/** Initializes the AccessControl member. */
private static synchronized AccessControl getaccessControl() {
if (accessControl == null) {
accessControl = SpringUtil.getAccessControl();
}
return accessControl;
}
// command line utility
public static void main(String[] args) throws IOException, DaoException {
if (args.length != 2) {
System.out.printf(
"command line usage: importGistic.pl <gistic-data-file.txt> <cancer-study-id>\n"
+ "\t <gistic-data-file.txt> Note that gistic-data-file.txt must be a massaged file, it does not come straight from the Broad\n"
+ "\t <cancer-study-id> e.g. 'tcga_gbm'");
return;
}
SpringUtil.initDataSource();
GisticReader gisticReader = new GisticReader();
File gistic_f = new File(args[0]);
int cancerStudyInternalId = gisticReader.getCancerStudyInternalId(args[1]);
ProgressMonitor.setConsoleMode(false);
System.out.println("Reading data from: " + gistic_f.getAbsolutePath());
System.out.println("CancerStudyId: " + cancerStudyInternalId);
int lines = FileUtil.getNumLines(gistic_f);
System.out.println(" --> total number of lines: " + lines);
ProgressMonitor.setMaxValue(lines);
ArrayList<Gistic> gistics = null;
gistics = gisticReader.parse(gistic_f, cancerStudyInternalId);
if (gistics == null) {
System.out.println("Error: didn't get any data");
return;
}
// add to CGDS database
for (Gistic g : gistics) {
try {
DaoGistic.addGistic(g);
} catch (validationException e) {
// only catching validationException, not DaoException
logger.debug(e);
} catch (DaoException e) {
System.err.println(e);
}
}
ConsoleUtil.showWarnings();
}
/**
* Initializes the servlet.
*
* @throws ServletException Serlvet Init Error.
*/
@Override
public void init() throws ServletException {
super.init();
accessControl = SpringUtil.getAccessControl();
}