EDIT

src/main/java/eu/etaxonomy/cdm/vaadin/component/ConceptRelationshipComposite.java -text

src/main/java/eu/etaxonomy/cdm/vaadin/jscomponent/D3ConceptRelationshipTree.java -text

src/main/java/eu/etaxonomy/cdm/vaadin/jscomponent/D3ConceptRelationshipTreeState.java -text

src/main/java/eu/etaxonomy/cdm/vaadin/presenter/ConceptRelationshipPresenter.java -text

src/main/java/eu/etaxonomy/cdm/vaadin/ui/ConceptRelationshipUI.java -text

src/main/java/eu/etaxonomy/cdm/vaadin/view/ConceptRelationshipView.java -text

src/main/java/eu/etaxonomy/cdm/vaadin/view/IConceptRelationshipComponentListener.java -text

src/main/webapp/VAADIN/themes/edit/favicon.ico -text

// $Id$

/**

* Copyright (C) 2015 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.vaadin.component;

import java.util.UUID;

import org.json.JSONException;

import com.vaadin.annotations.AutoGenerated;

import com.vaadin.ui.Alignment;

import com.vaadin.ui.Button;

import com.vaadin.ui.CustomComponent;

import com.vaadin.ui.HorizontalLayout;

import com.vaadin.ui.Notification;

import com.vaadin.ui.Notification.Type;

import com.vaadin.ui.VerticalLayout;

import eu.etaxonomy.cdm.vaadin.jscomponent.D3ConceptRelationshipTree;

import eu.etaxonomy.cdm.vaadin.presenter.ConceptRelationshipPresenter;

import eu.etaxonomy.cdm.vaadin.session.ISelectionListener;

import eu.etaxonomy.cdm.vaadin.session.SelectionEvent;

import eu.etaxonomy.cdm.vaadin.util.CdmVaadinSessionUtilities;

import eu.etaxonomy.cdm.vaadin.view.IConceptRelationshipComponentListener;

/**

 * @author cmathew

 * @date 9 Apr 2015

 *

 */

public class ConceptRelationshipComposite extends CustomComponent implements ISelectionListener {

    /*- VaadinEditorProperties={"grid":"RegularGrid,20","showGrid":true,"snapToGrid":true,"snapToObject":true,"movingGuides":false,"snappingDistance":10} */

    @AutoGenerated

    private VerticalLayout mainLayout;

    @AutoGenerated

    private D3ConceptRelationshipTree d3ConceptRelationShipTree;

    @AutoGenerated

    private HorizontalLayout updateHorizontalLayout;

    @AutoGenerated

    private Button deleteButton;

    @AutoGenerated

    private Button editButton;

    @AutoGenerated

    private Button newButton;

    private final IConceptRelationshipComponentListener listener;

    /**

     * The constructor should first build the main layout, set the

     * composition root and then do any custom initialization.

     *

     * The constructor will not be automatically regenerated by the

     * visual editor.

     */

    public ConceptRelationshipComposite() {

        buildMainLayout();

        setCompositionRoot(mainLayout);

        CdmVaadinSessionUtilities.getCurrentSelectionService().register(this);

        listener = new ConceptRelationshipPresenter(d3ConceptRelationShipTree);

        d3ConceptRelationShipTree.setImmediate(true);

    }

    /* (non-Javadoc)

     * @see eu.etaxonomy.cdm.vaadin.session.ISelectionListener#onSelect(eu.etaxonomy.cdm.vaadin.session.SelectionEvent)

     */

    @Override

    public void onSelect(SelectionEvent event) {

        if(event.getSourceType().equals(StatusComposite.class)) {

            UUID taxonUuid = (UUID)event.getSelectedObjects().get(0);

            try {

                listener.updateConceptRelationship(taxonUuid);

            } catch (JSONException e) {

               Notification.show("Error generating concept relation JSON",  e.getMessage(), Type.WARNING_MESSAGE);

            }

        }

    }

    @AutoGenerated

    private VerticalLayout buildMainLayout() {

        // common part: create layout

        mainLayout = new VerticalLayout();

        mainLayout.setImmediate(false);

        mainLayout.setWidth("100%");

        mainLayout.setHeight("100%");

        mainLayout.setMargin(true);

        mainLayout.setSpacing(true);

        // top-level component properties

        setWidth("100.0%");

        setHeight("100.0%");

        // updateHorizontalLayout

        updateHorizontalLayout = buildUpdateHorizontalLayout();

        mainLayout.addComponent(updateHorizontalLayout);

        mainLayout.setComponentAlignment(updateHorizontalLayout, new Alignment(20));

