/**
* Initialize options from properties object
*
* @param properties
* @throws IOException
* @throws FileNotFoundException
* @throws CmdLineException
*/
public MolgenisOptions(Properties properties) {
CmdLineParser parser;
try {
parser = new CmdLineParser(this);
parser.parse(properties);
Logger.getLogger(this.getClass().getSimpleName()).debug("parsed properties file.");
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
throw new RuntimeException("Cannot find property file: " + e.getMessage());
}
}
/**
* Initialize options from properties file
*
* @param propertiesFile the path string to molgenis.properties file
* @throws IOException
* @throws FileNotFoundException
* @throws CmdLineException
*/
public MolgenisOptions(String propertiesFile)
throws FileNotFoundException, IOException, CmdLineException {
this.molgenis_properties = propertiesFile;
Properties props = new Properties();
try {
// try to load from local files
props.load(new FileInputStream(propertiesFile.trim()));
} catch (FileNotFoundException e) {
try {
// try to load from classpath
props.load(ClassLoader.getSystemResourceAsStream(propertiesFile.trim()));
} catch (Exception e2) {
throw new IOException("couldn't find file " + new File(propertiesFile).getAbsolutePath());
}
}
CmdLineParser parser = new CmdLineParser(this);
parser.parse(props);
this.molgenis_properties = propertiesFile;
// parse passwordfile
String passwordFile = propertiesFile.replace(".properties", ".passwd");
this.molgenis_passwd = passwordFile;
props = new Properties();
try {
// try to load from local files
props.load(new FileInputStream(passwordFile.trim()));
} catch (FileNotFoundException e) {
try {
// try to load from classpath
props.load(ClassLoader.getSystemResourceAsStream(passwordFile.trim()));
} catch (Exception e2) {
// no biggie
}
}
parser = new CmdLineParser(this);
parser.parse(props);
// warn if no password was provided
if ("".equals(this.db_password))
System.err.println(
"WARNING: db_password was not provided in neither "
+ propertiesFile
+ " nor "
+ passwordFile);
Logger.getLogger(this.getClass().getSimpleName()).debug("parsed properties file.");
}