unibremen/informatik/OWL2Parser.java

	OWL2Parser.java revision 53680982da7898ae889870da416205a85f0bffad
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
53680982da7898ae889870da416205a85f0bffadJens Elkner    private static enum OPTION {
53680982da7898ae889870da416205a85f0bffadJens Elkner        OWL_XML, MANCHESTER, RDF_XML, OBO, TURTLE
53680982da7898ae889870da416205a85f0bffadJens Elkner    }
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner    private static Boolean quick = false;
53680982da7898ae889870da416205a85f0bffadJens Elkner    private static Boolean cyclic = false;
53680982da7898ae889870da416205a85f0bffadJens Elkner    protected static final Set<IRI> missingImports = new HashSet<IRI>();
53680982da7898ae889870da416205a85f0bffadJens Elkner    private static Set<OWLOntology> ontologies;
53680982da7898ae889870da416205a85f0bffadJens Elkner    private static final Set<OWLOntology> exported = new HashSet<OWLOntology>();
53680982da7898ae889870da416205a85f0bffadJens Elkner    private static OWLOntologyManager manager =
53680982da7898ae889870da416205a85f0bffadJens Elkner        setupManagerWithMissingImportListener();
53680982da7898ae889870da416205a85f0bffadJens Elkner    private static OWLOntologyIRIMapperImpl mapper =
53680982da7898ae889870da416205a85f0bffadJens Elkner        new OWLOntologyIRIMapperImpl();
53680982da7898ae889870da416205a85f0bffadJens Elkner    private static URI uri = null;
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner    public static void main(String[] args) {
53680982da7898ae889870da416205a85f0bffadJens Elkner        // A simple example of how to load and save an ontology
53680982da7898ae889870da416205a85f0bffadJens Elkner        try {
53680982da7898ae889870da416205a85f0bffadJens Elkner            OWLOutputHandler out = new OWLOutputHandler();
53680982da7898ae889870da416205a85f0bffadJens Elkner            parseArgs(args, out);
53680982da7898ae889870da416205a85f0bffadJens Elkner            URLConnection con = uri.toURL().openConnection();
53680982da7898ae889870da416205a85f0bffadJens Elkner            con.addRequestProperty("Accept", "text/plain");
53680982da7898ae889870da416205a85f0bffadJens Elkner            StreamDocumentSource sds =
53680982da7898ae889870da416205a85f0bffadJens Elkner                new StreamDocumentSource(con.getInputStream(), IRI.create(uri));
53680982da7898ae889870da416205a85f0bffadJens Elkner            OWLOntologyLoaderConfiguration config =
53680982da7898ae889870da416205a85f0bffadJens Elkner                new OWLOntologyLoaderConfiguration();
53680982da7898ae889870da416205a85f0bffadJens Elkner            config = config
53680982da7898ae889870da416205a85f0bffadJens Elkner                .setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT);
53680982da7898ae889870da416205a85f0bffadJens Elkner            OWLOntology ontology =
53680982da7898ae889870da416205a85f0bffadJens Elkner                manager.loadOntologyFromOntologyDocument(sds, config);
53680982da7898ae889870da416205a85f0bffadJens Elkner            if ( !missingImports.isEmpty()) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                IRI ontohub = IRI.create("https://ontohub.org/external/");
53680982da7898ae889870da416205a85f0bffadJens Elkner                for (IRI mi : missingImports) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                    mapper.addMapping(mi, ontohub.resolve(mi.toURI().getHost()
53680982da7898ae889870da416205a85f0bffadJens Elkner                        + mi.toURI().getPath()));
53680982da7898ae889870da416205a85f0bffadJens Elkner                }
53680982da7898ae889870da416205a85f0bffadJens Elkner                // reset the manager. clear out imports to avoid duplicates
53680982da7898ae889870da416205a85f0bffadJens Elkner                manager = setupManagerWithMissingImportListener();
53680982da7898ae889870da416205a85f0bffadJens Elkner                manager.addIRIMapper(mapper);
53680982da7898ae889870da416205a85f0bffadJens Elkner                // collect missing imports again to report them in output file.
