Added citation modal to Pathway Browser

pom.xml

@@ -48,7 +48,7 @@
         <reactome.web.carrousel>1.0.2</reactome.web.carrousel>
         <reactome.web.diagram>3.6.7</reactome.web.diagram>
         <reactome.web.fireworks>1.8.6</reactome.web.fireworks>
-        <reactome.web.model>2.1.20</reactome.web.model>
+        <reactome.web.model>2.1.21-SNAPSHOT</reactome.web.model>
         <reactome.web.pdb>2.3.1</reactome.web.pdb>
         <reactome.web.chebi>1.2.0</reactome.web.chebi>
         <reactome.web.rhea>1.3.1</reactome.web.rhea>

src/main/java/org/reactome/web/pwp/client/AppController.java

@@ -46,6 +46,9 @@
 import org.reactome.web.pwp.client.tools.analysis.AnalysisLauncher;
 import org.reactome.web.pwp.client.tools.analysis.AnalysisLauncherDisplay;
 import org.reactome.web.pwp.client.tools.analysis.AnalysisLauncherPresenter;
+import org.reactome.web.pwp.client.tools.citation.CitationLauncher;
+import org.reactome.web.pwp.client.tools.citation.CitationLauncherDisplay;
+import org.reactome.web.pwp.client.tools.citation.CitationLauncherPresenter;
 import org.reactome.web.pwp.client.tools.launcher.ToolLauncher;
 import org.reactome.web.pwp.client.tools.launcher.ToolLauncherDisplay;
 import org.reactome.web.pwp.client.tools.launcher.ToolLauncherPresenter;
@@ -207,6 +210,10 @@ private void initialiseDetailsTabsList(){
     private void initialiseTools(){
         AnalysisLauncher.Display analysisDisplay = new AnalysisLauncherDisplay();
         new AnalysisLauncherPresenter(this.eventBus, analysisDisplay);
+
+        CitationLauncher.Display citationDisplay = new CitationLauncherDisplay();
+        new CitationLauncherPresenter(this.eventBus, citationDisplay);
+
     }
 
     private void printMessage(){

src/main/java/org/reactome/web/pwp/client/common/PathwayPortalTool.java

@@ -6,7 +6,8 @@
 public enum PathwayPortalTool {
 
     NONE        ("XX", "No Tool"),
-    ANALYSIS    ("AT", "Analysis Tool");
+    ANALYSIS    ("AT", "Analysis Tool"),
+    CITATION     ("CT", "Cite Us!");
 
     private String code;
     private String title;

src/main/java/org/reactome/web/pwp/client/tools/citation/CitationLauncher.java

@@ -0,0 +1,33 @@
+package org.reactome.web.pwp.client.tools.citation;
+
+import org.reactome.web.pwp.client.common.module.BrowserModule;
+
+/**
+ * @author Yusra Haider <yhaider@ebi.ac.uk>
+ */
+
+public interface CitationLauncher {
+
+    interface Presenter extends BrowserModule.Presenter {
+        void displayClosed();
+    }
+
+    interface Display extends BrowserModule.Display {
+        void hide();
+
+        void center();
+
+        void show();
+
+        void setPresenter(CitationLauncher.Presenter presenter);
+
+        void setCitation(String citation);
+
+        void setExportBar(String id);
+    }
+}
+
+
+
+
+

src/main/java/org/reactome/web/pwp/client/tools/citation/CitationLauncherDisplay.java

