Java tutorial
/* * Copyright 2012 Fundaci Barcelona Media * * Licensed 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. */ package org.barcelonamedia.uima.tools.docanalyzer; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; import java.awt.Cursor; import java.awt.FlowLayout; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.WindowEvent; import java.io.ByteArrayInputStream; import java.io.ByteArrayOutputStream; import java.io.File; import java.io.FileInputStream; import java.io.FileNotFoundException; import java.io.FileOutputStream; import java.io.FileWriter; import java.io.FilenameFilter; import java.io.IOException; import java.io.InputStream; import java.util.ArrayList; import java.util.Collections; import java.util.List; import java.util.StringTokenizer; import java.util.zip.Inflater; import javax.swing.BorderFactory; import javax.swing.BoxLayout; import javax.swing.ButtonGroup; import javax.swing.ImageIcon; import javax.swing.JButton; import javax.swing.JDialog; import javax.swing.JFileChooser; import javax.swing.JFrame; import javax.swing.JLabel; import javax.swing.JList; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JRadioButton; import javax.swing.JScrollPane; import javax.swing.ListCellRenderer; import javax.swing.SpringLayout; import javax.swing.UIManager; import javax.swing.UnsupportedLookAndFeelException; import javax.xml.parsers.DocumentBuilder; import javax.xml.parsers.DocumentBuilderFactory; import javax.xml.parsers.FactoryConfigurationError; import javax.xml.parsers.ParserConfigurationException; import org.apache.commons.io.IOUtils; import org.apache.uima.UIMAException; import org.apache.uima.UIMAFramework; import org.apache.uima.UIMARuntimeException; import org.apache.uima.analysis_engine.AnalysisEngineDescription; import org.apache.uima.cas.CAS; import org.apache.uima.cas.TypeSystem; import org.apache.uima.cas.impl.XmiCasDeserializer; import org.apache.uima.internal.util.BrowserUtil; import org.apache.uima.resource.ResourceInitializationException; import org.apache.uima.tools.images.Images; import org.apache.uima.tools.stylemap.ColorParser; import org.apache.uima.tools.stylemap.StyleMapEditor; import org.apache.uima.tools.stylemap.StyleMapEntry; import org.apache.uima.tools.util.gui.Caption; import org.apache.uima.tools.util.gui.SpringUtilities; import org.apache.uima.tools.util.htmlview.AnnotationViewGenerator; import org.apache.uima.tools.viewer.CasAnnotationViewer; import org.apache.uima.util.CasCreationUtils; import org.apache.uima.util.CasToInlineXml; import org.apache.uima.util.FileUtils; import org.apache.uima.util.InvalidXMLException; import org.apache.uima.util.XMLInputSource; import org.apache.uima.util.XmlCasDeserializer; import org.barcelonamedia.uima.tools.DAO.DAOException; import org.barcelonamedia.uima.tools.DAO.XMIDAO; import org.w3c.dom.Document; import org.w3c.dom.Node; import org.w3c.dom.NodeList; import org.w3c.dom.Text; import org.xml.sax.SAXException; /** * Dialog that loads analyzed documents stored in XMI or XCAS format and allows them to be viewed * using the Java-based CAS viewer or a web browser, in either an HTML/Javascript format or in the * inline XML format. * */ public class DBAnnotationViewerDialog extends JDialog implements ActionListener { private static final long serialVersionUID = -7259891069111863433L; private File tempDir = createTempDir(); protected AnnotationViewGenerator annotationViewGenerator; // JMP private StyleMapEditor styleMapEditor; private DBPrefsMediator med1; /** XMI DAO object. */ private XMIDAO xmiDAO; private File styleMapFile; JList analyzedResultsList; String inputDirPath = null; TypeSystem typeSystem = null; String[] typesToDisplay = null; JRadioButton javaViewerRB = null; JRadioButton javaViewerUCRB = null; JRadioButton htmlRB = null; JRadioButton xmlRB = null; private CAS cas; private boolean processedStyleMap = false; private String defaultCasViewName = CAS.NAME_DEFAULT_SOFA; /** * Create an AnnotationViewer Dialog * * @param aParentFrame * frame containing this panel * @param aTitle * title to display for the dialog * @param aInputDir * directory containing input files (in XCAS foramt) to read * @param aStyleMapFile * filename of style map to be used to view files in HTML * @param aPerformanceStats * string representaiton of performance statistics, optional. * @param aTypeSystem * the CAS Type System to which the XCAS files must conform. * @param aTypesToDisplay * array of types that should be highlighted in the viewer. This can be set to the output * types of the Analysis Engine. A value of null means to display all types. */ /*public DBAnnotationViewerDialog(JFrame aParentFrame, String aDialogTitle, DBPrefsMediator med, File aStyleMapFile, String aPerformanceStats, TypeSystem aTypeSystem, final String[] aTypesToDisplay, String interactiveTempFN, boolean javaViewerRBisSelected, boolean javaViewerUCRBisSelected, boolean xmlRBisSelected, CAS cas) { super(aParentFrame, aDialogTitle); // create the AnnotationViewGenerator (for HTML view generation) this.med1 = med; this.cas = cas; annotationViewGenerator = new AnnotationViewGenerator(tempDir); launchThatViewer(med.getOutputDir(), interactiveTempFN, aTypeSystem, aTypesToDisplay, javaViewerRBisSelected, javaViewerUCRBisSelected, xmlRBisSelected, aStyleMapFile, tempDir); }*/ public DBAnnotationViewerDialog(JFrame aParentFrame, String aDialogTitle, DBPrefsMediator med, File aStyleMapFile, String aPerformanceStats, TypeSystem aTypeSystem, final String[] aTypesToDisplay, boolean generatedStyleMap, CAS cas) { super(aParentFrame, aDialogTitle); this.xmiDAO = med.getXmiDAO(); this.med1 = med; this.cas = cas; styleMapFile = aStyleMapFile; final String performanceStats = aPerformanceStats; typeSystem = aTypeSystem; typesToDisplay = aTypesToDisplay; // create the AnnotationViewGenerator (for HTML view generation) annotationViewGenerator = new AnnotationViewGenerator(tempDir); // create StyleMapEditor dialog styleMapEditor = new StyleMapEditor(aParentFrame, cas); JPanel resultsTitlePanel = new JPanel(); resultsTitlePanel.setLayout(new BoxLayout(resultsTitlePanel, BoxLayout.Y_AXIS)); resultsTitlePanel.add(new JLabel("These are the Analyzed Documents.")); resultsTitlePanel.add(new JLabel("Select viewer type and double-click file to open.")); try { String[] documents = this.xmiDAO.getXMIList(); analyzedResultsList = new JList(documents); JScrollPane scrollPane = new JScrollPane(); scrollPane.getViewport().add(analyzedResultsList, null); JPanel southernPanel = new JPanel(); southernPanel.setLayout(new BoxLayout(southernPanel, BoxLayout.Y_AXIS)); JPanel controlsPanel = new JPanel(); controlsPanel.setLayout(new SpringLayout()); Caption displayFormatLabel = new Caption("Results Display Format:"); controlsPanel.add(displayFormatLabel); JPanel displayFormatPanel = new JPanel(); displayFormatPanel.setLayout(new FlowLayout(FlowLayout.LEFT)); displayFormatPanel.setBorder(BorderFactory.createEmptyBorder(0, 0, 0, 0)); javaViewerRB = new JRadioButton("Java Viewer"); javaViewerUCRB = new JRadioButton("JV user colors"); htmlRB = new JRadioButton("HTML"); xmlRB = new JRadioButton("XML"); ButtonGroup displayFormatButtonGroup = new ButtonGroup(); displayFormatButtonGroup.add(javaViewerRB); displayFormatButtonGroup.add(javaViewerUCRB); displayFormatButtonGroup.add(htmlRB); displayFormatButtonGroup.add(xmlRB); // select the appropraite viewer button according to user's prefs javaViewerRB.setSelected(true); // default, overriden below if ("Java Viewer".equals(med.getViewType())) { javaViewerRB.setSelected(true); } else if ("JV