53680982da7898ae889870da416205a85f0bffadJens Elkner                missingImports.clear();
53680982da7898ae889870da416205a85f0bffadJens Elkner                ontology =
53680982da7898ae889870da416205a85f0bffadJens Elkner                    manager.loadOntologyFromOntologyDocument(sds, config);
53680982da7898ae889870da416205a85f0bffadJens Elkner            }
53680982da7898ae889870da416205a85f0bffadJens Elkner            ontologies = getImports(ontology, new HashSet<OWLOntology>());
53680982da7898ae889870da416205a85f0bffadJens Elkner            out._open();
53680982da7898ae889870da416205a85f0bffadJens Elkner            if (cyclic) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                String str = ontology.getOntologyID().getOntologyIRI().toString();
53680982da7898ae889870da416205a85f0bffadJens Elkner                // we must make a new name
53680982da7898ae889870da416205a85f0bffadJens Elkner                String merged_name = str + ".merged.owl";
53680982da7898ae889870da416205a85f0bffadJens Elkner                // System.out.println("NAME: " + merged_name + "\n");
53680982da7898ae889870da416205a85f0bffadJens Elkner                IRI mergedOntologyIRI = IRI.create(merged_name);
53680982da7898ae889870da416205a85f0bffadJens Elkner                // System.out.println("MERGED_IRI " + mergedOntologyIRI + "\n");
53680982da7898ae889870da416205a85f0bffadJens Elkner                OWLOntology merged;
53680982da7898ae889870da416205a85f0bffadJens Elkner                // Axioms can be excluded when 'quick' Option selected
53680982da7898ae889870da416205a85f0bffadJens Elkner                if (quick) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                    merged = manager.createOntology(mergedOntologyIRI);
53680982da7898ae889870da416205a85f0bffadJens Elkner                } else {
53680982da7898ae889870da416205a85f0bffadJens Elkner                    OWLOntologyMerger merger = new OWLOntologyMerger(manager);
53680982da7898ae889870da416205a85f0bffadJens Elkner                    merged =
53680982da7898ae889870da416205a85f0bffadJens Elkner                        merger.createMergedOntology(manager, mergedOntologyIRI);
53680982da7898ae889870da416205a85f0bffadJens Elkner                }
53680982da7898ae889870da416205a85f0bffadJens Elkner                out.renderUsingOption(merged);
53680982da7898ae889870da416205a85f0bffadJens Elkner            } else {
53680982da7898ae889870da416205a85f0bffadJens Elkner                ontologies.add(ontology);
53680982da7898ae889870da416205a85f0bffadJens Elkner                exportImports(out);
53680982da7898ae889870da416205a85f0bffadJens Elkner            }
53680982da7898ae889870da416205a85f0bffadJens Elkner            out._close();
53680982da7898ae889870da416205a85f0bffadJens Elkner        } catch (Exception ex) {
53680982da7898ae889870da416205a85f0bffadJens Elkner            System.err.println("OWL parse error: " + ex.getMessage());
53680982da7898ae889870da416205a85f0bffadJens Elkner            ex.printStackTrace();
53680982da7898ae889870da416205a85f0bffadJens Elkner        }
53680982da7898ae889870da416205a85f0bffadJens Elkner    }
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner    // print usage information screen
53680982da7898ae889870da416205a85f0bffadJens Elkner    private static void showHelpScreen() {
53680982da7898ae889870da416205a85f0bffadJens Elkner        System.out.println("Usage: processor [<options..>] <URI>\n"
53680982da7898ae889870da416205a85f0bffadJens Elkner            + "_>_options_<______________\n"
53680982da7898ae889870da416205a85f0bffadJens Elkner            + " | -o <tp> <fn>  ..write output to file\n"
53680982da7898ae889870da416205a85f0bffadJens Elkner            + " - - - tp  <- type [: owl xml omn rdf obo dol ttl]\n"
53680982da7898ae889870da416205a85f0bffadJens Elkner            + " - - - fn  <- filename\n"
53680982da7898ae889870da416205a85f0bffadJens Elkner            + " | -o-sys <tp> ..write output to system.out\n"
53680982da7898ae889870da416205a85f0bffadJens Elkner            + " - - - - - tp  <- type\n"
53680982da7898ae889870da416205a85f0bffadJens Elkner            + " | -qk  ..internal(!) sets 'quick' option\n"
53680982da7898ae889870da416205a85f0bffadJens Elkner            + " | -h  ..this helptext");
