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Merge pull request #4368 from dannysmyda/4519-control-tesseract-process-spawning

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4519 - Make tesseract.exe spawns for images cancellable
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Richard Cordovano 2018-12-14 09:51:08 -05:00 committed by GitHub
commit eb2029f199
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1 changed files with 212 additions and 40 deletions
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Core/src/org/sleuthkit/autopsy/textextractors/TikaTextExtractor.java
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@ -20,8 +20,12 @@ package org.sleuthkit.autopsy.textextractors;
import com.google.common.collect.ImmutableList;
import com.google.common.io.CharSource;
import com.google.common.util.concurrent.ThreadFactoryBuilder;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.io.PushbackReader;
import java.io.Reader;
import java.nio.file.Paths;
@ -29,9 +33,11 @@ import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
import java.util.Objects;
import java.util.concurrent.Callable;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Future;
import java.util.concurrent.ThreadFactory;
import java.util.concurrent.TimeUnit;
import java.util.concurrent.TimeoutException;
import java.util.logging.Level;
@ -50,8 +56,14 @@ import org.apache.tika.parser.pdf.PDFParserConfig;
import org.openide.util.NbBundle;
import org.openide.modules.InstalledFileLocator;
import org.openide.util.Lookup;
import org.sleuthkit.autopsy.casemodule.Case;
import org.sleuthkit.autopsy.casemodule.NoCurrentCaseException;
import org.sleuthkit.autopsy.coreutils.ExecUtil;
import org.sleuthkit.autopsy.coreutils.ExecUtil.ProcessTerminator;
import org.sleuthkit.autopsy.coreutils.PlatformUtil;
import org.sleuthkit.autopsy.datamodel.ContentUtils;
import org.sleuthkit.autopsy.textextractors.extractionconfigs.ImageFileExtractionConfig;
import org.sleuthkit.datamodel.AbstractFile;
import org.sleuthkit.datamodel.Content;
import org.sleuthkit.datamodel.ReadContentInputStream;
@ -110,7 +122,9 @@ final class TikaTextExtractor extends TextExtractor {
private static final java.util.logging.Logger tikaLogger = java.util.logging.Logger.getLogger("Tika"); //NON-NLS
private final ExecutorService tikaParseExecutor = Executors.newSingleThreadExecutor();
private final ThreadFactory tikaThreadFactory =
new ThreadFactoryBuilder().setNameFormat("tika-reader-%d").build();
private final ExecutorService executorService = Executors.newSingleThreadExecutor(tikaThreadFactory);
private static final String SQLITE_MIMETYPE = "application/x-sqlite3";
private final AutoDetectParser parser = new AutoDetectParser();
@ -121,6 +135,8 @@ final class TikaTextExtractor extends TextExtractor {
private static final String TESSERACT_EXECUTABLE = "tesseract.exe"; //NON-NLS
private static final File TESSERACT_PATH = locateTesseractExecutable();
private static final String LANGUAGE_PACKS = getLanguagePacks();
private ProcessTerminator processTerminator;
private static final String TESSERACT_OUTPUT_FILE_NAME = "output";
private static final List<String> TIKA_SUPPORTED_TYPES
= new Tika().getParser().getSupportedTypes(new ParseContext())
@ -132,6 +148,18 @@ final class TikaTextExtractor extends TextExtractor {
this.content = content;
}
/**
* If Tesseract has been installed and is set to be used through
* configuration, then ocr is enabled. OCR can only currently be run on
* Windows OS.
*
* @return Flag indicating if OCR is set to be used.
*/
private boolean ocrEnabled() {
return TESSERACT_PATH != null && tesseractOCREnabled
&& PlatformUtil.isWindowsOS() == true;
}
/**
* Returns a reader that will iterate over the text extracted from Apache
* Tika.
@ -145,12 +173,50 @@ final class TikaTextExtractor extends TextExtractor {
*/
@Override
public Reader getReader() throws ExtractionException {
ReadContentInputStream stream = new ReadContentInputStream(content);
InputStream stream = null;
Metadata metadata = new Metadata();
ParseContext parseContext = new ParseContext();
parseContext.set(Parser.class, parser);
if (ocrEnabled() && content instanceof AbstractFile) {
AbstractFile file = ((AbstractFile) content);
//Run OCR on images with Tesseract directly.
if (file.getMIMEType().toLowerCase().startsWith("image/")) {
stream = runOcrAndGetOutputStream(file);
} else {
//Otherwise, go through Tika for PDFs so that it can
//extract images and run Tesseract on them.
PDFParserConfig pdfConfig = new PDFParserConfig();
// Extracting the inline images and letting Tesseract run on each inline image.
