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/* Copyright (c) 2009 Peter Troshin
*
* JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0
*
* This library is free software; you can redistribute it and/or modify it under the terms of the
* Apache License version 2 as published by the Apache Software Foundation
*
* This library 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 Apache
* License for more details.
*
* A copy of the license is in apache_license.txt. It is also available here:
* @see: http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Any republication or derived work distributed in source code form
* must include this copyright and license notice.
*/
package compbio.engine.client;
import java.util.Collections;
import java.util.Map;
import org.apache.log4j.Logger;
import compbio.util.Util;
public class EnvVariableProcessor {
/**
* Special variable keys Absolute path(s) will be merged with the content of
* the system PATH variable
*/
public static final String PATH = "PATH";
private static Logger log = Logger.getLogger(EnvVariableProcessor.class);
private static final String PROP_NAME_VALUE_SEPARATOR = "#";
private static final String NEXT_ENV_PROPERTY_DELIMITER = ";";
static boolean containsMultipleVariables(String property) {
String[] arr = property.split(NEXT_ENV_PROPERTY_DELIMITER);
if (arr.length == 0) {
return false;
}
return true;
}
static String[] getEnvVariableList(String property) {
property = property.trim();
if (containsMultipleVariables(property)) {
return property.split(NEXT_ENV_PROPERTY_DELIMITER);
}
return new String[]{property};
}
static String getEnvVariableName(String property) {
return property.split(PROP_NAME_VALUE_SEPARATOR)[0];
}
static String getEnvVariableValue(String property) {
String[] vars = property.split(PROP_NAME_VALUE_SEPARATOR);
if (vars.length > 2) {
throw new IllegalArgumentException(
"Must be only one value per property! Make sure the property does not contain '"
+ PROP_NAME_VALUE_SEPARATOR + "' symbol!");
}
if (vars.length == 0 || vars.length==1) {
log.warn("Environmental variable '"+property+"' does not have a value!");
return "";
}
return vars[1];
}
static boolean isValidEnvVariableProperty(String property) {
if (property == null) {
return false;
}
return property.contains(PROP_NAME_VALUE_SEPARATOR);
}
/*
* This is a horrible hack, but it only requires to simplify configuration
* for users, could be removed at any time if proved to be a burden to
* maintanance.
*/
private final static String mafft_binaries = "MAFFT_BINARIES";
private final static String fasta4mafft = "FASTA_4_MAFFT";
private final static String iupred_path = "IUPred_PATH";
public static Map<String, String> getEnvVariables(String property,
Class<?> clazz) {
Map<String, String> vars = Util.getNewHashMap();
if (!isValidEnvVariableProperty(property)) {
return Collections.emptyMap();
}
for (String evar : getEnvVariableList(property)) {
if (!isValidEnvVariableProperty(evar)) {
log.error(clazz.getName()
+ " environment variable is specified by is NOT VALID! Skipping. "
+ "Valid format is propertyName"
+ PROP_NAME_VALUE_SEPARATOR + "propertyValue. "
+ "Given values is: " + evar);
}
evar=evar.trim();
String varName = getEnvVariableName(evar);
String varValue = getEnvVariableValue(evar);
// absolutise local paths to mafft env variables
if (!PathValidator.isAbsolutePath(varValue)) {
varName = varName.trim();
if (varName.equalsIgnoreCase(mafft_binaries)
|| varName.equalsIgnoreCase(fasta4mafft)
|| varName.equalsIgnoreCase(iupred_path)) {
varValue = EngineUtil.convertToAbsolute(varValue);
}
}
vars.put(varName, varValue);
}
return vars;
}
}
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