/**
* Blocking method that saves (if required) a finished workflow runs output.
*
* <p>Blocks until the workflow run has finished. Works even if the workflow result was not 0. The
* first time this method is called it saves the output to file.
*
* @return Output of this class including parameters passed to the bat.script and a capture of
* anything that sends to output or error streams. Does not include the results of the
* workflow run use getOutputFile() for these.
* @throws TavernaException Thrown if there is an InterruptedException, ProcessException or error
* saving the output.
* @throws ProcessException If the process was not started.
*/
public String getOutput() throws TavernaException, ProcessException {
if (outputFile == null) {
return saveOutput();
}
try {
return runner.getOutput();
} catch (InterruptedException ex) {
throw new TavernaException("Workflow was interrupted.", ex);
}
}
private String saveOutput() throws TavernaException, ProcessException {
String output = null;
FileWriter writer = null;
try {
output = runner.getOutput();
outputFile = new File(runDirectory, "Output.txt");
writer = new FileWriter(outputFile);
writer.write(output);
writer.close();
} catch (InterruptedException ex) {
throw new TavernaException("Workflow was interrupted.", ex);
} catch (IOException ex) {
throw new TavernaException("Workflow output could not be saved.", ex);
} finally {
try {
if (writer != null) {
writer.close();
}
} catch (IOException ex) {
throw new TavernaException("Workflow output could not be saved.", ex);
}
}
return output;
}
