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.
23 import jalview.urls.api.UrlProviderI;
24 import jalview.urls.desktop.DesktopUrlProviderFactory;
26 import java.io.BufferedWriter;
28 import java.io.FileWriter;
29 import java.io.IOException;
30 import java.util.List;
32 import org.testng.Assert;
33 import org.testng.annotations.BeforeMethod;
34 import org.testng.annotations.Test;
36 public class DesktopUrlProviderFactoryTest
38 // Test identifiers.org download file
39 private static final String testIdOrgString = "[{\"id\":\"MIR:00000002\",\"name\":\"ChEBI\",\"pattern\":\"^CHEBI:\\d+$\","
40 + "\"definition\":\"Chemical Entities of Biological Interest (ChEBI)\",\"prefix\":\"chebi\","
41 + "\"url\":\"http://identifiers.org/chebi\"},{\"id\":\"MIR:00000005\",\"name\":\"UniProt Knowledgebase\","
42 + "\"pattern\":\"^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$\","
43 + "\"definition\":\"The UniProt Knowledgebase (UniProtKB)\",\"prefix\":\"uniprot\",\"url\":\"http://identifiers.org/uniprot\"},"
44 + "{\"id\":\"MIR:00000011\",\"name\":\"InterPro\",\"pattern\":\"^IPR\\d{6}$\",\"definition\":\"InterPro\",\"prefix\":\"interpro\","
45 + "\"url\":\"http://identifiers.org/interpro\"},"
46 + "{\"id\":\"MIR:00000372\",\"name\":\"ENA\",\"pattern\":\"^[A-Z]+[0-9]+(\\.\\d+)?$\",\"definition\":\"The European Nucleotide Archive (ENA),\""
47 + "\"prefix\":\"ena.embl\",\"url\":\"http://identifiers.org/ena.embl\"}]";
49 @BeforeMethod(alwaysRun = true)
52 // make a dummy identifiers.org download file
57 temp = File.createTempFile("tempfile", ".tmp");
59 BufferedWriter bw = new BufferedWriter(new FileWriter(temp));
60 bw.write(testIdOrgString);
62 } catch (IOException e)
65 .println("Error initialising DesktopUrlProviderFactoryTest test: "
69 IdOrgSettings.setDownloadLocation(temp.getPath());
72 @Test(groups = { "Functional" })
73 public void testCreateUrlProvider()
75 String defaultUrlString = "Test1";
76 String defaultUrl = "http://blah.blah/$SEQUENCE_ID$";
77 String cachedUrlList = "MIR:00000005|MIR:00000011|Test1|http://blah.blah/$SEQUENCE_ID$|"
78 + "Test2|http://test2/$DB_ACCESSION$|Test3|http://test3/$SEQUENCE_ID$";
79 String userUrlList = "MIR:00000372|Test4|httpL//another.url/$SEQUENCE_ID$";
81 DesktopUrlProviderFactory factory = new DesktopUrlProviderFactory(
82 defaultUrlString, cachedUrlList, userUrlList);
83 UrlProviderI prov = factory.createUrlProvider();
85 // default url correctly set
86 Assert.assertEquals(prov.getPrimaryUrlId(), "Test1");
87 Assert.assertEquals(prov.getPrimaryUrl("FER_CAPAN"),
88 defaultUrl.replace("$SEQUENCE_ID$", "FER_CAPAN"));
90 List<String> menulinks = prov.getLinksForMenu();
91 List<UrlLinkDisplay> allLinks = prov.getLinksForTable();
93 // 8 links in provider - 4 from id file, 4 custom links
94 Assert.assertEquals(allLinks.size(), 8);
96 // 5 links in menu (cachedUrlList)
97 Assert.assertEquals(menulinks.size(), 5);
99 Assert.assertTrue(menulinks
100 .contains("Test1|http://blah.blah/$SEQUENCE_ID$"));
101 Assert.assertTrue(menulinks
102 .contains("Test2|http://test2/$DB_ACCESSION$"));
103 Assert.assertTrue(menulinks
104 .contains("Test3|http://test3/$SEQUENCE_ID$"));
105 Assert.assertTrue(menulinks
106 .contains("UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$"));
107 Assert.assertTrue(menulinks
108 .contains("InterPro|http://identifiers.org/interpro/$DB_ACCESSION$"));