// BridgeDb,
// An abstraction layer for identifier mapping services, both local and online.
//
// Copyright 2006-2009 BridgeDb developers
// Copyright 2012-2013 Christian Y. A. Brenninkmeijer
// Copyright 2012-2013 OpenPhacts
//
// 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 org.bridgedb.uri.tools;
import java.util.Collection;
import java.util.HashSet;
import java.util.Set;
import java.util.TreeSet;
import java.util.regex.Pattern;
import org.bridgedb.DataSource;
import org.bridgedb.DataSourcePatterns;
import org.bridgedb.rdf.UriPattern;
import org.bridgedb.rdf.UriPatternType;
import org.bridgedb.rdf.pairs.RdfBasedCodeMapper;
import org.bridgedb.utils.BridgeDBException;
/**
*
* @author Christian
*/
public class RegexUriPattern {
private final String prefix;
private final String postfix;
private final String sysCode;
private final Pattern regex;
static boolean initialized = false;
private RegexUriPattern(String prefix, String postfix, String sysCode, Pattern regex) throws BridgeDBException{
if (prefix == null || prefix.isEmpty()){
throw new BridgeDBException ("Illegal prefixe " + prefix);
}
this.prefix = prefix;
if (postfix != null){
this.postfix = postfix;
} else {
this.postfix = "";
}
this.sysCode = sysCode;
this.regex = regex;
}
/**
* @return the prefix
*/
public String getPrefix() {
return prefix;
}
/**
* @return the postfix
*/
public String getPostfix() {
return postfix;
}
/**
* @return the sysCode
*/
public String getSysCode() {
return sysCode;
}
public Pattern getRegex() {
return regex;
}
public String getUri(String id) {
return prefix + id + postfix;
}
public String toString(){
String result = getUri("$id");// + " -> " + sysCode;
if (regex != null){
result = result + " (" + regex.pattern() + ")";
}
result+= " for DataSource " + sysCode;
return result;
}
public String getUriPattern() {
//TODO handle regex
return getUri("$id");
}
public Set<UriPattern> mapsTo() throws BridgeDBException{
TreeSet<UriPattern> possibles = new TreeSet<UriPattern>(UriPattern.byCode(sysCode));
UriPattern asPattern = UriPattern.byPattern(getUriPattern());
possibles.remove(asPattern);
return possibles;
}
private static Pattern shortenRegex(Pattern regex, String sysCode) throws BridgeDBException{
if (regex == null){
return null;
}
String xrefPrefix = RdfBasedCodeMapper.getXrefPrefix(sysCode);
String fullPattern = regex.pattern();
if (fullPattern.startsWith(xrefPrefix)){
String partPattern = fullPattern.substring(xrefPrefix.length());
return Pattern.compile(partPattern);
} else if (fullPattern.startsWith("^" + xrefPrefix)){
String partPattern = "^" + fullPattern.substring(1 + xrefPrefix.length());
return Pattern.compile(partPattern);
} else {
throw new BridgeDBException ("Unable to convert Pattern " + regex.pattern() + " for code " + sysCode
+ " based on xrefprefix " + xrefPrefix);
}
}
public static RegexUriPattern factory(String prefix, String postfix, String sysCode) throws BridgeDBException {
return new RegexUriPattern(prefix, postfix, sysCode, null);
}
public static RegexUriPattern factory(String prefix, String postfix, String sysCode, Pattern regexPattern) throws BridgeDBException {
return new RegexUriPattern(prefix, postfix, sysCode, regexPattern);
}
public static RegexUriPattern factory(UriPattern uriPattern, String sysCode) throws BridgeDBException{
DataSource dataSource = DataSource.getExistingBySystemCode(sysCode);
Pattern regex = DataSourcePatterns.getPatterns().get(dataSource);
String xrefPrefix = RdfBasedCodeMapper.getXrefPrefix(sysCode);
String prefix;
String postfix = uriPattern.getPostfix();
if (xrefPrefix == null){
prefix = uriPattern.getPrefix();
} else if (uriPattern.getType() == UriPatternType.codeMapperPattern){
//prefix should not include the xrefPrefix
prefix = uriPattern.getPrefix();
regex = shortenRegex(regex, sysCode);
} else {
//prefix should include the xrefPrefix as regex and IDs no longer do
