Example usage for org.jdom2.input SAXBuilder SAXBuilder

List of usage examples for org.jdom2.input SAXBuilder SAXBuilder

  1. HOME
  2. Java
  3. org.jdom2
  4. org.jdom2.input.*
  5. SAXBuilder
  6. SAXBuilder

Introduction

In this page you can find the example usage for org.jdom2.input SAXBuilder SAXBuilder.

Prototype

public SAXBuilder()

Source Link

Document

Creates a new JAXP-based SAXBuilder.

Usage

From source file:es.ehu.si.ixa.pipe.convert.Convert.java

License:Apache License

public void absaSemEvalToMultiClassNER2015(String fileName) {
    SAXBuilder sax = new SAXBuilder();
    XPathFactory xFactory = XPathFactory.instance();
    try {//w w w . j a  v a 2s  .  co m
        Document doc = sax.build(fileName);
        XPathExpression<Element> expr = xFactory.compile("//sentence", Filters.element());
        List<Element> sentences = expr.evaluate(doc);
        for (Element sent : sentences) {

            String sentString = sent.getChildText("text");
            StringBuilder sb = new StringBuilder();
            sb = sb.append(sentString);
            Element opinionsElement = sent.getChild("Opinions");
            if (opinionsElement != null) {
                List<List<Integer>> offsetList = new ArrayList<List<Integer>>();
                HashSet<String> targetClassSet = new LinkedHashSet<String>();
                List<Integer> offsets = new ArrayList<Integer>();
                List<Element> opinionList = opinionsElement.getChildren();
                for (Element opinion : opinionList) {
                    if (!opinion.getAttributeValue("target").equals("NULL")) {
                        String className = opinion.getAttributeValue("category");
                        String targetString = opinion.getAttributeValue("target");
                        Integer offsetFrom = Integer.parseInt(opinion.getAttributeValue("from"));
                        Integer offsetTo = Integer.parseInt(opinion.getAttributeValue("to"));
                        offsets.add(offsetFrom);
                        offsets.add(offsetTo);
                        targetClassSet.add(targetString + "JAR!" + className + opinion.getAttributeValue("from")
                                + opinion.getAttributeValue("to"));
                    }
                }
                List<Integer> offsetsWithoutDuplicates = new ArrayList<Integer>(new HashSet<Integer>(offsets));
                Collections.sort(offsetsWithoutDuplicates);
                List<String> targetClassList = new ArrayList<String>(targetClassSet);

                for (int i = 0; i < offsetsWithoutDuplicates.size(); i++) {
                    List<Integer> offsetArray = new ArrayList<Integer>();
                    offsetArray.add(offsetsWithoutDuplicates.get(i++));
                    if (offsetsWithoutDuplicates.size() > i) {
                        offsetArray.add(offsetsWithoutDuplicates.get(i));
                    }
                    offsetList.add(offsetArray);
                }
                int counter = 0;
                for (int i = 0; i < offsetList.size(); i++) {
                    Integer offsetFrom = offsetList.get(i).get(0);
                    Integer offsetTo = offsetList.get(i).get(1);
                    String className = targetClassList.get(i);
                    String aspectString = sentString.substring(offsetFrom, offsetTo);
                    sb.replace(offsetFrom + counter, offsetTo + counter, "<START:"
                            + className.split("JAR!")[1].substring(0, 3) + "> " + aspectString + " <END>");
                    counter += 18;
                }
                System.out.println(sb.toString());
            }
        }
    } catch (JDOMException | IOException e) {
        e.printStackTrace();
    }
}

From source file:es.ehu.si.ixa.pipe.convert.Convert.java

License:Apache License

public void absaSemEvalText(Reader reader) {
    SAXBuilder sax = new SAXBuilder();
    XPathFactory xFactory = XPathFactory.instance();
    try {/* ww  w. j  av  a 2  s  .  c  o m*/
        Document doc = sax.build(reader);
        XPathExpression<Element> expr = xFactory.compile("//sentence", Filters.element());
        List<Element> sentences = expr.evaluate(doc);
        for (Element sent : sentences) {
            String sentString = sent.getChildText("text");
            System.out.println(sentString);
        }
    } catch (JDOMException | IOException e) {
        e.printStackTrace();
    }
}

From source file:es.ehu.si.ixa.pipe.convert.Convert.java

License:Apache License

public String absa15testToNAF(String fileName) {
    KAFDocument kaf = new KAFDocument("en", "v1.naf");
    Segmenter segmenter = new Segmenter();
    TokenFactory tokenFactory = new TokenFactory();
    Properties properties = setAnnotateProperties();
    SAXBuilder sax = new SAXBuilder();
    XPathFactory xFactory = XPathFactory.instance();
    try {/*from   w ww. ja  v  a  2s.co m*/
        Document doc = sax.build(fileName);
        XPathExpression<Element> expr = xFactory.compile("//sentence", Filters.element());
        List<Element> sentences = expr.evaluate(doc);

        int counter = 1;
        for (Element sent : sentences) {
            String sentId = sent.getAttributeValue("id");
            String sentString = sent.getChildText("text");
            StringReader stringReader = new StringReader(sentString);
            BufferedReader breader = new BufferedReader(stringReader);
            IxaPipeTokenizer<Token> tokenizer = new IxaPipeTokenizer<Token>(breader, tokenFactory, properties);
            List<Token> tokens = tokenizer.tokenize();
            List<List<Token>> segmentedSentences = segmenter.segment(tokens);
            for (List<Token> sentence : segmentedSentences) {
                for (Token token : sentence) {
                    WF wf = kaf.newWF(token.value(), token.startOffset(), counter);
                    wf.setXpath(sentId);
                }
            }
            counter++;
        }
    } catch (JDOMException | IOException e) {
        e.printStackTrace();
    }
    return kaf.toString();
}

From source file:es.ucm.fdi.ac.Analysis.java

License:Open Source License

/**
 * Reads an analysis from a file//  w w  w . j a va2  s  .c  o  m
 *
 * @param f the file to read from
 * @throws IOException on any error (may wrap invalid internal XML errors)
 */
public void loadFromFile(File f) throws IOException {
    try {
        SAXBuilder builder = new SAXBuilder();
        Document doc = builder.build(f);
        loadFromXML(doc.getRootElement());
    } catch (Exception e) {
        throw new IOException("Error loading from '" + f.getAbsolutePath() + "' xml save file", e);
    }
}

From source file:es.ucm.fdi.ac.gui.MainGui.java

License:Open Source License

/** 
 * Load a test help file, adhering to the following structure:
 * <helppairs>//from w  w w.  j  av  a 2s.  c o  m
 *  <testhelp>
 *   <testname>...</testname>
 *   <helpcontent>...</helpcontent>
 *  </testhelp>
 *  ...
 * </helppairs>
 * Notice that 'helpcontent' should be XHTML: old-fashioned HTML may fail to
 * validate.
 */
public HashMap<String, String> loadTestHelpFile(String fileName) throws IOException {
    HashMap<String, String> m = new HashMap<String, String>();
    XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat());
    URL url = getClass().getClassLoader().getResource(fileName);
    try {
        Document doc = (new SAXBuilder()).build(url);
        for (Element th : doc.getRootElement().getChildren()) {
            m.put(th.getChildTextTrim("testname"), outputter.outputString(th.getChild("helpcontent")));
        }
    } catch (JDOMException | NullPointerException e) {
        throw new IOException("Impossible to read XML file for " + url, e);
    }
    return m;
}

From source file:es.ucm.fdi.clover.gui.CloverSave.java

License:Open Source License

/**
 * Restores the CloverSave to a different XML file; totally changes the
 * 'views' (it is basically recreated) output array;
 *//*from  w  w  w . ja va2 s .c  o m*/
public static ArrayList<ClusterView> restore(BaseGraph base, ClusterViewFactory vf, File f) throws IOException {

    if (vf == null) {
        vf = new DefaultClusterViewFactory();
    }

    ArrayList<ClusterView> views = new ArrayList<ClusterView>();
    HashMap<String, Filter> filters = new HashMap<String, Filter>();
    HashMap<String, ClusterHierarchy> hierarchies = new HashMap<String, ClusterHierarchy>();

