From 55c6bfebcea8b011f95d1ca9b32fb02a7c46d66a Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 11 Apr 2018 11:56:16 +0200
Subject: [PATCH] OverviewImageView class removed
---
.../api/projects/ProjectMetaData.java | 14 +-
.../api/projects/ProjectRestImpl.java | 80 ++++-------
.../elements/ElementsRestImpl.java | 21 ---
.../publications/PublicationsRestImpl.java | 21 ---
.../services/view/OverviewImageView.java | 124 ------------------
.../view/OverviewImageViewFactory.java | 60 ---------
.../resources/applicationContext-service.xml | 1 -
.../mapviewer/services/view/AllViewTests.java | 2 -
.../view/OverviewImageViewFactoryTest.java | 47 -------
.../services/view/OverviewImageViewTest.java | 27 ----
10 files changed, 36 insertions(+), 361 deletions(-)
delete mode 100644 service/src/main/java/lcsb/mapviewer/services/view/OverviewImageView.java
delete mode 100644 service/src/main/java/lcsb/mapviewer/services/view/OverviewImageViewFactory.java
delete mode 100644 service/src/test/java/lcsb/mapviewer/services/view/OverviewImageViewFactoryTest.java
delete mode 100644 service/src/test/java/lcsb/mapviewer/services/view/OverviewImageViewTest.java
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectMetaData.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectMetaData.java
index 9f209f5307..ff880436c8 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectMetaData.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectMetaData.java
@@ -6,7 +6,7 @@ import java.util.Map;
import org.apache.log4j.Logger;
-import lcsb.mapviewer.services.view.OverviewImageView;
+import lcsb.mapviewer.model.map.OverviewImage;
public class ProjectMetaData implements Serializable {
@@ -51,12 +51,12 @@ public class ProjectMetaData implements Serializable {
/**
* List of overview images attached to this model.
*/
- private List<OverviewImageView> overviewImageViews;
+ private List<OverviewImage> overviewImageViews;
/**
* Top level overview image.
*/
- private OverviewImageView topOverviewImage;
+ private OverviewImage topOverviewImage;
/**
* Default constructor. Should be used only for deserialization.
@@ -102,7 +102,7 @@ public class ProjectMetaData implements Serializable {
* @return the overviewImageViews
* @see #overviewImageViews
*/
- public List<OverviewImageView> getOverviewImageViews() {
+ public List<OverviewImage> getOverviewImageViews() {
return overviewImageViews;
}
@@ -111,7 +111,7 @@ public class ProjectMetaData implements Serializable {
* the overviewImageViews to set
* @see #overviewImageViews
*/
- public void setOverviewImageViews(List<OverviewImageView> overviewImageViews) {
+ public void setOverviewImageViews(List<OverviewImage> overviewImageViews) {
this.overviewImageViews = overviewImageViews;
}
@@ -119,7 +119,7 @@ public class ProjectMetaData implements Serializable {
* @return the topOverviewImage
* @see #topOverviewImage
*/
- public OverviewImageView getTopOverviewImage() {
+ public OverviewImage getTopOverviewImage() {
return topOverviewImage;
}
@@ -128,7 +128,7 @@ public class ProjectMetaData implements Serializable {
* the topOverviewImage to set
* @see #topOverviewImage
*/
- public void setTopOverviewImage(OverviewImageView topOverviewImage) {
+ public void setTopOverviewImage(OverviewImage topOverviewImage) {
this.topOverviewImage = topOverviewImage;
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
index 15afbc55d2..589c2850ff 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
@@ -14,11 +14,11 @@ import java.security.NoSuchAlgorithmException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Comparator;
-import java.util.TreeMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
+import java.util.TreeMap;
import org.apache.commons.io.IOUtils;
import org.apache.log4j.Logger;
@@ -77,7 +77,6 @@ import lcsb.mapviewer.services.utils.ColorSchemaReader;
import lcsb.mapviewer.services.utils.CreateProjectParams;
import lcsb.mapviewer.services.utils.data.BuildInLayout;
import lcsb.mapviewer.services.utils.gmap.CoordinationConverter;
-import lcsb.mapviewer.services.view.OverviewImageViewFactory;
@Transactional(value = "txManager")
