Removed Baclava actions Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/repo Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/commit/a3483f50 Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/tree/a3483f50 Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/diff/a3483f50
Branch: refs/heads/master Commit: a3483f5072eff2d2e890d055045f67e3d3040ef1 Parents: b219f5d Author: Stian Soiland-Reyes <[email protected]> Authored: Fri Oct 21 12:27:19 2016 +0200 Committer: Stian Soiland-Reyes <[email protected]> Committed: Fri Oct 21 12:27:19 2016 +0200 ---------------------------------------------------------------------- .../ui/referenceactions/LoadInputsFromXML.java | 114 ----------- .../ui/referenceactions/SaveInputsAsXML.java | 201 ------------------- 2 files changed, 315 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/a3483f50/taverna-reference-ui/src/main/java/org/apache/taverna/reference/ui/referenceactions/LoadInputsFromXML.java ---------------------------------------------------------------------- diff --git a/taverna-reference-ui/src/main/java/org/apache/taverna/reference/ui/referenceactions/LoadInputsFromXML.java b/taverna-reference-ui/src/main/java/org/apache/taverna/reference/ui/referenceactions/LoadInputsFromXML.java deleted file mode 100644 index 19f238d..0000000 --- a/taverna-reference-ui/src/main/java/org/apache/taverna/reference/ui/referenceactions/LoadInputsFromXML.java +++ /dev/null @@ -1,114 +0,0 @@ -package org.apache.taverna.reference.ui.referenceactions; -/* - * Licensed to the Apache Software Foundation (ASF) under one or more - * contributor license agreements. See the NOTICE file distributed with - * this work for additional information regarding copyright ownership. - * The ASF licenses this file to You under the Apache License, Version 2.0 - * (the "License"); you may not use this file except in compliance with - * the License. You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - -import static javax.swing.JFileChooser.APPROVE_OPTION; -import static org.apache.taverna.workbench.icons.WorkbenchIcons.xmlNodeIcon; - -import java.awt.event.ActionEvent; -import java.io.File; -import java.io.FileInputStream; -import java.io.InputStreamReader; -import java.nio.charset.Charset; -import java.util.Iterator; -import java.util.Map; -import java.util.prefs.Preferences; - -import javax.swing.AbstractAction; -import javax.swing.JFileChooser; - -import org.apache.taverna.lang.ui.ExtensionFileFilter; -import org.apache.taverna.reference.ui.RegistrationPanel; - -import org.jdom.Document; -import org.jdom.input.SAXBuilder; - -/** - * Loads a set of input values from an XML document - */ -public class LoadInputsFromXML extends AbstractAction implements - ReferenceActionSPI { - private static final long serialVersionUID = -5031867688853589341L; - private static final String INPUT_DATA_DIR_PROPERTY = "inputDataValuesDir"; - - private Map<String, RegistrationPanel> inputPanelMap; - - public LoadInputsFromXML() { - super(); - putValue(NAME, "Load previous values"); - putValue(SMALL_ICON, xmlNodeIcon); - } - - @Override - public AbstractAction getAction() { - return new LoadInputsFromXML(); - } - - @Override - public void actionPerformed(ActionEvent e) { - Preferences prefs = Preferences.userNodeForPackage(getClass()); - String curDir = prefs.get(INPUT_DATA_DIR_PROPERTY, System.getProperty("user.home")); - - JFileChooser chooser = new JFileChooser(); - chooser.setDialogTitle("Select file to load input values from"); - - chooser.resetChoosableFileFilters(); - chooser.setFileFilter(new ExtensionFileFilter(new String[]{"xml"})); - chooser.setCurrentDirectory(new File(curDir)); - - if (chooser.showOpenDialog(null) != APPROVE_OPTION) - return; - prefs.put(INPUT_DATA_DIR_PROPERTY, chooser.getCurrentDirectory() - .toString()); - try { - File file = chooser.getSelectedFile(); - InputStreamReader stream; - stream = new InputStreamReader(new FileInputStream(file), - Charset.forName("UTF-8")); - Document inputDoc = new SAXBuilder(false).build(stream); - Map<String, DataThing> inputMap = DataThingXMLFactory.parseDataDocument(inputDoc); - for (String portName : inputMap.keySet()) { - RegistrationPanel panel = inputPanelMap.get(portName); - Object o = inputMap.get(portName).getDataObject(); - if (o != null) { - int objectDepth = getObjectDepth(o); - if ((panel != null) && (objectDepth <= panel.getDepth())) - panel.setValue(o, objectDepth); - } - } - } catch (Exception ex) { - // Nothing - } - } - - @Override - public void setInputPanelMap(Map<String, RegistrationPanel> inputPanelMap) { - this.inputPanelMap = inputPanelMap; - } - - private int getObjectDepth(Object o) { - int result = 0; - if (o instanceof Iterable) { - result++; - @SuppressWarnings("unchecked") - Iterator<Object> i = ((Iterable<Object>) o).iterator(); - if (i.hasNext()) - result = result + getObjectDepth(i.next()); - } - return result; - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/a3483f50/taverna-reference-ui/src/main/java/org/apache/taverna/reference/ui/referenceactions/SaveInputsAsXML.java ---------------------------------------------------------------------- diff --git a/taverna-reference-ui/src/main/java/org/apache/taverna/reference/ui/referenceactions/SaveInputsAsXML.java b/taverna-reference-ui/src/main/java/org/apache/taverna/reference/ui/referenceactions/SaveInputsAsXML.java deleted file mode 100644 index 3ebc2df..0000000 --- a/taverna-reference-ui/src/main/java/org/apache/taverna/reference/ui/referenceactions/SaveInputsAsXML.java +++ /dev/null @@ -1,201 +0,0 @@ -package org.apache.taverna.reference.ui.referenceactions; -/* - * Licensed to the Apache Software Foundation (ASF) under one or more - * contributor license agreements. See the NOTICE file distributed with - * this work for additional information regarding copyright ownership. - * The ASF licenses this file to You under the Apache License, Version 2.0 - * (the "License"); you may not use this file except in compliance with - * the License. You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - -import static java.lang.System.getProperty; -import static javax.swing.JFileChooser.APPROVE_OPTION; -import static javax.swing.JFileChooser.FILES_ONLY; -import static javax.swing.JOptionPane.ERROR_MESSAGE; -import static javax.swing.JOptionPane.YES_NO_OPTION; -import static javax.swing.JOptionPane.YES_OPTION; -import static javax.swing.JOptionPane.showConfirmDialog; -import static javax.swing.JOptionPane.showMessageDialog; -import static org.apache.taverna.workbench.icons.WorkbenchIcons.xmlNodeIcon; -import static org.jdom.Namespace.getNamespace; -import static org.jdom.output.Format.getPrettyFormat; - -import java.awt.event.ActionEvent; -import java.io.File; -import java.io.FileWriter; -import java.io.PrintWriter; -import java.util.HashMap; -import java.util.Map; -import java.util.prefs.Preferences; - -import javax.swing.AbstractAction; -import javax.swing.JFileChooser; - -import org.apache.taverna.invocation.InvocationContext; -import org.apache.taverna.lang.ui.ExtensionFileFilter; -import org.apache.taverna.reference.ui.RegistrationPanel; - -import org.apache.log4j.Logger; -import org.jdom.Document; -import org.jdom.Element; -import org.jdom.Namespace; -import org.jdom.output.XMLOutputter; - -/** - * Stores the entire map of result objects to disk - * as a single XML data document. - * - * @author Tom Oinn - * @author Alex Nenadic - */ -public class SaveInputsAsXML extends AbstractAction implements ReferenceActionSPI { - private static final long serialVersionUID = 452360182978773176L; - private static final String INPUT_DATA_DIR_PROPERTY = "inputDataValuesDir"; - private static final Logger logger = Logger - .getLogger(SaveInputsAsXML.class); - public static final String BACLAVA_NAMESPACE = "http://org.embl.ebi.escience/baclava/0.1alpha";; - /** {@value #BACLAVA_NAMESPACE} */ - private static final Namespace namespace = getNamespace("b", - BACLAVA_NAMESPACE); - - @SuppressWarnings("unused") - private InvocationContext context = null; - - private Map<String, RegistrationPanel> inputPanelMap; - - public