Example 1 with JSONParserException
use of beast.util.JSONParserException in project beast2 by CompEvol.
the class BeastMCMC method parseArgs.
/**
* parse command line arguments, and load file if specified
* @throws IOException
* @throws JSONException
* @throws JSONParserException
*/
public void parseArgs(String[] args) throws IOException, XMLParserException, JSONException {
int i = 0;
boolean resume = false;
boolean useStrictVersions = false;
Map<String, String> parserDefinitions = new HashMap<>();
File beastFile = null;
try {
while (i < args.length) {
int old = i;
if (i < args.length) {
if (args[i].equals("")) {
i += 1;
} else if (args[i].equals("-batch")) {
Logger.FILE_MODE = Logger.LogFileMode.only_new_or_exit;
i += 1;
} else if (args[i].equals("-resume")) {
resume = true;
Logger.FILE_MODE = Logger.LogFileMode.resume;
System.setProperty("beast.resume", "true");
System.setProperty("beast.debug", "false");
i += 1;
} else if (args[i].equals("-overwrite")) {
Logger.FILE_MODE = Logger.LogFileMode.overwrite;
i += 1;
} else if (args[i].equals("-seed")) {
if (args[i + 1].equals("random")) {
m_nSeed = Randomizer.getSeed();
} else {
m_nSeed = Long.parseLong(args[i + 1]);
}
i += 2;
} else if (args[i].equals("-threads")) {
m_nThreads = Integer.parseInt(args[i + 1]);
g_exec = Executors.newFixedThreadPool(m_nThreads);
i += 2;
// use BEAST environment variable to set Beast directories as colon separated list
// } else if (args[i].equals("-beastlib")) {
// ClassDiscovery.setJarPath(args[i + 1]);
// i += 2;
} else if (args[i].equals("-prefix")) {
System.setProperty("file.name.prefix", args[i + 1].trim());
i += 2;
} else if (args[i].equals("-D")) {
String[] strs = args[i + 1].split(",");
for (String str : strs) {
String[] strs2 = str.split("=");
if (strs2.length != 2) {
throw new IllegalArgumentException("Argument \"" + str + "\" is not well-formed: expecting name=value pairs");
}
String name = strs2[0];
String value = strs2[1];
parserDefinitions.put(name, value);
}
i += 2;
} else if (args[i].equals("-strictversions")) {
useStrictVersions = true;
i += 1;
}
if (i == old) {
if (i == args.length - 1) {
beastFile = new File(args[i]);
i++;
} else {
throw new IllegalArgumentException("Wrong argument");
}
}
}
}
} catch (Exception e) {
e.printStackTrace();
throw new IllegalArgumentException("Error parsing command line arguments: " + Arrays.toString(args) + "\nArguments ignored\n\n" + getUsage());
}
if (beastFile == null) {
// Not resuming so get starting options...
List<String> MCMCargs = new ArrayList<>();
Version version = new BEASTVersion2();
String titleString = "<html><center><p>Bayesian Evolutionary Analysis Sampling Trees<br>" + "Version " + version.getVersionString() + ", " + version.getDateString() + "</p></center></html>";
javax.swing.Icon icon = IconUtils.getIcon(BeastMain.class, "images/beast.png");
String nameString = "BEAST " + version.getVersionString();
BeastDialog dialog = new BeastDialog(new JFrame(), titleString, icon);
if (!dialog.showDialog(nameString, m_nSeed)) {
return;
}
switch(dialog.getLogginMode()) {
case 0:
/* do not ovewrite */
break;
case 1:
MCMCargs.add("-overwrite");
break;
case 2:
MCMCargs.add("-resume");
break;
}
MCMCargs.add("-seed");
MCMCargs.add(dialog.getSeed() + "");
if (dialog.getThreadPoolSize() > 0) {
MCMCargs.add("-threads");
MCMCargs.add(dialog.getThreadPoolSize() + "");
}
boolean useBeagle = dialog.useBeagle();
boolean beagleShowInfo = false;
long beagleFlags = 0;
if (useBeagle) {
beagleShowInfo = dialog.showBeagleInfo();
if (dialog.preferBeagleCPU()) {
beagleFlags |= BeagleFlag.PROCESSOR_CPU.getMask();
}
if (dialog.preferBeagleSSE()) {
beagleFlags |= BeagleFlag.VECTOR_SSE.getMask();
}
if (dialog.preferBeagleGPU()) {