public class ProjectRestImpl extends BaseRestImpl {
@@ -108,9 +107,6 @@ public class ProjectRestImpl extends BaseRestImpl {
@Autowired
private ProjectDao projectDao;
- @Autowired
- private OverviewImageViewFactory factory;
-
@Autowired
private UploadedFileEntryDao uploadedFileEntryDao;
@@ -136,7 +132,7 @@ public class ProjectRestImpl extends BaseRestImpl {
}
result.setProgress(project.getProgress());
- result.setOverviewImageViews(factory.createList(project.getOverviewImages()));
+ result.setOverviewImageViews(project.getOverviewImages());
Set<OverviewImage> set = new HashSet<>();
set.addAll(project.getOverviewImages());
@@ -151,11 +147,11 @@ public class ProjectRestImpl extends BaseRestImpl {
result.setDirectory(project.getDirectory());
result.setErrors(project.getErrors() != null && !project.getErrors().isEmpty());
if (set.size() > 0) {
- result.setTopOverviewImage(factory.create(set.iterator().next()));
+ result.setTopOverviewImage(set.iterator().next());
} else if (project.getOverviewImages().size() > 0) {
logger.warn(
"Cannot determine top level image. Taking first one. " + project.getOverviewImages().get(0).getFilename());
- result.setTopOverviewImage(factory.create(project.getOverviewImages().get(0)));
+ result.setTopOverviewImage(project.getOverviewImages().get(0));
}
if (project.getOrganism() != null) {
@@ -168,23 +164,6 @@ public class ProjectRestImpl extends BaseRestImpl {
return result;
}
- /**
- * @return the factory
- * @see #factory
- */
- public OverviewImageViewFactory getFactory() {
- return factory;
- }
-
- /**
- * @param factory
- * the factory to set
- * @see #factory
- */
- public void setFactory(OverviewImageViewFactory factory) {
- this.factory = factory;
- }
-
public FileEntry getSource(String token, String projectId) throws SecurityException, QueryException {
Project project = getProjectService().getProjectByProjectId(projectId, token);
if (project == null) {
@@ -331,14 +310,14 @@ public class ProjectRestImpl extends BaseRestImpl {
String backgroundOverlayId, String overlayIds, String zoomLevel, String polygonString)
throws SecurityException, QueryException, IOException, InvalidColorSchemaException, CommandExecutionException,
ConverterException, InconsistentModelException {
- User user = getUserService().getUserByToken(token);
+ User user = getUserService().getUserByToken(token);
Model topModel = getModelService().getLastModelByProjectId(projectId, token);
if (topModel == null) {
throw new ObjectNotFoundException("Project with given id doesn't exist");
}
-
+
Model originalModel = topModel.getSubmodelById(modelId);
-
+
if (originalModel == null) {
throw new ObjectNotFoundException("Model with given id doesn't exist");
}
@@ -349,31 +328,29 @@ public class ProjectRestImpl extends BaseRestImpl {
// create model bounded by the polygon
SubModelCommand subModelCommand = new SubModelCommand(originalModel, polygon);
Model part = subModelCommand.execute();
-
- //Get list of overlay ids
- String[] overlayIdsList;
- if (overlayIds == null || overlayIds.trim().isEmpty()) {
- overlayIdsList = new String[0];
- }
- else {
- overlayIdsList = overlayIds.split(",");
- }
+
+ // Get list of overlay ids
+ String[] overlayIdsList;
+ if (overlayIds == null || overlayIds.trim().isEmpty()) {
+ overlayIdsList = new String[0];
+ } else {
+ overlayIdsList = overlayIds.split(",");
+ }
// Remove all colors
- if (overlayIdsList.length > 0)
- {
-
- for (Element element: part.getElements()){
- element.setColor(Color.WHITE);
- }
+ if (overlayIdsList.length > 0) {
+
+ for (Element element : part.getElements()) {
+ element.setColor(Color.WHITE);
+ }
}
// Color with overlays
- for (String overlayId: overlayIdsList){
- Layout overlay = layoutService.getLayoutById(Integer.parseInt(overlayId.trim()), token);
-
- ColorSchemaReader reader = new ColorSchemaReader();
- Collection<ColorSchema> schemas = reader.readColorSchema(overlay.getInputData().getFileContent());
-
- new ColorModelCommand(part, schemas, getUserService().getColorExtractorForUser(user)).execute();
+ for (String overlayId : overlayIdsList) {
+ Layout overlay = layoutService.getLayoutById(Integer.parseInt(overlayId.trim()), token);
