1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.urls

File DesktopUrlProviderFactoryTest.java

 

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Classes

Class
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Actions
DesktopUrlProviderFactoryTest 36 26 3
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Contributing tests

This file is covered by 1 test. .

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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    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  1 toggle @BeforeMethod(alwaysRun = true)
49    public void setup()
50    {
51    // make a dummy identifiers.org download file
52  1 File temp = null;
53   
54  1 try
55    {
56  1 temp = File.createTempFile("tempfile", ".tmp");
57  1 temp.deleteOnExit();
58  1 BufferedWriter bw = new BufferedWriter(new FileWriter(temp));
59  1 bw.write(testIdOrgString);
60  1 bw.close();
61    } catch (IOException e)
62    {
63  0 System.out.println(
64    "Error initialising DesktopUrlProviderFactoryTest test: "
65    + e.getMessage());
66    }
67   
68  1 IdOrgSettings.setDownloadLocation(temp.getPath());
69    }
70   
 
71  1 toggle @Test(groups = { "Functional" })
72    public void testCreateUrlProvider()
73    {
74  1 String defaultUrlString = "Test1";
75  1 String defaultUrl = "http://blah.blah/$SEQUENCE_ID$";
76  1 String cachedUrlList = "MIR:00000005|MIR:00000011|Test1|http://blah.blah/$SEQUENCE_ID$|"
77    + "Test2|http://test2/$DB_ACCESSION$|Test3|http://test3/$SEQUENCE_ID$";
78  1 String userUrlList = "MIR:00000372|Test4|httpL//another.url/$SEQUENCE_ID$";
79   
80  1 DesktopUrlProviderFactory factory = new DesktopUrlProviderFactory(
81    defaultUrlString, cachedUrlList, userUrlList);
82  1 UrlProviderI prov = factory.createUrlProvider();
83   
84    // default url correctly set
85  1 Assert.assertEquals(prov.getPrimaryUrlId(), "Test1");
86  1 Assert.assertEquals(prov.getPrimaryUrl("FER_CAPAN"),
87    defaultUrl.replace("$SEQUENCE_ID$", "FER_CAPAN"));
88   
89  1 List<String> menulinks = prov.getLinksForMenu();
90  1 List<UrlLinkDisplay> allLinks = prov.getLinksForTable();
91   
92    // 8 links in provider - 4 from id file, 4 custom links
93  1 Assert.assertEquals(allLinks.size(), 8);
94   
95    // 5 links in menu (cachedUrlList)
96  1 Assert.assertEquals(menulinks.size(), 5);
97   
98  1 Assert.assertTrue(
99    menulinks.contains("Test1|http://blah.blah/$SEQUENCE_ID$"));
100  1 Assert.assertTrue(
101    menulinks.contains("Test2|http://test2/$DB_ACCESSION$"));
102  1 Assert.assertTrue(
103    menulinks.contains("Test3|http://test3/$SEQUENCE_ID$"));
104  1 Assert.assertTrue(menulinks.contains(
105    "UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$|uniprot"));
106  1 Assert.assertTrue(menulinks.contains(
107    "InterPro|http://identifiers.org/interpro/$DB_ACCESSION$|interpro"));
108    }
109    }