http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/QueryTest.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/QueryTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/QueryTest.java deleted file mode 100644 index b2b93cc..0000000 --- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/QueryTest.java +++ /dev/null @@ -1,303 +0,0 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: QueryTest.java,v $ - * Revision $Revision: 1.3 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/10/01 12:11:30 $ - * by $Author: davidwithers $ - * Created on 03-May-2006 - *****************************************************************/ -package org.biomart.martservice.query; - -import junit.framework.TestCase; - -/** - * - * @author David Withers - */ -public class QueryTest extends TestCase { - private String attributeName; - - private Attribute attribute; - - private String filterName; - - private String filterValue; - - private Filter filter; - - private Link link; - - private String datasetName; - - private Dataset dataset; - - private String virtualSchemaName; - - private String softwareVersion; - - private String formatter; - - private Query query; - - /* - * @see TestCase#setUp() - */ - protected void setUp() throws Exception { - super.setUp(); - attributeName = "attribute name"; - attribute = new Attribute(attributeName); - - filterName = "filter name"; - filterValue = "filter value"; - filter = new Filter(filterName, filterValue); - - link = new Link("source", "target", "id"); - - datasetName = "dataset name"; - dataset = new Dataset(datasetName); - - dataset.addAttribute(attribute); - dataset.addFilter(filter); - - virtualSchemaName = "default"; - - softwareVersion = "software version"; - - formatter = "page formatter"; - - query = new Query(virtualSchemaName); - } - - /* - * Test method for 'org.biomart.martservice.query.Query.Query(String)' - */ - public final void testQueryString() { - Query query = new Query(virtualSchemaName); - assertEquals("virtualSchemaName should be '" + virtualSchemaName + "'", - query.getVirtualSchemaName(), virtualSchemaName); - assertEquals("count should be '0'", query.getCount(), 0); - } - - /* - * Test method for 'org.biomart.martservice.query.Query.Query(String, int)' - */ - public final void testQueryStringInt() { - Query query = new Query(virtualSchemaName, 1); - assertEquals("virtualSchemaName should be '" + virtualSchemaName + "'", - query.getVirtualSchemaName(), virtualSchemaName); - assertEquals("count should be '1'", query.getCount(), 1); - } - - /* - * Test method for 'org.biomart.martservice.query.Query.Query(Query)' - */ - public final void testQueryQuery() { - query.addDataset(dataset); - query.addLink(link); - query.setCount(1); - query.setUniqueRows(1); - query.setSoftwareVersion(softwareVersion); - query.setFormatter(formatter); - Query copy = new Query(query); - assertEquals(copy.getDatasets().size(), 1); - assertEquals(copy.getAttributes().size(), 1); - assertEquals(copy.getFilters().size(), 1); - assertEquals(copy.getLinks().size(), 1); - assertEquals(copy.getCount(), 1); - assertEquals(copy.getUniqueRows(), 1); - assertEquals(copy.getSoftwareVersion(), softwareVersion); - assertEquals(copy.getFormatter(), formatter); - } - - /* - * Test method for - * 'org.biomart.martservice.query.Query.getVirtualSchemaName()' - */ - public final void testGetVirtualSchemaName() { - assertEquals("virtualSchemaName should be '" + virtualSchemaName + "'", - query.getVirtualSchemaName(), virtualSchemaName); - } - - /* - * Test method for - * 'org.biomart.martservice.query.Query.setVirtualSchemaName(String)' - */ - public final void testSetVirtualSchemaName() { - String newVirtualSchemaName = "new virtual schema name"; - query.setVirtualSchemaName(newVirtualSchemaName); - assertEquals("virtualSchemaName should be '" + newVirtualSchemaName - + "'", query.getVirtualSchemaName(), newVirtualSchemaName); - } - - /* - * Test method for 'org.biomart.martservice.query.Query.getCount()' - */ - public final void testGetCount() { - assertEquals("count should be '0'", query.getCount(), 0); - } - - /* - * Test method for 'org.biomart.martservice.query.Query.setCount(int)' - */ - public final void testSetCount() { - query.setCount(1); - assertEquals("count should be '1'", query.getCount(), 1); - } - - /* - * Test method for 'org.biomart.martservice.query.Query.getUniqueRows()' - */ - public final void testGetUniqueRows() { - assertEquals("uniqueRows should be '0'", query.getUniqueRows(), 0); - } - - /* - * Test method for 'org.biomart.martservice.query.Query.setUniqueRows(int)' - */ - public final void testSetUniqueRows() { - query.setUniqueRows(1); - assertEquals("uniqueRows should be '1'", query.getUniqueRows(), 1); - } - - /* - * Test method for 'org.biomart.martservice.query.Query.getSoftwareVersion()' - */ - public final void testGetSoftwareVersion() { - assertNull("softwareVersion should be null", query.getSoftwareVersion()); - } - - /* - * Test method for 'org.biomart.martservice.query.Query.setSoftwareVersion(String)' - */ - public final void testSetSoftwareVersion() { - String newSoftwareVersion = "new software version"; - query.setSoftwareVersion(newSoftwareVersion); - assertEquals("softwareVersion should be '" + newSoftwareVersion + "'", query.getSoftwareVersion(), newSoftwareVersion); - } - - /* - * Test method for 'org.biomart.martservice.query.Query.getFormatter()' - */ - public final void testGetFormatter() { - assertNull("formatter should be null", query.getFormatter()); - } - - /* - * Test method for 'org.biomart.martservice.query.Query.setFormatter(String)' - */ - public final void testSetFormatter() { - String newFormatter = "new formatter"; - query.setFormatter(newFormatter); - assertEquals("formatter should be '" + newFormatter + "'", query.getFormatter(), newFormatter); - } - - /* - * Test method for 'org.biomart.martservice.query.Query.getRequestId()' - */ - public final void testGetRequestId() { - assertNull("requestId should be null", query.getRequestId()); - } - - /* - * Test method for 'org.biomart.martservice.query.Query.setnewRequestId(String)' - */ - public final void testSetRequestId() { - String newRequestId = "new RequestId"; - query.setRequestId(newRequestId); - assertEquals("requestId should be '" + newRequestId + "'", query.getRequestId(), newRequestId); - } - - /* - * Test method for 'org.biomart.martservice.query.Query.addDataset(Dataset)' - */ - public final void testAddDataset() { - query.addDataset(dataset); - assertEquals(query.getDatasets().size(), 1); - assertSame(query.getDatasets().get(0), dataset); - } - - /* - * Test method for - * 