+
+ ColorSchemaReader reader = new ColorSchemaReader();
+ Collection<ColorSchema> schemas = reader.readColorSchema(overlay.getInputData().getFileContent());
+
+ new ColorModelCommand(part, schemas, getUserService().getColorExtractorForUser(user)).execute();
}
IConverter parser = getModelParser(handlerClass);
@@ -821,7 +798,8 @@ public class ProjectRestImpl extends BaseRestImpl {
return null;
}
- public List<Map<String, Object>> getSubmapConnections(String token, String projectId) throws ObjectNotFoundException, SecurityException {
+ public List<Map<String, Object>> getSubmapConnections(String token, String projectId)
+ throws ObjectNotFoundException, SecurityException {
List<Map<String, Object>> result = new ArrayList<>();
List<Model> models = getModels(projectId, "*", token);
List<Element> elements = new ArrayList<>();
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
index f5ff71b1b1..5aac8ca424 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
@@ -8,7 +8,6 @@ import java.util.Set;
import java.util.TreeMap;
import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.api.BaseRestImpl;
@@ -25,7 +24,6 @@ import lcsb.mapviewer.model.map.species.field.ElementModification;
import lcsb.mapviewer.model.map.species.field.Structure;
import lcsb.mapviewer.model.map.species.field.UniprotRecord;
import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.view.OverviewImageViewFactory;
@Transactional(value = "txManager")
public class ElementsRestImpl extends BaseRestImpl {
@@ -36,9 +34,6 @@ public class ElementsRestImpl extends BaseRestImpl {
@SuppressWarnings("unused")
private Logger logger = Logger.getLogger(ElementsRestImpl.class);
- @Autowired
- private OverviewImageViewFactory factory;
-
public List<Map<String, Object>> getElements(String projectId, String id, String columns, String modelId,
String token, String type, String includedCompartmentIds, String excludedCompartmentIds)
throws QueryException, SecurityException {
@@ -307,20 +302,4 @@ public class ElementsRestImpl extends BaseRestImpl {
return columnsSet;
}
- /**
- * @return the factory
- * @see #factory
- */
- public OverviewImageViewFactory getFactory() {
- return factory;
- }
-
- /**
- * @param factory
- * the factory to set
- * @see #factory
- */
- public void setFactory(OverviewImageViewFactory factory) {
- this.factory = factory;
- }
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
index 343de635ee..6565b23e84 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
@@ -27,7 +27,6 @@ import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.ISearchService;
-import lcsb.mapviewer.services.view.OverviewImageViewFactory;
@Transactional(value = "txManager")
public class PublicationsRestImpl extends BaseRestImpl {
@@ -43,9 +42,6 @@ public class PublicationsRestImpl extends BaseRestImpl {
@Autowired
private PubmedParser pubmedParser;
- @Autowired
- private OverviewImageViewFactory factory;
-
public SortedMap<MiriamData, List<BioEntity>> getPublications(Collection<Model> models) {
SortedMap<MiriamData, List<BioEntity>> publications = new TreeMap<>();
@@ -87,23 +83,6 @@ public class PublicationsRestImpl extends BaseRestImpl {
this.searchService = searchService;
}
- /**
- * @return the factory
- * @see #factory
- */
- public OverviewImageViewFactory getFactory() {
- return factory;
- }
-
- /**
- * @param factory
- * the factory to set
- * @see #factory
- */
- public void setFactory(OverviewImageViewFactory factory) {
- this.factory = factory;
- }
-
private enum SortColumn {
PUBMED_ID("pubmedId"), //
YEAR("year"), //
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/OverviewImageView.java b/service/src/main/java/lcsb/mapviewer/services/view/OverviewImageView.java
deleted file mode 100644
index d6a7ed977e..0000000000
--- a/service/src/main/java/lcsb/mapviewer/services/view/OverviewImageView.java
+++ /dev/null
@@ -1,124 +0,0 @@
-package lcsb.mapviewer.services.view;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.model.map.OverviewImage;
-
-/**
- * View representatin of a {@link OverviewImage}. It's a light structre that
- * present {@link OverviewImage} data to the client side.