@@ -0,0 +1,193 @@
+package org.reactome.web.pwp.client.tools.citation;
+
+import com.google.gwt.core.client.GWT;
+import com.google.gwt.event.logical.shared.CloseEvent;
+import com.google.gwt.event.logical.shared.CloseHandler;
+import com.google.gwt.event.logical.shared.ResizeEvent;
+import com.google.gwt.event.logical.shared.ResizeHandler;
+import com.google.gwt.i18n.client.DateTimeFormat;
+import com.google.gwt.resources.client.ClientBundle;
+import com.google.gwt.resources.client.CssResource;
+import com.google.gwt.resources.client.ImageResource;
+import com.google.gwt.safehtml.shared.SafeHtmlUtils;
+import com.google.gwt.user.client.Window;
+import com.google.gwt.user.client.ui.*;
+import org.reactome.web.pwp.client.tools.launcher.LauncherButton;
+
+import java.util.Date;
+
+public class CitationLauncherDisplay extends PopupPanel implements CitationLauncher.Display, CloseHandler<PopupPanel>,
+        ResizeHandler {
+
+    private CitationLauncher.Presenter presenter;
+    private Label citation;
+    private HorizontalPanel buttonBar;
+    private Label buttonBarHeading;
+
+    public CitationLauncherDisplay() {
+        super(true, true);
+        setAnimationEnabled(true);
+        setGlassEnabled(true);
+        setAutoHideOnHistoryEventsEnabled(false);
+        addStyleName(RESOURCES.getCSS().popupPanel());
+        Window.addResizeHandler(this);
+
+        int width = (int) Math.round(Window.getClientWidth() * 0.9);
+        int height = (int) Math.round(Window.getClientHeight() * 0.9);
+        this.setWidth(width + "px");
+        this.setHeight(height + "px");
+
+        FlowPanel mainPanel = new FlowPanel();                         // Main panel
+        mainPanel.addStyleName(RESOURCES.getCSS().mainPanel());
+        mainPanel.add(setTitlePanel());                                // Title panel with heading & close button
+
+        FlowPanel citationPanel = new FlowPanel();                     // panel that will contain the citation text
+        citationPanel.addStyleName(RESOURCES.getCSS().citationPanel());
+        citation = new Label();
+        citation.addStyleName(RESOURCES.getCSS().citationText());
+        citationPanel.add(citation);
+        mainPanel.add(citationPanel);
+
+        buttonBarHeading = new Label();
+        buttonBarHeading.addStyleName(RESOURCES.getCSS().buttonHeading());
+        mainPanel.add(buttonBarHeading);
+
+        buttonBar = new HorizontalPanel();                             // panel with all the export buttons
+        FlowPanel buttonPanel = new FlowPanel();
+        buttonPanel.addStyleName(RESOURCES.getCSS().buttonPanel());
+        buttonPanel.add(buttonBar);
+        mainPanel.add(buttonPanel);
+        this.addCloseHandler(this);
+        this.add(mainPanel);
+    }
+
+    @Override
+    public void show() {
+        super.show();
+    }
+
+    public void setCitation(String citation) {
+        this.citation.setText(citation);
+    }
+
+    @Override
+    public void onClose(CloseEvent<PopupPanel> event) {
+        presenter.displayClosed();
+        buttonBar = new HorizontalPanel();
+    }
+
+    @Override
+    public void onResize(ResizeEvent event) {
+        if (isVisible()) {
+            int width = (int) Math.round(RootLayoutPanel.get().getOffsetWidth() * 0.9);
+            int height = (int) Math.round(RootLayoutPanel.get().getOffsetHeight() * 0.9);
+            this.setWidth(width + "px");
+            this.setHeight(height + "px");
+        }
+    }
+
+    @Override
+    public void setPresenter(CitationLauncher.Presenter presenter) {
+        this.presenter = presenter;
+    }
+
+    // sets the panel title and close button
+    private Widget setTitlePanel() {
+        FlowPanel header = new FlowPanel();
+        header.setStyleName(RESOURCES.getCSS().header());
+        header.addStyleName(RESOURCES.getCSS().unselectable());
+        Label title = new Label("Cite Us!");
+        title.setStyleName(RESOURCES.getCSS().headerText());
+        Button closeBtn = new LauncherButton("Close citation modal", RESOURCES.getCSS().close(), clickEvent -> CitationLauncherDisplay.this.hide());
+        header.add(title);
+        header.add(closeBtn);
+        return header;
+    }
+
+    public void setExportBar(String id) {
+        this.buttonBarHeading.setText("Download As: ");
+        for (ExportType ef : ExportType.values()) {
+            this.buttonBar.add(getExportButton(ef.getIcon(), ef.getTitle(), ef.getUrl() + "&id=" + id
+                            + "&dateAccessed=" + DateTimeFormat.getFormat("E MMM dd yyyy").format(new Date()),
+                    "reactome_citation_" + id + ef.getExt()));
+        }
+    }
+
+    public FlowPanel getExportButton(ImageResource icon, String title, String url, String filename) {
+
+        FlowPanel button = new FlowPanel();
+        button.addStyleName(RESOURCES.getCSS().exportItem());
+        button.setTitle(title);
+
+        FlowPanel image = new FlowPanel();
+        image.add(new Image(icon));
+
+        Anchor anchor = new Anchor(SafeHtmlUtils.fromTrustedString(image.toString()), url, "_blank");
+        anchor.getElement().setAttribute("rel", "noindex,nofollow");
+        anchor.getElement().setAttribute("download", filename);
+
+        button.add(anchor);
+
+        return button;
+    }
+
+    public static CitationLauncherDisplay.Resources RESOURCES;
+
+    static {
+        RESOURCES = GWT.create(CitationLauncherDisplay.Resources.class);
+        RESOURCES.getCSS().ensureInjected();
+    }
+
+    /**
+     * A ClientBundle of resources used by this widget.
+     */
+    public interface Resources extends ClientBundle {
+        /**
+         * The styles used in this widget.
+         */
+        @Source(CitationLauncherDisplay.ResourceCSS.CSS)
+        CitationLauncherDisplay.ResourceCSS getCSS();
+
+        @Source("images/close_clicked.png")
+        ImageResource closeClicked();
+
+        @Source("images/close_hovered.png")
+        ImageResource closeHovered();
+
+        @Source("images/close_normal.png")
+        ImageResource closeNormal();
+    }
+
+    /**
+     * Styles used by this widget.
+     */
+    @CssResource.ImportedWithPrefix("pwp-CitationLauncher")
+    public interface ResourceCSS extends CssResource {
+        /**
+         * The path to the default CSS styles used by this resource.
+         */
+        String CSS = "org/reactome/web/pwp/client/tools/citation/CitationLauncher.css";
+
+        String popupPanel();
+
+        String mainPanel();
+
+        String citationPanel();
+
+        String header();
+
+        String headerText();
+
+        String citationText();
+
+        String close();
+
+        String unselectable();
+
+        String buttonPanel();
+
+        String exportItem();
+
+        String buttonHeading();
+    }
+}

