(groups = { "Functional" })...
122		public void testUrlLinks()
123		{
124		// creation from cached id list
125	1	String idList = "MIR:00000005|MIR:00000011|MIR:00000372";
126	1	UrlProviderI idProv = new IdentifiersUrlProvider(idList);
127
128	1	assertTrue(displayLinks.containsAll(idProv.getLinksForMenu()));
129
130		// because UrlProvider does not guarantee order of links, we can't just
131		// compare the output of writeUrlsAsString to a string, hence the hoops here
132	1	String result = idProv.writeUrlsAsString(true);
133	1	UrlProviderI up = new IdentifiersUrlProvider(result);
134	1	assertTrue(displayLinks.containsAll(up.getLinksForMenu()));
135
136	1	result = idProv.writeUrlsAsString(false);
137	1	up = new IdentifiersUrlProvider(result);
138	1	assertTrue(unselDisplayLinks.containsAll(up.getLinksForMenu()));
139
140		}
141
142		/*
143		* Test default is set and returned correctly
144		*/
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
145	1	@Test(groups = { "Functional" })...
146		public void testDefaultUrl()
147		{
148		// creation from cached id list
149	1	String idList = "MIR:00000005|MIR:00000011|MIR:00000372";
150	1	UrlProviderI idProv = new IdentifiersUrlProvider(idList);
151
152		// initially no default
153	1	assertEquals(null, idProv.getPrimaryUrl("seqid"));
154
155		// set and then retrieve default
156	1	assertTrue(idProv.setPrimaryUrl("MIR:00000005"));
157	1	assertEquals("http://identifiers.org/uniprot/seqid",
158		idProv.getPrimaryUrl("seqid"));
159
160		// ids less than length 4 return null
161	1	assertEquals(null, idProv.getPrimaryUrl("123"));
162
163		// attempt to set bad default
164	1	assertFalse(idProv.setPrimaryUrl("MIR:00001234"));
165		// default set to null (as default should have been set elsewhere)
166	1	assertEquals(null, idProv.getPrimaryUrl("seqid"));
167
168		// chooseDefaultUrl not implemented for IdentifiersUrlProvider
169	1	assertEquals(null, idProv.choosePrimaryUrl());
170		}
171		}