List of usage examples for org.dom4j Node getText
String getText();
Returns the text of this node.
From source file:edu.scripps.fl.pubchem.web.pug.PowerUserGateway.java
License:Apache License
private String makeRequest() throws Exception { InputStream is = fetchResponse(getRequest()); Document doc = getDocument(is); setResponse(doc);/*ww w . j av a 2s . c o m*/ Node node = doc.selectSingleNode("//PCT-Status[@value='server-error']"); if (node != null) { String msg = node.getParent().getParent().getText(); throw new Exception(String.format("PUG Error: %s", msg)); } node = doc.selectSingleNode("//*/PCT-Waiting_reqid"); String requestId = null; if (node != null) { requestId = node.getText(); log.debug("PCT-Waiting_reqid: " + requestId); } return requestId; }
From source file:edu.scripps.fl.pubchem.xml.extract.CategorizedCommentExtractor.java
License:Apache License
public List<CategorizedComment> getCategorizedCommentsFromXML(Document doc) throws Exception { List<CategorizedComment> comments = new ArrayList<CategorizedComment>(); List<Node> nodes = doc.selectNodes("//PC-AssayDescription_categorized-comment/PC-CategorizedComment"); PubChemXMLUtils utils = new PubChemXMLUtils(); for (Node nn : nodes) { CategorizedComment comment = new CategorizedComment(); comment.setCommentTag(nn.selectSingleNode("PC-CategorizedComment_title").getText()); List<Node> valueNodes = nn.selectNodes("PC-CategorizedComment_comment/PC-CategorizedComment_comment_E"); String text = ""; for (Node valeuNode : valueNodes) { if (null != valeuNode.getText()) text = text + valeuNode.getText() + "\n"; }// w w w .jav a2 s.c o m comment.setCommentValue(text); comments.add(comment); } return comments; }
From source file:edu.scripps.fl.pubchem.xml.extract.PanelExtractor.java
License:Apache License
private List<Integer> getXrefValues(String nodeName, Node parent) { List<Node> nodes = parent.selectNodes(nodeName); List<Integer> list = new ArrayList<Integer>(); if (nodes != null) { for (Node node : nodes) list.add(Integer.parseInt(node.getText())); }// ww w .j a v a 2 s . c o m return list; }
From source file:edu.scripps.fl.pubchem.xml.extract.ResultTidExtractor.java
License:Apache License
public List<ResultTid> getTidValuesFromXML(Document doc) throws IllegalAccessException, InvocationTargetException { List<ResultTid> tidValues = new ArrayList<ResultTid>(); List<Node> nodes = doc.selectNodes("//PC-AssayDescription_results/PC-ResultType"); for (Node nn : nodes) { ResultTid tidValue = new ResultTid(); tidValue.setTidName(nn.selectSingleNode("PC-ResultType_name").getText()); tidValue.setTidType(nn.selectSingleNode("PC-ResultType_type").valueOf("@value")); Node node = nn.selectSingleNode("PC-ResultType_unit"); if (node != null) tidValue.setTidUnit(node.valueOf("@value")); node = nn.selectSingleNode("PC-ResultType_description/PC-ResultType_description_E"); if (node != null) tidValue.setTidDescription(node.getText()); node = nn.selectSingleNode("PC-ResultType_ac"); if (node != null) tidValue.setIsActiveConcentration(true); node = nn.selectSingleNode("PC-ResultType_tc"); if (node != null) { Node node2 = node.selectSingleNode("PC-ConcentrationAttr/PC-ConcentrationAttr_dr-id"); if (node2 != null) { BeanUtils.setProperty(tidValue, "tidPlot", node2.getText()); }/* w w w . j a v a2 s. c om*/ BeanUtils.setProperty(tidValue, "tidConcentration", node.selectSingleNode("PC-ConcentrationAttr/PC-ConcentrationAttr_concentration").getText()); } node = nn.selectSingleNode("PC-ResultType_panel-info/PC-AssayPanelTestResult"); if (node != null) { BeanUtils.setProperty(tidValue, "tidPanelNum", node.selectSingleNode("PC-AssayPanelTestResult_mid").getText()); tidValue.setTidPanelReadout( node.selectSingleNode("PC-AssayPanelTestResult_readout-annot").valueOf("@value")); } tidValues.add(tidValue); } return tidValues; }
