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 }