Example usage for org.dom4j Node getText

Introduction

In this page you can find the example usage for org.dom4j Node getText.

Prototype

String getText();

Source Link

Document

Returns the text of this node.

Usage

From source file:architecture.common.xml.XmlWriter.java

License:Apache License

/**
 * This method is used to write out Nodes that contain text and still allow
 * for xml:space to be handled properly.
 *
 *//*from  ww  w .j a  v a2 s  . c  om*/
protected void writeNodeText(Node node) throws IOException {
    String text = node.getText();
    if (text != null && text.length() > 0) {
        if (escapeText) {
            text = escapeElementEntities(text);
        }

        lastOutputNodeType = Node.TEXT_NODE;
        writer.write(text);
    }
}

---

From source file:architecture.common.xml.XmlWriter.java

License:Apache License

protected void writeNode(Node node) throws IOException {
    int nodeType = node.getNodeType();
    switch (nodeType) {
    case Node.ELEMENT_NODE:
        writeElement((Element) node);
        break;/*w w  w  .ja v  a 2  s  .c  o m*/
    case Node.ATTRIBUTE_NODE:
        writeAttribute((Attribute) node);
        break;
    case Node.TEXT_NODE:
        writeNodeText(node);
        // write((Text) node);
        break;
    case Node.CDATA_SECTION_NODE:
        writeCDATA(node.getText());
        break;
    case Node.ENTITY_REFERENCE_NODE:
        writeEntity((Entity) node);
        break;
    case Node.PROCESSING_INSTRUCTION_NODE:
        writeProcessingInstruction((ProcessingInstruction) node);
        break;
    case Node.COMMENT_NODE:
        writeComment(node.getText());
        break;
    case Node.DOCUMENT_NODE:
        write((Document) node);
        break;
    case Node.DOCUMENT_TYPE_NODE:
        writeDocType((DocumentType) node);
        break;
    case Node.NAMESPACE_NODE:
        // Will be output with attributes
        // write((Namespace) node);
        break;
    default:
        throw new IOException("Invalid node type: " + node);
    }
}

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From source file:architecture.ee.plugin.impl.PluginManagerImpl.java

public List loadPlugin(File pluginDir, PluginEntityObject pluginDbBean) throws PluginException {

    if (!ApplicationHelper.isSetupComplete()) {
        return Collections.emptyList();
    }// w ww . ja v a2  s .  c om

    log.debug((new StringBuilder()).append("Loading action from: ").append(pluginDir.getName()).toString());
    Document pluginXML;
    try {
        pluginXML = PluginUtils.getPluginConfiguration(pluginDir);
    } catch (DocumentException e) {
        pluginXML = null;
    }

    if (pluginXML == null) {
        String msg = (new StringBuilder()).append("Plugin ").append(pluginDir.getName())
                .append(" could not be loaded: no plugin.xml file found").toString();
        log.error(msg);
        brokenPlugins.put(pluginDir.getName(), "No plugin.xml found.");
        throw new PluginException(msg);
    }

    ArrayList results = Lists.newArrayList();

    String pluginName;
    PluginClassLoader pluginLoader;

    Node pluginNameNode = pluginXML.selectSingleNode("/plugin/name");

    pluginName = pluginNameNode.getText();

    isValidVersion(pluginName, pluginXML, pluginDir);

    pluginLoader = getPluginClassloader(pluginName, pluginDir);
    if (pluginLoader == null) {
        return Collections.emptyList();
    }
    pluginLoader.initialize();
    log.debug("Plugin classloader urls:" + pluginLoader.getURLS());

    Plugin plugin;
    PluginMetaDataImpl metaData;
    ConfigurationContext context;
    Thread currentThread;
    ClassLoader oldLoader;

