@Override
public void setOptions(String[] options) throws Exception {
// these are options to the hadoop map task (especially the -names-file)
String existing = Utils.getOption("existing-header", options);
setPathToExistingHeader(existing);
String attNames = Utils.getOption('A', options);
setAttributeNames(attNames);
String namesFile = Utils.getOption("names-file", options);
setAttributeNamesFile(namesFile);
String outputName = Utils.getOption("header-file-name", options);
setOutputHeaderFileName(outputName);
super.setOptions(options);
// any options to pass on to the underlying Weka csv to arff map task?
CSVToARFFHeaderMapTask tempMap = new CSVToARFFHeaderMapTask();
tempMap.setOptions(options);
String optsToWekaMapTask = Utils.joinOptions(tempMap.getOptions());
if (!DistributedJobConfig.isEmpty(optsToWekaMapTask)) {
setCsvToArffTaskOptions(optsToWekaMapTask);
}
}
@Override
public Enumeration<Option> listOptions() {
Vector<Option> result = new Vector<Option>();
result.add(
new Option(
"\tPath to header file to use. Set this if you have\n\t"
+ "run previous jobs that have generated a header already. Setting this\n\t"
+ "prevents this job from running.",
"existing-header",
1,
"-existing-header"));
result.add(
new Option(
"\tComma separated list of attribute names to use.\n\t"
+ "Use either this option, -names-file or neither (in which case\n\t"
+ "attribute names will be generated).",
"A",
1,
"-A <attribute names>"));
result.add(
new Option(
"\tLocation of a names file to source attribute names\n\t"
+ "from. Can exist locally or in HDFS. "
+ "Use either this option, -A or neither (in which case\n\t"
+ "attribute names will be generated).",
"names-file",
1,
"-names-file <path to file>"));
result.add(
new Option(
"\tFile name for output ARFF header. Note that this is a name only\n\t"
+ "and not a path. This file will be created in the output directory\n\t"
+ "specified by the -output-path option. (default is a "
+ "randomly generated name)",
"header-file-name",
1,
"-header-file-name <name>"));
CSVToARFFHeaderMapTask tempTask = new CSVToARFFHeaderMapTask();
Enumeration<Option> mtOpts = tempTask.listOptions();
while (mtOpts.hasMoreElements()) {
result.addElement(mtOpts.nextElement());
}
result.add(new Option("", "", 0, "\nGeneral Hadoop job configuration options:"));
Enumeration<Option> superOpts = super.listOptions();
while (superOpts.hasMoreElements()) {
result.addElement(superOpts.nextElement());
}
return result.elements();
}
/**
* Adds options from the ARFF map task to the supplied list of options
*
* @param opts the list of options to add the ARFF options to
*/
protected void addArffMapTaskOpts(List<String> opts) {
String[] arffMapOpts = m_arffMapTask.getOptions();
for (String s : arffMapOpts) {
opts.add(s);
}
}
/**
* Adds a tab for the ARFF header job
*
* @param tabTitle the title for the tab
* @param arffJob the ARFF job
*/
protected void addTabForArffHeaderJob(String tabTitle, HadoopJob arffJob) {
JPanel jobHolder = new JPanel();
jobHolder.setLayout(new BorderLayout());
PropertySheetPanel arffJobEditor = new PropertySheetPanel();
arffJobEditor.setEnvironment(m_env);
arffJobEditor.setTarget(arffJob);
jobHolder.add(arffJobEditor, BorderLayout.NORTH);
m_arffMapTask = new CSVToARFFHeaderMapTask();
try {
m_arffMapTask.setOptions(Utils.splitOptions(m_optionsOrig));
} catch (Exception ex) {
ex.printStackTrace();
}
PropertySheetPanel mapTaskEditor = new PropertySheetPanel();
mapTaskEditor.setTarget(m_arffMapTask);
mapTaskEditor.setEnvironment(m_env);
jobHolder.add(mapTaskEditor, BorderLayout.CENTER);
// JScrollPane scroller = new JScrollPane(jobHolder);
m_configTabs.addTab(tabTitle, jobHolder);
}
@Override
public boolean runJob() throws DistributedWekaException {
boolean success = true;
m_finalHeader = null;
ClassLoader orig = Thread.currentThread().getContextClassLoader();
try {
Thread.currentThread().setContextClassLoader(this.getClass().getClassLoader());
if (!DistributedJobConfig.isEmpty(getPathToExistingHeader())) {
try {
handleExistingHeaderFile();
// done!!
return true;
} catch (DistributedWekaException ex) {
logMessage(
"Unable to laod existing header file from '"
+ getPathToExistingHeader()
+ "' (reason: "
+ ex.getMessage()
+ "). Running job to create header...");
}
}
setJobStatus(JobStatus.RUNNING);
if (m_env == null) {
m_env = Environment.getSystemWide();
}
// make sure that we save out to a subdirectory of the output directory
// so that the arff header doesn't get deleted by any jobs that invoke
// us first before themselves
String outputPath = m_mrConfig.getOutputPath();
outputPath += OUTPUT_SUBDIR;
m_mrConfig.setOutputPath(outputPath);
Random r = new Random();
String outHeadName = "" + Math.abs(r.nextInt());
if (!DistributedJobConfig.isEmpty(getOutputHeaderFileName())) {
outHeadName = environmentSubstitute(getOutputHeaderFileName());
}
if (!outHeadName.toLowerCase().endsWith(".arff")) {
outHeadName += ".arff";
}
outputPath += "/" + outHeadName;
// m_hdfsPathToAggregatedHeader = HDFSUtils.constructHDFSURI(
// m_mrConfig.getHDFSConfig(), outputPath, m_env);
m_hdfsPathToAggregatedHeader = outputPath;
// Where to write the consolidated ARFF file to
m_mrConfig.setUserSuppliedProperty(
CSVToArffHeaderHadoopReducer.CSV_TO_ARFF_HEADER_WRITE_PATH, outputPath);
// Now lets check to see whether this job needs to run at all - i.e.
