import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.Sequence;
+import jalview.gui.JvOptionPane;
import java.util.ArrayList;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class UrlLinkTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
final static String DB = "Test";
final static String URL_PREFIX = "http://www.jalview.org/";
// SEQUENCE_ID
UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
+ DELIM + URL_SUFFIX);
- assertEquals(DB.toUpperCase(), ul.getTarget());
+ assertEquals(DB, ul.getTarget());
assertEquals(DB, ul.getLabel());
- assertEquals(URL_PREFIX, ul.getUrl_prefix());
- assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+ assertEquals(URL_PREFIX, ul.getUrlPrefix());
+ assertEquals(URL_SUFFIX, ul.getUrlSuffix());
assertTrue(ul.isDynamic());
assertFalse(ul.usesDBAccession());
assertNull(ul.getRegexReplace());
// DB_ACCESSION
ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION + DELIM
+ URL_SUFFIX);
- assertEquals(DB.toUpperCase(), ul.getTarget());
+ assertEquals(DB, ul.getTarget());
assertEquals(DB, ul.getLabel());
- assertEquals(URL_PREFIX, ul.getUrl_prefix());
- assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+ assertEquals(URL_PREFIX, ul.getUrlPrefix());
+ assertEquals(URL_SUFFIX, ul.getUrlSuffix());
assertTrue(ul.isDynamic());
assertTrue(ul.usesDBAccession());
assertNull(ul.getRegexReplace());
// Not dynamic
ul = new UrlLink(DB + SEP + URL_PREFIX + URL_SUFFIX.substring(1));
- assertEquals(DB.toUpperCase(), ul.getTarget());
+ assertEquals(DB, ul.getTarget());
assertEquals(DB, ul.getLabel());
- assertEquals(URL_PREFIX + URL_SUFFIX.substring(1), ul.getUrl_prefix());
+ assertEquals(URL_PREFIX + URL_SUFFIX.substring(1), ul.getUrlPrefix());
assertFalse(ul.isDynamic());
assertFalse(ul.usesDBAccession());
assertNull(ul.getRegexReplace());
// SEQUENCE_ID
UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
+ REGEX_NESTED + DELIM + URL_SUFFIX);
- assertEquals(DB.toUpperCase(), ul.getTarget());
+ assertEquals(DB, ul.getTarget());
assertEquals(DB, ul.getLabel());
- assertEquals(URL_PREFIX, ul.getUrl_prefix());
- assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+ assertEquals(URL_PREFIX, ul.getUrlPrefix());
+ assertEquals(URL_SUFFIX, ul.getUrlSuffix());
assertTrue(ul.isDynamic());
assertFalse(ul.usesDBAccession());
assertEquals(REGEX_NESTED.substring(2, REGEX_NESTED.length() - 2),
// DB_ACCESSION
ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION
+ REGEX_NESTED + DELIM + URL_SUFFIX);
- assertEquals(DB.toUpperCase(), ul.getTarget());
+ assertEquals(DB, ul.getTarget());
assertEquals(DB, ul.getLabel());
- assertEquals(URL_PREFIX, ul.getUrl_prefix());
- assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+ assertEquals(URL_PREFIX, ul.getUrlPrefix());
+ assertEquals(URL_SUFFIX, ul.getUrlSuffix());
assertTrue(ul.isDynamic());
assertTrue(ul.usesDBAccession());
assertEquals(REGEX_NESTED.substring(2, REGEX_NESTED.length() - 2),
// invalid regex
ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION
+ REGEX_RUBBISH + DELIM + URL_SUFFIX);
- assertEquals(DB.toUpperCase(), ul.getTarget());
