org.apache.ctakes.ytex.tools.DBAnnotationViewerMain Maven / Gradle / Ivy
/**
* 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.
*/
package org.apache.ctakes.ytex.tools;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Container;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.io.BufferedInputStream;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.io.PrintWriter;
import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Properties;
import java.util.StringTokenizer;
import java.util.prefs.Preferences;
import java.util.zip.GZIPInputStream;
import javax.imageio.ImageIO;
import javax.swing.BorderFactory;
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.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
import javax.swing.JTextField;
import javax.swing.SpringLayout;
import javax.swing.UIManager;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.FactoryConfigurationError;
import javax.xml.parsers.ParserConfigurationException;
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.internal.util.BrowserUtil;
import org.apache.uima.resource.ResourceInitializationException;
import org.apache.uima.resource.metadata.FsIndexDescription;
import org.apache.uima.resource.metadata.TypeSystemDescription;
import org.apache.uima.tools.docanalyzer.AnnotationViewerDialog;
import org.apache.uima.tools.docanalyzer.PrefsMediator;
import org.apache.uima.tools.images.Images;
import org.apache.uima.tools.stylemap.ColorParser;
import org.apache.uima.tools.stylemap.StyleMapEntry;
import org.apache.uima.tools.util.gui.AboutDialog;
import org.apache.uima.tools.util.gui.Caption;
import org.apache.uima.tools.util.gui.FileSelector;
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.InvalidXMLException;
import org.apache.uima.util.XMLInputSource;
import org.apache.uima.util.XmlCasDeserializer;
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;
/**
* Main Annotation Viewer GUI. Allows user to choose directory of XCAS or XMI
* files, then launches the AnnotationViewerDialog.
*
* copied from AnnotationViewerMain. Modified to load CAS from database.
*/
public class DBAnnotationViewerMain extends JFrame {
private static final long serialVersionUID = -3201723535833938833L;
/**
* the descriptor file. Save this so that we can initialaze the
* casDescriptor just 1x. When view is pressed, we see if this has changed;
* if yes, then we reinitialize
*/
private String strDescriptorFile = null;
/**
* cas loaded from strDescriptorFile
*/
private CAS casDescriptor = null;
/**
* properties loaded from ytex.properties file
*/
private Properties jdbcProperties = null;
/**
* style map initialized with descriptor
*/
File styleMapFile;
// copied from AnnotationViewerDialog
protected AnnotationViewGenerator annotationViewGenerator = new AnnotationViewGenerator(
this.createTempDir());
private String defaultCasViewName = CAS.NAME_DEFAULT_SOFA;
private PrefsMediator prefsMed;
private boolean processedStyleMap = false;
JRadioButton javaViewerRB = null;
JRadioButton javaViewerUCRB = null;
JRadioButton htmlRB = null;
JRadioButton xmlRB = null;
// new
JTextField documentIDField = null;
private static final String HELP_MESSAGE = "Instructions for using Annotation Viewer:\n\n"
+ "1) In the \"TypeSystem or AE Descriptor File\" field, either type or use the browse\n"
+ "button to select the TypeSystem or AE descriptor for the AE that generated the\n"
+ "XMI or XCAS files. (This is needed for type system infornation only.\n"
+ "Analysis will not be redone.)\n\n"
+ "2) Specify a Document ID.\n\n"
+ "3) Click the \"View\" button at the buttom of the window.\n\n"
+ "4) Select the view type -- either the Java annotation viewer, HTML,\n"
+ "or XML. The Java annotation viewer is recommended.\n\n";
private File uimaHomeDir;
// private FileSelector jdbcPropertiesFileSelector;
private FileSelector taeDescriptorFileSelector;
private JButton viewButton;
private JDialog aboutDialog;
/** Stores user preferences */
private Preferences prefs = Preferences.userRoot().node(
"ytex/tools/DBAnnotationViewer");
/**
* Constructor. Sets up the GUI.
