number of publication should be in project scope

rest-api/src/main/java/lcsb/mapviewer/api/project/ModelMetaData.java

@@ -3,21 +3,15 @@ package lcsb.mapviewer.api.project;
 import java.awt.geom.Point2D;
 import java.io.Serializable;
 import java.util.ArrayList;
-import java.util.HashSet;
 import java.util.List;
-import java.util.Set;
 
 import org.primefaces.model.map.LatLng;
 
 import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.layout.Layout;
 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.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.services.utils.gmap.CoordinationConverter;
 import lcsb.mapviewer.services.view.LayoutView;
 import lcsb.mapviewer.services.view.LayoutViewFactory;
@@ -41,8 +35,6 @@ public class ModelMetaData implements Serializable {
 
 	private Integer							idObject;
 
-	private Integer							publicationCount;
-
 	/**
 	 * Size in pixels of the single square tile (small image used for graphical
 	 * representation).
@@ -119,31 +111,6 @@ public class ModelMetaData implements Serializable {
 		}
 		this.setSubmodels(submodels);
 
-		Set<MiriamData> publications = new HashSet<>();
-		List<ModelData> models = new ArrayList<>();
-		for (ModelSubmodelConnection connection : model.getSubmodels()) {
-			models.add(connection.getSubmodel());
-		}
-		models.add(model);
-		for (ModelData modelData : models) {
-			for (Element element : modelData.getElements()) {
-				for (MiriamData md : element.getMiriamData()) {
-					if (md.getDataType().equals(MiriamType.PUBMED)) {
-						publications.add(md);
-					}
-				}
-			}
-			for (Reaction reaction : modelData.getReactions()) {
-				for (MiriamData md : reaction.getMiriamData()) {
-					if (md.getDataType().equals(MiriamType.PUBMED)) {
-						publications.add(md);
-					}
-				}
-
-			}
-		}
-
-		this.setPublicationCount(publications.size());
 	}
 
 	protected ModelMetaData() {
@@ -370,20 +337,4 @@ public class ModelMetaData implements Serializable {
 		this.idObject = idObject;
 	}
 
-	/**
-	 * @return the publicationCount
-	 * @see #publicationCount
-	 */
-	public Integer getPublicationCount() {
-		return publicationCount;
-	}
-
-	/**
-	 * @param publicationCount
-	 *          the publicationCount to set
-	 * @see #publicationCount
-	 */
-	public void setPublicationCount(Integer publicationCount) {
-		this.publicationCount = publicationCount;
-	}
 }

rest-api/src/main/java/lcsb/mapviewer/api/project/ProjectMetaData.java

 package lcsb.mapviewer.api.project;
 
 import java.io.Serializable;
-import java.util.HashSet;
 import java.util.List;
-import java.util.Set;
 
 import org.apache.log4j.Logger;
 
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.model.map.OverviewImageLink;
-import lcsb.mapviewer.model.map.OverviewLink;
-import lcsb.mapviewer.model.map.model.ModelData;
 import lcsb.mapviewer.services.view.AnnotationView;
 import lcsb.mapviewer.services.view.OverviewImageView;
-import lcsb.mapviewer.services.view.OverviewImageViewFactory;
 
 public class ProjectMetaData implements Serializable {
 
@@ -53,6 +45,8 @@ public class ProjectMetaData implements Serializable {
 
 	private ModelMetaData						map;
 
+	private Integer									publicationCount;
+
 	/**
 	 * List of overview images attached to this model.
 	 */
@@ -69,7 +63,6 @@ public class ProjectMetaData implements Serializable {
 	protected ProjectMetaData() {
 	}
 
-
 	/**
 	 * @return the version
 	 * @see #version
@@ -240,4 +233,21 @@ public class ProjectMetaData implements Serializable {
 		this.organism = organism;
 	}
 
+	/**
+	 * @return the publicationCount
+	 * @see #publicationCount
+	 */
+	public Integer getPublicationCount() {
+		return publicationCount;
+	}
+
+	/**
+	 * @param publicationCount
+	 *          the publicationCount to set
+	 * @see #publicationCount
+	 */
+	public void setPublicationCount(Integer publicationCount) {
+		this.publicationCount = publicationCount;
+	}
+
 }

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

@@ -17,11 +17,14 @@ import org.springframework.web.bind.annotation.RequestParam;
 
 import lcsb.mapviewer.common.exception.InvalidStateException;
 import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.MiriamData;
+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.model.Model;
 import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
 import lcsb.mapviewer.model.map.reaction.Modifier;
 import lcsb.mapviewer.model.map.reaction.Product;
 import lcsb.mapviewer.model.map.reaction.Reactant;
@@ -106,8 +109,35 @@ public class ProjectRestImpl {
 				result.setTopOverviewImage(factory.create(model.getOverviewImages().get(0)));
 			}
 			result.setMap(new ModelMetaData(model));
+
+			Set<MiriamData> publications = new HashSet<>();
+			List<ModelData> models = new ArrayList<>();
+			for (ModelSubmodelConnection connection : model.getSubmodels()) {
+				models.add(connection.getSubmodel());
+			}
+			models.add(model);
+			for (ModelData modelData : models) {
+				for (Element element : modelData.getElements()) {
+					for (MiriamData md : element.getMiriamData()) {
+						if (md.getDataType().equals(MiriamType.PUBMED)) {
+							publications.add(md);
+						}
+					}
+				}
+				for (Reaction reaction : modelData.getReactions()) {
+					for (MiriamData md : reaction.getMiriamData()) {
+						if (md.getDataType().equals(MiriamType.PUBMED)) {
+							publications.add(md);
+						}
+					}
+
+				}
+			}
+
+			result.setPublicationCount(publications.size());
+
 		}
-		
+
 		return result;
 	}