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/**
* Copyright 2019 California Institute of Technology ("Caltech").
* U.S. Government sponsorship acknowledged.
*
* 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 io.opencaesar.owl.doc;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URI;
import java.net.URL;
import java.nio.file.Paths;
import java.time.LocalDateTime;
import java.time.format.DateTimeFormatter;
import java.util.ArrayDeque;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.Deque;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Scanner;
import java.util.Set;
import java.util.TreeMap;
import java.util.TreeSet;
import java.util.function.Function;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
import org.apache.jena.graph.Graph;
import org.apache.jena.ontology.AnnotationProperty;
import org.apache.jena.ontology.DatatypeProperty;
import org.apache.jena.ontology.Individual;
import org.apache.jena.ontology.ObjectProperty;
import org.apache.jena.ontology.OntClass;
import org.apache.jena.ontology.OntDocumentManager;
import org.apache.jena.ontology.OntModel;
import org.apache.jena.ontology.OntModelSpec;
import org.apache.jena.ontology.OntProperty;
import org.apache.jena.ontology.Ontology;
import org.apache.jena.ontology.Restriction;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.rdf.model.Property;
import org.apache.jena.rdf.model.RDFList;
import org.apache.jena.rdf.model.RDFNode;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.rdf.model.StmtIterator;
import org.apache.jena.riot.Lang;
import org.apache.jena.riot.RDFLanguages;
import org.apache.jena.vocabulary.OWL2;
import org.apache.jena.vocabulary.RDF;
import org.apache.jena.vocabulary.RDFS;
import org.apache.log4j.Appender;
import org.apache.log4j.AppenderSkeleton;
import org.apache.log4j.Level;
import org.apache.log4j.LogManager;
import org.apache.log4j.Logger;
import org.jgrapht.alg.TransitiveReduction;
import org.jgrapht.alg.cycle.TiernanSimpleCycles;
import org.jgrapht.graph.DefaultEdge;
import org.jgrapht.graph.SimpleDirectedGraph;
import org.jsoup.Jsoup;
import org.jsoup.nodes.Document;
import org.jsoup.nodes.Node;
import org.jsoup.nodes.TextNode;
import com.beust.jcommander.IParameterValidator;
import com.beust.jcommander.IStringConverter;
import com.beust.jcommander.JCommander;
import com.beust.jcommander.Parameter;
import com.beust.jcommander.ParameterException;
import net.sourceforge.plantuml.code.TranscoderUtil;
/**
* A utility for running a reasoner on the set of ontologies in scope of an OASIS XML catalog.
*/
public class OwlDocApp {
/**
* The default OWL file extensions
*/
public static final String[] DEFAULT_EXTENSIONS = {"owl", "ttl"};
private static final List extensions = Arrays.asList(
"fss", "owl", "rdf", "xml", "n3", "ttl", "rj", "nt", "jsonld", "trig", "trix", "nq"
);
private static final String CSS_DEFAULT = "default.css";
private static final String CSS_MAIN = "main.css";
private static final String IMG_ONTOLOGY = "https://help.eclipse.org/latest/topic/org.eclipse.jdt.doc.user/images/org.eclipse.jdt.ui/obj16/package_obj.svg";
private static final String IMG_CLASS = "https://help.eclipse.org/latest/topic/org.eclipse.jdt.doc.user/images/org.eclipse.jdt.ui/obj16/methpub_obj.svg";
private static final String IMG_DATATYPE = "https://help.eclipse.org/latest/topic/org.eclipse.jdt.doc.user/images/org.eclipse.jdt.ui/obj16/methpri_obj.svg";
private static final String IMG_PROPERTY = "https://help.eclipse.org/latest/topic/org.eclipse.jdt.doc.user/images/org.eclipse.jdt.ui/obj16/methpro_obj.svg";
private static final String IMG_INDIVIDUAL = "https://help.eclipse.org/latest/topic/org.eclipse.jdt.doc.user/images/org.eclipse.jdt.ui/obj16/field_public_obj.svg";
