JAL-2505 removed SequenceFeature constructor JAL-1641 include
[jalview.git] / test / jalview / urls / DesktopUrlProviderFactoryTest.java
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
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
48   @BeforeMethod(alwaysRun = true)
49   public void setup()
50   {
51     // make a dummy identifiers.org download file
52     File temp = null;
53
54     try
55     {
56       temp = File.createTempFile("tempfile", ".tmp");
57       temp.deleteOnExit();
58       BufferedWriter bw = new BufferedWriter(new FileWriter(temp));
59       bw.write(testIdOrgString);
60       bw.close();
61     } catch (IOException e)
62     {
63       System.out
64               .println("Error initialising DesktopUrlProviderFactoryTest test: "
65                       + e.getMessage());
66     }
67
68     IdOrgSettings.setDownloadLocation(temp.getPath());
69   }
70
71   @Test(groups = { "Functional" })
72   public void testCreateUrlProvider()
73   {
74     String defaultUrlString = "Test1";
75     String defaultUrl = "http://blah.blah/$SEQUENCE_ID$";
76     String cachedUrlList = "MIR:00000005|MIR:00000011|Test1|http://blah.blah/$SEQUENCE_ID$|"
77             + "Test2|http://test2/$DB_ACCESSION$|Test3|http://test3/$SEQUENCE_ID$";
78     String userUrlList = "MIR:00000372|Test4|httpL//another.url/$SEQUENCE_ID$";
79
80     DesktopUrlProviderFactory factory = new DesktopUrlProviderFactory(
81             defaultUrlString, cachedUrlList, userUrlList);
82     UrlProviderI prov = factory.createUrlProvider();
83
84     // default url correctly set
85     Assert.assertEquals(prov.getPrimaryUrlId(), "Test1");
86     Assert.assertEquals(prov.getPrimaryUrl("FER_CAPAN"),
87             defaultUrl.replace("$SEQUENCE_ID$", "FER_CAPAN"));
88
89     List<String> menulinks = prov.getLinksForMenu();
90     List<UrlLinkDisplay> allLinks = prov.getLinksForTable();
91
92     // 8 links in provider - 4 from id file, 4 custom links
93     Assert.assertEquals(allLinks.size(), 8);
94
95     // 5 links in menu (cachedUrlList)
96     Assert.assertEquals(menulinks.size(), 5);
97
98     Assert.assertTrue(menulinks
99             .contains("Test1|http://blah.blah/$SEQUENCE_ID$"));
100     Assert.assertTrue(menulinks
101             .contains("Test2|http://test2/$DB_ACCESSION$"));
102     Assert.assertTrue(menulinks
103             .contains("Test3|http://test3/$SEQUENCE_ID$"));
104     Assert.assertTrue(menulinks
105             .contains("UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$|uniprot"));
106     Assert.assertTrue(menulinks
107             .contains("InterPro|http://identifiers.org/interpro/$DB_ACCESSION$|interpro"));
108   }
109 }