http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/DatatypeMenuItem.java ---------------------------------------------------------------------- diff --git a/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/DatatypeMenuItem.java b/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/DatatypeMenuItem.java deleted file mode 100644 index c5a7468..0000000 --- a/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/DatatypeMenuItem.java +++ /dev/null @@ -1,196 +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.ui; - -import java.awt.BorderLayout; -import java.awt.Component; -import java.awt.Frame; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; - -import javax.swing.BorderFactory; -import javax.swing.ImageIcon; -import javax.swing.JDialog; -import javax.swing.JLabel; -import javax.swing.JMenuItem; -import javax.swing.JPanel; -import javax.swing.JProgressBar; - -import net.sf.taverna.t2.activities.biomoby.actions.MobyPanel; -import net.sf.taverna.t2.activities.biomoby.query.BiomobyObjectActivityItem; -import net.sf.taverna.t2.workbench.MainWindow; -import net.sf.taverna.t2.workbench.edits.EditManager; -import net.sf.taverna.t2.workbench.file.FileManager; -import net.sf.taverna.t2.workbench.helper.HelpEnabledDialog; - -import org.apache.log4j.Logger; -import org.biomoby.client.CentralImpl; -import org.biomoby.shared.MobyException; - -import com.sun.java.help.impl.SwingWorker; - -/** - * DatatypeMenuItem is a JMenuItem that onClick produces a biomoby datatype tree - * that workbench users can utilize to add datatypes to any workflow. - * - * @author Edward Kawas - * - */ -public class DatatypeMenuItem extends JMenuItem { - - private static Logger logger = Logger.getLogger(DatatypeMenuItem.class); - private static final long serialVersionUID = -1010828167358361441L; - - private String endpoint; - private String namespace; - - private final EditManager editManager; - private final FileManager fileManager; - - /** - * Default constructor; Creates a menu item for the default registry - */ - public DatatypeMenuItem(EditManager editManager, FileManager fileManager) { - this(CentralImpl.DEFAULT_ENDPOINT, CentralImpl.DEFAULT_NAMESPACE, editManager, fileManager); - } - - /** - * Create a Datatype menu item for a biomoby registry given a specific - * endpoint and namespace - * - * @param endpoint - * the registry endpoint - * @param namespace - * the registry namespace - */ - public DatatypeMenuItem(String endpoint, String namespace, EditManager editManager, FileManager fileManager) { - this(endpoint, namespace, endpoint, editManager, fileManager); - } - - /* - * A private constructor. Every constructor ends up here - */ - private DatatypeMenuItem(String endpoint, String namespace, String label, EditManager editManager, FileManager fileManager) { - // set up some specifics - this.endpoint = endpoint; - this.namespace = namespace; - this.editManager = editManager; - this.fileManager = fileManager; - // set up the name, label and icon for this menu item - setName(label); - setText(label); - setIcon(new ImageIcon(BiomobyObjectActivityItem.class - .getResource("/biomoby_object.png"))); - // enable the item - setEnabled(true); - // create an action listener to catch clicks - addActionListener(new ActionListener() { - public void actionPerformed(ActionEvent e) { - if (e.getSource() instanceof DatatypeMenuItem) { - final DatatypeMenuItem item = (DatatypeMenuItem) e - .getSource(); - // create a swing worker that creates our tree - SwingWorker worker = new SwingWorker() { - @Override - public Object construct() { - // create a progress bar ... - JProgressBar bar = new JProgressBar(); - bar.setIndeterminate(true); - bar.setString("Creating datatype tree ..."); - bar.setStringPainted(true); - // a dialog frame hold the bar - String title = "Datatype Tree Builder"; - JDialog frame = new HelpEnabledDialog(MainWindow.getMainWindow(), title, false, null); - JLabel label = new JLabel( - "Constructing tree for:\n\t" - + item.getEndpoint()); - JPanel panel = new JPanel(); - panel.add(bar); - // the panel that holds the label and bar - JPanel panel1 = new JPanel(); - panel1.setLayout(new BorderLayout()); - panel1.add(panel, BorderLayout.NORTH); - panel1.add(label, BorderLayout.CENTER); - panel1.setBorder(BorderFactory.createEmptyBorder( - 20, 20, 20, 20)); - frame.setContentPane(panel1); - frame.setResizable(false); - frame.pack(); - frame.setVisible(true); - // do our task - getTreeForRegistry(item.getEndpoint(), item - .getNamespace()); - // hide the progress bar ... - frame.setVisible(false); - frame.removeAll(); - frame = null; - return null; - } - }; - worker.start(); - } - } - }); - } - - /** - * Set the registry namespace - * - * @param namespace - * the registry namespace that this menu item will use - */ - public void setNamespace(String namespace) { - this.namespace = namespace; - } - - /** - * Set the registry endpoint - * - * @param endpoint - * the registry endpoint that this menu item will use - */ - public void setEndpoint(String endpoint) { - this.endpoint = endpoint; - } - - /** - * Get the registry endpoint - * - * @return the registry endpoint that this menu item is using - */ - public String getEndpoint() { - return endpoint; - } - - /** - * Get the registry namespace - * - * @return the registry namespace that this menu item is using - */ - public String getNamespace() { - return namespace; - } - - /* - * Creates a tree for a given registry - */ - private void getTreeForRegistry(String endpoint, String namespace) { - Frame f = MobyPanel.CreateFrame("Datatype Viewer for " + endpoint); - try { - Component c = new BiomobyObjectTree(endpoint, namespace, editManager, fileManager) - .getDatatypeTree(); - f.add(c); - f.setPreferredSize(c.getPreferredSize()); - f.setMinimumSize(c.getPreferredSize()); - f.pack(); - } catch (MobyException e) { - logger.error( - "Error encountered while constructing datatype viewer:\n", - e); - } - f.setVisible(true); - } -}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualView.java ---------------------------------------------------------------------- diff --git a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualView.java b/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualView.java deleted file mode 100644 index 4911721..0000000 --- a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualView.java +++ /dev/null @@ -1,106 +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.view; - -import java.awt.BorderLayout; -import java.awt.FlowLayout; -import java.awt.Frame; -import java.util.Map.Entry; - -import javax.swing.Action; -import javax.swing.JButton; -import javax.swing.JComponent; -import javax.swing.JPanel; - -import net.sf.taverna.t2.activities.biomoby.BiomobyActivity; -import net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean; -import net.sf.taverna.t2.activities.biomoby.actions.BiomobyActivityConfigurationAction; -import net.sf.taverna.t2.activities.biomoby.actions.MobyParserAction; -import net.sf.taverna.t2.activities.biomoby.actions.MobyServiceDetailsAction; -import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager; -import net.sf.taverna.t2.workbench.configuration.colour.ColourManager; -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.HTMLBasedActivityContextualView; -import net.sf.taverna.t2.workflowmodel.processor.activity.Activity; - -@SuppressWarnings("serial") -public class BiomobyActivityContextualView extends - HTMLBasedActivityContextualView<BiomobyActivityConfigurationBean> { - - private EditManager editManager; - private final FileManager fileManager; - private final ActivityIconManager activityIconManager; - - @Override - public Action getConfigureAction(Frame owner) { - BiomobyActivity activity = (BiomobyActivity) getActivity(); - if (activity.getMobyService() != null && activity.containsSecondaries()) { - return new BiomobyActivityConfigurationAction((BiomobyActivity) getActivity(), owner, - editManager, fileManager, activityIconManager); - } else { - return null; - } - } - - public BiomobyActivityContextualView(Activity<?> activity, EditManager editManager, - FileManager fileManager, ActivityIconManager activityIconManager, - ColourManager colourManager) { - super(activity, colourManager); - this.editManager = editManager; - this.editManager = editManager; - this.fileManager = fileManager; - this.activityIconManager = activityIconManager; - } - - @Override - protected String getRawTableRowsHtml() { - String html = "<tr><td>Endpoint</td><td>" + getConfigBean().getMobyEndpoint() - + "</td></tr>"; - html += "<tr><td>Authority</td><td>" + getConfigBean().getAuthorityName() + "</td></tr>"; - html += "<tr><td>Service</td><td>" + getConfigBean().getServiceName() + "</td></tr>"; - if (getConfigBean().getSecondaries().size() > 0) { - html += "<tr><th colspan='2' align='left'>Secondaries</th></tr>"; - for (Entry<String, String> entry : getConfigBean().getSecondaries().entrySet()) { - html += "<tr><td>" + entry.getKey() + "</td><td>" + entry.getValue() + "</td></tr>"; - } - } - return html; - } - - @Override - public String getViewTitle() { - return "Biomoby service"; - } - - /** - * Gets the component from the {@link HTMLBasedActivityContextualView} and adds buttons to it - * allowing Moby service details - */ - @Override - public JComponent getMainFrame() { - final JComponent mainFrame = super.getMainFrame(); - JPanel flowPanel = new JPanel(new FlowLayout()); - - BiomobyActivity activity = (BiomobyActivity) getActivity(); - - JButton button = new JButton(new MobyServiceDetailsAction(activity, null, editManager, - fileManager)); - flowPanel.add(button); - if (activity.getMobyService() != null) { - JButton button2 = new JButton(new MobyParserAction(activity, null, editManager, - fileManager)); - flowPanel.add(button2); - } - mainFrame.add(flowPanel, BorderLayout.SOUTH); - return mainFrame; - } - - @Override - public int getPreferredPosition() { - return 100; - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualViewFactory.java ---------------------------------------------------------------------- diff --git a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualViewFactory.java b/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualViewFactory.java deleted file mode 100644 index 942e52c..0000000 --- a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualViewFactory.java +++ /dev/null @@ -1,50 +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.view; - -import java.util.Arrays; -import java.util.List; - -import net.sf.taverna.t2.activities.biomoby.BiomobyActivity; -import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager; -import net.sf.taverna.t2.workbench.configuration.colour.ColourManager; -import net.sf.taverna.t2.workbench.edits.EditManager; -import net.sf.taverna.t2.workbench.file.FileManager; -import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView; -import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory; - -public class BiomobyActivityContextualViewFactory implements ContextualViewFactory<BiomobyActivity> { - - private EditManager editManager; - private FileManager fileManager; - private ActivityIconManager activityIconManager; - private ColourManager colourManager; - - public boolean canHandle(Object activity) { - return activity instanceof BiomobyActivity; - } - - public List<ContextualView> getViews(BiomobyActivity activity) { - return Arrays.asList(new ContextualView[] { new BiomobyActivityContextualView(activity, - editManager, fileManager, activityIconManager, colourManager) }); - } - - public void setEditManager(EditManager editManager) { - this.editManager = editManager; - } - - public void setFileManager(FileManager fileManager) { - this.fileManager = fileManager; - } - - public void setActivityIconManager(ActivityIconManager activityIconManager) { - this.activityIconManager = activityIconManager; - } - - public void setColourManager(ColourManager colourManager) { - this.colourManager = colourManager; - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyConfigView.java ---------------------------------------------------------------------- diff --git a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyConfigView.java b/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyConfigView.java deleted file mode 100644 index 0e08e0b..0000000 --- a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyConfigView.java +++ /dev/null @@ -1,108 +0,0 @@ -/** - * - */ -package net.sf.taverna.t2.activities.biomoby.view; - -import java.awt.BorderLayout; -import java.util.Map; - -import javax.swing.JComponent; - -import net.sf.taverna.t2.activities.biomoby.BiomobyActivity; -import net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean; -import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationPanel; - -import org.apache.log4j.Logger; -import org.biomoby.service.dashboard.data.ParametersTable; - -/** - * @author alanrw - * - */ -public class BiomobyConfigView extends ActivityConfigurationPanel<BiomobyActivity, BiomobyActivityConfigurationBean> { - - private BiomobyActivity activity; - private BiomobyActivityConfigurationBean configuration; - private boolean changed = false; - - private static Logger logger = Logger - .getLogger(BiomobyConfigView.class); - private ParametersTable parameterTable; - - public