Example usage for org.dom4j Node valueOf

List of usage examples for org.dom4j Node valueOf

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Introduction

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

Prototype

String valueOf(String xpathExpression);

Source Link

Document

valueOf evaluates an XPath expression and returns the textual representation of the results the XPath string-value of this node.

Usage

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

License:Open Source License

protected void populateAssayResultsFromXML(PCAssay assay, Node assayDescriptionNode) {
    List<Node> assayResultNodes = assayDescriptionNode
            .selectNodes("../../../PC-AssaySubmit_data/PC-AssayResults");
    if (assayResultNodes.size() == 0)
        return;/*from   w w w . jav  a 2s  .  c  o m*/

    for (Node resultNode : assayResultNodes) {
        PCAssayResult result = new PCAssayResult();

        String val = resultNode.selectSingleNode("PC-AssayResults_sid").valueOf("text()");
        result.setSID(Long.parseLong(val));

        val = resultNode.selectSingleNode("PC-AssayResults_outcome").valueOf("@value");
        val = val.substring(0, 1).toUpperCase() + val.substring(1);
        result.setOutcome(val);

        val = resultNode.selectSingleNode("PC-AssayResults_rank").valueOf("text()");
        result.setRankScore(Integer.parseInt(val));

        List<Node> assayDataNodes = resultNode.selectNodes("PC-AssayResults_data/PC-AssayData");

        List<String> all = GrowthList.decorate(new ArrayList<String>(assay.getColumns().size() - 2));
        result.setAllValues(all);
        for (Node node : assayDataNodes) {
            val = node.valueOf("PC-AssayData_tid/text()");
            int index = Integer.parseInt(val) - 1;
            val = node.selectSingleNode(".//*[starts-with(name(),'PC-AssayData_value_')]").getText();
            all.set(index, val);
        }
        assay.getResults().add(result);
    }

}

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;/*from  w ww.  j a va2 s  . co 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);/*  w w w. j  a  va 2  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);/*w  w  w .j  a v a  2 s.  c  o  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

private String nullSafeGet(Node node, String xpath, String expression) {
    Node node2 = node.selectSingleNode(xpath);
    if (null != node2)
        return node2.valueOf(expression);
    return "";
}

From source file:com.adobe.ac.maven.ncss.NcssAggregateReportGenerator.java

License:Apache License

private void doModuleAnalysis(final List<ModuleReport> reports) {
    getSink().table();//w  w  w .  j  a v a  2 s.co m
    getSink().tableRow();
    headerCellHelper(getResourceBundle().getString("report.javancss.header.module"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.packages"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.classetotal"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.functiontotal"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.ncsstotal"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.javadoc"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.javadoc_line"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.single_comment"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.multi_comment"));
    getSink().tableRow_();

    int packages = 0;
    int classes = 0;
    int methods = 0;
    int ncss = 0;
    int javadocs = 0;
    int jdlines = 0;
    int single = 0;
    int multi = 0;
    for (final Iterator<ModuleReport> it = reports.iterator(); it.hasNext();) {
        final ModuleReport report = (ModuleReport) it.next();
        final Document document = report.getJavancssDocument();
        getSink().tableRow();
        getLog().debug("Aggregating " + report.getModule().getArtifactId());
        tableCellHelper(report.getModule().getArtifactId());
        final int packageSize = document.selectNodes("//javancss/packages/package").size();
        packages += packageSize;
        tableCellHelper(String.valueOf(packageSize));

        final Node node = document.selectSingleNode("//javancss/packages/total");

        final String classSize = node.valueOf("classes");
        tableCellHelper(classSize);
        classes += Integer.parseInt(classSize);

        final String methodSize = node.valueOf("functions");
        tableCellHelper(methodSize);
        methods += Integer.parseInt(methodSize);

        final String ncssSize = node.valueOf("ncss");
        tableCellHelper(ncssSize);
        ncss += Integer.parseInt(ncssSize);

        final String javadocSize = node.valueOf("javadocs");
        tableCellHelper(javadocSize);
        javadocs += Integer.parseInt(javadocSize);

        final String jdlineSize = node.valueOf("javadoc_lines");
        tableCellHelper(jdlineSize);
        jdlines += Integer.parseInt(jdlineSize);

        final String singleSize = node.valueOf("single_comment_lines");
        tableCellHelper(singleSize);
        single += Integer.parseInt(singleSize);

        final String multiSize = node.valueOf("multi_comment_lines");
        tableCellHelper(multiSize);
        multi += Integer.parseInt(multiSize);

        getSink().tableRow_();
    }

    // Totals row
    getSink().tableRow();
    tableCellHelper(getResourceBundle().getString("report.javancss.header.totals"));
    tableCellHelper(String.valueOf(packages));
    tableCellHelper(String.valueOf(classes));
    tableCellHelper(String.valueOf(methods));
    tableCellHelper(String.valueOf(ncss));
    tableCellHelper(String.valueOf(javadocs));
    tableCellHelper(String.valueOf(jdlines));
    tableCellHelper(String.valueOf(single));
    tableCellHelper(String.valueOf(multi));
    getSink().tableRow_();