    SAXBuilder builder = new SAXBuilder();
    ClassLoader loader = base.getClass().getClassLoader();

    try {
        Document doc = builder.build(f.getAbsolutePath());
        Element root = doc.getRootElement();

        Element sharedElems = (Element) root.getChildren().get(0);

        for (Element e : (List<Element>) sharedElems.getChildren()) {
            if (e.getName().equals("filter")) {
                String className = e.getAttributeValue("filterClass");
                Filter filter = (Filter) loader.loadClass(className).newInstance();
                filter.restore(e);
                filters.put(e.getAttributeValue("id"), filter);
            } else if (e.getName().equals("hierarchy")) {
                Element cluster = (Element) e.getChildren().get(0);

                Element clusterer = (Element) e.getChildren().get(1);
                String className = clusterer.getAttributeValue("engineClass");
                ClusteringEngine engine = (ClusteringEngine) loader.loadClass(className).newInstance();
                engine.restore(clusterer);

                BaseGraph hb = base;
                if (e.getAttribute("filterId") != null) {
                    Filter filter = filters.get(e.getAttributeValue("filterId"));
                    hb = new FilteredGraph(base, filter);
                }

                ClusterHierarchy h = new ClusterHierarchy(e, hb, engine);
                hierarchies.put(e.getAttributeValue("id"), h);
            }
        }

        for (Element e : (List<Element>) root.getChildren()) {
            if (!e.getName().equals("view"))
                continue;

            // build view
            String hid = e.getAttributeValue("hierarchyId");
            ClusterView view = vf.createClusterView(hierarchies.get(hid), e);
            view.restore(e);

            Element layoutCache = (Element) e.getChildren().get(0);
            view.getAnimator().getLayoutCache().restore(layoutCache, view.getBase());

            Element animatorProps = (Element) e.getChildren().get(1);
            view.getAnimator().restore(animatorProps);

            views.add(view);
        }
    }

    // indicates a well-formedness error
    catch (JDOMException jde) {
        log.warn("Document is not well-formed XML");
        jde.printStackTrace();
    } catch (IOException ioe) {
        System.out.println(ioe);
        ioe.printStackTrace();
    } catch (Exception e) {
        System.out.println(e);
        e.printStackTrace();
    }

    return views;
}

From source file:es.upm.dit.xsdinferencer.extraction.extractorImpl.JSONTypesExtractorImpl.java

License:Apache License

/**
 * Method that performs the conversion between JSON and XML
 * @param jsonRoot the root of the JSON document. It must be either a {@link JSONObject} or a {@link JSONArray}
 * @param namespaceRoot the namespace of the resulting root element
 * @return a JDOM2 {@link Document} representing the obtained XML.
 * @throws JDOMException//  w w w .ja va2s  .co  m
 * @throws IOException
 */
protected Document convertJSONToXML(Object jsonRoot, Namespace namespaceRoot)
        throws JDOMException, IOException {
    if (!(jsonRoot instanceof JSONArray || jsonRoot instanceof JSONObject)) {
        throw new IllegalArgumentException("'jsonRoot' must be either a JSONObject or a JSONArray");
    }
    quoteStringsAtJSON(jsonRoot);
    addPrefixToJSONKeysEndingsRecursive(jsonRoot, XSDInferenceConfiguration.ARRAY_ELEMENT_NAME,
            XSDInferenceConfiguration.ARRAY_ELEMENT_ESCAPING_PREFIX);
    encapsulateArraysAtJSONRecursive(jsonRoot);
    String xmlString = "<" + XSDInferenceConfiguration.XML_ROOT_NAME + ">" + XML.toString(jsonRoot) + "</"
            + XSDInferenceConfiguration.XML_ROOT_NAME + ">";
    SAXBuilder saxBuilder = new SAXBuilder();
    Document xmlDocument = saxBuilder.build(new StringReader(xmlString));
    setNamespaceToElementsByName(XSDInferenceConfiguration.ARRAY_ELEMENT_NAME, xmlDocument.getRootElement(),
            XSDInferenceConfiguration.NAMESPACE_ARRAY_ELEMENT);
    removePrefixToElementNameEndings(xmlDocument.getRootElement(), XSDInferenceConfiguration.ARRAY_ELEMENT_NAME,
            XSDInferenceConfiguration.ARRAY_ELEMENT_ESCAPING_PREFIX);
    xmlDocument.getRootElement().setNamespace(namespaceRoot);
    sortElementsRecursive(xmlDocument.getRootElement());
    return xmlDocument;
}

