import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.Sequence;
+
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
import org.testng.annotations.Test;
public class UrlLinkTest
}
/**
- * Test construction of link by substituting sequence id or name
+ * Test construction of link by substituting sequence id or name using regular
+ * expression
*/
@Test(groups = { "Functional" })
public void testMakeUrlWithRegex()
assertNull(ul.getInvalidMessage());
}
+ /**
+ * Test creating links with null sequence
+ */
+ @Test(groups = { "Functional" })
+ public void testCreateLinksFromNullSequence()
+ {
+ UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_NAME
+ + DELIM + URL_SUFFIX);
+
+ Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+ ul.createLinksFromSeq(null, linkset);
+
+ 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);
+ }
+
+ /**
+ * Test creating links with non-dynamic urlLink
+ */
+ @Test(groups = { "Functional" })
+ public void testCreateLinksForNonDynamic()
+ {
+ UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + URL_SUFFIX);
+
+ Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+ ul.createLinksFromSeq(null, linkset);
+
+ 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);
+ }
+
+ /**
+ * Test creating links
+ */
+ @Test(groups = { "Functional" })
+ public void testCreateLinksFromSequence()
+ {
+
+ // create list of links and list of DBRefs
+ List<String> links = new ArrayList<String>();
+ List<DBRefEntry> refs = new ArrayList<DBRefEntry>();
+
+ // links as might be added into Preferences | Connections dialog
+ links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
+ + SEQUENCE_NAME + "$");
+ links.add("UNIPROT | http://www.uniprot.org/uniprot/$" + SEQUENCE_ID
+ + "$");
+ links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
+ + SEQUENCE_ID + "$");
+
+ // make seq0 dbrefs
+ refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
+ refs.add(new DBRefEntry("INTERPRO", "1", "IPR001041"));
+ refs.add(new DBRefEntry("INTERPRO", "1", "IPR006058"));
+ refs.add(new DBRefEntry("INTERPRO", "1", "IPR012675"));
+
+ Sequence seq0 = new Sequence("FER1", "AKPNGVL");
+
+ // add all the dbrefs to the sequence
+ seq0.addDBRef(refs.get(0));
+ seq0.addDBRef(refs.get(1));
+ seq0.addDBRef(refs.get(2));
+ seq0.addDBRef(refs.get(3));
+ seq0.createDatasetSequence();
+
+ // Test where link takes a sequence id as replacement
+ UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_NAME
+ + DELIM + URL_SUFFIX);
+
+ Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+ ul.createLinksFromSeq(seq0, linkset);
+
+ String key = seq0.getName() + SEP + URL_PREFIX + seq0.getName()
+ + 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);
+
+ // Test where link takes a db annotation id and only has one dbref
+ ul = new UrlLink(links.get(1));
+ linkset = new LinkedHashMap<String, List<String>>();
+ ul.createLinksFromSeq(seq0, linkset);
+
+ key = "P83527|http://www.uniprot.org/uniprot/P83527";
+ assertEquals(1, linkset.size());
+ 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");
+
+ // Test where link takes a db annotation id and has multiple dbrefs
+ ul = new UrlLink(links.get(2));
+ linkset = new LinkedHashMap<String, List<String>>();
+ ul.createLinksFromSeq(seq0, linkset);
+ assertEquals(3, linkset.size());
+
+ // 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");
+
+ 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");
+
+ 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");
+
+ // Test where there are no matching dbrefs for the link
+ ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID + DELIM
+ + URL_SUFFIX);
+ linkset = new LinkedHashMap<String, List<String>>();
+ ul.createLinksFromSeq(seq0, linkset);
+ assertTrue(linkset.isEmpty());
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff