Merge branch 'dev'

pom.xml

@@ -7,7 +7,7 @@
     <groupId>org.reactome.web</groupId>
     <artifactId>diagram</artifactId>
     <packaging>jar</packaging>
-    <version>3.6.2</version>
+    <version>3.6.3</version>
     <name>Reactome Diagram Viewer</name>
 
     <description>
@@ -44,7 +44,7 @@
         <webappDirectory>${project.build.directory}/${project.build.finalName}</webappDirectory>
 
         <reactome.web.analysis-client>1.4.0</reactome.web.analysis-client>
-        <reactome.web.model>2.0.4</reactome.web.model>
+        <reactome.web.model>2.0.6-SNAPSHOT</reactome.web.model>
         <reactome.web.carrousel>1.0.2</reactome.web.carrousel>
         <reactome.web.scroller>1.0.2</reactome.web.scroller>
         <reactome.web.quadtree>1.2.0</reactome.web.quadtree>

src/main/java/org/reactome/web/diagram/client/DiagramViewer.java

@@ -33,7 +33,7 @@ public interface DiagramViewer extends IsWidget, HasHandlers, RequiresResize {
 
     HandlerRegistration addAnalysisProfileChangedHandler(AnalysisProfileChangedHandler handler);
 
-    void flagItems(String identifier);
+    void flagItems(String identifier, Boolean includeInteractors);
 
     void highlightItem(String stableIdentifier);
 

src/main/java/org/reactome/web/diagram/client/DiagramViewerImpl.java

@@ -46,6 +46,7 @@ class DiagramViewerImpl extends AbstractDiagramViewer implements
     private AnalysisStatus analysisStatus;
     private InteractorsManager interactorsManager;
     private FlaggedElementsLoader flaggedElementsLoader = new FlaggedElementsLoader(this);
+    private Boolean includeInteractors = true;
 
     DiagramViewerImpl() {
         super();
@@ -101,13 +102,10 @@ private void initHandlers() {
     }
 
     @Override
-    public void flagItems(String identifier) {
-        if (context != null && identifier != null && !identifier.equals(viewerContainer.getFlagTerm())) {
-            Set<DiagramObject> flagged = context.getFlagged(identifier);
-            if (flagged == null) {
-                eventBus.fireEventFromSource(new DiagramObjectsFlagRequestedEvent(identifier), this);
-            } else {
-                eventBus.fireEventFromSource(new DiagramObjectsFlaggedEvent(identifier, flagged, false), this);
+    public void flagItems(String identifier, Boolean includeInteractors) {
+        if (context != null && identifier != null) {
+            if(!identifier.equalsIgnoreCase(context.getFlagTerm()) || !this.includeInteractors.equals(includeInteractors)) {
+                eventBus.fireEventFromSource(new DiagramObjectsFlagRequestedEvent(identifier, includeInteractors), this);
             }
         }
     }
@@ -203,7 +201,15 @@ public void onDiagramObjectsFlagged(DiagramObjectsFlaggedEvent event) {
     @Override
     public void onDiagramObjectsFlagRequested(DiagramObjectsFlagRequestedEvent event) {
         boolean notify = !event.getSource().equals(this);
-        flaggedElementsLoader.load(context.getContent(), event.getTerm(), notify);
+
+        context.setFlagTerm(event.getTerm());
+        this.includeInteractors = event.getIncludeInteractors();
+        Set<DiagramObject> flagged = context.getFlagged(context.getFlagTerm() + includeInteractors);
+        if(flagged == null) {
+            flaggedElementsLoader.load(context.getContent(), event.getTerm(), notify);
+        } else {
+            eventBus.fireEventFromSource(new DiagramObjectsFlaggedEvent(event.getTerm(), includeInteractors, flagged, notify), this);
+        }
     }
 
     @Override
@@ -226,7 +232,7 @@ public void flaggedElementsLoaded(String term, Occurrences toFlag, boolean notif
         }
 
         //Flag those diagram entities that interact with the term
-        if(toFlag != null && toFlag.getInteractsWith() != null) {
+        if(toFlag != null && toFlag.getInteractsWith() != null && includeInteractors) {
             for (String stId : toFlag.getInteractsWith()) {
                 GraphObject graphObject = context.getContent().getDatabaseObject(stId);
                 if (graphObject != null) {
@@ -235,12 +241,13 @@ public void flaggedElementsLoaded(String term, Occurrences toFlag, boolean notif
             }
         }
 
-        context.setFlagged(term, flagged);
-        eventBus.fireEventFromSource(new DiagramObjectsFlaggedEvent(term, flagged, notify), this);
+        context.setFlagged(term + includeInteractors, flagged);
+        eventBus.fireEventFromSource(new DiagramObjectsFlaggedEvent(term, includeInteractors, flagged, notify), this);
     }
 
     @Override
     public void onFlaggedElementsLoaderError(Throwable exception) {
+        context.setFlagTerm(null);
         Console.error(exception.getMessage());
     }
 

src/main/java/org/reactome/web/diagram/client/ViewerContainer.java

@@ -165,10 +165,6 @@ public void contentRequested() {
         context = null;
     }
 
-    public String getFlagTerm() {
-        return context.getFlagTerm();
-    }
-
     public void expressionColumnChanged() {
         activeVisualiser.expressionColumnChanged();
     }
@@ -194,8 +190,8 @@ public void interactorsResourceChanged(OverlayResource resource) {
     }
 
     @Override
-    public void onDiagramExportRequested(CanvasExportRequestedEvent event) {
-        activeVisualiser.exportView(event.getOption());
+    public void onCanvasExportRequested(CanvasExportRequestedEvent event) {
+        activeVisualiser.exportView();
     }
 
     @Override
@@ -209,7 +205,7 @@ public void onDiagramObjectsFlagRequested(DiagramObjectsFlagRequestedEvent event
     public void onDiagramObjectsFlagged(DiagramObjectsFlaggedEvent event) {
         context.setFlagTerm(event.getTerm());
         setWatermarkURL(context, activeVisualiser.getSelected());
-        activeVisualiser.flagItems(event.getFlaggedItems());
+        activeVisualiser.flagItems(event.getFlaggedItems(), event.getIncludeInteractors());
     }
 
     @Override
@@ -225,10 +221,10 @@ public void onControlAction(ControlActionEvent event) {
             case FIT_ALL:       activeVisualiser.fitDiagram(true);  break;
             case ZOOM_IN:       activeVisualiser.zoomIn();                    break;
             case ZOOM_OUT:      activeVisualiser.zoomOut();                   break;
-            case UP:            activeVisualiser.padding(0, 10);      break;
-            case RIGHT:         activeVisualiser.padding(-10, 0);     break;
-            case DOWN:          activeVisualiser.padding(0, -10);     break;
-            case LEFT:          activeVisualiser.padding(10, 0);      break;
+            case UP:            activeVisualiser.padding(0, 10);     break;
+            case RIGHT:         activeVisualiser.padding(-10, 0);    break;
+            case DOWN:          activeVisualiser.padding(0, -10);    break;
+            case LEFT:          activeVisualiser.padding(10, 0);     break;
             case FIREWORKS:     overview();                                   break;
         }
     }

src/main/java/org/reactome/web/diagram/client/visualisers/Visualiser.java

@@ -9,8 +9,6 @@
 
 import java.util.Set;
 
-import static org.reactome.web.diagram.events.CanvasExportRequestedEvent.Option;
-
 
 /**
  * @author Kostas Sidiropoulos <ksidiro@ebi.ac.uk>
@@ -27,7 +25,7 @@ public interface Visualiser extends IsWidget {
 
     void padding(int dX, int dY);
 
-    void exportView(Option option);
+    void exportView();
 
     void contentLoaded(Context context);
 
@@ -67,7 +65,7 @@ public interface Visualiser extends IsWidget {
 
     void setSize(int width, int height);
 
-    void flagItems(Set<DiagramObject> flaggedItems);
+    void flagItems(Set<DiagramObject> flaggedItems, Boolean includeInteractors);
 
     void resetFlag();
 }

src/main/java/org/reactome/web/diagram/client/visualisers/diagram/DiagramCanvas.java

@@ -7,15 +7,14 @@
 import com.google.gwt.event.dom.client.ContextMenuHandler;
 import com.google.gwt.event.shared.EventBus;
 import com.google.gwt.user.client.Timer;
-import com.google.gwt.user.client.Window;
 import com.google.gwt.user.client.ui.AbsolutePanel;
 import com.google.gwt.user.client.ui.Image;
 import org.reactome.web.analysis.client.model.AnalysisType;
-import org.reactome.web.diagram.client.DiagramFactory;
-import org.reactome.web.diagram.context.popups.ImageDownloadDialog;
+import org.reactome.web.diagram.context.popups.export.ExportDialog;
 import org.reactome.web.diagram.data.AnalysisStatus;
 import org.reactome.web.diagram.data.Context;
 import org.reactome.web.diagram.data.DiagramStatus;
+import org.reactome.web.diagram.data.graph.model.GraphObject;
 import org.reactome.web.diagram.data.interactors.model.DiagramInteractor;
 import org.reactome.web.diagram.data.interactors.model.InteractorEntity;
 import org.reactome.web.diagram.data.layout.*;
@@ -55,7 +54,6 @@
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Set;
-import java.util.stream.Collectors;
 
 /**
  * @author Antonio Fabregat <fabregat@ebi.ac.uk>
@@ -272,7 +270,7 @@ private void cleanCanvas(Context2d ctx) {
         ctx.clearRect(0, 0, ctx.getCanvas().getWidth(), ctx.getCanvas().getHeight());
     }
 
-    public void exportImage(final String diagramStId) {
+    public void showExportDialog(final Context context, final GraphObject selected, final String flagTerm, final Boolean includeInteractors) {
         final Context2d ctx = this.canvases.get(this.canvases.size() - 1).getContext2d();
         //This is silly but gives some visual feedback of the picture taking :D
         (new Timer() {
@@ -293,34 +291,18 @@ public void run() {
                     for (int i = 0; i < canvases.size() - 1; i++) {
                         ctx.drawImage(canvases.get(i).getCanvasElement(), 0, 0);
                     }
-                    Image image = new Image();
-                    image.setUrl(ctx.getCanvas().toDataUrl("image/png"));
-                    final ImageDownloadDialog downloadDialogBox = new ImageDownloadDialog(image, "png",diagramStId);
-                    downloadDialogBox.showCentered();
+                    Image snapshot = new Image();
+                    snapshot.setUrl(ctx.getCanvas().toDataUrl("image/png"));
+
+                    String sel = selected != null ? selected.getStId() : null;
+                    final ExportDialog dialog = new ExportDialog(context, sel, flagTerm, includeInteractors, snapshot);
+                    dialog.showCentered();
                     cleanCanvas(ctx);
                 }
             }
         }).scheduleRepeating(20);
     }
 
