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$",
- "InterPro|http://identifiers.org/interpro/$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$",
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());
}
}