JAL-2316 Unit test for IdentifiersUrlProvider

diff --git a/test/jalview/urls/CustomUrlProviderTest.java b/test/jalview/urls/CustomUrlProviderTest.java
index b536566..62d7806 100644 (file)
--- a/test/jalview/urls/CustomUrlProviderTest.java
+++ b/test/jalview/urls/CustomUrlProviderTest.java
@@ -118,6 +118,8 @@ public class CustomUrlProviderTest
     assertTrue(displayLinks.containsAll(customProv2.getLinksForDisplay()));
 
     // writing url links as a string works
+    // 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 = customProv.writeUrlsAsString();
     UrlProviderI up = new CustomUrlProvider(result);
     assertTrue(displayLinks.containsAll(up.getLinksForDisplay()));

diff --git a/test/jalview/urls/IdentifiersUrlProviderTest.java b/test/jalview/urls/IdentifiersUrlProviderTest.java
new file mode 100644 (file)
index 0000000..d8776f4
--- /dev/null
+++ b/test/jalview/urls/IdentifiersUrlProviderTest.java
@@ -0,0 +1,143 @@
+/*
+ * 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 java.util.Arrays;
+import java.util.HashMap;
+import java.util.Vector;
+
+import org.testng.annotations.Test;
+
+public class IdentifiersUrlProviderTest
+{
+  // Test identifiers.org download file
+  private static final String testIdOrgFile = "[{\"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 = {
+    "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 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 Vector<String> displayLinks = new Vector<String>(
+        Arrays.asList(dlinks));
+  
+  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/$DB_ACCESSION$");
+    }
+  };
+
+  /*
+   * 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, testIdOrgFile);
+    
+    assertTrue(displayLinks.containsAll(idProv.getLinksForDisplay()));
+
+    // 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();
+    UrlProviderI up = new IdentifiersUrlProvider(result, testIdOrgFile);
+    assertTrue(displayLinks.containsAll(up.getLinksForDisplay()));
+
+  }
+
+  /*
+   * 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, testIdOrgFile);
+    
+    // initially no default
+    assertEquals(null, idProv.getDefaultUrl());
+    
+    // set and then retrieve default
+    assertTrue(idProv.setDefaultUrl("MIR:00000005"));
+    assertEquals("MIR:00000005", idProv.getDefaultUrl());
+    assertEquals("http://identifiers.org/uniprot/id",
+            idProv.getDefaultUrl("id"));
+
+    // attempt to set bad default
+    assertFalse(idProv.setDefaultUrl("MIR:00001234"));
+    // default set to null (as default should have been set elsewhere)
+    assertEquals(null, idProv.getDefaultUrl());
+
+    // chooseDefaultUrl not implemented for IdentifiersUrlProvider
+    assertEquals(null, idProv.chooseDefaultUrl());
+  }
+
+  /*
+   * Test url setting works
+   */
+  @Test(groups = { "Functional" })
+  public void testSetUrlLinks()
+  {
+    // creation from cached id list
+    String idList = "MIR:00000005|MIR:00000011|MIR:00000372";
+    UrlProviderI idProv = new IdentifiersUrlProvider(idList, testIdOrgFile);
+
+    // set url links
+    String[] ids = { "MIR:00000372", "MIR:00000011" };
+    Vector<String> names = new Vector<String>(Arrays.asList(ids));
+    Vector<String> urls = null;
+    idProv.setUrlLinks(names, urls);
+    assertEquals(names, idProv.getLinksForDisplay());
+    
+    //set default url then reset url links, default should be unset if not present
+    String[] moreids = { "MIR:00000005", "MIR:00000011" };
+    names = new Vector<String>(Arrays.asList(moreids));
+    idProv.setDefaultUrl("MIR:00000372");
+    idProv.setUrlLinks(names, urls);
+    assertEquals(names, idProv.getLinksForDisplay());
+    assertEquals(null, idProv.getDefaultUrl());
+
+  }
+}