ElementMatcher is not a spring bean anymore

rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java

@@ -75,8 +75,7 @@ public abstract class BaseRestImpl {
   @Autowired
   private PubmedParser pubmedParser;
 
-  @Autowired
-  private ElementMatcher elementMatcher;
+  private ElementMatcher elementMatcher = new ElementMatcher();
 
   private Transformer mathMlTransformer;
 

service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java

@@ -41,8 +41,7 @@ public abstract class SearchResultFactory<T, S extends ISearchResultView> extend
    */
   public abstract List<ElementIdentifier> searchResultToElementIdentifier(S object, Model model);
 
-  @Autowired
-  private ElementMatcher elementMatcher;
+  private ElementMatcher elementMatcher = new ElementMatcher();
 
   protected boolean elementMatch(Target target, Element element) {
     return elementMatcher.elementMatch(target, element);

service/src/main/java/lcsb/mapviewer/services/view/AbstractView.java

-package lcsb.mapviewer.services.view;
-
-import java.io.Serializable;
-
-import lcsb.mapviewer.common.ObjectUtils;
-
-/**
- * Abstract interface of a view object for bean layer. It contains identifier of
- * the object that is represented by this view class.
- * 
- * @author Piotr Gawron
- * 
- * @param <T>
- *          type of class to be represented
- */
-public abstract class AbstractView<T> implements Serializable {
-	
-	/**
-	 * 
-	 */
-	private static final long	serialVersionUID	= 1L;
-
-	/**
-	 * Database identifier of the object that we pass to the bean layer.
-	 */
-	private Integer						idObject;
-
-	/**
-	 * Default constructor.
-	 * 
-	 * @param object
-	 *          object that we want to pass to bean layer
-	 */
-	protected AbstractView(T object) {
-		if (object != null) {
-			idObject = ObjectUtils.getIdOfObject(object);
-		}
-	}
-
-	/**
-	 * Default constructor. Should be used only for deserialization.
-	 */
-	protected AbstractView() {
-	}
-
-	/**
-	 * @return the idObject
-	 * @see #idObject
-	 */
-	public Integer getIdObject() {
-		return idObject;
-	}
-
-	/**
-	 * @param idObject
-	 *          the idObject to set
-	 * @see #idObject
-	 */
-	public void setIdObject(Integer idObject) {
-		this.idObject = idObject;
-	}
-
-}

service/src/main/java/lcsb/mapviewer/services/view/AbstractViewFactory.java

-package lcsb.mapviewer.services.view;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import org.springframework.transaction.annotation.Transactional;
-
-import com.google.gson.Gson;
-
-/**
- * This abstract class represents factory that should be used to create
- * {@link AbstractView} classes that are accessible from the client side.
- * 
- * @author Piotr Gawron
- * 
- * @param <T>
- *          original class
- * @param <S>
- *          {@link AbstractView} class of the original class
- */
-@Transactional(value = "txManager")
-public abstract class AbstractViewFactory<T, S> {
-
-	/**
-	 * Creates view object for the given parameter.
-	 * 
-	 * @param object
-	 *          object that should be transformed into {@link AbstractView}
-	 * @return {@link AbstractView} of the object
-	 */
-	public abstract S create(T object);
-
-	/**
-	 * Creates original object for the given view. Typical implementation should
-	 * retrieve it from db and update the information from parameter.
-	 * 
-	 * @param view
-	 *          {@link AbstractView} of the object
-	 * @return original object
-	 */
-	public abstract T viewToObject(S view);
-
-	/**
-	 * Creates Gson string representing {@link AbstractView<T>} element.
-	 * 
-	 * @param object
-	 *          object taht should be transformed into a string
-	 * @return string gson representation
-	 */
-	public abstract String createGson(S object);
-
-	/**
-	 * Creates Gson string representing list of {@link AbstractView<T>} elements.
-	 * 
-	 * @param list
-	 *          list of objects taht should be transformed into a string
-	 * @return {@link String} with gson representation
-	 */
-	public String createGson(List<S> list) {
-		return new Gson().toJson(list);
-	}
-
-	/**
-	 * Creates list of views for the given list of objects.
-	 * 
-	 * @param objects
-	 *          list of objects that should be transformed into list of
-	 *          {@link AbstractView views}
-	 * @return list of {@link AbstractView views} for the given list of objects.
-	 */
-	public List<S> createList(Collection<T> objects) {
-		List<S> result = new ArrayList<S>();
-		for (T object : objects) {
-			result.add(create(object));
-		}
-		return result;
-	}
-}

service/src/main/java/lcsb/mapviewer/services/view/package-info.java

-/**
- * This package contains structures used for passing data into the client side.
- * These structures are light-weighted and very often are modified by the bean
- * or client side. Sometimes the data in these structures is preformated.
- * <p/>
- * 
- * The main abstract interface is defined by
- * {@link lcsb.mapviewer.services.view.AbstractView AbstractView} class. All
- * other classes in this package extend this interface.
- * <p/>
- * Be carefull when refactoring classes in this package. Data are accessed not
- * directly (not via managable code) by client side.
- */
-package lcsb.mapviewer.services.view;
-

