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io.konig.core.impl.RdfUtil Maven / Gradle / Ivy
package io.konig.core.impl;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.io.Reader;
import java.io.StringWriter;
import java.io.Writer;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.StringTokenizer;
import org.openrdf.model.BNode;
import org.openrdf.model.Literal;
import org.openrdf.model.Namespace;
import org.openrdf.model.Resource;
import org.openrdf.model.URI;
import org.openrdf.model.Value;
import org.openrdf.model.datatypes.XMLDatatypeUtil;
import org.openrdf.model.impl.URIImpl;
import org.openrdf.model.util.Literals;
import org.openrdf.model.vocabulary.DCTERMS;
import org.openrdf.model.vocabulary.RDF;
import org.openrdf.model.vocabulary.RDFS;
import org.openrdf.model.vocabulary.XMLSchema;
import org.openrdf.rio.RDFHandler;
import org.openrdf.rio.RDFHandlerException;
import org.openrdf.rio.RDFParseException;
import org.openrdf.rio.RDFParser;
import org.openrdf.rio.helpers.BasicWriterSettings;
import org.openrdf.rio.turtle.TurtleParserFactory;
import org.openrdf.rio.turtle.TurtleUtil;
import io.konig.core.Context;
import io.konig.core.Edge;
import io.konig.core.Graph;
import io.konig.core.KonigException;
import io.konig.core.NamespaceManager;
import io.konig.core.Path;
import io.konig.core.Term;
import io.konig.core.Vertex;
import io.konig.core.io.CompactTurtleWriter;
import io.konig.core.io.CompositeRdfHandler;
import io.konig.core.io.GraphLoadHandler;
import io.konig.core.io.NamespaceRDFHandler;
import io.konig.core.io.PrettyPrintWriter;
import io.konig.core.io.TurtleConfig;
import io.konig.core.path.OutStep;
import io.konig.core.path.Step;
import io.konig.core.util.StringUtil;
import io.konig.core.vocab.Schema;
import io.konig.shacl.PropertyConstraint;
import io.konig.shacl.Shape;
import io.konig.shacl.ShapeManager;
import io.konig.shacl.io.ShapeLoader;
/*
* #%L
* konig-core
* %%
* Copyright (C) 2015 - 2016 Gregory McFall
* %%
* 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.
* #L%
*/
public class RdfUtil {
public static URI namespace(Graph graph, String value) {
NamespaceManager nsManager = graph.getNamespaceManager();
int index = value.length()-1;
for (index=value.lastIndexOf('/', index); index>0; index=value.lastIndexOf('/', --index)) {
String namespace = value.substring(0, index+1);
Namespace ns = nsManager.findByName(namespace);
if (ns != null) {
return (URI) graph.vertex(new URIImpl(namespace)).getId();
}
}
return null;
}
public static String compactId(Resource id, NamespaceManager nsManager) {
if (id == null) {
return null;
}
if (id instanceof BNode) {
return "_:" + ((BNode)id).getID();
}
if (id instanceof URI) {
URI iri = (URI) id;
if (nsManager != null) {
Namespace ns = nsManager.findByName(iri.getNamespace());
if (ns != null) {
return ns.getPrefix() + ":" + iri.getLocalName();
}
return "<" + iri.stringValue() + ">";
}
}
throw new IllegalArgumentException("Unsuppported Resource type: " + id.getClass().getName());
}
public static String localName(Resource id) {
if (id == null) {
return "null";
}
if (id instanceof BNode) {
return ((BNode)id).getID();
}
if (id instanceof URI) {
return ((URI)id).getLocalName();
}
throw new IllegalArgumentException("Unsuppported Resource type: " + id.getClass().getName());
}
/**
* Count the number of distinct PropertyConstraints within a given Shape
*/
public static int countDistinctProperties(Shape shape) {
Set memory = new HashSet<>();
return countProperties(memory, shape);
}
private static int countProperties(Set memory, Shape shape) {
int count = 0;
if (!memory.contains(shape)) {
memory.add(shape);
List list = shape.getProperty();
count += list.size();
for (PropertyConstraint p : list) {
Shape childShape = p.getShape();
if (childShape != null) {
count = countProperties(memory, childShape);
}
}
}
return count;
}
public static List collectNamespaces(NamespaceManager nsManager, Collection edgeList) {
Map map = new HashMap<>();
for (Edge e : edgeList) {
Resource subject = e.getSubject();
URI predicate = e.getPredicate();
Value object = e.getObject();
if (subject instanceof URI) {
addNamespace(map, nsManager, (URI)subject);
}
addNamespace(map, nsManager, predicate);
if (object instanceof URI) {
addNamespace(map, nsManager, (URI)object);
}
}
return new ArrayList(map.values());
}
/**
* Sort a list of properties alphabetically by local name.