*/
public DBAnnotationViewerMain() {
super("Annotation Viewer");
// set UIMA home dir
uimaHomeDir = new File(System.getProperty("uima.home",
"C:/Program Files/apache-uima"));
try {
UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
} catch (Exception e) {
// I don't think this should ever happen, but if it does just print
// error and continue
// with defalt look and feel
System.err
.println("Could not set look and feel: " + e.getMessage());
}
// UIManager.put("Panel.background",Color.WHITE);
// Need to set other colors as well
// Set frame icon image
try {
this.setIconImage(Images.getImage(Images.MICROSCOPE));
} catch (IOException e) {
System.err.println("Image could not be loaded: " + e.getMessage());
}
this.getContentPane().setBackground(Color.WHITE);
// create about dialog
aboutDialog = new AboutDialog(this, "About Annotation Viewer");
// Create Menu Bar
JMenuBar menuBar = new JMenuBar();
setJMenuBar(menuBar);
JMenu fileMenu = new JMenu("File");
JMenu helpMenu = new JMenu("Help");
// Menu Items
JMenuItem aboutMenuItem = new JMenuItem("About");
JMenuItem helpMenuItem = new JMenuItem("Help");
JMenuItem exitMenuItem = new JMenuItem("Exit");
fileMenu.add(exitMenuItem);
helpMenu.add(aboutMenuItem);
helpMenu.add(helpMenuItem);
menuBar.add(fileMenu);
menuBar.add(helpMenu);
// Labels to identify the text fields
// final Caption labelJdbcProps = new Caption("JDBC Properties File: ");
final Caption labelStyleMapFile = new Caption(
"TypeSystem or AE Descriptor File: ");
JPanel controlPanel = new JPanel();
controlPanel.setBorder(BorderFactory.createEmptyBorder(4, 4, 4, 4));
controlPanel.setLayout(new SpringLayout());
// Once we add components to controlPanel, we'll
// call SpringUtilities::makeCompactGrid on it.
// controlPanel.setLayout(new GridLayout(4, 2, 8, 4));
// // Set default values for input fields
taeDescriptorFileSelector = new FileSelector("", "TAE Descriptor File",
JFileChooser.FILES_ONLY, uimaHomeDir);
File descriptorFile = new File(uimaHomeDir,
"examples/descriptors/analysis_engine/PersonTitleAnnotator.xml");
taeDescriptorFileSelector.setSelected(descriptorFile.getAbsolutePath());
Caption labelDocumentID = new Caption("Document ID:");
this.documentIDField = new JTextField();
controlPanel.add(labelStyleMapFile);
controlPanel.add(taeDescriptorFileSelector);
controlPanel.add(labelDocumentID);
controlPanel.add(documentIDField);
// ------ copied here
Caption displayFormatLabel = new Caption("Results Display Format:");
controlPanel.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
displayFormatPanel.add(javaViewerRB);
displayFormatPanel.add(javaViewerUCRB);
displayFormatPanel.add(htmlRB);
displayFormatPanel.add(xmlRB);
controlPanel.add(displayFormatPanel);
// ------ END copied here
SpringUtilities.makeCompactGrid(controlPanel, 3, 2, // rows, cols
4, 4, // initX, initY
4, 4); // xPad, yPad
// Event Handlling of "Exit" Menu Item
exitMenuItem.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent ae) {
savePreferences();
System.exit(0);
}
});
// Event Handlling of "About" Menu Item
aboutMenuItem.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent ae) {
aboutDialog.setVisible(true);
}
});
// Event Handlling of "Help" Menu Item
helpMenuItem.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent ae) {
JOptionPane.showMessageDialog(DBAnnotationViewerMain.this,
HELP_MESSAGE, "Annotation Viewer Help",
JOptionPane.PLAIN_MESSAGE);
}
});
// Add the panels to the frame
Container contentPanel = getContentPane();
contentPanel.add(controlPanel, BorderLayout.CENTER);
// add banner
JLabel banner = new JLabel(new ImageIcon(this.getClass().getResource(
"/org/apache/ctakes/ctakes_logo.jpg")));
contentPanel.add(banner, BorderLayout.NORTH);
// Add the view Button to run TAE
viewButton = new JButton("View");
// Add the view button to another panel
JPanel lowerButtonsPanel = new JPanel();
lowerButtonsPanel.add(viewButton);
contentPanel.add(lowerButtonsPanel, BorderLayout.SOUTH);
setContentPane(contentPanel);
// Event Handling of view Button
viewButton.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent ee) {
try {
viewDocuments();
} catch (Exception e) {
displayError(e);
}
}
});
// load user preferences
if (System.getProperty("uima.noprefs") == null) {
restorePreferences();
}
}
public void viewDocuments() throws InvalidXMLException, IOException,
ResourceInitializationException {
String newDescriptorFile = taeDescriptorFileSelector.getSelected();
if (!newDescriptorFile.equals(this.strDescriptorFile)) {
// reset instance variables
this.strDescriptorFile = null;
this.casDescriptor = null;
this.styleMapFile = null;
File descriptorFile = new File(newDescriptorFile);
if (!descriptorFile.exists() || descriptorFile.isDirectory()) {
displayError("Descriptor File \"" + descriptorFile.getPath()
+ "\" does not exist.");
return;
}
// File inputDir = new File(inputFileSelector.getSelected());
// if (!inputDir.exists() || !inputDir.isDirectory()) {
// displayError("Input Directory \"" + inputDir.getPath() +
// "\" does not exist.");
// return;
// }
// parse descriptor. Could be either AE or TypeSystem descriptor
Object descriptor = UIMAFramework.getXMLParser().parse(
new XMLInputSource(descriptorFile));
// instantiate CAS to get type system. Also build style map file if
// there is none.
