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/*
* Copyright 2013-2024, Seqera Labs
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package nextflow.io;
/*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may not use this file except in compliance with
* the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
import java.io.IOException;
import java.io.InputStream;
import java.io.Reader;
import java.nio.ByteBuffer;
import java.nio.CharBuffer;
import java.nio.charset.Charset;
import java.nio.charset.CharsetEncoder;
import java.nio.charset.CoderResult;
import java.nio.charset.CodingErrorAction;
/**
* {@link InputStream} implementation that reads a character stream from a {@link Reader}
* and transforms it to a byte stream using a specified charset encoding. The stream
* is transformed using a {@link CharsetEncoder} object, guaranteeing that all charset
* encodings supported by the JRE are handled correctly. In particular for charsets such as
* UTF-16, the implementation ensures that one and only one byte order marker
* is produced.
*
* Since in general it is not possible to predict the number of characters to be read from the
* {@link Reader} to satisfy a read request on the {@link ReaderInputStream}, all reads from
* the {@link Reader} are buffered. There is therefore no well defined correlation
* between the current position of the {@link Reader} and that of the {@link ReaderInputStream}.
* This also implies that in general there is no need to wrap the underlying {@link Reader}
* in a {@link java.io.BufferedReader}.
*
* {@link ReaderInputStream} implements the inverse transformation of {@link java.io.InputStreamReader};
* in the following example, reading from in2 would return the same byte
* sequence as reading from in (provided that the initial byte sequence is legal
* with respect to the charset encoding):
*
* InputStream in = ...
* Charset cs = ...
* InputStreamReader reader = new InputStreamReader(in, cs);
* ReaderInputStream in2 = new ReaderInputStream(reader, cs);
* {@link ReaderInputStream} implements the same transformation as {@link java.io.OutputStreamWriter},
* except that the control flow is reversed: both classes transform a character stream
* into a byte stream, but {@link java.io.OutputStreamWriter} pushes data to the underlying stream,
* while {@link ReaderInputStream} pulls it from the underlying stream.
*
* Note that while there are use cases where there is no alternative to using
* this class, very often the need to use this class is an indication of a flaw
* in the design of the code. This class is typically used in situations where an existing
* API only accepts an {@link InputStream}, but where the most natural way to produce the data
* is as a character stream, i.e. by providing a {@link Reader} instance. An example of a situation
* where this problem may appear is when implementing the {@link javax.activation.DataSource}
* interface from the Java Activation Framework.
*
* Given the fact that the {@link Reader} class doesn't provide any way to predict whether the next
* read operation will block or not, it is not possible to provide a meaningful
* implementation of the {@link InputStream#available()} method. A call to this method
* will always return 0. Also, this class doesn't support {@link InputStream#mark(int)}.
*
* Instances of {@link ReaderInputStream} are not thread safe.
*
* @see WriterOutputStream
*
* @since 2.0
*/
public class ReaderInputStream extends InputStream {
private static final int DEFAULT_BUFFER_SIZE = 1024;
private final Reader reader;
private final CharsetEncoder encoder;
/**
* CharBuffer used as input for the decoder. It should be reasonably
* large as we read data from the underlying Reader into this buffer.
*/
private final CharBuffer encoderIn;
/**
* ByteBuffer used as output for the decoder. This buffer can be small
* as it is only used to transfer data from the decoder to the
* buffer provided by the caller.
*/
private final ByteBuffer encoderOut;
private CoderResult lastCoderResult;
private boolean endOfInput;
/**
* Construct a new {@link ReaderInputStream}.
*
* @param reader the target {@link Reader}
* @param encoder the charset encoder
* @since 2.1
*/
public ReaderInputStream(Reader reader, CharsetEncoder encoder) {
this(reader, encoder, DEFAULT_BUFFER_SIZE);
}
/**
* Construct a new {@link ReaderInputStream}.
*
* @param reader the target {@link Reader}
* @param encoder the charset encoder
* @param bufferSize the size of the input buffer in number of characters
* @since 2.1
*/
public ReaderInputStream(Reader reader, CharsetEncoder encoder, int bufferSize) {
this.reader = reader;
this.encoder = encoder;
this.encoderIn = CharBuffer.allocate(bufferSize);
this.encoderIn.flip();
this.encoderOut = ByteBuffer.allocate(128);
this.encoderOut.flip();
}
/**
* Construct a new {@link ReaderInputStream}.