* @param properties
*/
public static void sortByLocalName(List properties) {
Collections.sort(properties, new Comparator() {
@Override
public int compare(PropertyConstraint a, PropertyConstraint b) {
String aName = a.getPredicate()==null ? "" : a.getPredicate().getLocalName();
String bName = b.getPredicate()==null ? "" : b.getPredicate().getLocalName();
return aName.compareTo(bName);
}
});
}
public static boolean nearEqual(Object a, Object b) {
if (a instanceof Long && b instanceof Long) {
return a.equals(b);
}
if (a instanceof Number && b instanceof Number) {
Number x = (Number) a;
Number y = (Number) b;
double p = x.doubleValue();
double q = y.doubleValue();
double delta = Math.abs( q-p );
double base = (q+p)/2;
double fraction = delta/base;
if (fraction < 0.00000000000001) {
return true;
}
return false;
}
return a.equals(b);
}
public static Object javaValue(Value value) {
if (value instanceof Literal) {
return javaValue((Literal)value);
}
return value;
}
public static void append(StringBuilder builder, Resource id) {
if (id instanceof BNode) {
builder.append("_:");
builder.append(id.stringValue());
} else {
builder.append('<');
builder.append(id.stringValue());
builder.append('>');
}
}
public static void append(StringBuilder builder, Object value) {
if (value instanceof String) {
builder.append('"');
builder.append(value.toString());
builder.append('"');
} else {
builder.append(value);
}
}
public static String idValue(Resource id) {
StringBuilder builder = new StringBuilder();
append(builder, id);
return builder.toString();
}
public static Set toJavaValue(Set source) {
Set sink = new LinkedHashSet<>();
for (Value v : source) {
sink.add(javaValue(v));
}
return sink;
}
public static Object javaValue(Literal literal) {
String value = literal.getLabel();
URI type = literal.getDatatype();
if (
XMLSchema.INTEGER.equals(type) ||
XMLSchema.INT.equals(type) ||
XMLSchema.LONG.equals(type) ||
Schema.Integer.equals(type)
) {
return Long.parseLong(value);
} else if (
XMLSchema.DOUBLE.equals(type) ||
XMLSchema.FLOAT.equals(type) ||
XMLSchema.DECIMAL.equals(type) ||
Schema.Float.equals(type) ||
Schema.Number.equals(type)
) {
return Double.parseDouble(value);
}
return literal;
}
/**
* Filter the namespaces within a given NamespaceManager and produce a new manager that contains only those
* namespaces that are used within a certain reference graph.
* @param graph The reference graph
* @param nsManager The source NamespaceManager whose namespaces will be filtered based on the reference graph
* @return A new NamespaceManager that contains the subset of namespaces from nsManager that are used by the given graph.
*/
public static NamespaceManager filterNamespaces(Graph graph, NamespaceManager nsManager) {
NamespaceManager sink = new MemoryNamespaceManager();
for (Edge e : graph) {
Resource subject = e.getSubject();
URI predicate = e.getPredicate();
Value object = e.getObject();
copyNamespace(nsManager, subject, sink);
copyNamespace(nsManager, predicate, sink);
copyNamespace(nsManager, object, sink);
if (object instanceof Literal) {
Literal literal = (Literal) object;
URI type = literal.getDatatype();
if (type != null && !XMLSchema.STRING.equals(type)) {
copyNamespace(nsManager, type, sink);
}
}
}
return sink;
}
public static void deepCopy(Vertex v, Graph target) {
if (v != null) {
Graph g = v.getGraph();
Set>> out = v.outEdges();
for (Entry> entry : out) {
Set set = entry.getValue();
for (Edge e : set) {
target.edge(e);
Value object = e.getObject();
if (object instanceof BNode) {
BNode bnode = (BNode) object;
Vertex w = g.getVertex(bnode);
deepCopy(w, target);
}
}
}
}
}
private static void copyNamespace(NamespaceManager source, Value value, NamespaceManager sink) {
if (value instanceof URI && !RDF.TYPE.equals(value)) {
URI uri = (URI) value;
String name = uri.getNamespace();
Namespace ns = source.findByName(name);
if (ns != null) {
sink.add(ns);
}
}
}
public static void sortByPrefix(List list) {
Collections.sort(list, new Comparator() {
@Override
public int compare(Namespace a, Namespace b) {
String x = a.getPrefix();
String y = b.getPrefix();
return x.compareTo(y);
}
});
}
private static void addNamespace(Map map, NamespaceManager nsManager, URI uri) {
String key = uri.getNamespace();
Namespace ns = nsManager.findByName(key);
if (ns != null) {
map.put(key, ns);
}
}
public static URI expand(NamespaceManager nsManager, String curie) throws KonigException {
URI result = null;
if (curie != null) {
if (
!commonInternetScheme(curie) &&
!curie.startsWith("urn:")
) {
int colon = curie.indexOf(':');
if (colon >0) {
String prefix = curie.substring(0, colon);
Namespace ns = nsManager.findByPrefix(prefix);
