/**
* Delete directory with everything underneath. Note that in the case of *nix we use 'rm -fr
* <dir>, because of the known problems with recursive deletes, and because 'rm -fr' is probably
* faster.
*
* @param dir directory to delete.
* @throws IOException on any problem with delete.
*/
public static void deleteDirectory(File dir) throws IOException {
if (OsUtil.isNix()) {
OsUtil.runCommand("rm -fr " + dir.getPath());
} else {
FileUtils.deleteDirectory(dir);
}
}
@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();
}
private void mergeLuceneIndex() throws IOException {
String luceneDir = Settings.getSettings().getLuceneIndexDir();
String hdfsLuceneDir =
"/" + luceneDir + File.separator + Project.getProject().getProjectCode() + File.separator;
String localLuceneTempDir = luceneDir + File.separator + "tmp" + File.separator;
File localLuceneTempDirFile = new File(localLuceneTempDir);
if (localLuceneTempDirFile.exists()) {
Util.deleteDirectory(localLuceneTempDirFile);
}
localLuceneTempDirFile.mkdir();
// copy all zip lucene indexes, created by maps to local hd
String cmd = "hadoop fs -copyToLocal " + hdfsLuceneDir + "* " + localLuceneTempDir;
OsUtil.runCommand(cmd);
// remove the map indexes as they are now copied to local
String removeOldZips = "hadoop fs -rm " + hdfsLuceneDir + "*";
OsUtil.runCommand(removeOldZips);
logger.trace("Lucene index files collected to: {}", localLuceneTempDirFile.getAbsolutePath());
String[] zipFilesArr = localLuceneTempDirFile.list();
for (String indexZipFileStr : zipFilesArr) {
String indexZipFileName = localLuceneTempDir + indexZipFileStr;
String unzipToDir = localLuceneTempDir + indexZipFileStr.replace(".zip", "");
ZipUtil.unzipFile(indexZipFileName, unzipToDir);
File indexDir = new File(unzipToDir);
FSDirectory fsDir = FSDirectory.open(indexDir);
luceneIndex.addToIndex(fsDir);
}
// TODO check if we need to push the index to S3 or somewhere else
luceneIndex.destroy();
}
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;
}
