Examples with RDFFormat org.eclipse.rdf4j.rio.RDFFormat used on opensource projects

Example 56 with RDFFormat

use of org.eclipse.rdf4j.rio.RDFFormat in project d3web-KnowWE by denkbares.

the class InitTerminologyHandler method importAttachment.

private void importAttachment(OntologyCompiler compiler, Section<? extends AnnotationContentType> section, String attachmentFile, boolean silent) {
    long start = System.currentTimeMillis();
    Section<AttachmentType> importSection = Sections.successor(section, AttachmentType.class);
    String path = createPath(section, attachmentFile);
    WikiAttachment attachment;
    try {
        attachment = Environment.getInstance().getWikiConnector().getAttachment(path);
    } catch (IOException e) {
        Messages.storeMessage(compiler, section, this.getClass(), Messages.error("Error while retrieving attachment '" + attachmentFile + "': " + e.getMessage()));
        return;
    }
    Rdf2GoCore core = compiler.getRdf2GoCore();
    if (core == null) {
        Messages.storeMessage(compiler, section, this.getClass(), Messages.error("No ontology repository found '" + section.getText() + "'"));
        return;
    }
    if (attachment == null) {
        Messages.storeMessage(compiler, section, this.getClass(), Messages.error("Attachment '" + section.getText().trim() + "' not found"));
        return;
    }
    String fileName = attachment.getFileName();
    RDFFormat syntax = Rdf2GoUtils.syntaxForFileName(fileName);
    Future<?> mainReadFuture = executorService.submit(() -> readFrom(compiler, section, core, attachment, syntax));
    if (!silent) {
        Rdf2GoCore dummyCore = getDummyCore(compiler, section, attachment, syntax);
        // register the terminology imported in the cached empty dummy repository
        registerTerminology(compiler, dummyCore, importSection);
    }
    try {
        mainReadFuture.get();
    } catch (InterruptedException | ExecutionException e) {
        handleException(compiler, section, attachment, e);
    }
    long duration = System.currentTimeMillis() - start;
    if (duration > TimeUnit.SECONDS.toMillis(1)) {
        LOGGER.info("Loaded ontology from attachment " + path + " in " + duration + "ms");
    }
}

Example 57 with RDFFormat

use of org.eclipse.rdf4j.rio.RDFFormat in project d3web-KnowWE by denkbares.

the class InitTerminologyHandler method getDummyCore.

private Rdf2GoCore getDummyCore(OntologyCompiler compiler, Section<? extends AnnotationContentType> section, WikiAttachment attachment, RDFFormat syntax) {
    // we need rdfs reasoning for the SPARQLs to work
    TermCache cache;
    String key = attachment.getPath() + "_" + attachment.getDate();
    synchronized (importCache) {
        cache = importCache.computeIfAbsent(key, k -> {
            Rdf2GoCore dummy = new Rdf2GoCore(RepositoryConfigs.find("RDFS"));
            readFrom(compiler, section, dummy, attachment, syntax);
            return new TermCache(dummy, attachment.getPath(), attachment.getDate());
        });
        cache.referencingSections.add(section.getID());
        importCache.values().removeIf(rCache -> {
            boolean remove = noLongerReferenced(rCache) || attachmentOutDated(rCache);
            // if we remove, make sure to properly destroy to allow gc and free up memory
            if (remove) {
                rCache.core.close();
            }
            return remove;
        });
    }
    return cache.core;
}

Example 58 with RDFFormat

use of org.eclipse.rdf4j.rio.RDFFormat in project d3web-KnowWE by denkbares.

the class OntologyExporter method notify.

@Override
public void notify(Event event) {
    OntologyCompilerFinishedEvent finishedEvent = (OntologyCompilerFinishedEvent) event;
    if (!finishedEvent.isOntologyChanged())
        return;
    final OntologyCompiler compiler = finishedEvent.getCompiler();
    final Rdf2GoCore rdf2GoCore = compiler.getRdf2GoCore();
    Section<OntologyType> ontologySection = compiler.getCompileSection();
    synchronized (timers) {
        Timer lastTimer = timers.get(ontologySection.getID());
        if (lastTimer != null)
            lastTimer.cancel();
        // cleanup times of now longer existing sections
        timers.keySet().removeIf(sectionId -> Sections.get(sectionId) == null);
    }
    Section<?> exportAnnotation = DefaultMarkupType.getAnnotationContentSection(ontologySection, OntologyType.ANNOTATION_EXPORT);
    // no export specified, we are finished here
    if (exportAnnotation == null)
        return;
    String export = exportAnnotation.getText();
    String[] split = export.split("/");
    final String title;
    final String annotationName;
    if (split.length == 1) {
        title = ontologySection.getTitle();
        annotationName = split[0];
    } else if (split.length == 2) {
        title = split[0];
        annotationName = split[1];
    } else {
        Messages.storeMessage(exportAnnotation, this.getClass(), Messages.error("'" + export + "' is not" + " a valid annotation to export to. Use article-name/annotation-name.syntax or" + " only annotation-name.syntax instead."));
        return;
    }
    if (KnowWEUtils.getArticle(ontologySection.getWeb(), title) == null) {
        Messages.storeMessage(exportAnnotation, this.getClass(), Messages.error("Article '" + title + "' does not" + " exist, export has to point to an existing article."));
        return;
    }
    // if not failed yet, clean up messages
    Messages.clearMessages(exportAnnotation, this.getClass());
    RDFFormat parsedSyntax = Rdf2GoUtils.syntaxForFileName(annotationName);
    final RDFFormat syntax = parsedSyntax == null ? RDFFormat.TURTLE : parsedSyntax;
    long exportDelay = getExportDelay(ontologySection);
    Timer timer = new Timer();
    timer.schedule(new TimerTask() {

