2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
24 import static org.testng.AssertJUnit.assertEquals;
25 import static org.testng.AssertJUnit.assertFalse;
26 import static org.testng.AssertJUnit.assertTrue;
29 import java.io.FileWriter;
30 import java.util.Arrays;
31 import java.util.HashMap;
32 import java.util.Vector;
34 import org.testng.annotations.BeforeClass;
35 import org.testng.annotations.Test;
37 public class IdentifiersUrlProviderTest
39 // Test identifiers.org download file
40 private static final String testIdOrgFile = "[{\"id\":\"MIR:00000002\",\"name\":\"ChEBI\",\"pattern\":\"^CHEBI:\\d+$\","
41 + "\"definition\":\"Chemical Entities of Biological Interest (ChEBI)\",\"prefix\":\"chebi\","
42 + "\"url\":\"http://identifiers.org/chebi\"},{\"id\":\"MIR:00000005\",\"name\":\"UniProt Knowledgebase\","
43 + "\"pattern\":\"^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$\","
44 + "\"definition\":\"The UniProt Knowledgebase (UniProtKB)\",\"prefix\":\"uniprot\",\"url\":\"http://identifiers.org/uniprot\"},"
45 + "{\"id\":\"MIR:00000011\",\"name\":\"InterPro\",\"pattern\":\"^IPR\\d{6}$\",\"definition\":\"InterPro\",\"prefix\":\"interpro\","
46 + "\"url\":\"http://identifiers.org/interpro\"},"
47 + "{\"id\":\"MIR:00000372\",\"name\":\"ENA\",\"pattern\":\"^[A-Z]+[0-9]+(\\.\\d+)?$\",\"definition\":\"The European Nucleotide Archive (ENA),\""
48 + "\"prefix\":\"ena.embl\",\"url\":\"http://identifiers.org/ena.embl\"}]";
50 private static final String[] dlinks = {
51 "UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$",
52 "InterPro|http://identifiers.org/interpro/$DB_ACCESSION$",
53 "ENA|http://identifiers.org/ena.embl/$DB_ACCESSION$" };
55 private static final String[] dlinks1 = {
56 "MIR:00000011|http://identifiers.org/interpro/$DB_ACCESSION$",
57 "MIR:00000372|http://identifiers.org/ena.embl/$DB_ACCESSION$" };
59 private static final String[] dlinks2 = {
60 "MIR:00000005|http://identifiers.org/uniprot/$DB_ACCESSION$",
61 "MIR:00000011|http://identifiers.org/interpro/$DB_ACCESSION$" };
63 private static final String stringLinks = "MIR:00000005|http://identifiers.org/uniprot/$DB_ACCESSION$"
64 + "MIR:00000011|http://identifiers.org/interpro/$DB_ACCESSION$"
65 + "MIR:00000372|http://identifiers.org/ena.embl/$DB_ACCESSION$";
67 private static final Vector<String> displayLinks = new Vector<String>(
68 Arrays.asList(dlinks));
70 private static final Vector<String> displayLinks1 = new Vector<String>(
71 Arrays.asList(dlinks1));
73 private static final Vector<String> displayLinks2 = new Vector<String>(
74 Arrays.asList(dlinks2));
76 private static final HashMap<String, String> urlMap = new HashMap<String, String>()
79 put("MIR:00000005", "http://identifiers.org/uniprot/$DB_ACCESSION$");
80 put("MIR:00000011", "http://identifiers.org/interpro/$DB_ACCESSION$");
81 put("MIR:00000372", "http://identifiers.org/ena.embl/$DB_ACCESSION$");
85 private String testfile = "";
88 @BeforeClass(alwaysRun = true)
91 // setup test ids in a file
95 outFile = File.createTempFile("testidsfile", "txt");
96 outFile.deleteOnExit();
98 FileWriter fw = new FileWriter(outFile);
99 fw.write(testIdOrgFile);
102 testfile = outFile.getAbsolutePath();
104 } catch (Exception ex)
106 System.err.println(ex);
111 * Test urls are set and returned correctly
113 @Test(groups = { "Functional" })
114 public void testUrlLinks()
116 // creation from cached id list
117 String idList = "MIR:00000005|MIR:00000011|MIR:00000372";
118 UrlProviderI idProv = new IdentifiersUrlProvider(idList, testfile);
120 assertTrue(displayLinks.containsAll(idProv.getLinksForMenu()));
122 // because UrlProvider does not guarantee order of links, we can't just
123 // compare the output of writeUrlsAsString to a string, hence the hoops here
124 String result = idProv.writeUrlsAsString();
125 UrlProviderI up = new IdentifiersUrlProvider(result, testfile);
126 assertTrue(displayLinks.containsAll(up.getLinksForMenu()));
131 * Test default is set and returned correctly
133 @Test(groups = { "Functional" })
134 public void testDefaultUrl()
136 // creation from cached id list
137 String idList = "MIR:00000005|MIR:00000011|MIR:00000372";
138 UrlProviderI idProv = new IdentifiersUrlProvider(idList, testfile);
140 // initially no default
141 assertEquals(null, idProv.getDefaultUrl("seqid"));
143 // set and then retrieve default
144 assertTrue(idProv.setDefaultUrl("MIR:00000005"));
145 assertEquals("http://identifiers.org/uniprot/seqid",
146 idProv.getDefaultUrl("seqid"));
148 // ids less than length 4 return null
150 idProv.getDefaultUrl("123"));
152 // attempt to set bad default
153 assertFalse(idProv.setDefaultUrl("MIR:00001234"));
154 // default set to null (as default should have been set elsewhere)
155 assertEquals(null, idProv.getDefaultUrl("seqid"));
157 // chooseDefaultUrl not implemented for IdentifiersUrlProvider
158 assertEquals(null, idProv.chooseDefaultUrl());