org.coode.owlapi.obo12.parser.OBOIdType Maven / Gradle / Ivy
/*
* This file is part of the OWL API.
*
* The contents of this file are subject to the LGPL License, Version 3.0.
*
* Copyright (C) 2011, The University of Manchester
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see http://www.gnu.org/licenses/.
*
*
* Alternatively, the contents of this file may be used under the terms of the Apache License, Version 2.0
* in which case, the provisions of the Apache License Version 2.0 are applicable instead of those above.
*
* Copyright 2011, The University of Manchester
*
* 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
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* distributed under the License is distributed on an "AS IS" BASIS,
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package org.coode.owlapi.obo12.parser;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import javax.annotation.Nonnull;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLOntologyID;
/**
* Author: Matthew Horridge
* Stanford University
* Bio-Medical Informatics Research Group
* Date: 19/04/2012
*
* Describes the types of OBO IDs that can be found in OBO Files. Taken from
* Section 2.5 of the OBO Syntax and Semantics Specification.
*
*/
@SuppressWarnings("all")
enum OBOIdType {
/**
* Any string with an http: or https: prefix.
*/
URL_AS_ID(Pattern.compile("(http:|https:)[^\\s]*"), new OBOIIdTranslator() {
@Override
public IRI getIRIFromOBOId(OWLOntologyID ontologyID,
IDSpaceManager idSpaceManager, String id) {
return IRI.create(id);
}
}),
/**
* Any unprefixed ID. Does not contain a colon character. The spec implies
* the empty string matches this ID.
*/
UNPREFIXED_ID(Pattern.compile("[^\\s:]*"), new OBOIIdTranslator() {
@Override
public IRI getIRIFromOBOId(OWLOntologyID ontologyID,
IDSpaceManager idSpaceManager, String id) {
StringBuilder sb = new StringBuilder();
if (!ontologyID.isAnonymous()) {
sb.append(ontologyID.getOntologyIRI());
} else {
sb.append("anonymous");
}
sb.append("#");
sb.append(id);
return IRI.create(sb.toString());
}
}),
/**
* Must contain a colon character in the ID. The idspace must only consist
* of Alpha-Chars and possibly an underscore. The local id must only consist
* of digits (possibly none).
*/
CANONICAL_PREFIXED_ID(
Pattern.compile("([A-Za-z][A-Za-z_]*):([0-9]*)"),
new OBOIIdTranslator() {
@Override
public IRI getIRIFromOBOId(OWLOntologyID ontologyID,
IDSpaceManager idSpaceManager, String id) {
Matcher matcher = CANONICAL_PREFIXED_ID.getPattern()
.matcher(id);
matcher.matches();
String idspace = matcher.group(1);
String localid = matcher.group(2);
String iriPrefix = idSpaceManager.getIRIPrefix(idspace);
StringBuilder sb = new StringBuilder();
sb.append(iriPrefix);
sb.append(idspace);
sb.append("_");
sb.append(localid);
return IRI.create(sb.toString());
}
}),
/**
* Must contain a colon character somewhere in the ID. Any kind of prefix
* plus a local Id. The prefix doesn't contain a colon character.
*/
NON_CANONICAL_PREFIXED_ID(
Pattern.compile("([^\\s:]*):([^\\s]*)"),
new OBOIIdTranslator() {
@Override
public IRI getIRIFromOBOId(OWLOntologyID ontologyID,
IDSpaceManager idSpaceManager, String id) {
Matcher matcher = NON_CANONICAL_PREFIXED_ID.getPattern()
.matcher(id);
matcher.matches();
String idspace = matcher.group(1);
String localid = matcher.group(2);
String iriPrefix = idSpaceManager.getIRIPrefix(idspace);
StringBuilder sb = new StringBuilder();
sb.append(iriPrefix);
sb.append(idspace);
sb.append("#_");
sb.append(localid);
return IRI.create(sb.toString());
}
});
private Pattern pattern;
private OBOIIdTranslator translator;
private OBOIdType(Pattern pattern, OBOIIdTranslator translator) {
this.pattern = pattern;
this.translator = translator;
}
/** @return the pattern */
public Pattern getPattern() {
return pattern;
}
/**
* @param ontologyID
* @param idSpaceManager
* @param oboId
* @return the translated iri
*/
@Nonnull
public IRI getIRIFromOBOId(OWLOntologyID ontologyID,
IDSpaceManager idSpaceManager, String oboId) {
return translator.getIRIFromOBOId(ontologyID, idSpaceManager, oboId);
}
/**
* Gets the OBOIdType for a given OBO ID.
*
* @param oboId
* The OBO ID. Must not be null.
* @return The OBOIdType for the specified oboId, or null if
* the specified oboId does not conform to any OBO Id type.
*/
public static OBOIdType getIdType(String oboId) {
if (oboId == null) {
throw new NullPointerException("oboId must not be null");
}
for (OBOIdType idType : values()) {
Pattern pattern = idType.getPattern();
Matcher matcher = pattern.matcher(oboId);
if (matcher.matches()) {
return idType;
}
}
return null;
}
private static interface OBOIIdTranslator {
IRI getIRIFromOBOId(OWLOntologyID ontologyID,
IDSpaceManager idSpaceManager, String id);
}
}