Example usage for org.dom4j Node selectNodes

Introduction

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

Prototype

List<Node> selectNodes(String xpathExpression);

Source Link

Document

selectNodes evaluates an XPath expression and returns the result as a List of Node instances or String instances depending on the XPath expression.

Usage

From source file:org.mskcc.cbio.portal.scripts.ImportCaisesClinicalXML.java

License:Open Source License

private static void parseMedicalTherapies(List<ClinicalEvent> clinicalEvents, Node patientNode,
        String patientId, int cancerStudyId) {
    List<Node> treatmentNodes = patientNode.selectNodes("MedicalTherapies/MedicalTherapy");

    for (Node treatmentNode : treatmentNodes) {
        Patient patient = DaoPatient.getPatientByCancerStudyAndPatientId(cancerStudyId, patientId);
        ClinicalEvent clinicalEvent = new ClinicalEvent();
        clinicalEvent.setPatientId(patient.getInternalId());
        clinicalEvent.setEventType("TREATMENT");
        clinicalEvent.addEventDatum("TREATMENT_TYPE", "Medical Therapy");

        Node node = treatmentNode.selectSingleNode("MedTxDate");
        if (node == null) {
            System.err.println("no date");
            continue;
        }//from   w w w.ja  v  a2  s  .c  om
        clinicalEvent.setStartDate(Long.parseLong(node.getText()));

        node = treatmentNode.selectSingleNode("MedTxStopDate");
        if (node != null) {
            clinicalEvent.setStopDate(Long.parseLong(node.getText()));
        }

        node = treatmentNode.selectSingleNode("MedTxType");
        if (node != null) {
            clinicalEvent.addEventDatum("SUBTYPE", node.getText());
        }

        node = treatmentNode.selectSingleNode("MedTxIndication");
        if (node != null) {
            clinicalEvent.addEventDatum("INDICATION", node.getText());
        }

        node = treatmentNode.selectSingleNode("MedTxAgent");
        if (node != null) {
            clinicalEvent.addEventDatum("AGENT", node.getText());
        }

        node = treatmentNode.selectSingleNode("MedTxDose");
        if (node != null) {
            clinicalEvent.addEventDatum("DOSE", node.getText());
        }

        node = treatmentNode.selectSingleNode("MedTxTotalDose");
        if (node != null) {
            clinicalEvent.addEventDatum("TOTAL_DOSE", node.getText());
        }

        node = treatmentNode.selectSingleNode("MedTxUnits");
        if (node != null) {
            clinicalEvent.addEventDatum("UNIT", node.getText());
        }

        node = treatmentNode.selectSingleNode("MedTxSchedule");
        if (node != null) {
            clinicalEvent.addEventDatum("SCHEDULE", node.getText());
        }

        node = treatmentNode.selectSingleNode("MedTxRoute");
        if (node != null) {
            clinicalEvent.addEventDatum("ROUTE", node.getText());
        }

        clinicalEvents.add(clinicalEvent);
    }
}

---

From source file:org.mskcc.cbio.portal.scripts.ImportCaisesClinicalXML.java

License:Open Source License

private static void parseRadiationTherapies(List<ClinicalEvent> clinicalEvents, Node patientNode,
        String patientId, int cancerStudyId) {
    List<Node> treatmentNodes = patientNode.selectNodes("RadiationTherapies/RadiationTherapy");

    for (Node treatmentNode : treatmentNodes) {
        Patient patient = DaoPatient.getPatientByCancerStudyAndPatientId(cancerStudyId, patientId);
        ClinicalEvent clinicalEvent = new ClinicalEvent();
        clinicalEvent.setPatientId(patient.getInternalId());
        clinicalEvent.setEventType("TREATMENT");
        clinicalEvent.addEventDatum("TREATMENT_TYPE", "Radiation Therapy");

