/**
* Generates handles response. This is were we would pass stuff to cli or gui, etc
*
* @param n the processed policy object
* @return the policyObjected as accepted by user (potentially modified
*/
public PolicyObject userResponse(PolicyObject n) {
if ((parseAct(genProps.getProperty("userResponse", null)) == null)
&& !Boolean.parseBoolean(genProps.getProperty("blanketAccept", "false"))) {
return userInterface.userResponse(n);
} else {
if (Boolean.parseBoolean(genProps.getProperty("blanketAccept", "false"))) {
return n.setAction(n.getAction().setOverride(true));
} else {
return n.setAction(parseAct(genProps.getProperty("userResponse", null)));
}
}
}
private static Map<String, String> nodeAllocationToMap(AssociationEntry entry) {
final HashMap<String, String> map = new HashMap(8);
map.put(FIELD_HOSTNAME, entry.getHostname());
map.put(FIELD_IP, entry.getIpAddress());
map.put(FIELD_MAC, entry.getMac());
map.put(FIELD_BROADCAST, entry.getBroadcast());
map.put(FIELD_SUBNET_MASK, entry.getSubnetMask());
map.put(FIELD_GATEWAY, entry.getGateway());
map.put(FIELD_IN_USE, Boolean.toString(entry.isInUse()));
map.put(FIELD_EXPLICIT_MAC, Boolean.toString(entry.isExplicitMac()));
return map;
}
/**
* A constructor permitting a user interface class to launch everything and be in control.
*
* @param args any commandline arguements
* @param ui the known UserIO object
* @throws Exception Mostly from loadWeights, but should also happen for loadFromConfig
*/
public Gio(String[] args, UserIO ui) throws Exception {
userInterface = ui;
genProps = loadFromConfig("./PrivacyAdviser.cfg");
loadCLO(args);
// TODO add method to check validity of genProps (after each file load, clo load, and ui load).
if ((genProps.getProperty("genConfig") != null)
&& (genProps.getProperty("genConfig") != "./PrivacyAdvisor.cfg")) {
System.err.println("clo config call");
genProps = loadFromConfig(genProps.getProperty("genConfig")); // TODO merge, not override
loadCLO(args);
}
// start the logger
logger =
startLogger(
genProps.getProperty("loglocation", "./LOG.txt"),
genProps.getProperty("loglevel", "INFO"));
if (userInterface == null) {
selectUI(genProps.getProperty("userIO"));
}
selectPDB(genProps.getProperty("policyDB"));
// load the weights configuration file
origWeights = new Properties();
origWeights = loadWeights();
if (Boolean.parseBoolean(genProps.getProperty("useNet", "false"))) {
startNetwork();
} else {
nr = null;
}
}
/**
* Loads the case history into cache. This is where the background database chosen.
*
* @param dLoc the location of the database
*/
public void loadDB() {
try {
// TODO what about if we want to create a new db?
if (!Boolean.parseBoolean(genProps.getProperty("newDB"))) {
pdb.loadDB();
}
} catch (Exception e) {
System.err.println("Something wrong with loading DB");
}
try {
loadCLPolicies();
} catch (Exception e) {
System.err.println("Error. Probably wrong path to P3P folder");
}
}
private static Params parse(String[] args) {
Options options = generateCommandlineOptions();
CommandLineParser parser = new PosixParser();
Params params = new Params();
try {
CommandLine cmd = parser.parse(options, args);
String value;
if (cmd.hasOption("input")) {
params.input = cmd.getOptionValue("input");
}
if (cmd.hasOption("maxIter")) {
value = cmd.getOptionValue("maxIter");
params.maxIter = Integer.parseInt(value);
}
if (cmd.hasOption("tol")) {
value = cmd.getOptionValue("tol");
params.tol = Double.parseDouble(value);
}
if (cmd.hasOption("fitIntercept")) {
value = cmd.getOptionValue("fitIntercept");
params.fitIntercept = Boolean.parseBoolean(value);
}
if (cmd.hasOption("regParam")) {
value = cmd.getOptionValue("regParam");
params.regParam = Double.parseDouble(value);
}
if (cmd.hasOption("elasticNetParam")) {
value = cmd.getOptionValue("elasticNetParam");
params.elasticNetParam = Double.parseDouble(value);
}
if (cmd.hasOption("testInput")) {
value = cmd.getOptionValue("testInput");
params.testInput = value;
}
if (cmd.hasOption("fracTest")) {
value = cmd.getOptionValue("fracTest");
params.fracTest = Double.parseDouble(value);
}
} catch (ParseException e) {
