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/*
* The MIT License (MIT)
* Copyright (c) 2016-2017 Intel Corporation
*
* Permission is hereby granted, free of charge, to any person obtaining a copy of
* this software and associated documentation files (the "Software"), to deal in
* the Software without restriction, including without limitation the rights to
* use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
* the Software, and to permit persons to whom the Software is furnished to do so,
* subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
* FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
* COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
* IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
* CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.genomicsdb;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import java.io.*;
public class GenomicsDBLibLoader {
public final static String GENOMICSDB_LIBRARY_PATH = "genomicsdb.library.path";
private final static String GENOMICSDB_LIBRARY_NAME = "tiledbgenomicsdb";
private static boolean mIsLibraryLoaded = false;
private static Logger logger = LogManager.getLogger(GenomicsDBLibLoader.class);
private static native int jniGenomicsDBOneTimeInitialize();
public static synchronized boolean loadLibrary() {
if (mIsLibraryLoaded) return true;
try {
// If GENOMICSDB_LIBRARY_PATH is specified via -Dgenomicsdb.library.path=/path/to/lib then
// load library from GENOMICSDB_LIBRARY_PATH
String genomicsDBLibraryPath = System.getProperty(GENOMICSDB_LIBRARY_PATH);
if (genomicsDBLibraryPath != null && !genomicsDBLibraryPath.isEmpty()) {
File genomicsdbLibraryFile = new File(genomicsDBLibraryPath, System.mapLibraryName(GENOMICSDB_LIBRARY_NAME));
if (!genomicsdbLibraryFile.exists()) {
throw new RuntimeException("GenomicsDB library not found at " + genomicsDBLibraryPath);
}
System.load(genomicsdbLibraryFile.getAbsolutePath());
logger.info("GenomicsDB native library has been loaded from " + genomicsdbLibraryFile.getAbsolutePath());
} else {
loadLibraryFromJar("/" + System.mapLibraryName(GENOMICSDB_LIBRARY_NAME));
}
} catch (IOException e) {
logger.fatal("", e);
throw new RuntimeException("GenomicsDB native library could not be loaded", e);
}
jniGenomicsDBOneTimeInitialize();
mIsLibraryLoaded = true;
logger.info("GenomicsDB native library version : " + GenomicsDBUtils.nativeLibraryVersion());
return true;
}
//Copied from http://frommyplayground.com/how-to-load-native-jni-library-from-jar
/**
* Loads library from current JAR archive
* The file from JAR is copied into system temporary directory and then loaded. The temporary file is deleted after exiting.
* Method uses String as filename because the pathname is "abstract", not system-dependent.
*
* @param path The filename inside JAR as absolute path (beginning with '/'), e.g. /package/File.ext
* @throws IOException If temporary file creation or read/write operation fails
* @throws IllegalArgumentException If source file (param path) does not exist
* @throws IllegalArgumentException If the path is not absolute or if the filename is shorter than three characters (restriction of @see File#createTempFile(java.lang.String, java.lang.String)).
*/
private static void loadLibraryFromJar(String path) throws IOException {
if (!path.startsWith("/")) {
throw new IllegalArgumentException("The path should be absolute (start with '/').");
}
// Obtain filename from path
String[] parts = path.split("/");
String filename = (parts.length >= 1) ? parts[parts.length - 1] : null;
// Split filename to prefix and suffix (extension)
String prefix = "";
String suffix = null;
if (filename != null) {
parts = filename.split("\\.", 2);
prefix = parts[0];
suffix = (parts.length > 1) ? "." + parts[parts.length - 1] : null;
}
// Check if the filename is okay
if (filename == null || prefix.length() < 3) {
throw new IllegalArgumentException("The filename has to be at least 3 characters long.");
}
// Prepare temporary file
File temp = File.createTempFile(prefix, suffix);
temp.deleteOnExit();
if (!temp.exists()) {
throw new FileNotFoundException("File " + temp.getAbsolutePath() + " does not exist.");
}
// Prepare buffer for data copying
byte[] buffer = new byte[1024];
int readBytes;
// Open and check input stream
InputStream is = GenomicsDBLibLoader.class.getResourceAsStream(path);
if (is == null) {
throw new FileNotFoundException("File " + path + " was not found inside JAR.");
}
OutputStream os = null;
try {
os = new FileOutputStream(temp);
}
catch(FileNotFoundException e) {
is.close();
throw e;
}
try {
// Open output stream and copy data between source file in JAR and the temporary file
while ((readBytes = is.read(buffer)) != -1) {
os.write(buffer, 0, readBytes);
}
} finally {
IOException thrownException = null;
try {
os.flush();
}
catch(IOException e) {
thrownException = e;
}
// If read/write fails, close streams safely before throwing an exception
try {
os.close();
}
catch(IOException e) {
if(thrownException != null)
thrownException = e;
}
is.close();
if(thrownException != null)
throw thrownException;
}
// Finally, load the library
System.load(temp.getAbsolutePath());
}
}
