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+)?$\","
+ "{\"id\":\"MIR:00000011\",\"name\":\"InterPro\",\"pattern\":\"^IPR\\d{6}$\",\"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$|interpro",
+ "MIR:00000011|http://identifiers.org/interpro/$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));
private String testfile = "";
-
@BeforeClass(alwaysRun = true)
public void setup()
{
// 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
// 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"));