printHelpAndQuit(options);
}
return params;
}
public static void main(String args[])
throws ConfigurationException, IOException, WikiBrainException, DaoException {
Options options = new Options();
// Number of Max Results(otherwise take from config)
options.addOption(
new DefaultOptionBuilder()
.hasArg()
.withLongOpt("max-results")
.withDescription("maximum number of results")
.create("r"));
// Specify the Datasets
options.addOption(
new DefaultOptionBuilder()
.hasArgs()
.withLongOpt("gold")
.withDescription("the set of gold standard datasets to train on")
.create("g"));
// Delete existing data models
options.addOption(
new DefaultOptionBuilder()
.hasArg()
.withLongOpt("delete")
.withDescription(
"delete all existing SR data for the metric and its submetrics (true or false, default is true)")
.create("d"));
// Specify the Metrics
options.addOption(
new DefaultOptionBuilder()
.hasArg()
.withLongOpt("metric")
.withDescription("set a local metric")
.create("m"));
// Row and column ids for most similar caches
options.addOption(
new DefaultOptionBuilder()
.hasArg()
.withLongOpt("rowids")
.withDescription("page ids for rows of cosimilarity matrices (implies -s)")
.create("p"));
options.addOption(
new DefaultOptionBuilder()
.hasArg()
.withLongOpt("colids")
.withDescription("page ids for columns of cosimilarity matrices (implies -s)")
.create("q"));
// build the cosimilarity matrix
options.addOption(
new DefaultOptionBuilder()
.withLongOpt("cosimilarity")
.withDescription("build cosimilarity matrices")
.create("s"));
// sets the mode
options.addOption(
new DefaultOptionBuilder()
.withLongOpt("mode")
.hasArg()
.withDescription("mode: similarity, mostsimilar, or both")
.create("o"));
// add option for valid most similar ids
options.addOption(
new DefaultOptionBuilder()
.withLongOpt("validMostSimilarIds")
.withDescription("Set valid most similar ids")
.create("y"));
// when building pairwise cosine and ensembles, don't rebuild already built sub-metrics.
options.addOption(
new DefaultOptionBuilder()
.withLongOpt("skip-built")
.withDescription("Don't rebuild already built bmetrics (implies -d false)")
.create("k"));
// when building pairwise cosine and ensembles, don't rebuild already built sub-metrics.
options.addOption(
new DefaultOptionBuilder()
.withLongOpt("fake")
.withDescription("Create a fake gold standard for the language.")
.create("f"));
EnvBuilder.addStandardOptions(options);
CommandLineParser parser = new PosixParser();
CommandLine cmd;
try {
cmd = parser.parse(options, args);
} catch (ParseException e) {
System.err.println("Invalid option usage: " + e.getMessage());
new HelpFormatter().printHelp("SRBuilder", options);
return;
}
Env env = new EnvBuilder(cmd).build();
String metric = cmd.hasOption("m") ? cmd.getOptionValue("m") : null;
SRBuilder builder = new SRBuilder(env, metric);
if (cmd.hasOption("g")) {
builder.setDatasetNames(Arrays.asList(cmd.getOptionValues("g")));
}
if (cmd.hasOption("p")) {
builder.setRowIdsFromFile(cmd.getOptionValue("p"));
builder.setBuildCosimilarity(true);
}
if (cmd.hasOption("q")) {
builder.setColIdsFromFile(cmd.getOptionValue("q"));
builder.setBuildCosimilarity(true);
}
if (cmd.hasOption("y")) {
builder.setValidMostSimilarIdsFromFile(cmd.getOptionValue("y"));
}
if (cmd.hasOption("s")) {
builder.setBuildCosimilarity(true);
}
if (cmd.hasOption("k")) {
builder.setSkipBuiltMetrics(true);
builder.setDeleteExistingData(false);
}
if (cmd.hasOption("d")) {
builder.setDeleteExistingData(Boolean.valueOf(cmd.getOptionValue("d")));
}
if (cmd.hasOption("o")) {
builder.setMode(Mode.valueOf(cmd.getOptionValue("o").toUpperCase()));
}
if (cmd.hasOption("l")) {
builder.setLanguage(Language.getByLangCode(cmd.getOptionValue("l")));
}
if (cmd.hasOption("r")) {
builder.setMaxResults(Integer.valueOf(cmd.getOptionValue("r")));
}
if (cmd.hasOption("f")) {
builder.setCreateFakeGoldStandard(true);
}
builder.build();
}
/**
* call the user interface's general configuration method if the userInit option is true, and a
* user interface exists
*/
public void configUI() {
if (Boolean.parseBoolean(genProps.getProperty("userInit", "false"))