53680982da7898ae889870da416205a85f0bffadJens Elkner    }
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner    // parse arguments according to option set
53680982da7898ae889870da416205a85f0bffadJens Elkner    // fails for unknown or incomplete arguments, or when IRI is not set
53680982da7898ae889870da416205a85f0bffadJens Elkner    private static void parseArgs(String[] args, OWLOutputHandler out)
53680982da7898ae889870da416205a85f0bffadJens Elkner        throws Exception
53680982da7898ae889870da416205a85f0bffadJens Elkner    {
53680982da7898ae889870da416205a85f0bffadJens Elkner        String inp = "", msg = "OWL2Parser.parseArgs: ";
53680982da7898ae889870da416205a85f0bffadJens Elkner        if (args.length == 0) {
53680982da7898ae889870da416205a85f0bffadJens Elkner            throw new Exception(msg + "no arguments provided");
53680982da7898ae889870da416205a85f0bffadJens Elkner        }
53680982da7898ae889870da416205a85f0bffadJens Elkner        for (int i = 0; i < args.length; i++ ) {
53680982da7898ae889870da416205a85f0bffadJens Elkner            String arg = args[i].toLowerCase();
53680982da7898ae889870da416205a85f0bffadJens Elkner            if (arg.startsWith("-")) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                if (arg.equals("-o")) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                    if (!(i < args.length - 2)) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                        throw new Exception(msg
53680982da7898ae889870da416205a85f0bffadJens Elkner                            + "insufficient arguments (-o [format] [filename])");
53680982da7898ae889870da416205a85f0bffadJens Elkner                    }
53680982da7898ae889870da416205a85f0bffadJens Elkner                    out.add(parseOption(args[++i].toLowerCase(), msg), args[++i]);
53680982da7898ae889870da416205a85f0bffadJens Elkner                } else if (arg.equals("-o-sys")) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                    if (!(i < args.length - 1)) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                        throw new Exception(msg
53680982da7898ae889870da416205a85f0bffadJens Elkner                            + "insufficient arguments (-o-sys [format])");
53680982da7898ae889870da416205a85f0bffadJens Elkner                    }
53680982da7898ae889870da416205a85f0bffadJens Elkner                    out.add(parseOption(args[ ++i].toLowerCase(), msg));
53680982da7898ae889870da416205a85f0bffadJens Elkner                } else if (arg.equals("-qk") || arg.equals("-q")) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                    quick = true;
53680982da7898ae889870da416205a85f0bffadJens Elkner                } else if (arg.equals("-h") || arg.equals("--help")) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                    showHelpScreen();
53680982da7898ae889870da416205a85f0bffadJens Elkner                } else {
53680982da7898ae889870da416205a85f0bffadJens Elkner                    throw new Exception(msg + "unknown command <" + arg + ">");
53680982da7898ae889870da416205a85f0bffadJens Elkner                }
53680982da7898ae889870da416205a85f0bffadJens Elkner            } else {
53680982da7898ae889870da416205a85f0bffadJens Elkner                if (!inp.equals("")) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                    throw new Exception(msg + "ambigious IRI");
53680982da7898ae889870da416205a85f0bffadJens Elkner                }
53680982da7898ae889870da416205a85f0bffadJens Elkner                inp = args[i]; // read again to undo earlier 'toLowerCase'
53680982da7898ae889870da416205a85f0bffadJens Elkner                if (arg.startsWith("http:") || arg.startsWith("https:")) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                    uri = new URI(inp);
53680982da7898ae889870da416205a85f0bffadJens Elkner                } else {
53680982da7898ae889870da416205a85f0bffadJens Elkner                    uri = new File(inp).toURI();
53680982da7898ae889870da416205a85f0bffadJens Elkner                }
53680982da7898ae889870da416205a85f0bffadJens Elkner            }
53680982da7898ae889870da416205a85f0bffadJens Elkner        }