    Node classNode = pluginXML.selectSingleNode("/plugin/class");
    if (classNode != null) {
        String className = classNode.getText();
        try {
            log.debug("Plugin class:" + className);
            plugin = (Plugin) pluginLoader.loadClass(className).newInstance();
            log.debug("Plugin object:" + plugin);
            log.debug("******************************** ");
        } catch (Throwable e) {
            brokenPlugins.put(pluginDir.getName(), "Failed to configure class loader.");
            log.debug(e);
            throw new PluginException(e);
        }
    } else {
        plugin = new DummyPlugin(pluginName);
    }
    log.debug("===============================1============");
    metaData = new PluginMetaDataImpl(plugin, pluginLoader, this, pluginXML, pluginDir);
    log.debug("=========================2==================");
    metaData.setPluginDbBean(pluginDbBean);
    log.debug("=======================3====================");
    registerPlugin(plugin, pluginDir);
    log.debug("=======================4====================");
    pluginMeta.put(pluginName, metaData);
    log.debug("======================5=====================");
    pluginMeta.put(plugin, metaData);
    log.debug("====================6=======================");
    context = new ConfigurationContext(metaData);
    log.debug("=======================7====================");
    currentThread = Thread.currentThread();
    oldLoader = currentThread.getContextClassLoader();

    log.debug("===========================================");
    try {
        currentThread.setContextClassLoader(pluginLoader.getClassLoader());

        log.debug("Plugin configures:" + configurators.size());

        for (PluginConfigurator configurator : configurators) {
            log.debug("Plugin configure:" + configurator.getClass().getName());
            configurator.configure(context);
        }
    } catch (Exception e) {
        brokenPlugins.put(pluginDir.getName(), "Failed to configure class loader.");
        throw new PluginException(e);
    } finally {
        if (oldLoader != null)
            currentThread.setContextClassLoader(oldLoader);
    }

    log.debug("===========================================");

    int pluginDbVersion = getPluginDatabaseVersion(metaData);

    boolean init = true;
    if (pluginDbVersion > 0 && metaData.getDatabaseVersion() != pluginDbVersion) {
        brokenPlugins.put(pluginDir.getName(),
                (new StringBuilder()).append("Database version mismatches plugin version. Current: ")
                        .append(pluginDbVersion).append(", Required: ").append(metaData.getDatabaseVersion())
                        .toString());
        init = false;
    }
    if (init) {
        try {
            plugin.init();
            firePluginCreatedEvent(pluginDir.getName(), plugin);
        } catch (IncompatibleClassChangeError e) {
            log.error((new StringBuilder()).append("Unable to initialize plugin, plugin ").append(pluginName)
                    .append(" binds to an old class version needs to be required.").toString());
            results.add(PluginRequiresRebuildResult.getPluginRequiresRebuildResult());
            brokenPlugins.put(pluginDir.getName(), "Failed to initialize.");
        }
        results.addAll(context.getResults());
        ChainingClassLoader.clearCache();
    }
    return results;
}

---

From source file:architecture.ee.util.xml.XmlWriter.java

License:Apache License

/** Outputs the content of the given element. If whitespace trimming is
 * enabled then all adjacent text nodes are appended together before
 * the whitespace trimming occurs to avoid problems with multiple
 * text nodes being created due to text content that spans parser buffers
 * in a SAX parser.// w  ww  . j  av  a2  s.c o m
 */
protected void writeElementContent(Element element) throws IOException {
    boolean trim = format.isTrimText();
    boolean oldPreserve = preserve;
    if (trim) { //verify we have to before more expensive test
        preserve = isElementSpacePreserved(element);
        trim = !preserve;
    }
    if (trim) {
        // concatenate adjacent text nodes together
        // so that whitespace trimming works properly
        Text lastTextNode = null;
        StringBuilder buffer = null;
        boolean textOnly = true;
        for (int i = 0, size = element.nodeCount(); i < size; i++) {
            Node node = element.node(i);
            if (node instanceof Text) {
                if (lastTextNode == null) {
                    lastTextNode = (Text) node;
                } else {
                    if (buffer == null) {
                        buffer = new StringBuilder(lastTextNode.getText());
                    }
                    buffer.append(node.getText());
                }
            } else {
                if (!textOnly && format.isPadText()) {
                    writer.write(PAD_TEXT);
                }