User Colors".equals(med.getViewType())) { javaViewerUCRB.setSelected(true); } else if ("HTML".equals(med.getViewType())) { htmlRB.setSelected(true); } else if ("XML".equals(med.getViewType())) { xmlRB.setSelected(true); } displayFormatPanel.add(javaViewerRB); displayFormatPanel.add(javaViewerUCRB); displayFormatPanel.add(htmlRB); displayFormatPanel.add(xmlRB); controlsPanel.add(displayFormatPanel); SpringUtilities.makeCompactGrid(controlsPanel, 1, 2, // rows, cols 4, 4, // initX, initY 0, 0); // xPad, yPad JButton editStyleMapButton = new JButton("Edit Style Map"); // event for the editStyleMapButton button editStyleMapButton.addActionListener(this); southernPanel.add(controlsPanel); // southernPanel.add( new JSeparator() ); JPanel buttonsPanel = new JPanel(); buttonsPanel.setLayout(new FlowLayout(FlowLayout.RIGHT)); // APL: edit style map feature disabled for SDK buttonsPanel.add(editStyleMapButton); if (performanceStats != null) { JButton perfStatsButton = new JButton("Performance Stats"); perfStatsButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent ae) { JOptionPane.showMessageDialog((Component) ae.getSource(), performanceStats, null, JOptionPane.PLAIN_MESSAGE); } }); buttonsPanel.add(perfStatsButton); } JButton closeButton = new JButton("Close"); buttonsPanel.add(closeButton); southernPanel.add(buttonsPanel); // add list and panel container to Dialog getContentPane().add(resultsTitlePanel, BorderLayout.NORTH); getContentPane().add(scrollPane, BorderLayout.CENTER); getContentPane().add(southernPanel, BorderLayout.SOUTH); // event for the closeButton button closeButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent ae) { DBAnnotationViewerDialog.this.setVisible(false); } }); // event for analyzedResultsDialog window closing this.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); setLF(); // set default look and feel analyzedResultsList.setCellRenderer(new MyListCellRenderer()); // doubleclicking on document shows the annotated result MouseListener mouseListener = new ListMouseAdapter(); // styleMapFile, analyzedResultsList, // inputDirPath,typeSystem , typesToDisplay , // javaViewerRB , javaViewerUCRB ,xmlRB , // viewerDirectory , this); // add mouse Listener to the list analyzedResultsList.addMouseListener(mouseListener); } catch (DAOException e) { displayError(e.getMessage()); this.dispatchEvent(new WindowEvent(this, WindowEvent.WINDOW_CLOSING)); } } // unwound from small anonymous inner class public void actionPerformed(ActionEvent arg0) { // read style map XML file if it exists String styleMapXml = null; AnalysisEngineDescription selectedAE = null; try { if (styleMapFile.exists()) { styleMapXml = FileUtils.file2String(styleMapFile); } // have user select AE if they haven't done so already if (selectedAE == null) { selectedAE = promptForAE(); } if (selectedAE != null) { styleMapEditor.setAnalysisEngine(selectedAE); // launch StyleMapEditor GUI String newStyleMap = styleMapEditor.launchEditor(selectedAE.getAnalysisEngineMetaData(), styleMapXml, cas); if (newStyleMap != null) { // write new file using AE+StyleMap convention styleMapFile = med1.getStylemapFile(); // write new style map to disk FileWriter writer = new FileWriter(styleMapFile); writer.write(newStyleMap); writer.close(); // process generated style map annotationViewGenerator.processStyleMap(styleMapFile); } } } catch (Exception e) { displayError(e); } } /** * Filter to not show the two interactive-mode directories in the file list */ static class InteractiveFilter implements FilenameFilter { public boolean accept(File dir, String name) { if (name.equals("interactive_temp")) return false; if (name.equals("interactive_out")) return false; return true; } } /** * Gets the name of the CAS View that will be displayed first in * the annotation