List of usage examples for org.dom4j Node selectSingleNode
Node selectSingleNode(String xpathExpression);
selectSingleNode evaluates an XPath expression and returns the result as a single Node instance.
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; }//from ww w . j a va 2 s .com 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; }/*from w w w . j ava 2s . c om*/ 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; }//w w w . ja v a 2 s .com 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; }/* ww w . ja v a 2s.c o m*/ 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();/*from ww w . j a v a2 s . c o 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 .ja va 2 s .c o 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; }
From source file:org.onecmdb.core.utils.transform.xml.XPathAttributeSelector.java
License:Open Source License
public IAttributeValue getAttribute(IInstance row) { if (row instanceof XMLRow) { Node node = ((XMLRow) row).getNode(); Node selectedNode = null; try {//from www.jav a2s . co m selectedNode = node.selectSingleNode(getXpath()); } catch (InvalidXPathException e) { throw new IllegalArgumentException( "Invalid XPath '" + getXpath() + "' in attribute '" + getName() + "'", e); } if (selectedNode == null) { return (new EmptyAttributeValue(this)); //throw new IllegalArgumentException("Column '" + getXPath() + "' not found in row '" + node.getPath() +"'"); } TextAttributeValue col = new TextAttributeValue(this, selectedNode.getText()); return (col); } return (null); }
From source file:org.opencms.setup.xml.CmsSetupXmlHelper.java
License:Open Source License
/** * Sets the given value in all nodes identified by the given xpath of the given xml file.<p> * /* w w w .ja v a 2s . c o m*/ * If value is <code>null</code>, all nodes identified by the given xpath will be deleted.<p> * * If the node identified by the given xpath does not exists, the missing nodes will be created * (if <code>value</code> not <code>null</code>).<p> * * @param document the xml document * @param xPath the xpath to set * @param value the value to set (can be <code>null</code> for deletion) * @param nodeToInsert optional, if given it will be inserted after xPath with the given value * * @return the number of successful changed or deleted nodes */ public static int setValue(Document document, String xPath, String value, String nodeToInsert) { int changes = 0; // be naive and try to find the node Iterator<Node> itNodes = CmsCollectionsGenericWrapper.<Node>list(document.selectNodes(xPath)).iterator(); // if not found if (!itNodes.hasNext()) { if (value == null) { // if no node found for deletion return 0; } // find the node creating missing nodes in the way Iterator<String> it = CmsStringUtil.splitAsList(xPath, "/", false).iterator(); Node currentNode = document; while (it.hasNext()) { String nodeName = it.next(); // if a string condition contains '/' while ((nodeName.indexOf("='") > 0) && (nodeName.indexOf("']") < 0)) { nodeName += "/" + it.next(); } Node node = currentNode.selectSingleNode(nodeName); if (node != null) { // node found currentNode = node; if (!it.hasNext()) { currentNode.setText(value); } } else if (currentNode.getNodeType() == Node.ELEMENT_NODE) { Element elem = (Element) currentNode; if (!nodeName.startsWith("@")) { elem = handleNode(elem, nodeName); if (!it.hasNext() && CmsStringUtil.isNotEmptyOrWhitespaceOnly(value)) { elem.setText(value); } } else { // if node is attribute create it with given value elem.addAttribute(nodeName.substring(1), value); } currentNode = elem; } else { // should never happen if (LOG.isDebugEnabled()) { LOG.debug(Messages.get().getBundle().key(Messages.ERR_XML_SET_VALUE_2, xPath, value)); } break; } } if (nodeToInsert == null) { // if not inserting we are done return 1; } // if inserting, we just created the insertion point, so continue itNodes = CmsCollectionsGenericWrapper.<Node>list(document.selectNodes(xPath)).iterator(); } // if found while (itNodes.hasNext()) { Node node = itNodes.next(); if (nodeToInsert == null) { // if not inserting if (value != null) { // if found, change the value node.setText(value); } else { // if node for deletion is found node.getParent().remove(node); } } else { // first create the node to insert Element parent = node.getParent(); Element elem = handleNode(parent, nodeToInsert); if (value != null) { elem.setText(value); } // get the parent element list List<Node> list = CmsCollectionsGenericWrapper.<Node>list(parent.content()); // remove the just created element list.remove(list.size() - 1); // insert it back to the right position int pos = list.indexOf(node); list.add(pos + 1, elem); // insert after } changes++; } return changes; }
