From 5834ba7fa9f97e01018a88f49b1dab3e675ae12e Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 9 Jun 2017 13:59:03 +0200
Subject: [PATCH] api for getting reaction and element types
---
.../ConfigurationController.java | 2 +
.../configuration/ConfigurationRestImpl.java | 55 ++++++++++++++++++-
.../ConfigurationRestImplTest.java | 33 +++++++++++
3 files changed, 89 insertions(+), 1 deletion(-)
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java
index 4b582a14a8..abe96fcaf9 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java
+++ b/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;
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
index 7c32c55034..13560acbd5 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
@@ -1,20 +1,31 @@
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);
+ }
+
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/configuration/ConfigurationRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/configuration/ConfigurationRestImplTest.java
index 4d0c21c798..b88b846b41 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/configuration/ConfigurationRestImplTest.java
+++ b/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;
+ }
+
+ }
+
}
--
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