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;
import java.util.HashMap;
import java.util.Vector;
+import org.testng.annotations.BeforeClass;
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+)?$\","
+ "{\"id\":\"MIR:00000011\",\"name\":\"InterPro\",\"pattern\":\"^IPR\\d{6}$\",\"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$",
+ "MIR:00000372|http://identifiers.org/ena.embl/$DB_ACCESSION$" };
+
+ private static final String[] dlinks2 = {
+ "MIR:00000005|http://identifiers.org/uniprot/$DB_ACCESSION$",
+ "MIR:00000011|http://identifiers.org/interpro/$DB_ACCESSION$" };
private static final String stringLinks = "MIR:00000005|http://identifiers.org/uniprot/$DB_ACCESSION$"
+ "MIR:00000011|http://identifiers.org/interpro/$DB_ACCESSION$"
+ "MIR:00000372|http://identifiers.org/ena.embl/$DB_ACCESSION$";
+ private static final String[] unselDlinks = { "ChEBI|http://identifiers.org/chebi/$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));
+
+ private static final Vector<String> displayLinks2 = new Vector<String>(
+ Arrays.asList(dlinks2));
+
private static final HashMap<String, String> urlMap = new HashMap<String, String>()
{
{
}
};
+ private String testfile = "";
+
+
+ @BeforeClass(alwaysRun = true)
+ public void setup()
+ {
+ // setup test ids in a file
+ File outFile = null;
+ try
+ {
+ outFile = File.createTempFile("testidsfile", "txt");
+ outFile.deleteOnExit();
+
+ FileWriter fw = new FileWriter(outFile);
+ fw.write(testIdOrgFile);
+ fw.close();
+
+ testfile = outFile.getAbsolutePath();
+
+ } catch (Exception ex)
+ {
+ System.err.println(ex);
+ }
+
+ IdOrgSettings.setDownloadLocation(testfile);
+ }
+
/*
* Test urls are set and returned correctly
*/
{
// creation from cached id list
String idList = "MIR:00000005|MIR:00000011|MIR:00000372";
- UrlProviderI idProv = new IdentifiersUrlProvider(idList, testIdOrgFile);
+ 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, testIdOrgFile);
- 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()));
}
{
// creation from cached id list
String idList = "MIR:00000005|MIR:00000011|MIR:00000372";
- UrlProviderI idProv = new IdentifiersUrlProvider(idList, testIdOrgFile);
+ 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, testIdOrgFile);
-
- // 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);
- assertEquals(names, idProv.getLinksForDisplay());
-
- //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);
- assertEquals(names, idProv.getLinksForDisplay());
- assertEquals(null, idProv.getDefaultUrl());
-
+ assertEquals(null, idProv.choosePrimaryUrl());
}
}