                textOnly = false;

                if (lastTextNode != null) {
                    if (buffer != null) {
                        writeString(buffer.toString());
                        buffer = null;
                    } else {
                        writeString(lastTextNode.getText());
                    }
                    lastTextNode = null;

                    if (format.isPadText()) {
                        writer.write(PAD_TEXT);
                    }
                }
                writeNode(node);
            }
        }
        if (lastTextNode != null) {
            if (!textOnly && format.isPadText()) {
                writer.write(PAD_TEXT);
            }
            if (buffer != null) {
                writeString(buffer.toString());
                buffer = null;
            } else {
                writeString(lastTextNode.getText());
            }
            lastTextNode = null;
        }
    } else {
        Node lastTextNode = null;
        for (int i = 0, size = element.nodeCount(); i < size; i++) {
            Node node = element.node(i);
            if (node instanceof Text) {
                writeNode(node);
                lastTextNode = node;
            } else {
                if ((lastTextNode != null) && format.isPadText()) {
                    writer.write(PAD_TEXT);
                }
                writeNode(node);
                if ((lastTextNode != null) && format.isPadText()) {
                    writer.write(PAD_TEXT);
                }
                lastTextNode = null;
            }
        }
    }
    preserve = oldPreserve;
}

---

From source file:architecture.ee.util.xml.XmlWriter.java

License:Apache License

protected void writeNode(Node node) throws IOException {
    int nodeType = node.getNodeType();
    switch (nodeType) {
    case Node.ELEMENT_NODE:
        writeElement((Element) node);
        break;/*from  w  w  w.  j  av a 2 s. co  m*/
    case Node.ATTRIBUTE_NODE:
        writeAttribute((Attribute) node);
        break;
    case Node.TEXT_NODE:
        writeNodeText(node);
        //write((Text) node);
        break;
    case Node.CDATA_SECTION_NODE:
        writeCDATA(node.getText());
        break;
    case Node.ENTITY_REFERENCE_NODE:
        writeEntity((Entity) node);
        break;
    case Node.PROCESSING_INSTRUCTION_NODE:
        writeProcessingInstruction((ProcessingInstruction) node);
        break;
    case Node.COMMENT_NODE:
        writeComment(node.getText());
        break;
    case Node.DOCUMENT_NODE:
        write((Document) node);
        break;
    case Node.DOCUMENT_TYPE_NODE:
        writeDocType((DocumentType) node);
        break;
    case Node.NAMESPACE_NODE:
        // Will be output with attributes
        //write((Namespace) node);
        break;
    default:
        throw new IOException("Invalid node type: " + node);
    }
}

---

From source file:bard.pubchem.xml.PubChemXMLParserFactory.java

License:Open Source License

protected PCAssay populateAssayFromXMLNode(Node topNode) throws PubChemException {
    // String assayDescPath =
    // "PC-AssaySubmit_assay/PC-AssaySubmit_assay_descr/PC-AssayDescription";
    Node assayDescNode = null;/* w ww  . jav  a 2 s. c o  m*/
    if (topNode.getName().equals("PC-AssayDescription"))
        assayDescNode = topNode;
    else {
        assayDescNode = topNode.selectSingleNode(".//PC-AssayDescription");
    }
    if (assayDescNode == null)
        throw new PubChemException(
                String.format("Cannot find PC-AssayDescription node in provided node %s", topNode.getPath()));

    Node node = assayDescNode.selectSingleNode("PC-AssayDescription_aid/PC-ID/PC-ID_id");
    Integer aid = new Integer(node.getText());

    try {
        PCAssay assay = new PCAssay();
        if (aid > 0)
            assay.setAID(aid);

        node = assayDescNode.selectSingleNode("PC-AssayDescription_aid/PC-ID/PC-ID_version");
        Integer version = new Integer(node.getText());
        assay.setVersion(version);

        node = assayDescNode.selectSingleNode("PC-AssayDescription_revision");
        Integer revision = new Integer(node.getText());
        assay.setRevision(revision);

