OverviewLink serializers implemented

model/src/main/java/lcsb/mapviewer/model/map/OverviewImageLink.java

 package lcsb.mapviewer.model.map;
 
-import javax.persistence.*;
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.ManyToOne;
+
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
 
 import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.modelutils.serializer.model.map.OverviewImageLinkSerializer;
 
 /**
  * Link used in {@link OverviewImage parent OverviewImage} to link it to
@@ -13,6 +19,7 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
  */
 @Entity
 @DiscriminatorValue("IMAGE_LINK")
+@JsonSerialize(using = OverviewImageLinkSerializer.class)
 public class OverviewImageLink extends OverviewLink {
 
   /**

model/src/main/java/lcsb/mapviewer/model/map/OverviewModelLink.java

@@ -5,9 +5,12 @@ import javax.persistence.Entity;
 import javax.persistence.FetchType;
 import javax.persistence.ManyToOne;
 
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
+
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.modelutils.serializer.model.map.OverviewModelLinkSerializer;
 
 /**
  * Link used in {@link OverviewImage parent OverviewImage} to link it to
@@ -18,6 +21,7 @@ import lcsb.mapviewer.model.map.model.ModelData;
  */
 @Entity
 @DiscriminatorValue("MODEL_LINK")
+@JsonSerialize(using = OverviewModelLinkSerializer.class)
 public class OverviewModelLink extends OverviewLink {
 
   /**

model/src/main/java/lcsb/mapviewer/model/map/OverviewSearchLink.java

@@ -3,7 +3,10 @@ package lcsb.mapviewer.model.map;
 import javax.persistence.DiscriminatorValue;
 import javax.persistence.Entity;
 
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
+
 import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.modelutils.serializer.model.map.OverviewSearchLinkSerializer;
 
 /**
  * Link used in {@link OverviewImage parent OverviewImage} to link it to
@@ -14,6 +17,7 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
  */
 @Entity
 @DiscriminatorValue("SEARCH_LINK")
+@JsonSerialize(using = OverviewSearchLinkSerializer.class)
 public class OverviewSearchLink extends OverviewLink {
 
   /**

model/src/main/java/lcsb/mapviewer/modelutils/serializer/model/map/OverviewImageLinkSerializer.java

+package lcsb.mapviewer.modelutils.serializer.model.map;
+
+import java.io.IOException;
+
+import com.fasterxml.jackson.core.JsonGenerator;
+import com.fasterxml.jackson.databind.JsonSerializer;
+import com.fasterxml.jackson.databind.SerializerProvider;
+
+import lcsb.mapviewer.model.map.OverviewImageLink;
+
+public class OverviewImageLinkSerializer extends JsonSerializer<OverviewImageLink> {
+
+  @Override
+  public void serialize(final OverviewImageLink entry, final JsonGenerator gen,
+      final SerializerProvider serializers)
+      throws IOException {
+    gen.writeStartObject();
+
+    gen.writeNumberField("idObject", entry.getId());
+    gen.writeObjectField("polygon", entry.getPolygonCoordinates());
+    gen.writeNumberField("imageLinkId", entry.getLinkedOverviewImage().getId());
+    gen.writeStringField("type", entry.getClass().getSimpleName());
+    gen.writeEndObject();
+  }
+}
\ No newline at end of file

model/src/main/java/lcsb/mapviewer/modelutils/serializer/model/map/OverviewModelLinkSerializer.java

+package lcsb.mapviewer.modelutils.serializer.model.map;
+
+import java.awt.geom.Point2D;
+import java.io.IOException;
+
+import com.fasterxml.jackson.core.JsonGenerator;
+import com.fasterxml.jackson.databind.JsonSerializer;
+import com.fasterxml.jackson.databind.SerializerProvider;
+
+import lcsb.mapviewer.model.map.OverviewModelLink;
+
+public class OverviewModelLinkSerializer extends JsonSerializer<OverviewModelLink> {
+
+  @Override
+  public void serialize(final OverviewModelLink entry, final JsonGenerator gen,
+      final SerializerProvider serializers)
+      throws IOException {
+    gen.writeStartObject();
+
+    gen.writeNumberField("idObject", entry.getId());
+    gen.writeObjectField("polygon", entry.getPolygonCoordinates());
+    gen.writeNumberField("zoomLevel", entry.getZoomLevel());
+    gen.writeObjectField("modelPoint", new Point2D.Double(entry.getxCoord(), entry.getyCoord()));
+    gen.writeNumberField("modelLinkId", entry.getLinkedModel().getId());
+    gen.writeStringField("type", entry.getClass().getSimpleName());
+    gen.writeEndObject();
+  }
+}
\ No newline at end of file

model/src/main/java/lcsb/mapviewer/modelutils/serializer/model/map/OverviewSearchLinkSerializer.java