        Node node = treatmentNode.selectSingleNode("RadTxDate");
        if (node == null) {
            System.err.println("no date");
            continue;
        }/*from w ww .j a v a  2s .  c  o m*/
        clinicalEvent.setStartDate(Long.parseLong(node.getText()));

        node = treatmentNode.selectSingleNode("RadTxStopDate");
        if (node != null) {
            clinicalEvent.setStopDate(Long.parseLong(node.getText()));
        }

        node = treatmentNode.selectSingleNode("RadTxType");
        if (node != null) {
            clinicalEvent.addEventDatum("SUBTYPE", node.getText());
        }

        node = treatmentNode.selectSingleNode("RadTxIndication");
        if (node != null) {
            clinicalEvent.addEventDatum("INDICATION", node.getText());
        }

        node = treatmentNode.selectSingleNode("RadTxIntent");
        if (node != null) {
            clinicalEvent.addEventDatum("INTENT", node.getText());
        }

        node = treatmentNode.selectSingleNode("RadTxDosePerFraction");
        if (node != null) {
            clinicalEvent.addEventDatum("DOSE_PER_FRACTION", node.getText());
        }

        node = treatmentNode.selectSingleNode("RadTxTotalDose");
        if (node != null) {
            clinicalEvent.addEventDatum("TOTAL_DOSE", node.getText());
        }

        node = treatmentNode.selectSingleNode("RadTxUnits");
        if (node != null) {
            clinicalEvent.addEventDatum("UNIT", node.getText());
        }

        node = treatmentNode.selectSingleNode("RadTxNumFractions");
        if (node != null) {
            clinicalEvent.addEventDatum("NUM_FRACTIONS", node.getText());
        }

        node = treatmentNode.selectSingleNode("RadTxTarget");
        if (node != null) {
            clinicalEvent.addEventDatum("TARGET", node.getText());
        }

        clinicalEvents.add(clinicalEvent);
    }
}

---

From source file:org.mskcc.cbio.portal.scripts.ImportCaisesClinicalXML.java

License:Open Source License

private static void parseBrachyTherapies(List<ClinicalEvent> clinicalEvents, Node patientNode, String patientId,
        int cancerStudyId) {
    List<Node> treatmentNodes = patientNode.selectNodes("BrachyTherapies/BrachyTherapy");

    for (Node treatmentNode : treatmentNodes) {
        Patient patient = DaoPatient.getPatientByCancerStudyAndPatientId(cancerStudyId, patientId);
        ClinicalEvent clinicalEvent = new ClinicalEvent();
        clinicalEvent.setPatientId(patient.getInternalId());
        clinicalEvent.setEventType("TREATMENT");
        clinicalEvent.addEventDatum("TREATMENT_TYPE", "Brachytherapy");

        Node node = treatmentNode.selectSingleNode("BrachyDate");
        if (node == null) {
            System.err.println("no date");
            continue;
        }/*w w  w. j a  va 2 s .c  o m*/
        clinicalEvent.setStartDate(Long.parseLong(node.getText()));

        node = treatmentNode.selectSingleNode("BrachyIsotope");
        if (node != null) {
            clinicalEvent.addEventDatum("BRACHY_ISOTOPE", node.getText());
        }

        node = treatmentNode.selectSingleNode("BrachyPrescribedDose");
        if (node != null) {
            clinicalEvent.addEventDatum("DOSE", node.getText());
        }

        node = treatmentNode.selectSingleNode("BrachyDoseNotes");
        if (node != null) {
            clinicalEvent.addEventDatum("DOSE_NOTES", node.getText());
        }

        clinicalEvents.add(clinicalEvent);
    }
}

---

From source file:org.mskcc.cbio.portal.scripts.ImportCaisesClinicalXML.java

License:Open Source License

private static void parseDiagnostics(List<ClinicalEvent> clinicalEvents, Node patientNode, String patientId,
        int cancerStudyId) {
    List<Node> diagnosticNodes = patientNode.selectNodes("Diagnostics/Diagnostic");
    for (Node diagnosticNode : diagnosticNodes) {
        Patient patient = DaoPatient.getPatientByCancerStudyAndPatientId(cancerStudyId, patientId);
        ClinicalEvent clinicalEvent = new ClinicalEvent();
        clinicalEvent.setPatientId(patient.getInternalId());
        clinicalEvent.setEventType("DIAGNOSTIC");