SaveInputsAsXML(){ - super(); - putValue(NAME, "Save values"); - putValue(SMALL_ICON, xmlNodeIcon); - } - - @Override - public AbstractAction getAction() { - return new SaveInputsAsXML(); - } - - // Must be called before actionPerformed() - public void setInvocationContext(InvocationContext context) { - this.context = context; - } - - /** - * Shows a standard save dialog and dumps the entire input set to the - * specified XML file. - */ - @Override - public void actionPerformed(ActionEvent e) { - Preferences prefs = Preferences.userNodeForPackage(getClass()); - String curDir = prefs.get(INPUT_DATA_DIR_PROPERTY, getProperty("user.home")); - - JFileChooser fc = new JFileChooser(); - fc.setDialogTitle("Select file to save input values to"); - - fc.resetChoosableFileFilters(); - fc.setFileFilter(new ExtensionFileFilter(new String[] { "xml" })); - fc.setCurrentDirectory(new File(curDir)); - fc.setFileSelectionMode(FILES_ONLY); - - File file; - do { - if (fc.showSaveDialog(null) != APPROVE_OPTION) - return; - prefs.put(INPUT_DATA_DIR_PROPERTY, fc.getCurrentDirectory().toString()); - file = fc.getSelectedFile(); - - /* - * If the user did not use the .xml extension for the file - append - * it to the file name now - */ - if (!file.getName().toLowerCase().endsWith(".xml")) - file = new File(file.getParentFile(), file.getName() + ".xml"); - - // If the file exists, ask the user if they want to overwrite the file - } while (file.exists() - && showConfirmDialog(null, file.getAbsolutePath() - + " already exists. Do you want to overwrite it?", - "File already exists", YES_NO_OPTION) != YES_OPTION); - doSave(file); - } - - private void doSave(final File file) { - // Do this in separate thread to avoid hanging UI - new Thread("Save(InputsAsXML: Saving inputs to " + file) { - @Override - public void run() { - try { - synchronized (inputPanelMap) { - saveData(file); - } - } catch (Exception ex) { - showMessageDialog(null, "Problem saving input data", - "Save Inputs Error", ERROR_MESSAGE); - logger.error("Problem saving input data as XML", ex); - } - } - }.start(); - } - - /** - * Saves the input data to an XML Baclava file. - */ - private void saveData(File file) throws Exception { - // Build the DataThing map from the inputPanelMap - Map<String, Object> valueMap = new HashMap<>(); - for (String portName : inputPanelMap.keySet()) { - RegistrationPanel panel = inputPanelMap.get(portName); - Object obj = panel.getValue(); - if (obj != null) - valueMap.put(portName, obj); - } - Map<String, DataThing> dataThings = bakeDataThingMap(valueMap); - - // Build the string containing the XML document from the panel map - String xmlString = new XMLOutputter(getPrettyFormat()) - .outputString(getDataDocument(dataThings)); - try (PrintWriter out = new PrintWriter(new FileWriter(file))) { - out.print(xmlString); - } - } - - /** - * Returns a map of port names to DataThings from a map of port names to a - * list of (lists of ...) result objects. - */ - Map<String, DataThing> bakeDataThingMap(Map<String, Object> resultMap) { - Map<String, DataThing> dataThingMap = new HashMap<>(); - for (String portName : resultMap.keySet()) - dataThingMap.put(portName, bake(resultMap.get(portName))); - return dataThingMap; - } - - /** - * Returns a org.jdom.Document from a map of port named to DataThingS containing - * the port's results. - */ - public static Document getDataDocument(Map<String, DataThing> dataThings) { - Element rootElement = new Element("dataThingMap", namespace); - Document theDocument = new Document(rootElement); - for (String key : dataThings.keySet()) { - DataThing value = (DataThing) dataThings.get(key); - Element dataThingElement = new Element("dataThing", namespace); - dataThingElement.setAttribute("key", key); - dataThingElement.addContent(value.getElement()); - rootElement.addContent(dataThingElement); - } - return theDocument; - } - - @Override - public void setInputPanelMap(Map<String, RegistrationPanel> inputPanelMap) { - this.inputPanelMap = inputPanelMap; - } -}
