test/jalview/urls/UrlProviderTest.java

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