X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Furls%2FIdentifiersUrlProviderTest.java;h=eed58b0eeee55c1d15ef62785513c0acc9c8145a;hb=5f3fb4c5ccabbfd15911ca2d991be31fbb11a6dd;hp=8ea47c983ac22c536e96b509e63f8bd793454559;hpb=a889a61789f15e79ecde7043cddfdea18ad00166;p=jalview.git

diff --git a/test/jalview/urls/IdentifiersUrlProviderTest.java b/test/jalview/urls/IdentifiersUrlProviderTest.java
index 8ea47c9..eed58b0 100644
--- 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 = {
-      "UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$",
-      "InterPro|http://identifiers.org/interpro/$DB_ACCESSION$",
-      "ENA|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);
   }
 
   /*
@@ -115,16 +123,20 @@ 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.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);
+    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()));
+
   }
 
   /*
@@ -135,26 +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("seqid"));
+    assertEquals(null, idProv.getPrimaryUrl("seqid"));
     
     // set and then retrieve default
-    assertTrue(idProv.setDefaultUrl("MIR:00000005"));
+    assertTrue(idProv.setPrimaryUrl("MIR:00000005"));
     assertEquals("http://identifiers.org/uniprot/seqid",
-            idProv.getDefaultUrl("seqid"));
+            idProv.getPrimaryUrl("seqid"));
 
     // ids less than length 4 return null
     assertEquals(null,
-            idProv.getDefaultUrl("123"));
+            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("seqid"));
+    assertEquals(null, idProv.getPrimaryUrl("seqid"));
 
     // chooseDefaultUrl not implemented for IdentifiersUrlProvider
-    assertEquals(null, idProv.chooseDefaultUrl());
+    assertEquals(null, idProv.choosePrimaryUrl());
   }
 }