+package lcsb.mapviewer.modelutils.serializer.model.map;
+
+import java.io.IOException;
+
+import com.fasterxml.jackson.core.JsonGenerator;
+import com.fasterxml.jackson.databind.JsonSerializer;
+import com.fasterxml.jackson.databind.SerializerProvider;
+
+import lcsb.mapviewer.model.map.OverviewSearchLink;
+
+public class OverviewSearchLinkSerializer extends JsonSerializer<OverviewSearchLink> {
+
+  @Override
+  public void serialize(final OverviewSearchLink entry, final JsonGenerator gen,
+      final SerializerProvider serializers)
+      throws IOException {
+    gen.writeStartObject();
+
+    gen.writeNumberField("idObject", entry.getId());
+    gen.writeObjectField("polygon", entry.getPolygonCoordinates());
+    gen.writeStringField("query", entry.getQuery());
+    gen.writeStringField("type", entry.getClass().getSimpleName());
+    gen.writeEndObject();
+  }
+}
\ No newline at end of file

rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java

 package lcsb.mapviewer.api.projects;
 
-import java.awt.geom.Point2D;
 import java.io.IOException;
 import java.io.Serializable;
 import java.security.MessageDigest;
@@ -30,7 +29,6 @@ import lcsb.mapviewer.api.BaseRestImpl;
 import lcsb.mapviewer.api.OperationNotAllowedException;
 import lcsb.mapviewer.common.comparator.StringComparator;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.converter.Converter;
 import lcsb.mapviewer.converter.zip.GlyphZipEntryFile;
 import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
@@ -47,8 +45,6 @@ import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.OverviewImage;
 import lcsb.mapviewer.model.map.OverviewImageLink;
 import lcsb.mapviewer.model.map.OverviewLink;
-import lcsb.mapviewer.model.map.OverviewModelLink;
-import lcsb.mapviewer.model.map.OverviewSearchLink;
 import lcsb.mapviewer.model.map.layout.ProjectBackground;
 import lcsb.mapviewer.model.map.model.SubmodelType;
 import lcsb.mapviewer.model.map.species.Element;
@@ -72,7 +68,10 @@ import lcsb.mapviewer.services.utils.CreateProjectParams;
 public class ProjectRestImpl extends BaseRestImpl {
 
   public static enum ZipEntryFileType {
-    MAP, OVERLAY, IMAGE, GLYPH;
+    MAP,
+    OVERLAY,
+    IMAGE,
+    GLYPH;
 
     public static ZipEntryFileType getType(String entryType) {
       for (ZipEntryFileType type : ZipEntryFileType.values()) {
@@ -123,7 +122,7 @@ public class ProjectRestImpl extends BaseRestImpl {
   }
 
