Added STTICH annotator including unit tests.

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

@@ -27,6 +27,7 @@ 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.StitchAnnotator;
 import lcsb.mapviewer.annotation.services.annotators.TairAnnotator;
 import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
 import lcsb.mapviewer.common.IProgressUpdater;
@@ -140,6 +141,12 @@ public class ModelAnnotator {
 	@Autowired
 	private EnsemblAnnotator			 ensemblAnnotator;
 	
+	/**
+	 * STITCH annotator.
+	 */
+	@Autowired
+	private StitchAnnotator				stitchAnnotator;
+	
 	/**
 	 * TAIR annotator.
 	 */
@@ -177,6 +184,7 @@ public class ModelAnnotator {
 		addAnnotator(reconAnnotator);
 		addAnnotator(entrezAnnotator);
 		addAnnotator(ensemblAnnotator);
+		addAnnotator(stitchAnnotator);
 		addAnnotator(tairAnnotator);
 	}
 

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

+package lcsb.mapviewer.annotation.services.annotators;
+
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.data.Chebi;
+import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
+import lcsb.mapviewer.annotation.services.IExternalService;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+
+/**
+ * This is a class that implements STITCH annotation which is derived from existing ChEBI annotation.
+ * 
+ * @author David Hoksza
+ * 
+ */
+public class StitchAnnotator extends ElementAnnotator implements IExternalService {
+
+	/**
+	 * Default class logger.
+	 */
+	private static Logger	logger					= Logger.getLogger(StitchAnnotator.class);
+	
+	/**
+	 * Service used for annotation of entities using {@link MiriamType#STITCH STITCH}.
+	 */
+	@Autowired
+	private ChebiAnnotator		chebiAnnotator;
+
+	/**
+	 * Default constructor.
+	 */
+	public StitchAnnotator() {
+		super(StitchAnnotator.class, new Class[] { SimpleMolecule.class }, false);
+	}
+
+	@Override
+	public ExternalServiceStatus getServiceStatus() {
+		return chebiAnnotator.getServiceStatus();
+	}
+	
+	/**
+	 * Returns main layer of the InchKey, * i.e. everything 
+	 * before first hyphen: WBYWAXJHAXSJNI-VOTSOKGWSA-N -> WBYWAXJHAXSJNI	   
+	 * @param inchiKey Full inchiKey
+	 * @return Main layer of the InchiKey
+	 */
+	private String inchiKeyExtractMainLayer(String inchiKey){
+		return inchiKey.replaceFirst("-.*", "");
+	}
+
+	@Override
+	public void annotateElement(BioEntity object) throws AnnotatorException {
+		if (isAnnotatable(object)) {
+			
+			MiriamData mdChebi = null;
+			
+			for (MiriamData md : object.getMiriamData()) {
+				if (md.getDataType().equals(MiriamType.CHEBI)) {
+					mdChebi = md;
+				}
+				else if (md.getDataType().equals(MiriamType.STITCH)) {
+					return;
+				}				
+			}
+			
+			if (mdChebi == null) {
+				return;
+			}
+			
+			try {
+				
+				Chebi chebi = chebiAnnotator.getChebiElementForChebiId(mdChebi);
+				if (chebi == null) {
+					return;
+				}
+				String inchiKey = chebi.getInchiKey();
+				if (inchiKey == null) {
+					return;
+				}
+				
+				object.addMiriamData(new MiriamData(MiriamType.STITCH, inchiKeyExtractMainLayer(inchiKey)));				
+			} catch(ChebiSearchException exception) {
+				logger.warn("No ChEBI element retrieved fro ChEBI ID: " + mdChebi.getResource());
+			}			
+		}		
+	}
+
+	@Override
+	public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
+		return chebiAnnotator.refreshCacheQuery(query);
+	}
+	
+
+	@Override
+	public String getCommonName() {
+		return MiriamType.STITCH.getCommonName();
+	}
+
+	@Override
+	public String getUrl() {
+		return MiriamType.STITCH.getDbHomepage();
+	}
+
+	@Override
+	protected WebPageDownloader getWebPageDownloader() {
+		return super.getWebPageDownloader();
+	}
+
+	@Override
+	protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+		super.setWebPageDownloader(webPageDownloader);
+	}
+}