-    public void exportPPT(final String diagramStId, final List<DiagramObject> selected, final Set<DiagramObject> flagged) {
-        //The following uses the SERVER because the widget needs to work when stand-alone
-        String url = DiagramFactory.SERVER + "/ContentService/exporter/diagram/"
-                + diagramStId + ".pptx?profile="
-                + DiagramColours.get().getSelectedProfileName();
-        // Add selected items
-        if (selected != null && !selected.isEmpty()) {
-            String sel = "&sel=" + selected.stream().map(n -> n.getReactomeId().toString()).collect(Collectors.joining(","));
-            url = url + sel;
-        }
-        //Add flagged items
-        if (flagged != null && !flagged.isEmpty()) {
-            String flg = "&flg=" + flagged.stream().map(n -> n.getReactomeId().toString()).collect(Collectors.joining(","));
-            url = url + flg;
-        }
-        Window.open(url, "_self", "");
-    }
-
     public void notifyHoveredExpression(DiagramObject item, Coordinate model) {
         Renderer renderer = rendererManager.getRenderer(item);
         Double exp = (renderer != null) ? renderer.getExpressionHovered(item, model, column) : null;
@@ -493,7 +475,7 @@ public void render(Collection<DiagramObject> items, Context context) {
         items = itemsDistribution.getAll("Reaction");
         if (!items.isEmpty()) { //No need to check for null here
             Renderer reactionRenderer = rendererManager.getRenderer("Reaction");
-            reactionRenderer.setColourProperties(reactions, colourProfileType);
+            reactionRenderer.setColourProperties(reactions, ColourProfileType.NORMAL);
             reactionRenderer.setColourProperties(this.fadeOut, ColourProfileType.FADE_OUT);
             for (DiagramObject item : items) {
                 if (item.getIsFadeOut() != null) {

src/main/java/org/reactome/web/diagram/client/visualisers/diagram/DiagramVisualiser.java

@@ -34,8 +34,6 @@
 import java.util.Collection;
 import java.util.Set;
 
-import static org.reactome.web.diagram.events.CanvasExportRequestedEvent.Option;
-
 /**
  * @author Kostas Sidiropoulos <ksidiro@ebi.ac.uk>
  */
@@ -67,6 +65,8 @@ public class DiagramVisualiser extends SimplePanel implements Visualiser,
 
     private boolean forceDraw = false;
 
+    private Boolean includeInteractors;
+
     public DiagramVisualiser(EventBus eventBus) {
         super();
         this.eventBus = eventBus;
@@ -260,18 +260,15 @@ public void onAnalysisProfileChanged(AnalysisProfileChangedEvent event) {
     }
 
     @Override
-    public void exportView(Option option) {
+    public void exportView() {
         if (context != null) {
-            String stId = context.getContent().getStableId();
-            switch (option) {
-                case IMAGE: canvas.exportImage(stId); break;
-                case PPTX:  canvas.exportPPT(stId, layoutManager.getSelectedDiagramObjects(), layoutManager.getFlagged()); break;
-            }
+            canvas.showExportDialog(context, layoutManager.getSelected(), context.getFlagTerm(), includeInteractors);
         }
     }
 
     @Override
-    public void flagItems(Set<DiagramObject> flaggedItems){
+    public void flagItems(Set<DiagramObject> flaggedItems, Boolean includeInteractors){
+        this.includeInteractors = includeInteractors;
         layoutManager.setFlagged(flaggedItems);
         forceDraw = true;
     }

src/main/java/org/reactome/web/diagram/client/visualisers/ehld/AbstractSVGPanel.java

@@ -9,7 +9,8 @@
 import com.google.gwt.user.client.ui.Image;
 import org.reactome.web.diagram.client.visualisers.ehld.filters.FilterColour;
 import org.reactome.web.diagram.client.visualisers.ehld.filters.FilterFactory;
-import org.reactome.web.diagram.context.popups.ImageDownloadDialog;
+import org.reactome.web.diagram.context.popups.export.ExportDialog;
+import org.reactome.web.diagram.data.Context;
 import org.reactome.web.diagram.util.position.MousePosition;
 import org.reactome.web.diagram.util.svg.SVGUtil;
 import org.vectomatic.dom.svg.*;
@@ -65,6 +66,8 @@ public abstract class AbstractSVGPanel extends AbsolutePanel {
 
     protected boolean isSafari;
 