'org.biomart.martservice.query.Query.removeDataset(Dataset)' - */ - public final void testRemoveDataset() { - query.addDataset(dataset); - query.removeDataset(dataset); - assertEquals(query.getDatasets().size(), 0); - } - - /* - * Test method for 'org.biomart.martservice.query.Query.getDatasets()' - */ - public final void testGetDatasets() { - query.addDataset(dataset); - assertEquals(query.getDatasets().size(), 1); - assertSame(query.getDatasets().get(0), dataset); - } - - /* - * Test method for 'org.biomart.martservice.query.Query.getDataset(String)' - */ - public final void testGetDataset() { - query.addDataset(dataset); - assertSame(query.getDataset(dataset.getName()), dataset); - } - - /* - * Test method for 'org.biomart.martservice.query.Query.getAttributes()' - */ - public final void testGetAttributes() { - query.addDataset(dataset); - assertEquals(query.getAttributes().size(), 1); - assertSame(query.getAttributes().get(0), attribute); - } - - /* - * Test method for 'org.biomart.martservice.query.Query.getFilters()' - */ - public final void testGetFilters() { - query.addDataset(dataset); - assertEquals(query.getFilters().size(), 1); - assertSame(query.getFilters().get(0), filter); - } - - /* - * Test method for - * 'org.biomart.martservice.query.Query.addQueryListener(QueryListener)' - */ - public final void testAddQueryListener() { - } - - /* - * Test method for - * 'org.biomart.martservice.query.Query.removeQueryListener(QueryListener)' - */ - public final void testRemoveQueryListener() { - } - -}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/pom.xml ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/pom.xml b/taverna-biomoby-activity-ui/pom.xml deleted file mode 100644 index 8f92c83..0000000 --- a/taverna-biomoby-activity-ui/pom.xml +++ /dev/null @@ -1,86 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<project xmlns="http://maven.apache.org/POM/4.0.0"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd";> - <modelVersion>4.0.0</modelVersion> - <parent> - <groupId>net.sf.taverna</groupId> - <artifactId>taverna-parent</artifactId> - <version>3.0.1-SNAPSHOT</version> - </parent> - <groupId>net.sf.taverna.t2.ui-activities</groupId> - <artifactId>biomoby-activity-ui</artifactId> - <version>2.0.1-SNAPSHOT</version> - <name>Taverna 2 Biomoby Activity UI</name> - <dependencies> - <dependency> - <groupId>net.sf.taverna.t2.ui-api</groupId> - <artifactId>activity-icons-api</artifactId> - <version>${t2.ui.api.version}</version> - </dependency> - <dependency> - <groupId>net.sf.taverna.t2.ui-api</groupId> - <artifactId>activity-palette-api</artifactId> - <version>${t2.ui.api.version}</version> - </dependency> - <dependency> - <groupId>net.sf.taverna.t2.ui-impl</groupId> - <artifactId>activity-palette-impl</artifactId> - <version>${t2.ui.impl.version}</version> - </dependency> - <dependency> - <groupId>net.sf.taverna.t2.activities</groupId> - <artifactId>biomoby-activity</artifactId> - <version>${t2.activities.version}</version> - </dependency> - <dependency> - <groupId>net.sf.taverna.t2.ui-impl</groupId> - <artifactId>contextual-views-impl</artifactId> - <version>${t2.ui.impl.version}</version> - </dependency> - <dependency> - <groupId>net.sf.taverna.t2.ui-api</groupId> - <artifactId>contextual-views-api</artifactId> - <version>${t2.ui.api.version}</version> - </dependency> - <dependency> - <groupId>net.sf.taverna.t2.ui-api</groupId> - <artifactId>activity-tools</artifactId> - <version>${t2.ui.api.version}</version> - </dependency> - - <!-- testing dependencies --> - <dependency> - <groupId>junit</groupId> - <artifactId>junit</artifactId> - <version>${junit.version}</version> - <scope>test</scope> - </dependency> -<!-- <dependency> - <groupId>net.sf.taverna.t2.ui-impl</groupId> - <artifactId>activity-palette-impl</artifactId> - <version>${t2.ui.impl.version}</version> - <scope>test</scope> - </dependency> --> - </dependencies> - <repositories> - <repository> - <releases /> - <snapshots> - <enabled>false</enabled> - </snapshots> - <id>mygrid-repository</id> - <name>myGrid Repository</name> - <url>http://www.mygrid.org.uk/maven/repository - </url> - </repository> - <repository> - <releases> - <enabled>false</enabled> - </releases> - <snapshots /> - <id>mygrid-snapshot-repository</id> - <name>myGrid Snapshot Repository</name> - <url>http://www.mygrid.org.uk/maven/snapshot-repository</url> - </repository> - </repositories> -</project> - http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/AddParserActionHelper.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/AddParserActionHelper.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/AddParserActionHelper.java deleted file mode 100644 index b03b98c..0000000 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/AddParserActionHelper.java +++ /dev/null @@ -1,280 +0,0 @@ -/* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - */ -package net.sf.taverna.t2.activities.biomoby.actions; - -import java.awt.BorderLayout; -import java.awt.Dimension; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.awt.event.MouseEvent; -import java.awt.event.MouseListener; - -import javax.swing.ImageIcon; -import javax.swing.JComponent; -import javax.swing.JLabel; -import javax.swing.JMenuItem; -import javax.swing.JPanel; -import javax.swing.JPopupMenu; -import javax.swing.JScrollPane; -import javax.swing.JSeparator; -import javax.swing.JTree; -import javax.swing.ToolTipManager; -import javax.swing.tree.DefaultMutableTreeNode; -import javax.swing.tree.TreePath; -import javax.swing.tree.TreeSelectionModel; - -import net.sf.taverna.t2.activities.biomoby.BiomobyActivity; -import net.sf.taverna.t2.activities.biomoby.edits.AddMobyParseDatatypeEdit; -import net.sf.taverna.t2.workbench.edits.EditManager; -import net.sf.taverna.t2.workbench.file.FileManager; -import net.sf.taverna.t2.workflowmodel.Dataflow; -import net.sf.taverna.t2.workflowmodel.Edit; - -import org.apache.log4j.Logger; -import org.biomoby.shared.MobyData; -import org.biomoby.shared.MobyNamespace; -import org.biomoby.shared.MobyPrimaryDataSet; -import org.biomoby.shared.MobyPrimaryDataSimple; - -/** - * An action to add a parser from within the Workflow editor - * - * @author Eddie Kawas - * @author Stuart Owen - adapted for Taverna 2 - */ -public class AddParserActionHelper { - private static Logger logger = Logger.getLogger(AddParserActionHelper.class); - - private EditManager editManager; - - private final FileManager fileManager; - - public AddParserActionHelper(EditManager editManager, FileManager fileManager) { - this.editManager = editManager; - this.fileManager = fileManager; - } - - /* - * (non-Javadoc) - * - * @see