        Node trackingNode = assayDescNode
                .selectSingleNode("PC-AssayDescription_aid-source/PC-Source/PC-Source_db/PC-DBTracking");

        node = trackingNode.selectSingleNode("PC-DBTracking_name");
        assay.setSourceName(node.getText());

        node = trackingNode.selectSingleNode("PC-DBTracking_source-id/Object-id/Object-id_str");
        assay.setExtRegId(node.getText());

        // hold until date
        node = trackingNode.selectSingleNode("PC-DBTracking_date");
        if (node != null) {
            String year = node.selectSingleNode("Date/Date_std/Date-std/Date-std_year").getText();
            String month = node.selectSingleNode("Date/Date_std/Date-std/Date-std_month").getText();
            String day = node.selectSingleNode("Date/Date_std/Date-std/Date-std_day").getText();
            if (DEBUGGING)
                log.info("year: " + year + " month: " + month + " day: " + day);
            Calendar calendar = Calendar.getInstance();
            calendar.set(Integer.parseInt(year), Integer.parseInt(month) - 1, Integer.parseInt(day));
            assay.setHoldUntilDate(calendar.getTime());
            if (DEBUGGING)
                log.info(calendar.getTime().toString());
        }

        node = assayDescNode.selectSingleNode("PC-AssayDescription_name");
        assay.setName(node.getText());

        List<Node> nodes = assayDescNode
                .selectNodes("PC-AssayDescription_description/PC-AssayDescription_description_E");
        assay.setDescription(join(nodes, separator));

        nodes = assayDescNode.selectNodes("PC-AssayDescription_protocol/PC-AssayDescription_protocol_E");
        assay.setProtocol(join(nodes, separator));

        nodes = assayDescNode.selectNodes("PC-AssayDescription_comment/PC-AssayDescription_comment_E");
        assay.setComment(join(nodes, separator));

        node = assayDescNode.selectSingleNode("PC-AssayDescription_activity-outcome-method");
        if (node != null)
            assay.setActivityOutcomeMethod(node.valueOf("@value"));

        handlePlots(assay, assayDescNode);

        node = assayDescNode
                .selectSingleNode("PC-AssayDescription_grant-number/PC-AssayDescription_grant-number_E");
        if (node != null)
            assay.setGrantNumber(node.getText());

        node = assayDescNode.selectSingleNode("PC-AssayDescription_project-category");
        if (node != null)
            assay.setProjectCategory(node.valueOf("@value"));

        assay.getAssayXRefs().removeAll(assay.getAssayXRefs());

        nodes = assayDescNode.selectNodes("PC-AssayDescription_xref/PC-AnnotatedXRef");
        handleXRefs(assay, null, nodes);

        nodes = assayDescNode.selectNodes("PC-AssayDescription_target/PC-AssayTargetInfo");
        handleTargetXRefs(assay, null, nodes);

        handlePanels(assay, assayDescNode);

        handleColumns(assay, assayDescNode);

        handleComments(assay, assayDescNode);

        return assay;
    } catch (Exception ex) {
        throw new RuntimeException("Problem with AID " + aid, ex);
    }
}

---

From source file:bard.pubchem.xml.PubChemXMLParserFactory.java

License:Open Source License

protected void handlePanels(PCAssay assay, Node assayDescNode) {
    Node node = assayDescNode.selectSingleNode("PC-AssayDescription_is-panel");
    if (node == null)
        assay.setPanel(false);/*from  ww w.ja  v  a2  s. c o  m*/
    else
        assay.setPanel("true".equals(node.valueOf("@value")));

    if (assay.isPanel()) {
        node = assayDescNode
                .selectSingleNode("PC-AssayDescription_panel-info/PC-AssayPanel/PC-AssayPanel_name");
        assay.setPanelName(node.valueOf("text()"));
        node = assayDescNode
                .selectSingleNode("PC-AssayDescription_panel-info/PC-AssayPanel/PC-AssayPanel_descr");
        assay.setPanelDescription(node == null ? "" : node.valueOf("text()"));
    }

