4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignaziopackage de.unibremen.informatik;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport java.io.BufferedReader;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport java.io.BufferedWriter;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport java.io.File;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport java.io.FileReader;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport java.io.FileWriter;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport java.io.IOException;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport java.io.OutputStreamWriter;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport java.io.Writer;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport java.net.URI;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport java.net.URLConnection;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport java.util.ArrayList;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport java.util.HashSet;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport java.util.Set;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio

d25c69509848853b0b15b93e3cc180cab81047acChristian Maederimport org.coode.owlapi.owlxml.renderer.OWLXMLRenderer;

d25c69509848853b0b15b93e3cc180cab81047acChristian Maederimport org.coode.owlapi.rdf.rdfxml.RDFXMLRenderer;

2578a6d217296401d347302c9104fee179bd0470Francisc Nicolae Bungiuimport org.semanticweb.owlapi.apibinding.OWLManager;

d25c69509848853b0b15b93e3cc180cab81047acChristian Maederimport org.semanticweb.owlapi.io.OWLRendererException;

6f52b2f195d946649597c21e5888c70ccfeeb81eChristian Maederimport org.semanticweb.owlapi.io.StreamDocumentSource;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport org.semanticweb.owlapi.model.IRI;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport org.semanticweb.owlapi.model.MissingImportEvent;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport org.semanticweb.owlapi.model.MissingImportHandlingStrategy;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport org.semanticweb.owlapi.model.MissingImportListener;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport org.semanticweb.owlapi.model.OWLOntology;

43f8464f7a29c9609509b9c58925f0432263803dSimon Ulbrichtimport org.semanticweb.owlapi.model.OWLOntologyLoaderConfiguration;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport org.semanticweb.owlapi.model.OWLOntologyManager;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport org.semanticweb.owlapi.util.OWLOntologyMerger;

2578a6d217296401d347302c9104fee179bd0470Francisc Nicolae Bungiu

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport uk.ac.manchester.cs.owl.owlapi.OWLOntologyIRIMapperImpl;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxRenderer;

2578a6d217296401d347302c9104fee179bd0470Francisc Nicolae Bungiu

2578a6d217296401d347302c9104fee179bd0470Francisc Nicolae Bungiupublic class OWL2Parser {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio private static enum OPTION {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio OWL_XML, MANCHESTER, RDF_XML, OBO, TURTLE

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder

c7d44bc923b7eb1a01abd095cd004030fee589eanotanartist private static Boolean quick = false;

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder private static Boolean cyclic = false;

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist protected static final Set<IRI> missingImports = new HashSet<IRI>();

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder private static Set<OWLOntology> ontologies;

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder private static final Set<OWLOntology> exported = new HashSet<OWLOntology>();

2e08f62eab7a9bd9becf08ce32871a39306e4798Szaben private static OWLOntologyManager manager = setupManagerWithMissingImportListener();

43f8464f7a29c9609509b9c58925f0432263803dSimon Ulbricht private static OWLOntologyIRIMapperImpl mapper = new OWLOntologyIRIMapperImpl();

b1854c6c6cbc17bd15e317b7b787b29b0b788e8cnotanartist private static URI uri = null;

ae0124755bed317b3e11afe1c6275fdb488807acnotanartist

d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder public static void main(String[] args) {

d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder // A simple example of how to load and save an ontology

d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder try {

ae0124755bed317b3e11afe1c6275fdb488807acnotanartist OWLOutputHandler out = new OWLOutputHandler();

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio parseArgs(args, out);

a933696a057bd1ad025d2d8e6b7079cc8e979d6eChristian Maeder URLConnection con = uri.toURL().openConnection();

ebe1b5c42cea5468e66f088648362125cb3c2818Christian Maeder con.addRequestProperty("Accept", "text/plain");

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio StreamDocumentSource sds = new StreamDocumentSource(

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio con.getInputStream(), IRI.create(uri));

6f52b2f195d946649597c21e5888c70ccfeeb81eChristian Maeder OWLOntologyLoaderConfiguration config = new OWLOntologyLoaderConfiguration();

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio config = config

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio .setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT);

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio OWLOntology ontology = manager.loadOntologyFromOntologyDocument(

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio sds, config);

c1cca90cf3d763a48705ddaeeffb3c2d82e9e37eSimon Ulbricht if (!missingImports.isEmpty()) {

c1cca90cf3d763a48705ddaeeffb3c2d82e9e37eSimon Ulbricht IRI ontohub = IRI.create("https://ontohub.org/external/");

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio for (IRI mi : missingImports) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio mapper.addMapping(

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio mi,

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio ontohub.resolve(mi.toURI().getHost()

