Example usage for org.dom4j Node getText

List of usage examples for org.dom4j Node getText

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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:edu.scripps.fl.pubchem.PubChemFactory.java

License:Apache License

public void populateAssayFromSummaryDocument(PCAssay assay, Node docSumNode) throws Exception {
    Node errorNode = docSumNode.selectSingleNode("error");
    if (errorNode != null)
        throw new Exception("Entrez error: " + errorNode.getText());

    List<Node> list = docSumNode.selectNodes("*");
    String uid = docSumNode.valueOf("@uid");
    assay.setAID(Integer.parseInt(uid));
    for (Node node : list) {
        String name = node.getName();
        Object value = node.getText();
        if (node.selectNodes("*").size() > 0) {

        } else {/*from   w  ww  . j  a va  2s. co m*/
            String property = propMap.getProperty(name);
            if (null != property) {
                Class clazz = PropertyUtils.getPropertyType(assay, property);
                if (clazz.isAssignableFrom(Date.class))
                    value = parseDate(value);
                BeanUtils.setProperty(assay, property, value);
            } else {
                if (!unprocessedProperties.containsKey(name)) {
                    unprocessedProperties.put(name, "");
                    log.warn(String.format("Cannot determine PCAssay bean property '%s'", name));
                }
            }
        }
    }
    String desc = assay.getDescription();
    // eutils summary description doesn't contain new lines 
    // so don't update it if it already has a value (when we populate via xml first).
    if (desc == null || "".equals(desc) || !desc.contains("\n")) {
        Node node = docSumNode.selectSingleNode("AssayDescription");
        assay.setDescription(node.getText());
    }
    return;
}

From source file:edu.scripps.fl.pubchem.PubChemFactory.java

License:Apache License

public int populateRelations(Session session, Document document) throws IOException, DocumentException {
    String fromDb = document.selectSingleNode("/eLinkResult/LinkSet/DbFrom").getText();
    String idStr = document.selectSingleNode("/eLinkResult/LinkSet/IdList/Id").getText();
    Long id = Long.parseLong(idStr);
    List<Node> linkSetDbs = document.selectNodes("/eLinkResult/LinkSet/LinkSetDb");

    Transaction trx = session.beginTransaction();
    int counter = 0;
    for (Node linkSetDb : linkSetDbs) {
        String toDb = linkSetDb.selectSingleNode("DbTo").getText();
        String linkName = linkSetDb.selectSingleNode("LinkName").getText();
        List<Node> ids = linkSetDb.selectNodes("Link/Id");
        for (Node idNode : ids) {
            long relatedId = Long.parseLong(idNode.getText());
            if (id == relatedId)
                continue;
            Relation relation = new Relation();
            relation.setRelationName(linkName);
            relation.setFromDb(fromDb);//from  w  w w .  j a va  2  s.c  o m
            relation.setFromId(id);
            relation.setToDb(toDb);
            relation.setToId(relatedId);
            session.save(relation);
            if (counter++ % 100 == 0) {
                trx.commit();
                session.clear(); // cache grows hugely during very large
                // inserts
                trx = session.beginTransaction();
            }
        }
    }
    trx.commit();
    return counter;
}

From source file:edu.scripps.fl.pubchem.PubChemFactory.java

License:Apache License

public Collection<Long> getNeighbors(Long id) throws Exception {
    Document document = EUtilsWebSession.getInstance().getDocument(
            "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi", "dbfrom", "pcassay", "id", "" + id,
            "linkname", "pcassay_pcassay_neighbor_list");
    List<Node> linkSetDbs = document.selectNodes("/eLinkResult/LinkSet/LinkSetDb");
    Set<Long> relatedIds = new HashSet();
    int counter = 0;
    for (Node linkSetDb : linkSetDbs) {
        String linkName = linkSetDb.selectSingleNode("LinkName").getText();
        List<Node> ids = linkSetDb.selectNodes("Link/Id");
        for (Node idNode : ids) {
            Long relatedId = Long.parseLong(idNode.getText());
            relatedIds.add(relatedId);/*  ww  w.j a  v  a  2 s  .  c o  m*/
        }
    }
    return relatedIds;
}