prefix = uriPattern.getPrefix() + xrefPrefix;
regex = shortenRegex(regex, sysCode);
}
return new RegexUriPattern(prefix, postfix, sysCode, regex);
}
public static Collection<RegexUriPattern> getUriPatterns() throws BridgeDBException {
HashSet<RegexUriPattern> results = new HashSet<RegexUriPattern>();
for (UriPattern pattern:UriPattern.getUriPatterns()){
for (String sysCode:pattern.getSysCodes()){
RegexUriPattern regexPattern = factory(pattern, sysCode);
results.add(regexPattern);
}
}
return results;
}
public static Set<RegexUriPattern> existingByPattern(String pattern) throws BridgeDBException {
//todo regex in pattern
UriPattern uriPattern = UriPattern.existingByPattern(pattern);
return byPattern(uriPattern);
}
public static Set<RegexUriPattern> byPattern(UriPattern uriPattern) throws BridgeDBException {
Set<String> possibleSysCodes = uriPattern.getSysCodes();
HashSet<RegexUriPattern> results = new HashSet<RegexUriPattern>();
for (String possibleSysCode:possibleSysCodes){
results.add(factory(uriPattern, possibleSysCode));
}
return results;
}
/*private static String extractShortName (String full) throws BridgeDBException {
String withoutStart;
if (full.startsWith("ftp://")){
withoutStart = full.substring(6);
} else if (full.startsWith("http://")){
withoutStart = full.substring(7);
} else if (full.startsWith("https://")){
withoutStart = full.substring(8);
} else {
withoutStart = full;
}
if (withoutStart.startsWith("ftp.")){
withoutStart = withoutStart.substring(4);
}
if (withoutStart.startsWith("rdf.")){
withoutStart = withoutStart.substring(4);
}
if (withoutStart.startsWith("www.")){
withoutStart = withoutStart.substring(4);
}
if (withoutStart.indexOf("/") > 0){
return withoutStart.substring(0, withoutStart.indexOf("/"));
} else {
return withoutStart;
}
}*/
/*public static HashMap<String, Integer> getUriGroups() throws BridgeDBException {
Set<UriPattern> patterns = UriPattern.getUriPatterns();
HashMap<String, Integer> results = new HashMap<String, Integer>();
for (UriPattern pattern:UriPattern.getUriPatterns()){
String mid = extractShortName(pattern.getUriPattern());
Integer count = results.get(mid);
if (count == null){
count = pattern.getSysCodes().size();
} else {
count+= pattern.getSysCodes().size();
}
results.put(mid, count);
}
return results;
}*/
/*public static void refreshUriPatterns() throws BridgeDBException{
if (initialized){
return;
}
UriPattern.refreshUriPatterns();
init();
initialized = true;
}*/
/*public static void init() throws BridgeDBException {
Reporter.println("RegexUriPattern init");
Set<UriPattern> patterns = UriPattern.getUriPatterns();
HashMap<String, Integer> results = new HashMap<String, Integer>();
for (UriPattern pattern:UriPattern.getUriPatterns()){
String mid = extractShortName(pattern.getUriPattern());
Set<RegexUriPattern> byShortName = getByShortNames().get(mid);
if (byShortName == null){
byShortName = new HashSet<RegexUriPattern>();
}
byShortName.addAll(byPattern(pattern));
getByShortNames().put(mid, byShortName);
}
}*/
@Override
public boolean equals(Object otherObject){
if (!(otherObject instanceof RegexUriPattern)){
return false;
}
RegexUriPattern other = (RegexUriPattern)otherObject;
if (!this.prefix.equals(other.prefix)){
return false;
}
if (!this.sysCode.equals(other.sysCode)){
return false;
}
if (this.postfix == null){
if (other.postfix != null){
return false;
}
} else {
if (!other.postfix.equals(postfix)){
return false;
}
}
if (this.regex == null){
if (other.regex != null){
return false;
}
} else {
if (other.regex == null){
return false;
}
if (!this.regex.pattern().equals(other.regex.pattern())){
return false;
}
}
return true;
}
@Override
public int hashCode() {
String full = sysCode + "--" + prefix;
if (regex != null){
full = full + regex;
}
if (prefix != null){
full = full + prefix;
}
return full.hashCode();
}
}