/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.ws.seqfetcher;
-import static org.junit.Assert.*;
-
-import java.util.ArrayList;
-import java.util.List;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+import jalview.analysis.CrossRef;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
-import jalview.ws.DBRefFetcher;
+import jalview.datamodel.FeatureProperties;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.util.DBRefUtils;
import jalview.ws.SequenceFetcher;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
/**
* @author jimp
/**
* @throws java.lang.Exception
*/
- @BeforeClass
+ @BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
+ jalview.bin.Cache.initLogger();
}
/**
{
}
- @Test
+ /**
+ * Tests that standard protein database sources include Uniprot (as the first)
+ * and also PDB. (Additional sources are dependent on available of DAS
+ * services.)
+ */
+ @Test(groups = { "Functional" })
public void testStandardProtDbs()
{
String[] defdb = DBRefSource.PROTEINDBS;
srces.addAll(srcesfordb);
}
}
- DbSourceProxy uniprot = null;
+
int i = 0;
+ int uniprotPos = -1;
+ int pdbPos = -1;
// append the selected sequence sources to the default dbs
for (DbSourceProxy s : srces)
{
- if (s.getDbSource().equalsIgnoreCase(DBRefSource.UNIPROT))
+ if (s instanceof jalview.ws.dbsources.Uniprot)
{
- i++;
+ uniprotPos = i;
}
-
- if (s instanceof jalview.ws.dbsources.Uniprot)
+ if (s instanceof jalview.ws.dbsources.Pdb)
{
- uniprot = s;
- break;
+ pdbPos = i;
}
+ i++;
}
assertTrue("Failed to find Uniprot source as first source amongst "
- + srces.size() + " sources (source was at position " + i + ")",
- uniprot != null && i < 2);
+ + srces.size() + " sources (source was at position "
+ + uniprotPos + ")", uniprotPos == 0);
+ assertTrue("Failed to find PDB source amongst " + srces.size()
+ + " sources", pdbPos >= 0);
+ }
+
+ /**
+ * Tests retrieval of one entry from EMBL. Test is dependent on availability
+ * of network and the EMBL service.
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "External" })
+ public void testEmblUniprotProductRecovery() throws Exception
+ {
+ String retrievalId = "V00488";
+ DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
+ DBRefSource.EMBL).get(0);
+ assertNotNull("Couldn't find the EMBL retrieval client", embl);
+ verifyProteinNucleotideXref(retrievalId, embl);
}
+ /**
+ * Tests retrieval of one entry from EMBLCDS. Test is dependent on
+ * availability of network and the EMBLCDS service.
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "External" })
+ public void testEmblCDSUniprotProductRecovery() throws Exception
+ {
+ String retrievalId = "AAH29712";
+ DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
+ DBRefSource.EMBLCDS).get(0);
+ assertNotNull("Couldn't find the EMBL retrieval client", embl);
+ verifyProteinNucleotideXref(retrievalId, embl);
+ }
+
+ /**
+ * Helper method to perform database retrieval and verification of results.
+ *
+ * @param retrievalId
+ * @param embl
+ * @throws Exception
+ */
+ private void verifyProteinNucleotideXref(String retrievalId,
+ DbSourceProxy embl) throws Exception
+ {
+ AlignmentI alsq = embl.getSequenceRecords(retrievalId);
+ assertNotNull("Couldn't find the EMBL record " + retrievalId, alsq);
+ assertEquals("Didn't retrieve right number of records", 1,
+ alsq.getHeight());
+ SequenceI seq = alsq.getSequenceAt(0);
+ assertEquals("Wrong sequence name", embl.getDbSource() + "|"
+ + retrievalId, seq.getName());
+ SequenceFeature[] sfs = seq.getSequenceFeatures();
+ assertNotNull("Sequence features missing", sfs);
+ assertTrue(
+ "Feature not CDS",
+ FeatureProperties.isCodingFeature(embl.getDbSource(),
+ sfs[0].getType()));
+ assertEquals(embl.getDbSource(), sfs[0].getFeatureGroup());
+ DBRefEntry[] dr = DBRefUtils.selectRefs(seq.getDBRef(),
+ DBRefSource.PROTEINSEQ);
+ assertNotNull(dr);
+ assertEquals("Expected a single Uniprot cross reference", 1, dr.length);
+ assertEquals("Expected cross reference map to be one amino acid", dr[0]
+ .getMap().getMappedWidth(), 1);
+ assertEquals("Expected local reference map to be 3 nucleotides", dr[0]
+ .getMap().getWidth(), 3);
+ AlignmentI sprods = CrossRef.findXrefSequences(
+ alsq.getSequencesArray(), true, dr[0].getSource(),
+ alsq.getDataset());
+ assertNotNull(
+ "Couldn't recover cross reference sequence from dataset. Was it ever added ?",
+ sprods);
+ assertEquals("Didn't xref right number of records", 1,
+ sprods.getHeight());
+ SequenceI proteinSeq = sprods.getSequenceAt(0);
+ assertEquals(proteinSeq.getSequenceAsString(), dr[0].getMap().getTo()
+ .getSequenceAsString());
+ assertEquals(dr[0].getSource() + "|" + dr[0].getAccessionId(),
+ proteinSeq.getName());
+ }
}
git://source.jalview.org / jalview.git / blobdiff