53680982da7898ae889870da416205a85f0bffadJens Elkner        if (inp.equals("")) {
53680982da7898ae889870da416205a85f0bffadJens Elkner            throw new Exception(msg + "IRI not set");
53680982da7898ae889870da416205a85f0bffadJens Elkner        }
53680982da7898ae889870da416205a85f0bffadJens Elkner    }
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner    private static OPTION parseOption(String opt, String err) throws Exception {
53680982da7898ae889870da416205a85f0bffadJens Elkner        if (opt.equals("xml") || opt.equals("owl")) {
53680982da7898ae889870da416205a85f0bffadJens Elkner            return OPTION.OWL_XML;
53680982da7898ae889870da416205a85f0bffadJens Elkner        } else if (opt.equals("omn")) {
53680982da7898ae889870da416205a85f0bffadJens Elkner            return OPTION.MANCHESTER;
53680982da7898ae889870da416205a85f0bffadJens Elkner        } else if (opt.equals("rdf")) {
53680982da7898ae889870da416205a85f0bffadJens Elkner            return OPTION.RDF_XML;
53680982da7898ae889870da416205a85f0bffadJens Elkner        } else if (opt.equals("obo")) {
53680982da7898ae889870da416205a85f0bffadJens Elkner            return OPTION.OBO;
53680982da7898ae889870da416205a85f0bffadJens Elkner        } else if (opt.equals("ttl")) {
53680982da7898ae889870da416205a85f0bffadJens Elkner            return OPTION.TURTLE;
53680982da7898ae889870da416205a85f0bffadJens Elkner        }
53680982da7898ae889870da416205a85f0bffadJens Elkner        throw new Exception(err + "unrecognized owl-format: " + opt);
53680982da7898ae889870da416205a85f0bffadJens Elkner    }
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner    private static OWLOntologyManager setupManagerWithMissingImportListener() {
53680982da7898ae889870da416205a85f0bffadJens Elkner        OWLOntologyManager mgr = OWLManager.createOWLOntologyManager();
53680982da7898ae889870da416205a85f0bffadJens Elkner        mgr.addMissingImportListener(new HasMissingImports());
53680982da7898ae889870da416205a85f0bffadJens Elkner        return mgr;
53680982da7898ae889870da416205a85f0bffadJens Elkner    }
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner    private static class HasMissingImports implements MissingImportListener {
53680982da7898ae889870da416205a85f0bffadJens Elkner        @Override
53680982da7898ae889870da416205a85f0bffadJens Elkner        public void importMissing(MissingImportEvent event) {
53680982da7898ae889870da416205a85f0bffadJens Elkner            missingImports.add(event.getImportedOntologyURI());
53680982da7898ae889870da416205a85f0bffadJens Elkner        }
53680982da7898ae889870da416205a85f0bffadJens Elkner    }
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner    private static Set<OWLOntology> getImports(OWLOntology ontology,
53680982da7898ae889870da416205a85f0bffadJens Elkner        Set<OWLOntology> stop)
53680982da7898ae889870da416205a85f0bffadJens Elkner    {
53680982da7898ae889870da416205a85f0bffadJens Elkner        Set<OWLOntology> s = new HashSet<OWLOntology>();
53680982da7898ae889870da416205a85f0bffadJens Elkner        Set<OWLOntology> next = new HashSet<OWLOntology>(stop);
53680982da7898ae889870da416205a85f0bffadJens Elkner        next.add(ontology);
53680982da7898ae889870da416205a85f0bffadJens Elkner        for (OWLOntology imported : ontology.getDirectImports()) {
53680982da7898ae889870da416205a85f0bffadJens Elkner            if (cyclic || next.contains(imported)) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                cyclic = true;
53680982da7898ae889870da416205a85f0bffadJens Elkner            } else if (!s.contains(imported)) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                Set<OWLOntology> i = getImports(imported, next);
53680982da7898ae889870da416205a85f0bffadJens Elkner                s.add(imported);
53680982da7898ae889870da416205a85f0bffadJens Elkner                s.addAll(i);
53680982da7898ae889870da416205a85f0bffadJens Elkner            }
53680982da7898ae889870da416205a85f0bffadJens Elkner        }
53680982da7898ae889870da416205a85f0bffadJens Elkner        return s;
53680982da7898ae889870da416205a85f0bffadJens Elkner    }
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner    private static void exportImports(OWLOutputHandler out) throws IOException {