        Node node = diagnosticNode.selectSingleNode("DxDate");
        if (node == null) {
            System.err.println("no date");
            continue;
        }/* w w w  .  j  a va 2  s.com*/
        clinicalEvent.setStartDate(Long.parseLong(node.getText()));

        node = diagnosticNode.selectSingleNode("DxType");
        if (node != null) {
            clinicalEvent.addEventDatum("DIAGNOSTIC_TYPE", node.getText());
        }

        node = diagnosticNode.selectSingleNode("DxTarget");
        if (node != null) {
            clinicalEvent.addEventDatum("TARGET", node.getText());
        }

        node = diagnosticNode.selectSingleNode("DxResult");
        if (node != null) {
            clinicalEvent.addEventDatum("RESULT", node.getText());
        }

        node = diagnosticNode.selectSingleNode("DxNotes");
        if (node != null) {
            clinicalEvent.addEventDatum("NOTES", node.getText());
        }

        node = diagnosticNode.selectSingleNode("DxSide");
        if (node != null) {
            clinicalEvent.addEventDatum("SIDE", node.getText());
        }

        node = diagnosticNode.selectSingleNode("DxStatus");
        if (node != null) {
            clinicalEvent.addEventDatum("STATUS", node.getText());
        }

        node = diagnosticNode.selectSingleNode("ImgBaseline");
        if (node != null) {
            clinicalEvent.addEventDatum("BASELINE", node.getText());
        }

        node = diagnosticNode.selectSingleNode("DxNumNewTumors");
        if (node != null) {
            clinicalEvent.addEventDatum("NUM_NEW_TUMORS", node.getText());
        }

        clinicalEvents.add(clinicalEvent);
    }
}

---

From source file:org.mskcc.cbio.portal.scripts.ImportCaisesClinicalXML.java

License:Open Source License

private static void parseLabTests(List<ClinicalEvent> clinicalEvents, Node patientNode, String patientId,
        int cancerStudyId) {
    List<Node> labTestNodes = patientNode.selectNodes("LabTests/LabTest");
    for (Node labTestNode : labTestNodes) {
        Patient patient = DaoPatient.getPatientByCancerStudyAndPatientId(cancerStudyId, patientId);
        ClinicalEvent clinicalEvent = new ClinicalEvent();
        clinicalEvent.setPatientId(patient.getInternalId());
        clinicalEvent.setEventType("LAB_TEST");

        Node node = labTestNode.selectSingleNode("LabDate");
        if (node == null) {
            System.err.println("no date");
            continue;
        }/*from   www .  j av  a  2s.co m*/
        clinicalEvent.setStartDate(Long.parseLong(node.getText()));

        node = labTestNode.selectSingleNode("LabTest");
        if (node == null) {
            System.err.println("no lab test name");
            continue;
        }
        clinicalEvent.addEventDatum("TEST", node.getText());

        node = labTestNode.selectSingleNode("LabResult");
        if (node == null) {
            System.err.println("no lab result");
            continue;
        }
        clinicalEvent.addEventDatum("RESULT", node.getText());

        node = labTestNode.selectSingleNode("LabUnits");
        if (node != null) {
            clinicalEvent.addEventDatum("UNIT", node.getText());
        }

        node = labTestNode.selectSingleNode("LabNormalRange");
        if (node != null) {
            clinicalEvent.addEventDatum("NORMAL_RANGE", node.getText());
        }

        node = labTestNode.selectSingleNode("LabNotes");
        if (node != null) {
            clinicalEvent.addEventDatum("NOTES", node.getText());
        }

        clinicalEvents.add(clinicalEvent);
    }
}

---

From source file:org.mskcc.cbio.portal.scripts.ImportCaisesClinicalXML.java

License:Open Source License

private static void parseClinicalEventsFromSpecimen(List<ClinicalEvent> clinicalEvents, Node patientNode,
        String patientId, int cancerStudyId) {
    List<Node> specimenAccessionNodes = patientNode.selectNodes("SpecimenAccessions/SpecimenAccession");
    for (Node specimenAccessionNode : specimenAccessionNodes) {
        Node node = specimenAccessionNode.selectSingleNode("AccessionDate");
        if (node == null) {
            System.err.println("no date");
            continue;
        }/*from  w w w .  ja va2s  .  c  om*/
        long date = Long.parseLong(node.getText());