- *
- * @author Piotr Gawron
- *
- */
-public class OverviewImageView extends AbstractView<OverviewImage> implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Name of the file (relative to the main image data framework directory).
- */
- private String filename;
- /**
- * Width of the image.
- */
- private Integer width;
- /**
- * Height of the image.
- */
- private Integer height;
-
- /**
- * List of links that are accesible from this image.
- */
- private List<OverviewLinkView> links = new ArrayList<OverviewLinkView>();
-
- /**
- * Default constructor.
- *
- * @param object
- * original {@link OverviewImage}
- */
- protected OverviewImageView(OverviewImage object) {
- super(object);
- }
-
- /**
- * Default constructor. Should be used only for deserialization.
- */
- protected OverviewImageView() {
- }
-
- /**
- * @return the filename
- * @see #filename
- */
- public String getFilename() {
- return filename;
- }
-
- /**
- * @param filename
- * the filename to set
- * @see #filename
- */
- public void setFilename(String filename) {
- this.filename = filename;
- }
-
- /**
- * @return the width
- * @see #width
- */
- public Integer getWidth() {
- return width;
- }
-
- /**
- * @param width
- * the width to set
- * @see #width
- */
- public void setWidth(Integer width) {
- this.width = width;
- }
-
- /**
- * @return the height
- * @see #height
- */
- public Integer getHeight() {
- return height;
- }
-
- /**
- * @param height
- * the height to set
- * @see #height
- */
- public void setHeight(Integer height) {
- this.height = height;
- }
-
- /**
- * @return the links
- * @see #links
- */
- public List<OverviewLinkView> getLinks() {
- return links;
- }
-
- /**
- * @param links
- * the links to set
- * @see #links
- */
- public void setLinks(List<OverviewLinkView> links) {
- this.links = links;
- }
-}
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/OverviewImageViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/view/OverviewImageViewFactory.java
deleted file mode 100644
index 4b4bc5b150..0000000000
--- a/service/src/main/java/lcsb/mapviewer/services/view/OverviewImageViewFactory.java
+++ /dev/null
@@ -1,60 +0,0 @@
-package lcsb.mapviewer.services.view;
-
-import lcsb.mapviewer.model.map.OverviewImage;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-import com.google.gson.Gson;
-
-/**
- * Factory class for {@link OverviewImage} class.
- *
- * @author Piotr Gawron
- *
- */
-@Transactional(value = "txManager")
-public class OverviewImageViewFactory extends AbstractViewFactory<OverviewImage, OverviewImageView> {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(OverviewImageViewFactory.class);
-
- /**
- * Factory object used for creation of {@link OverviewImageView} elements.
