@Override
@SuppressWarnings("unchecked")
protected void setup(Reducer.Context context) throws IOException, InterruptedException {
this.context = context;
String settingsStr = context.getConfiguration().get(ParameterProcessing.SETTINGS_STR);
Settings settings = Settings.loadFromString(settingsStr);
Settings.setSettings(settings);
String projectStr = context.getConfiguration().get(ParameterProcessing.PROJECT);
Project project = Project.loadFromString(projectStr);
if (project.isEnvHadoop()) {
String metadataFileContents =
context.getConfiguration().get(ParameterProcessing.METADATA_FILE);
new File(ColumnMetadata.metadataNamesFile).getParentFile().mkdirs();
Files.write(metadataFileContents.getBytes(), new File(ColumnMetadata.metadataNamesFile));
}
columnMetadata = new ColumnMetadata();
String fileSeparatorStr = project.getFieldSeparator();
char fieldSeparatorChar = Delimiter.getDelim(fileSeparatorStr);
columnMetadata.setFieldSeparator(String.valueOf(fieldSeparatorChar));
columnMetadata.setAllMetadata(project.getMetadataCollect());
// write standard metadata fields
context.write(null, new Text(columnMetadata.delimiterSeparatedHeaders()));
zipFileWriter.setup();
zipFileWriter.openZipForWriting();
luceneIndex = new LuceneIndex(settings.getLuceneIndexDir(), project.getProjectCode(), null);
luceneIndex.init();
}
@Override
@SuppressWarnings("unchecked")
protected void cleanup(Reducer.Context context) throws IOException, InterruptedException {
if (!Project.getProject().isMetadataCollectStandard()) {
// write summary headers with all metadata, but for standard metadata don't write the last
// line
context.write(new Text("Hash"), new Text(columnMetadata.delimiterSeparatedHeaders()));
}
zipFileWriter.closeZip();
if (Project.getProject().isLuceneIndexEnabled()) {
mergeLuceneIndex();
}
Project project = Project.getProject();
if (project.isEnvHadoop()) {
String outputPath = Project.getProject().getProperty(ParameterProcessing.OUTPUT_DIR_HADOOP);
String zipFileName = zipFileWriter.getZipFileName();
if (project.isFsHdfs()) {
String cmd =
"hadoop fs -copyFromLocal "
+ zipFileName
+ " "
+ outputPath
+ File.separator
+ context.getTaskAttemptID()
+ ".zip";
OsUtil.runCommand(cmd);
} else if (project.isFsS3()) {
S3Agent s3agent = new S3Agent();
String run = project.getRun();
if (!run.isEmpty()) {
run = run + "/";
}
String s3key =
project.getProjectCode()
+ File.separator
+ "output/"
+ run
+ "results/"
+ context.getTaskAttemptID()
+ ".zip";
// Keep updating the hadoop progress
int refreshInterval = 60000;
Timer timer = new Timer(refreshInterval, this);
timer.start();
s3agent.putFileInS3(zipFileName, s3key);
timer.stop();
}
}
Stats.getInstance().setJobFinished();
}
@Override
public void actionPerformed(ActionEvent event) {
// inform Hadoop that we are alive
if (context != null) {
context.progress();
}
}
@Override
protected void setup(Reducer.Context context) throws IOException, InterruptedException {
super.setup(context);
Configuration conf = context.getConfiguration();
iteration = conf.getInt("iteration", -1);
System.out.println("Setting up Reducer " + iteration);
centroids = KMeansUtil.readCentroids(conf);
System.out.println("Reducer " + iteration + " Received " + centroids.size() + " centroids as");
KMeansUtil.showOutput(centroids);
}
protected void processMap(MapWritable value) throws IOException, InterruptedException {
columnMetadata.reinit();