    List<Node> nodes = assayDescNode.selectNodes(
            "PC-AssayDescription_panel-info/PC-AssayPanel/PC-AssayPanel_member/PC-AssayPanelMember");
    for (Node n : nodes) {
        String mid = n.selectSingleNode("PC-AssayPanelMember_mid").getText();
        Node node2 = n.selectSingleNode("PC-AssayPanelMember_name");
        String name = node2 == null ? "" : node2.getText();

        PCAssayPanel panel = new PCAssayPanel();
        panel.setAssay(assay);
        assay.getPanels().add(panel);
        panel.setPanelNumber(Integer.parseInt(mid));
        panel.setName(name);

        node2 = n.selectSingleNode("PC-AssayPanelMember_description");
        panel.setDescription(node2 == null ? "" : node2.getText());

        List<Node> nodes2 = n.selectNodes("PC-AssayPanelMember_protocol/PC-AssayPanelMember_protocol_E");
        panel.setProtocol(join(nodes2, separator));

        nodes2 = n.selectNodes("PC-AssayPanelMember_comment/PC-AssayPanelMember_comment_E");
        panel.setComment(join(nodes2, separator));

        List<Node> xrefNodes = n.selectNodes("PC-AssayPanelMember_xref/PC-AnnotatedXRef");
        handleXRefs(assay, panel, xrefNodes);

        List<Node> targetNodes = n.selectNodes("PC-AssayPanelMember_target/PC-AssayTargetInfo");
        handleTargetXRefs(assay, panel, targetNodes);
    }
}

---

From source file:bard.pubchem.xml.PubChemXMLParserFactory.java

License:Open Source License

protected void handleColumns(PCAssay assay, Node assayDescNode) {
    Map<Integer, PCAssayColumn> map = new HashMap<Integer, PCAssayColumn>();
    for (PCAssayColumn col : assay.getColumns())
        map.put(col.getTID(), col);/*from  ww w .ja  v  a  2 s  .  co  m*/

    ensureColumn(assay, -1, "Outcome", "string");
    ensureColumn(assay, 0, "Score", "float");

    Map<Integer, PCAssayPanel> mapPanels = new HashMap<Integer, PCAssayPanel>();
    for (PCAssayPanel panel : assay.getPanels())
        mapPanels.put(panel.getPanelNumber(), panel);

    List<Node> nodes = assayDescNode.selectNodes("PC-AssayDescription_results/PC-ResultType");
    for (Node n : nodes) {
        String tid = n.selectSingleNode("PC-ResultType_tid").getText();
        String name = n.selectSingleNode("PC-ResultType_name").getText();
        String type = n.selectSingleNode("PC-ResultType_type").valueOf("@value");
        PCAssayColumn column = ensureColumn(assay, Integer.parseInt(tid), name, type);

        Node node = n.selectSingleNode("PC-ResultType_unit");
        if (node != null)
            column.setUnit(node.valueOf("@value"));

        List<Node> descNodes = n.selectNodes("PC-ResultType_description/PC-ResultType_description_E");
        column.setDescription(join(descNodes, separator));
        if (DEBUGGING)
            log.info("Column description: " + join(descNodes, separator));

        node = n.selectSingleNode("PC-ResultType_ac");
        if (node != null)
            column.setActiveConcentration("true".equals(node.valueOf("@value")));

        node = n.selectSingleNode("PC-ResultType_tc");
        if (node != null) {
            Node node2 = node.selectSingleNode("PC-ConcentrationAttr/PC-ConcentrationAttr_dr-id");
            if (node2 != null) {
                column.setCurvePlotLabel(Integer.parseInt(node2.getText()));
            }
            String testedConc = node.selectSingleNode("PC-ConcentrationAttr/PC-ConcentrationAttr_concentration")
                    .getText();
            column.setTestedConcentration(Double.parseDouble(testedConc));
            String testedUnit = node.selectSingleNode("PC-ConcentrationAttr/PC-ConcentrationAttr_unit")
                    .valueOf("@value");
            column.setTestedConcentrationUnit(testedUnit);
        }

