List of usage examples for org.w3c.dom Document getChildNodes
public NodeList getChildNodes();
NodeList that contains all children of this node. From source file:plpwr.Task4.java
public Task4() throws Throwable { DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); DocumentBuilder db = dbf.newDocumentBuilder(); File file;// w ww . j a v a2 s. co m try { File[] files = {}; // files = new Task2.FileDialogFluent(Window.getWindow(), "Choose file", FileDialog.LOAD).setVisibleFluent(true).getFiles(); file = files[0]; } catch (Throwable e) { file = new File("book.xml"); } Document document = db.parse(file); // List<Node> nodes = XmlUtil.asList(document.getChildNodes().item(0).getChildNodes()); List<String> header = new ArrayList<>(); Node root = null; for (int i = 0; i < document.getChildNodes().getLength(); ++i) { if (document.getChildNodes().item(i).getNodeName().equals("#text")) continue; root = document.getChildNodes().item(i); } NodeList nodes; nodes = root.getChildNodes(); NodeList firstElement = null; for (int i = 0; i < nodes.getLength(); ++i) { if (nodes.item(i).getNodeName().equals("#text")) continue; firstElement = nodes.item(i).getChildNodes(); } // for (Node node : XmlUtil.asList(document.getChildNodes().item(0).getChildNodes().item(0).getChildNodes())) { // header.add(node.getNodeName()); // } for (int i = 0; i < firstElement.getLength(); ++i) { // System.out.println("ELO: "+firstElement.item(i).getNodeName()); if (nodes.item(i).getNodeName().equals("#text")) continue; Element node = (Element) firstElement.item(i); header.add(node.getNodeName()); } System.out.println("header: " + StringUtils.join(header.iterator(), '\t')); StringBuilder sb = new StringBuilder(); sb.append(StringUtils.join(header.iterator(), ';')); // for (Node node : nodes) { for (int i = 0; i < nodes.getLength(); i++) { // System.out.println(nodes.item(i).getNodeName()); if (nodes.item(i).getNodeName().equals("#text")) continue; Element node = (Element) nodes.item(i); NodeList inNodes = node.getChildNodes(); // for(Node n : XmlUtil.asList(e.getChildNodes())) { List<String> row = new ArrayList<>(); for (int j = 0; j < inNodes.getLength(); j++) { // System.out.println(inNodes.item(j).getNodeName()); if (inNodes.item(j).getNodeType() != Node.ELEMENT_NODE) continue; String content = (inNodes.item(j).getChildNodes().item(0)).getNodeValue(); content = content.replaceAll("\\s+", " "); row.add(content); } System.out.println("\nrow:\t" + StringUtils.join(row.iterator(), '\t')); sb.append(StringUtils.join(row.iterator(), '\t')); } setAns(sb.toString()); }
From source file:psidev.psi.mi.filemakers.xsd.AbstractXsdTreeStruct.java
public void loadSchema(URL schemaUrl) throws FileNotFoundException, IOException { emptySelectionLists();// w w w . j av a2 s. com this.schemaURL = schemaUrl; InputStream in = schemaURL.openStream(); /* test: get keyz/keyref */ try { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); DocumentBuilder parser = factory.newDocumentBuilder(); Document d = parser.parse(in); for (int i = 0; i < d.getChildNodes().getLength(); i++) { getKeys(d.getChildNodes().item(i)); } } catch (ParserConfigurationException e) { JOptionPane.showMessageDialog(new JFrame(), "Cannot load the schema.", "ERROR", JOptionPane.ERROR_MESSAGE); log.error(e); } catch (SAXException e) { JOptionPane.showMessageDialog(new JFrame(), "Cannot load the schema.", "ERROR", JOptionPane.ERROR_MESSAGE); log.error(e); } catch (IOException e) { JOptionPane.showMessageDialog(new JFrame(), "Cannot load the schema.", "ERROR", JOptionPane.ERROR_MESSAGE); log.error(e); } in = schemaURL.openStream(); SchemaReader reader = new SchemaReader(new InputSource(in)); schema = reader.read(); createTree(); Utils.lastVisitedDirectory = schemaURL.getPath(); Utils.lastVisitedSchemaDirectory = schemaURL.getPath(); }
From source file:ru.codeinside.adm.ui.UploadDeployer.java