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

@@ -48,8 +48,5 @@
 	<bean id="FullAliasViewFactory" class="lcsb.mapviewer.services.search.data.FullAliasViewFactory"/>
 	<bean id="FullReactionViewFactory" class="lcsb.mapviewer.services.search.data.FullReactionViewFactory"/>
 	<bean id="LightAliasViewFactory" class="lcsb.mapviewer.services.search.data.LightAliasViewFactory"/>
-
-	<bean id="ElementMatcher" class="lcsb.mapviewer.services.search.ElementMatcher"/>
-	
 	
 </beans>
\ No newline at end of file

service/src/test/java/lcsb/mapviewer/services/AllServicesTests.java

@@ -8,13 +8,11 @@ import lcsb.mapviewer.services.impl.AllImplServiceTests;
 import lcsb.mapviewer.services.overlay.AllOverlayTests;
 import lcsb.mapviewer.services.search.AllSearchTests;
 import lcsb.mapviewer.services.utils.AllUtilsTests;
-import lcsb.mapviewer.services.view.AllViewTests;
 
 @RunWith(Suite.class)
 @SuiteClasses({ AllImplServiceTests.class, //
     AllOverlayTests.class, //
     AllSearchTests.class, //
-    AllViewTests.class, //
     AllUtilsTests.class, //
 })
 public class AllServicesTests {

service/src/test/java/lcsb/mapviewer/services/search/ElementMatcherTest.java

@@ -7,7 +7,6 @@ import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
 
 import lcsb.mapviewer.annotation.data.Chemical;
 import lcsb.mapviewer.annotation.data.Target;
@@ -22,47 +21,47 @@ import lcsb.mapviewer.services.search.db.DbSearchCriteria;
 
 public class ElementMatcherTest extends ServiceTestFunctions {
 
-	@Autowired
-	ElementMatcher elementMatcher;
+  ElementMatcher elementMatcher = new ElementMatcher();
 
-	@AfterClass
-	public static void tearDownAfterClass() throws Exception {
-	}
+  @AfterClass
+  public static void tearDownAfterClass() throws Exception {
+  }
 
-	@Before
-	public void setUp() throws Exception {
-	}
+  @Before
+  public void setUp() throws Exception {
+  }
 
-	@After
-	public void tearDown() throws Exception {
-	}
+  @After
+  public void tearDown() throws Exception {
+  }
 
-	@Test
-	public void testMatchOther() {
-		Target target = new Target();
+  @Test
+  public void testMatchOther() {
+    Target target = new Target();
 
-		target.setType(TargetType.OTHER);
-		assertFalse(elementMatcher.elementMatch(target, new GenericProtein("s1")));
-	}
+    target.setType(TargetType.OTHER);
+    assertFalse(elementMatcher.elementMatch(target, new GenericProtein("s1")));
+  }
 
-	@Test
-	public void testElementMatch() {
-		String geneName = "GDNF";
-		Chemical view = chemicalService.getByName("Amphetamine", new DbSearchCriteria().disease(new MiriamData(MiriamType.MESH_2012, "D010300")));
-		Target target = null;
-		for (Target t : view.getInferenceNetwork()) {
-			for (MiriamData row : t.getGenes()) {
-				if (row.getResource().equals(geneName)) {
-					target = t;
-				}
-			}
-		}
+  @Test
+  public void testElementMatch() {
+    String geneName = "GDNF";
+    Chemical view = chemicalService.getByName("Amphetamine",
+        new DbSearchCriteria().disease(new MiriamData(MiriamType.MESH_2012, "D010300")));
+    Target target = null;
+    for (Target t : view.getInferenceNetwork()) {
+      for (MiriamData row : t.getGenes()) {
+        if (row.getResource().equals(geneName)) {
+          target = t;
+        }
+      }
+    }
 
-		Element element = new Rna("id");
-		element.setName(geneName);
+    Element element = new Rna("id");
+    element.setName(geneName);
 
-		assertTrue(elementMatcher.elementMatch(target, element));
+    assertTrue(elementMatcher.elementMatch(target, element));
 
-	}
+  }
 
 }

service/src/test/java/lcsb/mapviewer/services/view/AllViewTests.java

-package lcsb.mapviewer.services.view;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ FrameworkVersionViewTest.class, //
-})
-public class AllViewTests {
-
-}

service/src/test/java/lcsb/mapviewer/services/view/FrameworkVersionViewTest.java

-package lcsb.mapviewer.services.view;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.FrameworkVersion;
-
-public class FrameworkVersionViewTest {
-
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	@Test
-	public void testSerialization() {
-		try {
-			SerializationUtils.serialize(new FrameworkVersion());
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-}