api for getting reaction and element types

rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java

@@ -26,6 +26,8 @@ public class ConfigurationController extends BaseController {
 		result.put("imageFormats", configurationController.getImageFormats(token));
 		result.put("modelFormats", configurationController.getModelFormats(token));
 		result.put("overlayTypes", configurationController.getOverlayTypes(token));
+		result.put("elementTypes", configurationController.getElementTypes(token));
+		result.put("reactionTypes", configurationController.getReactionTypes(token));
 		return result;
 	}
 

rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java

 package lcsb.mapviewer.api.configuration;
 
+import java.lang.reflect.InvocationTargetException;
 import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
+import java.util.Queue;
+import java.util.Set;
 
+import org.apache.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.annotation.Transactional;
-import org.springframework.web.bind.annotation.RequestParam;
 
+import javassist.Modifier;
 import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.converter.IConverter;
 import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
 import lcsb.mapviewer.converter.graphics.ImageGenerators;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
 import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
+import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.modelutils.map.ClassTreeNode;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
 import lcsb.mapviewer.services.SecurityException;
 import lcsb.mapviewer.services.interfaces.IConfigurationService;
 import lcsb.mapviewer.services.interfaces.IUserService;
@@ -23,6 +34,7 @@ import lcsb.mapviewer.services.view.ConfigurationView;
 
 @Transactional(value = "txManager")
 public class ConfigurationRestImpl {
+	private Logger								logger = Logger.getLogger(ConfigurationRestImpl.class);
 
 	@Autowired
 	private IUserService					userService;
@@ -112,4 +124,45 @@ public class ConfigurationRestImpl {
 		return result;
 	}
 
+	public Set<String> getElementTypes(String token) throws SecurityException {
+		userService.getToken(token);
+
+		return getClassStringTypesList(Element.class);
+	}
+
+	private Set<String> getClassStringTypesList(Class<?> elementClass) {
+		Set<String> result = new HashSet<>();
+		ElementUtils elementUtils = new ElementUtils();
+		ClassTreeNode top = elementUtils.getAnnotatedElementClassTree();
+		Queue<ClassTreeNode> queue = new LinkedList<>();
+		queue.add(top);
+		while (!queue.isEmpty()) {
+			ClassTreeNode clazz = queue.poll();
+			for (ClassTreeNode child : clazz.getChildren()) {
+				queue.add(child);
+			}
+			if (elementClass.isAssignableFrom(clazz.getClazz())) {
+				if (!Modifier.isAbstract(clazz.getClazz().getModifiers())) {
+					try {
+						if (elementClass.isAssignableFrom(Reaction.class)) {
+							result.add(((AnnotatedObject) (clazz.getClazz().getDeclaredConstructor().newInstance())).getStringType());
+						} else {
+							result.add(((AnnotatedObject) (clazz.getClazz().getDeclaredConstructor(String.class).newInstance("id"))).getStringType());
+						}
+					} catch (InstantiationException | IllegalAccessException | IllegalArgumentException | InvocationTargetException | NoSuchMethodException
+							| java.lang.SecurityException e) {
+						throw new RuntimeException(e);
+					}
+				}
+			}
+		}
+		return result;
+	}
+
+	public Set<String> getReactionTypes(String token) throws SecurityException {
+		userService.getToken(token);
+
+		return getClassStringTypesList(Reaction.class);
+	}
+
 }

rest-api/src/test/java/lcsb/mapviewer/api/configuration/ConfigurationRestImplTest.java

@@ -4,7 +4,9 @@ import static org.junit.Assert.assertTrue;
 
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
+import org.apache.log4j.Logger;
 import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.Before;
@@ -12,9 +14,14 @@ import org.junit.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import lcsb.mapviewer.api.RestTestFunctions;
+import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
+import lcsb.mapviewer.model.map.species.GenericProtein;
 import lcsb.mapviewer.services.view.ConfigurationView;
 
 public class ConfigurationRestImplTest extends RestTestFunctions {
+
+	private Logger							 logger	= Logger.getLogger(ConfigurationRestImplTest.class);
+
 	@Autowired
 	public ConfigurationRestImpl configurationRestImpl;
 
@@ -63,4 +70,30 @@ public class ConfigurationRestImplTest extends RestTestFunctions {
 		}
 	}
 
+	@Test
+	public void testGetElementTypes() throws Exception {
+		try {
+			Set<String> list = configurationRestImpl.getElementTypes(token.getId());
+			GenericProtein protein = new GenericProtein("id");
+			assertTrue(list.contains(protein.getStringType()));
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testGetReactionTypes() throws Exception {
+		try {
+			Set<String> list = configurationRestImpl.getReactionTypes(token.getId());
+			StateTransitionReaction protein = new StateTransitionReaction();
+			assertTrue(list.contains(protein.getStringType()));
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
 }