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package org.semanticweb.owlapi.util;
import static org.semanticweb.owlapi.util.OWLAPIPreconditions.verifyNotNull;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.util.Collection;
import java.util.Collections;
import java.util.Set;
import java.util.function.BiFunction;
import java.util.function.Function;
import java.util.function.Supplier;
import java.util.stream.Collectors;
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
import org.semanticweb.owlapi.io.XMLUtils;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyID;
import org.semanticweb.owlapi.model.OWLOntologyStorageException;
/**
* Class for saving ontologies to zip files with an optional index.
*
* @author ignazio
*/
public class OWLZipSaver {
/** YAML entry name */
public static final String YAML_INDEX_NAME = "owlzip.yaml";
/** Properties entry name */
public static final String PROPERTIES_INDEX_NAME = "owlzip.properties";
/** Catalog entry name */
public static final String CATALOG_INDEX_NAME = "catalog.xml";
private Function entryPath = this::entryPath;
private BiFunction, Collection, String> index =
this::yamlIndex;
private Supplier indexName = () -> YAML_INDEX_NAME;
/**
* @param entryPath function to use to generate the path in the zip file for an ontology. The
* default strategy is to use the last part of the ontology IRI.
*/
public void setEntryPath(Function entryPath) {
this.entryPath = entryPath;
}
/**
* @param index function to use to generate the index content. The default strategy is to create
* a YAML file. The methods on this class can be passed here to switch to different
* strategies, or a user defined strategy can be used.
*/
public void setIndex(
BiFunction, Collection, String> index) {
this.index = index;
}
/**
* @param indexName the name for the index entry. This defaults to owlzip.yaml; other known
* values are owlzip.poperties and catalog-v001.xml. A supplier that returns a null or
* empty string will cause the class to skip creating an index; in that case, the
* ontologies will just be compressed.
*/
public void setIndexName(Supplier indexName) {
this.indexName = indexName;
}
/**
* Save the root ontology as root in the index and its imports closure as companion ontologies.
*
* @param root root ontology to save
* @param out output stream; to be created by the caller, closed in this method
* @throws IOException if writing to the file fails
* @throws OWLOntologyStorageException if serializing the ontologies fails
*/
public void saveImportsClosure(OWLOntology root, OutputStream out)
throws IOException, OWLOntologyStorageException {
Set importsClosure = root.getImportsClosure();
importsClosure.remove(root);
saveOntologies(Collections.singletonList(root), importsClosure, out);
}
/**
* Save the root ontologies as root in the index and their imports closures as companion
* ontologies.
*
* @param roots root ontologies to save
* @param out output stream; to be created by the caller, closed in this method
* @throws IOException if writing to the file fails
* @throws OWLOntologyStorageException if serializing the ontologies fails
*/
public void saveImportsClosures(Collection roots, OutputStream out)
throws IOException, OWLOntologyStorageException {
Set set =
roots.stream().flatMap(o -> o.getImportsClosure().stream()).collect(Collectors.toSet());
set.removeAll(roots);
saveOntologies(roots, set, out);
}
/**
* Save the ontologies in the index and their content as companion ontologies; no ontology will
* be marked as root.
*
* @param ontologies ontologies to save
* @param out output stream; to be created by the caller, closed in this method
* @throws IOException if writing to the file fails
* @throws OWLOntologyStorageException if serializing the ontologies fails
*/
public void saveOntologies(Collection ontologies, OutputStream out)
throws IOException, OWLOntologyStorageException {
saveOntologies(Collections.emptyList(), ontologies, out);
}
/**
* Save the ontologies in the index, marking as root the ontologies in the roots collection; the
* other ontologies will be saved as companion ontologies. This method assumes the caller takes
* care of flattening ontology imports closures, and will not navigate imports statements.