private static final String IMG_ITEM = "https://help.eclipse.org/latest/topic/org.eclipse.jdt.doc.user/images/org.eclipse.jdt.ui/obj16/methdef_obj.svg";
private static class Options {
@Parameter(
names = { "--input-catalog-path", "-c"},
description = "path to the input OWL catalog (Required)",
validateWith = CatalogPathValidator.class,
required = true)
private String inputCatalogPath;
@Parameter(
names={"--input-catalog-title", "-t"},
description="Title of OML input catalog (Optional)")
private String inputCatalogTitle = "OWL Ontology Index";
@Parameter(
names={"--input-catalog-version", "-v"},
description="Version of OML input catalog (Optional)")
private String inputCatalogVersion = "";
@Parameter(
names = { "--input-ontology-iri", "-i"},
description = "iri of input OWL ontology (Optional, by default all ontologies in catalog)")
private List inputOntologyIris = new ArrayList<>();
@Parameter(
names = {"--input-file-extension", "-e"},
description = "input file extension (owl and ttl by default, options: owl, rdf, xml, rj, ttl, n3, nt, trig, nq, trix, jsonld, fss)",
validateWith = FileExtensionValidator.class)
private List inputFileExtensions = new ArrayList<>(Arrays.asList(DEFAULT_EXTENSIONS));
@Parameter(
names= { "--output-folder-path", "-o" },
description="Path of Bikeshed output folder",
validateWith=OutputFolderPathValidator.class,
required=true)
private String outputFolderPath = ".";
@Parameter(
names= { "--output-case-sensitive","-s" },
description="Whether output paths are case sensitive",
help=true)
private boolean outputCaseSensitive;
@Parameter(
names= { "--css-file-path","-css" },
description="Path of a css file",
converter = URLConverter.class,
help=true)
private URL cssFilePath = OwlDocApp.class.getClassLoader().getResource(CSS_DEFAULT);
@Parameter(
names = {"--debug", "-d"},
description = "Shows debug logging statements")
private boolean debug;
@Parameter(
names = {"--help", "-h"},
description = "Displays summary of options",
help = true)
private boolean help;
}
private final Options options = new Options();
private class OwlModel {
private OntModel ontModel;
private List ontologies;
private List classes;
private List datatypes;
private List annotationProperties;
private List datatypeProperties;
private List objectProperties;
private List individuals;
public OwlModel(OntModel ontModel) {
this.ontModel = ontModel;
ontologies = sortByIri(ontModel.listOntologies().filterKeep(i-> hasTerms(i)).toList());
classes = sortByName(ontModel.listNamedClasses().toList());
datatypes = sortByName(ontModel.listSubjectsWithProperty(RDF.type, RDFS.Datatype).toList());
annotationProperties = sortByName(ontModel.listAnnotationProperties().toList());
objectProperties = sortByName(ontModel.listObjectProperties().toList());
datatypeProperties = sortByName(ontModel.listDatatypeProperties().toList());
individuals = sortByName(ontModel.listIndividuals().toList());
// Ignore DC elements to avoid clutter
ontologies.removeIf(i -> i.hasURI("http://purl.org/dc/elements/1.1"));
annotationProperties.removeIf(i -> i.getURI().startsWith("http://purl.org/dc/elements/1.1"));
// Ignore OML to avoid clutter
ontologies.removeIf(i -> i.hasURI("http://opencaesar.io/oml"));
annotationProperties.removeIf(i -> i.getURI().startsWith("http://opencaesar.io/oml"));
}
private boolean hasTerms(Ontology o) {
var iri = o.getURI();
var resources = ontModel.listResourcesWithProperty(RDF.type)
.filterDrop(i -> i.isAnon())
.filterKeep(i -> i.getURI().startsWith(iri))
.toList();
resources.removeIf(i -> ontModel.getOntology(i.getURI()) != null);
return !resources.isEmpty();
}
}
private final static Logger LOGGER = Logger.getLogger(OwlDocApp.class);
/**
* Application for running a reasoner on the set of ontologies in scope of an OASIS XML catalog.
* @param args Application arguments.
