STRING annotator including unit tests.

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

@@ -28,6 +28,7 @@ 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.StitchAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.StringAnnotator;
 import lcsb.mapviewer.annotation.services.annotators.TairAnnotator;
 import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
 import lcsb.mapviewer.common.IProgressUpdater;
@@ -147,6 +148,12 @@ public class ModelAnnotator {
 	@Autowired
 	private StitchAnnotator				stitchAnnotator;
 	
+	/**
+	 * STRING annotator.
+	 */
+	@Autowired
+	private StringAnnotator				stringAnnotator;
+	
 	/**
 	 * TAIR annotator.
 	 */
@@ -185,6 +192,7 @@ public class ModelAnnotator {
 		addAnnotator(entrezAnnotator);
 		addAnnotator(ensemblAnnotator);
 		addAnnotator(stitchAnnotator);
+		addAnnotator(stringAnnotator);
 		addAnnotator(tairAnnotator);
 	}
 

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

+package lcsb.mapviewer.annotation.services.annotators;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
+import lcsb.mapviewer.annotation.services.IExternalService;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+
+/**
+ * This is a class that implements a mapping to STRING database.
+ * 
+ * @author David Hoksza
+ * 
+ */
+public class StringAnnotator extends ElementAnnotator implements IExternalService {
+	
+	/**
+	 * Service used for annotation of entities using {@link MiriamType#TAIR_LOCUS
+	 * TAIR}.
+	 */
+	@Autowired
+	private TairAnnotator		tairAnnotator;	
+	
+	/**
+	 * Default constructor.
+	 */
+	public StringAnnotator() {
+		super(StringAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, false);
+	}
+
+	@Override
+	public ExternalServiceStatus getServiceStatus() {
+		return tairAnnotator.getServiceStatus();
+	}
+
+	@Override
+	public void annotateElement(BioEntity object) throws AnnotatorException {
+		if (isAnnotatable(object)) {
+			
+			MiriamData mdTair = null;			
+			for (MiriamData md : object.getMiriamData()) {
+				if (md.getDataType().equals(MiriamType.STRING)) {
+					return;			
+				}
+				if (md.getDataType().equals(MiriamType.TAIR_LOCUS)) {
+					mdTair = md;
+				} 
+			}			
+			if (mdTair != null) {
+				tairAnnotator.annotateElement(object);
+			}
+			
+			List<MiriamData> mdUniprots = new ArrayList<MiriamData>();
+			for (MiriamData md : object.getMiriamData()) {
+				if (md.getDataType().equals(MiriamType.UNIPROT)) {
+					mdUniprots.add(md);
+				}			
+			}
+			
+			List<String> stringIds = new ArrayList<String>();
+			for (MiriamData mdUniprot: mdUniprots) {
+				MiriamData mdString = uniprotToString(mdUniprot);
+				if (mdString != null && stringIds.indexOf(mdString.getResource()) < 0) {
+					stringIds.add(mdString.getResource());
+					object.addMiriamData(mdString);
+				}								
+			}
+		}		
+	}
+
+	/**
+	 * Transform UniProt {@link MiriamData} data to STRING {@link MiriamData}.
+	 * 
+	 * @param UniProt
+	 *          {@link MiriamData} with UniProt identifier
+	 * @return {@link MiriamData} with STRING identifier
+	 * @throws AnnotatorException
+	 *           thrown when there is a problem with accessing external database
+	 */
+	public MiriamData uniprotToString(MiriamData uniprot) throws AnnotatorException {
+		if (uniprot == null) {
+			return null;
+		}
+
+		if (!MiriamType.UNIPROT.equals(uniprot.getDataType())) {
+			throw new InvalidArgumentException(MiriamType.UNIPROT + " expected.");
+		}
+
+		return new MiriamData(MiriamType.STRING, uniprot.getResource());
+	}
+
+	@Override
+	public String getCommonName() {
+		return MiriamType.STRING.getCommonName();
+	}
+
+	@Override
+	public String getUrl() {
+		return MiriamType.STRING.getDbHomepage();
+	}
+}

annotation/src/main/resources/applicationContext-annotation.xml

@@ -24,6 +24,7 @@
 	<bean id="ReconAnnotator" class="lcsb.mapviewer.annotation.services.annotators.ReconAnnotator"/>
 	<bean id="PdbAnnotator" class="lcsb.mapviewer.annotation.services.annotators.PdbAnnotator"/>
 	<bean id="StitchAnnotator" class="lcsb.mapviewer.annotation.services.annotators.StitchAnnotator"/>
+	<bean id="StringAnnotator" class="lcsb.mapviewer.annotation.services.annotators.StringAnnotator"/>
 	<bean id="TairAnnotator" class="lcsb.mapviewer.annotation.services.annotators.TairAnnotator"/>
 	<bean id="UniprotAnnotator" class="lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator"/>
 	