        String site = null, type = null, instrument = null;
        node = specimenAccessionNode.selectSingleNode("AccessionAnatomicSite");
        if (node != null) {
            site = node.getText();
        }
        node = specimenAccessionNode.selectSingleNode("AccessionVisitType");
        if (node != null) {
            type = node.getText();
        }
        node = specimenAccessionNode.selectSingleNode("AccessionProcInstrument");
        if (node != null) {
            instrument = node.getText();
        }

        List<Node> specimenNodes = specimenAccessionNode.selectNodes("Specimens/Specimen");
        for (Node specimenNode : specimenNodes) {
            Patient patient = DaoPatient.getPatientByCancerStudyAndPatientId(cancerStudyId, patientId);

            ClinicalEvent clinicalEvent = new ClinicalEvent();
            clinicalEvent.setPatientId(patient.getInternalId());
            clinicalEvent.setEventType("SPECIMEN");
            clinicalEvent.setStartDate(date);
            if (site != null) {
                clinicalEvent.addEventDatum("SPECIMEN_SITE", site);
            }
            if (type != null) {
                clinicalEvent.addEventDatum("ANATOMIC_SITE", type);
            }
            if (instrument != null) {
                clinicalEvent.addEventDatum("PROC_INSTRUMENT", instrument);
            }

            addAllDataUnderNode(clinicalEvent, Element.class.cast(specimenNode));

            clinicalEvents.add(clinicalEvent);
        }
    }
}

---

From source file:org.mskcc.cbio.portal.scripts.ImportCaisesClinicalXML.java

License:Open Source License

private static List<ClinicalData> parseClinicalDataFromSpecimen(Node patientNode, int cancerStudyId,
        Map<String, String> mapSu2cSampleIdSampleId) {
    List<ClinicalData> clinicalData = new ArrayList<ClinicalData>();
    List<Node> specimenAccessionNodes = patientNode.selectNodes("SpecimenAccessions/SpecimenAccession");
    for (Node specimenAccessionNode : specimenAccessionNodes) {
        String site = null, instrument = null;
        Node node = specimenAccessionNode.selectSingleNode("AccessionAnatomicSite");
        if (node != null) {
            site = node.getText();/* w  ww  . ja  v  a 2 s  .co  m*/
        }
        node = specimenAccessionNode.selectSingleNode("AccessionProcInstrument");
        if (node != null) {
            instrument = node.getText();
        }

        List<Node> specimenNodes = specimenAccessionNode.selectNodes("Specimens/Specimen");
        for (Node specimenNode : specimenNodes) {
            node = specimenNode.selectSingleNode("SpecimenReferenceNumber");
            if (node == null) {
                continue;
            }
            String su2cSampleId = node.getText();
            String sampleId = mapSu2cSampleIdSampleId.get(su2cSampleId);
            if (sampleId == null) {
                continue;
            }

            if (site != null) {
                ClinicalData clinicalDatum = new ClinicalData(cancerStudyId, sampleId, "TUMOR_SITE", site);
                clinicalData.add(clinicalDatum);
            }

            if (instrument != null) {
                ClinicalData clinicalDatum = new ClinicalData(cancerStudyId, sampleId, "PROC_INSTRUMENT",
                        instrument);
                clinicalData.add(clinicalDatum);
            }
        }
    }
    return clinicalData;
}