53680982da7898ae889870da416205a85f0bffadJens Elkner        Boolean changed;
53680982da7898ae889870da416205a85f0bffadJens Elkner        do {
53680982da7898ae889870da416205a85f0bffadJens Elkner            changed = false;
53680982da7898ae889870da416205a85f0bffadJens Elkner            for (OWLOntology onto : ontologies) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                if (exported.containsAll(onto.getDirectImports())) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                    if (!exported.contains(onto)) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                        changed = exported.add(onto);
53680982da7898ae889870da416205a85f0bffadJens Elkner                        out.renderUsingOption(onto);
53680982da7898ae889870da416205a85f0bffadJens Elkner                    }
53680982da7898ae889870da416205a85f0bffadJens Elkner                }
53680982da7898ae889870da416205a85f0bffadJens Elkner            }
53680982da7898ae889870da416205a85f0bffadJens Elkner        } while (changed);
53680982da7898ae889870da416205a85f0bffadJens Elkner    }
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner    // output handler allows and handles a list of output-requests
53680982da7898ae889870da416205a85f0bffadJens Elkner    protected static class OWLOutputHandler {
53680982da7898ae889870da416205a85f0bffadJens Elkner        static ArrayList<OWLOntologyWriter> writer =
53680982da7898ae889870da416205a85f0bffadJens Elkner            new ArrayList<OWLOntologyWriter>();
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner        void add(OPTION op) throws Exception {
53680982da7898ae889870da416205a85f0bffadJens Elkner            writer.add(new OWLOntologyWriter(op));
53680982da7898ae889870da416205a85f0bffadJens Elkner        }
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner        void add(OPTION op, String filename) throws Exception {
53680982da7898ae889870da416205a85f0bffadJens Elkner            writer.add(new OWLOntologyWriter(filename, op));
53680982da7898ae889870da416205a85f0bffadJens Elkner        }
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner        void _open() throws IOException {
53680982da7898ae889870da416205a85f0bffadJens Elkner            for (OWLOntologyWriter out : writer) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                out._open();
53680982da7898ae889870da416205a85f0bffadJens Elkner            }
53680982da7898ae889870da416205a85f0bffadJens Elkner        }
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner        void _close() throws IOException {
53680982da7898ae889870da416205a85f0bffadJens Elkner            for (OWLOntologyWriter out : writer) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                out._close();
53680982da7898ae889870da416205a85f0bffadJens Elkner            }
53680982da7898ae889870da416205a85f0bffadJens Elkner        }
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner        // function need to be called once to render and close every output
53680982da7898ae889870da416205a85f0bffadJens Elkner        void renderUsingOption(OWLOntology onto) throws IOException {
53680982da7898ae889870da416205a85f0bffadJens Elkner            for (OWLOntologyWriter out : writer) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                out.renderUsingOption(onto);
53680982da7898ae889870da416205a85f0bffadJens Elkner            }
53680982da7898ae889870da416205a85f0bffadJens Elkner        }
53680982da7898ae889870da416205a85f0bffadJens Elkner    }
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner    // custem OntolgyWriter bundles a BufferedWriter with an OWL output format
53680982da7898ae889870da416205a85f0bffadJens Elkner    protected static class OWLOntologyWriter extends BufferedWriter {
53680982da7898ae889870da416205a85f0bffadJens Elkner        protected static OPTION option;
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner        OWLOntologyWriter(String fn, OPTION op) throws Exception {
53680982da7898ae889870da416205a85f0bffadJens Elkner            super(new FileWriter(fn));
53680982da7898ae889870da416205a85f0bffadJens Elkner            option = op;
53680982da7898ae889870da416205a85f0bffadJens Elkner        }
