-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
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 jalview.ws.dbsources.Pdb;
+import jalview.ws.dbsources.Uniprot;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
/**
* @author jimp
- *
+ *
*/
public class DbRefFetcherTest
{
/**
* @throws java.lang.Exception
*/
- @BeforeClass
+ @BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
+ jalview.bin.Cache.initLogger();
}
/**
* @throws java.lang.Exception
*/
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
}
- @Test
+ /**
+ * Tests that standard protein database sources include Uniprot (as the first)
+ * and also PDB. (Additional sources are dependent on availability of DAS
+ * services.)
+ */
+ @Test(groups = { "Functional" })
public void testStandardProtDbs()
{
- String[] defdb = DBRefSource.PROTEINDBS;
- List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
- for (String ddb : defdb)
- {
- SequenceFetcher sfetcher= new SequenceFetcher();
- List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
-
- if (srcesfordb != null)
+ List<String> defdb = new ArrayList<String>();
+ defdb.addAll(Arrays.asList(DBRefSource.PROTEINDBS));
+ defdb.add(DBRefSource.PDB);
+ List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
+ SequenceFetcher sfetcher = new SequenceFetcher();
+ boolean pdbFound = false;
+
+ for (String ddb : defdb)
{
- srces.addAll(srcesfordb);
+ List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
+
+ if (srcesfordb != null)
+ {
+ // TODO is this right? get duplicate entries
+ srces.addAll(srcesfordb);
+ }
}
- }
- DbSourceProxy uniprot=null;
- int i=0;
- // append the selected sequence sources to the default dbs
- for (DbSourceProxy s:srces)
- {
- if (s.getDbSource().equalsIgnoreCase(DBRefSource.UNIPROT))
+
+ int i = 0;
+ int uniprotPos = -1;
+ for (DbSourceProxy s : srces)
{
+ if (s instanceof Uniprot && uniprotPos == -1)
+ {
+ uniprotPos = i;
+ }
+ if (s instanceof Pdb)
+ {
+ pdbFound = true;
+ }
i++;
}
-
- if (s instanceof jalview.ws.dbsources.Uniprot)
- {
- uniprot = s;
- break;
- }
+
+ assertTrue("Failed to find Uniprot source as first source amongst "
+ + srces.size() + " sources (source was at position "
+ + uniprotPos + ")", uniprotPos == 0);
+ assertTrue("Failed to find PDB source amongst " + srces.size()
+ + " sources", pdbFound);
}
-
- assertTrue("Failed to find Uniprot source as first source amongst "+srces.size()+" sources (source was at position "+i+")", uniprot!=null && i<2);
+
+ /**
+ * 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.getDBRefs(),
+ new String[] { DBRefSource.UNIPROT });
+ 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 = new CrossRef(alsq.getSequencesArray(), alsq)
+ .findXrefSequences(dr[0].getSource(), true);
+ 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