if (ns != null) {
StringBuilder builder = new StringBuilder();
builder.append(ns.getName());
builder.append(curie.substring(colon+1));
result = new URIImpl(builder.toString());
} else {
throw new KonigException("Namespace not found for prefix: " + prefix);
}
}
} else {
result = new URIImpl(curie);
}
}
return result;
}
private static final int WORD = 1;
private static final int COLON = 2;
private static final int SLASH = 3;
private static boolean commonInternetScheme(String curie) {
int state = WORD;
for (int i=0; i listSubtypes(List typeList) {
Graph graph = null;
if (!typeList.isEmpty()) {
graph = typeList.get(0).getGraph();
}
Set set = new HashSet<>();
for (Vertex v : typeList) {
set.add(v.getId());
Set subTypes = RdfUtil.subTypes(v);
set.addAll(subTypes);
}
List result = new ArrayList<>();
for (Resource r : set) {
result.add(graph.getVertex(r));
}
return result;
}
public static String normalize(String value) {
if (value != null) {
StringTokenizer tokens = new StringTokenizer(value, "\r\n\t ");
StringBuilder builder = new StringBuilder();
while (tokens.hasMoreTokens()) {
builder.append(tokens.nextToken());
if (tokens.hasMoreTokens()) {
builder.append(' ');
}
}
value = builder.toString();
}
return value;
}
public static void prettyPrintTurtle(Graph graph, OutputStream out) throws IOException, RDFHandlerException {
OutputStreamWriter writer = new OutputStreamWriter(out);
prettyPrintTurtle(graph.getNamespaceManager(), graph, writer);
writer.flush();
}
public static void prettyPrintTurtle(Graph graph, Writer writer) throws IOException, RDFHandlerException {
prettyPrintTurtle(graph.getNamespaceManager(), graph, writer);
}
public static void prettyPrintTurtle(String baseIri, Graph graph, Writer writer) throws IOException, RDFHandlerException {
prettyPrintTurtle(graph.getNamespaceManager(), baseIri, graph, writer);
}
public static void prettyPrintTurtle(NamespaceManager nsManager, Graph graph, Writer writer) throws IOException, RDFHandlerException {
prettyPrintTurtle(nsManager, null, graph, writer);
}
public static void prettyPrintTurtle(NamespaceManager nsManager, String baseIRI, Graph graph, Writer writer) throws IOException, RDFHandlerException {
prettyPrintTurtle(nsManager, baseIRI, graph, writer, null);
}
public static void prettyPrintTurtle(NamespaceManager nsManager, String baseIRI, Graph graph, Writer writer, TurtleConfig config) throws IOException, RDFHandlerException {
nsManager = nsManager==null ? null : filterNamespaces(graph, nsManager);
CompactTurtleWriter turtle = new CompactTurtleWriter(writer);
if (config != null) {
turtle.setConfig(config);
}
turtle.setBaseIRI(baseIRI);
turtle.getWriterConfig().set(BasicWriterSettings.PRETTY_PRINT, true);
NaturalEdgeIterable sequence = new NaturalEdgeIterable(graph);
turtle.startRDF();
printNamespaces(nsManager, turtle);
for (Edge e : sequence) {
turtle.handleStatement(e);
}
turtle.endRDF();
}
public static void prettyPrintTurtle(NamespaceManager nsManager, Graph graph, File file) throws IOException, RDFHandlerException {
file.getParentFile().mkdirs();
FileWriter writer = new FileWriter(file);
try {
prettyPrintTurtle(nsManager, graph, writer);
} finally {
writer.close();
}
}
private static void printNamespaces(NamespaceManager namespaceManager, CompactTurtleWriter turtle) throws RDFHandlerException {
if (namespaceManager != null) {
List list = new ArrayList<>(namespaceManager.listNamespaces());
Collections.sort(list, new Comparator() {
@Override
public int compare(Namespace a, Namespace b) {
return a.getPrefix().compareTo(b.getPrefix());
}
});
for (Namespace n : list) {
turtle.handleNamespace(n.getPrefix(), n.getName());
}
}
}
public static void loadTurtle(Graph graph, NamespaceManager nsManager, InputStream input, String baseURL)
throws IOException, RDFParseException, RDFHandlerException {
CompositeRdfHandler handler = new CompositeRdfHandler(
new GraphLoadHandler(graph),
new NamespaceRDFHandler(nsManager)
);
RDFParser parser = new TurtleParserFactory().getParser();
parser.setRDFHandler(handler);
Reader reader = new InputStreamReader(input);
parser.parse(reader, baseURL);
}
public static void loadTurtle(File sourceDir, Graph graph, ShapeManager shapeManager)
throws RDFParseException, RDFHandlerException, IOException {
loadTurtle(sourceDir, graph, graph.getNamespaceManager());
ShapeLoader shapeLoader = new ShapeLoader(shapeManager);
shapeLoader.load(graph);
}
public static void loadTurtle(File sourceDir, Graph graph) throws RDFParseException, RDFHandlerException, IOException {
loadTurtle(sourceDir, graph, graph.getNamespaceManager());
}
/**
* From a given source directory, load all files with the *.ttl suffix into a given Graph.