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner        OWLOntologyWriter(OPTION op) throws Exception {
53680982da7898ae889870da416205a85f0bffadJens Elkner            super(new OutputStreamWriter(System.out));
53680982da7898ae889870da416205a85f0bffadJens Elkner            option = op;
53680982da7898ae889870da416205a85f0bffadJens Elkner        }
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner        void writeMissingImports() throws IOException {
53680982da7898ae889870da416205a85f0bffadJens Elkner            for (IRI mi : missingImports) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                write("<Missing>" + mi + "</Missing>\n");
53680982da7898ae889870da416205a85f0bffadJens Elkner            }
53680982da7898ae889870da416205a85f0bffadJens Elkner        }
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner        void _open() throws IOException {
53680982da7898ae889870da416205a85f0bffadJens Elkner            if (option == OPTION.OWL_XML) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                write("<Ontologies>\n");
53680982da7898ae889870da416205a85f0bffadJens Elkner            }
53680982da7898ae889870da416205a85f0bffadJens Elkner        }
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner        void _close() throws IOException {
53680982da7898ae889870da416205a85f0bffadJens Elkner            if (option == OPTION.OWL_XML) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                writeMissingImports();
53680982da7898ae889870da416205a85f0bffadJens Elkner                write("\n</Ontologies>\n");
53680982da7898ae889870da416205a85f0bffadJens Elkner            }
53680982da7898ae889870da416205a85f0bffadJens Elkner            _close(this);
53680982da7898ae889870da416205a85f0bffadJens Elkner        }
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner        void _close(Writer pointer) throws IOException {
53680982da7898ae889870da416205a85f0bffadJens Elkner            pointer.flush();
53680982da7898ae889870da416205a85f0bffadJens Elkner            pointer.close();
53680982da7898ae889870da416205a85f0bffadJens Elkner        }
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner        void renderUsingOption(OWLOntology onto) throws IOException {
53680982da7898ae889870da416205a85f0bffadJens Elkner            switch (option) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                case OWL_XML:
53680982da7898ae889870da416205a85f0bffadJens Elkner                    renderAsXml(onto);
53680982da7898ae889870da416205a85f0bffadJens Elkner                    break;
53680982da7898ae889870da416205a85f0bffadJens Elkner                case MANCHESTER:
53680982da7898ae889870da416205a85f0bffadJens Elkner                    renderAsOmn(onto);
53680982da7898ae889870da416205a85f0bffadJens Elkner                    break;
53680982da7898ae889870da416205a85f0bffadJens Elkner                case RDF_XML:
53680982da7898ae889870da416205a85f0bffadJens Elkner                    renderAsRdf(onto);
53680982da7898ae889870da416205a85f0bffadJens Elkner                    break;
53680982da7898ae889870da416205a85f0bffadJens Elkner                // TODO: the below still need implementation!
53680982da7898ae889870da416205a85f0bffadJens Elkner                case OBO:
53680982da7898ae889870da416205a85f0bffadJens Elkner                    renderAsXml(onto);
53680982da7898ae889870da416205a85f0bffadJens Elkner                    break;
53680982da7898ae889870da416205a85f0bffadJens Elkner                case TURTLE:
53680982da7898ae889870da416205a85f0bffadJens Elkner                    renderAsXml(onto);
53680982da7898ae889870da416205a85f0bffadJens Elkner                    break;
53680982da7898ae889870da416205a85f0bffadJens Elkner            }
53680982da7898ae889870da416205a85f0bffadJens Elkner        }
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner        void renderAsOmn(OWLOntology onto) {
53680982da7898ae889870da416205a85f0bffadJens Elkner            try {
53680982da7898ae889870da416205a85f0bffadJens Elkner                ManchesterOWLSyntaxRenderer omnrend =
53680982da7898ae889870da416205a85f0bffadJens Elkner                    new ManchesterOWLSyntaxRenderer();
