List of usage examples for org.dom4j Node selectNodes
List<Node> selectNodes(String xpathExpression);
selectNodes evaluates an XPath expression and returns the result as a List of Node instances or String instances depending on the XPath expression.
From source file:edu.scripps.fl.pubchem.web.pug.PUGRequest.java
License:Apache License
public static void setResponseIds(Document document, Type type, Collection<Object> ids) throws Exception { String idTypePath = "//PCT-QueryAssayData_"; idTypePath += Type.AID.equals(type) ? "aids" : "scids"; Node localRoot = document.selectSingleNode(idTypePath); Node node = localRoot.selectSingleNode(".//PCT-ID-List_db"); node.setText(type.getDatabase());/*from ww w .ja v a 2 s.c o m*/ node = localRoot.selectSingleNode(".//PCT-ID-List_uids"); // if (node == null) // throw new Exception("Cannot find PCT-ID-List_uids node"); for (Node child : (List<Node>) node.selectNodes("*")) child.detach(); for (Object id : ids) { Element aidElem = DocumentHelper.createElement("PCT-ID-List_uids_E"); aidElem.setText(id.toString()); ((Element) node).add(aidElem); } }
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"; }/*from www . j a v a 2s . com*/ comment.setCommentValue(text); comments.add(comment); } return comments; }
From source file:edu.scripps.fl.pubchem.xml.extract.PanelExtractor.java
License:Apache License
public List<Panel> getPanelValuesFromXML(Document doc) throws Exception { List<Panel> panelValues = new ArrayList<Panel>(); List<Node> nodes = doc.selectNodes( "//PC-AssayDescription_panel-info/PC-AssayPanel/PC-AssayPanel_member/PC-AssayPanelMember"); for (Node nn : nodes) { Panel panelValue = new Panel(); panelValue.setPanelName(nn.selectSingleNode("PC-AssayPanelMember_name").getText()); List<Node> targetNodes = nn.selectNodes("PC-AssayPanelMember_target/PC-AssayTargetInfo"); if (targetNodes != null && targetNodes.size() > 0) { List<PanelTarget> targets = new ArrayList<PanelTarget>(); for (Node targetNode : targetNodes) { PanelTarget target = new PanelTarget(); target.setPanelTargetName(targetNode.selectSingleNode("PC-AssayTargetInfo_name").getText()); BeanUtils.setProperty(target, "panelTargetGi", targetNode.selectSingleNode("PC-AssayTargetInfo_mol-id").getText()); target.setPanelTargetType( targetNode.selectSingleNode("PC-AssayTargetInfo_molecule-type").valueOf("@value")); targets.add(target);/*from w w w. j a v a 2 s . co m*/ } panelValue.setPanelTarget(targets); } Node p = nn.selectSingleNode("PC-AssayPanelMember_xref"); if (p != null) { List<Integer> taxonomies = getXrefValues( "PC-AnnotatedXRef/PC-AnnotatedXRef_xref/PC-XRefData/PC-XRefData_taxonomy", p); panelValue.setPanelTaxonomy(taxonomies); List<Integer> genes = getXrefValues( "PC-AnnotatedXRef/PC-AnnotatedXRef_xref/PC-XRefData/PC-XRefData_gene", p); panelValue.setPanelGene(genes); } panelValues.add(panelValue); } return panelValues; }
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())); }/*from ww w .ja v a2 s . com*/ return list; }
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;/*from ww w . j a va 2 s .co 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"); }
From source file:edu.umd.cs.findbugs.xml.XMLUtil.java
License:Open Source License
@SuppressWarnings("unchecked") public static <T> List<T> selectNodes(Node node, String arg0) { return node.selectNodes(arg0); }
From source file:eleyzhu.facetid.common.PluginManager.java
License:Open Source License