* @throws Exception Error
*/
public static void main(final String... args) throws Exception {
final OwlDocApp app = new OwlDocApp();
final JCommander builder = JCommander.newBuilder().addObject(app.options).build();
builder.parse(args);
if (app.options.help) {
builder.usage();
return;
}
if (app.options.debug) {
final Appender appender = LogManager.getRootLogger().getAppender("stdout");
((AppenderSkeleton) appender).setThreshold(Level.DEBUG);
}
app.run();
}
/**
* Creates a new OwlDocApp object
*/
public OwlDocApp() {
}
private void run() throws Exception {
LOGGER.info("=================================================================");
LOGGER.info(" S T A R T");
LOGGER.info(" OWL Doc " + getAppVersion());
LOGGER.info("=================================================================");
LOGGER.info(("Input Catalog Path = " + options.inputCatalogPath));
LOGGER.info(("Input Catalog Title = " + options.inputCatalogTitle));
LOGGER.info(("Input Catalog Version = " + options.inputCatalogVersion));
LOGGER.info(("Input Ontology Iris = " + options.inputOntologyIris));
LOGGER.info(("Input File Extensions = " + options.inputFileExtensions));
LOGGER.info(("Output Folder Path = " + options.outputFolderPath));
LOGGER.info(("Output Case Sensitive = " + options.outputCaseSensitive));
OwlCatalog catalog = OwlCatalog.create(new File(options.inputCatalogPath).toURI());
Map fileMap = catalog.getFileUriMap(options.inputFileExtensions);
OntDocumentManager mgr = new OntDocumentManager();
for (var entry : fileMap.entrySet()) {
mgr.addAltEntry(entry.getKey(), entry.getValue().toString());
}
if (options.inputOntologyIris.isEmpty()) {
options.inputOntologyIris.addAll(fileMap.keySet());
}
OntModelSpec s = new OntModelSpec(OntModelSpec.OWL_MEM);
s.setDocumentManager(mgr);
OntModel ontModel = ModelFactory.createOntologyModel(s);
for (var iri : options.inputOntologyIris) {
mgr.getFileManager().readModelInternal(ontModel, iri);
}
OwlModel owlModel = new OwlModel(ontModel);
final var outputFiles = new HashMap();
outputFiles.putAll(copyCssFile());
// create output files
outputFiles.putAll(generateIndexFile(owlModel));
outputFiles.putAll(generateSummaryFile(owlModel));
outputFiles.putAll(generateNavigationFile(owlModel));
outputFiles.putAll(generateClassHierarchyFile(owlModel));
outputFiles.putAll(generateClassesFile(owlModel));
outputFiles.putAll(generateDatatypesFile(owlModel));
outputFiles.putAll(generatePropertiesFile(owlModel.annotationProperties, "Annotation Properties"));
outputFiles.putAll(generatePropertiesFile(owlModel.datatypeProperties, "Datatype Properties"));
outputFiles.putAll(generatePropertiesFile(owlModel.objectProperties, "Object Properties"));
outputFiles.putAll(generateIndividualsFile(owlModel));
// save output files
outputFiles.forEach((file, result) -> {
BufferedWriter out = null;
try {
file.getParentFile().mkdirs();
final var filePath = file.getCanonicalPath();
out = new BufferedWriter(new FileWriter(filePath));
LOGGER.info("Saving: "+filePath);
out.write(result.toString());
if (file.getName().endsWith(".sh")) {
file.setExecutable(true);
}
}
catch (IOException e) {
System.out.println(e);
}
finally {
if (out != null) {
try {
out.close();
} catch (IOException e) {
// no handling
}
}
}
});
ontModel.close();
LOGGER.info("=================================================================");
LOGGER.info(" E N D");
LOGGER.info("=================================================================");
}
//----------------------------------------------------------------------------------
private Map copyCssFile() throws IOException {
var inputStream = options.cssFilePath.openStream();
Scanner s = new Scanner(inputStream);
String content = s.useDelimiter("\\A").hasNext() ? s.next() : "";
s.close();
var file = new File(options.outputFolderPath+File.separator+CSS_MAIN);
return Collections.singletonMap(file, content);
}
private Map generateIndexFile(OwlModel owlModel) throws IOException {
final var content = new StringBuffer();
content.append(
"""
Ontology Documentation
""");
final var file = new File(options.outputFolderPath+File.separator+"index.html").getCanonicalFile();
return Collections.singletonMap(file, content.toString());
}
private Map generateSummaryFile(OwlModel owlModel) throws IOException {