From source file:edu.scripps.fl.pubchem.xml.extract.XrefExtractor.java
License:Apache License
public List<Xref> getXrefValuesFromXML(Document doc, List<Panel> panel) throws Exception { List<Xref> xrefs = new ArrayList<Xref>(); List<Node> nodes = doc.selectNodes("//PC-AssayDescription_xref/PC-AnnotatedXRef"); for (Node nn : nodes) { Xref xref = new Xref(); Node node = nn.selectSingleNode("PC-AnnotatedXRef_xref/PC-XRefData"); selectXref(xref, node, "PC-XRefData_aid", "AID"); selectXref(xref, node, "PC-XRefData_protein-gi", "Protein"); selectXref(xref, node, "PC-XRefData_gene", "Gene"); selectXref(xref, node, "PC-XRefData_taxonomy", "Taxonomy"); selectXref(xref, node, "PC-XRefData_mim", "OMIM"); selectXref(xref, node, "PC-XRefData_dburl", "Source Database Homepage"); selectXref(xref, node, "PC-XRefData_mesh", "MESH"); selectXref(xref, node, "PC-XRefData_sburl", "Substance Homepage"); selectXref(xref, node, "PC-XRefData_asurl", "Assay Homepage"); selectXref(xref, node, "PC-XRefData_rn", "Substance Registry #"); selectXref(xref, node, "PC-XRefData_pmid", "PMID"); selectXref(xref, node, "PC-XRefData_sid", "SID"); selectXref(xref, node, "PC-XRefData_cid", "CID"); selectXref(xref, node, "PC-XRefData_nucleotide-gi", "Nucleotide"); selectXref(xref, node, "PC-XRefData_gi", "GenBank"); selectXref(xref, node, "PC-XRefData_mmdb", "MMDB"); selectXref(xref, node, "PC-XRefData_biosystem", "Biosystems Id"); if (nn.selectSingleNode("PC-AnnotatedXRef_comment") != null) xref.setXrefComment(nn.selectSingleNode("PC-AnnotatedXRef_comment").getText()); Node citationNode = nn.selectSingleNode("PC-AnnotatedXRef_type"); if (citationNode != null) { if (citationNode.getText().equals("1")) xref.setIsPrimaryCitation(true); }// www . jav a 2 s. c o m xrefs.add(xref); } nodes = doc.selectNodes("//PC-AssayDescription_target/PC-AssayTargetInfo"); for (Node nn : nodes) { Xref xref = new Xref(); BeanUtils.setProperty(xref, "xrefValue", nn.selectSingleNode("PC-AssayTargetInfo_mol-id").getText()); BeanUtils.setProperty(xref, "xrefTargetValue", nn.selectSingleNode("PC-AssayTargetInfo_molecule-type").getText()); BeanUtils.setProperty(xref, "isTarget", true); xrefs.add(xref); } if (panel != null) checkXrefAgainstPanel(xrefs, panel); return xrefs; }
From source file:edu.ucsd.library.xdre.imports.RDFDAMS4ImportHandler.java
/** * Procedure to populate the RDF metadata and ingest the files *//*from w ww.j a va2 s. c om*/ public boolean execute() throws Exception { if (filesPaths != null) { File file = null; // List the source files for (int i = 0; i < filesPaths.length; i++) { file = new File(filesPaths[i]); if (file.exists()) { listFile(filesMap, file); } } } String message = ""; Document doc = null; DamsURI damsURI = null; String oid = null; int fLen = rdfFiles.length; String currFile = null; SAXReader saxReader = new SAXReader(); for (int i = 0; i < fLen && !interrupted; i++) { currFile = rdfFiles[i].getName(); setStatus( "Processing external import for file " + currFile + " (" + (i + 1) + " of " + fLen + ") ... "); try { doc = saxReader.read(rdfFiles[i]); List<Node> nodes = doc.selectNodes("//@rdf:about"); for (int j = 0; j < nodes.size(); j++) { Node nUri = nodes.get(j); String iUri = nUri.getStringValue(); Node parentNode = nUri.getParent(); String nName = parentNode.getName(); if (iUri.endsWith("/COL") || !