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Merge branch 'documentation/JAL-3766_relnotes' into releases/Release_2_11_1_Branch
[jalview.git] / test / jalview / urls / IdentifiersUrlProviderTest.java
diff --git a/test/jalview/urls/IdentifiersUrlProviderTest.java b/test/jalview/urls/IdentifiersUrlProviderTest.java
index 843e2d5..eed58b0 100644 (file)
--- a/test/jalview/urls/IdentifiersUrlProviderTest.java
+++ b/test/jalview/urls/IdentifiersUrlProviderTest.java
@@ -25,6 +25,8 @@ 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;
@@ -36,8 +38,7 @@ 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+$\","
+  private static final String testIdOrgFile = "{\"Local\": [{\"id\":\"MIR:00000002\",\"name\":\"ChEBI\",\"pattern\":\"^CHEBI:\\d+$\","
           + "\"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+)?$\","
@@ -45,12 +46,12 @@ public class IdentifiersUrlProviderTest
           + "{\"id\":\"MIR:00000011\",\"name\":\"InterPro\",\"pattern\":\"^IPR\\d{6}$\",\"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\"}]";
+          + "\"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/$DB_ACCESSION$|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/$DB_ACCESSION$",
@@ -64,9 +65,14 @@ public class IdentifiersUrlProviderTest
           + "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));
 
@@ -105,6 +111,8 @@ public class IdentifiersUrlProviderTest
     {
       System.err.println(ex);
     }
+
+    IdOrgSettings.setDownloadLocation(testfile);
   }
 
   /*
@@ -115,15 +123,19 @@ public class IdentifiersUrlProviderTest
   {
     // creation from cached id list
     String idList = "MIR:00000005|MIR:00000011|MIR:00000372";
-    UrlProviderI idProv = new IdentifiersUrlProvider(idList, testfile);
+    UrlProviderI idProv = new IdentifiersUrlProvider(idList);
     
-    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, testfile);
-    assertTrue(displayLinks.containsAll(up.getLinksForDisplay()));
+    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()));
 
   }
 
@@ -135,54 +147,26 @@ public class IdentifiersUrlProviderTest
   {
     // creation from cached id list
     String idList = "MIR:00000005|MIR:00000011|MIR:00000372";
-    UrlProviderI idProv = new IdentifiersUrlProvider(idList, testfile);
+    UrlProviderI idProv = new IdentifiersUrlProvider(idList);
     
     // initially no default
-    assertEquals(null, idProv.getDefaultUrl());
+    assertEquals(null, idProv.getPrimaryUrl("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"));
+    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.setDefaultUrl("MIR:00001234"));
+    assertFalse(idProv.setPrimaryUrl("MIR:00001234"));
     // default set to null (as default should have been set elsewhere)
-    assertEquals(null, idProv.getDefaultUrl());
+    assertEquals(null, idProv.getPrimaryUrl("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, testfile);
-
-    // 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);
-    Vector<String> result = idProv.getLinksForDisplay();
-    assertEquals(displayLinks1.size(), result.size());
-    assertTrue(displayLinks1.containsAll(result));
-    
-    //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);
-    result = idProv.getLinksForDisplay();
-    assertEquals(displayLinks2.size(), result.size());
-    assertTrue(displayLinks2.containsAll(result));
-    assertEquals(null, idProv.getDefaultUrl());
-
+    assertEquals(null, idProv.choosePrimaryUrl());
   }
 }