/*
* 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, 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
*
* 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.coode.owlapi.obo12.parser;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.semanticweb.owlapi.model.HasIRI;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLRuntimeException;
import org.semanticweb.owlapi.vocab.DublinCoreVocabulary;
import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
/**
* Author: Matthew Horridge<br>
* The University Of Manchester<br>
* Bio-Health Informatics Group<br>
* Date: 10-Jan-2007<br>
* <br>
*/
@SuppressWarnings("javadoc")
public enum OBOVocabulary implements HasIRI {
DATA_VERSION("data-version"), VERSION("version"), DATE("date",
DublinCoreVocabulary.DATE.getIRI()), SAVED_BY("saved-by"), AUTO_GENERATED_BY(
"auto-generated-by"), ONTOLOGY("ontology"), SUBSETDEF(
"subsetdef", OBOPrefix.OBO_IN_OWL,
"SubsetProperty"), IMPORT(
"import"), SYNONYM_TYPE_DEF(
"synonymtypedef",
OBOPrefix.OBO_IN_OWL,
"SynonymTypeProperty"), SYNONYM_TYPE(
"synonym-type",
OBOPrefix.OBO_IN_OWL,
"hasSynonymType"), ID_SPACE(
"id_space"), DEFAULT_RELATIONSHIP_ID_PREFIX(
"default-relationship-id-prefix"), ID_MAPPING(
"id-mapping"), REMARK(
"remark"), ID("id"), NAME(
"name",
OWLRDFVocabulary.RDFS_LABEL
.getIRI()), FORMAT_VERSION(
"format-version"), TYPEDEF(
"Typedef"), ALT_ID(
"alt_id",
OBOPrefix.OBO_IN_OWL,
"hasAlternativeId"), SHORT_HAND(
"shorthand",
OBOPrefix.OBO_IN_OWL,
"shorthand"), ALT_NAME(
"alt_name"), NAMESPACE(
"namespace"), DEFAULT_NAMESPACE(
"default-namespace"), DEF(
"def"), COMMENT("comment",
OWLRDFVocabulary.RDFS_COMMENT
.getIRI()), SUBSET(
"subset",
OBOPrefix.OBO_IN_OWL,
"inSubset"), SYNONYM(
"synonym"), HAS_SCOPE(
"hasScope",
OBOPrefix.OBO_IN_OWL), RELATED_SYNONYM(
"relatedSynonym",
OBOPrefix.OBO_IN_OWL,
"hasRelatedSynonym"), EXACT_SYNONYM(
"exactSynonym",
OBOPrefix.OBO_IN_OWL,
"hasExactSynonym"), BROAD_SYNONYM(
"broadSynonym",
OBOPrefix.OBO_IN_OWL,
"hasBroadSynonym"), NARROW_SYNONYM(
"narrowSynonym",
OBOPrefix.OBO_IN_OWL,
"hasNarrowSynonym"), XREF(
"xref",
OBOPrefix.OBO_IN_OWL), XREF_ANALOGUE(
"xref_analogue"), XREF_UNKNOWN(
"xref_unk"), IS_A(
"is_a"), IS_OBSOLETE(
"is_obsolete",
OWLRDFVocabulary.OWL_DEPRECATED
.getIRI()), PART_OF(
"part_of"), RELATIONSHIP(
"relationship"), REPLACED_BY(
"replaced_by"), CONSIDER(
"consider",
OBOPrefix.OBO_IN_OWL,
"consider"), USE_TERM(
"use_term"), DOMAIN(
"domain"), RANGE(
"range"), IS_CYCLIC(
"is_cyclic"), IS_TRANSITIVE(
"is_transitive"), IS_SYMMETRIC(
"is_symmetric"), IS_ASYMMETRIC(
"is_asymmetric"), IS_REFLEXIVE(
"is_reflexive"), INVERSE(
"inverse"), TRANSITIVE_OVER(
"transitive_over"), INTERSECTION_OF(
"intersection_of"), UNION_OF(
"union_of"), DISJOINT_FROM(
"disjoint_from"), TERM(
"Term"), BUILTIN(
"builtin"), IS_METADATA_TAG(
"is_metadata_tag"), CARDINALITY(
"cardinality"), MAX_CARDINALITY(
"maxCardinality"), MIN_CARDINALITY(
"minCardinality"), INSTANCE(
"Instance"), INSTANCE_OF(
"instance_of"), PROPERTY_VALUE(