if (descriptor instanceof AnalysisEngineDescription) {
casDescriptor = CasCreationUtils
.createCas((AnalysisEngineDescription) descriptor);
styleMapFile = getStyleMapFile(
(AnalysisEngineDescription) descriptor,
descriptorFile.getPath());
} else if (descriptor instanceof TypeSystemDescription) {
TypeSystemDescription tsDesc = (TypeSystemDescription) descriptor;
tsDesc.resolveImports();
casDescriptor = CasCreationUtils.createCas(tsDesc, null,
new FsIndexDescription[0]);
styleMapFile = getStyleMapFile(
(TypeSystemDescription) descriptor,
descriptorFile.getPath());
} else {
displayError("Invalid Descriptor File \""
+ descriptorFile.getPath()
+ "\""
+ "Must be either an AnalysisEngine or TypeSystem descriptor.");
return;
}
// everything ok - save the desc file name
this.strDescriptorFile = newDescriptorFile;
}
// create Annotation Viewer Main Panel
prefsMed = new PrefsMediator();
// set OUTPUT dir in PrefsMediator, not input dir.
// PrefsMediator is also used in DocumentAnalyzer, where the
// output dir is the directory containing XCAS files.
// prefsMed.setOutputDir(inputDir.toString());
prefsMed.setOutputDir(System.getProperty("user.home"));
/*
* DBAnnotationViewerDialog viewerDialog = new
* DBAnnotationViewerDialog(this, "Analyzed Documents", prefsMed,
* styleMapFile, null, cas.getTypeSystem(), null, false, cas);
* viewerDialog.pack(); viewerDialog.setModal(true);
* viewerDialog.setVisible(true);
*/
this.launchThatViewer(this.documentIDField.getText(),
casDescriptor.getTypeSystem(), null, javaViewerRB.isSelected(),
javaViewerUCRB.isSelected(), xmlRB.isSelected(), styleMapFile,
createTempDir());
}
/**
* @param tae
* // *
* @param taeDescFileName
* @return
* @throws IOException
*/
private File getStyleMapFile(AnalysisEngineDescription tad,
String descFileName) throws IOException {
File styleMapFile = getStyleMapFileName(descFileName);
if (!styleMapFile.exists()) {
// generate default style map
String xml = AnnotationViewGenerator.autoGenerateStyleMap(tad
.getAnalysisEngineMetaData());
PrintWriter writer;
writer = new PrintWriter(new BufferedWriter(new FileWriter(
styleMapFile)));
writer.println(xml);
writer.close();
}
return styleMapFile;
}
/**
* @param tae
* // *
* @param taeDescFileName
* @return
* @throws IOException
*/
private File getStyleMapFile(TypeSystemDescription tsd, String descFileName)
throws IOException {
File styleMapFile = getStyleMapFileName(descFileName);
if (!styleMapFile.exists()) {
// generate default style map
String xml = AnnotationViewGenerator.autoGenerateStyleMap(tsd);
PrintWriter writer;
writer = new PrintWriter(new BufferedWriter(new FileWriter(
styleMapFile)));
writer.println(xml);
writer.close();
}
return styleMapFile;
}
/**
* Gets the name of the style map file for the given AE or TypeSystem
* descriptor filename.
*/
public File getStyleMapFileName(String aDescriptorFileName) {
String baseName;
int index = aDescriptorFileName.lastIndexOf(".");
if (index > 0) {
baseName = aDescriptorFileName.substring(0, index);
} else {
baseName = aDescriptorFileName;
}
return new File(baseName + "StyleMap.xml");
}
public static void main(String[] args) {
final DBAnnotationViewerMain frame = new DBAnnotationViewerMain();
frame.addWindowListener(new WindowAdapter() {
public void windowClosing(WindowEvent e) {
frame.savePreferences();
System.exit(0);
}
});
frame.pack();
frame.setVisible(true);
}
/**
* Save user's preferences using Java's Preference API.
*/
public void savePreferences() {
// prefs.put("inDir", inputFileSelector.getSelected());
prefs.put("taeDescriptorFile",
this.taeDescriptorFileSelector.getSelected());
}
/**
* Reset GUI to preferences last saved via {@link #savePreferences}.
*/
public void restorePreferences() {
// figure defaults
File defaultTaeDescriptorFile = new File(uimaHomeDir,
"examples/descriptors/analysis_engine/PersonTitleAnnotator.xml");
// restore preferences
this.taeDescriptorFileSelector.setSelected(prefs.get(
"taeDescriptorFile", defaultTaeDescriptorFile.toString()));
}
/**
* 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(DBAnnotationViewerMain.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);
}
/*
* (non-Javadoc)
*
* @see java.awt.Component#getPreferredSize()
*/
public Dimension getPreferredSize() {
return new Dimension(640, 270);
}
/**
* copied from AnnotationViewerDialog. Modified to load document from db.