+ assertEquals(DB, ul.getTarget());
assertEquals(DB, ul.getLabel());
- assertEquals(URL_PREFIX, ul.getUrl_prefix());
- assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+ assertEquals(URL_PREFIX, ul.getUrlPrefix());
+ assertEquals(URL_SUFFIX, ul.getUrlSuffix());
assertTrue(ul.isDynamic());
assertTrue(ul.usesDBAccession());
assertEquals(REGEX_RUBBISH.substring(2, REGEX_RUBBISH.length() - 2),
String key = DB + SEP + URL_PREFIX;
assertEquals(1, linkset.size());
assertTrue(linkset.containsKey(key));
- assertEquals(linkset.get(key).get(0), DB.toUpperCase());
- assertEquals(linkset.get(key).get(1), DB);
- assertEquals(linkset.get(key).get(2), null);
- assertEquals(linkset.get(key).get(3), URL_PREFIX);
+ assertEquals(DB, linkset.get(key).get(0));
+ assertEquals(DB, linkset.get(key).get(1));
+ assertEquals(null, linkset.get(key).get(2));
+ assertEquals(URL_PREFIX, linkset.get(key).get(3));
}
/**
String key = DB + SEP + URL_PREFIX + URL_SUFFIX;
assertEquals(1, linkset.size());
assertTrue(linkset.containsKey(key));
- assertEquals(linkset.get(key).get(0), DB.toUpperCase());
- assertEquals(linkset.get(key).get(1), DB);
- assertEquals(linkset.get(key).get(2), null);
- assertEquals(linkset.get(key).get(3), URL_PREFIX + URL_SUFFIX);
+ assertEquals(DB, linkset.get(key).get(0));
+ assertEquals(DB, linkset.get(key).get(1));
+ assertEquals(null, linkset.get(key).get(2));
+ assertEquals(URL_PREFIX + URL_SUFFIX, linkset.get(key).get(3));
}
/**
+ URL_SUFFIX;
assertEquals(1, linkset.size());
assertTrue(linkset.containsKey(key));
- assertEquals(linkset.get(key).get(0), DB.toUpperCase());
- assertEquals(linkset.get(key).get(1), DB);
- assertEquals(linkset.get(key).get(2), seq0.getName());
- assertEquals(linkset.get(key).get(3), URL_PREFIX + seq0.getName()
- + URL_SUFFIX);
+ assertEquals(DB, linkset.get(key).get(0));
+ assertEquals(DB, linkset.get(key).get(1));
+ assertEquals(seq0.getName(), linkset.get(key).get(2));
+ assertEquals(URL_PREFIX + seq0.getName() + URL_SUFFIX, linkset.get(key)
+ .get(3));
// Test where link takes a db annotation id and only has one dbref
ul = new UrlLink(links.get(1));
ul.createLinksFromSeq(seq0, linkset);
key = "P83527|http://www.uniprot.org/uniprot/P83527";
- assertEquals(1, linkset.size());
+ assertEquals(linkset.size(), 1);
assertTrue(linkset.containsKey(key));
- assertEquals(linkset.get(key).get(0), DBRefSource.UNIPROT);
- assertEquals(linkset.get(key).get(1), DBRefSource.UNIPROT + SEP
- + "P83527");
- assertEquals(linkset.get(key).get(2), "P83527");
- assertEquals(linkset.get(key).get(3),
- "http://www.uniprot.org/uniprot/P83527");
+ assertEquals(DBRefSource.UNIPROT, linkset.get(key).get(0));
+ assertEquals(DBRefSource.UNIPROT + SEP + "P83527", linkset.get(key)
+ .get(1));
+ assertEquals("P83527", linkset.get(key).get(2));
+ assertEquals("http://www.uniprot.org/uniprot/P83527", linkset.get(key)
+ .get(3));
// Test where link takes a db annotation id and has multiple dbrefs
ul = new UrlLink(links.get(2));
// check each link made it in correctly
key = "IPR001041|http://www.ebi.ac.uk/interpro/entry/IPR001041";
