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A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
/*
* Copyright 2013-2019, Centre for Genomic Regulation (CRG)
*
* 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;
/*
* This source is a derivation of the
* https://commons.apache.org/proper/commons-exec/apidocs/src-html/org/apache/commons/exec/LogOutputStream.html
*
* @author Paolo Di Tommaso
*/
/*
* 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.ByteArrayOutputStream;
import java.io.IOException;
import java.io.OutputStream;
/**
* Base class to connect a logging system to the output and/or
* error stream of then external process. The implementation
* parses the incoming data to construct a line and passes
* the complete line to an user-defined implementation.
*
* @version $Id: LogOutputStream.java 1636056 2014-11-01 21:12:52Z ggregory $
*/
public abstract class LogOutputStream
extends OutputStream {
/** Initial buffer size. */
private static final int INTIAL_SIZE = 132;
/** Carriage return */
private static final int CR = 0x0d;
/** Linefeed */
private static final int LF = 0x0a;
/** the internal buffer */
private final ByteArrayOutputStream buffer = new ByteArrayOutputStream(
INTIAL_SIZE);
private boolean skip = false;
private final int level;
/**
* Creates a new instance of this class.
* Uses the default level of 999.
*/
public LogOutputStream() {
this(999);
}
/**
* Creates a new instance of this class.
*
* @param level loglevel used to log data written to this stream.
*/
public LogOutputStream(final int level) {
this.level = level;
}
/**
* Write the data to the buffer and flush the buffer, if a line separator is
* detected.
*
* @param cc data to log (byte).
* @see java.io.OutputStream#write(int)
*/
@Override
public void write(final int cc) throws IOException {
final byte c = (byte) cc;
if (c == '\n' || c == '\r') {
if (!skip) {
processBuffer();
}
} else {
buffer.write(cc);
}
skip = c == '\r';
}
/**
* Flush this log stream.
*
* @see java.io.OutputStream#flush()
*/
@Override
public void flush() {
if (buffer.size() > 0) {
processBuffer();
}
}
/**
* Writes all remaining data from the buffer.
*
* @see java.io.OutputStream#close()
*/
@Override
public void close() throws IOException {
if (buffer.size() > 0) {
processBuffer();
}
super.close();
}
/**
* @return the trace level of the log system
*/
public int getMessageLevel() {
return level;
}
/**
* Write a block of characters to the output stream
*
* @param b the array containing the data
* @param off the offset into the array where data starts
* @param len the length of block
* @throws java.io.IOException if the data cannot be written into the stream.
* @see java.io.OutputStream#write(byte[], int, int)
*/
@Override
public void write(final byte[] b, final int off, final int len)
throws IOException {
// find the line breaks and pass other chars through in blocks
int offset = off;
int blockStartOffset = offset;
int remaining = len;
while (remaining > 0) {
while (remaining > 0 && b[offset] != LF && b[offset] != CR) {
offset++;
remaining--;
}
// either end of buffer or a line separator char
final int blockLength = offset - blockStartOffset;
if (blockLength > 0) {
buffer.write(b, blockStartOffset, blockLength);
}
while (remaining > 0 && (b[offset] == LF || b[offset] == CR)) {
write(b[offset]);
offset++;
remaining--;
}
blockStartOffset = offset;
}
}
/**
* Converts the buffer to a string and sends it to {@code processLine}.
*/
protected void processBuffer() {
processLine(buffer.toString());
buffer.reset();
}
/**
* Logs a line to the log system of the user.
*
* @param line
* the line to log.
*/
protected void processLine(final String line) {
processLine(line, level);
}
/**
* Logs a line to the log system of the user.
*
* @param line the line to log.
* @param logLevel the log level to use
*/
protected abstract void processLine(final String line, final int logLevel);
}