test/jalview/urls/UrlProviderTest.java

   1 package jalview.urls;
   2
   3 import jalview.urls.api.UrlProviderI;
   4 import jalview.urls.desktop.DesktopUrlProviderFactory;
   5 import jalview.util.UrlConstants;
   6
   7 import java.io.BufferedWriter;
   8 import java.io.File;
   9 import java.io.FileWriter;
  10 import java.io.IOException;
  11 import java.util.List;
  12 import java.util.Vector;
  13
  14 import org.testng.Assert;
  15 import org.testng.annotations.BeforeMethod;
  16 import org.testng.annotations.Test;
  17
  18
  19 public class UrlProviderTest {
  20
  21   // Test identifiers.org download file
  22   private static final String testIdOrgString = "[{\"id\":\"MIR:00000002\",\"name\":\"ChEBI\",\"pattern\":\"^CHEBI:\\d+$\","
  23          + "\"definition\":\"Chemical Entities of Biological Interest (ChEBI)\",\"prefix\":\"chebi\","
  24          + "\"url\":\"http://identifiers.org/chebi\"},{\"id\":\"MIR:00000005\",\"name\":\"UniProt Knowledgebase\","
  25          + "\"pattern\":\"^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$\","
  26          + "\"definition\":\"The UniProt Knowledgebase (UniProtKB)\",\"prefix\":\"uniprot\",\"url\":\"http://identifiers.org/uniprot\"},"
  27          + "{\"id\":\"MIR:00000011\",\"name\":\"InterPro\",\"pattern\":\"^IPR\\d{6}$\",\"definition\":\"InterPro\",\"prefix\":\"interpro\","
  28          + "\"url\":\"http://identifiers.org/interpro\"},"
  29          + "{\"id\":\"MIR:00000372\",\"name\":\"ENA\",\"pattern\":\"^[A-Z]+[0-9]+(\\.\\d+)?$\",\"definition\":\"The European Nucleotide Archive (ENA),\""
  30          + "\"prefix\":\"ena.embl\",\"url\":\"http://identifiers.org/ena.embl\"}]";
  31
  32   private UrlProviderI prov;
  33
  34   @BeforeMethod(alwaysRun = true)
  35   public void setup()
  36   {
  37    // make a dummy identifiers.org download file
  38    File temp = null;
  39
  40    try
  41    {
  42      temp = File.createTempFile("tempfile", ".tmp");
  43      temp.deleteOnExit();
  44      BufferedWriter bw = new BufferedWriter(new FileWriter(temp));
  45      bw.write(testIdOrgString);
  46      bw.close();
  47    } catch (IOException e)
  48    {
  49       System.out.println("Error initialising UrlProviderTest test: "
  50               + e.getMessage());
  51    }
  52
  53    IdOrgSettings.setDownloadLocation(temp.getPath());
  54
  55     String defaultUrlString = "No default";
  56     String cachedUrlList = "MIR:00000005|MIR:00000011|Test1|http://blah.blah/$SEQUENCE_ID$|"
  57             + "Test2|http://test2/$DB_ACCESSION$|Test3|http://test3/$SEQUENCE_ID$";
  58     String userUrlList = "MIR:00000372|Test4|httpL//another.url/$SEQUENCE_ID$";
  59
  60     DesktopUrlProviderFactory factory = new DesktopUrlProviderFactory(
  61             defaultUrlString, cachedUrlList, userUrlList);
  62     prov = factory.createUrlProvider();
  63  }
  64
  65   @Test(groups = { "Functional" })
  66   public void testInitUrlProvider()
  67   {
  68     String emblUrl = UrlConstants.DEFAULT_STRING.substring(
  69             UrlConstants.DEFAULT_STRING.indexOf(UrlConstants.SEP) + 1,
  70             UrlConstants.DEFAULT_STRING.length());
  71
  72     // chooses EMBL url when default Url id does not exist in provided url lists
  73     Assert.assertEquals(prov.getDefaultUrlId(), UrlConstants.DEFAULT_LABEL);
  74     Assert.assertEquals(prov.getDefaultUrl("FER_CAPAN"),
  75             emblUrl.replace("$SEQUENCE_ID$", "FER_CAPAN"));
  76
  77     Vector<String> menulinks = prov.getLinksForMenu();
  78     List<UrlLinkDisplay> allLinks = prov.getLinksForTable();
  79
  80     // 9 links in provider - 4 from id file, 4 custom links, 1 additional
  81     // default
  82     Assert.assertEquals(allLinks.size(), 9);
  83
  84     // 6 links in menu (cachedUrlList) + new default
  85     Assert.assertEquals(menulinks.size(), 6);
  86
  87     Assert.assertTrue(menulinks
  88             .contains("Test1|http://blah.blah/$SEQUENCE_ID$"));
  89     Assert.assertTrue(menulinks
  90             .contains("Test2|http://test2/$DB_ACCESSION$"));
  91     Assert.assertTrue(menulinks
  92             .contains("Test3|http://test3/$SEQUENCE_ID$"));
  93     Assert.assertTrue(menulinks
  94             .contains("UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$"));
  95     Assert.assertTrue(menulinks
  96             .contains("InterPro|http://identifiers.org/interpro/$DB_ACCESSION$"));
  97     Assert.assertTrue(menulinks.contains(UrlConstants.DEFAULT_LABEL
  98             + UrlConstants.SEP + emblUrl));
  99   }
 100
 101   @Test(groups = { "Functional" })
 102   public void testSetDefaultUrl()
 103   {
 104     // set custom url as default
 105     Assert.assertTrue(prov.setDefaultUrl("Test1"));
 106     Assert.assertEquals(prov.getDefaultUrlId(), "Test1");
 107
 108     // set identifiers url as default
 109     Assert.assertTrue(prov.setDefaultUrl("MIR:00000011"));
 110     Assert.assertEquals(prov.getDefaultUrlId(), "MIR:00000011");
 111   }
 112
 113   @Test(
 114     groups = { "Functional" },
 115     expectedExceptions = { IllegalArgumentException.class })
 116   public void testSetDefaultUrlWrongly()
 117   {
 118     // don't allow default to be a non-key
 119     prov.setDefaultUrl("not-a-key");
 120   }
 121 }