BiomobyConfigView(BiomobyActivity activity) { - this.activity = activity; - initialise(); - } - - private void initialise() { - configuration = activity.getConfiguration(); - this.setLayout(new BorderLayout()); - parameterTable = activity.getParameterTable(); - JComponent component = parameterTable.scrollable(); - this.add(component, BorderLayout.NORTH); - validate(); - } - - /* (non-Javadoc) - * @see net.sf.taverna.t2.workbench.ui.views.contextualviews.ActivityConfigurationPanel#getConfiguration() - */ - @Override - public BiomobyActivityConfigurationBean getConfiguration() { - return configuration; - } - - /* (non-Javadoc) - * @see net.sf.taverna.t2.workbench.ui.views.contextualviews.ActivityConfigurationPanel#isConfigurationChanged() - */ - @Override - public boolean isConfigurationChanged() { - Map<String,String> secondaries = configuration.getSecondaries(); - int rows = parameterTable.getModel().getRowCount(); - for (int i = 0; i < rows; i++) { - String key = (String)parameterTable.getModel().getValueAt(i,0); - String newValue = parameterTable.getModel().getValueAt(i,1).toString(); - String currentValue = secondaries.get(key); - if (!currentValue.equals(newValue)) { - return true; - } - } - return false; - } - - /* (non-Javadoc) - * @see net.sf.taverna.t2.workbench.ui.views.contextualviews.ActivityConfigurationPanel#noteConfiguration() - */ - @Override - public void noteConfiguration() { - BiomobyActivityConfigurationBean newConfiguration = - (BiomobyActivityConfigurationBean) cloneBean(configuration); - Map<String,String> secondaries = newConfiguration.getSecondaries(); - int rows = parameterTable.getModel().getRowCount(); - for (int i = 0; i < rows; i++) { - String key = (String)parameterTable.getModel().getValueAt(i,0); - String value = parameterTable.getModel().getValueAt(i,1).toString(); - secondaries.put(key, value); - } -// logger.info(convertBeanToString(configuration)); -// logger.info("COnfiguration was " + configuration.hashCode()); -// logger.info(convertBeanToString(newConfiguration)); -// logger.info("New configuration is " + newConfiguration.hashCode()); - configuration = newConfiguration; - } - - @Override - public void refreshConfiguration() { - logger.info(convertBeanToString(activity.getConfiguration())); - removeAll(); - initialise(); - } - - @Override - public boolean checkValues() { - // TODO Not yet implemented - return true; - } - - - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualView.java ---------------------------------------------------------------------- diff --git a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualView.java b/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualView.java deleted file mode 100644 index 4ceed9b..0000000 --- a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualView.java +++ /dev/null @@ -1,95 +0,0 @@ -/** - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * 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. - * - */ -package net.sf.taverna.t2.activities.biomoby.view; - -import java.awt.BorderLayout; -import java.awt.FlowLayout; - -import javax.swing.JButton; -import javax.swing.JComponent; -import javax.swing.JPanel; - -import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity; -import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityConfigurationBean; -import net.sf.taverna.t2.activities.biomoby.actions.MobyObjectDetailsAction; -import net.sf.taverna.t2.workbench.configuration.colour.ColourManager; -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.HTMLBasedActivityContextualView; -import net.sf.taverna.t2.workflowmodel.processor.activity.Activity; - -/** - * @author Stuart Owen - * - */ -@SuppressWarnings("serial") -public class BiomobyObjectActivityContextualView extends - HTMLBasedActivityContextualView<BiomobyObjectActivityConfigurationBean> { - - private EditManager editManager; - private final FileManager fileManager; - - public BiomobyObjectActivityContextualView(Activity<?