*
* @param roots root ontologies
* @param ontologies ontologies to save
* @param out output stream; to be created by the caller, closed in this method
* @throws IOException if writing to the file fails
* @throws OWLOntologyStorageException if serializing the ontologies fails
*/
public void saveOntologies(Collection roots, Collection ontologies,
OutputStream out) throws IOException, OWLOntologyStorageException {
try (ZipOutputStream f = new ZipOutputStream(out)) {
addIndex(roots, ontologies, f);
for (OWLOntology o : roots) {
ZipEntry next = new ZipEntry(entryPath.apply(o.getOntologyID()));
f.putNextEntry(next);
ByteArrayOutputStream temp = new ByteArrayOutputStream();
o.saveOntology(temp);
f.write(temp.toByteArray());
}
for (OWLOntology o : ontologies) {
ZipEntry next = new ZipEntry(entryPath.apply(o.getOntologyID()));
f.putNextEntry(next);
ByteArrayOutputStream temp = new ByteArrayOutputStream();
o.saveOntology(temp);
f.write(temp.toByteArray());
}
f.close();
}
}
protected void addIndex(Collection roots, Collection ontologies,
ZipOutputStream f) throws IOException {
String name = indexName.get();
if (name != null && !name.isEmpty()) {
ZipEntry e = new ZipEntry(name);
f.putNextEntry(e);
String entrydata = index.apply(roots, ontologies);
f.write(entrydata.getBytes());
f.closeEntry();
}
}
/**
* Prepare a catalog index; this method can be used as a {@link java.util.function.BiFunction}
* for {@link #setIndex(BiFunction)}. Imports statements are not navigated; all ontologies
* required have to appear explicitly in the collections.
*
* @param roots collection of roots, if any
* @param ontologies collection of ontologies, if any
* @return content of a catalog index for the input ontologies
*/
public String catalogIndex(Collection roots, Collection ontologies) {
StringBuilder b = new StringBuilder(1000).append(
"\n\n \n");
int id = 1;
if (roots.size() + ontologies.size() > 0) {
for (OWLOntology o : roots) {
b.append(" \n");
id++;
}
for (OWLOntology o : ontologies) {
b.append(" \n");
id++;
}
}
b.append(" \n\n");
return b.toString();
}
/**
* Prepare a yaml index; this method can be used as a {@link java.util.function.BiFunction} for
* {@link #setIndex(BiFunction)}. Imports statements are not navigated; all ontologies required
* have to appear explicitly in the collections.
*
* @param roots collection of roots, if any
* @param ontologies collection of ontologies, if any
* @return content of a yaml index for the input ontologies
*/
public String yamlIndex(Collection roots, Collection ontologies) {
StringBuilder b = new StringBuilder();
if (roots.size() + ontologies.size() > 0) {
b.append("ontologies:\n");
roots.stream().map(OWLOntology::getOntologyID)
.forEach(o -> b.append("- iri: ").append(o.getOntologyIRI().get())
.append("\n path: ").append(entryPath.apply(o)).append("\n root: true\n"));
ontologies.stream().map(OWLOntology::getOntologyID)
.forEach(o -> b.append("- iri: ").append(o.getOntologyIRI().get())
.append("\n path: ").append(entryPath.apply(o)).append("\n"));
}
return b.toString();
}
/**
* Prepare a properties index; this method can be used as a
* {@link java.util.function.BiFunction} for {@link #setIndex(BiFunction)}. Imports statements
* are not navigated; all ontologies required have to appear explicitly in the collections.
*
* @param roots collection of roots, if any
* @param ontologies collection of ontologies, if any
* @return content of a properties index for the input ontologies
*/
public String propertiesIndex(Collection roots,
Collection ontologies) {
StringBuilder b = new StringBuilder();
if (!roots.isEmpty()) {
String rootsEntry = roots.stream().map(OWLOntology::getOntologyID).map(entryPath)
.collect(Collectors.joining(", "));
b.append("roots=").append(rootsEntry).append("\n");
}
ontologies.stream().map(OWLOntology::getOntologyID).forEach(o -> b
.append(entryPath.apply(o)).append("=").append(o.getOntologyIRI().get()).append("\n"));
return b.toString();
}
/**
* Prepare a zip name for an ontology id; this method can be used as a Function for
* {@link #setEntryPath(Function)}.
*
* @param id ontology id
* @return zip entry name for the ontology
*/
public String entryPath(OWLOntologyID id) {
String string = id.getOntologyIRI().get().toString();
if (string.endsWith("/") || string.endsWith("#")) {
string = XMLUtils.getNCNameSuffix(string.subSequence(0, string.length() - 1));
}
return verifyNotNull(string);
}
}