private boolean hasApiServer(String supportedInterface, JarInputStream jarStream) throws IOException, SAXException, ParserConfigurationException { for (String xmlPath : jarStream.getManifest().getMainAttributes().getValue("Service-Component") .split(",")) { ZipEntry nextZipEntry = jarStream.getNextEntry(); while (nextZipEntry != null && !xmlPath.equals(nextZipEntry.getName())) { nextZipEntry = jarStream.getNextEntry(); }/* www . j a v a2 s .co m*/ Document xmlDoc = readXml(jarStream); Node node = getChildForNlByNames(xmlDoc.getChildNodes(), "component", "service", "provide"); if (node != null) { String interfaceValue = node.getAttributes().getNamedItem("interface").getNodeValue(); if (StringUtils.isNotEmpty(interfaceValue) && supportedInterface.equals(interfaceValue.trim())) { return true; } } } return false; }
From source file:slash.navigation.converter.gui.services.CrossingWays.java
String extractResult(String result) throws IOException { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); DocumentBuilder builder;/*from w ww. j a v a 2 s.c o m*/ try { builder = factory.newDocumentBuilder(); } catch (ParserConfigurationException e) { throw new IOException(e); } Document document; try { document = builder.parse(new InputSource(new StringReader(result))); } catch (SAXException e) { throw new IOException(e); } NodeList nodeList = document.getChildNodes(); if (nodeList.getLength() > 0) { Node node = nodeList.item(0); return node.getTextContent(); } return null; }
From source file:ubic.gemma.core.image.aba.AllenBrainAtlasServiceImpl.java
private Collection<ImageSeries> extractSeries(Document imageSeriesDoc) { NodeList sectionDataSets = imageSeriesDoc.getChildNodes().item(0).getChildNodes().item(0).getChildNodes(); Collection<ImageSeries> series = new LinkedList<>(); for (int i = 0; i < sectionDataSets.getLength(); i++) { Node node = sectionDataSets.item(i); if (node.getNodeName().equals("section-data-set")) { String idText = XMLUtils.extractOneChildText(node, "id"); if (idText == null) { continue; }//from w ww .j a v a 2 s . c o m ImageSeries is = new ImageSeries(Integer.parseInt(idText)); Node images = XMLUtils.extractOneChild(node, "section-images"); if (images == null) { AllenBrainAtlasServiceImpl.log.warn("ABA series " + idText + " did not contain any images."); continue; } is.setImages(this.getImageSeriesImages(images.getChildNodes())); series.add(is); } } return series; }
From source file:ubic.gemma.image.aba.AllenBrainAtlasServiceImpl.java
/** * Given a gene too look for for will return the coressponding abaGene (useful for finding images) * //from w ww . ja v a2 s . c o m * @param givenGene symbol of gene that will be used to search ABA. * @return */ protected AbaGene getGene(String givenGene, boolean correctCase) throws IOException { String gene = givenGene; if (correctCase) { gene = correctCase(gene); } File outputFile = getFile(gene); Document geneDoc = null; try { FileOutputStream out = new FileOutputStream(outputFile); this.getGene(gene, out); out.close(); geneDoc = XMLUtils.openAndParse(new FileInputStream(outputFile)); } catch (ParserConfigurationException pce) { log.warn(pce); return null; } catch (SAXException se) { log.warn(se); } catch (FileNotFoundException fnfe) { return null; } if (geneDoc == null) { return null; } Collection<String> xmlData = XMLUtils.extractTagData(geneDoc, "geneid"); Integer geneId = xmlData.isEmpty() ? null : Integer.parseInt(xmlData.iterator().next()); xmlData = XMLUtils.extractTagData(geneDoc, "genename"); String geneName = xmlData.isEmpty() ? null : xmlData.iterator().next(); xmlData = XMLUtils.extractTagData(geneDoc, "genesymbol"); String geneSymbol = xmlData.isEmpty() ? null : xmlData.iterator().next(); xmlData = XMLUtils.extractTagData(geneDoc, "entrezgeneid"); Integer entrezGeneId = xmlData.isEmpty() ? null : Integer.parseInt(xmlData.iterator().next()); xmlData = XMLUtils.extractTagData(geneDoc, "ncbiaccessionnumber"); String ncbiAccessionNumber = xmlData.isEmpty() ? null : xmlData.iterator().next(); String geneUrl = (geneSymbol == null) ? null : this.getGeneUrl(geneSymbol); if (geneId == null && geneSymbol == null) return null; AbaGene geneData = new AbaGene(geneId, geneSymbol, geneName, entrezGeneId, ncbiAccessionNumber, geneUrl, null); NodeList idList = geneDoc.getChildNodes().item(0).getChildNodes(); // log.debug( "Got " + idList.getLength() ); for (int i = 0; i < idList.getLength(); i++) { Node item = idList.item(i); if (!item.getNodeName().equals("image-series")) continue; NodeList imageSeriesList = item.getChildNodes(); for (int j = 0; j < imageSeriesList.getLength(); j++) { Node imageSeries = imageSeriesList.item(j); NodeList childNodes = imageSeries.getChildNodes(); Integer imageSeriesId = null; String plane = null; for (int m = 0; m < childNodes.getLength(); m++) { Node c = childNodes.item(m); // log.info( c.getNodeName() ); String n = c.getNodeName(); try { if (n.equals("imageseriesid")) { imageSeriesId = Integer.parseInt(XMLUtils.getTextValue((Element) c)); } else if (n.equals("plane")) { plane = XMLUtils.getTextValue((Element) c); } else { // Just skip and check the next one. } } catch (IOException ioe) { log.warn(ioe); } } if (imageSeriesId != null && plane != null) { ImageSeries is = new ImageSeries(imageSeriesId, plane); geneData.addImageSeries(is); log.debug("added image series to gene data"); } else { log.debug("Skipping adding imageSeries to gene cause data missing"); } } } return geneData; }
From source file:ubic.gemma.image.aba.AllenBrainAtlasServiceImpl.java
@Override public Collection<Image> getImageseries(Integer imageseriesId) { File outputFile = getFile("ImageseriesId_" + imageseriesId.toString()); Document imageSeriesDoc = null; try {/* w w w. ja v a2 s .c om*/ FileOutputStream out = new FileOutputStream(outputFile); this.getImageseries(imageseriesId, out); imageSeriesDoc = XMLUtils.openAndParse(new FileInputStream(outputFile)); } catch (Exception e) { log.error(e.getMessage(), e.getCause()); return null; } NodeList idList = imageSeriesDoc.getChildNodes().item(0).getChildNodes(); Collection<Image> results = new HashSet<Image>(); for (int i = 0; i < idList.getLength(); i++) { Node item = idList.item(i); if (!item.getNodeName().equals("images")) continue; NodeList imageList = item.getChildNodes(); for (int j = 0; j < imageList.getLength(); j++) { Node image = imageList.item(j); if (!image.getNodeName().equals("image")) continue; NodeList childNodes = image.getChildNodes(); Integer imageId = null; String displayName = null; Integer position = null; Integer referenceAtlasIndex = null; String thumbnailUrl = null; String zoomifiedNisslUrl = null; String expressionThumbnailUrl = null; String downloadImagePath = null; String downloadExpressionPath = null; for (int m = 0; m < childNodes.getLength(); m++) { Node c = childNodes.item(m); // log.info( c.getNodeName() ); String n = c.getNodeName(); try { if (n.equals("#text")) { continue; // added to make faster as half of comparisions are empty nodes of this type! } else if (n.equals("imageid")) { imageId = Integer.parseInt(XMLUtils.getTextValue((Element) c)); } else if (n.equals("imagedisplayname")) { displayName = XMLUtils.getTextValue((Element) c); } else if (n.equals("position")) { position = Integer.parseInt(XMLUtils.getTextValue((Element) c)); } else if (n.equals("referenceatlasindex")) { referenceAtlasIndex = Integer.parseInt(XMLUtils.getTextValue((Element) c)); } else if (n.equals("thumbnailurl")) { thumbnailUrl = XMLUtils.getTextValue((Element) c); } else if (n.equals("zoomifiednisslurl")) { zoomifiedNisslUrl = XMLUtils.getTextValue((Element) c); } else if (n.equals("expressthumbnailurl")) { expressionThumbnailUrl = XMLUtils.getTextValue((Element) c); } else if (n.equals("downloadImagePath")) { downloadImagePath = XMLUtils.getTextValue((Element) c); } else if (n.equals("downloadExpressionPath")) { downloadExpressionPath = XMLUtils.getTextValue((Element) c); } else { continue; } } catch (IOException ioe) { log.warn(ioe); } } // for loop if (imageId != null && downloadImagePath != null) { Image img = new Image(displayName, imageId, position, referenceAtlasIndex, thumbnailUrl, zoomifiedNisslUrl, expressionThumbnailUrl, downloadImagePath, downloadExpressionPath, 0, 0); results.add(img); } else { log.info( "Skipping adding image to collection cause necessary data missing after parsing image xml"); } } } return results; }