        // d3ConceptRelationShipTree

        d3ConceptRelationShipTree = new D3ConceptRelationshipTree();

        d3ConceptRelationShipTree.setImmediate(false);

        d3ConceptRelationShipTree.setWidth("-1px");

        d3ConceptRelationShipTree.setHeight("-1px");

        mainLayout.addComponent(d3ConceptRelationShipTree);

        mainLayout.setExpandRatio(d3ConceptRelationShipTree, 1.0f);

        mainLayout.setComponentAlignment(d3ConceptRelationShipTree, new Alignment(20));

        return mainLayout;

    }

    @AutoGenerated

    private HorizontalLayout buildUpdateHorizontalLayout() {

        // common part: create layout

        updateHorizontalLayout = new HorizontalLayout();

        updateHorizontalLayout.setImmediate(false);

        updateHorizontalLayout.setWidth("-1px");

        updateHorizontalLayout.setHeight("-1px");

        updateHorizontalLayout.setMargin(true);

        updateHorizontalLayout.setSpacing(true);

        // newButton

        newButton = new Button();

        newButton.setCaption("new");

        newButton.setImmediate(true);

        newButton.setWidth("-1px");

        newButton.setHeight("-1px");

        updateHorizontalLayout.addComponent(newButton);

        // editButton

        editButton = new Button();

        editButton.setCaption("edit");

        editButton.setImmediate(true);

        editButton.setWidth("-1px");

        editButton.setHeight("-1px");

        updateHorizontalLayout.addComponent(editButton);

        // deleteButton

        deleteButton = new Button();

        deleteButton.setCaption("delete");

        deleteButton.setImmediate(true);

        deleteButton.setWidth("-1px");

        deleteButton.setHeight("-1px");

        updateHorizontalLayout.addComponent(deleteButton);

        return updateHorizontalLayout;

    }

}

// $Id$

/**

 * Copyright (C) 2015 EDIT

 * European Distributed Institute of Taxonomy

 * http://www.e-taxonomy.eu

 *

 * The contents of this file are subject to the Mozilla Public License Version 1.1

 * See LICENSE.TXT at the top of this package for the full license terms.

 */

package eu.etaxonomy.cdm.vaadin.jscomponent;

import java.util.ArrayList;

import java.util.HashMap;

import java.util.List;

import java.util.Map;

import java.util.Set;

import org.apache.log4j.Logger;

import org.json.JSONArray;

import org.json.JSONException;

import org.json.JSONObject;

import com.vaadin.annotations.JavaScript;

import com.vaadin.annotations.StyleSheet;

import com.vaadin.ui.AbstractJavaScriptComponent;

import com.vaadin.ui.JavaScriptFunction;

import com.vaadin.ui.Notification;

import com.vaadin.ui.Notification.Type;

import eu.etaxonomy.cdm.model.taxon.Taxon;

import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;

import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;

/**

 * @author cmathew

 * @date 8 Apr 2015

 *

 */

@StyleSheet({"css/d3.conceptrelationshiptree.css"})

@JavaScript({"extlib/d3.min.js", "lib/d3.conceptrelationshiptree_connector.js"})

public class D3ConceptRelationshipTree extends AbstractJavaScriptComponent {

    private static final Logger logger = Logger.getLogger(D3ConceptRelationshipTree.class);

    public D3ConceptRelationshipTree() {

        addFunction("test", new JavaScriptFunction() {

            @Override

            public void call(JSONArray arguments) throws JSONException {

                Notification.show("Store selected","uuid : " + arguments.getString(0), Type.WARNING_MESSAGE);

            }

        });

        //String expected = "{\"name\":\"Taxon D sec. ???\",\"children\":[{\"name\":\"Includes\",\"children\":[{\"name\":\"Taxon A sec. Journal Reference 1\",\"uuid\":\"eaac797e-cac7-4649-97cf-c7b580076895\"},{\"name\":\"Taxon B sec. ???\",\"uuid\":\"77e7d93e-75c6-4dd4-850d-7b5809654378\"}],\"uuid\":\"0501c385-cab1-4fbe-b945-fc747419bb13\"},{\"name\":\"Excludes\",\"children\":[{\"name\":\"Taxon C sec. ???\",\"uuid\":\"3d71c8b8-3bec-4f5f-ba23-6f9d55ef84e9\"}],\"uuid\":\"4535a63c-4a3f-4d69-9350-7bf02e2c23be\"}],\"uuid\":\"5f713f69-e03e-4a11-8a55-700fbbf44805\"}";

        //setConceptRelationshipTree(expected);

        setConceptRelationshipTree("");

    }

    public void updateConceptRelationshipTree(Taxon fromTaxon) throws JSONException {

        Set<TaxonRelationship> relationsFromThisTaxon = fromTaxon.getRelationsFromThisTaxon();

        Map<TaxonRelationshipType, List<Taxon>> relToTaxonMap = new HashMap<TaxonRelationshipType, List<Taxon>>();