&& !(userInterface == null)) {
userInterface.user_init(genProps);
}
}
/** make menu bar a separate component */
private void buildMenuToolBar() {
// get property manager
PrideInspectorContext context = (PrideInspectorContext) getDesktopContext();
// create all the actions
// file open action
Icon openFileIcon = GUIUtilities.loadIcon(context.getProperty("open.file.icon.small"));
String openFileDesc = context.getProperty("open.file.title");
String openFileTooltip = context.getProperty("open.file.tooltip");
PrideAction openFileAction = new OpenFileAction(openFileDesc, openFileIcon);
// database open action
Icon openDbIcon = GUIUtilities.loadIcon(context.getProperty("open.database.icon.small"));
String openDbDesc = context.getProperty("open.database.title");
String openDbTooltip = context.getProperty("open.database.tooltip");
PrideAction openDbAction = new OpenDatabaseAction(openDbDesc, openDbIcon);
// open reviewer
Icon openReviewerIcon =
GUIUtilities.loadIcon(context.getProperty("reviewer.download.icon.small"));
String openReviewerDesc = context.getProperty("reviewer.download.title");
String openReviewerTooltip = context.getProperty("reviewer.download.tooltip");
PrideAction openReviewerAction = new OpenReviewAction(openReviewerDesc, openReviewerIcon);
// close
String closeDesc = context.getProperty("close.source.title");
String closeAllDesc = context.getProperty("close.all.soruce.title");
PrideAction closeAction = new CloseControllerAction(closeDesc, null);
PrideAction closeAllAction = new CloseAllControllersAction(closeAllDesc, null);
context.addPropertyChangeListenerToDataAccessMonitor((PropertyChangeListener) closeAction);
context.addPropertyChangeListenerToDataAccessMonitor((PropertyChangeListener) closeAllAction);
// try pride xml sample
String openPrideXmlExampleDesc = context.getProperty("open.pride.xml.example.title");
File prideXmlExampleFile =
getExampleFiles(context.getProperty("pride.inspector.pride.example.file"));
java.util.List<File> prideXmlFiles = new ArrayList<File>();
if (prideXmlExampleFile != null) {
prideXmlFiles.add(prideXmlExampleFile);
}
PrideAction openPrideXmlExampleAction =
new OpenFileAction(openPrideXmlExampleDesc, null, prideXmlFiles);
openPrideXmlExampleAction.setEnabled(
prideXmlExampleFile != null && prideXmlExampleFile.exists());
// try mzml sample
String openMzMLExampleDesc = context.getProperty("open.mzml.example.title");
File mzMLExampleFile =
getExampleFiles(context.getProperty("pride.inspector.mzml.example.file"));
java.util.List<File> mzMLFiles = new ArrayList<File>();
if (mzMLExampleFile != null) {
mzMLFiles.add(mzMLExampleFile);
}
PrideAction openMzMLExampleAction = new OpenFileAction(openMzMLExampleDesc, null, mzMLFiles);
openMzMLExampleAction.setEnabled(mzMLExampleFile != null && mzMLExampleFile.exists());
// help
Icon helpIcon = GUIUtilities.loadIcon(context.getProperty("help.icon.small"));
String helpDesc = context.getProperty("help.title");
String helpTooltip = context.getProperty("help.tooltip");
PrideAction helpAction = new OpenHelpAction(helpDesc, helpIcon);
// faq
String faqDesc = context.getProperty("faq.title");
PrideAction faqAction = new OpenFAQAction(faqDesc, null);
// pride website
String prideWeb = context.getProperty("open.pride.website.title");
String prideWebUrl = context.getProperty("pride.website");
PrideAction prideWebAction = new OpenUrlAction(prideWeb, null, prideWebUrl);
// pride website
String inspectorWeb = context.getProperty("open.pride.inspector.website.title");
String inspectorWebUrl = context.getProperty("pride.inspector.website");
PrideAction inspectorWebAction = new OpenUrlAction(inspectorWeb, null, inspectorWebUrl);
// feedback
String feedbackDesc = context.getProperty("feedback.title");
PrideAction feedBackAction = new FeedbackAction(feedbackDesc, null);
// export
String exportDesc = context.getProperty("export.title");
PrideAction exportAction = new ExportSpectrumAction(exportDesc, null);
context.addPropertyChangeListenerToDataAccessMonitor((PropertyChangeListener) exportAction);
// export identification
String exportIdentDesc = context.getProperty("export.identification.title");
