/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* 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.broad.igv.util.stream;
import htsjdk.samtools.seekablestream.SeekableStream;
import org.apache.log4j.Logger;
import org.broad.igv.util.HttpUtils;
import java.io.EOFException;
import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
/**
* A SeekableStream implementation for the "range" webservice. The purpose of this class is to serve range-byte
* requests to clients who are unable to use the http header for this.
* <p/>
* /xchip/igv/data/public/annotations/seq/hg18/chr1.txt
*/
public class SeekableServiceStream extends SeekableStream {
static Logger log = Logger.getLogger(SeekableServiceStream.class);
public static final String WEBSERVICE_URL = "https://portals.broadinstitute.org/webservices/igv/range";
private long position = 0;
private long contentLength = Long.MAX_VALUE;
private URL wrappedURL;
public SeekableServiceStream(URL url) {
this.wrappedURL = url;
}
public long length() {
if(contentLength == Long.MAX_VALUE) {
try {
contentLength = HttpUtils.getInstance().getContentLength(wrappedURL);
} catch (IOException e) {
log.error("Error fetching content length for: " + wrappedURL, e);
}
}
return contentLength;
}
public boolean eof() throws IOException {
return position >= contentLength;
}
@Override
public String getSource() {
return this.wrappedURL.toExternalForm();
}
public void seek(long position) {
this.position = position;
}
public long position() {
return position;
}
@Override
public long skip(long n) throws IOException {
position += n;
return n;
}
public int read(byte[] buffer, int offset, int length) throws IOException {
if (offset < 0 || length < 0 || (offset + length) > buffer.length) {
throw new IndexOutOfBoundsException();
}
InputStream is = null;
URL url = new URL(WEBSERVICE_URL + "?file=" + wrappedURL.toExternalForm() + "&position=" + position + "&length=" + length);
int n = 0;
try {
is = HttpUtils.getInstance().openConnectionStream(url);
while (n < length) {
int count = is.read(buffer, offset + n, length - n);
if (count < 0) {
return n;
}
n += count;
}
position += n;
return n;
} catch (IOException e) {
// THis is a bit of a hack, but its not clear how else to handle this. If a byte range is specified
// that goes past the end of the file the response code will be 416. The MAC os translates this to
// an IOException with the 416 code in the message. Windows translates the error to an EOFException.
//
// The BAM file iterator uses the return value to detect end of file (specifically looks for n == 0).
if (e.getMessage().contains("416") || (e instanceof EOFException)) {
return n;
} else {
throw e;
}
} finally {
if (is != null) {
is.close();
}
}
}
public void close() throws IOException {
// Nothing to do
}
public byte[] readBytes(long position, int nBytes) throws IOException {
this.position = position;
byte[] buffer = new byte[nBytes];
read(buffer, 0, nBytes);
return buffer;
}
public int read() throws IOException {
throw new UnsupportedOperationException("read() is not supported on SeekableServiceStream. Must read in blocks.");
}
}