List of usage examples for java.io PrintWriter write
public void write(String s)
From source file:nersc.greenseas.portlet.GreenseasPortlet.java
@Override public void serveResource(ResourceRequest resourceRequest, ResourceResponse resourceResponse) throws IOException, PortletException { System.out.println("Calling serveResource"); resourceResponse.setContentType("text/javascript"); String uri = resourceRequest.getParameter("fileID"); String requestType = resourceRequest.getParameter("requestType"); System.out.println("requestType:'" + requestType + "'"); String opendapDataURL = resourceRequest.getParameter("opendapDataURL"); if (requestType != null) { if (requestType.equals("serveNetCDFFile")) { String location = resourceRequest.getParameter("fileID"); if (location != null) { String[] folders = { "content", "gsadbc", "createdFiles" }; String filePath = createDirectory(System.getProperty("catalina.base"), folders); for (int i = 0; i < location.length(); i++) { char c = uri.charAt(i); if (c < '0' || (c > '9' && c < 'A') || (c > 'Z' && c < 'a') || c > 'z') throw new InvalidFileNameException( "Invalid file name (illegal character:'" + c + "'):" + uri); }/* w w w . j av a 2 s . c o m*/ String fileExtension = ".nc"; location = filePath + location + fileExtension; resourceResponse.setContentType("application/octet-stream"); resourceResponse.setProperty("Content-Disposition", "attachment;filename=\"Greenseas_Downloaded_Parameters.nc\""); OutputStream out = resourceResponse.getPortletOutputStream(); // Content-Type: application/octet-stream // Content-Disposition: attachment;filename=\"filename.xxx\" InputStream in = null; try { in = new FileInputStream(new File(location)); if (in != null) { byte[] buffer = new byte[4096]; int len; while ((len = in.read(buffer)) != -1) { out.write(buffer, 0, len); } out.flush(); System.out.println("Wrote nc file to outputstream"); } } catch (Exception e) { // TODO: handle exception } finally { if (in != null) in.close(); if (out != null) out.close(); } } return; } if (uri != null || opendapDataURL != null) { if (opendapDataURL == null) { String[] folders = { "content", "gsadbc", "uploadedFiles" }; String filePath = createDirectory(System.getProperty("catalina.base"), folders); for (int i = 0; i < uri.length(); i++) { char c = uri.charAt(i); if (c < '0' || (c > '9' && c < 'A') || (c > 'Z' && c < 'a') || c > 'z') throw new InvalidFileNameException( "Invalid file name (illegal character:'" + c + "'):" + uri); } String fileExtension = ".nc"; uri = filePath + uri + fileExtension; } else { uri = opendapDataURL; } if (requestType.startsWith("getDataValuesOf:")) { System.out.println("requestType is getDataValuesOf:"); Map<String, String[]> parameterMap = resourceRequest.getParameterMap(); Map<Integer, Map<String, Double>> values = NetCDFReader.getDatavaluesFromNetCDFFile(uri, parameterMap); if (values == null) return; JSONObject jsonObject = new JSONObject(values); // System.out.println("Returning with jsonObject:"); // System.out.println(jsonObject.toJSONString()); PrintWriter writer = resourceResponse.getWriter(); writer.write(jsonObject.toString()); return; } else if (requestType.equals("getLayersFromNetCDFFile")) { System.out.println("requestType is getLayersFromNetCDFFile:"); System.out.println("opendapDataURL:" + opendapDataURL); System.out.println("uri:" + uri); Map<String, String> values = NetCDFReader.getLayersFromRaster(uri); if (values == null) { System.out.println("No values found!"); return; } JSONObject jsonObject = new JSONObject(values); System.out.println("Returning with jsonObject:"); System.out.println(jsonObject.toJSONString()); PrintWriter writer = resourceResponse.getWriter(); writer.write(jsonObject.toString()); return; } else if (requestType.equals("getMetaDimensions")) { System.out.println("getMetaDimensions:" + uri); String parameter = resourceRequest.getParameter("rasterParameter"); if (parameter == null) return; Map<String, Map<String, String>> values = NetCDFReader.getDimensionsFromRasterParameter(uri, parameter); if (values == null) return; JSONObject jsonObject = new JSONObject(values); System.out.println("Returning with jsonObject:"); System.out.println(jsonObject.toJSONString()); PrintWriter writer = resourceResponse.getWriter(); writer.write(jsonObject.toString()); return; } else if (requestType.equals("loadFileFromID")) { //TODO: fix security hole System.out.println(uri); JSONObject jsonObject = new JSONObject(); File f = new File(uri); boolean exists = f.exists(); // sleep for 1 seconds to mitigate brute force attacks try { Thread.sleep(1000); } catch (InterruptedException e) { } jsonObject.put("fileIDExists", exists); PrintWriter writer = resourceResponse.getWriter(); writer.write(jsonObject.toString()); return; } } if (requestType.equals("getLonghurstPolygon")) { Map<String, String> values = new HashMap<String, String>(); String region = resourceRequest.getParameter("longhurstRegion"); System.out.println("getLonghurstPolygon:" + region); String polygon = DatabaseProperties.getLonghurstPolygon(region); values.put(region, polygon); JSONObject jsonObject = new JSONObject(values); System.out.println("Returning with polygon!=null:" + (polygon != null)); PrintWriter writer = resourceResponse.getWriter(); writer.write(jsonObject.toString()); return; } else if (requestType.equals("createNetCDFUsingH.1")) { JSONParser parser = new JSONParser(); JSONArray jsonA = null; JSONObject jsonO = null; int numberOfFeatures = 0; try { jsonA = (JSONArray) parser.parse(resourceRequest.getParameter("data")); String variablesString = resourceRequest.getParameter("variables"); numberOfFeatures = Integer.parseInt(resourceRequest.getParameter("numberOfFeatures")); System.out.println(variablesString); jsonO = (JSONObject) parser.parse(variablesString); } catch (ParseException e) { } String[] folders = { "content", "gsadbc", "createdFiles" }; String filePath = createDirectory(System.getProperty("catalina.base"), folders); String fileID = NetCDFWriter.createNetCDF(jsonA, jsonO, numberOfFeatures, filePath); Map<String, String> values = new HashMap<String, String>(); values.put("fileID", fileID); JSONObject jsonObject = new JSONObject(values); /*resourceResponse.setContentType("application/x-netcdf"); resourceResponse.addProperty(HttpHeaders.CACHE_CONTROL, "max-age=3600, must-revalidate"); OutputStream out = resourceResponse.getPortletOutputStream(); InputStream in = new FileInputStream(new File(location)); byte[] buffer = new byte[4096]; int len; while ((len = in.read(buffer)) != -1) { out.write(buffer, 0, len); } out.flush(); in.close(); out.close();*/ System.out.println("Returning with fileID" + fileID); PrintWriter writer = resourceResponse.getWriter(); writer.write(jsonObject.toString()); return; } else if (requestType.equals("getLonghurstPolygon")) { Map<String, String> values = new HashMap<String, String>(); String region = resourceRequest.getParameter("longhurstRegion"); System.out.println("getLonghurstPolygon:" + region); String polygon = DatabaseProperties.getLonghurstPolygon(region); values.put(region, polygon); JSONObject jsonObject = new JSONObject(values); System.out.println("Returning with polygon!=null:" + (polygon != null)); PrintWriter writer = resourceResponse.getWriter(); writer.write(jsonObject.toString()); return; } else if (requestType.equals("updateTreeWithInventoryNumbers")) { String urlS = resourceRequest.getParameter("url"); String region = resourceRequest.getParameter("gsadbcRegionFilterPlaceHolder"); if (region != null) { region = region.substring(51, region.length() - 13); } JSONParser parser = new JSONParser(); JSONObject jsonO = null; try { jsonO = (JSONObject) parser.parse(resourceRequest.getParameter("data")); } catch (ParseException e) { } String charset = "UTF-8"; int numberOfThreads = 4; Set<?