53680982da7898ae889870da416205a85f0bffadJens Elkner                omnrend.render(onto, this);
53680982da7898ae889870da416205a85f0bffadJens Elkner            } catch (OWLRendererException ex) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                System.err.println("Error by ManchesterParser!");
53680982da7898ae889870da416205a85f0bffadJens Elkner                ex.printStackTrace();
53680982da7898ae889870da416205a85f0bffadJens Elkner            }
53680982da7898ae889870da416205a85f0bffadJens Elkner        }
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner        void renderAsXml(OWLOntology onto) {
53680982da7898ae889870da416205a85f0bffadJens Elkner            try {
53680982da7898ae889870da416205a85f0bffadJens Elkner                OWLXMLRenderer xmlren = new OWLXMLRenderer();
53680982da7898ae889870da416205a85f0bffadJens Elkner                File tempFile = File.createTempFile("owlTemp_1", ".xml");
53680982da7898ae889870da416205a85f0bffadJens Elkner                FileWriter buf = new FileWriter(tempFile);
53680982da7898ae889870da416205a85f0bffadJens Elkner                if (quick) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                    onto.getOWLOntologyManager()
53680982da7898ae889870da416205a85f0bffadJens Elkner                        .removeAxioms(onto,onto.getAxioms());
53680982da7898ae889870da416205a85f0bffadJens Elkner                }
53680982da7898ae889870da416205a85f0bffadJens Elkner                xmlren.render(onto, buf);
53680982da7898ae889870da416205a85f0bffadJens Elkner                _close(buf);
53680982da7898ae889870da416205a85f0bffadJens Elkner                BufferedReader rBuf =
53680982da7898ae889870da416205a85f0bffadJens Elkner                    new BufferedReader(new FileReader(tempFile));
53680982da7898ae889870da416205a85f0bffadJens Elkner                rBuf.readLine(); // ignore the first line containing <?xml version="1.0"?>
53680982da7898ae889870da416205a85f0bffadJens Elkner                while (rBuf.ready()) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                    append(rBuf.readLine()).append("\n");
53680982da7898ae889870da416205a85f0bffadJens Elkner                }
53680982da7898ae889870da416205a85f0bffadJens Elkner                rBuf.close();
53680982da7898ae889870da416205a85f0bffadJens Elkner                tempFile.deleteOnExit();
53680982da7898ae889870da416205a85f0bffadJens Elkner                append("<Loaded name=\"")
53680982da7898ae889870da416205a85f0bffadJens Elkner                    .append(manager.getOntologyDocumentIRI(onto));
53680982da7898ae889870da416205a85f0bffadJens Elkner                append("\" ontiri=\"")
53680982da7898ae889870da416205a85f0bffadJens Elkner                    .append(onto.getOntologyID().getOntologyIRI());
53680982da7898ae889870da416205a85f0bffadJens Elkner                append("\"/>\n");
53680982da7898ae889870da416205a85f0bffadJens Elkner            } catch (Exception ex) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                System.err.println("Error by XMLParser!");
53680982da7898ae889870da416205a85f0bffadJens Elkner                ex.printStackTrace();
53680982da7898ae889870da416205a85f0bffadJens Elkner            }
53680982da7898ae889870da416205a85f0bffadJens Elkner        }
53680982da7898ae889870da416205a85f0bffadJens Elkner
53680982da7898ae889870da416205a85f0bffadJens Elkner        void renderAsRdf(OWLOntology onto) {
53680982da7898ae889870da416205a85f0bffadJens Elkner            try {
53680982da7898ae889870da416205a85f0bffadJens Elkner                RDFXMLRenderer rdfrend = new RDFXMLRenderer(onto, this);
53680982da7898ae889870da416205a85f0bffadJens Elkner                rdfrend.render();
53680982da7898ae889870da416205a85f0bffadJens Elkner            } catch (IOException ex) {
53680982da7898ae889870da416205a85f0bffadJens Elkner                System.err.println("Error by RDFParser!");
53680982da7898ae889870da416205a85f0bffadJens Elkner                ex.printStackTrace();
53680982da7898ae889870da416205a85f0bffadJens Elkner            }
53680982da7898ae889870da416205a85f0bffadJens Elkner        }
53680982da7898ae889870da416205a85f0bffadJens Elkner    }
2578a6d217296401d347302c9104fee179bd0470Francisc Nicolae Bungiu}