++outputFileCount;
DocumentMetadata allMetadata = getAllMetadata(value);
Metadata standardMetadata = getStandardMetadata(allMetadata, outputFileCount);
columnMetadata.addMetadata(standardMetadata);
columnMetadata.addMetadata(allMetadata);
// documents other than the first one in this loop are either duplicates or attachments
if (first) {
masterOutputFileCount = outputFileCount;
} else {
if (allMetadata.hasParent()) {
columnMetadata.addMetadataValue(
DocumentMetadataKeys.ATTACHMENT_PARENT, UPIFormat.format(masterOutputFileCount));
} else {
columnMetadata.addMetadataValue(
DocumentMetadataKeys.MASTER_DUPLICATE, UPIFormat.format(masterOutputFileCount));
}
}
// String uniqueId = allMetadata.getUniqueId();
String originalFileName =
new File(allMetadata.get(DocumentMetadataKeys.DOCUMENT_ORIGINAL_PATH)).getName();
// add the text to the text folder
String documentText = allMetadata.get(DocumentMetadataKeys.DOCUMENT_TEXT);
String textEntryName =
ParameterProcessing.TEXT
+ "/"
+ UPIFormat.format(outputFileCount)
+ "_"
+ originalFileName
+ ".txt";
if (textEntryName != null) {
zipFileWriter.addTextFile(textEntryName, documentText);
}
columnMetadata.addMetadataValue(DocumentMetadataKeys.LINK_TEXT, textEntryName);
// add the native file to the native folder
String nativeEntryName =
ParameterProcessing.NATIVE
+ "/"
+ UPIFormat.format(outputFileCount)
+ "_"
+ originalFileName;
BytesWritable bytesWritable = (BytesWritable) value.get(new Text(ParameterProcessing.NATIVE));
if (bytesWritable != null) { // some large exception files are not passed
zipFileWriter.addBinaryFile(
nativeEntryName, bytesWritable.getBytes(), bytesWritable.getLength());
logger.trace("Processing file: {}", nativeEntryName);
}
columnMetadata.addMetadataValue(DocumentMetadataKeys.LINK_NATIVE, nativeEntryName);
// add the pdf made from native to the PDF folder
String pdfNativeEntryName =
ParameterProcessing.PDF_FOLDER
+ "/"
+ UPIFormat.format(outputFileCount)
+ "_"
+ new File(allMetadata.get(DocumentMetadataKeys.DOCUMENT_ORIGINAL_PATH)).getName()
+ ".pdf";
BytesWritable pdfBytesWritable =
(BytesWritable) value.get(new Text(ParameterProcessing.NATIVE_AS_PDF));
if (pdfBytesWritable != null) {
zipFileWriter.addBinaryFile(
pdfNativeEntryName, pdfBytesWritable.getBytes(), pdfBytesWritable.getLength());
logger.trace("Processing file: {}", pdfNativeEntryName);
}
processHtmlContent(value, allMetadata, UPIFormat.format(outputFileCount));
// add exception to the exception folder
String exception = allMetadata.get(DocumentMetadataKeys.PROCESSING_EXCEPTION);
if (exception != null) {
String exceptionEntryName =
"exception/"
+ UPIFormat.format(outputFileCount)
+ "_"
+ new File(allMetadata.get(DocumentMetadataKeys.DOCUMENT_ORIGINAL_PATH)).getName();
if (bytesWritable != null) {
zipFileWriter.addBinaryFile(
exceptionEntryName, bytesWritable.getBytes(), bytesWritable.getLength());
}
columnMetadata.addMetadataValue(DocumentMetadataKeys.LINK_EXCEPTION, exceptionEntryName);
}
// write this all to the reduce map
// context.write(new Text(outputKey), new Text(columnMetadata.delimiterSeparatedValues()));
// drop the key altogether, because it messes up the format - but put it in the value
// TODO use NullWritable
if (OsUtil.isNix()) {
context.write(null, new Text(columnMetadata.delimiterSeparatedValues()));
}
// prepare for the next file with the same key, if there is any
first = false;
}