test/jalview/urls/UrlProviderTest.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 import jalview.util.UrlConstants;
  26
  27 import java.io.BufferedWriter;
  28 import java.io.File;
  29 import java.io.FileWriter;
  30 import java.io.IOException;
  31 import java.util.List;
  32
  33 import org.testng.Assert;
  34 import org.testng.annotations.BeforeMethod;
  35 import org.testng.annotations.Test;
  36
  37 public class UrlProviderTest
  38 {
  39
  40   // Test identifiers.org download file
  41   private static final String testIdOrgString = "{\"Local\": [{\"id\":\"MIR:00000002\",\"name\":\"ChEBI\",\"pattern\":\"^CHEBI:\\d+$\","
  42           + "\"definition\":\"Chemical Entities of Biological Interest (ChEBI)\",\"prefix\":\"chebi\","
  43           + "\"url\":\"http://identifiers.org/chebi\"},{\"id\":\"MIR:00000005\",\"name\":\"UniProt Knowledgebase\","
  44           + "\"pattern\":\"^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$\","
  45           + "\"definition\":\"The UniProt Knowledgebase (UniProtKB)\",\"prefix\":\"uniprot\",\"url\":\"http://identifiers.org/uniprot\"},"
  46           + "{\"id\":\"MIR:00000011\",\"name\":\"InterPro\",\"pattern\":\"^IPR\\d{6}$\",\"definition\":\"InterPro\",\"prefix\":\"interpro\","
  47           + "\"url\":\"http://identifiers.org/interpro\"},"
  48           + "{\"id\":\"MIR:00000372\",\"name\":\"ENA\",\"pattern\":\"^[A-Z]+[0-9]+(\\.\\d+)?$\",\"definition\":\"The European Nucleotide Archive (ENA),\""
  49           + "\"prefix\":\"ena.embl\",\"url\":\"http://identifiers.org/ena.embl\"}]}";
  50
  51   private UrlProviderI prov;
  52
  53   @BeforeMethod(alwaysRun = true)
  54   public void setup()
  55   {
  56     // make a dummy identifiers.org download file
  57     File temp = null;
  58
  59     try
  60     {
  61       temp = File.createTempFile("tempfile", ".tmp");
  62       temp.deleteOnExit();
  63       BufferedWriter bw = new BufferedWriter(new FileWriter(temp));
  64       bw.write(testIdOrgString);
  65       bw.close();
  66     } catch (IOException e)
  67     {
  68       System.out.println(
  69               "Error initialising UrlProviderTest test: " + e.getMessage());
  70     }
  71
  72     IdOrgSettings.setDownloadLocation(temp.getPath());
  73
  74     String defaultUrlString = "No default";
  75     String cachedUrlList = "MIR:00000005|MIR:00000011|Test1|http://blah.blah/$SEQUENCE_ID$|"
  76             + "Test2|http://test2/$DB_ACCESSION$|Test3|http://test3/$SEQUENCE_ID$";
  77     String userUrlList = "MIR:00000372|Test4|httpL//another.url/$SEQUENCE_ID$";
  78
  79     DesktopUrlProviderFactory factory = new DesktopUrlProviderFactory(
  80             defaultUrlString, cachedUrlList, userUrlList);
  81     prov = factory.createUrlProvider();
  82   }
  83
  84   @Test(groups = { "Functional" })
  85   public void testInitUrlProvider()
  86   {
  87     String emblUrl = UrlConstants.DEFAULT_STRING.substring(
  88             UrlConstants.DEFAULT_STRING.indexOf(UrlConstants.SEP) + 1,
  89             UrlConstants.DEFAULT_STRING.length());
  90
  91     // chooses EMBL url when default Url id does not exist in provided url lists
  92     Assert.assertEquals(prov.getPrimaryUrlId(), UrlConstants.DEFAULT_LABEL);
  93     Assert.assertEquals(prov.getPrimaryUrl("FER_CAPAN"),
  94             emblUrl.replace("$SEQUENCE_ID$", "FER_CAPAN"));
  95
  96     List<String> menulinks = prov.getLinksForMenu();
  97     List<UrlLinkDisplay> allLinks = prov.getLinksForTable();
  98
  99     // 9 links in provider - 4 from id file, 4 custom links, 1 additional
 100     // default
 101     Assert.assertEquals(allLinks.size(), 9);
 102
 103     // 6 links in menu (cachedUrlList) + new default
 104     Assert.assertEquals(menulinks.size(), 6);
 105
 106     Assert.assertTrue(
 107             menulinks.contains("Test1|http://blah.blah/$SEQUENCE_ID$"));
 108     Assert.assertTrue(
 109             menulinks.contains("Test2|http://test2/$DB_ACCESSION$"));
 110     Assert.assertTrue(
 111             menulinks.contains("Test3|http://test3/$SEQUENCE_ID$"));
 112     Assert.assertTrue(menulinks.contains(
 113             "UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$|uniprot"));
 114     Assert.assertTrue(menulinks.contains(
 115             "InterPro|http://identifiers.org/interpro/$DB_ACCESSION$|interpro"));
 116     Assert.assertTrue(menulinks.contains(
 117             UrlConstants.DEFAULT_LABEL + UrlConstants.SEP + emblUrl));
 118   }
 119
 120   @Test(groups = { "Functional" })
 121   public void testSetDefaultUrl()
 122   {
 123     // set custom url as default
 124     Assert.assertTrue(prov.setPrimaryUrl("Test1"));
 125     Assert.assertEquals(prov.getPrimaryUrlId(), "Test1");
 126
 127     // set identifiers url as default
 128     Assert.assertTrue(prov.setPrimaryUrl("MIR:00000011"));
 129     Assert.assertEquals(prov.getPrimaryUrlId(), "MIR:00000011");
 130   }
 131
 132   @Test(
 133     groups =
 134     { "Functional" },
 135     expectedExceptions =
 136     { IllegalArgumentException.class })
 137   public void testSetDefaultUrlWrongly()
 138   {
 139     // don't allow default to be a non-key
 140     prov.setPrimaryUrl("not-a-key");
 141   }
 142 }