"property_value"), IS_ANONYMOUS(
"is_anonymous");
/**
* @deprecated Use {@link #OBO_IRI_BASE}
*/
@Deprecated
public static final String ONTOLOGY_URI_BASE = "http://purl.org/obo/owl";
/**
* @deprecated Use {@link #OBO_IRI_BASE}
*/
@Deprecated
public static final String ANNOTATION_URI_BASE = OBOPrefix.OBO_IN_OWL.getPrefix();
public static final String OBO_IRI_BASE = OBOPrefix.OBO.getPrefix();
public static final String LEGACY_OBO_IRI_BASE = "http://purl.org/obo/owl/";//
/**
* The pattern for OBO IDs. Specified at
* <a href="http://www.obofoundry.org/id-policy.shtml" >http://www.
* obofoundry.org/id-policy.shtml</a>
*/
public static final Pattern OBO_ID_PATTERN = Pattern.compile("(([^:]+):)?(.+)");
private static final String bases = Pattern.quote(OBO_IRI_BASE) + "|"
+ Pattern.quote(ONTOLOGY_URI_BASE + "/") + "|"
+ Pattern.quote(LEGACY_OBO_IRI_BASE) + "|" + Pattern.quote(ANNOTATION_URI_BASE);
public static final Pattern OBO_IRI_PATTERN =
Pattern.compile("(" + bases + ")" + "(([^\\_]*)\\_)?([A-Za-z0-9\\_\\-]*)");
private static final IDSpaceManager DEFAULT_ID_SPACE_MANAGER = new IDSpaceManager() {
@Override
public void setIRIPrefix(String idPrefix, String iriPrefix) {
throw new OWLRuntimeException(
"The default id space manager must not be used for custom prefixes.");
}
};
private static final List<OBOVocabulary> headerTags = Arrays.asList(FORMAT_VERSION,
DATA_VERSION, DATE, SAVED_BY, AUTO_GENERATED_BY, SUBSETDEF, IMPORT,
SYNONYM_TYPE_DEF, ID_SPACE, DEFAULT_RELATIONSHIP_ID_PREFIX, ID_MAPPING, REMARK);
private static final List<OBOVocabulary> termStanzaTags = Arrays.asList(ID, NAME, NAMESPACE,
ALT_ID, DEF, COMMENT, SUBSET, SYNONYM, XREF, IS_A, INTERSECTION_OF, UNION_OF,
DISJOINT_FROM, RELATIONSHIP, IS_OBSOLETE, REPLACED_BY, CONSIDER);
private static final List<OBOVocabulary> typeDefStanzaTags = Arrays.asList(ID, NAME, NAMESPACE,
ALT_ID, DEF, COMMENT, SUBSET, SYNONYM, XREF, DOMAIN, RANGE, IS_ASYMMETRIC,
IS_CYCLIC, IS_REFLEXIVE, IS_SYMMETRIC, IS_TRANSITIVE, IS_A, INVERSE,
TRANSITIVE_OVER, RELATIONSHIP, IS_METADATA_TAG, IS_OBSOLETE, REPLACED_BY,
CONSIDER);
private static final List<OBOVocabulary> instanceStanzaTags = Arrays.asList(ID, NAME, NAMESPACE,
ALT_ID, DEF, COMMENT, SYNONYM, XREF, INSTANCE_OF, PROPERTY_VALUE, IS_OBSOLETE,
REPLACED_BY, CONSIDER);
private final String name;
private final IRI iri;
OBOVocabulary(String name) {
this.name = name;
iri = IRI.create(OBOPrefix.OBO.getPrefix(), name);
}
OBOVocabulary(String name, OBOPrefix prefix) {
this.name = name;
iri = IRI.create(prefix.getPrefix(), name);
}
OBOVocabulary(String name, OBOPrefix prefix, String localName) {
this.name = name;
iri = IRI.create(prefix.getPrefix(), localName);
}
OBOVocabulary(String name, IRI iri) {
this.name = name;
this.iri = iri;
}
public String getName() {
return name;
}
@Override
public IRI getIRI() {
return iri;
}
@Override
public String toString() {
return name;
}
/**
* Converts OBO Ids to IRIs. The conversion is defined at
* <a href="http://www.obofoundry.org/id-policy.shtml" >http://www.