beagleFlags |= BeagleFlag.PROCESSOR_GPU.getMask();
}
if (dialog.preferBeagleDouble()) {
beagleFlags |= BeagleFlag.PRECISION_DOUBLE.getMask();
}
if (dialog.preferBeagleSingle()) {
beagleFlags |= BeagleFlag.PRECISION_SINGLE.getMask();
}
}
if (beagleFlags != 0) {
System.setProperty("beagle.preferred.flags", Long.toString(beagleFlags));
}
if (!useBeagle) {
System.setProperty("java.only", "true");
}
File inputFile = dialog.getInputFile();
if (!beagleShowInfo && inputFile == null) {
System.err.println("No input file specified");
System.exit(1);
}
MCMCargs.add(inputFile.getAbsolutePath());
// BeastStartDialog dlg = new BeastStartDialog();
// if (dlg.m_bOK) {
// parseArgs(dlg.getArgs());
// }
parseArgs(MCMCargs.toArray(new String[0]));
return;
}
Log.warning.println("File: " + beastFile.getName() + " seed: " + m_nSeed + " threads: " + m_nThreads);
if (resume) {
Log.info.println("Resuming from file");
}
if (useStrictVersions) {
// grab "required" attribute from beast spec
if (beastFile.getPath().toLowerCase().endsWith(".json")) {
throw new IllegalArgumentException("The -strictversions flag is not implemented for JSON files yet (only XML files are supported).");
} else {
BufferedReader fin = new BufferedReader(new FileReader(beastFile));
StringBuffer buf = new StringBuffer();
String str = null;
int lineCount = 0;
while (fin.ready() && lineCount < 100) {
str = fin.readLine();
buf.append(str);
buf.append(' ');
}
fin.close();
str = buf.toString();
int start = str.indexOf("required=");
if (start < 0) {
throw new IllegalArgumentException("Could not find a 'required' attribute in the XML. Add the required attribute, or run without the -strictversions flag");
}
char c = str.charAt(start + 9);
start += 10;
int end = str.indexOf(c, start);
String packages = str.substring(start, end);
PackageManager.loadExternalJars(packages);
}
} else {
PackageManager.loadExternalJars();
}
// parse xml
Randomizer.setSeed(m_nSeed);
if (beastFile.getPath().toLowerCase().endsWith(".json")) {
m_runnable = new JSONParser(parserDefinitions).parseFile(beastFile);
} else {
try {
m_runnable = new XMLParser(parserDefinitions).parseFile(beastFile);
} catch (SAXException | ParserConfigurationException e) {
throw new IllegalArgumentException(e);
}
}
m_runnable.setStateFile(beastFile.getName() + ".state", resume);
}
Also used :
HashMap(java.util.HashMap)
ArrayList(java.util.ArrayList)
SAXException(org.xml.sax.SAXException)
Version(beast.app.util.Version)
JFrame(javax.swing.JFrame)
FileReader(java.io.FileReader)
ParserConfigurationException(javax.xml.parsers.ParserConfigurationException)
XMLParser(beast.util.XMLParser)
JSONException(org.json.JSONException)
XMLParserException(beast.util.XMLParserException)
SAXException(org.xml.sax.SAXException)
JSONParserException(beast.util.JSONParserException)
IOException(java.io.IOException)
ParserConfigurationException(javax.xml.parsers.ParserConfigurationException)
BeastDialog(beast.app.beastapp.BeastDialog)
BufferedReader(java.io.BufferedReader)
JSONParser(beast.util.JSONParser)
File(java.io.File)
Aggregations
BeastDialog (beast.app.beastapp.BeastDialog)1
Version (beast.app.util.Version)1
JSONParser (beast.util.JSONParser)1
JSONParserException (beast.util.JSONParserException)1
XMLParser (beast.util.XMLParser)1
XMLParserException (beast.util.XMLParserException)1
BufferedReader (java.io.BufferedReader)1
File (java.io.File)1
FileReader (java.io.FileReader)1
IOException (java.io.IOException)1
ArrayList (java.util.ArrayList)1
HashMap (java.util.HashMap)1
JFrame (javax.swing.JFrame)1
ParserConfigurationException (javax.xml.parsers.ParserConfigurationException)1
JSONException (org.json.JSONException)1
SAXException (org.xml.sax.SAXException)1
