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IdentifiersUrlProviderTest | 39 | 31 | 5 |
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 | ||
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 | { | |
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 | ||
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 | */ | |
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 | */ | |
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 | } |