        JSONObject fromTaxonJO = new JSONObject();

        fromTaxonJO.put("name", fromTaxon.getTitleCache());

        fromTaxonJO.put("uuid", fromTaxon.getUuid().toString());

        if(relationsFromThisTaxon !=null && !relationsFromThisTaxon.isEmpty()) {

            for(TaxonRelationship tr : relationsFromThisTaxon) {

                if(fromTaxon.equals(tr.getFromTaxon())) {

                    if(relToTaxonMap.containsKey(tr.getType())) {

                        relToTaxonMap.get(tr.getType()).add(tr.getToTaxon());

                    } else {

                        List<Taxon> toTaxonList = new ArrayList<Taxon>();

                        toTaxonList.add(tr.getToTaxon());

                        relToTaxonMap.put(tr.getType(), toTaxonList);

                    }

                }

            }

            int typeIndex = 0;

            JSONArray ftChildren = new JSONArray();

            fromTaxonJO.put("children", ftChildren);

            for (Map.Entry<TaxonRelationshipType, List<Taxon>> entry : relToTaxonMap.entrySet()) {

                JSONObject crJO = new JSONObject();

                crJO.put("name", entry.getKey().getTitleCache());

                crJO.put("uuid", entry.getKey().getUuid());

                JSONArray crChildrenJA = new JSONArray();

                crJO.put("children", crChildrenJA);

                int toTaxonIndex = 0;

                for(Taxon toTaxon: entry.getValue()) {

                    JSONObject toTaxonJO = new JSONObject();

                    toTaxonJO.put("name", toTaxon.getTitleCache());

                    toTaxonJO.put("uuid", toTaxon.getUuid());

                    crChildrenJA.put(toTaxonIndex, toTaxonJO);

                    toTaxonIndex++;

                }

                ftChildren.put(typeIndex, crJO);

                typeIndex++;

            }

        }

        setConceptRelationshipTree(fromTaxonJO.toString());;

    }

    public void setConceptRelationshipTree(String conceptRelationshipTree) {

        getState().setConceptRelationshipTree(conceptRelationshipTree);;

    }

    @Override

    public D3ConceptRelationshipTreeState getState() {

        return (D3ConceptRelationshipTreeState) super.getState();

    }

}

// $Id$

/**

* Copyright (C) 2015 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.vaadin.jscomponent;

import com.vaadin.shared.ui.JavaScriptComponentState;

/**

 * @author cmathew

 * @date 8 Apr 2015

 *

 */

public class D3ConceptRelationshipTreeState extends JavaScriptComponentState {

    private String conceptRelationshipTree;

    public String getConceptRelationshipTree() {

        return conceptRelationshipTree;

    }

    public void setConceptRelationshipTree(String conceptRelationshipTree) {

        this.conceptRelationshipTree = conceptRelationshipTree;

    }

}

// $Id$

/**

* Copyright (C) 2015 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.vaadin.presenter;

import java.util.Arrays;

import java.util.List;

import java.util.UUID;

import org.json.JSONException;

import eu.etaxonomy.cdm.api.service.ITaxonService;

import eu.etaxonomy.cdm.model.common.CdmBase;

import eu.etaxonomy.cdm.model.taxon.Taxon;

import eu.etaxonomy.cdm.vaadin.jscomponent.D3ConceptRelationshipTree;

import eu.etaxonomy.cdm.vaadin.util.CdmSpringContextHelper;

import eu.etaxonomy.cdm.vaadin.view.IConceptRelationshipComponentListener;

/**

 * @author cmathew

 * @date 9 Apr 2015

 *

 */

public class ConceptRelationshipPresenter implements IConceptRelationshipComponentListener {

    private final ITaxonService taxonService;

    private final D3ConceptRelationshipTree crTree;

    public ConceptRelationshipPresenter(D3ConceptRelationshipTree crTree) {

        taxonService = CdmSpringContextHelper.getTaxonService();

        this.crTree = crTree;

    }

    @Override

    public void updateConceptRelationship(UUID taxonUuid) throws JSONException {

        List<String> FROM_TAXON_INIT_STRATEGY = Arrays.asList(new String []{

                "relationsFromThisTaxon"

        });

        Taxon taxon = CdmBase.deproxy(taxonService.load(taxonUuid, FROM_TAXON_INIT_STRATEGY), Taxon.class);

        crTree.updateConceptRelationshipTree(taxon);

    }

}

// $Id$

/**

* Copyright (C) 2015 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.vaadin.ui;

import java.util.logging.Logger;

import javax.servlet.annotation.WebServlet;

import com.vaadin.annotations.Theme;

import com.vaadin.annotations.VaadinServletConfiguration;

import com.vaadin.navigator.Navigator;

import com.vaadin.server.VaadinServlet;

import com.vaadin.ui.UI;

import eu.etaxonomy.cdm.vaadin.view.ConceptRelationshipView;