*
* @see AnnotationViewerDialog
*/
public void launchThatViewer(String documentID, TypeSystem typeSystem,
final String[] aTypesToDisplay, boolean javaViewerRBisSelected,
boolean javaViewerUCRBisSelected, boolean xmlRBisSelected,
File styleMapFile, File viewerDirectory) {
try {
CAS cas = this.loadDocumentCas(documentID, typeSystem);
// get the specified view
cas = cas.getView(this.defaultCasViewName);
// launch appropriate viewer
if (javaViewerRBisSelected || javaViewerUCRBisSelected) { // JMP
// record preference for next time
prefsMed.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(this,
"Annotation Results for Document ID " + documentID); // 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
prefsMed.setViewType("XML");
BrowserUtil.openUrlInDefaultBrowser(inlineXmlFile
.getAbsolutePath());
} else
// HTML view
{
prefsMed.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);
}
}
/**
* copied from AnnotationViewerDialog.
*
* If the current AE filename is not know ask for it. Then parse the
* selected file and return the AnalysisEngineDescription object.
*
* @see AnnotationViewerDialog
* @return the selected AnalysisEngineDescription, null if the user
* cancelled
*/
protected AnalysisEngineDescription promptForAE() throws IOException,
InvalidXMLException, ResourceInitializationException {
if (prefsMed.getTAEfile() != null) {
File taeFile = new File(prefsMed.getTAEfile());
XMLInputSource in = new XMLInputSource(taeFile);
AnalysisEngineDescription aed = UIMAFramework.getXMLParser()
.parseAnalysisEngineDescription(in);
return aed;
} else {
String taeDir = prefsMed.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;
}
}
}
/**
* copied from AnnotationViewerDialog.
*/
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);
}
}
/**
* copied from AnnotationViewerDialog.
*/
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;
}
private Properties loadJDBCProperties() throws IOException {
InputStream is = null;
try {
is = this.getClass().getResourceAsStream(
"/org/apache/ctakes/ytex/ytex.properties");
this.jdbcProperties = new Properties();
this.jdbcProperties.load(is);
// make sure required properties are specified
if (!jdbcProperties.containsKey("db.url")
|| !jdbcProperties.containsKey("db.driver")) {
// null out properties
this.jdbcProperties = null;
throw new IOException(
"Error: required jdbc properties (db.url / db.driver) not specified");
}
// set jdbcproperties file name to avoid reloading, return
// properties
return jdbcProperties;
} finally {
if (is != null) {
try {
is.close();
} catch (Exception ignore) {
}
}
}
}
/**
* load document from db
*/
private CAS loadDocumentCas(String documentID, TypeSystem typeSystem)
throws SQLException, IOException, SAXException,
ResourceInitializationException, ClassNotFoundException {
Connection conn = null;
PreparedStatement ps = null;
ResultSet rs = null;
GZIPInputStream gzIS = null;
Properties jdbcProperties = loadJDBCProperties();
CAS cas = CasCreationUtils.createCas(Collections.EMPTY_LIST,
typeSystem,
UIMAFramework.getDefaultPerformanceTuningProperties());
try {
Class.forName(jdbcProperties.getProperty("db.driver"));
conn = DriverManager.getConnection(
jdbcProperties.getProperty("db.url"),
jdbcProperties.containsKey("db.username") ? jdbcProperties
.getProperty("db.username") : null,
jdbcProperties.containsKey("db.password") ? jdbcProperties
.getProperty("db.password") : null);
String strSQL = jdbcProperties.containsKey("db.schema") ? "select cas from "
+ jdbcProperties.getProperty("db.schema")
+ ".document where document_id = ?"
: "select cas from document where document_id = ?";
ps = conn.prepareStatement(strSQL);
ps.setInt(1, Integer.parseInt(documentID));
rs = ps.executeQuery();
if (rs.next()) {
gzIS = new GZIPInputStream(new BufferedInputStream(
rs.getBinaryStream(1)));
XmlCasDeserializer.deserialize(gzIS, cas, true);
} else {
throw new RuntimeException("No document with id = "
+ documentID);
}
} finally {
try {
if (rs != null)
rs.close();
} catch (SQLException e) {
}
try {
if (ps != null)
ps.close();
} catch (SQLException e) {
}
try {
if (conn != null)
conn.close();
} catch (SQLException e) {
}
try {
if (gzIS != null)
gzIS.close();
} catch (IOException e) {
}
}
return cas;
}
/**
* copied from AnnotationViewerDialog.
*/
private File createTempDir() {
File temp = new File(System.getProperty("java.io.tmpdir"),
System.getProperty("user.name"));
temp.mkdir();
return temp;
}
}
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