// https://wiki.apache.org/tika/PDFParser%20%28Apache%20PDFBox%29
// https://tika.apache.org/1.7/api/org/apache/tika/parser/pdf/PDFParserConfig.html
pdfConfig.setExtractInlineImages(true);
// Multiple pages within a PDF file might refer to the same underlying image.
pdfConfig.setExtractUniqueInlineImagesOnly(true);
parseContext.set(PDFParserConfig.class, pdfConfig);
// Configure Tesseract parser to perform OCR
TesseractOCRConfig ocrConfig = new TesseractOCRConfig();
String tesseractFolder = TESSERACT_PATH.getParent();
ocrConfig.setTesseractPath(tesseractFolder);
/*
* Tesseract expects language data packs to be in a
* subdirectory of tesseractFolder, in a folder called
* "tessdata". If they are stored somewhere else, use
* ocrConfig.setTessdataPath(String tessdataPath) to point
* to them
*/
ocrConfig.setLanguage(LANGUAGE_PACKS);
parseContext.set(TesseractOCRConfig.class, ocrConfig);
stream = new ReadContentInputStream(content);
}
} else {
stream = new ReadContentInputStream(content);
}
Metadata metadata = new Metadata();
// Use the more memory efficient Tika SAX parsers for DOCX and
// PPTX files (it already uses SAX for XLSX).
OfficeParserConfig officeParserConfig = new OfficeParserConfig();
@ -158,60 +224,163 @@ final class TikaTextExtractor extends TextExtractor {
officeParserConfig.setUseSAXDocxExtractor(true);
parseContext.set(OfficeParserConfig.class, officeParserConfig);
// configure OCR if it is enabled in KWS settings and installed on the machine
if (TESSERACT_PATH != null && tesseractOCREnabled && PlatformUtil.isWindowsOS() == true) {
// configure PDFParser.
PDFParserConfig pdfConfig = new PDFParserConfig();
// Extracting the inline images and letting Tesseract run on each inline image.
// https://wiki.apache.org/tika/PDFParser%20%28Apache%20PDFBox%29
// https://tika.apache.org/1.7/api/org/apache/tika/parser/pdf/PDFParserConfig.html
pdfConfig.setExtractInlineImages(true);
// Multiple pages within a PDF file might refer to the same underlying image.
pdfConfig.setExtractUniqueInlineImagesOnly(true);
parseContext.set(PDFParserConfig.class, pdfConfig);
// Configure Tesseract parser to perform OCR
TesseractOCRConfig ocrConfig = new TesseractOCRConfig();
String tesseractFolder = TESSERACT_PATH.getParent();
ocrConfig.setTesseractPath(tesseractFolder);
// Tesseract expects language data packs to be in a subdirectory of tesseractFolder, in a folder called "tessdata".
// If they are stored somewhere else, use ocrConfig.setTessdataPath(String tessdataPath) to point to them
ocrConfig.setLanguage(LANGUAGE_PACKS);
parseContext.set(TesseractOCRConfig.class, ocrConfig);
}
//Parse the file in a task, a convenient way to have a timeout...
final Future<Reader> future = tikaParseExecutor.submit(() -> new ParsingReader(parser, stream, metadata, parseContext));
//Make the creation of a TikaReader a cancellable future in case it takes too long
Future<Reader> future = executorService.submit(
new GetTikaReader(parser, stream, metadata, parseContext));
try {
final Reader tikaReader = future.get(getTimeout(content.getSize()), TimeUnit.SECONDS);
final Reader tikaReader = future.get(getTimeout(content.getSize()),
TimeUnit.SECONDS);
//check if the reader is empty
PushbackReader pushbackReader = new PushbackReader(tikaReader);
int read = pushbackReader.read();
if (read == -1) {
throw new ExtractionException("Unable to extract text: Tika returned empty reader for " + content);
throw new ExtractionException("Unable to extract text: "
+ "Tika returned empty reader for " + content);
}
pushbackReader.unread(read);
//concatenate parsed content and meta data into a single reader.
