/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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/>.
+ * 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.Assert.assertNotEquals;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+import jalview.analysis.CrossRef;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
+import jalview.datamodel.FeatureProperties;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+import jalview.util.DBRefUtils;
import jalview.ws.DBRefFetcher;
import jalview.ws.SequenceFetcher;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.ws.dbsources.EBIAlfaFold;
+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.junit.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
/**
* @author jimp
- *
+ *
*/
public class DbRefFetcherTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* @throws java.lang.Exception
*/
- @BeforeClass
+ @BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
+ jalview.bin.Console.initLogger();
}
/**
* @throws java.lang.Exception
*/
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
}
- @Test
- public void testStandardProtDbs()
+ @Test(groups = { "Network" })
+ public void checkUniprotCanonicalFlagSet()
{
- 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)
+ // TODO - mock this - for moment it is a live request.
+ SequenceI uniprotSeq = new Sequence("FER1_SPIOL",
+ "MAATTTTMMGMATTFVPKPQAPPMMAALPSNTGRSLFGLKTGSRGGRMTMAAYKVTLVTPTGNVEFQCPDDV"
+ + "YILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEE"
+ + "LTA");
+ DBRefFetcher dbr = new DBRefFetcher(new SequenceI[] { uniprotSeq });
+ dbr.fetchDBRefs(true);
+ List<DBRefEntry> primRefs = uniprotSeq.getPrimaryDBRefs();
+ assertNotNull(primRefs);
+ assertTrue(primRefs.size() > 0);
+ boolean canonicalUp = false;
+ for (DBRefEntry ref : primRefs)
{
- srces.addAll(srcesfordb);
+ assertEquals(DBRefSource.UNIPROT, ref.getCanonicalSourceName());
+ canonicalUp |= ref.isCanonical();
}
+ assertTrue("No Canonical Uniprot reference detected", canonicalUp);
}
- DbSourceProxy uniprot=null;
- int i=0;
- // append the selected sequence sources to the default dbs
- for (DbSourceProxy s:srces)
+
+ /**
+ * 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()
{
- if (s.getDbSource().equalsIgnoreCase(DBRefSource.UNIPROT))
+ 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)
{
- i++;
+ List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
+
+ if (srcesfordb != null)
+ {
+ // TODO is this right? get duplicate entries
+ srces.addAll(srcesfordb);
+ }
}
-
- if (s instanceof jalview.ws.dbsources.Uniprot)
+
+ int i = 0;
+ int uniprotPos = -1;
+ for (DbSourceProxy s : srces)
{
- uniprot = s;
- break;
+ if (s instanceof Uniprot && uniprotPos == -1)
+ {
+ uniprotPos = i;
+ }
+ if (s instanceof Pdb)
+ {
+ pdbFound = true;
+ }
+ i++;
}
+
+ 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);
+ }
+
+ /**
+ * 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);
}
-
- assertTrue("Failed to find Uniprot source as first source amongst "+srces.size()+" sources (source was at position "+i+")", uniprot!=null && i<2);
+
+ /**
+ * 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());
+ List<SequenceFeature> sfs = seq.getSequenceFeatures();
+ assertFalse("Sequence features missing", sfs.isEmpty());
+ assertTrue("Feature not CDS", FeatureProperties
+ .isCodingFeature(embl.getDbSource(), sfs.get(0).getType()));
+ assertEquals(embl.getDbSource(), sfs.get(0).getFeatureGroup());
+ List<DBRefEntry> dr = DBRefUtils.selectRefs(seq.getDBRefs(),
+ new String[]
+ { DBRefSource.UNIPROT });
+ assertNotNull(dr);
+ assertEquals("Expected a single Uniprot cross reference", 1, dr.size());
+ assertEquals("Expected cross reference map to be one amino acid",
+ dr.get(0).getMap().getMappedWidth(), 1);
+ assertEquals("Expected local reference map to be 3 nucleotides",
+ dr.get(0).getMap().getWidth(), 3);
+ AlignmentI sprods = new CrossRef(alsq.getSequencesArray(), alsq)
+ .findXrefSequences(dr.get(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.get(0).getMap().getTo().getSequenceAsString());
+ assertEquals(dr.get(0).getSource() + "|" + dr.get(0).getAccessionId(),
+ proteinSeq.getName());
+ }
+
+ /**
+ * 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 testAlphaFoldClien() throws Exception
+ {
+ DbSourceProxy alphafold = new EBIAlfaFold();
+ AlignmentI resp = alphafold.getSequenceRecords(alphafold.getTestQuery());
+ assertNotNull(resp);
+ assertEquals("One sequence only",resp.getHeight(), 1);
+ for (AlignmentAnnotation aa:resp.getAlignmentAnnotation()) {
+ if (aa.graph == AlignmentAnnotation.CUSTOMRENDERER)
+ {
+ assertTrue("Contact map didn't provide valid contact",resp.getContactListFor(aa, 1).getContactAt(1)!=-1d);
+ // test passes
+ return;
+ }
+ }
+ Assert.fail();
}
}
git://source.jalview.org / jalview.git / blobdiff