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio + mi.toURI().getPath()));

c1cca90cf3d763a48705ddaeeffb3c2d82e9e37eSimon Ulbricht }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio // reset the manager. clear out imports to avoid duplicates

2e08f62eab7a9bd9becf08ce32871a39306e4798Szaben manager = setupManagerWithMissingImportListener();

c1cca90cf3d763a48705ddaeeffb3c2d82e9e37eSimon Ulbricht manager.addIRIMapper(mapper);

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist // collect missing imports again to report them in output file.

c1cca90cf3d763a48705ddaeeffb3c2d82e9e37eSimon Ulbricht missingImports.clear();

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio ontology = manager

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio .loadOntologyFromOntologyDocument(sds, config);

43f8464f7a29c9609509b9c58925f0432263803dSimon Ulbricht }

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder ontologies = getImports(ontology, new HashSet<OWLOntology>());

ea200f8484810ec6d7436f8c1b8286e7e61f4551notanartist out._open();

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder if (cyclic) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio String str = ontology.getOntologyID().getOntologyIRI()

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio .toString();

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio String merged_name = str + ".merged.owl"; // we must make a new

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio // name!

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder // System.out.println("NAME: " + merged_name + "\n");

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder IRI mergedOntologyIRI = IRI.create(merged_name);

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder // System.out.println("MERGED_IRI " + mergedOntologyIRI + "\n");

91e24fc45834b35f2a3830d72565640251149bf3Christian Maeder OWLOntology merged;

c7d44bc923b7eb1a01abd095cd004030fee589eanotanartist // Axioms can be excluded when 'quick' Option selected

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio if (quick) {

91e24fc45834b35f2a3830d72565640251149bf3Christian Maeder merged = manager.createOntology(mergedOntologyIRI);

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio } else {

91e24fc45834b35f2a3830d72565640251149bf3Christian Maeder OWLOntologyMerger merger = new OWLOntologyMerger(manager);

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio merged = merger.createMergedOntology(manager,

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio mergedOntologyIRI);

91e24fc45834b35f2a3830d72565640251149bf3Christian Maeder }

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist out.renderUsingOption(merged);

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder } else {

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder ontologies.add(ontology);

b1854c6c6cbc17bd15e317b7b787b29b0b788e8cnotanartist exportImports(out);

d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder }

ea200f8484810ec6d7436f8c1b8286e7e61f4551notanartist out._close();

d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder } catch (Exception ex) {

d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder System.err.println("OWL parse error: " + ex.getMessage());

d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder ex.printStackTrace();

d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder }

d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder }

d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder

ae0124755bed317b3e11afe1c6275fdb488807acnotanartist // print usage information screen

ae0124755bed317b3e11afe1c6275fdb488807acnotanartist private static void showHelpScreen() {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio System.out.println("Usage: processor [<options..>] <URI>\n"

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio + "_>_options_<______________\n"

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio + " | -o <tp> <fn> ..write output to file\n"

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio + " - - - tp <- type [: owl xml omn rdf obo dol ttl]\n"

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio + " - - - fn <- filename\n"

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio + " | -o-sys <tp> ..write output to system.out\n"

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio + " - - - - - tp <- type\n"

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio + " | -qk ..internal(!) sets 'quick' option\n"

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio + " | -h ..this helptext");

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

c7d44bc923b7eb1a01abd095cd004030fee589eanotanartist

c7d44bc923b7eb1a01abd095cd004030fee589eanotanartist // parse arguments according to option set

b1854c6c6cbc17bd15e317b7b787b29b0b788e8cnotanartist // fails for unknown or incomplete arguments, or when IRI is not set

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio private static void parseArgs(String[] args, OWLOutputHandler out)

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio throws Exception {

ae0124755bed317b3e11afe1c6275fdb488807acnotanartist String inp = "", msg = "OWL2Parser.parseArgs: ";

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio if (args.length == 0) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio throw new Exception(msg + "no arguments provided");

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

c7d44bc923b7eb1a01abd095cd004030fee589eanotanartist for (int i = 0; i < args.length; i++) {

c7d44bc923b7eb1a01abd095cd004030fee589eanotanartist String arg = args[i].toLowerCase();

c7d44bc923b7eb1a01abd095cd004030fee589eanotanartist if (arg.startsWith("-")) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio if (arg.equals("-o")) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio if (!(i < args.length - 2)) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio throw new Exception(

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio msg

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio + "insufficient arguments (-o [format] [filename])");

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio out.add(parseOption(args[++i].toLowerCase(), msg),

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio args[++i]);

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio } else if (arg.equals("-o-sys")) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio if (!(i < args.length - 1)) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio throw new Exception(msg