   private Project getProjectByProjectId(String projectId) throws ObjectNotFoundException {
-    Project project = getProjectService().getProjectByProjectId(projectId);
+    Project project = getProjectService().getProjectByProjectId(projectId, true);
     if (project == null) {
       throw new ObjectNotFoundException("Project with given id doesn't exist");
     }
@@ -192,44 +191,7 @@ public class ProjectRestImpl extends BaseRestImpl {
     result.put("filename", image.getProject().getDirectory() + "/" + image.getFilename());
     result.put("width", image.getWidth());
     result.put("height", image.getHeight());
-    List<Map<String, Object>> links = new ArrayList<>();
-    for (OverviewLink link : image.getLinks()) {
-      links.add(overviewLinkToMap(link));
-    }
-    result.put("links", links);
-    return result;
-  }
-
-  private Map<String, Object> overviewLinkToMap(OverviewLink link) {
-    Map<String, Object> result = new LinkedHashMap<>();
-    result.put("idObject", link.getId());
-    result.put("polygon", polygonToMap(link.getPolygon()));
-    if (link instanceof OverviewModelLink) {
-      OverviewModelLink modelLink = (OverviewModelLink) link;
-      result.put("zoomLevel", modelLink.getZoomLevel());
-      result.put("modelPoint", new Point2D.Double(modelLink.getxCoord(), modelLink.getyCoord()));
-      result.put("modelLinkId", modelLink.getLinkedModel().getId());
-
-    } else if (link instanceof OverviewImageLink) {
-      result.put("imageLinkId", ((OverviewImageLink) link).getLinkedOverviewImage().getId());
-    } else if (link instanceof OverviewSearchLink) {
-      result.put("query", ((OverviewSearchLink) link).getQuery());
-    } else {
-      throw new NotImplementedException("Not implemented behaviour for class: " + link.getClass());
-    }
-    result.put("type", link.getClass().getSimpleName());
-    return result;
-  }
-
-  private List<Map<String, Double>> polygonToMap(String polygon) {
-    List<Map<String, Double>> result = new ArrayList<>();
-    for (String string : polygon.split(" ")) {
-      String tmp[] = string.split(",");
-      Map<String, Double> point = new TreeMap<>();
-      point.put("x", Double.parseDouble(tmp[0]));
-      point.put("y", Double.parseDouble(tmp[1]));
-      result.add(point);
-    }
+    result.put("links", image.getLinks());
     return result;
   }
 
@@ -258,7 +220,7 @@ public class ProjectRestImpl extends BaseRestImpl {
   }
 
   public List<Map<String, Object>> getProjects() {
-    List<Project> projects = getProjectService().getAllProjects();
+    List<Project> projects = getProjectService().getAllProjects(true);
     List<Map<String, Object>> result = new ArrayList<>();
     for (Project project : projects) {
       result.add(createData(project));
@@ -447,36 +409,36 @@ public class ProjectRestImpl extends BaseRestImpl {
         throw new QueryException("Unknown type for zip entry: zip-entries[" + fileIndex + "]");
       }
       switch (type) {
-        case MAP:
-          String submodelTypeKey = "zip-entries[" + fileIndex + "][_data][type][id]";
-          String rootKey = "zip-entries[" + fileIndex + "][_data][root]";
-          String mappingKey = "zip-entries[" + fileIndex + "][_data][mapping]";
-
-          String mapTypeString = getStringValue(data.get(submodelTypeKey), SubmodelType.UNKNOWN.name());
-          SubmodelType mapType = SubmodelType.valueOf(mapTypeString);
-
-          name = (String) data.get("zip-entries[" + fileIndex + "][_data][name]").get(0);
-          Boolean root = getBoolValue(data.get(rootKey), false);
-          Boolean mapping = getBoolValue(data.get(mappingKey), false);
-
-          entry = new ModelZipEntryFile(filename, name, root, mapping, mapType);
-          break;
-        case OVERLAY:
-          name = getFirstEntry(data, "zip-entries[" + fileIndex + "][_data][name]");
-          String description = getFirstEntry(data, "zip-entries[" + fileIndex + "][_data][description]");
-          if (name == null || name.trim().isEmpty()) {
-            throw new QueryException("zip-entries[" + fileIndex + "][_data][name] cannot be empty");
-          }
-          entry = new LayoutZipEntryFile(filename, name, description);
-          break;
-        case IMAGE:
-          entry = new ImageZipEntryFile(filename);
-          break;
-        case GLYPH:
-          entry = new GlyphZipEntryFile(filename);
-          break;
-        default:
-          throw new QueryException("Unknown entry type: " + entryType);
+      case MAP:
+        String submodelTypeKey = "zip-entries[" + fileIndex + "][_data][type][id]";
+        String rootKey = "zip-entries[" + fileIndex + "][_data][root]";
+        String mappingKey = "zip-entries[" + fileIndex + "][_data][mapping]";
+
+        String mapTypeString = getStringValue(data.get(submodelTypeKey), SubmodelType.UNKNOWN.name());
+        SubmodelType mapType = SubmodelType.valueOf(mapTypeString);
+
+        name = (String) data.get("zip-entries[" + fileIndex + "][_data][name]").get(0);
+        Boolean root = getBoolValue(data.get(rootKey), false);
+        Boolean mapping = getBoolValue(data.get(mappingKey), false);
+
+        entry = new ModelZipEntryFile(filename, name, root, mapping, mapType);
+        break;
+      case OVERLAY:
+        name = getFirstEntry(data, "zip-entries[" + fileIndex + "][_data][name]");
+        String description = getFirstEntry(data, "zip-entries[" + fileIndex + "][_data][description]");
+        if (name == null || name.trim().isEmpty()) {
+          throw new QueryException("zip-entries[" + fileIndex + "][_data][name] cannot be empty");
+        }
+        entry = new LayoutZipEntryFile(filename, name, description);
+        break;
+      case IMAGE:
+        entry = new ImageZipEntryFile(filename);
+        break;
+      case GLYPH:
+        entry = new GlyphZipEntryFile(filename);
+        break;
+      default:
+        throw new QueryException("Unknown entry type: " + entryType);
       }
       fileIndex++;
       result.add(entry);
@@ -737,8 +699,14 @@ public class ProjectRestImpl extends BaseRestImpl {
   }
 