/** * Loads public plugins.//from w w w. j ava2s . c o m * * @param pluginDir the directory of the expanded public plugin. * @return the new Plugin model for the Public Plugin. */ private Plugin loadPublicPlugin(File pluginDir) { File pluginFile = new File(pluginDir, "plugin.xml"); SAXReader saxReader = new SAXReader(); Document pluginXML = null; try { pluginXML = saxReader.read(pluginFile); } catch (DocumentException e) { Log.error(e); } Plugin pluginClass = null; List<? extends Node> plugins = pluginXML.selectNodes("/plugin"); for (Node plugin1 : plugins) { PublicPlugin publicPlugin = new PublicPlugin(); String clazz = null; String name; String minVersion; try { name = plugin1.selectSingleNode("name").getText(); clazz = plugin1.selectSingleNode("class").getText(); try { String lower = name.replaceAll("[^0-9a-zA-Z]", "").toLowerCase(); // Dont load the plugin if its on the Blacklist if (_blacklistPlugins.contains(lower) || _blacklistPlugins.contains(clazz) || SettingsManager.getLocalPreferences().getDeactivatedPlugins().contains(name)) { return null; } } catch (Exception e) { // Whatever^^ return null; } // Check for minimum Spark version try { minVersion = plugin1.selectSingleNode("minSparkVersion").getText(); String buildNumber = JiveInfo.getVersion(); boolean ok = buildNumber.compareTo(minVersion) >= 0; if (!ok) { return null; } } catch (Exception e) { Log.error("Unable to load plugin " + name + " due to missing <minSparkVersion>-Tag in plugin.xml."); return null; } // Check for minimum Java version try { String javaversion = plugin1.selectSingleNode("java").getText().replaceAll("[^0-9]", ""); javaversion = javaversion == null ? "0" : javaversion; int jv = Integer.parseInt(attachMissingZero(javaversion)); String myversion = System.getProperty("java.version").replaceAll("[^0-9]", ""); int mv = Integer.parseInt(attachMissingZero(myversion)); boolean ok = (mv >= jv); if (!ok) { Log.error("Unable to load plugin " + name + " due to old JavaVersion.\nIt Requires " + plugin1.selectSingleNode("java").getText() + " you have " + System.getProperty("java.version")); return null; } } catch (NullPointerException e) { Log.warning("Plugin " + name + " has no <java>-Tag, consider getting a newer Version"); } // set dependencies try { List<? extends Node> dependencies = plugin1.selectNodes("depends/plugin"); for (Node depend1 : dependencies) { Element depend = (Element) depend1; PluginDependency dependency = new PluginDependency(); dependency.setVersion(depend.selectSingleNode("version").getText()); dependency.setName(depend.selectSingleNode("name").getText()); publicPlugin.addDependency(dependency); } } catch (Exception e) { e.printStackTrace(); } // Do operating system check. boolean operatingSystemOK = isOperatingSystemOK(plugin1); if (!operatingSystemOK) { return null; } publicPlugin.setPluginClass(clazz); publicPlugin.setName(name); try { String version = plugin1.selectSingleNode("version").getText(); publicPlugin.setVersion(version); String author = plugin1.selectSingleNode("author").getText(); publicPlugin.setAuthor(author); String email = plugin1.selectSingleNode("email").getText(); publicPlugin.setEmail(email); String description = plugin1.selectSingleNode("description").getText(); publicPlugin.setDescription(description); String homePage = plugin1.selectSingleNode("homePage").getText(); publicPlugin.setHomePage(homePage); } catch (Exception e) { Log.debug("We can ignore these."); } try { pluginClass = (Plugin) getParentClassLoader().loadClass(clazz).newInstance(); Log.debug(name + " has been loaded."); publicPlugin.setPluginDir(pluginDir); publicPlugins.add(publicPlugin); registerPlugin(pluginClass); } catch (Throwable e) { Log.error("Unable to load plugin " + clazz + ".", e); } } catch (Exception ex) { Log.error("Unable to load plugin " + clazz + ".", ex); } } return pluginClass; }
From source file:Emporium.Servlet.ServImportaImpressaoPLP.java