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio + "insufficient arguments (-o-sys [format])");

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio out.add(parseOption(args[++i].toLowerCase(), msg));

25f163f5755534f518718981c8b160fdf5097773notanartist } else if (arg.equals("-qk") || arg.equals("-q")) {

c7d44bc923b7eb1a01abd095cd004030fee589eanotanartist quick = true;

25f163f5755534f518718981c8b160fdf5097773notanartist } else if (arg.equals("-h") || arg.equals("--help")) {

25f163f5755534f518718981c8b160fdf5097773notanartist showHelpScreen();

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio } else {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio throw new Exception(msg + "unknown command <" + arg + ">");

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

c7d44bc923b7eb1a01abd095cd004030fee589eanotanartist } else {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio if (!inp.equals("")) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio throw new Exception(msg + "ambigious IRI");

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

b1854c6c6cbc17bd15e317b7b787b29b0b788e8cnotanartist inp = args[i]; // read again to undo earlier 'toLowerCase'

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio if (arg.startsWith("http:") || arg.startsWith("https:")) {

b1854c6c6cbc17bd15e317b7b787b29b0b788e8cnotanartist uri = new URI(inp);

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio } else {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio uri = new File(inp).toURI();

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio if (inp.equals("")) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio throw new Exception(msg + "IRI not set");

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

2e08f62eab7a9bd9becf08ce32871a39306e4798Szaben }

c7d44bc923b7eb1a01abd095cd004030fee589eanotanartist

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio private static OPTION parseOption(String opt, String err) throws Exception {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio if (opt.equals("xml") || opt.equals("owl")) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio return OPTION.OWL_XML;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio } else if (opt.equals("omn")) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio return OPTION.MANCHESTER;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio } else if (opt.equals("rdf")) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio return OPTION.RDF_XML;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio } else if (opt.equals("obo")) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio return OPTION.OBO;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio } else if (opt.equals("ttl")) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio return OPTION.TURTLE;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio throw new Exception(err + "unrecognized owl-format: " + opt);

c7d44bc923b7eb1a01abd095cd004030fee589eanotanartist }

ae0124755bed317b3e11afe1c6275fdb488807acnotanartist

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio private static OWLOntologyManager setupManagerWithMissingImportListener() {

2e08f62eab7a9bd9becf08ce32871a39306e4798Szaben OWLOntologyManager mgr = OWLManager.createOWLOntologyManager();

2e08f62eab7a9bd9becf08ce32871a39306e4798Szaben mgr.addMissingImportListener(new HasMissingImports());

2e08f62eab7a9bd9becf08ce32871a39306e4798Szaben return mgr;

2e08f62eab7a9bd9becf08ce32871a39306e4798Szaben }

2e08f62eab7a9bd9becf08ce32871a39306e4798Szaben

7ca6e1b0867fc982f00128017f530b433ea8a37fChristian Maeder private static class HasMissingImports implements MissingImportListener {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio

7ca6e1b0867fc982f00128017f530b433ea8a37fChristian Maeder @Override

7ca6e1b0867fc982f00128017f530b433ea8a37fChristian Maeder public void importMissing(MissingImportEvent event) {

7ca6e1b0867fc982f00128017f530b433ea8a37fChristian Maeder missingImports.add(event.getImportedOntologyURI());

7ca6e1b0867fc982f00128017f530b433ea8a37fChristian Maeder }

7ca6e1b0867fc982f00128017f530b433ea8a37fChristian Maeder }

7ca6e1b0867fc982f00128017f530b433ea8a37fChristian Maeder

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio private static Set<OWLOntology> getImports(OWLOntology ontology,

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio Set<OWLOntology> stop) {

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder Set<OWLOntology> s = new HashSet<OWLOntology>();

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder Set<OWLOntology> next = new HashSet<OWLOntology>(stop);

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder next.add(ontology);

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio for (OWLOntology imported : ontology.getDirectImports()) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio if (cyclic || next.contains(imported)) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio cyclic = true;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio } else if (!s.contains(imported)) {

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder Set<OWLOntology> i = getImports(imported, next);

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder s.add(imported);

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder s.addAll(i);

d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder return s;

d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder }

d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio private static void exportImports(OWLOutputHandler out) throws IOException {

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder Boolean changed;

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder do {

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder changed = false;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio for (OWLOntology onto : ontologies) {

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder if (exported.containsAll(onto.getDirectImports())) {

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder if (!exported.contains(onto)) {

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder changed = exported.add(onto);

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist out.renderUsingOption(onto);

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder }

d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder } while (changed);

d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder }

d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio // output handler allows and handles a list of output-requests