From source file:es.upm.dit.xsdinferencer.XSDInferencer.java

License:Apache License

/**
 * Method that, given an args array, does the whole inference process by calling the appropriate submodules.
 * @param args the args array, as provided by {@link XSDInferencer#main(String[])}
 * @return a {@link Results} object with the inference results (both statistics and XSDs)
 * @throws XSDConfigurationException if there is a problem with the configuration
 * @throws IOException if there is an I/O problem while reading the input XML files or writing the output files
 * @throws JDOMException if there is any problem while parsing the input XML files 
 *//*from ww  w .  j a  v a2 s.  c o m*/
public Results inferSchema(String[] args) throws XSDInferencerException {
    try {
        XSDInferenceConfiguration configuration = new XSDInferenceConfiguration(args);
        FilenameFilter filenameFilter;
        if (configuration.getWorkingFormat().equals("xml")) {
            filenameFilter = FILE_NAME_FILTER_XML_EXTENSION;
            List<File> xmlFiles = getInstanceFileNames(args, filenameFilter);
            List<Document> xmlDocuments = new ArrayList<>(xmlFiles.size());
            SAXBuilder saxBuilder = new SAXBuilder();
            for (int i = 0; i < xmlFiles.size(); i++) {
                File xmlFile = xmlFiles.get(i);
                System.out.print("Reading input file " + xmlFile.getName() + "...");
                FileInputStream fis = new FileInputStream(xmlFile);
                //BufferedReader reader = new BufferedReader(new InputStreamReader(fis, Charsets.UTF_8));
                Document xmlDocument = saxBuilder.build(fis);
                xmlDocuments.add(xmlDocument);
                System.out.println("OK");
            }
            return inferSchema(xmlDocuments, configuration);
        } else if (configuration.getWorkingFormat().equals("json")) {
            filenameFilter = FILE_NAME_FILTER_JSON_EXTENSION;
            List<File> jsonFiles = getInstanceFileNames(args, filenameFilter);
            List<JSONObject> jsonDocumentWithRootObjects = new ArrayList<>(jsonFiles.size());
            List<JSONArray> jsonDocumentWithRootArrays = new ArrayList<>(jsonFiles.size());
            for (int i = 0; i < jsonFiles.size(); i++) {
                File jsonFile = jsonFiles.get(i);
                String jsonString = Joiner.on(System.lineSeparator())
                        .join(Files.readAllLines(jsonFile.toPath()));
                JSONObject jsonObject = null;
                try {
                    jsonObject = new JSONObject(jsonString);
                } catch (JSONException e) {
                }

                if (jsonObject != null) {
                    jsonDocumentWithRootObjects.add(jsonObject);
                } else {
                    JSONArray jsonArray = null;
                    try {
                        jsonArray = new JSONArray(jsonString);
                    } catch (JSONException e) {
                    }
                    if (jsonArray != null) {
                        jsonDocumentWithRootArrays.add(jsonArray);
                    } else {
                        throw new JSONException("Invalid JSON Document " + jsonFile);
                    }

                }
            }
            return inferSchema(jsonDocumentWithRootObjects, jsonDocumentWithRootArrays, configuration);
        } else {
            throw new InvalidXSDConfigurationParameterException(
                    "Unknown working format. Impossible to load files");
        }
    } catch (IOException | JDOMException | RuntimeException e) {
        throw new XSDInferencerException(e);
    }

}

From source file:es.uvigo.ei.sing.rubioseq.gui.view.models.configuration.ConfigProgramPathsChipSeq.java

