OWL2Parser.java revision be8a364e20bf080501e6b7b76664c33b649ffac7
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.MissingImportEvent;
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport org.semanticweb.owlapi.model.MissingImportHandlingStrategy;
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport org.semanticweb.owlapi.model.MissingImportListener;
43f8464f7a29c9609509b9c58925f0432263803dSimon Ulbrichtimport org.semanticweb.owlapi.model.OWLOntologyLoaderConfiguration;
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport org.semanticweb.owlapi.model.OWLOntologyManager;
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport org.semanticweb.owlapi.util.OWLOntologyMerger;
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport uk.ac.manchester.cs.owl.owlapi.OWLOntologyIRIMapperImpl;
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazioimport uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxRenderer;
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio private static enum OPTION {
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();
d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder // A simple example of how to load and save an ontology
a933696a057bd1ad025d2d8e6b7079cc8e979d6eChristian Maeder URLConnection con = uri.toURL().openConnection();
ebe1b5c42cea5468e66f088648362125cb3c2818Christian Maeder con.addRequestProperty("Accept", "text/plain");
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio StreamDocumentSource sds = new StreamDocumentSource(
6f52b2f195d946649597c21e5888c70ccfeeb81eChristian Maeder OWLOntologyLoaderConfiguration config = new OWLOntologyLoaderConfiguration();
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio .setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT);
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio OWLOntology ontology = manager.loadOntologyFromOntologyDocument(
c1cca90cf3d763a48705ddaeeffb3c2d82e9e37eSimon Ulbricht IRI ontohub = IRI.create("https://ontohub.org/external/");
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio // reset the manager. clear out imports to avoid duplicates
b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist // collect missing imports again to report them in output file.
4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder ontologies = getImports(ontology, new HashSet<OWLOntology>());
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio String str = ontology.getOntologyID().getOntologyIRI()
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio String merged_name = str + ".merged.owl"; // we must make a new
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");
c7d44bc923b7eb1a01abd095cd004030fee589eanotanartist // Axioms can be excluded when 'quick' Option selected
91e24fc45834b35f2a3830d72565640251149bf3Christian Maeder merged = manager.createOntology(mergedOntologyIRI);
91e24fc45834b35f2a3830d72565640251149bf3Christian Maeder OWLOntologyMerger merger = new OWLOntologyMerger(manager);
d25c69509848853b0b15b93e3cc180cab81047acChristian Maeder System.err.println("OWL parse error: " + ex.getMessage());
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");
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)
ae0124755bed317b3e11afe1c6275fdb488807acnotanartist String inp = "", msg = "OWL2Parser.parseArgs: ";
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio + "insufficient arguments (-o [format] [filename])");
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio + "insufficient arguments (-o-sys [format])");
25f163f5755534f518718981c8b160fdf5097773notanartist } else if (arg.equals("-qk") || arg.equals("-q")) {
25f163f5755534f518718981c8b160fdf5097773notanartist } else if (arg.equals("-h") || arg.equals("--help")) {
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio throw new Exception(msg + "unknown command <" + arg + ">");
b1854c6c6cbc17bd15e317b7b787b29b0b788e8cnotanartist inp = args[i]; // read again to undo earlier 'toLowerCase'
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio if (arg.startsWith("http:") || arg.startsWith("https:")) {
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio private static OPTION parseOption(String opt, String err) throws Exception {
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio throw new Exception(err + "unrecognized owl-format: " + opt);
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio private static OWLOntologyManager setupManagerWithMissingImportListener() {
2e08f62eab7a9bd9becf08ce32871a39306e4798Szaben OWLOntologyManager mgr = OWLManager.createOWLOntologyManager();
2e08f62eab7a9bd9becf08ce32871a39306e4798Szaben mgr.addMissingImportListener(new HasMissingImports());
7ca6e1b0867fc982f00128017f530b433ea8a37fChristian Maeder private static class HasMissingImports implements MissingImportListener {
7ca6e1b0867fc982f00128017f530b433ea8a37fChristian Maeder public void importMissing(MissingImportEvent event) {
7ca6e1b0867fc982f00128017f530b433ea8a37fChristian Maeder missingImports.add(event.getImportedOntologyURI());
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio private static Set<OWLOntology> getImports(OWLOntology ontology,
4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder Set<OWLOntology> s = new HashSet<OWLOntology>();
4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder Set<OWLOntology> next = new HashSet<OWLOntology>(stop);
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio for (OWLOntology imported : ontology.getDirectImports()) {
4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder Set<OWLOntology> i = getImports(imported, next);
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio private static void exportImports(OWLOutputHandler out) throws IOException {
4efb09a1f46a0b322633b729c9a9fd50bf270125Christian Maeder if (exported.containsAll(onto.getDirectImports())) {
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio // output handler allows and handles a list of output-requests
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio protected static class OWLOutputHandler {
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio static ArrayList<OWLOntologyWriter> writer = new ArrayList<OWLOntologyWriter>();
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio void add(OPTION op, String filename) throws Exception {
b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist // function need to be called once to render and close every output
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio void renderUsingOption(OWLOntology onto) throws IOException {
b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist // custem OntolgyWriter bundles a BufferedWriter with an OWL output format
b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist protected static class OWLOntologyWriter extends BufferedWriter {
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio OWLOntologyWriter(String fn, OPTION op) throws Exception {
4ffc423a7df8af7e7d7e563a15471da4505ddeb5ignazio void renderUsingOption(OWLOntology onto) throws IOException {
b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist // TODO: the below still need implementation!
b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist ManchesterOWLSyntaxRenderer omnrend = new ManchesterOWLSyntaxRenderer();
b1d1bda618f7b145c28645f39b0ca651b8001ebanotanartist System.err.println("Error by ManchesterParser!");
be8a364e20bf080501e6b7b76664c33b649ffac7Jens Elkner File tempFile = File.createTempFile("owlTemp_1", ".xml.gz",
be8a364e20bf080501e6b7b76664c33b649ffac7Jens Elkner out = new OutputStreamWriter(new GZIPOutputStream(fos, 4096),
be8a364e20bf080501e6b7b76664c33b649ffac7Jens Elkner in = new InputStreamReader(new GZIPInputStream(fis, 4096),
be8a364e20bf080501e6b7b76664c33b649ffac7Jens Elkner // ignore the first line containing <?xml version="1.0"?>
be8a364e20bf080501e6b7b76664c33b649ffac7Jens Elkner while ((chomp != -2) && (c = in.read(buf, 0, 8192)) != -1) {
be8a364e20bf080501e6b7b76664c33b649ffac7Jens Elkner for (int i=0; i < c; i++) {
be8a364e20bf080501e6b7b76664c33b649ffac7Jens Elkner // chomp trailing LF and CR
be8a364e20bf080501e6b7b76664c33b649ffac7Jens Elkner for (int i=n; i < c; i++) {
be8a364e20bf080501e6b7b76664c33b649ffac7Jens Elkner // copy the remaining stuff as is
be8a364e20bf080501e6b7b76664c33b649ffac7Jens Elkner try { out.close(); } catch (Exception e) { /* nwcd */ }
be8a364e20bf080501e6b7b76664c33b649ffac7Jens Elkner try { fos.close(); } catch (Exception e) { /* nwcd */ }
be8a364e20bf080501e6b7b76664c33b649ffac7Jens Elkner try { in.close(); } catch (Exception e) { /* nwcd */ }
be8a364e20bf080501e6b7b76664c33b649ffac7Jens Elkner try { fis.close(); } catch (Exception e) { /* nwcd */ }