PrideAction exportIdentAction = new ExportIdentificationPeptideAction(exportIdentDesc, null);
// export spectrum description
String exportSpectrumDesc = context.getProperty("export.spectrum.desc.title");
PrideAction exportSpectrumDescAction = new ExportSpectrumDescAction(exportSpectrumDesc, null);
// export identification description
String exportIdentDescTitle = context.getProperty("export.identification.desc.title");
PrideAction exportIdentDescAction =
new ExportIdentificationDescAction(exportIdentDescTitle, null);
// export peptide description
String exportPeptideDescTitle = context.getProperty("export.peptide.desc.title");
PrideAction exportPeptideAction = new ExportPeptideDescAction(exportPeptideDescTitle, null);
// make experiment public
String makeExpPublicTitle = context.getProperty("make.experiment.public.title");
PrideAction makeExpPublicAction = new MakeExperimentPublicAction(makeExpPublicTitle, null);
String createReviewerTitle = context.getProperty("create.reviewer.title");
PrideAction createReviewerAction = new CreateReviewerAction(createReviewerTitle, null);
// check update
String updateDescTitle = context.getProperty("check.update.desc.title");
PrideAction updateAction = new UpdateAction(updateDescTitle, null);
// about
String aboutDesc = context.getProperty("about.title");
PrideAction aboutAction = new AboutAction(aboutDesc, null);
// exit
String exitDesc = context.getProperty("exit.title");
PrideAction exitAction = new ExitAction(exitDesc, null);
// menu items
menuBar = new JMenuBar();
// file menu
JMenu fileMenu =
MenuFactory.createMenu(
"File",
openFileAction,
openDbAction,
openReviewerAction,
MenuFactory.ACTION_SEPARATOR,
closeAction,
closeAllAction,
MenuFactory.ACTION_SEPARATOR,
exitAction);
fileMenu.setMnemonic(java.awt.event.KeyEvent.VK_F);
menuBar.add(fileMenu);
// try samples
JMenu trySampleMenu =
MenuFactory.createMenu("Examples", openPrideXmlExampleAction, openMzMLExampleAction);
trySampleMenu.setMnemonic(java.awt.event.KeyEvent.VK_X);
menuBar.add(trySampleMenu);
// export menu
JMenu exportMenu =
MenuFactory.createMenu(
"Export",
exportAction,
exportSpectrumDescAction,
exportIdentAction,
exportIdentDescAction,
exportPeptideAction);
exportMenu.setMnemonic(java.awt.event.KeyEvent.VK_E);
menuBar.add(exportMenu);
// curation menu
boolean showCurationMenu = Boolean.parseBoolean(context.getProperty("include.curation.menu"));
if (showCurationMenu) {
JMenu curationMenu =
MenuFactory.createMenu("Curation", makeExpPublicAction, createReviewerAction);
curationMenu.setMnemonic(java.awt.event.KeyEvent.VK_C);
menuBar.add(curationMenu);
}
// help menu
JMenu helpMenu =
MenuFactory.createMenu(
"Help",
helpAction,
faqAction,
MenuFactory.ACTION_SEPARATOR,
prideWebAction,
inspectorWebAction,
MenuFactory.ACTION_SEPARATOR,
feedBackAction,
MenuFactory.ACTION_SEPARATOR,
updateAction,
aboutAction);
helpMenu.setMnemonic(java.awt.event.KeyEvent.VK_H);
menuBar.add(helpMenu);
// add menus
mainFrame.setJMenuBar(menuBar);
// tool bar
toolBar = new JToolBar();
// open file
JButton openFileButton = new JButton();
openFileButton.setAction(openFileAction);
openFileButton.setText("");
openFileButton.setToolTipText(openFileTooltip);
openFileButton.setFocusable(false);
toolBar.add(openFileButton);
// open database
JButton openDbButton = new JButton();
openDbButton.setAction(openDbAction);
openDbButton.setText("");
openDbButton.setToolTipText(openDbTooltip);
openDbButton.setFocusable(false);
toolBar.add(openDbButton);
// open reviewer download
JButton openReviewerButton = new JButton();
openReviewerButton.setAction(openReviewerAction);
openReviewerButton.setText("");
openReviewerButton.setToolTipText(openReviewerTooltip);
openReviewerButton.setFocusable(false);
toolBar.add(openReviewerButton);
// separator
toolBar.addSeparator();
// help
JButton helpButton = new JButton(helpIcon);
helpButton.setAction(helpAction);
helpButton.setText("");
helpButton.setToolTipText(helpTooltip);
helpButton.setFocusable(false);
toolBar.add(helpButton);
mainFrame.getContentPane().add(toolBar, BorderLayout.PAGE_START);
}