JAL-3858 improved contactInterval computation and added detailed test coverage for...

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

diff --git a/test/jalview/urls/IdentifiersUrlProviderTest.java b/test/jalview/urls/IdentifiersUrlProviderTest.java
index 9c8c96a..1fb3146 100644 (file)
--- a/test/jalview/urls/IdentifiersUrlProviderTest.java
+++ b/test/jalview/urls/IdentifiersUrlProviderTest.java
@@ -38,8 +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+)?$\","
@@ -47,8 +46,8 @@ public class IdentifiersUrlProviderTest
           + "{\"id\":\"MIR:00000011\",\"name\":\"InterPro\",\"pattern\":\"^IPR\\d{6}$\",\"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$|uniprot",
       "InterPro|http://identifiers.org/interpro/$DB_ACCESSION$|interpro",
@@ -66,11 +65,12 @@ public class IdentifiersUrlProviderTest
           + "MIR:00000011|http://identifiers.org/interpro/$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 String[] unselDlinks = {
+      "ChEBI|http://identifiers.org/chebi/$DB_ACCESSION$" };
 
   private static final Vector<String> displayLinks = new Vector<String>(
-        Arrays.asList(dlinks));
-  
+          Arrays.asList(dlinks));
+
   private static final Vector<String> unselDisplayLinks = new Vector<String>(
           Arrays.asList(unselDlinks));
 
@@ -91,7 +91,6 @@ public class IdentifiersUrlProviderTest
 
   private String testfile = "";
 
-
   @BeforeClass(alwaysRun = true)
   public void setup()
   {
@@ -125,7 +124,7 @@ public class IdentifiersUrlProviderTest
     // 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
@@ -149,18 +148,17 @@ public class IdentifiersUrlProviderTest
     // 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"));
+    assertEquals(null, idProv.getPrimaryUrl("123"));
 
     // attempt to set bad default
     assertFalse(idProv.setPrimaryUrl("MIR:00001234"));