final var content = new StringBuffer();
final var path = options.outputFolderPath+File.separator+"summary.html";
DateTimeFormatter dtf = DateTimeFormatter.ofPattern("yyyy/MM/dd HH:mm:ss");
LocalDateTime now = LocalDateTime.now();
var timestamp = dtf.format(now);
var image = getOntologiesImage(CSS_DEFAULT, owlModel);
content.append(String.format(
"""
%s
%s v%s
Updated on: %s
""",
options.inputCatalogTitle,
getRelativeCSSPath(path),
options.inputCatalogTitle,
options.inputCatalogVersion,
timestamp,
image));
final var file = new File(path).getCanonicalFile();
return Collections.singletonMap(file, content.toString());
}
private Map generateNavigationFile(OwlModel owlModel) throws IOException {
final var files = new HashMap();
final var path = options.outputFolderPath+File.separator+"navigation.html";
final var elements = new StringBuffer();
for (var s : owlModel.ontologies) {
var iri = s.getURI();
var uri = URI.create(iri);
var relativePath = uri.getAuthority()+uri.getPath()+hashCode(iri);
var path1 = options.outputFolderPath+File.separator+relativePath+".html";
var path2 = options.outputFolderPath+File.separator+relativePath+"_2.html";
elements.append(String.format(
"""
""",
getRelativeCSSPath(path),
elements.toString().replaceAll("\n", "\n\t\t\t\t\t"));
final var file = new File(path).getCanonicalFile();
files.put(file, content.toString());
return files;
}
private Map generateClassesFile(OwlModel owlModel) throws IOException {
final var files = new HashMap();
final var path = options.outputFolderPath+File.separator+"classes.html";
final var elements = new StringBuffer();
Function qualifiedType = i -> {
if (i.getOnProperty().isDatatypeProperty())
return i.getProperty(OWL2.onDataRange).getObject().asResource();
else
return i.getProperty(OWL2.onClass).getObject().asResource();
};
for (var s : owlModel.classes) {
var localName = localName(s);
var iri = s.getURI();
var uri = URI.create(iri);
var relativePath = uri.getAuthority()+uri.getPath()+(uri.getFragment() == null ? "" : File.separator+uri.getFragment())+hashCode(iri);
var path1 = options.outputFolderPath+File.separator+relativePath+".html";
elements.append(String.format(
"""
""",
getRelativeCSSPath(path),
elements.toString().replaceAll("\n", "\n\t\t\t\t\t"));
final var file = new File(path).getCanonicalFile();
files.put(file, content.toString());
return files;
}
private Map generateClassHierarchyFile(OwlModel owlModel) throws IOException {
final var path = options.outputFolderPath+File.separator+"class-hierarchy.html";
final var elements = new StringBuffer();
Deque stack = new ArrayDeque<>();
Map levels = new HashMap<>();
stack.addAll(owlModel.ontModel.listHierarchyRootClasses().filterDrop(i -> i.isAnon()).toList());
stack.forEach(i -> levels.put(i, 0));
while (!stack.isEmpty()) {
OntClass aClass = stack.pop();
StringBuffer spaces = new StringBuffer();
int indentLevel = levels.get(aClass);
for (int i = 0; i < indentLevel; i++) {
spaces.append(" ");
}
var iri = aClass.getURI();
var uri = URI.create(iri);
var relativePath = uri.getAuthority()+uri.getPath()+(uri.getFragment() == null ? "" : File.separator+uri.getFragment())+hashCode(iri);
var path1 = options.outputFolderPath+File.separator+relativePath+".html";
elements.append(String.format(
"""
""",
spaces.toString(),
IMG_CLASS,
getRelativePath(path, path1),
aClass.getLocalName()));
List subClasses = aClass.listSubClasses(true).filterDrop(i -> i.isAnon()).toList();
for (OntClass subClass : subClasses) {
levels.put(subClass, indentLevel+1);
stack.push(subClass);
}
}
final var contents = String.format(
"""
Class Hierarchy
Class Hierarchy
%s
""",
getRelativeCSSPath(path),
elements.toString().replaceAll("\n", "\n\t\t\t\t\t"));
final var file = new File(path).getCanonicalFile();
return Collections.singletonMap(file, contents.toString());
}
private Map generateDatatypesFile(OwlModel owlModel) throws IOException {
final var files = new HashMap();
final var path = options.outputFolderPath+File.separator+"datatypes.html";
final var elements = new StringBuffer();
for (var s : owlModel.datatypes) {
var localName = localName(s);
var iri = s.getURI();
var uri = URI.create(iri);
var relativePath = uri.getAuthority()+uri.getPath()+(uri.getFragment() == null ? "" : File.separator+uri.getFragment())+hashCode(iri);