> entrySet = jsonO.keySet(); ArrayList<Map<String, String>> responseMaps = new ArrayList<Map<String, String>>(); ArrayList<Map<String, String>> requestMaps = new ArrayList<Map<String, String>>(); for (int i = 0; i < numberOfThreads; i++) { responseMaps.add(new HashMap<String, String>()); requestMaps.add(new HashMap<String, String>()); } int thredd = 0; for (Object o : entrySet) { String key = (String) o; String request = (String) jsonO.get(key); requestMaps.get(thredd).put(key, request); thredd = (thredd + 1) % numberOfThreads; } ArrayList<GetNumberOfFeatures> threadds = new ArrayList<GetNumberOfFeatures>(); for (int i = 0; i < numberOfThreads; i++) { GetNumberOfFeatures runnable = new GetNumberOfFeatures(responseMaps.get(i), requestMaps.get(i), charset, urlS, i, region); Thread thread = new Thread(runnable); thread.start(); threadds.add(runnable); } while (true) { try { Thread.sleep(2000); } catch (InterruptedException e) { e.printStackTrace(); } boolean done = true; for (int i = 0; i < numberOfThreads; i++) { if (!threadds.get(i).done) { done = false; break; } } if (done) break; } Map<String, String> responseMap = new HashMap<String, String>(); for (int i = 0; i < numberOfThreads; i++) { responseMap.putAll(responseMaps.get(i)); } JSONObject jsonObject = new JSONObject(responseMap); PrintWriter writer = resourceResponse.getWriter(); writer.write(jsonObject.toString()); return; } } else { } }
From source file:com.globalsight.connector.blaise.BlaiseCreateJobHandler.java
@ActionHandler(action = "uploadAttachment", formClass = "") public void uploadAttachment(HttpServletRequest request, HttpServletResponse response, Object form) throws Exception { FileUploader uploader = new FileUploader(); File file = uploader.upload(request); getSessionManager(request).setAttribute("uploadAttachment", file.getAbsolutePath()); PrintWriter writer = response.getWriter(); writer.write("<script type='text/javascript'>window.parent.addAttachment(' ')</script>;"); pageReturn();//from w ww .ja v a2s .com }
From source file:com.cognifide.aet.rest.ConfigsServlet.java
/*** * Returns JSON representation of Suite based on correlationId or suite name. * If suite name is provided, then newest version of JSON is returned. * * @param req//from w ww . j a v a 2 s .c o m * @param resp */ @Override protected void doGet(HttpServletRequest req, HttpServletResponse resp) { LOGGER.debug("GET, req: '{}'", req); PrintWriter responseWriter = retrieveResponseWriter(req, resp); if (responseWriter != null) { resp.setContentType("application/json"); String configType = StringUtils.substringAfter(req.getRequestURI(), Helper.getConfigsPath()) .replace(Helper.PATH_SEPARATOR, ""); String reportDomain = reportConfigurationManager.getReportDomain(); if (COMMUNICATION_SETTINGS_PARAM.equals(configType)) { JmsEndpointConfig jmsEndpointConfig = jmsConnection.getEndpointConfig(); CommunicationSettings communicationSettings = new CommunicationSettings(jmsEndpointConfig, reportDomain); responseWriter.write(new Gson().toJson(communicationSettings)); } else if (LIST_PARAM.equals(configType)) { resp.setContentType("text/html; charset=utf-8"); resp.setHeader("User-Agent", "Mozilla/5.0 (Windows NT 6.3; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/49.0.2623.112 Safari/537.36"); responseWriter.write(new SuitesListProvider(metadataDAO, reportDomain).listSuites()); } else if (LOCKS_PARAM.equals(configType)) { responseWriter.write(getLocks()); } else { resp.setStatus(HttpURLConnection.HTTP_BAD_REQUEST); responseWriter.write("Unable to get given config."); } } else { resp.setStatus(HttpServletResponse.SC_INTERNAL_SERVER_ERROR); } flushResponseBuffer(req, resp); }