/**

 * @author cmathew

 * @date 9 Apr 2015

 *

 */

@Theme("edit")

public class ConceptRelationshipUI extends AbstractAuthenticatedUI {

    Navigator navigator;

    private static final String FIRST_VIEW = "editcr";

    private final static Logger logger =

            Logger.getLogger(ConceptRelationshipUI.class.getName());

    @WebServlet(value = {"/app/editcr/*"}, asyncSupported = true)

    @VaadinServletConfiguration(productionMode = false, ui = ConceptRelationshipUI.class, widgetset = "eu.etaxonomy.cdm.vaadin.AppWidgetSet")

    public static class Servlet extends VaadinServlet {

    }

    @Override

    protected void doInit() {

        // FIXME: remove this when testing is done

        setIgnoreAuthentication(true);

        getPage().setTitle("Concept Relationship Editor");

        ConceptRelationshipView crEditor = new ConceptRelationshipView();

        UI.getCurrent().getNavigator().addView(FIRST_VIEW, crEditor);

    }

    @Override

    public String getFirstViewName() {

        return FIRST_VIEW;

    }

}

// $Id$

/**

* Copyright (C) 2015 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.vaadin.view;

import com.vaadin.annotations.AutoGenerated;

import com.vaadin.navigator.View;

import com.vaadin.navigator.ViewChangeListener.ViewChangeEvent;

import com.vaadin.ui.Alignment;

import com.vaadin.ui.CustomComponent;

import com.vaadin.ui.HorizontalLayout;

import eu.etaxonomy.cdm.vaadin.component.ConceptRelationshipComposite;

import eu.etaxonomy.cdm.vaadin.component.StatusComposite;

/**

 * @author cmathew

 * @date 9 Apr 2015

 *

 */

public class ConceptRelationshipView extends CustomComponent implements View {

    /*- VaadinEditorProperties={"grid":"RegularGrid,20","showGrid":true,"snapToGrid":true,"snapToObject":true,"movingGuides":false,"snappingDistance":10} */

    @AutoGenerated

    private HorizontalLayout mainLayout;

    @AutoGenerated

    private StatusComposite statusCompositeRight;

    @AutoGenerated

    private ConceptRelationshipComposite conceptRelationshipComposite;

    @AutoGenerated

    private StatusComposite statusCompositeLeft;

    /**

     * The constructor should first build the main layout, set the

     * composition root and then do any custom initialization.

     *

     * The constructor will not be automatically regenerated by the

     * visual editor.

     */

    public ConceptRelationshipView() {

        buildMainLayout();

        setCompositionRoot(mainLayout);

        conceptRelationshipComposite.setSizeFull();

    }

    /* (non-Javadoc)

     * @see com.vaadin.navigator.View#enter(com.vaadin.navigator.ViewChangeListener.ViewChangeEvent)

     */

    @Override

    public void enter(ViewChangeEvent event) {

        // TODO Auto-generated method stub

    }

    @AutoGenerated

    private HorizontalLayout buildMainLayout() {

        // common part: create layout

        mainLayout = new HorizontalLayout();

        mainLayout.setImmediate(false);

        mainLayout.setWidth("100%");

        mainLayout.setHeight("100%");

        mainLayout.setMargin(true);

        // top-level component properties

        setWidth("100.0%");

        setHeight("100.0%");

        // statusCompositeLeft

        statusCompositeLeft = new StatusComposite();

        statusCompositeLeft.setImmediate(false);

        statusCompositeLeft.setWidth("-1px");

        statusCompositeLeft.setHeight("-1px");

        mainLayout.addComponent(statusCompositeLeft);

        // conceptRelationshipComposite

        conceptRelationshipComposite = new ConceptRelationshipComposite();

        conceptRelationshipComposite.setImmediate(false);

        conceptRelationshipComposite.setWidth("-1px");

        conceptRelationshipComposite.setHeight("-1px");

        mainLayout.addComponent(conceptRelationshipComposite);

        mainLayout.setExpandRatio(conceptRelationshipComposite, 1.0f);

        mainLayout.setComponentAlignment(conceptRelationshipComposite, new Alignment(20));

        // statusCompositeRight

        statusCompositeRight = new StatusComposite();

        statusCompositeRight.setImmediate(false);

        statusCompositeRight.setWidth("-1px");

        statusCompositeRight.setHeight("-1px");

        mainLayout.addComponent(statusCompositeRight);

        return mainLayout;

    }

}

// $Id$

/**

* Copyright (C) 2015 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.vaadin.view;

import java.util.UUID;

import org.json.JSONException;

/**

 * @author cmathew

 * @date 9 Apr 2015

 *

 */

public interface IConceptRelationshipComponentListener {

    /**

     * @param taxonUuid

     * @throws JSONException

     */

    public void updateConceptRelationship(UUID taxonUuid) throws JSONException;

}