From source file:org.opencms.util.ant.CmsSetupXmlHelper.java
License:Open Source License
/** * Sets the given value in all nodes identified by the given xpath of the given xml file.<p> * /*from ww w . j ava 2s . c om*/ * If value is <code>null</code>, all nodes identified by the given xpath will be deleted.<p> * * If the node identified by the given xpath does not exists, the missing nodes will be created * (if <code>value</code> not <code>null</code>).<p> * * @param document the xml document * @param xPath the xpath to set * @param value the value to set (can be <code>null</code> for deletion) * @param nodeToInsert optional, if given it will be inserted after xPath with the given value * * @return the number of successful changed or deleted nodes */ @SuppressWarnings("unchecked") public static int setValue(Document document, String xPath, String value, String nodeToInsert) { int changes = 0; // be naive and try to find the node Iterator<Node> itNodes = document.selectNodes(xPath).iterator(); // if not found if (!itNodes.hasNext()) { if (value == null) { // if no node found for deletion return 0; } // find the node creating missing nodes in the way Iterator<String> it = CmsStringUtil.splitAsList(xPath, "/", false).iterator(); Node currentNode = document; while (it.hasNext()) { String nodeName = it.next(); // if a string condition contains '/' while ((nodeName.indexOf("='") > 0) && (nodeName.indexOf("']") < 0)) { nodeName += "/" + it.next(); } Node node = currentNode.selectSingleNode(nodeName); if (node != null) { // node found currentNode = node; if (!it.hasNext()) { currentNode.setText(value); } } else if (currentNode.getNodeType() == Node.ELEMENT_NODE) { Element elem = (Element) currentNode; if (!nodeName.startsWith("@")) { elem = handleNode(elem, nodeName); if (!it.hasNext() && !CmsStringUtil.isEmptyOrWhitespaceOnly(value)) { elem.setText(value); } } else { // if node is attribute create it with given value elem.addAttribute(nodeName.substring(1), value); } currentNode = elem; } else { // should never happen break; } } if (nodeToInsert == null) { // if not inserting we are done return 1; } // if inserting, we just created the insertion point, so continue itNodes = document.selectNodes(xPath).iterator(); } // if found while (itNodes.hasNext()) { Node node = itNodes.next(); if (nodeToInsert == null) { // if not inserting if (value != null) { // if found, change the value node.setText(value); } else { // if node for deletion is found node.getParent().remove(node); } } else { // first create the node to insert Element parent = node.getParent(); Element elem = handleNode(parent, nodeToInsert); if (value != null) { elem.setText(value); } // get the parent element list List<Node> list = parent.content(); // remove the just created element list.remove(list.size() - 1); // insert it back to the right position int pos = list.indexOf(node); list.add(pos + 1, elem); // insert after } changes++; } return changes; }
From source file:org.pdfsam.console.business.pdf.handlers.ConcatCmdExecutor.java
License:Open Source License
/** * given a fileset node returns the PdfFile objects * //www . ja v a 2s. c o m * @param fileSetNode * @param parentDir * @return a list of PdfFile objects * @throws Exception */ private List getFileNodesFromFileset(Node fileSetNode, String parentDir) throws Exception { String parentPath = null; Node useCurrentDir = fileSetNode.selectSingleNode("@usecurrentdir"); Node dir = fileSetNode.selectSingleNode("@dir"); if (dir != null && dir.getText().trim().length() > 0) { parentPath = dir.getText(); } else { if (useCurrentDir != null && Boolean.valueOf(useCurrentDir.getText()).booleanValue()) { parentPath = parentDir; } } return getPdfFileListFromNode(fileSetNode.selectNodes("file"), parentPath); }