public static String leXmlPLP(String xml, String idPLP, int idCliente, int idDepto, String nomeBD) throws DocumentException, HeadlessException { String ret = ""; xml = xml.replaceAll("&", "E"); //System.out.println(xml); if (xml != null && !xml.isEmpty()) { SAXReader reader = new SAXReader(); StringReader sr = new StringReader(xml); Document doc = reader.read(sr); List<Node> eventos = (List<Node>) doc.selectNodes("//correioslog"); // processa eventos for (Node node : eventos) { String contrato = node.valueOf("remetente/numero_contrato"); String cartaoPostagem = "";//node.valueOf(""); String codigoAdministrativo = node.valueOf("remetente/codigo_administrativo"); String nomeRemetente = node.valueOf("remetente/nome_remetente"); String cepRemetente = node.valueOf("remetente/cep_remetente"); String enderecoRemetente = node.valueOf("remetente/logradouro_remetente"); String numeroRemetente = node.valueOf("remetente/numero_remetente"); String complementoRemetente = node.valueOf("remetente/complemento_remetente"); String bairroRemetente = node.valueOf("remetente/bairro_remetente"); String cidadeRemetente = node.valueOf("remetente/cidade_remetente"); String ufRemetente = node.valueOf("remetente/uf_remetente"); Endereco endRemetente = new Endereco(nomeRemetente, enderecoRemetente, numeroRemetente, complementoRemetente, bairroRemetente, cidadeRemetente, ufRemetente, cepRemetente); List<Node> evnt = (List<Node>) node.selectNodes("objeto_postal"); for (Node nd : evnt) { String notaFiscal = nd.valueOf("nacional/numero_nota_fiscal"); int codECT = Integer.parseInt(nd.valueOf("codigo_servico_postagem").trim()); String servico = ContrServicoECT.consultaGrupoServicoByCodECT(codECT); String nomeDestinatario = nd.valueOf("destinatario/nome_destinatario"); String cepDestinatario = nd.valueOf("nacional/cep_destinatario"); String enderecoDestinatario = nd.valueOf("destinatario/logradouro_destinatario"); String numeroDestinatario = nd.valueOf("destinatario/numero_end_destinatario"); String complementoDestinatario = nd.valueOf("destinatario/complemento_destinatario"); String bairroDestinatario = nd.valueOf("nacional/bairro_destinatario"); String cidadeDestinatario = nd.valueOf("nacional/cidade_destinatario"); String ufDestinatario = nd.valueOf("nacional/uf_destinatario"); Endereco endDestinatario = new Endereco(nomeDestinatario, enderecoDestinatario, numeroDestinatario, complementoDestinatario, bairroDestinatario, cidadeDestinatario, ufDestinatario, cepDestinatario); int ar = 0; int mp = 0; int rg = 0; int rm = 0; int pr = 0; float vd = 0; List<Node> evtAdicionais = (List<Node>) node.selectNodes("servico_adicional"); for (Node nda : evtAdicionais) { int codAd = Integer.parseInt(nda.valueOf("codigo_servico_adicional").trim()); switch (codAd) { case 1: ar = 1;// w ww. j a v a 2 s .c o m break; case 2: mp = 1; break; case 4: rm = 1; break; case 15: pr = 1; break; case 19: case 35: vd = Float.parseFloat(nda.valueOf("valor_declarado").trim().replace(",", ".")); break; default: break; } } String sro = nd.valueOf("numero_etiqueta"); ContrImpressaoPLP.inserePLP(sro, idPLP, 0, contrato, cartaoPostagem, codigoAdministrativo, codECT, servico, idCliente, idDepto, ar, mp, vd, pr, rg, rm, notaFiscal, endRemetente, endDestinatario, nomeBD); } } } else { ret = "XML da PLP est vazio!"; } return ret; }
From source file:fr.gouv.culture.vitam.utils.XmlDom.java
License:Open Source License