* This method will search subdirectories recursively for Turtle files.
* @param sourceDir The source directory containing Turtle files.
* @param graph The graph into which RDF statements will be placed.
*/
public static void loadTurtle(File sourceDir, Graph graph, NamespaceManager nsManager)
throws IOException, RDFParseException, RDFHandlerException {
RDFHandler handler = new GraphLoadHandler(graph);
if (nsManager != null) {
handler = new CompositeRdfHandler(handler, new NamespaceRDFHandler(nsManager));
}
RDFParser parser = new TurtleParserFactory().getParser();
parser.setRDFHandler(handler);
loadTurtle(sourceDir, parser);
}
private static void loadTurtle(File sourceDir, RDFParser parser) throws RDFParseException, RDFHandlerException, IOException {
File[] array = sourceDir.listFiles();
if (array != null) {
for (File file : array) {
if (file.isDirectory()) {
loadTurtle(file, parser);
} else if (file.getName().endsWith(".ttl")){
try {
FileReader input = new FileReader(file);
parser.parse(input, "");
} catch (RDFParseException e) {
throw new RDFParseException("Failed to parse file: " + file.getAbsolutePath(), e);
} catch (RDFHandlerException e) {
throw new RDFHandlerException("Failed to parse file: " + file.getAbsolutePath(), e);
} catch (IOException e) {
throw new IOException("Failed to parse file: " + file.getAbsolutePath(), e);
}
}
}
}
}
public static void loadTurtle(Graph graph, Reader input, String baseURL) throws RDFParseException, RDFHandlerException, IOException {
GraphLoadHandler handler = new GraphLoadHandler(graph);
RDFParser parser = new TurtleParserFactory().getParser();
parser.setRDFHandler(handler);
parser.parse(input, baseURL);
}
public static void loadTurtle(Graph graph, InputStream input, String baseURL)
throws IOException, RDFParseException, RDFHandlerException {
InputStreamReader reader = new InputStreamReader(input);
loadTurtle(graph, reader, baseURL);
}
/**
* Find the super types of a given OWL Class.
* @param owlClass The OWL class whose super types are to be found.
* @return The set of super types of the given class.
*/
public static Set superTypes(Vertex owlClass) {
Set result = new HashSet<>();
List stack = new ArrayList<>();
stack.add(owlClass);
for (int i=0; i list = target.asTraversal().out(RDFS.SUBCLASSOF).toVertexList();
for (Vertex v : list) {
Resource id = v.getId();
if (!id.equals(owlClass.getId()) && !result.contains(id)) {
result.add(id);
stack.add(v);
}
}
}
return result;
}
/**
* Compute the transitive closure of the subtypes of a given OWL Class.
* @param owlClass The OWL Class whose transitive closure is to be computed.
* @return The transitive closure of the given OWL Class.