   private enum LogSortColumn {
-    ID("id"), LEVEL("level"), TYPE("type"), OBJECT_IDENTIFIER("objectIdentifier"), OBJECT_CLASS("objectClass"), MAP_NAME("mapName"), SOURCE("source"), CONTENT(
-        "content");
+    ID("id"),
+    LEVEL("level"),
+    TYPE("type"),
+    OBJECT_IDENTIFIER("objectIdentifier"),
+    OBJECT_CLASS("objectClass"),
+    MAP_NAME("mapName"),
+    SOURCE("source"),
+    CONTENT("content");
 
     private String commonName;
 

service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java

 package lcsb.mapviewer.services.impl;
 
-import java.io.*;
-import java.util.*;
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+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 java.util.concurrent.CountDownLatch;
 
 import javax.mail.MessagingException;
@@ -11,33 +23,67 @@ import org.apache.commons.io.FileUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.core.LogEvent;
+import org.hibernate.Hibernate;
 import org.primefaces.model.DefaultTreeNode;
 import org.primefaces.model.TreeNode;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 
-import lcsb.mapviewer.annotation.services.*;
+import lcsb.mapviewer.annotation.services.MeSHParser;
+import lcsb.mapviewer.annotation.services.ModelAnnotator;
+import lcsb.mapviewer.annotation.services.ProblematicAnnotation;
+import lcsb.mapviewer.annotation.services.TaxonomyBackend;
+import lcsb.mapviewer.annotation.services.TaxonomySearchException;
 import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
 import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
-import lcsb.mapviewer.commands.*;
-import lcsb.mapviewer.common.*;
+import lcsb.mapviewer.commands.ClearColorModelCommand;
+import lcsb.mapviewer.commands.CommandExecutionException;
+import lcsb.mapviewer.commands.CopyCommand;
+import lcsb.mapviewer.commands.CreateHierarchyCommand;
+import lcsb.mapviewer.commands.SetFixedHierarchyLevelCommand;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.common.MinervaLoggerAppender;
+import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.*;
+import lcsb.mapviewer.converter.ColorSchemaReader;
+import lcsb.mapviewer.converter.ComplexZipConverter;
+import lcsb.mapviewer.converter.ComplexZipConverterParams;
+import lcsb.mapviewer.converter.Converter;
+import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.ProjectFactory;
 import lcsb.mapviewer.converter.graphics.DrawingException;
 import lcsb.mapviewer.converter.graphics.MapGenerator;
 import lcsb.mapviewer.converter.graphics.MapGenerator.MapGeneratorParams;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
 import lcsb.mapviewer.converter.zip.ZipEntryFile;
-import lcsb.mapviewer.model.*;
+import lcsb.mapviewer.model.IgnoredLogMarker;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.ProjectLogEntry;
+import lcsb.mapviewer.model.ProjectLogEntryType;
+import lcsb.mapviewer.model.ProjectStatus;
 import lcsb.mapviewer.model.cache.UploadedFileEntry;
-import lcsb.mapviewer.model.map.*;
-import lcsb.mapviewer.model.map.layout.*;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.ProjectBackground;
+import lcsb.mapviewer.model.map.layout.ProjectBackgroundImageLayer;
+import lcsb.mapviewer.model.map.layout.ProjectBackgroundStatus;
 import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.model.*;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
 import lcsb.mapviewer.model.overlay.DataOverlay;
 import lcsb.mapviewer.model.overlay.InvalidDataOverlayException;
-import lcsb.mapviewer.model.user.*;
