X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Furls%2FIdentifiersUrlProviderTest.java;fp=test%2Fjalview%2Furls%2FIdentifiersUrlProviderTest.java;h=eed58b0eeee55c1d15ef62785513c0acc9c8145a;hb=2595e9d4ee0dbbd3406a98c4e49a61ccde806479;hp=0000000000000000000000000000000000000000;hpb=e20075ba805d744d7cc4976e2b8d5e5840fb0a8d;p=jalview.git

diff --git a/test/jalview/urls/IdentifiersUrlProviderTest.java b/test/jalview/urls/IdentifiersUrlProviderTest.java
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+++ b/test/jalview/urls/IdentifiersUrlProviderTest.java
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+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+package jalview.urls;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.urls.api.UrlProviderI;
+
+import java.io.File;
+import java.io.FileWriter;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Vector;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class IdentifiersUrlProviderTest
+{
+  private static final String testIdOrgFile = "{\"Local\": [{\"id\":\"MIR:00000002\",\"name\":\"ChEBI\",\"pattern\":\"^CHEBI:\\d+$\","
+          + "\"definition\":\"Chemical Entities of Biological Interest (ChEBI)\",\"prefix\":\"chebi\","
+          + "\"url\":\"http://identifiers.org/chebi\"},{\"id\":\"MIR:00000005\",\"name\":\"UniProt Knowledgebase\","
+          + "\"pattern\":\"^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$\","
+          + "\"definition\":\"The UniProt Knowledgebase (UniProtKB)\",\"prefix\":\"uniprot\",\"url\":\"http://identifiers.org/uniprot\"},"
+          + "{\"id\":\"MIR:00000011\",\"name\":\"InterPro\",\"pattern\":\"^IPR\\d{6}$\",\"definition\":\"InterPro\",\"prefix\":\"interpro\","
+          + "\"url\":\"http://identifiers.org/interpro\"},"
+          + "{\"id\":\"MIR:00000372\",\"name\":\"ENA\",\"pattern\":\"^[A-Z]+[0-9]+(\\.\\d+)?$\",\"definition\":\"The European Nucleotide Archive (ENA),\""
+          + "\"prefix\":\"ena.embl\",\"url\":\"http://identifiers.org/ena.embl\"}]}";
+  
+  private static final String[] dlinks = {
+      "UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$|uniprot",
+      "InterPro|http://identifiers.org/interpro/$DB_ACCESSION$|interpro",
+      "ENA|http://identifiers.org/ena.embl/$DB_ACCESSION$|ena.embl" };
+
+  private static final String[] dlinks1 = {
+      "MIR:00000011|http://identifiers.org/interpro/$DB_ACCESSION$",
+      "MIR:00000372|http://identifiers.org/ena.embl/$DB_ACCESSION$" };
+
+  private static final String[] dlinks2 = {
+      "MIR:00000005|http://identifiers.org/uniprot/$DB_ACCESSION$",
+      "MIR:00000011|http://identifiers.org/interpro/$DB_ACCESSION$" };
+
+  private static final String stringLinks = "MIR:00000005|http://identifiers.org/uniprot/$DB_ACCESSION$"
+          + "MIR:00000011|http://identifiers.org/interpro/$DB_ACCESSION$"
+          + "MIR:00000372|http://identifiers.org/ena.embl/$DB_ACCESSION$";
+
+  private static final String[] unselDlinks = { "ChEBI|http://identifiers.org/chebi/$DB_ACCESSION$" };
+
+  private static final Vector<String> displayLinks = new Vector<String>(
+        Arrays.asList(dlinks));
+  
+  private static final Vector<String> unselDisplayLinks = new Vector<String>(
+          Arrays.asList(unselDlinks));
+
+  private static final Vector<String> displayLinks1 = new Vector<String>(
+          Arrays.asList(dlinks1));
+
+  private static final Vector<String> displayLinks2 = new Vector<String>(
+          Arrays.asList(dlinks2));
+
+  private static final HashMap<String, String> urlMap = new HashMap<String, String>()
+  {
+    {
+      put("MIR:00000005", "http://identifiers.org/uniprot/$DB_ACCESSION$");
+      put("MIR:00000011", "http://identifiers.org/interpro/$DB_ACCESSION$");
+      put("MIR:00000372", "http://identifiers.org/ena.embl/$DB_ACCESSION$");
+    }
+  };
+
+  private String testfile = "";
+
+
+  @BeforeClass(alwaysRun = true)
+  public void setup()
+  {
+    // setup test ids in a file
+    File outFile = null;
+    try
+    {
+      outFile = File.createTempFile("testidsfile", "txt");
+      outFile.deleteOnExit();
+
+      FileWriter fw = new FileWriter(outFile);
+      fw.write(testIdOrgFile);
+      fw.close();
+
+      testfile = outFile.getAbsolutePath();
+
+    } catch (Exception ex)
+    {
+      System.err.println(ex);
+    }
+
+    IdOrgSettings.setDownloadLocation(testfile);
+  }
+
+  /*
+   * Test urls are set and returned correctly
+   */
+  @Test(groups = { "Functional" })
+  public void testUrlLinks()
+  {
+    // creation from cached id list
+    String idList = "MIR:00000005|MIR:00000011|MIR:00000372";
+    UrlProviderI idProv = new IdentifiersUrlProvider(idList);
+    
+    assertTrue(displayLinks.containsAll(idProv.getLinksForMenu()));
+
+    // because UrlProvider does not guarantee order of links, we can't just
+    // compare the output of writeUrlsAsString to a string, hence the hoops here
+    String result = idProv.writeUrlsAsString(true);
+    UrlProviderI up = new IdentifiersUrlProvider(result);
+    assertTrue(displayLinks.containsAll(up.getLinksForMenu()));
+
+    result = idProv.writeUrlsAsString(false);
+    up = new IdentifiersUrlProvider(result);
+    assertTrue(unselDisplayLinks.containsAll(up.getLinksForMenu()));
+
+  }
+
+  /*
+   * Test default is set and returned correctly
+   */
+  @Test(groups = { "Functional" })
+  public void testDefaultUrl()
+  {
+    // creation from cached id list
+    String idList = "MIR:00000005|MIR:00000011|MIR:00000372";
+    UrlProviderI idProv = new IdentifiersUrlProvider(idList);
+    
+    // initially no default
+    assertEquals(null, idProv.getPrimaryUrl("seqid"));
+    
+    // set and then retrieve default
+    assertTrue(idProv.setPrimaryUrl("MIR:00000005"));
+    assertEquals("http://identifiers.org/uniprot/seqid",
+            idProv.getPrimaryUrl("seqid"));
+
+    // ids less than length 4 return null
+    assertEquals(null,
+            idProv.getPrimaryUrl("123"));
+
+    // attempt to set bad default
+    assertFalse(idProv.setPrimaryUrl("MIR:00001234"));
+    // default set to null (as default should have been set elsewhere)
+    assertEquals(null, idProv.getPrimaryUrl("seqid"));
+
+    // chooseDefaultUrl not implemented for IdentifiersUrlProvider
+    assertEquals(null, idProv.choosePrimaryUrl());
+  }
+}