> activity, EditManager editManager, - FileManager fileManager, ColourManager colourManager) { - super(activity, colourManager); - this.editManager = editManager; - this.fileManager = fileManager; - } - - @Override - protected String getRawTableRowsHtml() { - String html = "<tr><td>Endpoint</td><td>" + getConfigBean().getMobyEndpoint() - + "</td></tr>"; - html += "<tr><td>Authority</td><td>" + getConfigBean().getAuthorityName() + "</td></tr>"; - html += "<tr><td>Datatype</td><td>" + getConfigBean().getServiceName() + "</td></tr>"; - return html; - } - - @Override - public String getViewTitle() { - return "Biomoby Object service"; - } - - /** - * Gets the component from the {@link HTMLBasedActivityContextualView} and adds buttons to it - * allowing Moby object details - */ - @Override - public JComponent getMainFrame() { - final JComponent mainFrame = super.getMainFrame(); - BiomobyObjectActivity activity = (BiomobyObjectActivity) getActivity(); - if (activity.getMobyObject() != null) { - JPanel flowPanel = new JPanel(new FlowLayout()); - JButton button = new JButton(new MobyObjectDetailsAction(activity, null, editManager, - fileManager)); - flowPanel.add(button); - mainFrame.add(flowPanel, BorderLayout.SOUTH); - } - return mainFrame; - } - - @Override - public int getPreferredPosition() { - return 100; - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualViewFactory.java ---------------------------------------------------------------------- diff --git a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualViewFactory.java b/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualViewFactory.java deleted file mode 100644 index 0e6ea55..0000000 --- a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualViewFactory.java +++ /dev/null @@ -1,67 +0,0 @@ -/** - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * 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. - * - */ -package net.sf.taverna.t2.activities.biomoby.view; - -import java.util.Arrays; -import java.util.List; - -import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity; -import net.sf.taverna.t2.workbench.configuration.colour.ColourManager; -import net.sf.taverna.t2.workbench.edits.EditManager; -import net.sf.taverna.t2.workbench.file.FileManager; -import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView; -import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory; - -/** - * @author Stuart Owen - * - */ -public class BiomobyObjectActivityContextualViewFactory implements - ContextualViewFactory<BiomobyObjectActivity> { - - private EditManager editManager; - private FileManager fileManager; - private ColourManager colourManager; - - public boolean canHandle(Object activity) { - return activity instanceof BiomobyObjectActivity; - } - - public List<ContextualView> getViews(BiomobyObjectActivity activity) { - return Arrays.asList(new ContextualView[] { new BiomobyObjectActivityContextualView( - activity, editManager, fileManager, colourManager) }); - } - - public void setEditManager(EditManager editManager) { - this.editManager = editManager; - } - - public void setFileManager(FileManager fileManager) { - this.fileManager = fileManager; - } - - public void setColourManager(ColourManager colourManager) { - this.colourManager = colourManager; - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualView.java ---------------------------------------------------------------------- diff --git a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualView.java b/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualView.java deleted file mode 100644 index 91d4cd6..0000000 --- a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualView.java +++ /dev/null @@ -1,62 +0,0 @@ -/** - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * 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. - * - */ -package net.sf.taverna.t2.activities.biomoby.view; - -import net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivityConfigurationBean; -import net.sf.taverna.t2.workbench.configuration.colour.ColourManager; -import net.sf.taverna.t2.workbench.ui.actions.activity.HTMLBasedActivityContextualView; -import net.sf.taverna.t2.workflowmodel.processor.activity.Activity; - -/** - * @author Stuart Owen - * - */ -@SuppressWarnings("serial") -public class MobyParseDatatypeContextualView extends - HTMLBasedActivityContextualView<MobyParseDatatypeActivityConfigurationBean> { - - public MobyParseDatatypeContextualView(Activity<?