Examples with SystemCommandExecutor org.nextprot.api.commons.utils.SystemCommandExecutor used on opensource projects

Example 1 with SystemCommandExecutor

use of org.nextprot.api.commons.utils.SystemCommandExecutor in project nextprot-api by calipho-sib.

the class BlastProgram method process.

private O process(List<String> commandLine) throws ExceptionWithReason {
    SystemCommandExecutor commandExecutor = new SystemCommandExecutor(commandLine);
    try {
        commandExecutor.executeCommand();
        String stderr = commandExecutor.getLastExecutionStandardError();
        if (!stderr.isEmpty()) {
            ExceptionWithReason ewr = new ExceptionWithReason();
            ewr.getReason().addCause(name + " exception", stderr.replace("\n", " "));
            ewr.getReason().setMessage("Error while executing " + name);
            throw ewr;
        }
        return buildOutputFromStdout(commandExecutor.getLastExecutionStandardOutput());
    } catch (InterruptedException | IOException e) {
        throw new NextProtException("Internal error: cannot process " + name + " command line " + commandLine, e);
    }
}