JAL-2316 Adjusted unit tests. Tidied UrlLinkProviderI interface.

[jalview.git] / test / jalview / urls / IdentifiersUrlProviderTest.java

diff --git a/test/jalview/urls/IdentifiersUrlProviderTest.java b/test/jalview/urls/IdentifiersUrlProviderTest.java
index d8776f4..8ea47c9 100644 (file)
--- a/test/jalview/urls/IdentifiersUrlProviderTest.java
+++ b/test/jalview/urls/IdentifiersUrlProviderTest.java
@@ -25,10 +25,13 @@ import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
 
+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
@@ -45,18 +48,31 @@ public class IdentifiersUrlProviderTest
           + "\"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/$DB_ACCESSION$"};
+      "UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$",
+      "InterPro|http://identifiers.org/interpro/$DB_ACCESSION$",
+      "ENA|http://identifiers.org/ena.embl/$DB_ACCESSION$" };
+
+  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 Vector<String> displayLinks = new Vector<String>(
         Arrays.asList(dlinks));
   
+  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>()
   {
     {
@@ -66,6 +82,31 @@ public class IdentifiersUrlProviderTest
     }
   };
 
+  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);
+    }
+  }
+
   /*
    * Test urls are set and returned correctly
    */
@@ -74,15 +115,15 @@ public class IdentifiersUrlProviderTest
   {
     // creation from cached id list
     String idList = "MIR:00000005|MIR:00000011|MIR:00000372";
-    UrlProviderI idProv = new IdentifiersUrlProvider(idList, testIdOrgFile);
+    UrlProviderI idProv = new IdentifiersUrlProvider(idList, testfile);
     
-    assertTrue(displayLinks.containsAll(idProv.getLinksForDisplay()));
+    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();
-    UrlProviderI up = new IdentifiersUrlProvider(result, testIdOrgFile);
-    assertTrue(displayLinks.containsAll(up.getLinksForDisplay()));
+    UrlProviderI up = new IdentifiersUrlProvider(result, testfile);
+    assertTrue(displayLinks.containsAll(up.getLinksForMenu()));
 
   }
 
@@ -94,50 +135,26 @@ public class IdentifiersUrlProviderTest
   {
     // creation from cached id list
     String idList = "MIR:00000005|MIR:00000011|MIR:00000372";
-    UrlProviderI idProv = new IdentifiersUrlProvider(idList, testIdOrgFile);
+    UrlProviderI idProv = new IdentifiersUrlProvider(idList, testfile);
     
     // initially no default
-    assertEquals(null, idProv.getDefaultUrl());
+    assertEquals(null, idProv.getDefaultUrl("seqid"));
     
     // set and then retrieve default
     assertTrue(idProv.setDefaultUrl("MIR:00000005"));
-    assertEquals("MIR:00000005", idProv.getDefaultUrl());
-    assertEquals("http://identifiers.org/uniprot/id",
-            idProv.getDefaultUrl("id"));
+    assertEquals("http://identifiers.org/uniprot/seqid",
+            idProv.getDefaultUrl("seqid"));
+
+    // ids less than length 4 return null
+    assertEquals(null,
+            idProv.getDefaultUrl("123"));
 
     // 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());
+    assertEquals(null, idProv.getDefaultUrl("seqid"));
 
     // 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());
-
-  }
 }