src/main/java/org/reactome/web/pwp/client/tools/citation/CitationLauncherPresenter.java

@@ -0,0 +1,96 @@
+package org.reactome.web.pwp.client.tools.citation;
+
+import com.google.gwt.event.shared.EventBus;
+import org.reactome.web.pwp.client.common.PathwayPortalTool;
+import org.reactome.web.pwp.client.common.events.BrowserReadyEvent;
+import org.reactome.web.pwp.client.common.events.StateChangedEvent;
+import org.reactome.web.pwp.client.common.events.ToolSelectedEvent;
+import org.reactome.web.pwp.client.common.handlers.BrowserReadyHandler;
+import org.reactome.web.pwp.client.common.module.AbstractPresenter;
+import org.reactome.web.pwp.model.client.common.ContentClientHandler;
+import org.reactome.web.pwp.model.client.content.ContentClient;
+import org.reactome.web.pwp.model.client.content.ContentClientError;
+
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+
+
+public class CitationLauncherPresenter extends AbstractPresenter implements CitationLauncher.Presenter, BrowserReadyHandler {
+
+    private CitationLauncher.Display display;
+    private static final Map<String, String> CITATIONS;
+    private static final String PATHWAY_ANALYSIS_CITATION_ID = "28249561";
+    private static final String DIAGRAM_VIEWER_CITATION_ID = "29186351";
+
+    static {
+        Map<String, String> citations = new HashMap<>();
+        citations.put("28249561", "Fabregat A, Sidiropoulos K, Viteri G, Forner O, Marin-Garcia P, Arnau V, D'Eustachio P, Stein L, Hermjakob H. Reactome pathway analysis: a high-performance in-memory approach. BMC Bioinformatics. 2017 Mar 2;18(1):142. doi: 10.1186/s12859-017-1559-2. PubMed PMID: 28249561");
+        citations.put("29186351", "Fabregat A, Sidiropoulos K, Viteri G, Marin-Garcia P, Ping P, Stein L, D'Eustachio P, Hermjakob H. Reactome diagram viewer: data structures and strategies to boost performance. Bioinformatics. 2018 Apr 1;34(7):1208-1214. doi: 10.1093/bioinformatics/btx752. PubMed PMID: 29186351");
+        CITATIONS = Collections.unmodifiableMap(citations);
+    }
+
+
+    public CitationLauncherPresenter(EventBus eventBus, CitationLauncher.Display display) {
+        super(eventBus);
+        this.display = display;
+        this.display.setPresenter(this);
+        this.eventBus.addHandler(BrowserReadyEvent.TYPE, this);
+    }
+
+    @Override
+    public void displayClosed() {
+        this.eventBus.fireEventFromSource(new ToolSelectedEvent(PathwayPortalTool.NONE), this);
+    }
+
+    @Override
+    public void onBrowserReady(BrowserReadyEvent event) {
+        // do your stuff
+    }
+
+    @Override
+    public void onStateChanged(StateChangedEvent event) {
+        PathwayPortalTool tool = event.getState().getTool();
+        if (tool.equals(PathwayPortalTool.CITATION)) {
+            if (event.getState().getAnalysisStatus().getToken() != null) getCitation(PATHWAY_ANALYSIS_CITATION_ID);
+            else getCitation(DIAGRAM_VIEWER_CITATION_ID);
+        } else {
+            display.hide();
+        }
+    }
+
+    private void showDisplay() {
+        display.show();
+        display.center();
+    }
+
+    private void getCitation(String id) {
+        ContentClient.getStaticCitation(id, new ContentClientHandler.Citation() {
+            @Override
+            public void onCitationTextLoaded(String citation) {
+                // happy flow
+                display.setCitation(citation);
+                // call method for including the export buttons on display
+                display.setExportBar(id);
+                showDisplay();
+            }
+
+            @Override
+            public void onContentClientException(Type type, String message) {
+                display.setCitation(CITATIONS.get(id));
+                showDisplay();
+                //TODO add code for showing banner
+            }
+
+            @Override
+            public void onContentClientError(ContentClientError error) {
+                display.setCitation(CITATIONS.get(id));
+                showDisplay();
+                //TODO add code for showing banner
+            }
+        });
+    }
+
+}
+
+