> activity, ColourManager colourManager) { - super(activity, colourManager); - } - - @Override - protected String getRawTableRowsHtml() { - String html = "<tr><td>Article name used by service</td><td>" - + getConfigBean().getArticleNameUsedByService() + "</td></tr>"; - html += "<tr><td>Datatype</td><td>" + getConfigBean().getDatatypeName() + "</td></tr>"; - html += "<tr><td>Registry endpoint</td><td>" + getConfigBean().getRegistryEndpoint() - + "</td></tr>"; - return html; - } - - @Override - public String getViewTitle() { - return "Moby parse datatype service"; - } - - @Override - public int getPreferredPosition() { - return 100; - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualViewFactory.java ---------------------------------------------------------------------- diff --git a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualViewFactory.java b/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualViewFactory.java deleted file mode 100644 index 5179642..0000000 --- a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualViewFactory.java +++ /dev/null @@ -1,69 +0,0 @@ -/** - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * 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. - * - */ -package net.sf.taverna.t2.activities.biomoby.view; - -import java.util.Arrays; -import java.util.List; - -import net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivity; -import net.sf.taverna.t2.workbench.configuration.colour.ColourManager; -import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView; -import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory; - -/** - * @author Stuart Owen - * - */ -public class MobyParseDatatypeContextualViewFactory implements - ContextualViewFactory<MobyParseDatatypeActivity> { - - private ColourManager colourManager; - - /* - * (non-Javadoc) - * - * @see - * net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory#canHandle - * (java.lang.Object) - */ - public boolean canHandle(Object activity) { - return activity instanceof MobyParseDatatypeActivity; - } - - /* - * (non-Javadoc) - * - * @see - * net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory#getView - * (java.lang.Object) - */ - public List<ContextualView> getViews(MobyParseDatatypeActivity activity) { - return Arrays.asList(new ContextualView[] { new MobyParseDatatypeContextualView(activity, - colourManager) }); - } - - public void setColourManager(ColourManager colourManager) { - this.colourManager = colourManager; - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/resources/Add24.gif ---------------------------------------------------------------------- diff --git a/src/main/resources/Add24.gif b/src/main/resources/Add24.gif deleted file mode 100644 index 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a/src/main/resources/META-INF/services/net.sf.taverna.t2.partition.PropertyExtractorSPI b/src/main/resources/META-INF/services/net.sf.taverna.t2.partition.PropertyExtractorSPI deleted file mode 100644 index afaed0e..0000000 --- a/src/main/resources/META-INF/services/net.sf.taverna.t2.partition.PropertyExtractorSPI +++ /dev/null @@ -1 +0,0 @@ -net.sf.taverna.t2.activities.biomoby.partition.BiomobyPropertyExtractor \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/resources/META-INF/services/net.sf.taverna.t2.partition.QueryFactory ---------------------------------------------------------------------- diff --git a/src/main/resources/META-INF/services/net.sf.taverna.t2.partition.QueryFactory b/src/main/resources/META-INF/services/net.sf.taverna.t2.partition.QueryFactory deleted file mode 100644 index 12241b2..0000000 --- a/src/main/resources/META-INF/services/net.sf.taverna.t2.partition.QueryFactory +++ /dev/null @@ -1 +0,0 @@ -net.sf.taverna.t2.activities.biomoby.query.BiomobyQueryFactory \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider ---------------------------------------------------------------------- diff --git a/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider b/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider deleted file mode 100644 index 604022f..0000000 --- a/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider +++ /dev/null @@ -1 +0,0 @@ -net.sf.taverna.t2.activities.biomoby.servicedescriptions.BiomobyServiceProvider http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent ---------------------------------------------------------------------- diff --git a/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent b/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent deleted file mode 100644 index 312b88c..0000000 --- a/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent +++ /dev/null @@ -1,5 +0,0 @@ -net.sf.taverna.t2.activities.biomoby.menu.BiomobyActivityDetailsMenuAction -net.sf.taverna.t2.activities.biomoby.menu.BiomobyActivityParserMenuAction -#net.sf.taverna.t2.activities.biomoby.actions.BiomobyAdvancedMenuAction -net.sf.taverna.t2.activities.biomoby.menu.ConfigureBiomobyMenuAction - http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI ---------------------------------------------------------------------- diff --git a/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI b/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI deleted file mode 100644 index cca5a06..0000000 --- a/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI +++ /dev/null @@ -1,2 +0,0 @@ -net.sf.taverna.t2.activities.biomoby.query.BiomobyActivityIcon -net.sf.taverna.t2.activities.biomoby.query.BiomobyObjectActivityIcon \ No newline at end of file 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newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/resources/META-INF/spring/biomoby-activity-ui-context-osgi.xml ---------------------------------------------------------------------- diff --git a/src/main/resources/META-INF/spring/biomoby-activity-ui-context-osgi.xml b/src/main/resources/META-INF/spring/biomoby-activity-ui-context-osgi.xml deleted file mode 100644 index c67a55b..0000000 --- a/src/main/resources/META-INF/spring/biomoby-activity-ui-context-osgi.xml +++ /dev/null @@ -1,28 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<beans:beans xmlns="http://www.springframework.org/schema/osgi"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; - xmlns:beans="http://www.springframework.org/schema/beans"; - xsi:schemaLocation="http://www.springframework.org/schema/beans - http://www.springframework.org/schema/beans/spring-beans.xsd - http://www.springframework.org/schema/osgi - http://www.springframework.org/schema/osgi/spring-osgi.xsd";> - - <service ref="BiomobyActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" /> - <service ref="BiomobyObjectActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" /> - - <service ref="BiomobyServiceProvider" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider" /> - - <service ref="BiomobyActivityDetailsMenuAction" auto-export="interfaces" /> - <service ref="BiomobyActivityParserMenuAction" auto-export="interfaces" /> - <service ref="ConfigureBiomobyMenuAction" auto-export="interfaces" /> - - <service ref="BiomobyActivityContextualViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" /> - <service ref="BiomobyObjectActivityContextualViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" /> - <service ref="MobyParseDatatypeContextualViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" /> - - <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" /> - <reference id="fileManager" interface="net.sf.taverna.t2.workbench.file.FileManager" /> - <reference id="activityIconManager" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconManager" /> - <reference id="colourManager" interface="net.sf.taverna.t2.workbench.configuration.colour.ColourManager" /> - <reference id="serviceDescriptionRegistry" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry" /> - -</beans:beans> http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/resources/META-INF/spring/biomoby-activity-ui-context.xml ---------------------------------------------------------------------- diff --git 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ref="serviceDescriptionRegistry" /> - </bean> - - <bean id="BiomobyActivityDetailsMenuAction" class="net.sf.taverna.t2.activities.biomoby.menu.BiomobyActivityDetailsMenuAction"> - <property name="editManager" ref="editManager" /> - <property name="fileManager" ref="fileManager" /> - </bean> - <bean id="BiomobyActivityParserMenuAction" class="net.sf.taverna.t2.activities.biomoby.menu.BiomobyActivityParserMenuAction"> - <property name="editManager" ref="editManager" /> - <property name="fileManager" ref="fileManager" /> - </bean> - <bean id="ConfigureBiomobyMenuAction" class="net.sf.taverna.t2.activities.biomoby.menu.ConfigureBiomobyMenuAction"> - <property name="editManager" ref="editManager" /> - <property name="fileManager" ref="fileManager" /> - <property name="activityIconManager" ref="activityIconManager" /> - </bean> - - <bean id="BiomobyActivityContextualViewFactory" class="net.sf.taverna.t2.activities.biomoby.view.BiomobyActivityContextualViewFactory"> - <property name="editManager" ref="editManager" /> - <property name="fileManager" ref="fileManager" /> - <property name="activityIconManager" ref="activityIconManager" /> - <property