/**
* Run a shell command.
*
* @param args shell arguments to call
* @return the result of running the command
* @throws ProcessRunException if there's an error running the process
*/
public RunResult run(List<String> args) throws ProcessRunException {
for (int i = 0; i < retries; i++) {
LOG.debug("Running: " + args);
ProcessRunner runner = new ProcessRunner(args);
RunResult result = runner.run();
if (result.getReturnCode() == 0) {
return result;
}
LOG.error("Error running command! Got return code: " + result.getReturnCode());
if (i + 1 == retries) {
return result;
}
try {
LOG.debug("Sleeping for " + RETRY_SLEEP_TIME / 1000 + "s");
Thread.sleep(RETRY_SLEEP_TIME);
} catch (InterruptedException e) {
throw new RuntimeException("Shouldn't happen!");
}
}
throw new RuntimeException("Shouldn't happen");
}
@Override
public void shutDown() {
synchronized (this.extensionToRunnerMap) {
for (ProcessRunner runner : this.extensionToRunnerMap.values()) {
for (Process p : runner.getProcesses()) p.destroy();
}
}
}
@Override
public void directoryChanged(DirectoryEvent e) {
// Only interested in file create event
if (e.getEventType() != DirectoryEvent.ENTRY_CREATE) return;
String[] parts = e.getFile().toString().split("\\.");
if (parts.length == 0) return;
ProcessRunner runner = this.extensionToRunnerMap.get(parts[parts.length - 1]);
if (runner == null) return;
try {
runner.execute(e.getFile());
} catch (IOException ex) {
ex.printStackTrace();
}
}
/**
* 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);
}
}
/**
* Blocks until the workflow run has finished and then reports if it was successful.
*
* <p>A workflow run is considered successful if it returns with a 0 result.
*
* @return True is and only if the workflow run ended with a 0.
* @throws TavernaException Wrapper around any InterruptedException, or if the process was never
* started.
* @throws ProcessException If the process was not started.
*/
public boolean wasSuccessful() throws TavernaException, ProcessException {
try {
boolean result = runner.waitFor() == 0;
if (outputFile == null) {
saveOutput();
}
return result;
} catch (InterruptedException ex) {
throw new TavernaException("Error checking if run was successfull", 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;
}
/**
* Starts a run of Tavernas Command Line tool based on the provided parameters.
*
* @param tavernaHome Location of the bat or sh file to be run.
* @param outputRoot Location where the different outputs will be written. This are:
* <dl>
* <dt>BaclavaOutput.xml
* <dd>Output saved by the workflow
* <dt>Output.txt
* <dd>Output of this class including parameters passed to the bat.script and a capture of
* anything that sends to output or error streams.
* <dt>TavernaLog.txt
* <dd>Log file generated by the workflow
* </dl>
*
* @param inputs Array of the inputs plus the values provided by the users. If not null this is
* the preferred source of inputs.
* @param inputsURI URI to a Baclava file that holds the inputs. File uris should begin with
* "file:" Ignored if null or "inputs" not null. If both "inputs" and "inputsURI" are null
* workflow is assumed not to have any inputs.
* @param workflowURI URI to a workflow file that holds the inputs. File uris should begin with
* "file:"
* @throws TavernaException Throw if the inputs passed in are determined as incorrect before the
* workflow is run.
* @throws IOException Throw if accessing any of the File parameters, or child files created,
* causes such an exception.
*/
public CommandLineRun(
File tavernaHome,
File outputRoot,
TavernaInput[] inputs,
String inputsURI,
String workflowURI)
throws TavernaException, IOException, URISyntaxException {
ArrayList<String> cmd = getLaunch(tavernaHome);
runDirectory = Utils.createCalendarBasedDirectory(outputRoot);
baclavaFile = new File(runDirectory, "BaclavaOutput.xml");
cmd.add("-outputdoc=" + baclavaFile.getAbsolutePath());
File logFile = new File(runDirectory, "TavernaLog.txt");
cmd.add("-logfile=" + logFile.getAbsolutePath());
if (inputs != null) { // the useris passing all inputs individually
System.out.append("Running workflow with individual inputs.");
// for (TavernaInput input:inputs){
// cmd.addAll(input.getInputArguments());
// }
// Create Baclava input file from all the inputs gathered and pass that as an input to
// the Taverna Command Line Tool/Server - this is more convenient as we use just one file
// for all the inputs and we can also pass more complex inputs rather than just one-line
// strings
Map<String, Object> valueMap = new HashMap<String, Object>();
for (TavernaInput input : inputs) {
valueMap.put(input.getName(), input.getValue());
}
Map<String, DataThing> dataThingsMap = DataThingBasedBaclava.bakeDataThingMap(valueMap);
// Build the XML Baclava document containing the workflow inputs
Document document = DataThingBasedBaclava.getDataDocument(dataThingsMap);
Random randomGenerator = new Random();
File baclavaInputFile =
new File(
System.getProperty("java.io.tmpdir"),
Integer.toString(randomGenerator.nextInt(999999)) + "-baclava.xml");
java.io.FileWriter writer = null;
try {
XMLOutputter out = new XMLOutputter();
writer = new java.io.FileWriter(baclavaInputFile);
out.output(document, writer);
writer.flush();
writer.close();
} catch (Exception ex) {
System.out.println(
"Failed to save Baclava inputs to file " + baclavaInputFile.getAbsolutePath());
ex.printStackTrace();
} finally {
try {
if (writer != null) {
writer.close();
}
} catch (Exception ex2) {
// Ignore
}
}
// Probably won't work on Windows
String baclavaInputURL =
"file://" + new URI(baclavaInputFile.getAbsolutePath()).toASCIIString();
System.out.println(
"Converted all individual inputs to a local Baclava file : " + baclavaInputURL);
cmd.add("-inputdoc=" + baclavaInputURL);
} else if (inputsURI != null) { // the user is passing a Baclava file with all the inputs
System.out.println("Running workflow with Baclava inputs from " + inputsURI);
cmd.add("-inputdoc=" + inputsURI);
}
cmd.add(workflowURI);
String[] command = new String[0];
command = cmd.toArray(command);
System.out.println("Executing command " + cmd.toString());
runner = new ProcessRunner(command, tavernaHome);
runner.start();
}
/**
* Used to destroy a workflow run.
*
* <p>Stops a workflow run by passing a destroy request to the process that is running it.
*/
public void destroy() {
runner.destroy();
}
/**
* Returns the output of the workflow run up to this point.
*
* <p>Non blocking method that returns the output of the workflow up to this point. Expected to
* hold the parameters used to start the workflow. Depending on when it is called may (but is
* never guaranteed to) include intermediate workflow output or even results.
*
* <p>Unlike other methods this one is not expected to fail or throw an Exception even if the run
* fails or was interrupted but this behaviour is not guaranteed.
*
* @return Partial workflow output
*/
public String getRunInfo() {
return runner.getRunInfo();
}