org.embl.ebi.escience.scuflui.processoractions.AbstractProcessorAction#getComponent(org.embl.ebi.escience.scufl.Processor) - */ - public JComponent getComponent(final BiomobyActivity activity) { - - - // set up the root node - String serviceName = activity.getMobyService().getName(); - String description = activity.getMobyService().getDescription(); - MobyServiceTreeNode service = new MobyServiceTreeNode(serviceName, - description); - DefaultMutableTreeNode rootNode = new DefaultMutableTreeNode(service); - - // now add the child nodes containing useful information about the - // service - DefaultMutableTreeNode output = new DefaultMutableTreeNode("Parse:"); - rootNode.add(output); - // process outputs - MobyData[] outputs = activity.getMobyService().getPrimaryOutputs(); - for (int i = 0; i < outputs.length; i++) { - if (outputs[i] instanceof MobyPrimaryDataSimple) { - MobyPrimaryDataSimple simple = (MobyPrimaryDataSimple) outputs[i]; - StringBuffer sb = new StringBuffer( - "Namespaces used by this object: "); - MobyNamespace[] namespaces = simple.getNamespaces(); - for (int j = 0; j < namespaces.length; j++) { - sb.append(namespaces[j].getName() + " "); - } - if (namespaces.length == 0) - sb.append(" ANY "); - MobyObjectTreeNode mobyObjectTreeNode = new MobyObjectTreeNode( - simple.getDataType().getName() + "('" - + simple.getName() + "')", sb.toString()); - mobyObjectTreeNode.setNamespaces(simple.getNamespaces()); - output.insert(new DefaultMutableTreeNode(mobyObjectTreeNode), - output.getChildCount()); - } else { - // we have a collection - MobyPrimaryDataSet collection = (MobyPrimaryDataSet) outputs[i]; - DefaultMutableTreeNode collectionNode = new DefaultMutableTreeNode( - "Collection('" + collection.getName() + "')"); - output.insert(collectionNode, output.getChildCount()); - MobyPrimaryDataSimple[] simples = collection.getElements(); - for (int j = 0; j < simples.length; j++) { - MobyPrimaryDataSimple simple = simples[j]; - StringBuffer sb = new StringBuffer( - "Namespaces used by this object: "); - MobyNamespace[] namespaces = simple.getNamespaces(); - for (int k = 0; k < namespaces.length; k++) { - sb.append(namespaces[k].getName() + " "); - } - if (namespaces.length == 0) - sb.append("ANY "); - MobyObjectTreeNode mobyObjectTreeNode = new MobyObjectTreeNode( - simple.getDataType().getName() + "('" - + simple.getName() + "')", sb.toString()); - mobyObjectTreeNode.setNamespaces(simple.getNamespaces()); - collectionNode - .insert(new DefaultMutableTreeNode( - mobyObjectTreeNode), collectionNode - .getChildCount()); - } - - } - } - if (outputs.length == 0) { - output.add(new DefaultMutableTreeNode(" None ")); - } - - // finally return a tree describing the object - final JTree tree = new JTree(rootNode); - tree.setCellRenderer(new BioMobyServiceTreeCustomRenderer()); - ToolTipManager.sharedInstance().registerComponent(tree); - tree.addMouseListener(new MouseListener() { - public void mouseClicked(MouseEvent me) { - } - - public void mousePressed(MouseEvent me) { - mouseReleased(me); - } - - public void mouseReleased(MouseEvent me) { - if (me.isPopupTrigger()) // right click, show popup menu - { - TreePath path = tree.getPathForLocation(me.getX(), me - .getY()); - if (path == null) - return; - if (path.getPathCount() >= 3) { - if (path.getParentPath().toString().indexOf("Parse:") >= 0 - && path.getLastPathComponent().toString() - .indexOf(" None ") == -1) { - DefaultMutableTreeNode node = (DefaultMutableTreeNode) tree - .getLastSelectedPathComponent(); - if (node == null) - return; - final String selectedObject = node.toString(); - if (!selectedObject.equals(path - .getLastPathComponent().toString())) - return; - - logger.debug("TreePath " + path.toString()); - if ( - // path has a collection in it - (path.getPathCount() == 4 - && path.getParentPath() - .getLastPathComponent().toString() - .startsWith("Collection(") && (path - .getParentPath().toString()) - .indexOf("Parse:") > 0) - // or path is just a simple - || (path.toString().indexOf("Collection(") < 0)) { - - final JPopupMenu menu = new JPopupMenu(); - - final String potentialCollectionString = path - .getParentPath().getLastPathComponent() - .toString(); - final boolean isCollection = potentialCollectionString - .indexOf("Collection('") >= 0; - JMenuItem item3 = new JMenuItem( - "Add parser for " + selectedObject - + " to the workflow"); - item3 - .setIcon(getIcon("/Cut24.gif")); - item3.addActionListener(new ActionListener() { - - public void actionPerformed(ActionEvent ae) { - // you would like to search for - // selectedObject - try { - try { - Dataflow currentDataflow = fileManager.getCurrentDataflow(); - Edit<?> edit = new AddMobyParseDatatypeEdit( - currentDataflow, activity, - selectedObject,isCollection, potentialCollectionString, editManager.getEdits()); - editManager.doDataflowEdit( - currentDataflow, edit); - - } catch (Exception e) { - logger.error("", e); - } - - } catch (Exception e) { - logger.error("", e); - } - - } - }); - - menu.add(new JSeparator()); - menu.add(new JLabel("Parse Moby Data ... ", - JLabel.CENTER)); - menu.add(new JSeparator()); - menu.add(item3); - menu.show(me.getComponent(), me.getX(), me - .getY()); - } else { - logger - .debug("unexpected situation occured; '" - + selectedObject - + "' was the object selected and the path is: " - + path.toString()); - } - } - } - } - } - - public void mouseEntered(MouseEvent me) { - } - - public void mouseExited(MouseEvent me) { - } - }); - - tree.getSelectionModel().setSelectionMode( - TreeSelectionModel.SINGLE_TREE_SELECTION); - JScrollPane jsp = new JScrollPane(tree); - JPanel thePanel = new JPanel(new BorderLayout()); - thePanel.add(jsp, BorderLayout.CENTER); - return thePanel; - } - - /* - * (non-Javadoc) - * - * @see org.embl.ebi.escience.scuflui.processoractions.ProcessorActionSPI#getDescription() - */ - public String getDescription() { - return "Add BioMOBY Parser ..."; - } - - /* - * (non-Javadoc) - * - * @see org.embl.ebi.escience.scuflui.processoractions.ProcessorActionSPI#getIcon() - */ - public ImageIcon getIcon() { - return MobyPanel.getIcon("/Cut24.gif"); - } - - /** - * returns the frame size as a dimension for the content pane housing - * this action - */ - public Dimension getFrameSize() { - return new Dimension(450, 450); - } - - /** - * Return an Icon to represent this action - * - * @param loc - * the location of the image to use as an icon - */ - private ImageIcon getIcon(String loc) { - return MobyPanel.getIcon(loc); - } -} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyObjectTreeCustomRenderer.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyObjectTreeCustomRenderer.