model annotator coverage tests

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

@@ -378,7 +378,7 @@ public class ModelAnnotator {
 	 *          {@link AnnotatedObject}
 	 * @return list of improper annotations
 	 */
-	protected Collection<ImproperAnnotations> findImproperAnnotations(AnnotatedObject element, Collection<MiriamType> validClasses) {
+	protected List<ImproperAnnotations> findImproperAnnotations(AnnotatedObject element, Collection<MiriamType> validClasses) {
 		List<ImproperAnnotations> result = new ArrayList<>();
 		for (MiriamData md : element.getMiriamData()) {
 			boolean valid = false;
@@ -498,7 +498,7 @@ public class ModelAnnotator {
 	 *          class for which list of annotators will be returned
 	 * @return annotators names for a given class
 	 */
-	public Collection<String> getAvailableAnnotatorNames(Class<?> clazz) {
+	public List<String> getAvailableAnnotatorNames(Class<?> clazz) {
 		List<String> result = new ArrayList<>();
 		for (ElementAnnotator annotator : getAvailableAnnotators(clazz)) {
 			result.add(annotator.getCommonName());
@@ -514,8 +514,8 @@ public class ModelAnnotator {
 	 *          class for which list of default annotators will be returned
 	 * @return annotators names for a given class
 	 */
-	public Collection<String> getAvailableDefaultAnnotatorNames(Class<?> clazz) {
-		List<String> result = new ArrayList<String>();
+	public List<String> getAvailableDefaultAnnotatorNames(Class<?> clazz) {
+		List<String> result = new ArrayList<>();
 		for (ElementAnnotator annotator : getAvailableDefaultAnnotators(clazz)) {
 			result.add(annotator.getCommonName());
 		}
@@ -530,8 +530,8 @@ public class ModelAnnotator {
 	 *          class for which list of default annotators will be returned
 	 * @return annotators for a given class
 	 */
-	public Collection<ElementAnnotator> getAvailableDefaultAnnotators(Class<?> clazz) {
-		List<ElementAnnotator> result = new ArrayList<ElementAnnotator>();
+	public List<ElementAnnotator> getAvailableDefaultAnnotators(Class<?> clazz) {
+		List<ElementAnnotator> result = new ArrayList<>();
 		for (ElementAnnotator annotator : availableAnnotators) {
 			if (annotator.isAnnotatable(clazz) && annotator.isDefault()) {
 				result.add(annotator);
@@ -549,7 +549,7 @@ public class ModelAnnotator {
 	 * @return list of {@link ElementAnnotator annotators}
 	 */
 	public List<ElementAnnotator> getAnnotatorsFromCommonNames(List<String> list) {
-		List<ElementAnnotator> result = new ArrayList<ElementAnnotator>();
+		List<ElementAnnotator> result = new ArrayList<>();
 		for (String string : list) {
 			boolean added = false;
 			for (ElementAnnotator annotator : availableAnnotators) {

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

@@ -29,6 +29,7 @@ import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
 import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
 import lcsb.mapviewer.annotation.services.annotators.ReconAnnotator;
 import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.map.AnnotatedObject;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamRelationType;
@@ -239,6 +240,36 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
 		}
 	}
 
+	@Test
+	public void testFindInmproperAnnotations2() throws Exception {
+		try {
+			List<MiriamType> list = new ArrayList<>();
+			list.add(MiriamType.PUBMED);
+			Reaction reaction = new Reaction();
+			reaction.addMiriamData(new MiriamData(MiriamType.PUBMED, "12345"));
+			List<ImproperAnnotations> result = modelAnnotator.findImproperAnnotations(reaction, list);
+			assertEquals(0, result.size());
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testFindInmproperAnnotations3() throws Exception {
+		try {
+			List<MiriamType> list = new ArrayList<>();
+			list.add(MiriamType.PUBMED);
+			Reaction reaction = new Reaction();
+			reaction.addMiriamData(new MiriamData(MiriamType.PUBMED, "inv_id"));
+			List<ImproperAnnotations> result = modelAnnotator.findImproperAnnotations(reaction, list);
+			assertEquals(1, result.size());
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
 	@Test
 	public void testFindMissingAnnotations() throws Exception {
 		try {
@@ -252,6 +283,21 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
 		}
 	}
 
+	@Test
+	public void testFindMissingAnnotations2() throws Exception {
+		try {
+			Model model = getModelForFile("testFiles/annotation/missingAnnotations.xml", false);
+			Map<Class<? extends AnnotatedObject>, Set<MiriamType>> requestedAnnotations = new HashMap<>();;
+			requestedAnnotations.put(GenericProtein.class, new HashSet<>());
+			Collection<? extends ProblematicAnnotation> results = modelAnnotator.findMissingAnnotations(model, requestedAnnotations);
+			assertEquals(1, results.size());
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
 	@Test
 	public void testAnnotateModelWithDrugMolecule() throws Exception {
 		try {
@@ -336,4 +382,75 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
 		}
 	}
 
+	@Test
+	public void testGetAvailableAnnotatorNamess() {
+		try {
+			List<String> list = modelAnnotator.getAvailableAnnotatorNames(Protein.class);
+			assertTrue(list.size() > 0);
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testGetAvailableAnnotators2() {
+		try {
+			List<ElementAnnotator> list = modelAnnotator.getAvailableAnnotators();
+			assertTrue(list.size() > 0);
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testGetAvailableDefaultAnnotators() {
+		try {
+			List<ElementAnnotator> list = modelAnnotator.getAvailableDefaultAnnotators(Protein.class);
+			assertTrue(list.size() > 0);
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testGetAvailableDefaultAnnotatorNamess() {
+		try {
+			List<String> list = modelAnnotator.getAvailableDefaultAnnotatorNames(Protein.class);
+			assertTrue(list.size() > 0);
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testGetAnnotatorsFromCommonNames() {
+		try {
+			List<ElementAnnotator> list = modelAnnotator.getAnnotatorsFromCommonNames(modelAnnotator.getAvailableAnnotatorNames(Protein.class));
+			assertTrue(list.size() > 0);
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testGetAnnotatorsFromInvalidName() {
+		try {
+			String name = "unkName";
+			List<String> names = new ArrayList<>();
+			names.add(name);
+			modelAnnotator.getAnnotatorsFromCommonNames(names);
+			fail();
+		} catch (InvalidArgumentException e) {
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+
 }