var path1 = options.outputFolderPath+File.separator+relativePath+".html";
elements.append(String.format(
"""
""",
getRelativeCSSPath(path),
elements.toString().replaceAll("\n", "\n\t\t\t\t\t"));
final var file = new File(path).getCanonicalFile();
files.put(file, content.toString());
return files;
}
private Map generatePropertiesFile(List properties, String title) throws IOException {
final var files = new HashMap();
final var path = options.outputFolderPath+File.separator+title.replace(' ', '_').toLowerCase()+".html";
final var elements = new StringBuffer();
for (var s : properties) {
var localName = localName(s);
var iri = s.getURI();
var uri = URI.create(iri);
var relativePath = uri.getAuthority()+uri.getPath()+(uri.getFragment() == null ? "" : File.separator+uri.getFragment())+hashCode(iri);
var path1 = options.outputFolderPath+File.separator+relativePath+".html";
elements.append(String.format(
"""
""",
IMG_PROPERTY,
getRelativePath(path, path1),
localName));
var axioms = getAxioms(path1, s.listProperties());
final var content = new StringBuffer(String.format(
"""
%s
""",
title,
getRelativeCSSPath(path),
title,
elements.toString().replaceAll("\n", "\n\t\t\t\t\t"));
final var file = new File(path).getCanonicalFile();
files.put(file, content.toString());
return files;
}
private Map generateIndividualsFile(OwlModel owlModel) throws IOException {
final var files = new HashMap();
final var path = options.outputFolderPath+File.separator+"individuals.html";
final var elements = new StringBuffer();
for (var s : owlModel.individuals) {
var localName = localName(s);
var iri = s.getURI();
var uri = URI.create(iri);
var relativePath = uri.getAuthority()+uri.getPath()+(uri.getFragment() == null ? "" : File.separator+uri.getFragment())+hashCode(iri);
var path1 = options.outputFolderPath+File.separator+relativePath+".html";
elements.append(String.format(
"""
""",
IMG_INDIVIDUAL,
getRelativePath(path, path1),
localName));
var axioms = getAxioms(path1, s.listProperties());
final var content = new StringBuffer(String.format(
"""
%s
""", s);
}
private String getClassImage(String contextFilePath, OntClass ontClass) {
String thisClass = String.format(
"""
class "%s" [[%s]]
""",
abbreviatedIri(ontClass),
path(contextFilePath, ontClass.getURI()));
var superClasses = String.join("\n", ontClass.listSuperClasses(true).filterKeep(i -> i.isURIResource()).mapWith(i -> String.format(
"""
class "%s" [[%s]]
"%s" -up-|> "%s"
""",
abbreviatedIri(i),
path(contextFilePath, ontClass.getURI()),
abbreviatedIri(ontClass),
abbreviatedIri(i)
)).toList());
var subClasses = String.join("\n", ontClass.listSubClasses(true).filterKeep(i -> i.isURIResource()).mapWith(i -> String.format(
"""
class "%s" [[%s]]
hide "%s" members
"%s" -up-|> "%s"
""",
abbreviatedIri(i),
path(contextFilePath, ontClass.getURI()),
abbreviatedIri(i),
abbreviatedIri(i),
abbreviatedIri(ontClass)
)).toList());
return plantUmlImage(thisClass+superClasses+subClasses);
}
/**
* Import Edge
*/
public static class Import extends DefaultEdge {
private static final long serialVersionUID = 1L;
/** Default Constructor */
public Import() {}
public Ontology getSource() {return (Ontology)super.getSource();}
public Ontology getTarget() {return (Ontology)super.getTarget();}
};
private String getOntologiesImage(String contextFilePath, OwlModel owlModel) {
var graph = new SimpleDirectedGraph(Import.class);
var packages = String.join("\n", owlModel.ontologies.stream().map(i -> {
graph.addVertex(i);
return String.format(
"""
package "%s" {}
""",
i.getURI());
}).toList());
owlModel.ontologies.stream().forEach(i -> i.listImports().filterKeep(k -> owlModel.ontologies.contains(k)).mapWith(k -> k.asOntology()).forEach(j -> {
graph.addEdge(i, j);
}));
var algorithm = new TiernanSimpleCycles(graph);
var cycles = algorithm.findSimpleCycles();
while (!cycles.isEmpty()) {
var maxCycle = cycles.stream().max(Comparator.comparingInt(List::size)).orElse(null);
graph.removeEdge(maxCycle.get(0), maxCycle.get(1));
cycles = algorithm.findSimpleCycles();
}
TransitiveReduction.INSTANCE.reduce(graph);
var imports = String.join("\n", graph.edgeSet().stream().map(i -> String.format(
"""
"%s" -.> "%s"
""",
i.getSource().getURI(),
i.getTarget().getURI())
).collect(Collectors.toList()));