+import lcsb.mapviewer.model.user.ConfigurationElementType;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.model.user.UserAnnotationSchema;
+import lcsb.mapviewer.model.user.UserClassAnnotators;
+import lcsb.mapviewer.model.user.UserClassRequiredAnnotations;
+import lcsb.mapviewer.model.user.UserClassValidAnnotations;
 import lcsb.mapviewer.model.user.annotator.AnnotatorData;
 import lcsb.mapviewer.modelutils.map.ClassTreeNode;
 import lcsb.mapviewer.modelutils.map.ElementUtils;
@@ -47,7 +93,11 @@ import lcsb.mapviewer.persist.dao.ProjectDao;
 import lcsb.mapviewer.persist.dao.map.ModelDao;
 import lcsb.mapviewer.persist.dao.map.ProjectBackgroundDao;
 import lcsb.mapviewer.persist.dao.user.UserDao;
-import lcsb.mapviewer.services.interfaces.*;
+import lcsb.mapviewer.services.interfaces.ICommentService;
+import lcsb.mapviewer.services.interfaces.IConfigurationService;
+import lcsb.mapviewer.services.interfaces.IModelService;
+import lcsb.mapviewer.services.interfaces.IProjectService;
+import lcsb.mapviewer.services.interfaces.IUserService;
 import lcsb.mapviewer.services.overlay.AnnotatedObjectTreeRow;
 import lcsb.mapviewer.services.search.chemical.IChemicalService;
 import lcsb.mapviewer.services.search.drug.IDrugService;
@@ -598,8 +648,8 @@ public class ProjectService implements IProjectService {
 
   /**
    * When we encountered hibernate exception we need to handle error reporting
-   * differently (hibernate session is broken). This method handles such case when
-   * hibernate exception occurred when removing project.
+   * differently (hibernate session is broken). This method handles such case
+   * when hibernate exception occurred when removing project.
    *
    * @param originalProject
    *          project that was being removed
@@ -1247,4 +1297,26 @@ public class ProjectService implements IProjectService {
     }
     validator.fixValidationIssues(project);
   }
+
+  @Override
+  public Project getProjectByProjectId(String projectId, boolean initializeLazy) {
+    Project result = getProjectByProjectId(projectId);
+    if (result != null && initializeLazy) {
+      for (ModelData model: result.getModels()) {
+        Hibernate.initialize(model);
+      }
+    }
+    return result;
+  }
+
+  @Override
+  public List<Project> getAllProjects(boolean initializeLazy) {
+    List<Project> result = getAllProjects();
+    for (Project project : result) {
+      for (ModelData model: project.getModels()) {
+        Hibernate.initialize(model);
+      }
+    }
+    return result;
+  }
 }

service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java

@@ -26,6 +26,8 @@ public interface IProjectService {
    *         doesn't exist.
    */
   Project getProjectByProjectId(String projectId);
+  
+  Project getProjectByProjectId(String projectId, boolean initializeLazy);
 
   /**
    * Checks if project with a given {@link Project#projectId identifier} exists.
@@ -43,6 +45,8 @@ public interface IProjectService {
    * @return list of all projects.
    */
   List<Project> getAllProjects();
+  
+  List<Project> getAllProjects(boolean initializeLazy);
 
   /**
    * Removes project from the system.

web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTest.java

@@ -134,7 +134,6 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
     MockHttpSession session = createSession(CURATOR_LOGIN, CURATOR_PASSWORD);
 
     RequestBuilder request = get("/api/projects/")
-        .contentType(MediaType.APPLICATION_FORM_URLENCODED)
         .session(session);
 
     String response = mockMvc.perform(request)