From source file:edu.vt.vbi.patric.portlets.GenomeFinder.java
@SuppressWarnings("unchecked") public void serveResource(ResourceRequest request, ResourceResponse response) throws PortletException, IOException { String sraction = request.getParameter("sraction"); if (sraction != null) { if (sraction.equals("save_params")) { Map<String, String> key = new HashMap<>(); String genomeId = request.getParameter("genomeId"); String taxonId = request.getParameter("taxonId"); String cType = request.getParameter("cType"); String cId = request.getParameter("cId"); if (cType != null && cId != null && cType.equals("taxon") && !cId.equals("")) { taxonId = cId;//w w w. j av a2 s.c om } String keyword = request.getParameter("keyword"); String state = request.getParameter("state"); String exact_search_term = request.getParameter("exact_search_term"); String search_on = request.getParameter("search_on"); if (genomeId != null && !genomeId.equals("")) { key.put("genomeId", genomeId); } if (taxonId != null && !taxonId.equals("")) { key.put("taxonId", taxonId); } if (keyword != null) { key.put("keyword", keyword.trim()); } if (state != null) { key.put("state", state); } if (exact_search_term != null) { key.put("exact_search_term", exact_search_term); } if (search_on != null) { key.put("search_on", search_on); } if (!key.containsKey("genomeId") && cType != null && cType.equals("genome") && cId != null && !cId.equals("")) { key.put("genomeId", cId); } if (!key.containsKey("taxonId") && cType != null && cType.equals("taxon") && cId != null && !cId.equals("")) { key.put("taxonId", cId); } long pk = (new Random()).nextLong(); SessionHandler.getInstance().set(SessionHandler.PREFIX + pk, jsonWriter.writeValueAsString(key)); PrintWriter writer = response.getWriter(); writer.write("" + pk); writer.close(); } else if (sraction.equals("get_params")) { String ret = ""; String pk = request.getParameter("pk"); String json = SessionHandler.getInstance().get(SessionHandler.PREFIX + pk); if (json != null) { Map<String, String> key = jsonReader.readValue(json); ret = key.get("keyword"); } PrintWriter writer = response.getWriter(); writer.write("" + ret); writer.close(); } } else { String need = request.getParameter("need"); JSONObject jsonResult = new JSONObject(); switch (need) { case "0": { // Getting Genome List String pk = request.getParameter("pk"); Map data = processGenomeTab(request); Map<String, String> key = (Map) data.get("key"); int numFound = (Integer) data.get("numFound"); List<Genome> records = (List<Genome>) data.get("genomes"); JSONArray docs = new JSONArray(); for (Genome item : records) { docs.add(item.toJSONObject()); } if (data.containsKey("facets")) { JSONObject facets = FacetHelper.formatFacetTree((Map) data.get("facets")); key.put("facets", facets.toJSONString()); SessionHandler.getInstance().set(SessionHandler.PREFIX + pk, jsonWriter.writeValueAsString(key)); } jsonResult.put("results", docs); jsonResult.put("total", numFound); response.setContentType("application/json"); PrintWriter writer = response.getWriter(); jsonResult.writeJSONString(writer); writer.close(); break; } case "1": { // getting Genome Sequence List Map data = processSequenceTab(request); int numFound = (Integer) data.get("numFound"); List<GenomeSequence> sequences = (List<GenomeSequence>) data.get("sequences"); JSONArray docs = new JSONArray(); for (GenomeSequence item : sequences) { docs.add(item.toJSONObject()); } jsonResult.put("results", docs); jsonResult.put("total", numFound); response.setContentType("application/json"); PrintWriter writer = response.getWriter(); jsonResult.writeJSONString(writer); writer.close(); break; } case "tree": { String pk = request.getParameter("pk"); String state; Map<String, String> key = jsonReader .readValue(SessionHandler.getInstance().get(SessionHandler.PREFIX + pk)); if (key.containsKey("state")) { state = key.get("state"); } else { state = request.getParameter("state"); } key.put("state", state); SessionHandler.getInstance().set(SessionHandler.PREFIX + pk, jsonWriter.writeValueAsString(key)); JSONArray tree = new JSONArray(); try { if (key.containsKey("facets") && !key.get("facets").isEmpty()) { JSONObject facet_fields = (JSONObject) (new JSONParser()).parse(key.get("facets")); DataApiHandler dataApi = new DataApiHandler(request); tree = FacetHelper.processStateAndTree(dataApi, SolrCore.GENOME, key, need, facet_fields, key.get("facet"), state, key.get("join"), 4); } } catch (ParseException e) { LOGGER.error(e.getMessage(), e); } response.setContentType("application/json"); PrintWriter writer = response.getWriter(); tree.writeJSONString(writer); writer.close(); break; } case "tree_for_taxon": { // This is called by Taxon Overview page to faceted summary of genome under a specific taxa. String facet = request.getParameter("facet"); String keyword = request.getParameter("keyword"); Map<String, String> key = new HashMap<>(); key.put("keyword", keyword); DataApiHandler dataApi = new DataApiHandler(request); SolrQuery query = dataApi.buildSolrQuery(key, null, facet, 0, 0, false); // build solr query LOGGER.debug("tree_for_taxon: [{}] {}", SolrCore.GENOME.getSolrCoreName(), query.toString()); String apiResponse = dataApi.solrQuery(SolrCore.GENOME, query); Map resp = jsonReader.readValue(apiResponse); JSONObject facet_fields = FacetHelper.formatFacetTree((Map) resp.get("facet_counts")); JSONArray tree = FacetHelper.processStateAndTree(dataApi, SolrCore.GENOME, key, need, facet_fields, facet, "", null, 4); response.setContentType("application/json"); PrintWriter writer = response.getWriter(); tree.writeJSONString(writer); writer.close(); break; } case "getGenome": { // This is called by Genome Overview page to display genome metadata. DataApiHandler dataApi = new DataApiHandler(request); Genome genome = dataApi.getGenome(request.getParameter("id")); response.setContentType("application/json"); PrintWriter writer = response.getWriter(); if (genome != null) { genome.toJSONObject().writeJSONString(writer); } writer.close(); break; } case "download": { List<String> tableHeader = new ArrayList<>(); List<String> tableField = new ArrayList<>(); JSONArray tableSource = new JSONArray(); String fileName = "GenomeFinder"; String fileFormat = request.getParameter("fileformat"); // String _tablesource = request.getParameter("tablesource"); String aT = request.getParameter("aT"); switch (aT) { case "0": { // genome Map data = processGenomeTab(request); List<Genome> genomes = (List<Genome>) data.get("genomes"); for (Genome genome : genomes) { tableSource.add(genome.toJSONObject()); } tableHeader.addAll(DownloadHelper.getHeaderForGenomes()); tableField.addAll(DownloadHelper.getFieldsForGenomes()); break; } case "1": { // sequence Map data = processSequenceTab(request); List<GenomeSequence> sequences = (List<GenomeSequence>) data.get("sequences"); for (GenomeSequence sequence : sequences) { tableSource.add(sequence.toJSONObject()); } tableHeader.addAll(DownloadHelper.getHeaderForGenomeSequence()); tableField.addAll(DownloadHelper.getFieldsForGenomeSequence()); break; } } ExcelHelper excel = new ExcelHelper("xssf", tableHeader, tableField, tableSource); excel.buildSpreadsheet(); if (fileFormat.equalsIgnoreCase("xlsx")) { response.setContentType("application/octetstream"); response.addProperty("Content-Disposition", "attachment; filename=\"" + fileName + "." + fileFormat + "\""); excel.writeSpreadsheettoBrowser(response.getPortletOutputStream()); } else if (fileFormat.equalsIgnoreCase("txt")) { response.setContentType("application/octetstream"); response.addProperty("Content-Disposition", "attachment; filename=\"" + fileName + "." + fileFormat + "\""); response.getPortletOutputStream().write(excel.writeToTextFile().getBytes()); } } } } }