- */
- @Autowired
- private OverviewLinkViewFactory overviewLinkViewFactory;
-
- @Override
- public OverviewImageView create(OverviewImage object) {
- OverviewImageView result = new OverviewImageView(object);
- if (object == null) {
- logger.warn("Empty image...");
- return result;
- }
- if (object.getProject() != null) {
- result.setFilename(object.getProject().getDirectory() + "/" + object.getFilename());
- } else {
- result.setFilename(object.getFilename());
- }
- result.setWidth(object.getWidth());
- result.setHeight(object.getHeight());
- result.setLinks(overviewLinkViewFactory.createList(object.getLinks()));
-
- return result;
- }
-
- @Override
- public String createGson(OverviewImageView object) {
- return new Gson().toJson(object);
- }
-
- @Override
- public OverviewImage viewToObject(OverviewImageView view) {
- throw new NotImplementedException();
- }
-}
diff --git a/service/src/main/resources/applicationContext-service.xml b/service/src/main/resources/applicationContext-service.xml
index ef8ea2b837..4eafac2052 100644
--- a/service/src/main/resources/applicationContext-service.xml
+++ b/service/src/main/resources/applicationContext-service.xml
@@ -45,7 +45,6 @@
<bean id="PasswordEncoder" class="lcsb.mapviewer.services.impl.Md5PasswordEncoder"/>
<!-- View factories -->
- <bean id="OverviewImageViewFactory" class="lcsb.mapviewer.services.view.OverviewImageViewFactory"/>
<bean id="OverviewLinkViewFactory" class="lcsb.mapviewer.services.view.OverviewLinkViewFactory"/>
<bean id="ReferenceGenomeViewFactory" class="lcsb.mapviewer.services.view.ReferenceGenomeViewFactory"/>
<bean id="ReferenceGenomeGeneMappingViewFactory" class="lcsb.mapviewer.services.view.ReferenceGenomeGeneMappingViewFactory"/>
diff --git a/service/src/test/java/lcsb/mapviewer/services/view/AllViewTests.java b/service/src/test/java/lcsb/mapviewer/services/view/AllViewTests.java
index 16b074840b..de944a5cb3 100644
--- a/service/src/test/java/lcsb/mapviewer/services/view/AllViewTests.java
+++ b/service/src/test/java/lcsb/mapviewer/services/view/AllViewTests.java
@@ -6,8 +6,6 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ FrameworkVersionViewTest.class, //
- OverviewImageViewFactoryTest.class, //
- OverviewImageViewTest.class, //
OverviewLinkViewFactoryTest.class, //
OverviewLinkViewTest.class, //
ReferenceGenomeViewFactoryTest.class, //
diff --git a/service/src/test/java/lcsb/mapviewer/services/view/OverviewImageViewFactoryTest.java b/service/src/test/java/lcsb/mapviewer/services/view/OverviewImageViewFactoryTest.java
deleted file mode 100644
index 61a2c7772a..0000000000
--- a/service/src/test/java/lcsb/mapviewer/services/view/OverviewImageViewFactoryTest.java
+++ /dev/null
@@ -1,47 +0,0 @@
-package lcsb.mapviewer.services.view;
-
-import static org.junit.Assert.assertNotNull;
-import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-public class OverviewImageViewFactoryTest extends ServiceTestFunctions {
- @Autowired
- OverviewImageViewFactory overviewImageViewFactory;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testCreateNull() throws Exception {
- try {
- OverviewImageView result = overviewImageViewFactory.create(null);
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreate() throws Exception {
- try {
- OverviewImage oi = new OverviewImage();
- OverviewImageView result = overviewImageViewFactory.create(oi);
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
diff --git a/service/src/test/java/lcsb/mapviewer/services/view/OverviewImageViewTest.java b/service/src/test/java/lcsb/mapviewer/services/view/OverviewImageViewTest.java
deleted file mode 100644
index 3922449a9a..0000000000
--- a/service/src/test/java/lcsb/mapviewer/services/view/OverviewImageViewTest.java
+++ /dev/null
@@ -1,27 +0,0 @@
-package lcsb.mapviewer.services.view;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class OverviewImageViewTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new OverviewImageView());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
--
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