package jalview.ws.seqfetcher;
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.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.Pdb;
+import jalview.ws.dbsources.Uniprot;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.List;
import org.testng.annotations.AfterClass;
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.Cache.initLogger();
/**
* @throws java.lang.Exception
*/
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
}
- @Test(groups ={ "Functional" })
+ @Test(groups= {"Network"})
+ public void checkUniprotCanonicalFlagSet()
+ {
+ // 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) {
+ assertEquals(DBRefSource.UNIPROT, ref.getCanonicalSourceName());
+ canonicalUp |= ref.isCanonical();
+ }
+ assertTrue("No Canonical Uniprot reference detected", canonicalUp);
+ }
+ /**
+ * 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<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)
{
- SequenceFetcher sfetcher = new SequenceFetcher();
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
+ int uniprotPos = -1;
for (DbSourceProxy s : srces)
{
- if (s.getDbSource().equalsIgnoreCase(DBRefSource.UNIPROT))
+ if (s instanceof Uniprot && uniprotPos == -1)
{
- i++;
+ uniprotPos = i;
}
-
- if (s instanceof jalview.ws.dbsources.Uniprot)
+ if (s instanceof Pdb)
{
- uniprot = s;
- break;
+ pdbFound = true;
}
+ 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", pdbFound);
}
- @Test(groups =
- { "External" })
+ /**
+ * 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 = "CAA23748"; // "V00488";
- DbSourceProxy embl = new SequenceFetcher().getSourceProxy(DBRefSource.EMBL).get(0);
+ String retrievalId = "V00488";
+ DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
+ DBRefSource.EMBL).get(0);
assertNotNull("Couldn't find the EMBL retrieval client", embl);
verifyProteinNucleotideXref(retrievalId, embl);
}
- @Test(groups =
- { "External" })
+ /**
+ * 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";
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());
- DBRefEntry[] dr = DBRefUtils.selectRefs(alsq.getSequenceAt(0).getDBRef(), DBRefSource.PROTEINSEQ);
+ 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.length);
- assertEquals("Expected cross refernce map to be one amino acid", dr[0]
+ 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 refernce map to be 3 nucleotides", dr[0]
+ assertEquals("Expected local reference map to be 3 nucleotides", dr.get(0)
.getMap().getWidth(), 3);
- AlignmentI sprods = CrossRef.findXrefSequences(alsq.getSequencesArray(), true, dr[0].getSource(), alsq.getDataset());
+ 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());
}
}
git://source.jalview.org / jalview.git / blobdiff