/** * Attached file accessibility test/*from w w w .j ava2 s . c o m*/ * * @param current_file * @param task * optional * @param config * @param argument * @param checkDigest * @param checkFormat * @param showFormat * @return VitamResult */ static final public VitamResult all_tests_in_one(File current_file, RunnerLongTask task, ConfigLoader config, VitamArgument argument, boolean checkDigest, boolean checkFormat, boolean showFormat) { SAXReader saxReader = new SAXReader(); VitamResult finalResult = new VitamResult(); Element root = initializeCheck(argument, finalResult, current_file); try { Document document = saxReader.read(current_file); removeAllNamespaces(document); Node nodesrc = document.selectSingleNode("/digests"); String src = null; String localsrc = current_file.getParentFile().getAbsolutePath() + File.separator; if (nodesrc != null) { nodesrc = nodesrc.selectSingleNode("@source"); if (nodesrc != null) { src = nodesrc.getText() + "/"; } } if (src == null) { src = localsrc; } @SuppressWarnings("unchecked") List<Node> nodes = document.selectNodes("//" + config.DOCUMENT_FIELD); if (nodes == null) { Element result = fillInformation(argument, root, "result", "filefound", "0"); addDate(argument, config, result); } else { String number = "" + nodes.size(); Element result = fillInformation(argument, root, "result", "filefound", number); XMLWriter writer = null; writer = new XMLWriter(System.out, StaticValues.defaultOutputFormat); int currank = 0; for (Node node : nodes) { currank++; Node attachment = node.selectSingleNode(config.ATTACHMENT_FIELD); if (attachment == null) { continue; } Node file = attachment.selectSingleNode(config.FILENAME_ATTRIBUTE); if (file == null) { continue; } Node mime = null; Node format = null; if (checkFormat) { mime = attachment.selectSingleNode(config.MIMECODE_ATTRIBUTE); format = attachment.selectSingleNode(config.FORMAT_ATTRIBUTE); } String sfile = null; String smime = null; String sformat = null; String sintegrity = null; String salgo = null; if (file != null) { sfile = file.getText(); } if (mime != null) { smime = mime.getText(); } if (format != null) { sformat = format.getText(); } // Now check // first existence check String ficname = src + sfile; Element check = fillInformation(argument, root, "check", "filename", sfile); File fic1 = new File(ficname); File fic2 = new File(localsrc + sfile); File fic = null; if (fic1.canRead()) { fic = fic1; } else if (fic2.canRead()) { fic = fic2; } if (fic == null) { fillInformation(argument, check, "find", "status", StaticValues.LBL.error_filenotfile.get()); addDate(argument, config, result); finalResult.values[AllTestsItems.FileError.ordinal()]++; finalResult.values[AllTestsItems.GlobalError.ordinal()]++; } else { Element find = fillInformation(argument, check, "find", "status", "ok"); addDate(argument, config, find); finalResult.values[AllTestsItems.FileSuccess.ordinal()]++; if (checkDigest) { @SuppressWarnings("unchecked") List<Node> integrities = node.selectNodes(config.INTEGRITY_FIELD); for (Node integrity : integrities) { Node algo = integrity.selectSingleNode(config.ALGORITHME_ATTRIBUTE); salgo = null; sintegrity = null; if (integrity != null) { sintegrity = integrity.getText(); if (algo != null) { salgo = algo.getText(); } else { salgo = config.DEFAULT_DIGEST; } } // Digest check if (salgo == null) { // nothing } else if (salgo.equals(StaticValues.XML_SHA1)) { salgo = "SHA-1"; } else if (salgo.equals(StaticValues.XML_SHA256)) { salgo = "SHA-256"; } else if (salgo.equals(StaticValues.XML_SHA512)) { salgo = "SHA-512"; } else { salgo = null; } if (algo != null) { Element eltdigest = Commands.checkDigest(fic, salgo, sintegrity); if (eltdigest.selectSingleNode(".