    getSink().table_();
}

From source file:com.adobe.ac.maven.ncss.NcssReportGenerator.java

License:Apache License

private void doMainPackageAnalysis(final Document document) {
    subtitleHelper(getResourceBundle().getString("report.javancss.package.text"));
    getSink().table();//from w w  w  . j  a  v  a2s . com
    getSink().tableRow();
    // HEADER
    headerCellHelper(getResourceBundle().getString("report.javancss.header.package"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.classe"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.function"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.ncss"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.javadoc"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.javadoc_line"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.single_comment"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.multi_comment"));
    getSink().tableRow_();
    // DATA
    final List list = document.selectNodes("//javancss/packages/package");
    Collections.sort(list, new NumericNodeComparator("ncss"));
    final Iterator nodeIterator = list.iterator();
    while (nodeIterator.hasNext()) {
        final Node node = (Node) nodeIterator.next();
        getSink().tableRow();
        tableCellHelper(node.valueOf("name"));
        tableCellHelper(node.valueOf("classes"));
        tableCellHelper(node.valueOf("functions"));
        tableCellHelper(node.valueOf("ncss"));
        tableCellHelper(node.valueOf("javadocs"));
        tableCellHelper(node.valueOf("javadoc_lines"));
        tableCellHelper(node.valueOf("single_comment_lines"));
        tableCellHelper(node.valueOf("multi_comment_lines"));
        getSink().tableRow_();
    }
    getSink().table_();
}

From source file:com.adobe.ac.maven.ncss.NcssReportGenerator.java

License:Apache License

private void doTotalPackageAnalysis(final Document document) {
    getSink().table();//from  ww w  .j  av a  2  s . c  o m
    getSink().tableRow();
    headerCellHelper(getResourceBundle().getString("report.javancss.header.classetotal"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.functiontotal"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.ncsstotal"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.javadoc"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.javadoc_line"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.single_comment"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.multi_comment"));
    getSink().tableRow_();
    final Node node = document.selectSingleNode("//javancss/packages/total");
    getSink().tableRow();
    tableCellHelper(node.valueOf("classes"));
    tableCellHelper(node.valueOf("functions"));
    tableCellHelper(node.valueOf("ncss"));
    tableCellHelper(node.valueOf("javadocs"));
    tableCellHelper(node.valueOf("javadoc_lines"));
    tableCellHelper(node.valueOf("single_comment_lines"));
    tableCellHelper(node.valueOf("multi_comment_lines"));
    getSink().tableRow_();
    getSink().table_();
}

From source file:com.adobe.ac.maven.ncss.NcssReportGenerator.java

License:Apache License

private void doTopObjectGeneric(final List nodeList) {
    getSink().table();/*from   w  w  w. j a v  a 2s .  c o m*/
    getSink().tableRow();
    headerCellHelper(getResourceBundle().getString("report.javancss.header.object"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.ncss"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.function"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.classe"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.javadoc"));
    getSink().tableRow_();
    final Iterator nodeIterator = nodeList.iterator();
    int i = 0;
    while (nodeIterator.hasNext() && (i++ < lineThreshold)) {
        final Node node = (Node) nodeIterator.next();
        getSink().tableRow();
        getSink().tableCell();
        getSink().tableCell_();
        tableCellHelper(node.valueOf("ncss"));
        tableCellHelper(node.valueOf("functions"));
        tableCellHelper(node.valueOf("classes"));
        tableCellHelper(node.valueOf("javadocs"));
        getSink().tableRow_();
    }
    getSink().table_();
}

From source file:com.adobe.ac.maven.ncss.NcssReportGenerator.java

License:Apache License

private void doObjectAverage(final Document document) {
    subtitleHelper(getResourceBundle().getString("report.javancss.averages"));
    getSink().table();/*  ww w.  j ava 2 s .com*/
    getSink().tableRow();
    headerCellHelper(getResourceBundle().getString("report.javancss.header.ncssaverage"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.programncss"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.classeaverage"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.functionaverage"));
    headerCellHelper(getResourceBundle().getString("report.javancss.header.javadocaverage"));
    getSink().tableRow_();
    final Node node = document.selectSingleNode("//javancss/objects/averages");
    final String totalNcss = document.selectSingleNode("//javancss/objects/ncss").getText();
    getSink().tableRow();
    tableCellHelper(node.valueOf("ncss"));
    tableCellHelper(totalNcss);
    tableCellHelper(node.valueOf("classes"));
    tableCellHelper(node.valueOf("functions"));
    tableCellHelper(node.valueOf("javadocs"));
    getSink().tableRow_();
    getSink().table_();
}