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyObjectTreeCustomRenderer.java deleted file mode 100644 index 46b4d5a..0000000 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyObjectTreeCustomRenderer.java +++ /dev/null @@ -1,97 +0,0 @@ -/* - * This file is a component of the Taverna project, - * and is licensed under the GNU LGPL. - * Copyright Edward Kawas, The BioMoby Project - */ -package net.sf.taverna.t2.activities.biomoby.actions; - -import java.awt.Color; -import java.awt.Component; - -import javax.swing.JComponent; -import javax.swing.JTree; -import javax.swing.tree.DefaultMutableTreeNode; -import javax.swing.tree.DefaultTreeCellRenderer; - -public class BioMobyObjectTreeCustomRenderer extends DefaultTreeCellRenderer { - - private static final long serialVersionUID = 1L; - - private Color leafForeground = Color.blue; - - private Color rootColor = Color.black; - - @SuppressWarnings("unused") - private Color feedsIntoColor = Color.gray; - - @SuppressWarnings("unused") - private Color producedColor = Color.lightGray; - - @SuppressWarnings("unused") - private Color authorityColor = Color.orange; - - private Color serviceColor = Color.magenta; - - private Color objectColor = Color.green; - - public Component getTreeCellRendererComponent(JTree tree, Object value, - boolean selected, boolean expanded, boolean leaf, int row, - boolean hasFocus) { - // Allow the original renderer to set up the label - Component c = super.getTreeCellRendererComponent(tree, value, selected, - expanded, leaf, row, hasFocus); - - if (value instanceof DefaultMutableTreeNode) { - DefaultMutableTreeNode node = (DefaultMutableTreeNode) value; - if (node.getUserObject() instanceof MobyServiceTreeNode) { - // service node - c.setForeground(serviceColor); - ((JComponent) c).setToolTipText(((MobyServiceTreeNode) node - .getUserObject()).getDescription()); - setIcon(MobyPanel.getIcon("/service.png")); - } else if (node.getUserObject() instanceof MobyObjectTreeNode) { - // object node - c.setForeground(objectColor); - ((JComponent) c).setToolTipText(((MobyObjectTreeNode) node - .getUserObject()).getDescription()); - } else if (node.isRoot()) { - // root node - setIcon(MobyPanel.getIcon("/moby.png")); - ((JComponent) c).setToolTipText(" Description of " - + node.getUserObject()); - c.setForeground(rootColor); - } else if (node.getUserObject() instanceof String) { - // check for feeds into and produced by nodes - String string = (String) node.getUserObject(); - if (string.equalsIgnoreCase("feeds into")) { - setIcon(MobyPanel.getIcon("/input.png")); - ((JComponent) c).setToolTipText(null); - } else if (string.equalsIgnoreCase("produced by")) { - setIcon(MobyPanel.getIcon("/output.png")); - ((JComponent) c).setToolTipText(null); - } else if (string.equalsIgnoreCase("produces")) { - ((JComponent) c).setToolTipText(null); - } else { - - ((JComponent) c).setToolTipText(null); - - if (!leaf) { - if (string.startsWith("Collection('")) { - setIcon(MobyPanel.getIcon("/collection.png")); - } else { - setIcon(MobyPanel.getIcon("/authority.png")); - } - } - } - - } else { - ((JComponent) c).setToolTipText("nothing node"); - } - } - if (selected) - c.setBackground(Color.lightGray); - if (leaf) - c.setForeground(this.leafForeground); - return c; - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyServiceTreeCustomRenderer.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyServiceTreeCustomRenderer.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyServiceTreeCustomRenderer.java deleted file mode 100644 index ecce3ca..0000000 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyServiceTreeCustomRenderer.java +++ /dev/null @@ -1,86 +0,0 @@ -/* - * This file is a component of the Taverna project, - * and is licensed under the GNU LGPL. - * Copyright Edward Kawas, The BioMoby Project - */ -package net.sf.taverna.t2.activities.biomoby.actions; - -import java.awt.Color; -import java.awt.Component; - -import javax.swing.JComponent; -import javax.swing.JTree; -import javax.swing.tree.DefaultMutableTreeNode; -import javax.swing.tree.DefaultTreeCellRenderer; - -public class BioMobyServiceTreeCustomRenderer extends DefaultTreeCellRenderer { - - private static final long serialVersionUID = 1L; - - private Color leafForeground = Color.blue; - - @SuppressWarnings("unused") - private Color rootColor = Color.black; - - @SuppressWarnings("unused") - private Color feedsIntoColor = Color.gray; - - @SuppressWarnings("unused") - private Color producedColor = Color.lightGray; - - @SuppressWarnings("unused") - private Color authorityColor = Color.orange; - - private Color serviceColor = Color.magenta; - - private Color objectColor = Color.green; - - public Component getTreeCellRendererComponent(JTree tree, Object value, - boolean selected, boolean expanded, boolean leaf, int row, - boolean hasFocus) { - // Allow the original renderer to set up the label - Component c = super.getTreeCellRendererComponent(tree, value, selected, - expanded, leaf, row, hasFocus); - - if (value instanceof DefaultMutableTreeNode) { - DefaultMutableTreeNode node = (DefaultMutableTreeNode) value; - if (node.getUserObject() instanceof MobyServiceTreeNode) { - // service node - c.setForeground(serviceColor); - ((JComponent) c).setToolTipText(((MobyServiceTreeNode) node - .getUserObject()).getDescription()); - setIcon(MobyPanel.getIcon("/service.png")); - } else if (node.getUserObject() instanceof MobyObjectTreeNode) { - // object node - c.setForeground(objectColor); - ((JComponent) c).setToolTipText(((MobyObjectTreeNode) node - .getUserObject()).getDescription()); - } else if (node.getUserObject() instanceof String) { - // check for feeds into and produced by nodes - String string = (String) node.getUserObject(); - if (string.equalsIgnoreCase("inputs")) { - setIcon(MobyPanel.getIcon("/input.png")); - ((JComponent) c).setToolTipText(null); - } else if (string.equalsIgnoreCase("outputs")) { - setIcon(MobyPanel.getIcon("/output.png")); - ((JComponent) c).setToolTipText(null); - } else { - - ((JComponent) c).setToolTipText(null); - - if (!leaf) { - if (string.startsWith("Collection('")) { - setIcon(MobyPanel.getIcon("/collection.png")); - } - } - } - - } else { - ((JComponent) c).setToolTipText("nothing node"); - } - } - if (leaf) - c.setForeground(this.leafForeground); - return c; - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActionHelper.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActionHelper.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActionHelper.java deleted file mode 100644 index 9579627..0000000 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActionHelper.java +++ /dev/null @@ -1,852 +0,0 @@ -/* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - */ -package net.sf.taverna.t2.activities.biomoby.actions; - -import java.awt.BorderLayout; -import java.awt.Component; -import java.awt.Dimension; -import java.awt.Frame; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.awt.event.MouseEvent; -import java.awt.event.MouseListener; - -import javax.swing.ImageIcon; -import javax.swing.JComponent; -import javax.swing.JFrame; -import javax.swing.JLabel; -import javax.swing.JMenuItem; -import javax.swing.JPanel; -import javax.swing.JPopupMenu; -import javax.swing.JProgressBar; -import javax.swing.JScrollPane; -import javax.swing.JSeparator; -import javax.swing.JTree; -import javax.swing.ToolTipManager; -import javax.swing.tree.DefaultMutableTreeNode; -import javax.swing.tree.TreePath; -import javax.swing.tree.TreeSelectionModel; - -import net.sf.taverna.t2.activities.biomoby.BiomobyActivity; -import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity; -import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityConfigurationBean; -import net.sf.taverna.t2.activities.biomoby.edits.AddBiomobyCollectionDataTypeEdit; -import net.sf.taverna.t2.activities.biomoby.edits.AddBiomobyDataTypeEdit; -import net.sf.taverna.t2.activities.biomoby.edits.AddMobyParseDatatypeEdit; -import net.sf.taverna.t2.workbench.edits.EditManager; -import net.sf.taverna.t2.workbench.file.FileManager; -import net.sf.taverna.t2.workflowmodel.Dataflow; -import net.sf.taverna.t2.workflowmodel.Edit; -import net.sf.taverna.t2.workflowmodel.OutputPort; -import net.sf.taverna.t2.workflowmodel.utils.Tools; - -import org.apache.log4j.Logger; -import org.biomoby.client.CentralImpl; -import org.biomoby.shared.Central; -import org.biomoby.shared.MobyData; -import org.biomoby.shared.MobyDataType; -import org.biomoby.shared.MobyException; -import org.biomoby.shared.MobyNamespace; -import org.biomoby.shared.MobyPrimaryDataSet; -import org.biomoby.shared.MobyPrimaryDataSimple; -import org.biomoby.shared.NoSuccessException; - - -/** - * - * @author Eddie An action that for BioMobyProcessors - * @auther Stuart Owen - helped port to T2 - but with the minimum code changes possible! - */ -public class BiomobyActionHelper { - - private static Logger logger = Logger - .getLogger(BiomobyActionHelper.class); - - JProgressBar progressBar = new JProgressBar(); - - private EditManager editManager; - - private final FileManager fileManager; - - public BiomobyActionHelper(EditManager editManager, FileManager fileManager) { - this.editManager = editManager; - this.fileManager = fileManager; - } - - /* - * (non-Javadoc) - * - * @see - * org.embl.ebi.escience.scuflui.processoractions.AbstractProcessorAction - * #getComponent(org.embl.ebi.escience.scufl.Processor) - */ - - public JComponent getComponent(final BiomobyActivity activity) { - // variables i need - - final String endpoint = activity.getConfiguration().getMobyEndpoint(); - // set up the root node - String serviceName = activity.getMobyService().getName(); - String description = activity.getMobyService().getDescription(); - - MobyServiceTreeNode service = new MobyServiceTreeNode(serviceName, - description); - DefaultMutableTreeNode rootNode = new DefaultMutableTreeNode(service); - - // now add the child nodes containing useful information about the - // service - DefaultMutableTreeNode input = new DefaultMutableTreeNode("Inputs"); - DefaultMutableTreeNode output = new DefaultMutableTreeNode("Outputs"); - rootNode.add(input); - rootNode.add(output); - - // process inputs - MobyData[] inputs = activity.getMobyService().getPrimaryInputs(); - for (int i = 0; i < inputs.length; i++) { - if (inputs[i] instanceof MobyPrimaryDataSimple) { - MobyPrimaryDataSimple simple = (MobyPrimaryDataSimple) inputs[i]; - StringBuffer sb = new StringBuffer( - "Namespaces used by this object: "); - MobyNamespace[] namespaces = simple.getNamespaces(); - for (int j = 0; j < namespaces.length; j++) { - sb.append(namespaces[j].getName() + " "); - } - if (namespaces.length == 0) - sb.append(" ANY "); - MobyObjectTreeNode mobyObjectTreeNode = new MobyObjectTreeNode( - simple.getDataType().getName() + "('" - + simple.getName() + "')", sb.toString()); - input.insert(new DefaultMutableTreeNode(mobyObjectTreeNode), - input.getChildCount()); - } else { - // we have a collection - MobyPrimaryDataSet collection = (MobyPrimaryDataSet) inputs[i]; - DefaultMutableTreeNode collectionNode = new DefaultMutableTreeNode( - "Collection('" + collection.getName() + "')"); - input.insert(collectionNode, input.getChildCount()); - MobyPrimaryDataSimple[] simples = collection.getElements(); - for (int j = 0; j < simples.length; j++) { - MobyPrimaryDataSimple simple = simples[j]; - StringBuffer sb = new StringBuffer( - "Namespaces used by this object: "); - MobyNamespace[] namespaces = simple.getNamespaces(); - for (int k = 0; k < namespaces.length; k++) { - sb.append(namespaces[k].getName() + " "); - } - if (namespaces.length == 0) - sb.append(" ANY "); - MobyObjectTreeNode mobyObjectTreeNode = new MobyObjectTreeNode( - simple.getDataType().getName() + "('" - + simple.getName() + "')", sb.toString()); - collectionNode - .insert(new DefaultMutableTreeNode( - mobyObjectTreeNode), collectionNode - .getChildCount()); - } - - } - } - if (inputs.length == 0) { - input.add(new DefaultMutableTreeNode(" None ")); - } - - // process outputs - MobyData[] outputs = activity.getMobyService().getPrimaryOutputs(); - for (int i = 0; i < outputs.length; i++) { - if (outputs[i] instanceof MobyPrimaryDataSimple) { - MobyPrimaryDataSimple simple = (MobyPrimaryDataSimple) outputs[i]; - StringBuffer sb = new StringBuffer( - "Namespaces used by this object: "); - MobyNamespace[] namespaces = simple.getNamespaces(); - for (int j = 0; j < namespaces.length; j++) { - sb.append(namespaces[j].getName() + " "); - } - if (namespaces.length == 0) - sb.append(" ANY "); - MobyObjectTreeNode mobyObjectTreeNode = new MobyObjectTreeNode( - simple.getDataType().getName() + "('" - + simple.getName() + "')", sb.toString()); - mobyObjectTreeNode.setNamespaces(simple.getNamespaces()); - output.insert(new DefaultMutableTreeNode(mobyObjectTreeNode), - output.getChildCount()); - } else { - // we have a collection - MobyPrimaryDataSet collection = (MobyPrimaryDataSet) outputs[i]; - DefaultMutableTreeNode collectionNode = new DefaultMutableTreeNode( - "Collection('" + collection.getName() + "')"); - output.insert(collectionNode, output.getChildCount()); - MobyPrimaryDataSimple[] simples = collection.getElements(); - for (int j = 0; j < simples.length; j++) { - MobyPrimaryDataSimple simple = simples[j]; - StringBuffer sb = new StringBuffer( - "Namespaces used by this object: "); - MobyNamespace[] namespaces = simple.getNamespaces(); - for (int k = 0; k < namespaces.length; k++) { - sb.append(namespaces[k].getName() + " "); - } - if (namespaces.length == 0) - sb.append("ANY "); - MobyObjectTreeNode mobyObjectTreeNode = new MobyObjectTreeNode( - simple.getDataType().getName() + "('" - + simple.getName() + "')", sb.toString()); - mobyObjectTreeNode.setNamespaces(simple.getNamespaces()); - collectionNode - .insert(new DefaultMutableTreeNode( - mobyObjectTreeNode), collectionNode - .getChildCount()); - } - - } - } - if (outputs.length == 0) { - output.add(new DefaultMutableTreeNode(" None ")); - } - - // finally return a tree describing the object - final JTree tree = new JTree(rootNode); - tree.setCellRenderer(new BioMobyServiceTreeCustomRenderer()); - ToolTipManager.sharedInstance().registerComponent(tree); - tree.addMouseListener(new MouseListener() { - public void mouseClicked(MouseEvent me) { - } - - public void mousePressed(MouseEvent me) { - mouseReleased(me); - } - - public void mouseReleased(MouseEvent me) { - if (me.isPopupTrigger()) // right click, show popup menu - { - TreePath path = tree.getPathForLocation(me.getX(), me - .getY()); - if (path == null) - return; - if (path.getPathCount() >= 3) { - if (path.getPathCount() == 4 - && path.getParentPath().getLastPathComponent() - .toString().startsWith("Collection(") - && (path.getParentPath().toString()) - .indexOf("Inputs") > 0) { - // we have a collection input - DefaultMutableTreeNode node = (DefaultMutableTreeNode) tree - .getLastSelectedPathComponent(); - final String selectedObject = node.toString(); - // ensure that the last selected item is an object! - if (!selectedObject.equals(path - .getLastPathComponent().toString())) - return; - String collectionName = ""; - if (path.getParentPath().getLastPathComponent() - .toString().indexOf("('") > 0 - && path.getParentPath() - .getLastPathComponent().toString() - .indexOf("')") > 0) { - collectionName = path.getParentPath() - .getLastPathComponent().toString() - .substring( - path.getParentPath() - .getLastPathComponent() - .toString().indexOf( - "('") + 2, - path.getParentPath() - .getLastPathComponent() - .toString().indexOf( - "')")); - } - final String theCollectionName = collectionName; - final JPopupMenu menu = new JPopupMenu(); - // Create and add a menu item for adding to the item - // to the workflow - JMenuItem item = new JMenuItem("Add Datatype - " - + selectedObject + " to the workflow?"); - item - .setIcon(MobyPanel.getIcon("/Add24.gif")); - item.addActionListener(new ActionListener() { - // private boolean added = false; - - public void actionPerformed(ActionEvent ae) { - - try { - Dataflow currentDataflow = fileManager.getCurrentDataflow(); - Edit<?> edit = new AddBiomobyCollectionDataTypeEdit( - currentDataflow, activity, - selectedObject, - theCollectionName, editManager.getEdits()); - editManager.doDataflowEdit( - currentDataflow, edit); - - } catch (Exception e) { - logger.error("", e); - } - } - }); - // Create and add a menu item for service details - JMenuItem details = new JMenuItem("Find out about " - + selectedObject); - details - .setIcon(MobyPanel.getIcon("/Information24.gif")); - details.addActionListener(new ActionListener() { - public void actionPerformed(ActionEvent ae) { - - // TODO Create a frame - Frame frame = MobyPanel.CreateFrame("A BioMoby Object Description"); - JPanel panel = new MobyPanel( - selectedObject, - "A BioMoby Object Description", ""); - - frame.add(panel); - frame.setSize(getFrameSize()); - frame.pack(); - frame.setVisible(true); - } - }); - // add the components to the menu - menu.add(new JLabel("Add to workflow ... ", - JLabel.CENTER)); - menu.add(new JSeparator()); - menu.add(item); - menu.add(new JSeparator()); - menu.add(new JLabel("Datatype Details ... ", - JLabel.CENTER)); - menu.add(new JSeparator()); - menu.add(details); - // show the window - menu.show(me.getComponent(), me.getX(), me.getY()); - } else if (path.getPathCount() == 3 - && path.getParentPath().getLastPathComponent() - .toString().startsWith("Inputs") - && !path.getLastPathComponent().toString() - .startsWith("Collection(") - && !path.getLastPathComponent().toString() - .equals(" None ")) { - // we have a simple input - DefaultMutableTreeNode node = (DefaultMutableTreeNode) tree - .getLastSelectedPathComponent(); - if (node == null) - return; - final String selectedObject = node.toString(); - // ensure that the last selected item is an object! - if (!selectedObject.equals(path - .getLastPathComponent().toString())) - return; - - final JPopupMenu menu = new JPopupMenu(); - // Create and add a menu item for adding to the item - // to the workflow - JMenuItem item = new JMenuItem("Add Datatype - " - + selectedObject + " to the workflow?"); - item - .setIcon(MobyPanel.getIcon("/Add24.gif")); - item.addActionListener(new ActionListener() { - // private boolean added = false; - - public void actionPerformed(ActionEvent ae) { - - try { - Dataflow currentDataflow = fileManager.getCurrentDataflow(); - Edit<?> edit = new AddBiomobyDataTypeEdit( - currentDataflow, activity, - selectedObject, editManager.getEdits()); - editManager.doDataflowEdit( - currentDataflow, edit); - - } catch (Exception e) { - logger.error("Could not perform action", e); - } - } - }); - - // Create and add a menu item for service details - JMenuItem details = new JMenuItem( - "Find out about 1 " + selectedObject); - details - .setIcon(MobyPanel.getIcon("/Information24.gif")); - details.addActionListener(new ActionListener() { - public void actionPerformed(ActionEvent ae) { - // TODO Create a frame - Frame frame = MobyPanel.CreateFrame("A BioMoby Object Description"); - JPanel panel = new MobyPanel( - // TODO create a valid description - selectedObject, - "A BioMoby Object Description", - createDataDescription( - selectedObject.split("\\(")[0], - activity.getConfiguration() - .getMobyEndpoint())); - frame.add(panel); - frame.setSize(getFrameSize()); - frame.pack(); - frame.setVisible(true); - } - - private String createDataDescription( - String dataName, String mobyEndpoint) { - MobyDataType data; - try { - Central central = new CentralImpl( - mobyEndpoint); - data = central.getDataType(dataName); - - } catch (MobyException e) { - return "Couldn't retrieve a description on the BioMoby service '" - + dataName + "'"; - } catch (NoSuccessException e) { - return "Couldn't retrieve a description on the BioMoby service '" - + dataName + "'"; - } - return data.toString(); - } - }); - // add the components to the menu - menu.add(new JLabel("Add to workflow ... ", - JLabel.CENTER)); - menu.add(new JSeparator()); - menu.add(item); - menu.add(new JSeparator()); - menu.add(new JLabel("Datatype Details ... ", - JLabel.CENTER)); - menu.add(new JSeparator()); - menu.add(details); - // show the window - menu.show(me.getComponent(), me.getX(), me.getY()); - - } else if (path.getParentPath().toString().indexOf( - "Outputs") >= 0 - && path.getLastPathComponent().toString() - .indexOf(" None ") == -1) { - DefaultMutableTreeNode node = (DefaultMutableTreeNode) tree - .getLastSelectedPathComponent(); - if (node == null) - return; - final String selectedObject = node.toString(); - if (!selectedObject.equals(path - .getLastPathComponent().toString())) - return; - - if ((path.getPathCount() == 4 - && path.getParentPath() - .getLastPathComponent().toString() - .startsWith("Collection(") && (path - .getParentPath().toString()) - .indexOf("Outputs") > 0) - || (path.toString().indexOf("Collection(") < 0)) { - final JPopupMenu menu = new JPopupMenu(); - JMenuItem item = new JMenuItem( - "Find Services that Consume " - + selectedObject - + " - brief search"); - item - .setIcon(MobyPanel.getIcon("/Information24.gif")); - final String potentialCollectionString = path - .getParentPath().getLastPathComponent() - .toString(); - final boolean isCollection = potentialCollectionString - .indexOf("Collection('") >= 0; - final Object selectedMobyObjectTreeNodeHolder = (DefaultMutableTreeNode) tree - .getLastSelectedPathComponent(); - item.addActionListener(new ActionListener() { - - public void actionPerformed(ActionEvent ae) { - // you would like to search for - // selectedObject - new Thread("Finding biomoby services") { - public void run() { - try { - // FIXME: ignored for now - - // Stuart - String name = selectedObject; - if (name.indexOf("(") > 0) - name = name - .substring( - 0, - name - .indexOf("(")); - String articlename = ""; - if (isCollection) { - articlename = potentialCollectionString - .substring( - potentialCollectionString - .indexOf("('") + 2, - potentialCollectionString - .lastIndexOf("'")); - } else { - articlename = selectedObject - .substring( - selectedObject - .indexOf("'") + 1, - selectedObject - .lastIndexOf("'")); - } - - BiomobyObjectActivity boAct = new BiomobyObjectActivity(); - BiomobyObjectActivityConfigurationBean bean = new BiomobyObjectActivityConfigurationBean(); - MobyDataType dataType = new MobyDataType( - name); - bean - .setAuthorityName(dataType - .getAuthority()); - bean - .setServiceName(dataType - .getName()); - bean - .setMobyEndpoint(endpoint); - boAct.configure(bean); - - OutputPort theServiceport = null; - - try { - if (isCollection) - theServiceport = Tools - .getActivityOutputPort( - activity, - name - + "(Collection - '" - + (articlename - .equals("") ? "MobyCollection" - : articlename) - + "' As Simples)"); - - else - theServiceport = Tools - .getActivityOutputPort( - activity, - name - + "(" - + articlename - + ")"); - } catch (Exception except) { - } - BiomobyObjectActionHelper boa = null; - - if (theServiceport == null) { - boa = new BiomobyObjectActionHelper( - false, editManager, fileManager); - } else { - boa = new BiomobyObjectActionHelper( - theServiceport, - false, editManager, fileManager); - } - - if (selectedMobyObjectTreeNodeHolder instanceof DefaultMutableTreeNode - && ((DefaultMutableTreeNode) selectedMobyObjectTreeNodeHolder) - .getUserObject() instanceof MobyObjectTreeNode) { - DefaultMutableTreeNode dmtn = (DefaultMutableTreeNode) selectedMobyObjectTreeNodeHolder; - MobyObjectTreeNode motn = (MobyObjectTreeNode) dmtn - .getUserObject(); - boa - .setNamespaces(motn - .getNamespaces()); - } - PopupThread popupthread = new PopupThread( - boAct, boa); - progressBar - .setStringPainted(true); - progressBar - .setVisible(true); - popupthread.start(); - - while (popupthread - .isAlive()) { - Thread.sleep(4000); - } - - progressBar - .setVisible(false); - Component c = popupthread - .getComponent(); - Dimension loc = getFrameLocation(); - Dimension size = getFrameSize(); - JPanel frame = new SimpleActionFrame( - c, - "Moby Object Details"); - createFrame( - frame, - (int) loc - .getWidth(), - (int) loc - .getHeight(), - (int) size - .getWidth(), - (int) size - .getHeight()); - } catch (Exception e) { - } - } - }.start(); - - } - }); - - JMenuItem item2 = new JMenuItem( - "Find Services that Consume " - + selectedObject - + " - semantic search"); - item2 - .setIcon(MobyPanel.getIcon("/Search24.gif")); - item2.addActionListener(new ActionListener() { - public void actionPerformed(ActionEvent ae) { - // you would like to search for - // selectedObject - new Thread("Finding BioMoby services") { - - public void run() { - try { - String name = selectedObject; - if (name.indexOf("(") > 0) - name = name - .substring( - 0, - name - .indexOf("(")); - String articlename = ""; - if (isCollection) { - articlename = potentialCollectionString - .substring( - potentialCollectionString - .indexOf("('") + 2, - potentialCollectionString - .lastIndexOf("'")); - } else { - articlename = selectedObject - .substring( - selectedObject - .indexOf("'") + 1, - selectedObject - .lastIndexOf("'")); - } - BiomobyObjectActivity boAct = new BiomobyObjectActivity(); - BiomobyObjectActivityConfigurationBean bean = new BiomobyObjectActivityConfigurationBean(); - MobyDataType dataType = new MobyDataType( - name); - bean - .setAuthorityName(dataType - .getAuthority()); - bean - .setServiceName(dataType - .getName()); - bean - .setMobyEndpoint(endpoint); - boAct.configure(bean); - - OutputPort theServiceport = null; - - try { - - if (isCollection) - theServiceport = Tools - .getActivityOutputPort( - activity, - name - + "(Collection - '" - + (articlename - .equals("") ? "MobyCollection" - : articlename) - + "' As Simples)"); - - else - theServiceport = Tools - .getActivityOutputPort( - activity, - name - + "(" - + articlename - + ")"); - } catch (Exception except) { - } - BiomobyObjectActionHelper boa = null; - - if (theServiceport == null) - boa = new BiomobyObjectActionHelper( - true, editManager, fileManager); - else - boa = new BiomobyObjectActionHelper( - theServiceport, - true, editManager, fileManager); - if (selectedMobyObjectTreeNodeHolder instanceof DefaultMutableTreeNode - && ((DefaultMutableTreeNode) selectedMobyObjectTreeNodeHolder) - .getUserObject() instanceof MobyObjectTreeNode) { - DefaultMutableTreeNode dmtn = (DefaultMutableTreeNode) selectedMobyObjectTreeNodeHolder; - MobyObjectTreeNode motn = (MobyObjectTreeNode) dmtn - .getUserObject(); - boa - .setNamespaces(motn - .getNamespaces()); - } - - PopupThread popupthread = new PopupThread( - boAct, boa); - progressBar - .setStringPainted(true); - progressBar - .setVisible(true); - popupthread.start(); - - while (popupthread - .isAlive()) { - Thread.sleep(4000); - } - - progressBar - .setVisible(false); - Component c = popupthread - .getComponent(); - Dimension loc = getFrameLocation(); - Dimension size = getFrameSize(); - JPanel frame = new SimpleActionFrame( - c, - "Moby Object Details"); - createFrame( - frame, - (int) loc - .getWidth(), - (int) loc - .getHeight(), - (int) size - .getWidth(), - (int) size - .getHeight()); - } catch (Exception e) { - } - } - }.start(); - } - }); - - // string may be needed to extract the - // collection article name - // final String potentialCollectionString = - // path.getParentPath() - // .getLastPathComponent().toString(); - // final boolean isCollection = - // potentialCollectionString - // .indexOf("Collection('") >= 0; - - JMenuItem item3 = new JMenuItem( - "Add parser for " + selectedObject - + " to the workflow"); - item3 - .setIcon(MobyPanel.getIcon("/Cut24.gif")); - item3.addActionListener(new ActionListener() { - - public void actionPerformed(ActionEvent ae) { - - try { - Dataflow currentDataflow = fileManager.getCurrentDataflow(); - Edit<?> edit = new AddMobyParseDatatypeEdit( - currentDataflow, activity, - selectedObject,isCollection, potentialCollectionString, editManager.getEdits()); - editManager.doDataflowEdit( - currentDataflow, edit); - - } catch (Exception e) { - logger.error("Could not perform action", e); - } - - } - }); - - menu.add(new JLabel( - "Moby Service Discovery ... ", - JLabel.CENTER)); - menu.add(new JSeparator()); - menu.add(item); - menu.add(new JSeparator()); - menu.add(item2); - menu.add(new JLabel("Parse Moby Data ... ", - JLabel.CENTER)); - menu.add(new JSeparator()); - menu.add(item3); - - menu.show(me.getComponent(), me.getX(), me - .getY()); - } - } - } - } - } - - public void mouseEntered(MouseEvent me) { - } - - public void mouseExited(MouseEvent me) { - } - }); - - tree.getSelectionModel().setSelectionMode( - TreeSelectionModel.SINGLE_TREE_SELECTION); - JScrollPane jsp = new JScrollPane(tree); - JPanel thePanel = new JPanel(new BorderLayout()); - thePanel.add(jsp, BorderLayout.CENTER); - progressBar = new JProgressBar(); - progressBar.setValue(0); - progressBar.setString("Finding Services ... "); - progressBar.setStringPainted(true); - progressBar.setIndeterminate(true); - progressBar.setVisible(false); - thePanel.add(progressBar, BorderLayout.PAGE_END); - return thePanel; - } - - /* - * (non-Javadoc) - * - * @seeorg.embl.ebi.escience.scuflui.processoractions.ProcessorActionSPI# - * getDescription() - */ - public String getDescription() { - return "Moby Service Details"; - } - - /* - * (non-Javadoc) - * - * @see - * org.embl.ebi.escience.scuflui.processoractions.ProcessorActionSPI#getIcon - * () - */ - public ImageIcon getIcon() { - return MobyPanel.getIcon("/moby_small.gif"); - } - - /** - * returns the frame size as a dimension for the content pane housing this - * action - */ - public Dimension getFrameSize() { - return new Dimension(450, 450); - } - - /** - * Return an Icon to represent this action - * - * @param loc - * the location of the image to use as an icon - */ - public ImageIcon getIcon(String loc) { - return MobyPanel.getIcon(loc); - } - - /** - * Where should the frame open? - */ - public Dimension getFrameLocation() { - return new Dimension(100, 100); - } - - public void createFrame(JPanel targetComponent, - int posX, int posY, int sizeX, int sizeY) { - final JPanel component = targetComponent; - JFrame newFrame = new JFrame(component.getName()); - newFrame.getContentPane().setLayout(new BorderLayout()); - newFrame.getContentPane().add( - new JScrollPane((JComponent) targetComponent), - BorderLayout.CENTER); - newFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); - newFrame.setSize(sizeX, sizeY); - newFrame.setLocation(posX, posY); - newFrame.setVisible(true); - } - -} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActivityConfigurationAction.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActivityConfigurationAction.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActivityConfigurationAction.java deleted file mode 100644 index f74c76a..0000000 --- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActivityConfigurationAction.java +++ /dev/null @@ -1,60 +0,0 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ -package net.sf.taverna.t2.activities.biomoby.actions; - -import java.awt.Frame; -import java.awt.event.ActionEvent; - -import net.sf.taverna.t2.activities.biomoby.BiomobyActivity; -import net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean; -import net.sf.taverna.t2.activities.biomoby.view.BiomobyConfigView; -import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager; -import net.sf.taverna.t2.workbench.edits.EditManager; -import net.sf.taverna.t2.workbench.file.FileManager; -import net.sf.taverna.t2.workbench.ui.actions.activity.ActivityConfigurationAction; -import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationDialog; - -import org.apache.log4j.Logger; - -@SuppressWarnings("serial") -public class BiomobyActivityConfigurationAction extends - ActivityConfigurationAction<BiomobyActivity, BiomobyActivityConfigurationBean> { - - private final Frame owner; - private static Logger logger = Logger.getLogger(BiomobyActivityConfigurationAction.class); - private final EditManager editManager; - private final FileManager fileManager; - - public BiomobyActivityConfigurationAction(BiomobyActivity activity, Frame owner, - EditManager editManager, FileManager fileManager, - ActivityIconManager activityIconManager) { - super(activity, activityIconManager); - this.owner = owner; - this.editManager = editManager; - this.fileManager = fileManager; - } - - public void actionPerformed(ActionEvent arg0) { - ActivityConfigurationDialog<BiomobyActivity, BiomobyActivityConfigurationBean> currentDialog = ActivityConfigurationAction - .getDialog(getActivity()); - if (currentDialog != null) { - currentDialog.toFront(); - return; - } - - final BiomobyConfigView biomobyConfigView = new BiomobyConfigView( - (BiomobyActivity) getActivity()); - final ActivityConfigurationDialog<BiomobyActivity, BiomobyActivityConfigurationBean> dialog = new ActivityConfigurationDialog<BiomobyActivity, BiomobyActivityConfigurationBean>( - getActivity(), biomobyConfigView, editManager, fileManager); - - ActivityConfigurationAction.setDialog(getActivity(), dialog, fileManager); - } - - public boolean isEnabled() { - BiomobyActivity activity = (BiomobyActivity) getActivity(); - return (activity.getMobyService() != null && activity.containsSecondaries()); - } - -}