// if the header can be produced immediately (no nominal values need to
// be determined) then we can just write ARFF header directly to the
// output location in HDFS and quit
CSVToARFFHeaderMapTask tempMapTask = new CSVToARFFHeaderMapTask();
if (!DistributedJobConfig.isEmpty(getCsvToArffTaskOptions())) {
String[] tempOpts = Utils.splitOptions(getCsvToArffTaskOptions());
tempMapTask.setOptions(tempOpts);
}
boolean haveAttributeNames = false;
List<String> tempAttNames = null;
if (!DistributedJobConfig.isEmpty(getAttributeNames())) {
tempAttNames = new ArrayList<String>();
String[] n = environmentSubstitute(getAttributeNames()).split(",");
for (String nn : n) {
nn = nn.trim();
if (nn.length() > 0) {
tempAttNames.add(nn);
}
}
haveAttributeNames = true;
} else if (!DistributedJobConfig.isEmpty(getAttributeNamesFile())) {
// handle names file - bail out if there are no atts or names file
String namesFile = environmentSubstitute(getAttributeNamesFile());
if (namesFile.startsWith("hdfs://")) {
namesFile = namesFile.replace("hdfs://", "");
// strip the host and port (if provided)
namesFile = namesFile.substring(namesFile.indexOf("/"));
String pathS = HDFSUtils.resolvePath(namesFile, m_env);
Configuration tempConf = new Configuration();
m_mrConfig.getHDFSConfig().configureForHadoop(tempConf, m_env);
FileSystem fs = FileSystem.get(tempConf);
Path path = new Path(pathS);
InputStream is = fs.open(path);
InputStreamReader isr = new InputStreamReader(is);
BufferedReader br = new BufferedReader(isr);
// this closes the stream for us
tempAttNames = CSVToArffHeaderHadoopMapper.readNames(br);
} else {
// local file
URI uri = new URI(namesFile);
File path = new File(uri.getPath());
BufferedReader br = new BufferedReader(new FileReader(path));
tempAttNames = CSVToArffHeaderHadoopMapper.readNames(br);
}
haveAttributeNames = true;
}
// can't generate header immediately if we have to compute summary
// stats
if (haveAttributeNames && !tempMapTask.getComputeSummaryStats()) {
if (tempMapTask.headerAvailableImmediately(
tempAttNames.size(), tempAttNames, new StringBuffer())) {
Instances finalHeader = tempMapTask.getHeader(tempAttNames.size(), tempAttNames);
m_finalHeader = finalHeader;
Configuration tempConf = new Configuration();
m_mrConfig.getHDFSConfig().configureForHadoop(tempConf, m_env);
CSVToArffHeaderHadoopReducer.writeHeaderToDestination(finalHeader, outputPath, tempConf);
// done!
return true;
}
}
// Otherwise, go ahead with the job...
Configuration conf = new Configuration();
// Options to the map task and the underlying general Weka map
// task
StringBuilder csvToArffTaskOptions = new StringBuilder();
if (!DistributedJobConfig.isEmpty(getAttributeNames())) {
csvToArffTaskOptions.append(" -A ").append(environmentSubstitute(getAttributeNames()));
} else if (!DistributedJobConfig.isEmpty(getAttributeNamesFile())) {
String filenameOnly = handleNamesFile(conf);
csvToArffTaskOptions.append(" -names-file ").append(filenameOnly);
}
if (!DistributedJobConfig.isEmpty(getCsvToArffTaskOptions())) {
csvToArffTaskOptions.append(" ").append(getCsvToArffTaskOptions());
}
if (csvToArffTaskOptions.length() > 0) {
m_mrConfig.setUserSuppliedProperty(
CSVToArffHeaderHadoopMapper.CSV_TO_ARFF_HEADER_MAP_TASK_OPTIONS,
environmentSubstitute(csvToArffTaskOptions.toString()));
setJobName(getJobName() + " " + csvToArffTaskOptions.toString());
}
// install the weka libraries and any user-selected packages
// to HDFS and add to the distributed cache/classpath for
// the job
installWekaLibrariesInHDFS(conf);
Job job = m_mrConfig.configureForHadoop(environmentSubstitute(getJobName()), conf, m_env);
cleanOutputDirectory(job);
statusMessage("Submitting job: " + getJobName());
logMessage("Submitting job: " + getJobName());
success = runJob(job);
if (success) {
getFinalHeaderFromHDFS(conf, outputPath);
}
setJobStatus(success ? JobStatus.FINISHED : JobStatus.FAILED);
} catch (Exception ex) {
setJobStatus(JobStatus.FAILED);
throw new DistributedWekaException(ex);
} finally {
Thread.currentThread().setContextClassLoader(orig);
}
return success;
}