License:Open Source License

public void loadDataFromFile(File editFile) {

    loadDefaultParameters(editFile);/*from  w  w w .ja v a 2 s  . com*/

    SAXBuilder saxBuilder = new SAXBuilder();
    try {
        Document document = saxBuilder.build(editFile);
        Element configData = document.getRootElement();

        Element bwaPath = configData.getChild(BWA_PATH);
        if (validElement(bwaPath)) {
            this.setBwaPath(Utils.getRUbioSeqFile(bwaPath.getValue()));
        }

        Element samtoolsPath = configData.getChild(SAMTOOLS_PATH);
        if (validElement(samtoolsPath)) {
            this.setSamtoolsPath(Utils.getRUbioSeqFile(samtoolsPath.getValue()));
        }

        Element picardPath = configData.getChild(PICARD_PATH);
        if (validElement(picardPath)) {
            this.setPicardPath(Utils.getRUbioSeqFile(picardPath.getValue()));
        }

        Element MACSPath = configData.getChild(MACS_PATH);
        if (validElement(MACSPath)) {
            this.setMacsPath(Utils.getRUbioSeqFile(MACSPath.getValue()));
        }

        Element PythonPath = configData.getChild(PYTHON_PATH);
        if (validElement(PythonPath)) {
            this.setPythonPath(Utils.getRUbioSeqFile(PythonPath.getValue()));
        }

        Element fastqcPath = configData.getChild(FASTQC_PATH);
        if (validElement(fastqcPath)) {
            this.setFastqcPath(Utils.getRUbioSeqFile(fastqcPath.getValue()));
        }

        Element BEDToolsPath = configData.getChild(BED_TOOLS_PATH);
        if (validElement(BEDToolsPath)) {
            this.setBedtoolsPath(Utils.getRUbioSeqFile(BEDToolsPath.getValue()));
        }

        Element BedgraphtoWigPath = configData.getChild(BGTW_PATH);
        if (validElement(BedgraphtoWigPath)) {
            this.setBedgraphtobigwigPath(Utils.getRUbioSeqFile(BedgraphtoWigPath.getValue()));
        }

        Element IDRPath = configData.getChild(IDR_PATH);
        if (validElement(IDRPath)) {
            this.setIdrPath(Utils.getRUbioSeqFile(IDRPath.getValue()));
        }

        Element PeakAnnotatorPath = configData.getChild(PEAKANNOTATOR_PATH);
        if (validElement(PeakAnnotatorPath)) {
            this.setPeakannotatorPath(Utils.getRUbioSeqFile(PeakAnnotatorPath.getValue()));
        }

        Element CCATPath = configData.getChild(CCAT_PATH);
        if (validElement(CCATPath)) {
            this.setCcatPath(Utils.getRUbioSeqFile(CCATPath.getValue()));
        }

        Element nthr = configData.getChild(NTHR);
        if (validElement(nthr)) {
            try {
                this.setNthr(Integer.valueOf(nthr.getValue()));
            } catch (Exception e) {
            }
        }

        Element javaRam = configData.getChild(JAVA_RAM);
        if (validElement(javaRam)) {
            this.setJavaRam(javaRam.getValue());
        }

        Element queueSystem = configData.getChild(QUEUE_SYSTEM);
        System.err.println("\n\n\t QUEUE_SYSTEM = " + queueSystem + "\n");
        if (validElement(queueSystem)) {
            String queueSystemValue = queueSystem.getValue().toUpperCase();
            if (queueSystemValue.equals("SGE")) {
                this.setQueueSystem(QueueSystem.SGE);
            } else if (queueSystemValue.equals("PBS")) {
                this.setQueueSystem(QueueSystem.PBS);
            } else if (queueSystemValue.equals("NONE")) {
                this.setQueueSystem(QueueSystem.NONE);
            }
        }

        Element queueName = configData.getChild(QUEUE_NAME);
        if (validElement(queueName)) {
            this.setQueueName(queueName.getValue());
        }

        Element multicoreName = configData.getChild(MULTICORE_NAME);
        if (validElement(multicoreName)) {
            this.setMulticoreName(multicoreName.getValue());
        }