(iUri.startsWith("http") && iUri.indexOf("/ark:/") > 0)) { // Assign ARK if (nName.endsWith("Object") || nName.endsWith("Component") || nName.endsWith("File") || (((Element) parentNode).isRootElement() || (parentNode.getParent().isRootElement() && parentNode.getParent().getName().equals("RDF")))) { String objId = iUri; if (nName.endsWith("Component") || nName.endsWith("File")) { damsURI = DamsURI.toParts(iUri, null); objId = damsURI.getObject(); } String srcObjKey = objId + "::" + rdfFiles[i].getAbsolutePath(); oid = idsMap.get(srcObjKey); // Assign new ARK if (oid == null) { oid = getNewId(); idsMap.put(srcObjKey, oid); } if (nName.endsWith("Object")) { objId = oid; objRecords.put(objId, currFile); } else if (nName.endsWith("Component") || nName.endsWith("File")) { damsURI.setObject(oid); // XXX // Assign cid and fid for Component and FIle if required objId = damsURI.toString(); } else objId = oid; nUri.setText(objId); updateReference(doc, iUri, objId); } else { String field = null; Node tNode = null; String xPath = null; Map<String, String> props = new TreeMap<String, String>(); String elemXPath = parentNode.getPath(); if (nName.endsWith("Collection") || nName.endsWith("CollectionPart")) { // Retrieve the Collection record field = "title_tesim"; xPath = "dams:title/mads:Title/mads:authoritativeLabel"; tNode = parentNode.selectSingleNode(xPath); if (tNode == null) { // Loop through to locate the rdfs:label if not selected by xPath. Node n = parentNode.selectSingleNode("dams:title"); for (Iterator<Element> it = ((Element) n).elementIterator(); it.hasNext();) { Element elem = it.next(); if (elem.getNamespacePrefix().equals("mads") && elem.getName().equals("Title")) tNode = elem.selectSingleNode("mads:authoritativeLabel"); } } } /* else if (nName.endsWith("Language") || nName.endsWith("Authority") || nName.endsWith("Subject") || nName.endsWith("Name") || nName.endsWith("Topic") || nName.endsWith("GenreForm") || nName.endsWith("Temporal") || nName.endsWith("Geographic")){ // Subject, Authority records use mads:authoritativeLabel field = "name_tesim"; xPath = "mads:authoritativeLabel"; tNode = parentNode.selectSingleNode(xPath); } */else if (nName.endsWith(COPYRIGHT)) { // Copyright records use dams:copyrightStatus, plus other properties in the next step. field = "status_tesim"; xPath = "dams:copyrightStatus"; tNode = parentNode.selectSingleNode(xPath); props = copyrightProperties(parentNode); } else if (nName.endsWith(LICENSE)) { // License records use dams:LicenseNote, plus other properties in the next step. field = "note_tesim"; xPath = "dams:licenseNote"; tNode = parentNode.selectSingleNode(xPath); props = licenseProperties(parentNode); } else if (nName.endsWith(OTHERRIGHTS)) { // Copyright records use dams:copyrightStatus, plus other properties in the next step. field = "otherRightsBasis_tesim"; xPath = "dams:otherRightsBasis"; tNode = parentNode.selectSingleNode(xPath); props = licenseProperties(parentNode); } else if (nName.endsWith(RELATEDRESOURCE)) { // RelatedResource records use dams:description, plus other properties in the next step. field = "description_tesim"; xPath = "dams:description"; tNode = parentNode.selectSingleNode(xPath); props = relatedResourceProperties(parentNode); } else if (nName.endsWith(SOURCECAPTURE)) { // SourceCapture records use dams:sourceType, plus other properties in the next step. field = "sourceType_tesim"; xPath = "dams:sourceType"; tNode = parentNode.selectSingleNode(xPath); props = sourceCaptureProperties(parentNode); } else if (elemXPath.indexOf("mads", elemXPath.lastIndexOf('/') + 1) >= 0) { // MADSScheme and Language if (nName.endsWith(MADSSCHEME) || nName.equals(LANGUAGE)) { field = "code_tesim"; xPath = "mads:code"; tNode = parentNode.selectSingleNode(xPath); if (tNode == null) { field = "name_tesim"; xPath = "rdfs:label"; tNode = parentNode.selectSingleNode(xPath); if (tNode == null) { // Loop through to locate the rdfs:label if not selected by xPath. for (Iterator<Element> it = ((Element) parentNode).elementIterator(); it .hasNext();) { Element elem = it.next(); if (elem.getNamespacePrefix().equals("rdfs") && elem.getName().equals("label")) tNode = elem; } } } } else { // Subject, Authority records use mads:authoritativeLabel field = "name_tesim"; xPath = "mads:authoritativeLabel"; tNode = parentNode.selectSingleNode(xPath); if (tNode == null) { // Try to use the mads:code