return plantUmlImage("set separator none\n"+ packages + imports);
}
//----------------------------------------------------------------------------------
private static List sortNodes(Collection nodes, Function getLabel) {
var sorted = new ArrayList<>(nodes);
sorted.sort((x1, x2) -> getLabel.apply(x1).compareTo(getLabel.apply(x2)));
return sorted;
}
private static List sortResourcesi(List resources, Function getLabel) {
var filtered = resources.stream().filter(i -> !i.isAnon()).collect(Collectors.toList());
filtered.sort((x1, x2) -> getLabel.apply(x1).compareTo(getLabel.apply(x2)));
return filtered;
}
private static List sortByIri(List resources) {
return sortResourcesi(resources, i -> ((Resource)i).getURI());
}
private static List sortByName(List resources) {
return sortResourcesi(resources, i -> localName((Resource)i));
}
private static final Pattern LINK = Pattern.compile("\\{\\{([^\\s\\}]+)\s*(.*?)\\}\\}");
private String replaceLinks(String contextFilePath, String input, OntModel ontModel) {
Matcher matcher = LINK.matcher(input);
return matcher.replaceAll(match -> {
String url = match.group(1);
String text = match.group(2);
String name = url;
if (url.contains("#")) {
String[] iri = url.split("#");
name = iri[1];
} else if (url.contains("/")) {
int index = url.lastIndexOf('/');
name = url.substring(index+1);
} else {
String[] iri = url.split(":");
if (iri.length == 2) {
String prefix = iri[0];
name = iri[1];
String ns = null;
for (Graph g : ontModel.getSubGraphs()) {
ns = g.getPrefixMapping().getNsPrefixURI(prefix);
if (ns != null) {
break;
}
}
url = ns+name;
}
}
if (text.length() == 0) {
text = name;
}
return String.format("%s", path(contextFilePath, url), text);
});
}
private static String plantUmlImage(String diagram) {
try {
return TranscoderUtil.getDefaultTranscoder().encode(diagram);
} catch (IOException e) {
e.printStackTrace();
return "";
}
}
private String hashCode(String s) {
return options.outputCaseSensitive ? "" : "_"+Math.abs(s.hashCode());
}
private String asString(String contextFilePath, RDFNode node) {
if (node.isResource()) {
var resource = node.asResource();
var iri = resource.getURI();
var label = abbreviatedIri(resource);
if (isExternalResource(resource)) {
return String.format("%s", iri, label);
} else {
var path = path(contextFilePath, iri);
return String.format("%s", path, label);
}
}
return replaceLinks(contextFilePath, wrapUntaggedTextWithPreTag(node.toString()), (OntModel)node.getModel());
}
private String asLocalName(String contextFilePath, Resource resource) {
var iri = resource.getURI();
var label = resource.getLocalName();
if (isExternalResource(resource)) {
return String.format("%s", iri, label);
} else {
var path = path(contextFilePath, iri);
return String.format("%s", path, label);
}
}
private String asString(String contextFilePath, List nodes) {
return String.join(" & ", nodes.stream()
.map(i -> asString(contextFilePath, i))
.collect(Collectors.toList()));
}
private boolean isExternalResource(Resource r) {
var uri = r.getURI();
var ontModel = (OntModel) r.getModel();
var ontologies = ontModel.listOntologies().toList();
for (var ontology : ontologies) {
var ontologyURI = ontology.getURI();
if (uri.startsWith(ontologyURI)) {
return false;
}
}
return true;
}
private String path(String contextFilePath, String iri) {
var uri = URI.create(iri);
var relativePath = uri.getAuthority()+uri.getPath()+(uri.getFragment() == null ? "" : File.separator+uri.getFragment())+hashCode(iri);
var path = options.outputFolderPath+File.separator+relativePath+".html";
return getRelativePath(contextFilePath, path);
}
private static String abbreviatedIri(Resource resource) {
var localName = localName(resource);
String prefix = prefix(resource);
return (prefix != null) ? prefix+":"+localName : resource.getURI();
}
private static String prefix(Resource resource) {
var namespace = namespace(resource);
String prefix = resource.getModel().getGraph().getPrefixMapping().getNsURIPrefix(namespace);
return prefix;
}
private static String localName(Resource resource) {
var iri = resource.getURI();
int index = iri.lastIndexOf("#");
if (index == -1) {
index = iri.lastIndexOf("/");
}
return (index != -1) ? iri.substring(index+1) : resource.getLocalName();
}
private static String namespace(Resource resource) {