CharSource metaDataCharSource = getMetaDataCharSource(metadata);
return CharSource.concat(new ReaderCharSource(pushbackReader), metaDataCharSource).openStream();
return CharSource.concat(new ReaderCharSource(pushbackReader),
metaDataCharSource).openStream();
} catch (TimeoutException te) {
final String msg = NbBundle.getMessage(this.getClass(), "AbstractFileTikaTextExtract.index.tikaParseTimeout.text", content.getId(), content.getName());
final String msg = NbBundle.getMessage(this.getClass(),
"AbstractFileTikaTextExtract.index.tikaParseTimeout.text",
content.getId(), content.getName());
throw new ExtractionException(msg, te);
} catch (ExtractionException ex) {
throw ex;
} catch (Exception ex) {
tikaLogger.log(Level.WARNING, "Exception: Unable to Tika parse the content" + content.getId() + ": " + content.getName(), ex.getCause()); //NON-NLS
final String msg = NbBundle.getMessage(this.getClass(), "AbstractFileTikaTextExtract.index.exception.tikaParse.msg", content.getId(), content.getName());
tikaLogger.log(Level.WARNING, "Exception: Unable to Tika parse the "
+ "content" + content.getId() + ": " + content.getName(),
ex.getCause()); //NON-NLS
final String msg = NbBundle.getMessage(this.getClass(),
"AbstractFileTikaTextExtract.index.exception.tikaParse.msg",
content.getId(), content.getName());
throw new ExtractionException(msg, ex);
} finally {
future.cancel(true);
}
}
/**
* Run OCR and return the file stream produced by Tesseract.
*
* @param file Image file to run OCR on
*
* @return InputStream connected to the output file that Tesseract produced.
*
* @throws
* org.sleuthkit.autopsy.textextractors.TextExtractor.ExtractionException
*/
private InputStream runOcrAndGetOutputStream(AbstractFile file) throws ExtractionException {
File inputFile = null;
File outputFile = null;
try {
//Appending file id makes the name unique
String tempFileName = file.getId() + file.getName();
inputFile = Paths.get(Case.getCurrentCaseThrows().getTempDirectory(),
tempFileName).toFile();
ContentUtils.writeToFile(content, inputFile);
String tempOutputName = file.getId() + TESSERACT_OUTPUT_FILE_NAME;
String outputFilePath = Paths.get(Case.getCurrentCaseThrows().getTempDirectory(),
tempOutputName).toString();
String executeablePath = TESSERACT_PATH.toString();
//Build tesseract commands
ProcessBuilder process = new ProcessBuilder();
process.command(executeablePath,
String.format("\"%s\"", inputFile.getAbsolutePath()),
String.format("\"%s\"", outputFilePath),
//language pack command flag
"-l", LANGUAGE_PACKS);
//If the ProcessTerminator was supplied during
//configuration apply it here.
if (processTerminator != null) {
ExecUtil.execute(process, 1, TimeUnit.SECONDS, processTerminator);
} else {
ExecUtil.execute(process);
}
outputFile = new File(outputFilePath + ".txt");
//Open a stream of the Tesseract text file and send this to Tika
return new CleanUpStream(outputFile);
} catch (NoCurrentCaseException | IOException ex) {
if (outputFile != null) {
outputFile.delete();
}
throw new ExtractionException("Could not successfully run Tesseract", ex);
} finally {
if (inputFile != null) {
inputFile.delete();
}
}
}
/**
* Wraps the creation of a TikaReader into a Future so that it can be
* cancelled.
*/
private class GetTikaReader implements Callable<Reader> {
private final AutoDetectParser parser;
private final InputStream stream;
private final Metadata metadata;
private final ParseContext parseContext;
public GetTikaReader(AutoDetectParser parser, InputStream stream,
Metadata metadata, ParseContext parseContext) {
this.parser = parser;
this.stream = stream;
this.metadata = metadata;
this.parseContext = parseContext;
}
@Override
public Reader call() throws Exception {
return new ParsingReader(parser, stream, metadata, parseContext);
}
}
/**
* Automatically deletes the underlying File when the close() method is
* called. This is used to delete the Output file produced from Tesseract
* once it has been read by Tika.
*/
private class CleanUpStream extends FileInputStream {
private File file;
/**
* Store a reference to file on construction
*
* @param file
* @throws FileNotFoundException
*/
public CleanUpStream(File file) throws FileNotFoundException {
super(file);
this.file = file;
}
/**
* Delete this underlying file when close is called.
*
* @throws IOException
*/
@Override
public void close() throws IOException {
try {
super.close();
} finally {
if (file != null) {
file.delete();
file = null;
}
}
}
}
/**
* Finds and returns the path to the Tesseract executable, if able.
*
@ -339,12 +508,15 @@ final class TikaTextExtractor extends TextExtractor {
public void setExtractionSettings(Lookup context) {
if (context != null) {
ImageFileExtractionConfig configInstance = context.lookup(ImageFileExtractionConfig.class);
if (configInstance == null) {
return;
}
if (Objects.nonNull(configInstance.getOCREnabled())) {
if (configInstance != null && Objects.nonNull(configInstance.getOCREnabled())) {
this.tesseractOCREnabled = configInstance.getOCREnabled();
}
ProcessTerminator terminatorInstance = context.lookup(ProcessTerminator.class);
if (terminatorInstance != null) {
this.processTerminator = terminatorInstance;
}
}
}