*/
public static List subtypeList(Vertex owlClass) {
return owlClass.asTraversal().inTransitive(RDFS.SUBCLASSOF).toVertexList();
}
public static Set subTypes(Vertex owlClass) {
Set result = new HashSet<>();
List stack = new ArrayList<>();
stack.add(owlClass);
for (int i=0; i list = target.asTraversal().in(RDFS.SUBCLASSOF).toVertexList();
for (Vertex v : list) {
Resource id = v.getId();
if (!id.equals(owlClass.getId()) && !result.contains(id)) {
result.add(id);
stack.add(v);
}
}
}
return result;
}
public static URI out(Path path, int index) {
if (path != null) {
List list = path.asList();
if (index < list.size()) {
Step s = list.get(index);
if (s instanceof OutStep) {
return ((OutStep) s).getPredicate();
}
}
}
return null;
}
public static boolean isSubClassOf(Vertex subject, Resource target) {
List list = subject.asTraversal().out(RDFS.SUBCLASSOF).toVertexList();
for (Vertex v : list) {
if (v.getId().equals(target)) {
return true;
}
}
for (Vertex v : list) {
if (isSubClassOf(v, target)) {
return true;
}
}
return false;
}
public static String toTurtle(Literal literal) {
StringWriter writer = new StringWriter();
PrettyPrintWriter out = new PrettyPrintWriter(writer);
writeLiteral(out, literal);
out.flush();
return writer.toString();
}
public static void writeLiteral(PrettyPrintWriter writer, Literal literal) {
String label = literal.getLabel();
URI datatype = literal.getDatatype();
if (XMLSchema.INTEGER.equals(datatype) || XMLSchema.DECIMAL.equals(datatype)
|| XMLSchema.DOUBLE.equals(datatype) || XMLSchema.BOOLEAN.equals(datatype))
{
try {
writer.write(XMLDatatypeUtil.normalize(label, datatype));
return; // done
}
catch (IllegalArgumentException e) {
// not a valid numeric typed literal. ignore error and write
// as
// quoted string instead.
}
}
if (label.indexOf('\n') != -1 || label.indexOf('\r') != -1 || label.indexOf('\t') != -1) {
// Write label as long string
writer.write("\"\"\"");
writer.write(TurtleUtil.encodeLongString(label));
writer.write("\"\"\"");
}
else {
// Write label as normal string
writer.write("\"");
writer.write(TurtleUtil.encodeString(label));
writer.write("\"");
}
if (Literals.isLanguageLiteral(literal)) {
// Append the literal's language
writer.write("@");
writer.write(literal.getLanguage());
}
else if (!XMLSchema.STRING.equals(datatype) ) {
// Append the literal's datatype (possibly written as an abbreviated
// URI)
writer.write("^^");
writeURI(writer, datatype);
}
}
public static void writeURI(PrettyPrintWriter out, URI uri) {
NamespaceManager nsManager = out.getNamespaceManager();
if (nsManager != null) {
Namespace ns = nsManager.findByName(uri.getNamespace());
if (ns != null) {
out.print(ns.getPrefix());
out.print(':');
out.print(uri.getLocalName());
return;
}
}
out.print('<');
out.print(uri.stringValue());
out.print('>');
}
public static String compactName(NamespaceManager nsManager, Resource resource) {
if (resource==null) {
return null;
}
if (resource instanceof BNode) {
return "_:" + ((BNode)resource).getID();
}
String iriValue = resource.stringValue();
if (nsManager != null) {
URI id = (URI) resource;
Namespace ns = nsManager.findByName(id.getNamespace());
if (ns != null) {
String prefix = ns.getPrefix();
StringBuilder builder = new StringBuilder();
builder.append(prefix);
builder.append(':');
builder.append(id.getLocalName());
return builder.toString();
}
}
StringBuilder builder = new StringBuilder();
builder.append('<');
builder.append(iriValue);
builder.append('>');
return builder.toString();
}
public static String compactName(Context context, URI resource) {
String iriValue = resource.stringValue();
if (context != null) {
Context inverse = context.inverse();
Term term = inverse.getTerm(iriValue);
if (term != null) {
return term.getId();
}
term = inverse.getTerm(resource.getNamespace());
if (term != null) {
StringBuilder builder = new StringBuilder();
builder.append(term.getId());
builder.append(':');
builder.append(resource.getLocalName());
return builder.toString();
}
}
StringBuilder builder = new StringBuilder();
builder.append('<');
builder.append(iriValue);
builder.append('>');
return builder.toString();
}
public static URI uri(Value value) {
return value instanceof URI ? (URI) value : null;
}
public static String shortShapeName(Resource id) {
URI uri = uri(id);
if (uri != null) {
String name = uri.getLocalName();
if (name.endsWith("Shape")) {
name = name.substring(0, name.length()-5);
}
return name;
}
return null;
}
public static String getName(Vertex v) {
if (v != null) {
Value name = v.getValue(Schema.name);
if (name == null) {
name = v.getValue(RDFS.LABEL);
}
if (name != null) {
return name.stringValue();
}
String localName = localName(v.getId());
return StringUtil.label(localName);
}
return null;
}
}