var iri = resource.getURI();
int index = iri.lastIndexOf("#");
if (index == -1) {
index = iri.lastIndexOf("/");
}
return (index != -1) ? iri.substring(0, index+1) : resource.getNameSpace();
}
private static String wrapUntaggedTextWithPreTag(String html) {
Document document = Jsoup.parseBodyFragment(html);
StringBuilder processedHtml = new StringBuilder();
if (document.body().childNodes().size() == 1) {
return html;
}
for (Node node : document.body().childNodes()) {
if (node instanceof TextNode) {
String untaggedText = ((TextNode)node).getWholeText();
if (!untaggedText.isEmpty()) {
processedHtml.append("
").append(untaggedText).append("
");
}
} else {
processedHtml.append(node.outerHtml());
}
}
return processedHtml.toString();
}
private String getRelativeCSSPath(String contextFilePath) {
return getRelativePath(contextFilePath, options.outputFolderPath+File.separator+CSS_MAIN);
}
private String getRelativePath(String contextFilePath, String targetFilePath) {
var path1 = Paths.get(contextFilePath).getParent();
var path2 = Paths.get(targetFilePath);
return path1.relativize(path2).toString();
}
//----------------------------------------------------------------------------------
/**
* A parameter validator for an OASIS XML catalog path.
*/
public static class CatalogPathValidator implements IParameterValidator {
/**
* Creates a new CatalogPath object
*/
public CatalogPathValidator() {
}
@Override
public void validate(final String name, final String value) throws ParameterException {
File file = new File(value);
if (!file.exists() || !file.getName().endsWith("catalog.xml")) {
throw new ParameterException("Parameter " + name + " should be a valid OWL catalog path");
}
}
}
/**
* A parameter validator for a file with one of the supported extensions
*/
public static class FileExtensionValidator implements IParameterValidator {
/**
* Creates a new FileExtensionValidator object
*/
public FileExtensionValidator() {
}
@Override
public void validate(final String name, final String value) throws ParameterException {
if (!extensions.contains(value)) {
throw new ParameterException("Parameter " + name + " should be a valid extension, got: " + value +
" recognized extensions are: " +
extensions.stream().reduce( (x,y) -> x + " " + y) );
}
}
}
/**
* A parameter validator for an output RDF file.
*/
public static class OutputFileExtensionValidator implements IParameterValidator {
/**
* Creates a new OutputFileExtensionValidator object
*/
public OutputFileExtensionValidator() {
}
@Override
public void validate(final String name, final String value) throws ParameterException {
Lang lang = RDFLanguages.fileExtToLang(value);
if (lang == null) {
throw new ParameterException("Parameter " + name + " should be a valid RDF output extension, got: " + value +
" recognized RDF extensions are: "+extensions);
}
}
}
/**
* The validator for output folder paths
*/
public static class OutputFolderPathValidator implements IParameterValidator {
/**
* Creates a new OutputFolderPath object
*/
public OutputFolderPathValidator() {}
@Override
public void validate(String name, String value) throws ParameterException {
final var directory = new File(value).getAbsoluteFile();
if (!directory.isDirectory()) {
final var created = directory.mkdirs();
if (!created) {
throw new ParameterException("Parameter " + name + " should be a valid folder path");
}
}
}
}
/**
* The converter for URL params
*/
public static class URLConverter implements IStringConverter{
/**
* Creates a new URLConverter object
*/
public URLConverter() {}
@Override
public URL convert(String value) {
try {
return new URL(value);
} catch (MalformedURLException e) {
return OwlDocApp.class.getClassLoader().getResource(CSS_DEFAULT);
}
}
}
/**
* Get application version id from properties file.
*
* @return version string from build.properties or UNKNOWN
*/
private String getAppVersion() {
var version = this.getClass().getPackage().getImplementationVersion();
return (version != null) ? version : "";
}
}
""",
options.inputCatalogTitle,
getRelativeCSSPath(path),
options.inputCatalogTitle,
options.inputCatalogVersion,
timestamp,
image));
final var file = new File(path).getCanonicalFile();
return Collections.singletonMap(file, content.toString());
}
private Map