[@status='ok']") != null) { finalResult.values[AllTestsItems.DigestSuccess.ordinal()]++; } else { finalResult.values[AllTestsItems.DigestError.ordinal()]++; finalResult.values[AllTestsItems.GlobalError.ordinal()]++; } addDate(argument, config, eltdigest); addElement(writer, argument, check, eltdigest); } } } // Check format if (checkFormat && config.droidHandler != null) { try { // Droid List<DroidFileFormat> list = config.droidHandler.checkFileFormat(fic, argument); Element cformat = Commands.droidFormat(list, smime, sformat, sfile, fic); if (config.droidHandler != null) { cformat.addAttribute("pronom", config.droidHandler.getVersionSignature()); } if (config.droidHandler != null) { cformat.addAttribute("droid", "6.1"); } if (cformat.selectSingleNode(".[@status='ok']") != null) { finalResult.values[AllTestsItems.FormatSuccess.ordinal()]++; } else if (cformat.selectSingleNode(".[@status='warning']") != null) { finalResult.values[AllTestsItems.FormatWarning.ordinal()]++; finalResult.values[AllTestsItems.GlobalWarning.ordinal()]++; } else { finalResult.values[AllTestsItems.FormatError.ordinal()]++; finalResult.values[AllTestsItems.GlobalError.ordinal()]++; } addDate(argument, config, cformat); addElement(writer, argument, check, cformat); } catch (Exception e) { Element cformat = fillInformation(argument, check, "format", "status", "Error " + e.toString()); addDate(argument, config, cformat); finalResult.values[AllTestsItems.SystemError.ordinal()]++; } } // Show format if (showFormat && config.droidHandler != null) { Element showformat = Commands.showFormat(sfile, smime, sformat, fic, config, argument); if (showformat.selectSingleNode(".[@status='ok']") != null) { finalResult.values[AllTestsItems.ShowSuccess.ordinal()]++; } else if (showformat.selectSingleNode(".[@status='warning']") != null) { finalResult.values[AllTestsItems.ShowWarning.ordinal()]++; finalResult.values[AllTestsItems.GlobalWarning.ordinal()]++; } else { finalResult.values[AllTestsItems.ShowError.ordinal()]++; finalResult.values[AllTestsItems.GlobalError.ordinal()]++; } addDate(argument, config, showformat); addElement(writer, argument, check, showformat); } } addDate(argument, config, result); root = finalizeOneCheck(argument, finalResult, current_file, number); if (root != null) { result = root.element("result"); } if (task != null) { float value = ((float) currank) / (float) nodes.size(); value *= 100; task.setProgressExternal((int) value); } } } document = null; } catch (DocumentException e1) { Element result = fillInformation(argument, root, "result", "parsererror", StaticValues.LBL.error_error.get() + " " + e1 + " - " + StaticValues.LBL.error_parser.get() + " (" + SAXReader.class.getName() + ")"); addDate(argument, config, result); finalResult.values[AllTestsItems.SystemError.ordinal()]++; } catch (UnsupportedEncodingException e1) { Element result = fillInformation(argument, root, "result", "parsererror", StaticValues.LBL.error_error.get() + " " + e1 + " - " + StaticValues.LBL.error_parser.get() + " (" + XMLWriter.class.getName() + ")"); addDate(argument, config, result); finalResult.values[AllTestsItems.SystemError.ordinal()]++; } finalizeAllCheck(argument, finalResult); return finalResult; }
From source file:fr.isima.ponge.wsprotocol.xml.XmlIOManager.java
License:Open Source License
/** * Reads extra properties.//from w w w. j a va2 s . c o m * * @param keeper The object having extra properties. * @param rootNode The XML node to gather the properties from. */ protected void readExtraProperties(ExtraPropertiesKeeper keeper, Node rootNode) { for (Object o : rootNode.selectNodes("extra-property")) { Node node = (Node) o; String className = node.valueOf("@type"); if (className == null) { className = String.class.getName(); } ExtraPropertyHandler handler = getExtraPropertyHandler(className); if (handler != null) { handler.readExtraProperty((Element) node, keeper); } } }