assertTrue(linkset.containsKey(key));
- assertEquals(linkset.get(key).get(0), "INTERPRO");
- assertEquals(linkset.get(key).get(1), "INTERPRO" + SEP + "IPR001041");
- assertEquals(linkset.get(key).get(2), "IPR001041");
- assertEquals(linkset.get(key).get(3),
- "http://www.ebi.ac.uk/interpro/entry/IPR001041");
+ assertEquals("INTERPRO", linkset.get(key).get(0));
+ assertEquals("INTERPRO" + SEP + "IPR001041", linkset.get(key).get(1));
+ assertEquals("IPR001041", linkset.get(key).get(2));
+ assertEquals("http://www.ebi.ac.uk/interpro/entry/IPR001041", linkset
+ .get(key).get(3));
key = "IPR006058|http://www.ebi.ac.uk/interpro/entry/IPR006058";
assertTrue(linkset.containsKey(key));
- assertEquals(linkset.get(key).get(0), "INTERPRO");
- assertEquals(linkset.get(key).get(1), "INTERPRO" + SEP + "IPR006058");
- assertEquals(linkset.get(key).get(2), "IPR006058");
- assertEquals(linkset.get(key).get(3),
- "http://www.ebi.ac.uk/interpro/entry/IPR006058");
+ assertEquals("INTERPRO", linkset.get(key).get(0));
+ assertEquals("INTERPRO" + SEP + "IPR006058", linkset.get(key).get(1));
+ assertEquals("IPR006058", linkset.get(key).get(2));
+ assertEquals("http://www.ebi.ac.uk/interpro/entry/IPR006058", linkset
+ .get(key).get(3));
key = "IPR012675|http://www.ebi.ac.uk/interpro/entry/IPR012675";
assertTrue(linkset.containsKey(key));
- assertEquals(linkset.get(key).get(0), "INTERPRO");
- assertEquals(linkset.get(key).get(1), "INTERPRO" + SEP + "IPR012675");
- assertEquals(linkset.get(key).get(2), "IPR012675");
- assertEquals(linkset.get(key).get(3),
- "http://www.ebi.ac.uk/interpro/entry/IPR012675");
+ assertEquals("INTERPRO", linkset.get(key).get(0));
+ assertEquals("INTERPRO" + SEP + "IPR012675", linkset.get(key).get(1));
+ assertEquals("IPR012675", linkset.get(key).get(2));
+ assertEquals("http://www.ebi.ac.uk/interpro/entry/IPR012675", linkset
+ .get(key).get(3));
// Test where there are no matching dbrefs for the link
ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION + DELIM
assertTrue(linkset.isEmpty());
}
+ /**
+ * Test links where label and target are both included
+ */
+ @Test(groups = { "Functional" })
+ public void testLinksWithTargets()
+ {
+ UrlLink ul = new UrlLink(
+ "Protein Data Bank | http://www.identifiers.org/pdb/$"
+ + DB_ACCESSION + "$" + " | pdb");
+
+ assertEquals("Protein Data Bank", ul.getLabel());
+ assertEquals("pdb", ul.getTarget());
+ assertEquals("http://www.identifiers.org/pdb/$" + DB_ACCESSION + "$",
+ ul.getUrlWithToken());
+
+ assertEquals("Protein Data Bank|http://www.identifiers.org/pdb/$"
+ + DB_ACCESSION + "$" + "|pdb", ul.toStringWithTarget());
+
+ ul = new UrlLink("Protein Data Bank",
+ "http://www.identifiers.org/pdb/$" + DB_ACCESSION + "$", "pdb");
+
+ assertEquals("Protein Data Bank", ul.getLabel());
+ assertEquals("pdb", ul.getTarget());
+ assertEquals("http://www.identifiers.org/pdb/$" + DB_ACCESSION + "$",
+ ul.getUrlWithToken());
+
+ assertEquals("Protein Data Bank|http://www.identifiers.org/pdb/$"
+ + DB_ACCESSION + "$" + "|pdb", ul.toStringWithTarget());
+
+ }
+
}