name="colourManager" ref="colourManager" /> - </bean> - <bean id="BiomobyObjectActivityContextualViewFactory" class="net.sf.taverna.t2.activities.biomoby.view.BiomobyObjectActivityContextualViewFactory"> - <property name="editManager" ref="editManager" /> - <property name="fileManager" ref="fileManager" /> - <property name="colourManager" ref="colourManager" /> - </bean> - <bean id="MobyParseDatatypeContextualViewFactory" class="net.sf.taverna.t2.activities.biomoby.view.MobyParseDatatypeContextualViewFactory"> - <property name="colourManager" ref="colourManager" /> - </bean> - -</beans> http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/resources/Search24.gif ---------------------------------------------------------------------- diff --git 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a/src/main/resources/service.png b/src/main/resources/service.png deleted file mode 100644 index 912efb2..0000000 Binary files a/src/main/resources/service.png and /dev/null differ http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/test/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyContextualViewFactoryTest.java ---------------------------------------------------------------------- diff --git a/src/test/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyContextualViewFactoryTest.java b/src/test/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyContextualViewFactoryTest.java deleted file mode 100644 index a9c51c6..0000000 --- a/src/test/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyContextualViewFactoryTest.java +++ /dev/null @@ -1,49 +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.view; - -import static org.junit.Assert.assertNull; -import static org.junit.Assert.assertTrue; - -import java.util.List; - -import net.sf.taverna.t2.activities.biomoby.BiomobyActivity; -import net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean; -import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView; -import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory; -import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactoryRegistry; -import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException; - -import org.junit.Before; -import org.junit.Test; - -public class BiomobyContextualViewFactoryTest { - BiomobyActivity activity; - @Before - public void setup() throws ActivityConfigurationException { - activity=new BiomobyActivity() { //need to prevent the activity trying to configure itself, but store a copy of the config bean - - @Override - public void configure( - BiomobyActivityConfigurationBean configurationBean) - throws ActivityConfigurationException { - this.configurationBean=configurationBean; - } - - }; - BiomobyActivityConfigurationBean b = new BiomobyActivityConfigurationBean(); - b.setAuthorityName("a"); - b.setMobyEndpoint("e"); - b.setServiceName("s"); - activity.configure(b); - } - - @Test - public void testGetConfigureAction() throws Exception { - ContextualView view = new BiomobyActivityContextualView(activity, null, null, null, null); - //will be null because its not a valid activity so therefore has no secondaries - assertNull("The action should be null",view.getConfigureAction(null)); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/taverna-biomoby-activity-ui/pom.xml ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity-ui/pom.xml b/taverna-biomoby-activity-ui/pom.xml new file mode 100644 index 0000000..8f92c83 --- /dev/null +++ b/taverna-biomoby-activity-ui/pom.xml @@ -0,0 +1,86 @@ +<?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/fd2e9765/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 new file mode 100644 index 0000000..b03b98c --- /dev/null +++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/AddParserActionHelper.java @@ -0,0 +1,280 @@ +/* + * 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/fd2e9765/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 new file mode 100644 index 0000000..46b4d5a --- /dev/null +++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyObjectTreeCustomRenderer.java @@ -0,0 +1,97 @@ +/* + * 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/fd2e9765/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 new file mode 100644 index 0000000..ecce3ca --- /dev/null +++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyServiceTreeCustomRenderer.java @@ -0,0 +1,86 @@ +/* + * 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; + } +}
