/** * @param restTemplate REST Template for making HTTP calls */ public PathwayCommons2Client(RestTemplate restTemplate) { this(restTemplate, new SimpleIOHandler()); }
@Override public void run() { // try { model[0] = handler.convertFromOWL(stream); // } catch (Throwable e) { // log.warn("Import failed: " + e); // } } }, com.ctc.wstx.stax.WstxInputFactory.class);
@Override public void run() { model[0] = (new SimpleIOHandler()).convertFromOWL(stream); } });
public void importModel(Validation validation, InputStream inputStream) { // add the parser SimpleIOHandler simpleReader = new SimpleIOHandler(); simpleReader.mergeDuplicates(true); associate(inputStream, validation); associate(simpleReader, validation); /* * build a model and associate it with the validation (for post-validation later on); * during this, many errors/warnings may be caught and reported via AOP ;)) */ Model model = simpleReader.convertFromOWL(inputStream); if(model == null) throw new BiopaxValidatorException( "Failed importing a BioPAX model!"); associate(model, validation); }
private String convertToOWL(Model model) { ByteArrayOutputStream out = new ByteArrayOutputStream(); (new SimpleIOHandler(model.getLevel())).convertToOWL(model, out); return out.toString(); }
/** * Constructor */ public Normalizer() { biopaxReader = new SimpleIOHandler(BioPAXLevel.L3); biopaxReader.mergeDuplicates(true); copier = new ShallowCopy(BioPAXLevel.L3); options = new NormalizerOptions(); // with default settings subs = new HashMap<BioPAXElement, BioPAXElement>(); subsModel = biopaxReader.getFactory().createModel(); }
private static Model convertFromOwl(final InputStream stream) { final Model[] model = new Model[1]; final SimpleIOHandler handler = new SimpleIOHandler(); handler.mergeDuplicates(true); // a workaround (illegal) BioPAX data having duplicated rdf:ID... ClassLoaderHack.runWithHack(new Runnable() { @Override public void run() { // try { model[0] = handler.convertFromOWL(stream); // } catch (Throwable e) { // log.warn("Import failed: " + e); // } } }, com.ctc.wstx.stax.WstxInputFactory.class); return model[0]; }
private static String toOwl(BioPAXElement bpe) { StringWriter writer = new StringWriter(); try { SimpleIOHandler simpleExporter = new SimpleIOHandler(BioPAXLevel.L3); simpleExporter.writeObject(writer, bpe); } catch (Exception e) { log.error("Failed printing '" + bpe.getRDFId() + "' to OWL", e); } return writer.toString(); }
private Model readBioPAXfromURL(String urlName) throws IOException { return ioHandler.convertFromOWL(openURL(urlName)); }
@Around("execution(* org.biopax.paxtools.io.SimpleIOHandler.processIndividual(*)) " + "&& args(model)") public String adviseProcessIndividual(ProceedingJoinPoint jp, Model model) { String id = null; SimpleIOHandler reader = (SimpleIOHandler) jp.getThis(); String bpeId = null; try { bpeId = reader.getId(); } catch (NullPointerException e) { bpeId = reader.getXmlStreamInfo(); } try { id = (String) jp.proceed(); } catch (Throwable ex) { reportException(ex, reader, bpeId); } return id; }
private static Model getModel(BioPAXIOHandler io, String fName) throws FileNotFoundException { FileInputStream file = new FileInputStream(fName); return io.convertFromOWL(file); }
if(el != null) { o = el; PropertyEditor<?,?> editor = reader.getEditorMap() .getEditorForProperty(triple.property, el.getModelInterface()); if (editor == null) { jp.proceed(); } catch (Throwable t) { reportException(t, o, "syntax.error", "SimpleIOHandler.bindValue interceptor", triple.toString());
@Before("execution(* org.biopax.paxtools.io.SimpleIOHandler.skip(..))") public void adviseUnknownClass(JoinPoint jp) { SimpleIOHandler reader = (SimpleIOHandler) jp.getTarget(); String loc = reader.getXmlStreamInfo(); report(reader, loc, "unknown.class", "reader", Behavior.ERROR, false, loc); }
@Override public void run() { try { simpleExporter.writeObject(writer, bpe); } catch (Exception e) { log.error("Failed printing '" + bpe.getRDFId() + "' to OWL", e); } } }, com.ctc.wstx.stax.WstxInputFactory.class);
public void importModel(Validation validation, InputStream inputStream) { // add the parser SimpleIOHandler simpleReader = new SimpleIOHandler(); simpleReader.mergeDuplicates(true); associate(inputStream, validation); associate(simpleReader, validation); /* * build a model and associate it with the validation (for post-validation later on); * during this, many errors/warnings may be caught and reported via AOP ;)) */ Model model = simpleReader.convertFromOWL(inputStream); if(model == null) throw new ValidatorException( "Failed importing a BioPAX model!"); associate(model, validation); }
public static void main(String[] args) throws FileNotFoundException { SimpleIOHandler reader = new SimpleIOHandler(); Model model = reader.convertFromOWL(new FileInputStream( "/home/ozgun/Projects/biopax-pattern/All-Data.owl")); new ChemicalNameNormalizer(model); }
/** * This is to refresh 'modelSerialized' property: * generates BioPAX OWL from current model. */ public void updateModelSerialized() { Model model = getModel(); if (model != null) { try { // export to OWL ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); (new SimpleIOHandler(model.getLevel())).convertToOWL(model, outputStream); this.modelSerialized = outputStream.toString("UTF-8"); } catch (IOException e) { throw new BiopaxValidatorException( "Failed to export modified model!", e); } } }
/** * Gets the OWL (RDF/XML) representation * of the BioPAX element. * * @param bpe * @return */ public static String toOwl(final BioPAXElement bpe) { final StringWriter writer = new StringWriter(); final SimpleIOHandler simpleExporter = new SimpleIOHandler(BioPAXLevel.L3); ClassLoaderHack.runWithHack(new Runnable() { @Override public void run() { try { simpleExporter.writeObject(writer, bpe); } catch (Exception e) { log.error("Failed printing '" + bpe.getRDFId() + "' to OWL", e); } } }, com.ctc.wstx.stax.WstxInputFactory.class); return writer.toString(); }
@Before("execution(* org.biopax.paxtools.io.SimpleIOHandler.skip(..))") public void adviseUnknownClass(JoinPoint jp) { SimpleIOHandler reader = (SimpleIOHandler) jp.getTarget(); String loc = reader.getXmlStreamInfo(); report(reader, "unknown.class", "SimpleIOHandler.skip interceptor", false, loc); }
public static void main(String[] args) throws IOException { // A blacklist file is available at http://www.pathwaycommons.org/pc2/downloads/blacklist.txt // This is for avoiding ubiquitous small molecules like ATP Blacklist black = new Blacklist("blacklist.txt"); DeltaFeatureExtractor dfe = new DeltaFeatureExtractor(); dfe.setBlacklist(black); SimpleIOHandler io = new SimpleIOHandler(); // The large model file is available at // http://www.pathwaycommons.org/pc2/downloads/Pathway%20Commons.5.Detailed_Process_Data.BIOPAX.owl.gz Model model = io.convertFromOWL(new FileInputStream( "Pathway Commons.5.Detailed_Process_Data.BIOPAX.owl")); dfe.mineAndCollect(model); dfe.writeResults("DeltaFeatures.txt"); }