From source file:edu.vt.vbi.patric.portlets.PathwayFinder.java
@SuppressWarnings("unchecked") public void serveResource(ResourceRequest request, ResourceResponse response) throws PortletException, IOException { String sraction = request.getParameter("sraction"); if (sraction != null && sraction.equals("save_params")) { String search_on = request.getParameter("search_on"); String keyword = request.getParameter("keyword"); String taxonId = request.getParameter("taxonId"); String algorithm = request.getParameter("algorithm"); String genomeId = request.getParameter("genomeId"); String feature_id = request.getParameter("feature_id"); Map<String, String> key = new HashMap<>(); if (search_on != null) { key.put("search_on", search_on.trim()); if (search_on.equalsIgnoreCase("Map_ID")) { key.put("map", keyword.trim()); } else if (search_on.equalsIgnoreCase("Ec_Number")) { key.put("ec_number", keyword.trim()); } else if (search_on.equalsIgnoreCase("Keyword")) { key.put("keyword", keyword.trim()); }/*ww w . j a va2s . c o m*/ } if (taxonId != null && !taxonId.equals("")) { key.put("taxonId", taxonId); } if (genomeId != null && !genomeId.equals("")) { key.put("genomeId", genomeId); } if (algorithm != null && !algorithm.equals("")) { key.put("algorithm", algorithm); } if (feature_id != null && !feature_id.equals("")) { key.put("feature_id", feature_id); } long pk = (new Random()).nextLong(); SessionHandler.getInstance().set(SessionHandler.PREFIX + pk, jsonWriter.writeValueAsString(key)); PrintWriter writer = response.getWriter(); writer.write("" + pk); writer.close(); } else { String need = request.getParameter("need"); String pk = request.getParameter("pk"); Map<String, String> key = null; if (pk != null && !pk.isEmpty()) { key = jsonReader.readValue(SessionHandler.getInstance().get(SessionHandler.PREFIX + pk)); } DataApiHandler dataApi = new DataApiHandler(request); switch (need) { case "0": JSONObject jsonResult = processPathwayTab(dataApi, key.get("map"), key.get("ec_number"), key.get("algorithm"), key.get("taxonId"), key.get("genomeId"), key.get("keyword")); response.setContentType("application/json"); jsonResult.writeJSONString(response.getWriter()); break; case "1": jsonResult = processEcNumberTab(dataApi, key.get("map"), key.get("ec_number"), key.get("algorithm"), key.get("taxonId"), key.get("genomeId"), key.get("keyword")); response.setContentType("application/json"); jsonResult.writeJSONString(response.getWriter()); break; case "2": jsonResult = processGeneTab(dataApi, key.get("map"), key.get("ec_number"), key.get("algorithm"), key.get("taxonId"), key.get("genomeId"), key.get("keyword")); response.setContentType("application/json"); jsonResult.writeJSONString(response.getWriter()); break; case "download": processDownload(request, response); break; case "downloadMapFeatureTable": processDownloadMapFeatureTable(request, response); break; } } }
From source file:gr.demokritos.iit.cru.creativity.reasoning.diagrammatic.DiagrammaticComputationalTools.java