for mapping when mads:authoritativeLabel is not available field = "code_tesim"; xPath = "mads:code"; tNode = parentNode.selectSingleNode(xPath); } // Mapping for mads:isMemberOfMADSScheme String madsScheme = null; Node madsSchemeNode = parentNode.selectSingleNode("mads:isMemberOfMADSScheme"); if (madsSchemeNode != null) { Node msValueNode = madsSchemeNode.selectSingleNode("@rdf:resource"); if (msValueNode != null) { madsScheme = madsSchemeNode.getStringValue(); props.put("scheme_tesim", madsScheme); } else if ((madsSchemeNode = madsSchemeNode .selectSingleNode("mads:MADSScheme")) != null && madsSchemeNode.hasContent()) { if ((msValueNode = madsSchemeNode .selectSingleNode("mads:code")) != null) { madsScheme = msValueNode.getText(); props.put("scheme_code_tesim", madsScheme); } else if ((msValueNode = madsSchemeNode .selectSingleNode("rdfs:label")) != null) { madsScheme = msValueNode.getText(); props.put("scheme_name_tesim", madsScheme); } } else { props.put("scheme_tesim", ""); } } else { props.put("scheme_tesim", null); } } } else { // XXX Other Rights records like Statute, License, Other Rights etc. field = "value_tesim"; xPath = "rdf:value"; tNode = parentNode.selectSingleNode(xPath); field = "code_tesim"; if (tNode == null) { xPath = "dams:code"; tNode = parentNode.selectSingleNode(xPath); } } if (tNode == null) { throw new Exception("Element " + xPath + " is missing from the " + nName + " record " + iUri + " in file " + currFile + "."); } updateDocument(doc, parentNode, field, tNode.getText(), props); } } else if (nName.endsWith("Object")) { objRecords.put(iUri, currFile); } } String dams4Rdf = doc.asXML(); logData("dams4_" + rdfFiles[i].getName(), dams4Rdf); // Ingest the records String subjectId = null; DamsURI objURI = null; List<DamsURI> objURIs = null; RDFStore graph = null; rdfStore = new RDFStore(); Model rdf = rdfStore.loadRDFXML(dams4Rdf); initHandler(); Model iRdf = null; int jLen = items.size(); for (int j = 0; j < jLen && !interrupted; j++) { graph = new RDFStore(); recordsCount++; // Add subject subjectId = items.get(j); try { setStatus("Processing metadata for record " + subjectId + " (" + (j + 1) + " of " + jLen + ") in file " + currFile + " ... "); boolean succeeded = false; objURIs = objects.get(subjectId); for (int k = 0; k < objURIs.size(); k++) { objURI = objURIs.get(k); iRdf = rdfStore.querySubject(objURI.toString()); graph.merge(iRdf); } // Update object //log.info(j + " ingesting record " + subjectId + ":\n" + graph.export(RDFStore.RDFXML_ABBREV_FORMAT) + "\n\n"); succeeded = damsClient.updateObject(subjectId, graph.export(RDFStore.RDFXML_ABBREV_FORMAT), Constants.IMPORT_MODE_ADD); if (!succeeded) { if (metadataFailed.indexOf(currFile) < 0) failedCount++; metadataFailed.append(subjectId + " (" + currFile + "), \n"); message = "Metadata import for record " + subjectId + " failed (" + (j + 1) + " of " + jLen + ") in file " + currFile + "."; setStatus(message); logError(message + "\n Error RDF: \n" + graph.export(RDFStore.RDFXML_ABBREV_FORMAT)); } else { recordsIngested.add(subjectId); message = "Metadata import for record " + subjectId + " succeeded (" + (j + 1) + " of " + jLen + ") in file " + currFile + ". "; setStatus(message); logMessage(message); log.info(message); // Update SOLR fre records ingested. updateSOLR(subjectId); } } catch (Exception e) { e.printStackTrace(); if (metadataFailed.indexOf(currFile) < 0) failedCount++; metadataFailed.append(subjectId + " (" + currFile + "), \n"); message = "Metadata import failed: " + e.getMessage(); setStatus(message + " (" + (j + 1) + " of " + jLen + ") in file " + currFile + "."); logError(message); } try { Thread.sleep(10); } catch (InterruptedException e) { e.printStackTrace(); interrupted = true; failedCount++; metadataFailed.append(subjectId + " (" + currFile + ") \n"); message = "Metadata import