TAIR annotation called even when Uniprot annotation already exists (can come...

TAIR annotation called even when Uniprot annotation already exists (can come from different annotator and correspond to, e.g., different species)

annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java

@@ -25,6 +25,7 @@ import lcsb.mapviewer.annotation.services.annotators.GoAnnotator;
 import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
 import lcsb.mapviewer.annotation.services.annotators.PdbAnnotator;
 import lcsb.mapviewer.annotation.services.annotators.ReconAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.TairAnnotator;
 import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
 import lcsb.mapviewer.common.IProgressUpdater;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -124,6 +125,13 @@ public class ModelAnnotator {
 	 */
 	@Autowired
 	private EnsemblAnnotator			 ensemblAnnotator;
+	
+	/**
+	 * TAIR annotator.
+	 */
+	@Autowired
+	private TairAnnotator				tairAnnotator;
+
 
 	/**
 	 * List of all avaliable {@link ElementAnnotator} objects.
@@ -153,6 +161,7 @@ public class ModelAnnotator {
 		addAnnotator(reconAnnotator);
 		addAnnotator(entrezAnnotator);
 		addAnnotator(ensemblAnnotator);
+		addAnnotator(tairAnnotator);
 	}
 
 	/**

annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java

 package lcsb.mapviewer.annotation.services.annotators;
 
 import java.io.IOException;
+import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
-import java.util.Set;
+import java.util.List;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
 import org.apache.log4j.Logger;
-import org.kohsuke.rngom.ast.builder.Annotations;
 
 import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
 import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
@@ -47,7 +47,7 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
 	 * Default constructor.
 	 */
 	public TairAnnotator() {
-		super(TairAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, false); //TODO - check with Simone
+		super(TairAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, false);
 	}
 
 	@Override
@@ -75,34 +75,36 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
 	@Override
 	public void annotateElement(BioEntity object) throws AnnotatorException {
 		if (isAnnotatable(object)) {
-			boolean uniprotFound = false;
+//			boolean uniprotFound = false;
+			List<MiriamData> mdUniProts = new ArrayList<MiriamData>();
 			MiriamData mdTair = null;
 			for (MiriamData md : object.getMiriamData()) {
 				if (md.getDataType().equals(MiriamType.TAIR_LOCUS)) {
 					mdTair = md;
 				}
 				if (md.getDataType().equals(MiriamType.UNIPROT)) {
-					uniprotFound = true;
+					mdUniProts.add(md);
+//					uniprotFound = true;
 				}
 			}
 
-			if (mdTair == null || uniprotFound) {
+			if (mdTair == null /*|| uniprotFound*/) {
 				return;
 			}
 			
 			MiriamData mdUniprot = tairToUniprot(mdTair);			
-			if (mdUniprot != null) {
+			if (mdUniprot != null && mdUniProts.indexOf(mdUniprot) == -1) {
 				object.addMiriamData(mdUniprot);
 			}
 		}		
 	}
 
 	/**
-	 * Returns url to TAIR page about TAIR entry.
+	 * Returns URL to TAIR page about TAIR entry.
 	 * 
 	 * @param tairId
-	 *          tair identifier
-	 * @return url to TAIR page about the TAIR entry
+	 *          TAIR identifier
+	 * @return URL to TAIR page about the TAIR entry
 	 */
 	private String getTairUrl(String tairId) {
 		return "http://arabidopsis.org/servlets/TairObject?type=locus&name=" + tairId;
@@ -147,11 +149,11 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
 	}
 
 	/**
-	 * Transform tair identifier into uniprot identifier.
+	 * Transform TAIR identifier into uniprot identifier.
 	 * 
 	 * @param tair
-	 *          {@link MiriamData} with tair identifier
-	 * @return {@link MiriamData} with uniprot identifier
+	 *          {@link MiriamData} with TAIR identifier
+	 * @return {@link MiriamData} with UniProt identifier
 	 * @throws UniprotSearchException
 	 *           thrown when there is a problem with accessing external database
 	 */
@@ -180,7 +182,6 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
 		} catch (IOException exception) {
 			throw new AnnotatorException(exception);
 		}
-
 	}
 
 	@Override

annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java

@@ -69,6 +69,33 @@ public class TairAnnotatorTest extends AnnotationTestFunctions {
 		}
 	}
 	
+	@Test
+	public void testAnnotateExistingUniprot() throws Exception {
+		try {
+
+			Species protein = new GenericProtein("id");
+			protein.setName("bla");
+			protein.addMiriamData(new MiriamData(MiriamType.TAIR_LOCUS, "AT1G15950"));
+			protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "P32246")); // Human version of the protein
+			
+			tairAnnotator.annotateElement(protein);
+
+			int cntUniProts = 0;
+
+			for (MiriamData md : protein.getMiriamData()) {
+				if (md.getDataType().equals(MiriamType.UNIPROT)) {
+					cntUniProts++;
+				}
+			}
+			
+			assertTrue("No UNIPROT annotation extracted from TAIR annotator", cntUniProts > 1);
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+	
 	
 	@Test
 	public void testAnnotateInvalidTair() throws Exception {