*
* @param reader the target {@link Reader}
* @param charset the charset encoding
* @param bufferSize the size of the input buffer in number of characters
*/
public ReaderInputStream(Reader reader, Charset charset, int bufferSize) {
this(reader,
charset.newEncoder()
.onMalformedInput(CodingErrorAction.REPLACE)
.onUnmappableCharacter(CodingErrorAction.REPLACE),
bufferSize);
}
/**
* Construct a new {@link ReaderInputStream} with a default input buffer size of
* 1024 characters.
*
* @param reader the target {@link Reader}
* @param charset the charset encoding
*/
public ReaderInputStream(Reader reader, Charset charset) {
this(reader, charset, DEFAULT_BUFFER_SIZE);
}
/**
* Construct a new {@link ReaderInputStream}.
*
* @param reader the target {@link Reader}
* @param charsetName the name of the charset encoding
* @param bufferSize the size of the input buffer in number of characters
*/
public ReaderInputStream(Reader reader, String charsetName, int bufferSize) {
this(reader, Charset.forName(charsetName), bufferSize);
}
/**
* Construct a new {@link ReaderInputStream} with a default input buffer size of
* 1024 characters.
*
* @param reader the target {@link Reader}
* @param charsetName the name of the charset encoding
*/
public ReaderInputStream(Reader reader, String charsetName) {
this(reader, charsetName, DEFAULT_BUFFER_SIZE);
}
/**
* Construct a new {@link ReaderInputStream} that uses the default character encoding
* with a default input buffer size of 1024 characters.
*
* @param reader the target {@link Reader}
*/
public ReaderInputStream(Reader reader) {
this(reader, Charset.defaultCharset());
}
/**
* Fills the internal char buffer from the reader.
*
* @throws IOException
* If an I/O error occurs
*/
private void fillBuffer() throws IOException {
if (!endOfInput && (lastCoderResult == null || lastCoderResult.isUnderflow())) {
encoderIn.compact();
int position = encoderIn.position();
// We don't use Reader#read(CharBuffer) here because it is more efficient
// to write directly to the underlying char array (the default implementation
// copies data to a temporary char array).
int c = reader.read(encoderIn.array(), position, encoderIn.remaining());
if (c == -1) {
endOfInput = true;
} else {
encoderIn.position(position+c);
}
encoderIn.flip();
}
encoderOut.compact();
lastCoderResult = encoder.encode(encoderIn, encoderOut, endOfInput);
encoderOut.flip();
}
/**
* Read the specified number of bytes into an array.
*
* @param b the byte array to read into
* @param off the offset to start reading bytes into
* @param len the number of bytes to read
* @return the number of bytes read or -1
* if the end of the stream has been reached
* @throws IOException if an I/O error occurs
*/
@Override
public int read(byte[] b, int off, int len) throws IOException {
if (b == null) {
throw new NullPointerException("Byte array must not be null");
}
if (len < 0 || off < 0 || (off + len) > b.length) {
throw new IndexOutOfBoundsException("Array Size=" + b.length +
", offset=" + off + ", length=" + len);
}
int read = 0;
if (len == 0) {
return 0; // Always return 0 if len == 0
}
while (len > 0) {
if (encoderOut.hasRemaining()) {
int c = Math.min(encoderOut.remaining(), len);
encoderOut.get(b, off, c);
off += c;
len -= c;
read += c;
} else {
fillBuffer();
if (endOfInput && !encoderOut.hasRemaining()) {
break;
}
}
}
return read == 0 && endOfInput ? -1 : read;
}
/**
* Read the specified number of bytes into an array.
*
* @param b the byte array to read into
* @return the number of bytes read or -1
* if the end of the stream has been reached
* @throws IOException if an I/O error occurs
*/
@Override
public int read(byte[] b) throws IOException {
return read(b, 0, b.length);
}
/**
* Read a single byte.
*
* @return either the byte read or -1 if the end of the stream
* has been reached
* @throws IOException if an I/O error occurs
*/
@Override
public int read() throws IOException {
for (;;) {
if (encoderOut.hasRemaining()) {
return encoderOut.get() & 0xFF;
} else {
fillBuffer();
if (endOfInput && !encoderOut.hasRemaining()) {
return -1;
}
}
}
}
/**
* Close the stream. This method will cause the underlying {@link Reader}
* to be closed.
* @throws IOException if an I/O error occurs
*/
@Override
public void close() throws IOException {
reader.close();
}
}