Merge branch '201-exception-when-running-annotations' into 'master'

Resolve "exception when running annotations"

Closes #201

See merge request !108

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

@@ -19,9 +19,9 @@ import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.Species;
 
 /**
- * Interface that allows to annotate {@link BioEntity elements} in the
- * system. Different implementation use different resources to perform
- * annotation. They can annotate different types of elements.
+ * Interface that allows to annotate {@link BioEntity elements} in the system.
+ * Different implementation use different resources to perform annotation. They
+ * can annotate different types of elements.
  * 
  * @author Piotr Gawron
  * 
@@ -31,7 +31,7 @@ public abstract class ElementAnnotator extends CachableInterface {
 	/**
 	 * Default class logger.
 	 */
-	private final Logger																 logger				= Logger.getLogger(ElementAnnotator.class);
+	private final Logger													 logger				= Logger.getLogger(ElementAnnotator.class);
 
 	/**
 	 * List of classes that can be annotated by this {@link IElementAnnotator
@@ -42,7 +42,7 @@ public abstract class ElementAnnotator extends CachableInterface {
 	/**
 	 * Should be this annotator used as a default annotatior.
 	 */
-	private boolean																			 isDefault		= false;
+	private boolean																 isDefault		= false;
 
 	/**
 	 * Default constructor.
@@ -61,8 +61,7 @@ public abstract class ElementAnnotator extends CachableInterface {
 			if (BioEntity.class.isAssignableFrom(validClass)) {
 				addValidClass((Class<? extends BioEntity>) validClass);
 			} else {
-				throw new InvalidArgumentException(
-						"Cannot pass class of type: " + validClass + ". Only classes extending " + BioEntity.class + " are accepted.");
+				throw new InvalidArgumentException("Cannot pass class of type: " + validClass + ". Only classes extending " + BioEntity.class + " are accepted.");
 			}
 		}
 		this.isDefault = isDefault;
@@ -193,7 +192,7 @@ public abstract class ElementAnnotator extends CachableInterface {
 			List<String> sortedSynonyms = new ArrayList<>();
 			sortedSynonyms.addAll(synonyms);
 			Collections.sort(sortedSynonyms);
-			
+
 			element.setSynonyms(sortedSynonyms);
 		} else {
 			logger.warn(prefix + "Synonyms don't match: \"" + synonyms + "\", \"" + element.getSynonyms() + "\"");
@@ -227,10 +226,12 @@ public abstract class ElementAnnotator extends CachableInterface {
 	 *          value to set
 	 */
 	protected void setDescription(BioEntity element, String description) {
-		if (element.getNotes() == null || element.getNotes().equals("") || element.getNotes().equals(description)) {
-			element.setNotes(description);
-		} else if (!element.getNotes().toLowerCase().contains(description.toLowerCase())) {
-			element.setNotes(element.getNotes() + "\n" + description);
+		if (description != null) {
+			if (element.getNotes() == null || element.getNotes().equals("") || element.getNotes().equals(description)) {
+				element.setNotes(description);
+			} else if (!element.getNotes().toLowerCase().contains(description.toLowerCase())) {
+				element.setNotes(element.getNotes() + "\n" + description);
+			}
 		}
 	}
 

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

@@ -41,7 +41,7 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
 	/**
 	 * Version of the rest API that is supported by this annotator.
 	 */
-	static final String					SUPPORTED_VERSION				 = "6.0";
+	static final String					SUPPORTED_VERSION				 = "6.1";
 
 	/**
 	 * Url address of ensembl restfull service.

annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java

@@ -92,7 +92,7 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
 	}
 
 	@Test
-	public void test3FindDrug() throws Exception {
+	public void testFindRapamycin() throws Exception {
 		try {
 			// finding synonym
 			Drug rapamycinDrug = drugBankHTMLParser.findDrug("Rapamycin");
@@ -100,8 +100,7 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
 			assertEquals("Sirolimus", rapamycinDrug.getName());
 			assertEquals("DB00877", rapamycinDrug.getSources().get(0).getResource());
 			assertTrue(rapamycinDrug.getBloodBrainBarrier().equalsIgnoreCase("NO"));
-			boolean res = rapamycinDrug.getDescription().contains(
-					"A macrolide compound obtained from Streptomyces hygroscopicus that acts by selectively blocking the transcriptional activation of cytokines thereby inhibiting cytokine production. It is bioactive only when bound to immunophilins. Sirolimus is a potent immunosuppressant and possesses both antifungal and antineoplastic properties. [PubChem]");
+			boolean res = rapamycinDrug.getDescription().contains("A macrolide compound obtained from Streptomyces");
 			assertTrue(res);
 			assertEquals(3, rapamycinDrug.getTargets().size());
 

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

@@ -85,6 +85,14 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
 		assertEquals(0, getWarnings().size());
 	}
 
+	@Test
+	public void testSetEmptyDescription() {
+		GenericProtein species = new GenericProtein("id");
+		species.setNotes("X");
+		annotator.setDescription(species, null);
+		assertEquals("X", species.getNotes());
+	}
+
 	@Test
 	public void testSetNotMatchingIchi() {
 		Ion species = new Ion("id");