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
  13 import org.testng.Assert;
  14 import org.testng.annotations.BeforeMethod;
  15 import org.testng.annotations.Test;
  16
  17 public class UrlProviderTest
  18 {
  19
  20   // Test identifiers.org download file
  21   private static final String testIdOrgString = "{\"Local\": [{\"id\":\"MIR:00000002\",\"name\":\"ChEBI\",\"pattern\":\"^CHEBI:\\d+$\","
  22           + "\"definition\":\"Chemical Entities of Biological Interest (ChEBI)\",\"prefix\":\"chebi\","
  23           + "\"url\":\"http://identifiers.org/chebi\"},{\"id\":\"MIR:00000005\",\"name\":\"UniProt Knowledgebase\","
  24           + "\"pattern\":\"^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$\","
  25           + "\"definition\":\"The UniProt Knowledgebase (UniProtKB)\",\"prefix\":\"uniprot\",\"url\":\"http://identifiers.org/uniprot\"},"
  26           + "{\"id\":\"MIR:00000011\",\"name\":\"InterPro\",\"pattern\":\"^IPR\\d{6}$\",\"definition\":\"InterPro\",\"prefix\":\"interpro\","
  27           + "\"url\":\"http://identifiers.org/interpro\"},"
  28           + "{\"id\":\"MIR:00000372\",\"name\":\"ENA\",\"pattern\":\"^[A-Z]+[0-9]+(\\.\\d+)?$\",\"definition\":\"The European Nucleotide Archive (ENA),\""
  29           + "\"prefix\":\"ena.embl\",\"url\":\"http://identifiers.org/ena.embl\"}]}";
  30
  31   private UrlProviderI prov;
  32
  33   @BeforeMethod(alwaysRun = true)
  34   public void setup()
  35   {
  36     // make a dummy identifiers.org download file
  37     File temp = null;
  38
  39     try
  40     {
  41       temp = File.createTempFile("tempfile", ".tmp");
  42       temp.deleteOnExit();
  43       BufferedWriter bw = new BufferedWriter(new FileWriter(temp));
  44       bw.write(testIdOrgString);
  45       bw.close();
  46     } catch (IOException e)
  47     {
  48       System.out.println(
  49               "Error initialising UrlProviderTest test: " + e.getMessage());
  50     }
  51
  52     IdOrgSettings.setDownloadLocation(temp.getPath());
  53
  54     String defaultUrlString = "No default";
  55     String cachedUrlList = "MIR:00000005|MIR:00000011|Test1|http://blah.blah/$SEQUENCE_ID$|"
  56             + "Test2|http://test2/$DB_ACCESSION$|Test3|http://test3/$SEQUENCE_ID$";
  57     String userUrlList = "MIR:00000372|Test4|httpL//another.url/$SEQUENCE_ID$";
  58
  59     DesktopUrlProviderFactory factory = new DesktopUrlProviderFactory(
  60             defaultUrlString, cachedUrlList, userUrlList);
  61     prov = factory.createUrlProvider();
  62   }
  63
  64   @Test(groups = { "Functional" })
  65   public void testInitUrlProvider()
  66   {
  67     String emblUrl = UrlConstants.DEFAULT_STRING.substring(
  68             UrlConstants.DEFAULT_STRING.indexOf(UrlConstants.SEP) + 1,
  69             UrlConstants.DEFAULT_STRING.length());
  70
  71     // chooses EMBL url when default Url id does not exist in provided url lists
  72     Assert.assertEquals(prov.getPrimaryUrlId(), UrlConstants.DEFAULT_LABEL);
  73     Assert.assertEquals(prov.getPrimaryUrl("FER_CAPAN"),
  74             emblUrl.replace("$SEQUENCE_ID$", "FER_CAPAN"));
  75
  76     List<String> menulinks = prov.getLinksForMenu();
  77     List<UrlLinkDisplay> allLinks = prov.getLinksForTable();
  78
  79     // 9 links in provider - 4 from id file, 4 custom links, 1 additional
  80     // default
  81     Assert.assertEquals(allLinks.size(), 9);
  82
  83     // 6 links in menu (cachedUrlList) + new default
  84     Assert.assertEquals(menulinks.size(), 6);
  85
  86     Assert.assertTrue(
  87             menulinks.contains("Test1|http://blah.blah/$SEQUENCE_ID$"));
  88     Assert.assertTrue(
  89             menulinks.contains("Test2|http://test2/$DB_ACCESSION$"));
  90     Assert.assertTrue(
  91             menulinks.contains("Test3|http://test3/$SEQUENCE_ID$"));
  92     Assert.assertTrue(menulinks.contains(
  93             "UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$|uniprot"));
  94     Assert.assertTrue(menulinks.contains(
  95             "InterPro|http://identifiers.org/interpro/$DB_ACCESSION$|interpro"));
  96     Assert.assertTrue(menulinks.contains(
  97             UrlConstants.DEFAULT_LABEL + UrlConstants.SEP + emblUrl));
  98   }
  99
 100   @Test(groups = { "Functional" })
 101   public void testSetDefaultUrl()
 102   {
 103     // set custom url as default
 104     Assert.assertTrue(prov.setPrimaryUrl("Test1"));
 105     Assert.assertEquals(prov.getPrimaryUrlId(), "Test1");
 106
 107     // set identifiers url as default
 108     Assert.assertTrue(prov.setPrimaryUrl("MIR:00000011"));
 109     Assert.assertEquals(prov.getPrimaryUrlId(), "MIR:00000011");
 110   }
 111
 112   @Test(
 113     groups =
 114     { "Functional" },
 115     expectedExceptions =
 116     { IllegalArgumentException.class })
 117   public void testSetDefaultUrlWrongly()
 118   {
 119     // don't allow default to be a non-key
 120     prov.setPrimaryUrl("not-a-key");
 121   }
 122 }