        @Override
        public void run() {
            Stopwatch stopwatch = new Stopwatch();
            WikiConnector connector = Environment.getInstance().getWikiConnector();
            ByteArrayInputStream stream;
            try {
                ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
                // cleanup so the versions don't stack to bad...
                rdf2GoCore.writeModel(outputStream, syntax);
                stream = new ByteArrayInputStream(outputStream.toByteArray());
            } catch (Exception e) {
                if (e.getCause() instanceof ClosedChannelException) {
                    LOGGER.warn("Export of ontology from '" + compiler.getCompileSection().getTitle() + "' aborted due to repository shutdown.");
                } else {
                    LOGGER.error("Unable to export ontology from '" + compiler.getCompileSection().getTitle() + "'", e);
                }
                return;
            }
            try {
                connector.deleteAttachment(title, annotationName, "SYSTEM");
                connector.storeAttachment(title, annotationName, "SYSTEM", stream);
            } catch (IOException e) {
                LOGGER.error("Unable to save exported ontology as an attachment in '" + title + "/" + annotationName + "'", e);
                return;
            }
            LOGGER.info("Exported ontology to attachment '" + title + "/" + annotationName + "' in " + stopwatch.getDisplay() + " after a delay of " + Stopwatch.getDisplay(exportDelay));
        }
    }, exportDelay);
    synchronized (timers) {
        timers.put(ontologySection.getID(), timer);
    }
}

Example 59 with RDFFormat

use of org.eclipse.rdf4j.rio.RDFFormat in project commons-rdf by apache.

the class RDF4JParser method parseSynchronusly.

@Override
protected void parseSynchronusly() throws IOException {
    final Optional<RDFFormat> formatByMimeType = getContentType().flatMap(Rio::getParserFormatForMIMEType);
    final String base = getBase().map(IRI::getIRIString).orElse(null);
    final ParserConfig parserConfig = getParserConfig();
    // TODO: Should we need to set anything?
    final RDFLoader loader = new RDFLoader(parserConfig, rdf4jTermFactory.getValueFactory());
    final RDFHandler rdfHandler = makeRDFHandler();
    if (getSourceFile().isPresent()) {
        // NOTE: While we could have used
        // loader.load(sourcePath.toFile()
        // if the path fs provider == FileSystems.getDefault(),
        // that RDFLoader method does not use absolute path
        // as the base URI, so to be consistent
        // we'll always do it with our own input stream
        // 
        // That means we may have to guess format by extensions:
        final Optional<RDFFormat> formatByFilename = getSourceFile().map(Path::getFileName).map(Path::toString).flatMap(Rio::getParserFormatForFileName);
        // TODO: for the excited.. what about the extension after following
        // symlinks?
        final RDFFormat format = formatByMimeType.orElse(formatByFilename.orElse(null));
        try (InputStream in = Files.newInputStream(getSourceFile().get())) {
            loader.load(in, base, format, rdfHandler);
        }
    } else if (getSourceIri().isPresent()) {
        try {
            // TODO: Handle international IRIs properly
            // (Unicode support for for hostname, path and query)
            final URL url = new URL(getSourceIri().get().getIRIString());
            // TODO: This probably does not support https:// -> http://
            // redirections
            loader.load(url, base, formatByMimeType.orElse(null), makeRDFHandler());
        } catch (final MalformedURLException ex) {
            throw new IOException("Can't handle source URL: " + getSourceIri().get(), ex);
        }
    }
    // must be getSourceInputStream then, this is guaranteed by
    // super.checkSource();
    loader.load(getSourceInputStream().get(), base, formatByMimeType.orElse(null), rdfHandler);
}

Example 60 with RDFFormat

use of org.eclipse.rdf4j.rio.RDFFormat in project AJAN-service by aantakli.

the class MAJANServiceHandler method ExecuteAgent.

@Override
public String ExecuteAgent(String agentId, String endpoint, MRDFGraph content) throws TException {
    try {
        Agent agent = agentManager.getAgent(agentId);
        if (endpoint == null) {
            agent.execute();
        } else {
            // add content graph to endpoint
            RDFFormat format = getRDFFormat(content.ContentType);
            if (format == null) {
                return "null";
            }
            LinkedHashModel model = string2Model(content.Graph, format);
            agent.setEndpointEvent(endpoint, model);
        }
        return agent.getUrl();
    } catch (AgentNotFoundException e) {
        return "null";
    }
}