interrupted for subject " + subjectId + ". \n Error: " + e.getMessage() + "\n"; setStatus("Canceled"); clearSession(); logError(message); } } // Ingest the source file if (importOption.equalsIgnoreCase("metadataAndFiles")) { uploadFiles(rdf, currFile); } } catch (Exception e) { e.printStackTrace(); failedCount++; message = "Import failed for " + currFile + ": " + e.getMessage(); setStatus(message + " (" + (i + 1) + " of " + fLen + ")."); logError(message); } finally { // Update SOLR for files uploaded int iLen = objWithFiles.size(); for (int j = 0; j < iLen && !interrupted; j++) { updateSOLR(objWithFiles.get(j)); } } setProgressPercentage(((i + 1) * 100) / fLen); try { Thread.sleep(10); } catch (InterruptedException e) { e.printStackTrace(); interrupted = true; failedCount++; message = "Import interrupted for oject in " + currFile + ". \n Error: " + e.getMessage() + "\n"; setStatus("Canceled"); clearSession(); logError(message); } } return exeResult; }
From source file:edu.ucsd.library.xdre.imports.RDFDAMS4ImportHandler.java
private Map<String, String> getProperties(Node record, Map<String, String> propNames) { Map<String, String> props = new TreeMap<String, String>(); String key = null;//from w ww. j av a 2 s . co m String solrName = null; String propValue = null; for (Iterator<String> it = propNames.keySet().iterator(); it.hasNext();) { propValue = null; key = it.next(); solrName = propNames.get(key); Node tNode = record.selectSingleNode(key); if (tNode != null) propValue = tNode.getText().trim(); props.put(solrName, propValue); } return props; }
From source file:edu.ucsd.library.xdre.imports.RDFDAMS4ImportTsHandler.java
private String encodeLiteralValue(Node node) { String value = null;/*from w ww .j a v a 2 s. c o m*/ if (node != null) { value = "\"" + StringEscapeUtils.escapeJava(Normalizer.normalize(node.getText(), Normalizer.Form.NFC)) .replace("'", "\\'").replace("\"", "\\\"") + "\""; Node langAttr = node.selectSingleNode("@xml:lang"); if (langAttr != null) value += "@" + langAttr.getStringValue(); } return value; }
From source file:edu.ucsd.library.xdre.web.CollectionOperationController.java
private static String getTitle(Document doc) { String title = ""; Node node = doc.selectSingleNode("//dams:Object/dams:title/mads:Title/mads:authoritativeLabel"); if (node != null) { title = node.getText(); }//w w w. ja va 2 s. co m return title; }
From source file:edu.umd.cs.buildServer.inspection.PMDRunner.java
License:Apache License
private void readPMDTestOutcomes(XMLDocumentBuilder stdoutMonitor) { Document document = stdoutMonitor.getDocument(); if (document == null) return;//ww w . j a v a 2 s. c o m int count = TestOutcome.FIRST_TEST_NUMBER; Iterator<?> fileNodeIter = document.selectNodes("//pmd/file").iterator(); while (fileNodeIter.hasNext()) { Node fileElement = (Node) fileNodeIter.next(); String fileName = fileElement.valueOf("@name"); Iterator<?> violationIter = fileElement.selectNodes("./violation").iterator(); while (violationIter.hasNext()) { Node violationElement = (Node) violationIter.next(); String line = violationElement.valueOf("@line"); String rule = violationElement.valueOf("@rule"); String description = violationElement.getText(); String priority = violationElement.valueOf("@priority"); // Turn the warning into a TestOutcome TestOutcome testOutcome = new TestOutcome(); testOutcome.setTestType(TestOutcome.TestType.PMD); testOutcome.setTestName(rule); testOutcome.setOutcome(TestOutcome.STATIC_ANALYSIS); testOutcome.setShortTestResult(fileName + ":" + line); testOutcome.setLongTestResultCompressIfNeeded(description); testOutcome.setTestNumber(Integer.toString(count++)); testOutcome.setExceptionClassName(priority); // XXX: HACK! testOutcomeCollection.add(testOutcome); } } projectSubmission.getLog().info("Recorded " + count + " PMD warnings as test outcomes"); }