        node = n.selectSingleNode("PC-ResultType_panel-info/PC-AssayPanelTestResult");
        if (node != null) {
            String panelId = node.selectSingleNode("PC-AssayPanelTestResult_mid").getText();
            PCAssayPanel panel = mapPanels.get(Integer.parseInt(panelId));
            column.setPanel(panel);
            String panelColumnType = node.selectSingleNode("PC-AssayPanelTestResult_readout-annot")
                    .valueOf("@value");
            column.setPanelReadoutType(panelColumnType);
        }
    }
}

---

From source file:bard.pubchem.xml.PubChemXMLParserFactory.java

License:Open Source License

protected void handleXRefs(PCAssay assay, PCAssayPanel panel, List<Node> nodes) {
    for (Node n : nodes) {
        Node node = n.selectSingleNode("PC-AnnotatedXRef_comment");
        String comment = node == null ? "" : node.getText();

        node = n.selectSingleNode("PC-AnnotatedXRef_xref/PC-XRefData/*");

        String type = node.getName();
        type = type.substring(type.lastIndexOf("_") + 1, type.length());
        String database = targetType.containsKey(type) ? targetType.get(type) : type;
        String id = node.getText();

        XRef xref = new XRef();
        xref.setXRefId(id);// w ww.  ja  v  a  2  s.  com
        xref.setDatabase(database);
        xref.setType(type);

        PCAssayXRef aXref = new PCAssayXRef();
        aXref.setPanel(panel);
        aXref.setAssay(assay);
        aXref.setComment(comment);
        aXref.setXRef(xref);
        aXref.setTarget(false);
        assay.getAssayXRefs().add(aXref);
    }
}

---

From source file:bard.pubchem.xml.PubChemXMLParserFactory.java

License:Open Source License

protected void handleTargetXRefs(PCAssay assay, PCAssayPanel panel, List<Node> nodes) {
    for (Node n : nodes) {
        String name = n.selectSingleNode("PC-AssayTargetInfo_name").getText();
        String id = n.selectSingleNode("PC-AssayTargetInfo_mol-id").getText();
        String type = n.selectSingleNode("PC-AssayTargetInfo_molecule-type").valueOf("@value");
        String database = targetType.containsKey(type) ? targetType.get(type) : type;
        Node taxonNode = n.selectSingleNode("PC-AssayTargetInfo_organism/BioSource/BioSource_org/Org-ref");
        String taxonName = "", taxonCommon = "", taxon = "";
        if (taxonNode != null) {
            taxonName = nullSafeGet(taxonNode, "Org-ref_taxname", "text()");
            taxonCommon = nullSafeGet(taxonNode, "Org-ref_common", "text()");
            String db = nullSafeGet(taxonNode, "Org-ref_db/Dbtag/Dbtag_db", "text()");
            if (!"taxon".equals(db))
                throw new RuntimeException("Non taxon BioSource Org-ref_db (was " + db + ")");
            taxonNode = taxonNode.selectSingleNode("Org-ref_db/Dbtag/Dbtag_tag/Object-id/Object-id_id");
            taxon = taxonNode.getText();
        }//from   ww w.j av  a 2  s .  c  om

        XRef xref = new XRef();
        xref.setXRefId(id);
        xref.setDatabase(database);
        xref.setType(type);
        xref.setName(name);

        PCAssayXRef aXref = new PCAssayXRef();
        aXref.setTarget(true);
        aXref.setPanel(panel);
        aXref.setAssay(assay);
        aXref.setXRef(xref);
        if (!taxon.equals("")) {
            aXref.setTaxon(Long.parseLong(taxon));
            aXref.setTaxonName(taxonName);
            aXref.setTaxonCommon(taxonCommon);
        }
        assay.getAssayXRefs().add(aXref);
    }
}

---

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