---

From source file:org.mskcc.cbio.portal.scripts.ImportCaisesClinicalXML.java

License:Open Source License

private static long parseStatusesAndReturnDiagnosisDate(List<ClinicalEvent> clinicalEvents, Node patientNode,
        String patientId, int cancerStudyId) {
    List<Node> statusNodes = patientNode.selectNodes("Statuses/Status");
    long diagnosisDate = 0;
    for (Node statusNode : statusNodes) {
        Patient patient = DaoPatient.getPatientByCancerStudyAndPatientId(cancerStudyId, patientId);
        ClinicalEvent clinicalEvent = new ClinicalEvent();
        clinicalEvent.setPatientId(patient.getInternalId());
        clinicalEvent.setEventType("STATUS");

        Node node = statusNode.selectSingleNode("StatusDate");
        if (node == null) {
            System.err.println("no date");
            continue;
        }/*w  ww. j a  v a2s. co m*/
        long statusDate = Long.parseLong(node.getText());
        clinicalEvent.setStartDate(statusDate);

        node = statusNode.selectSingleNode("Status");
        if (node == null) {
            System.err.println("no status");
            continue;
        }
        clinicalEvent.addEventDatum("STATUS", node.getText());
        if (node.getText().equalsIgnoreCase("Diagnosis Date")) {
            diagnosisDate = statusDate;
        }

        clinicalEvents.add(clinicalEvent);
    }
    return diagnosisDate;
}

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From source file:org.onecmdb.core.utils.transform.xml.XPathInstanceSelector.java

License:Open Source License

public List<IInstance> getInstances(DataSet ds) throws IOException {
    if (ds.getDataSource() instanceof XMLDataSource) {
        List<IInstance> rows = new ArrayList<IInstance>();
        for (Node node : ((XMLDataSource) ds.getDataSource()).getNodes()) {
            List<Node> selectedNodes = node.selectNodes(getXpath());
            for (Node selectedNode : selectedNodes) {

                XMLRow row = new XMLRow(ds, selectedNode);
                row.setAutoCreate(isAutoCreate());
                String temp = null;
                if (templatePath != null) {
                    Node n = row.getNode();

                    Object sNode = n.selectObject(templatePath);

                    if (sNode instanceof Node) {
                        temp = ((Node) sNode).getText();
                    } else if (sNode instanceof String) {
                        temp = (String) sNode;
                    }//from   ww w .j  a va2  s  . c om
                }
                if (temp == null) {
                    temp = getTemplate();
                }
                row.setTemplate(temp);

                rows.add(row);
            }
        }
        return (rows);
    }
    throw new IllegalArgumentException("XPath selector must operate on an XML data source");
}

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From source file:org.openadaptor.auxil.convertor.xml.XmlToOrderedMapConvertor.java

License:Open Source License

/**
 * Select Elements using an XPATH expression. Firstly the expression is used to select
 * Nodes. Then the Element subset of selected Nodes is returned.
 *
 * @param node the root node containing the elements to select
 *
 * @param xpathExpression the XPath expression used to selected the elements
 *
 * @return a possibly empty Element[]//from   w  ww .ja  va2  s  .co  m
 *
 * @throws RecordException if there was an XPath error
 */
private Element[] selectElements(Node node, String xpathExpression) throws RecordException {
    List selectedNodes = node.selectNodes(xpathExpression);
    List selectedElements = new ArrayList();

    Iterator it = selectedNodes.iterator();
    while (it.hasNext()) {
        Object entry = it.next();
        if (entry instanceof Node) {
            if (entry instanceof Element)
                selectedElements.add(entry);
        } else {
            String exceptionDetail = "XPATH selection using expression " + xpathExpression
                    + " failed to return nodes.";
            if (throwRecordExceptionOnBadSelection) {
                log.warn(exceptionDetail);
                log.warn(
                        "set throwRecordExceptionOnBadSelection to false to prevent an exception in this case.");
                throw new RecordException(exceptionDetail);
            } else {
                log.warn(exceptionDetail);
                log.warn("set throwRecordExceptionOnBadSelection to true to force an exception in this case.");
            }
        }
    }

    return (Element[]) selectedElements.toArray(new Element[selectedElements.size()]);
}

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