From source file:edu.scripps.fl.pubchem.PubChemFactory.java

License:Apache License

public List<Relation> getRelations(Document document) {
    String fromDb = document.selectSingleNode("/eLinkResult/LinkSet/DbFrom").getText();
    String idStr = document.selectSingleNode("/eLinkResult/LinkSet/IdList/Id").getText();
    Long id = Long.parseLong(idStr);
    List<Node> linkSetDbs = document.selectNodes("/eLinkResult/LinkSet/LinkSetDb");
    ArrayList<Relation> list = new ArrayList();
    for (Node linkSetDb : linkSetDbs) {
        String toDb = linkSetDb.selectSingleNode("DbTo").getText();
        String linkName = linkSetDb.selectSingleNode("LinkName").getText();
        List<Node> ids = linkSetDb.selectNodes("Link/Id");
        list.ensureCapacity(list.size() + ids.size());
        for (Node idNode : ids) {
            long relatedId = Long.parseLong(idNode.getText());
            if (id == relatedId)
                continue;
            Relation relation = new Relation();
            relation.setRelationName(linkName);
            relation.setFromDb(fromDb);//  www  . jav  a 2s  .  c  o m
            relation.setFromId(id);
            relation.setToDb(toDb);
            relation.setToId(relatedId);
            list.add(relation);
        }
    }
    return list;
}

From source file:edu.scripps.fl.pubchem.PubChemXMLParserFactory.java

License:Apache License

protected PCAssay populateAssayFromXMLNode(Node topNode) throws Exception {
    //      String assayDescPath = "PC-AssaySubmit_assay/PC-AssaySubmit_assay_descr/PC-AssayDescription";
    Node assayDescNode = null;/*from   ww w. ja  v a 2  s .c om*/
    if (topNode.getName().equals("PC-AssayDescription"))
        assayDescNode = topNode;
    else {
        assayDescNode = topNode.selectSingleNode(".//PC-AssayDescription");
    }
    if (assayDescNode == null)
        throw new Exception(
                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"));

        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:edu.scripps.fl.pubchem.PubChemXMLParserFactory.java

License:Apache License

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

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

    Map<Integer, PCAssayPanel> mapPanels = new HashMap();
    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:edu.scripps.fl.pubchem.PubChemXMLParserFactory.java

License:Apache 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 = taxonNode.selectSingleNode("Org-ref_taxname").getText();
            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();
        }/*w  w  w .j  av a  2s .  c o  m*/

        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);
    }
}

From source file:edu.scripps.fl.pubchem.web.entrez.EUtilsWebSession.java

License:Apache License

public Document getDocument(InputStream in) throws Exception {
    DocumentBuilder builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
    DOMReader reader = new DOMReader();
    Document document = reader.read(builder.parse(new BufferedInputStream(in)));
    // SAXReader reader = new SAXReader();
    // Document document = reader.read(in);
    in.close();/* w  w  w  .  ja  v a 2 s .  c  o  m*/
    if (DEBUGGING)
        new XMLWriter().write(document);
    Node node = document.selectSingleNode("/eSearchResult/ERROR");
    if (node != null)
        throw new Exception(node.getText());
    return document;
}

From source file:edu.scripps.fl.pubchem.web.entrez.EUtilsWebSession.java

License:Apache License

public Set<String> getDatabases() throws Exception {
    Document document = getDocument("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi");
    List<Node> list = document.selectNodes("/eInfoResult/DbList/DbName", ".");
    Set dbs = new HashSet(list.size());
    for (Node node : list)
        dbs.add(node.getText());
    return dbs;// w  w  w .j a  v a2s .  c om
}

From source file:edu.scripps.fl.pubchem.web.pug.PowerUserGateway.java

License:Apache License

public URL getResponseURL() throws IOException {
    URL url = null;//  w ww.ja  v a2 s .  com
    Node node = getResponse().selectSingleNode("//*/PCT-Download-URL_url");
    if (node != null)
        url = new URL(node.getText());
    return url;
}