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

@@ -123,7 +123,7 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
 		Matcher m = tairToUniprot.matcher(pageContent);
 		if (m.find()) {
 			result.add(new MiriamData(MiriamType.UNIPROT, m.group(1)));
-		}
+		}		
 		return result;
 	}
 

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

@@ -23,6 +23,7 @@
 	<bean id="HgncAnnotator" class="lcsb.mapviewer.annotation.services.annotators.HgncAnnotator"/>
 	<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="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

@@ -17,6 +17,7 @@ import org.junit.runners.Suite.SuiteClasses;
 		HgncAnnotatorTest.class, //
 		PdbAnnotatorTest.class, //
 		ReconAnnotatorTest.class, //
+		StitchAnnotatorTest.class, //
 		TairAnnotatorTest.class, //
 		UniprotAnnotatorTest.class, //
 })

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

@@ -40,7 +40,7 @@ public class BrendaAnnotatorTest extends AnnotationTestFunctions {
 	}
 	
 	@Test
-	public void testUniprotToCazy() throws Exception {
+	public void testUniprotToBrenda() throws Exception {
 		try {
 			Collection<MiriamData> mds = brendaAnnotator.uniprotToBrenda(new MiriamData(MiriamType.UNIPROT, "P12345"));
 			assertEquals(mds.size(), 2);			

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;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class StitchAnnotatorTest extends AnnotationTestFunctions {
+	
+	@Autowired
+	StitchAnnotator testedAnnotator;
+
+	@Before
+	public void setUp() throws Exception {
+	}
+
+	@After
+	public void tearDown() throws Exception {
+	}
+
+	@Test
+	public void testAnnotate() throws Exception {
+		try {
+
+			Species bioEntity = new SimpleMolecule("id");
+			bioEntity.addMiriamData(new MiriamData(MiriamType.CHEBI, "CHEBI:35697"));
+			
+			testedAnnotator.annotateElement(bioEntity);
+
+			MiriamData mdStitch = null;
+
+			for (MiriamData md : bioEntity.getMiriamData()) {
+				if (md.getDataType().equals(MiriamType.STITCH)) {
+					mdStitch = md; //there should be only one EC number for that TAIR<->UNIPROT record
+				}
+			}
+			
+			assertTrue("No STITCH annotation extracted from STITCH annotator", mdStitch != null);
+			assertTrue("Wrong number of annotations extract from STITCH annotator", bioEntity.getMiriamData().size() == 2);
+			assertTrue("Invalid STITCH annotation extracted from STITCH annotator based on CHEBI ID", mdStitch.getResource().equalsIgnoreCase("WBYWAXJHAXSJNI") );
+			
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+	
+	@Test
+	public void testExtractInchiMainLayer() throws Exception {
+		try {
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+		
+	@Test
+	public void testAnnotateInvalidEmpty() throws Exception {
+		try {
+			Species bioEntity = new SimpleMolecule("id");			
+			testedAnnotator.annotateElement(bioEntity);
+
+			assertEquals(0, bioEntity.getMiriamData().size());
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+	
+	@Test
+	public void testAnnotateInvalidChebi() throws Exception {
+		try {
+			Species bioEntity = new SimpleMolecule("id");
+			bioEntity.addMiriamData(new MiriamData(MiriamType.CHEBI, "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 STTICH annotator 
+	//internally calls ChEBI annotator which has it own set of tests 
+
+}

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

@@ -356,6 +356,14 @@ public enum MiriamType {
 			"http://www.yeastgenome.org/", //
 			"urn:miriam:sgd", //
 			new Class<?>[] {}, "MIR:00000023"),
+	
+	/**
+	 * STITCH: http://stitch.embl.de/.
+	 */
+	STITCH("STITCH", //
+			"http://stitch.embl.de/", //
+			"urn:miriam:stitch", //
+			new Class<?>[] {}, "MIR:00100343"),
 
 	/**
 	 * The Arabidopsis Information Resource (TAIR) maintains a database of genetic

persist/src/db/11.1.1/fix_db_20171114.sql

@@ -6,3 +6,7 @@ INSERT INTO cache_type(validity, classname) VALUES (365, 'lcsb.mapviewer.annotat
 
 DELETE FROM cache_type WHERE classname = 'lcsb.mapviewer.annotation.services.annotators.BrendaAnnotator';
 INSERT INTO cache_type(validity, classname) VALUES (365, 'lcsb.mapviewer.annotation.services.annotators.BrendaAnnotator');
+
+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');
+