* obofoundry.org/id-policy.shtml</a>
*
* @param oboId The Id to convert
* @return The IRI of the converted Id
*/
public static IRI ID2IRI(String oboId) {
return ID2IRI(oboId, DEFAULT_ID_SPACE_MANAGER);
}
/**
* Converts OBO Ids to IRIs. The conversion is defined at
* <a href="http://www.obofoundry.org/id-policy.shtml" >http://www.
* obofoundry.org/id-policy.shtml</a>.
*
* @param oboId The OBO Id to convert.
* @param idSpaceManager An {@link IDSpaceManager} which can be used to customise the IRI
* prefixes used in the conversion.
* @return The IRI of the converted Id.
*/
public static IRI ID2IRI(String oboId, IDSpaceManager idSpaceManager) {
Matcher matcher = OBO_ID_PATTERN.matcher(oboId);
if (matcher.matches()) {
String idSpace = matcher.group(2);
String localId = matcher.group(3);
StringBuilder sb = new StringBuilder();
String iriPrefix = idSpaceManager.getIRIPrefix(idSpace);
sb.append(iriPrefix);
if (idSpace != null && !idSpace.isEmpty()) {
sb.append(idSpace);
sb.append("_");
}
sb.append(localId);
return IRI.create(sb.toString());
} else {
return IRI.create(oboId);
}
}
// Format of Foundry-compliant URIs
// FOUNDRY_OBO_URI ::= "http://purl.obolibrary.org/obo/" IDSPACE "_" LOCALID
// Format of OBO legacy URIs
// Those are found in documents that were natively authored using the OBO
// format and which were converted using the NCBOoboInOwl script before this
// policy was put in place.
// LEGACY_OBO_URI ::= "http://purl.org/obo/owl/" IDSPACE "#" IDSPACE "_"
// LOCALID
public static String IRI2ID(IRI oboIRI) {
Matcher matcher = OBO_IRI_PATTERN.matcher(oboIRI.toString());
if (matcher.matches()) {
String idSpace = matcher.group(3);
String localId = matcher.group(4);
StringBuilder sb = new StringBuilder();
if (idSpace != null) {
sb.append(idSpace);
sb.append(":");
}
sb.append(localId);
return sb.toString();
} else {
throw new OWLRuntimeException("Not an OBO IRI");
}
}
public static boolean isOBOIRI(IRI oboIRI) {
return OBO_ID_PATTERN.matcher(oboIRI.toString()).matches();
}
public static List<OBOVocabulary> getHeaderTags() {
return new ArrayList<>(headerTags);
}
public static List<OBOVocabulary> getTermStanzaTags() {
return new ArrayList<>(termStanzaTags);
}
public static List<OBOVocabulary> getTypeDefStanzaTags() {
return new ArrayList<>(typeDefStanzaTags);
}
public static List<OBOVocabulary> getInstanceStanzaTags() {
return new ArrayList<>(instanceStanzaTags);
}
}