/**
* Copyright (C) 2012-2013 Selventa, Inc.
*
* This file is part of the OpenBEL Framework.
*
* This program is free software; you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* The OpenBEL Framework is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
* License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with the OpenBEL Framework. If not, see <http://www.gnu.org/licenses/>.
*
* Additional Terms under LGPL v3:
*
* This license does not authorize you and you are prohibited from using the
* name, trademarks, service marks, logos or similar indicia of Selventa, Inc.,
* or, in the discretion of other licensors or authors of the program, the
* name, trademarks, service marks, logos or similar indicia of such authors or
* licensors, in any marketing or advertising materials relating to your
* distribution of the program or any covered product. This restriction does
* not waive or limit your obligation to keep intact all copyright notices set
* forth in the program as delivered to you.
*
* If you distribute the program in whole or in part, or any modified version
* of the program, and you assume contractual liability to the recipient with
* respect to the program or modified version, then you will indemnify the
* authors and licensors of the program for any liabilities that these
* contractual assumptions directly impose on those licensors and authors.
*/
package org.openbel.framework.core.df.beldata;
import java.io.File;
import java.io.IOException;
import java.io.RandomAccessFile;
import java.util.LinkedHashMap;
import java.util.Map;
import java.util.Properties;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
/**
* BELDataHeaderParser represents a BEL data document parser for the header
* section. This parser understands header blocks and block properties like
*
* <pre>
* [SomeValue]
* PropertyKey1=PropertyValue1
* PropertyKey2=PropertyValue2
* </pre>
*
* Block header values, property key, and property values are all trimmed of
* leading/trailing whitespace using {@link String#trim()}. Additionally, lines
* that are blank or start with the comment character '#' are ignored.
*
* @author Anthony Bargnesi {@code <abargnesi@selventa.com>}
*/
public abstract class BELDataHeaderParser {
private static final Pattern PROPERTY_LINE_REGEX = Pattern
.compile("([a-zA-Z0-9\\s]+)\\=(.*)");
private static final String VALUES_BLOCK = "Values";
/**
* Defines the next character stop offset and initializes it to -1.
*/
private long nextCharacterOffset = -1;
/**
* Retrieves the next character offset of the file parsed.
*
* @return long, the character stop offset, some positive number indicating
* the offset of the next character to read, which could be -1 if
* the file was fully read
*/
public long getNextCharacterOffset() {
return nextCharacterOffset;
}
/**
* Parse the BEL Data header {@link File} to a {@link Map} of block name
* to block properties held in a {@link Properties} object.
*
* @param belDataFile {@link File}, the BEL data document file to parse
* @return {@link Map} of {@link String} to {@link Properties} the
* properties indexed in a block name
* @throws IOException, if there was an error reading from {@code belDataFile}
*/
public Map<String, Properties> parse(File belDataFile) throws IOException {
RandomAccessFile raf = null;
try {
raf = new RandomAccessFile(belDataFile, "r");
Map<String, Properties> blockProperties =
new LinkedHashMap<String, Properties>();
String line;
String currentBlock = null;
boolean aborted = false;
while (!aborted && (line = raf.readLine()) != null) {
line = line.trim();
if (line.startsWith("#") || line.equals("")) {
// skip commented or blank lines.
continue;
} else if (line.charAt(0) == '['
&& line.charAt(line.length() - 1) == ']') {
currentBlock = line.substring(1, line.length() - 1).trim();
// if we have reached the VALUE_BLOCK then we're done
// parsing the header.
if (VALUES_BLOCK.equals(currentBlock)) {
nextCharacterOffset = raf.getFilePointer();
aborted = true;
continue;
}
blockProperties.put(currentBlock, new Properties());
} else {
Matcher propertyLineMatcher = PROPERTY_LINE_REGEX
.matcher(line);
if (propertyLineMatcher.matches()) {
blockProperties.get(currentBlock).put(
propertyLineMatcher.group(1).trim(),
propertyLineMatcher.group(2).trim());
}
}
}
return blockProperties;
} finally {
if (raf != null) {
raf.close();
}
}
}
}