From f4e370375df3d78318f2caf71d7061f06e75eaf1 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 10 Apr 2017 15:36:23 +0200
Subject: [PATCH] number of publication should be in project scope
---
.../mapviewer/api/project/ModelMetaData.java | 49 -------------------
.../api/project/ProjectMetaData.java | 28 +++++++----
.../api/project/ProjectRestImpl.java | 32 +++++++++++-
3 files changed, 50 insertions(+), 59 deletions(-)
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/project/ModelMetaData.java b/rest-api/src/main/java/lcsb/mapviewer/api/project/ModelMetaData.java
index a771a5e150..3fc4c467e5 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/project/ModelMetaData.java
+++ b/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;
- }
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/project/ProjectMetaData.java b/rest-api/src/main/java/lcsb/mapviewer/api/project/ProjectMetaData.java
index 090b6d0dc1..6c946ee3d0 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/project/ProjectMetaData.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/project/ProjectMetaData.java
@@ -1,20 +1,12 @@
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;
+ }
+
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/project/ProjectRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/project/ProjectRestImpl.java
index 27157aa2be..71d93d6ba7 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/project/ProjectRestImpl.java
+++ b/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;
}
--
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