+    protected Boolean includeInteractors;
+
     public AbstractSVGPanel(EventBus eventBus) {
         this.eventBus = eventBus;
         getElement().getStyle().setBackgroundColor("white");
@@ -76,23 +79,13 @@ public AbstractSVGPanel(EventBus eventBus) {
         sb = new StringBuilder();
     }
 
-    public void exportView(String stableId){
+    public void showExportDialog(final Context context, final String selected, final String flagged) {
         if(svg != null) {
             OMSVGSVGElement auxSVG = (OMSVGSVGElement) svg.cloneNode(true);
-            auxSVG.setViewBox(initialBB);
-
-            //Reset all transformations
-            sb.setLength(0);
-            sb.append("matrix(").append(initialTM.getA()).append(",").append(initialTM.getB()).append(",").append(initialTM.getC()).append(",")
-                    .append(initialTM.getD()).append(",").append(initialTM.getE()).append(",").append(initialTM.getF()).append(")");
-            for (OMSVGElement svgLayer : getRootLayers(auxSVG)) {
-                svgLayer.setAttribute(SVGConstants.SVG_TRANSFORM_ATTRIBUTE, sb.toString());
-            }
-
-            Image image = new Image();
-            image.setUrl("data:image/svg+xml;base64," + btoa(auxSVG.getMarkup()));
-            final ImageDownloadDialog downloadDialogBox = new ImageDownloadDialog(image, "svg", stableId);
-            downloadDialogBox.showCentered();
+            Image snapshot = new Image();
+            snapshot.setUrl("data:image/svg+xml;base64," + btoa(auxSVG.getMarkup()));
+            final ExportDialog dialog = new ExportDialog(context, selected, flagged, includeInteractors, snapshot);
+            dialog.showCentered();
         }
     }
 
@@ -283,4 +276,17 @@ private OMElement getAnalysisText(OMElement element){
         }
         return rtn;
     }
+
+    private void resetAllTransformations(OMSVGSVGElement auxSVG) {
+        auxSVG.setViewBox(initialBB);
+
+        //Reset all transformations
+        sb.setLength(0);
+        sb.append("matrix(").append(initialTM.getA()).append(",").append(initialTM.getB()).append(",").append(initialTM.getC()).append(",")
+                .append(initialTM.getD()).append(",").append(initialTM.getE()).append(",").append(initialTM.getF()).append(")");
+        for (OMSVGElement svgLayer : getRootLayers(auxSVG)) {
+            svgLayer.setAttribute(SVGConstants.SVG_TRANSFORM_ATTRIBUTE, sb.toString());
+        }
+
+    }
 }

src/main/java/org/reactome/web/diagram/client/visualisers/ehld/SVGVisualiser.java

@@ -53,9 +53,6 @@
 
 import java.util.*;
 
-import static org.reactome.web.diagram.events.CanvasExportRequestedEvent.Option;
-
-
 /**
  * @author Kostas Sidiropoulos <ksidiro@ebi.ac.uk>
  */
@@ -159,9 +156,15 @@ public void padding(int dX, int dY) {
     }
 
     @Override
-    public void exportView(Option option) {
+    public void exportView() {
         if (context != null) {
-            exportView(context.getContent().getStableId());
+
+            String sel = null;
+            if (selected != null) {
+                sel = selected.getId().replace("REGION-", "");
+            }
+
+            showExportDialog(context, sel, context.getFlagTerm());
         }
     }
 
@@ -1192,8 +1195,9 @@ private void unFlagElement(OMElement element) {
     }
 
     @Override
-    public void flagItems(Set<DiagramObject> flaggedItems){
+    public void flagItems(Set<DiagramObject> flaggedItems, Boolean includeInteractors){
         resetFlag();
+        this.includeInteractors = includeInteractors;
         for (DiagramObject diagramObject : flaggedItems) {
             if(diagramObject instanceof EHLDObject){
                 EHLDObject item = (EHLDObject) diagramObject;