        Element multicoreNumber = configData.getChild(MULTICORE_NUMBER);
        if (validElement(multicoreNumber)) {
            try {
                this.setMulticoreNumber(Integer.valueOf(multicoreNumber.getValue()));
            } catch (Exception e) {
            }
        }

    } catch (JDOMException e) {
        e.printStackTrace();
    } catch (IOException e) {
        e.printStackTrace();
    }
}

From source file:es.uvigo.ei.sing.rubioseq.gui.view.models.configuration.ConfigProgramPathsCNV.java

License:Open Source License

public void loadDataFromFile(File editFile) {

    loadDefaultParameters(editFile);//from ww  w.  ja  v  a2  s  .com

    SAXBuilder saxBuilder = new SAXBuilder();
    try {
        Document document = saxBuilder.build(editFile);
        Element configData = document.getRootElement();

        Element bwaPath = configData.getChild(BWA_PATH);
        if (validElement(bwaPath)) {
            this.setBwaPath(Utils.getRUbioSeqFile(bwaPath.getValue()));
        }

        Element samtoolsPath = configData.getChild(SAMTOOLS_PATH);
        if (validElement(samtoolsPath)) {
            this.setSamtoolsPath(Utils.getRUbioSeqFile(samtoolsPath.getValue()));
        }

        Element gatkpath = configData.getChild(GATK_PATH);
        if (validElement(gatkpath)) {
            this.setGatkpath(Utils.getRUbioSeqFile(gatkpath.getValue()));
        }

        Element picardPath = configData.getChild(PICARD_PATH);
        if (validElement(picardPath)) {
            this.setPicardPath(Utils.getRUbioSeqFile(picardPath.getValue()));
        }

        Element BFASTPath = configData.getChild(BFAST_PATH);
        if (validElement(BFASTPath)) {
            this.setBfastPath(Utils.getRUbioSeqFile(BFASTPath.getValue()));
        }

        Element fastqcPath = configData.getChild(FASTQC_PATH);
        if (validElement(fastqcPath)) {
            this.setFastqcPath(Utils.getRUbioSeqFile(fastqcPath.getValue()));
        }

        Element BEDToolsPath = configData.getChild(BED_TOOLS_PATH);
        if (validElement(BEDToolsPath)) {
            this.setBedtoolsPath(Utils.getRUbioSeqFile(BEDToolsPath.getValue()));
        }

        Element CONTRAPath = configData.getChild(CONTRA_PATH);
        if (validElement(CONTRAPath)) {
            this.setContraPath(Utils.getRUbioSeqFile(CONTRAPath.getValue()));
        }

        Element nthr = configData.getChild(NTHR);
        if (validElement(nthr)) {
            try {
                this.setNthr(Integer.valueOf(nthr.getValue()));
            } catch (Exception e) {
            }
        }

        Element javaRam = configData.getChild(JAVA_RAM);
        if (validElement(javaRam)) {
            this.setJavaRam(javaRam.getValue());
        }

        Element queueSystem = configData.getChild(QUEUE_SYSTEM);
        if (validElement(queueSystem)) {
            String queueSystemValue = queueSystem.getValue().toUpperCase();
            if (queueSystemValue.equals("SGE")) {
                this.setQueueSystem(QueueSystem.SGE);
            } else if (queueSystemValue.equals("PBS")) {
                this.setQueueSystem(QueueSystem.PBS);
            } else if (queueSystemValue.equals("NONE")) {
                this.setQueueSystem(QueueSystem.NONE);
            }
        }

        Element queueName = configData.getChild(QUEUE_NAME);
        if (validElement(queueName)) {
            this.setQueueName(queueName.getValue());
        }

        Element multicoreName = configData.getChild(MULTICORE_NAME);
        if (validElement(multicoreName)) {
            this.setMulticoreName(multicoreName.getValue());
        }

        Element multicoreNumber = configData.getChild(MULTICORE_NUMBER);
        if (validElement(multicoreNumber)) {
            try {
                this.setMulticoreNumber(Integer.valueOf(multicoreNumber.getValue()));
            } catch (Exception e) {
            }
        }

    } catch (JDOMException e) {
        e.printStackTrace();
    } catch (IOException e) {
        e.printStackTrace();
    }
}