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio protected static class OWLOutputHandler {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio static ArrayList<OWLOntologyWriter> writer = new ArrayList<OWLOntologyWriter>();

d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio void add(OPTION op) throws Exception {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio writer.add(new OWLOntologyWriter(op));

d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio void add(OPTION op, String filename) throws Exception {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio writer.add(new OWLOntologyWriter(filename, op));

d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio void _open() throws IOException {

ea200f8484810ec6d7436f8c1b8286e7e61f4551notanartist for (OWLOntologyWriter out : writer) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio out._open();

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio void _close() throws IOException {

ea200f8484810ec6d7436f8c1b8286e7e61f4551notanartist for (OWLOntologyWriter out : writer) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio out._close();

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist // function need to be called once to render and close every output

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio void renderUsingOption(OWLOntology onto) throws IOException {

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist for (OWLOntologyWriter out : writer) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio out.renderUsingOption(onto);

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist // custem OntolgyWriter bundles a BufferedWriter with an OWL output format

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist protected static class OWLOntologyWriter extends BufferedWriter {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist protected static OPTION option;

d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio OWLOntologyWriter(String fn, OPTION op) throws Exception {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio super(new FileWriter(fn));

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio option = op;

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio OWLOntologyWriter(OPTION op) throws Exception {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio super(new OutputStreamWriter(System.out));

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist option = op;

d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio void writeMissingImports() throws IOException {

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist for (IRI mi : missingImports) {

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist write("<Missing>" + mi + "</Missing>\n");

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

ea200f8484810ec6d7436f8c1b8286e7e61f4551notanartist }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio void _open() throws IOException {

ea200f8484810ec6d7436f8c1b8286e7e61f4551notanartist if (option == OPTION.OWL_XML) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio write("<Ontologies>\n");

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio void _close() throws IOException {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio if (option == OPTION.OWL_XML) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio writeMissingImports();

ea200f8484810ec6d7436f8c1b8286e7e61f4551notanartist write("\n</Ontologies>\n");

ea200f8484810ec6d7436f8c1b8286e7e61f4551notanartist }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio _close(this);

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio void _close(Writer pointer) throws IOException {

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist pointer.flush();

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist pointer.close();

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio void renderUsingOption(OWLOntology onto) throws IOException {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio switch (option) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio case OWL_XML:

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist renderAsXml(onto);

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist break;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio case MANCHESTER:

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio renderAsOmn(onto);

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio break;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio case RDF_XML:

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio renderAsRdf(onto);

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio break;

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist // TODO: the below still need implementation!

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio case OBO:

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio renderAsXml(onto);

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio break;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio case TURTLE:

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio renderAsXml(onto);

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio break;

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio void renderAsOmn(OWLOntology onto) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio try {

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist ManchesterOWLSyntaxRenderer omnrend = new ManchesterOWLSyntaxRenderer();

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist omnrend.render(onto, this);

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist } catch (OWLRendererException ex) {

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist System.err.println("Error by ManchesterParser!");

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist ex.printStackTrace();

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio void renderAsXml(OWLOntology onto) {

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist try {

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist OWLXMLRenderer xmlren = new OWLXMLRenderer();

c21fdc9d17fd00d8433cfc75895dc081bfa7a586notanartist File tempFile = File.createTempFile("owlTemp_1", ".xml");

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist FileWriter buf = new FileWriter(tempFile);

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist if (quick) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio onto.getOWLOntologyManager().removeAxioms(onto,

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio onto.getAxioms());

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist }

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist xmlren.render(onto, buf);

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio _close(buf);

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio BufferedReader rBuf = new BufferedReader(new FileReader(

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio tempFile));

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio rBuf.readLine(); // ignore the first line containing <?xml

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio // version="1.0"?>

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio while (rBuf.ready()) {

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio append(rBuf.readLine()).append("\n");

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist rBuf.close();

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist tempFile.deleteOnExit();

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio append("<Loaded name=\"").append(

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio manager.getOntologyDocumentIRI(onto));

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio append("\" ontiri=\"").append(

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio onto.getOntologyID().getOntologyIRI());

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist append("\"/>\n");

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist } catch (Exception ex) {

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist System.err.println("Error by XMLParser!");

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist ex.printStackTrace();

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio void renderAsRdf(OWLOntology onto) {

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist try {

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist RDFXMLRenderer rdfrend = new RDFXMLRenderer(onto, this);

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist rdfrend.render();

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist } catch (IOException ex) {

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist System.err.println("Error by RDFParser!");

b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist ex.printStackTrace();

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio }

d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder }

2578a6d217296401d347302c9104fee179bd0470Francisc Nicolae Bungiu}