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

@@ -18,6 +18,7 @@ import org.junit.runners.Suite.SuiteClasses;
 		PdbAnnotatorTest.class, //
 		ReconAnnotatorTest.class, //
 		StitchAnnotatorTest.class, //
+		StringAnnotatorTest.class, //
 		TairAnnotatorTest.class, //
 		UniprotAnnotatorTest.class, //
 })

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

 package lcsb.mapviewer.annotation.services.annotators;
 
 import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.Matchers.anyString;
-import static org.mockito.Mockito.when;
-
-import java.io.IOException;
 
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
-import org.mockito.Mockito;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.cache.WebPageDownloader;
-import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.species.SimpleMolecule;

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

+package lcsb.mapviewer.annotation.services.annotators;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class StringAnnotatorTest extends AnnotationTestFunctions {
+	
+	@Autowired
+	StringAnnotator testedAnnotator;
+
+	@Before
+	public void setUp() throws Exception {
+	}
+
+	@After
+	public void tearDown() throws Exception {
+	}
+
+	@Test
+	public void testAnnotateUniprot() throws Exception {
+		try {
+
+			Species bioEntity = new GenericProtein("id");
+			bioEntity.addMiriamData(new MiriamData(MiriamType.UNIPROT, "P53350"));
+			
+			testedAnnotator.annotateElement(bioEntity);
+
+			MiriamData mdString = null;
+
+			for (MiriamData md : bioEntity.getMiriamData()) {
+				if (md.getDataType().equals(MiriamType.STRING)) {
+					mdString = md; //there should be only one EC number for that TAIR<->UNIPROT record
+				}
+			}
+			
+			assertTrue("No STRING annotation extracted from STRING annotator", mdString != null);
+			assertTrue("Wrong number of annotations extract from STRING annotator", bioEntity.getMiriamData().size() == 2);
+			assertTrue("Invalid STRING annotation extracted from STRING annotator based on the UniProt annotation", mdString.getResource().equalsIgnoreCase("P53350") );
+			
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+	
+	@Test
+	public void testAnnotateTair() throws Exception {
+		try {
+
+			Species bioEntity = new GenericProtein("id");
+			bioEntity.addMiriamData(new MiriamData(MiriamType.TAIR_LOCUS, "AT1G01030"));
+			
+			testedAnnotator.annotateElement(bioEntity);
+
+			MiriamData mdString = null;
+
+			for (MiriamData md : bioEntity.getMiriamData()) {
+				if (md.getDataType().equals(MiriamType.STRING)) {
+					mdString = md; //there should be only one EC number for that TAIR<->UNIPROT record
+				}
+			}
+			
+			assertTrue("No STRING annotation extracted from STRING annotator", mdString != null);
+			assertTrue("Wrong number of annotations extract from STRING annotator", bioEntity.getMiriamData().size() == 3);
+			
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+	
+	
+		
+	@Test
+	public void testAnnotateInvalidEmpty() throws Exception {
+		try {
+			Species bioEntity = new GenericProtein("id");			
+			testedAnnotator.annotateElement(bioEntity);
+
+			assertEquals(0, bioEntity.getMiriamData().size());
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+	
+	@Test
+	public void testAnnotateInvalidTair() throws Exception {
+		try {
+			Species bioEntity = new GenericProtein("id");
+			bioEntity.addMiriamData(new MiriamData(MiriamType.TAIR_LOCUS, "bla"));
+			testedAnnotator.annotateElement(bioEntity);
+
+			assertEquals(1, bioEntity.getMiriamData().size());
+
+			assertEquals(1, getWarnings().size());
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	//All the service status tests are not necessary, since STRING annotator 
+	//internally calls TAIR annotator which has it own set of tests
+}

model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java

@@ -373,6 +373,14 @@ public enum MiriamType {
 			"http://stitch.embl.de/", //
 			"urn:miriam:stitch", //
 			new Class<?>[] {}, "MIR:00100343"),
+	
+	/**
+	 * STRING: 	http://string-db.org/.
+	 */
+	STRING("STRING", //
+			"http://string-db.org/", //
+			"urn:miriam:string", //
+			new Class<?>[] {}, "MIR:00000265"),
 
   /**
    * The Arabidopsis Information Resource (TAIR) maintains a database of genetic

persist/src/db/11.1.1/fix_db_20171114.sql

@@ -10,3 +10,6 @@ INSERT INTO cache_type(validity, classname) VALUES (365, 'lcsb.mapviewer.annotat
 DELETE FROM cache_type WHERE classname = 'lcsb.mapviewer.annotation.services.annotators.StitchAnnotator';
 INSERT INTO cache_type(validity, classname) VALUES (365, 'lcsb.mapviewer.annotation.services.annotators.StitchAnnotator');
 
+DELETE FROM cache_type WHERE classname = 'lcsb.mapviewer.annotation.services.annotators.StringAnnotator';
+INSERT INTO cache_type(validity, classname) VALUES (365, 'lcsb.mapviewer.annotation.services.annotators.StringAnnotator');
+