viewer. */ public String getDefaultCasViewName() { return defaultCasViewName; } /** * Sets the name of the CAS View that will be displayed first in * the annotation viewer. It not set, defaults to {@link CAS#NAME_DEFAULT_SOFA}. */ public void setDefaultCasViewName(String defaultCasViewName) { this.defaultCasViewName = defaultCasViewName; } // Common code to launch viewer for both the Run (file-based) and // Interactive modes // JMP public void launchThatViewer(String xmi_id, TypeSystem typeSystem, final String[] aTypesToDisplay, boolean javaViewerRBisSelected, boolean javaViewerUCRBisSelected, boolean xmlRBisSelected, File styleMapFile, File viewerDirectory) { try { InputStream xmiDocument = this.xmiDAO.getXMI(xmi_id); // create a new CAS CAS cas = CasCreationUtils.createCas(Collections.EMPTY_LIST, typeSystem, UIMAFramework.getDefaultPerformanceTuningProperties()); if (this.med1.isUmcompress()) { //Descomprime el XMI //Create the decompressor and give it the data to compress Inflater decompressor = new Inflater(); byte[] documentDataByteArray = IOUtils.toByteArray(xmiDocument); decompressor.setInput(documentDataByteArray); //Create an expandable byte array to hold the decompressed data ByteArrayOutputStream bos = new ByteArrayOutputStream(documentDataByteArray.length); //Decompress the data byte[] buf = new byte[1024]; while (!decompressor.finished()) { int count = decompressor.inflate(buf); bos.write(buf, 0, count); } bos.close(); //Get the decompressed data byte[] decompressedData = bos.toByteArray(); XmiCasDeserializer.deserialize(new ByteArrayInputStream(decompressedData), cas, true); } else { XmlCasDeserializer.deserialize(xmiDocument, cas, true); } //get the specified view cas = cas.getView(this.defaultCasViewName); //launch appropriate viewer if (javaViewerRBisSelected || javaViewerUCRBisSelected) { // JMP // record preference for next time med1.setViewType(javaViewerRBisSelected ? "Java Viewer" : "JV User Colors"); //create tree viewer component CasAnnotationViewer viewer = new CasAnnotationViewer(); viewer.setDisplayedTypes(aTypesToDisplay); if (javaViewerUCRBisSelected) getColorsForTypesFromFile(viewer, styleMapFile); else viewer.setHiddenTypes(new String[] { "uima.cpm.FileLocation" }); // launch viewer in a new dialog viewer.setCAS(cas); JDialog dialog = new JDialog(DBAnnotationViewerDialog.this, "Annotation Results for " + xmi_id + " in " + inputDirPath); // JMP dialog.getContentPane().add(viewer); dialog.setSize(850, 630); dialog.pack(); dialog.show(); } else { CAS defaultView = cas.getView(CAS.NAME_DEFAULT_SOFA); if (defaultView.getDocumentText() == null) { displayError( "The HTML and XML Viewers can only view the default text document, which was not found in this CAS."); return; } // generate inline XML File inlineXmlFile = new File(viewerDirectory, "inline.xml"); String xmlAnnotations = new CasToInlineXml().generateXML(defaultView); FileOutputStream outStream = new FileOutputStream(inlineXmlFile); outStream.write(xmlAnnotations.getBytes("UTF-8")); outStream.close(); if (xmlRBisSelected) // JMP passed in { // record preference for next time med1.setViewType("XML"); BrowserUtil.openUrlInDefaultBrowser(inlineXmlFile.getAbsolutePath()); } else // HTML view { med1.setViewType("HTML"); // generate HTML view // first process style map if not done already if (!processedStyleMap) { if (!styleMapFile.exists()) { annotationViewGenerator.autoGenerateStyleMapFile( promptForAE().getAnalysisEngineMetaData(), styleMapFile); } annotationViewGenerator.processStyleMap(styleMapFile); processedStyleMap = true; } annotationViewGenerator.processDocument(inlineXmlFile); File genFile = new File(viewerDirectory, "index.html"); // open in browser BrowserUtil.openUrlInDefaultBrowser(genFile.getAbsolutePath()); } } // end LTV here } catch (Exception ex) { displayError(ex); } } /** * Assumes node has a text field and extracts its value. JMP */ static public String getTextValue(Node node) { Node first = node.getFirstChild(); if (first != null) { Text text = (Text) node.getFirstChild(); return text.getNodeValue().trim(); } else return null; } /** * Gets the first child with a given name. JMP */ static public Node getFirstChildByName(Node node, String name) { NodeList children = node.getChildNodes(); for (int c = 0; c < children.getLength(); ++c) { Node n = children.item(c); if (n.getNodeName().equals(name)) return n; } return null; } /** * Reads in annotation-color associations from stylemap file. JMP Also reads checked value if * present. */ public void getColorsForTypesFromFile(CasAnnotationViewer viewer, File aStyleMapFile) { List colorList = new ArrayList(); ArrayList typeList = new ArrayList(); ArrayList notCheckedList = new ArrayList(); ArrayList hiddenList = new ArrayList(); hiddenList.add("uima.cpm.FileLocation"); if (aStyleMapFile.exists()) { FileInputStream stream = null; Document parse = null; try { stream = new FileInputStream(aStyleMapFile); DocumentBuilder db = DocumentBuilderFactory.newInstance().newDocumentBuilder(); parse = db.parse(stream); } catch (FileNotFoundException e) { throw new UIMARuntimeException(e); } catch (ParserConfigurationException e) { throw new UIMARuntimeException(e); } catch (FactoryConfigurationError e) { throw new UIMARuntimeException(e); } catch (SAXException e) { throw new UIMARuntimeException(e); } catch (IOException e) { throw new UIMARuntimeException(e); } Node node0 = parse.getDocumentElement(); // Node node1 = getFirstChildByName(parse.getDocumentElement(), // "styleMap"); // String node1Name = node1.getNodeName(); NodeList nodeList = node0.getChildNodes(); ColorParser cParser = new ColorParser(); for (int i = 0; i < nodeList.getLength(); i++) { Node node = nodeList.item(i); String nodeName = node.getNodeName(); if (nodeName.equals("rule")) { NodeList childrenList = node.getChildNodes(); String type = ""; String label = ""; StyleMapEntry sme = null; String colorText = ""; for (int j = 0; j < childrenList.getLength(); j++) { Node child = childrenList.item(j); String childName = child.getNodeName(); if (childName.equals("pattern")) { type = getTextValue(child); } if (childName.equals("label")) { label = getTextValue(child); } if (childName.equals("style")) { colorText = getTextValue(child); } } sme = cParser.parseAndAssignColors(type, label, label, colorText); if (!sme.getChecked()) { notCheckedList.add(sme.getAnnotationTypeName()); } if (!sme.getHidden()) { colorList.add(sme.getBackground()); typeList.add(sme.getAnnotationTypeName()); } else { hiddenList.add(sme.getAnnotationTypeName()); } } } if (stream != null) try { stream.close(); } catch (IOException e) { e.printStackTrace(); } viewer.assignColorsFromList(colorList, typeList); viewer.assignCheckedFromList(notCheckedList); String[] hiddenArr = new String[hiddenList.size()]; hiddenList.toArray(hiddenArr); viewer.setHiddenTypes(hiddenArr); } } /** * Displays an error message to the user. * * @param aErrorString * error message to display */ public void displayError(String aErrorString) { // word-wrap long mesages StringBuffer buf = new StringBuffer(aErrorString.length()); final int CHARS_PER_LINE = 80; int charCount = 0; StringTokenizer tokenizer = new StringTokenizer(aErrorString, " \n", true); while (tokenizer.hasMoreTokens()) { String tok = tokenizer.nextToken(); if (tok.equals("\n")) { buf.append("\n"); charCount = 0; } else if ((charCount > 0) && ((charCount + tok.length()) > CHARS_PER_LINE)) { buf.append("\n").append(tok); charCount = tok.length(); } else { buf.append(tok); charCount += tok.length(); } } JOptionPane.showMessageDialog(DBAnnotationViewerDialog.this, buf.toString(), "Error", JOptionPane.ERROR_MESSAGE); } /** * Displays an error message to the user. * * @param aThrowable * Throwable whose message is to be displayed. */ public void displayError(Throwable aThrowable) { aThrowable.printStackTrace(); String message = aThrowable.toString(); // For UIMAExceptions or UIMARuntimeExceptions, add cause info. // We have to go through this nonsense to support Java 1.3. // In 1.4 all exceptions can have a cause, so this wouldn't involve // all of this typecasting. while ((aThrowable instanceof UIMAException) || (aThrowable instanceof UIMARuntimeException)) { if (aThrowable instanceof UIMAException) { aThrowable = ((UIMAException) aThrowable).getCause(); } else if (aThrowable instanceof UIMARuntimeException) { aThrowable = ((UIMARuntimeException) aThrowable).getCause(); } if (aThrowable != null) { message += ("\nCausedBy: " + aThrowable.toString()); } } displayError(message); } /** * If the current AE filename is not know ask for it. Then parse the selected file and return the * AnalysisEngineDescription object. * * @return the selected AnalysisEngineDescription, null if the user cancelled */ protected AnalysisEngineDescription promptForAE() throws IOException, InvalidXMLException, ResourceInitializationException { if (med1.getTAEfile() != null) { File taeFile = new File(med1.getTAEfile()); XMLInputSource in = new XMLInputSource(taeFile); AnalysisEngineDescription aed = UIMAFramework.getXMLParser().parseAnalysisEngineDescription(in); return aed; } else { String taeDir = med1.getTAEfile(); JFileChooser chooser = new JFileChooser(taeDir); chooser.setDialogTitle("Select the Analysis Engine that Generated this Output"); chooser.setFileSelectionMode(JFileChooser.FILES_ONLY); int returnVal = chooser.showOpenDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { XMLInputSource in = new XMLInputSource(chooser.getSelectedFile()); return UIMAFramework.getXMLParser().parseAnalysisEngineDescription(in); } else { return null; } } } /** set default look and feel */ private static void setLF() { // Force SwingApp to come up in the System L&F String laf = UIManager.getSystemLookAndFeelClassName(); try { UIManager.setLookAndFeel(laf); } catch (UnsupportedLookAndFeelException exc) { System.err.println("Warning: UnsupportedLookAndFeel: " + laf); } catch (Exception exc) { System.err.println("Error loading " + laf + ": " + exc); } } private File createTempDir() { File temp = new File(System.getProperty("java.io.tmpdir"), System.getProperty("user.name")); temp.mkdir(); return temp; } // create and call the list cell renderer to set the selected color and // image icon static class MyListCellRenderer extends JLabel implements ListCellRenderer { private static final long serialVersionUID = 7231915634689270693L; public MyListCellRenderer() { setOpaque(true); } public Component getListCellRendererComponent(JList analyzedResultsList, Object value, int index, boolean isSelected, boolean cellHasFocus) { ImageIcon xmlIcon = Images.getImageIcon(Images.XML_DOC); setIcon(xmlIcon); setText(value.toString()); setBackground(isSelected ? Color.orange : Color.white); setForeground(isSelected ? Color.black : Color.black); return this; } } class ListMouseAdapter extends MouseAdapter { public void mouseClicked(MouseEvent e) { try { if (e.getClickCount() == 2) { String xmi_id = ((String) analyzedResultsList.getSelectedValue()); if (xmi_id != null) { analyzedResultsList.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); // Start LTV here launchThatViewer(xmi_id, typeSystem, typesToDisplay, javaViewerRB.isSelected(), javaViewerUCRB.isSelected(), xmlRB.isSelected(), styleMapFile, tempDir); analyzedResultsList.setCursor(Cursor.getDefaultCursor()); } } } catch (Exception ex) { displayError(ex); } } } }