public HashSet<String> Graphs(JSONArray triples1, JSONArray triples2) throws FileNotFoundException, UnsupportedEncodingException, URISyntaxException, IOException, ParserConfigurationException, SAXException, XPathExpressionException, SQLException { // JSON a=new JSON(); /*/*from w w w. j a v a 2 s .c o m*/ JSONArray users = new JSONArray(); JSONObject obj1 = new JSONObject(); obj1.put("c1", "rambo"); obj1.put("rel", "likes"); obj1.put("c2", "mambo"); users.add(obj1); JSONObject obj2 = new JSONObject(); obj2.put("c1", "rambo"); obj2.put("rel", "likes"); obj2.put("c2", "mambo"); users.add(obj2); Object[] m = users.toArray();*/ String filenameSource = "C:\\Users\\George\\Desktop\\projects\\diagrammatic\\triples1.rdf";// + System.currentTimeMillis() + PrintWriter writer = new PrintWriter(filenameSource, "UTF-8"); writer.write("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" + "<rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\"\n" + " xmlns=\"http://c2learn.eu/onto1#\"\n"///http://www.semagrow.eu/schemas/family# + "xmlns:rdfs=\"http://www.w3.org/2000/01/rdf-schema#\"\n" + " xmlns:owl=\"http://www.w3.org/2002/07/owl#\">\n" + "\n" + "<owl:Ontology rdf:about=\"\">\n" + "</owl:Ontology>\n" + "\n"); for (Object triple : triples1) { // System.out.println(triple.toString()); JSONObject jtriple = (JSONObject) triple; String concept = jtriple.get("c1").toString().toLowerCase(); String relation = jtriple.get("rel").toString().toLowerCase(); String subject = jtriple.get("c2").toString().toLowerCase(); // writer.write(" <owl:Class rdf:about=" + concept + ">\n" // + "</owl:Class>\n"); if (relation.equalsIgnoreCase("isA")) { writer.write("<owl:Class rdf:ID=\"" + concept + "\">\n"); writer.write("<rdfs:label>" + concept + "</rdfs:label>\n"); writer.write("<owl:subclassof rdf:resource=\"#" + subject + "\"/>\n"); writer.write("</owl:Class>\n"); } /*else { writer.write("<owl:ObjectProperty rdf:ID=\"" + relation + "\">\n"); writer.write("<rdfs:range rdf:resource=\"#" + subject + "\"/>\n"); writer.write("<rdfs:domain rdf:resource=\"#" + concept + "\"/>\n"); writer.write("<rdfs:label>" + relation + "</rdfs:label>\n"); writer.write("</owl:ObjectProperty>\n"); }*/ writer.write("\n"); } writer.write("</rdf:RDF>"); writer.close(); String filenameTarget = "C:\\Users\\George\\Desktop\\projects\\diagrammatic\\triples2.rdf";////" + System.currentTimeMillis() + " writer = new PrintWriter(filenameTarget, "UTF-8"); writer.write("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" + "<rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\"\n" + " xmlns=\"http://c2learn.eu/onto2#\"\n"//http://www.semagrow.eu/schemas/family# + "xmlns:rdfs=\"http://www.w3.org/2000/01/rdf-schema#\"\n" + " xmlns:owl=\"http://www.w3.org/2002/07/owl#\">\n" + "\n" + "<owl:Ontology rdf:about=\"\">\n" + "</owl:Ontology>\n" + "\n"); for (Object triple : triples1) { // System.out.println(triple.toString()); JSONObject jtriple = (JSONObject) triple; String concept = jtriple.get("c1").toString().toLowerCase(); String relation = jtriple.get("rel").toString().toLowerCase(); String subject = jtriple.get("c2").toString().toLowerCase(); // writer.write(" <owl:Class rdf:about=" + concept + ">\n" // + "</owl:Class>\n"); if (relation.equalsIgnoreCase("isA")) { writer.write("<owl:Class rdf:ID=\"" + concept + "\">\n"); writer.write("<rdfs:label>" + concept + "</rdfs:label>\n"); writer.write("<owl:subclassof rdf:resource=\"#" + subject + "\"/>\n"); writer.write("</owl:Class>\n"); } /*else { writer.write("<owl:ObjectProperty rdf:ID=\"" + relation + "\">\n"); writer.write("<rdfs:range rdf:resource=\"#" + subject + "\"/>\n"); writer.write("<rdfs:domain rdf:resource=\"#" + concept + "\"/>\n"); writer.write("<rdfs:label>" + relation + "</rdfs:label>\n"); writer.write("</owl:ObjectProperty>\n"); }*/ writer.write("\n"); } writer.write("</rdf:RDF>"); writer.close(); String fileSeparator = "\\"; //String oaeiDirectorySubsConceptsOnly = "C:/Users/antonis/Documents/NetBeansProjects/Synthesis/benchmarks"; // String oaeiDirectoryEqualsConceptsOnly = "C:/Users/antonis/Documents/NetBeansProjects/Synthesis/benchmarks"; //String onto1 = "http://oaei.ontologymatching.org/2011/benchmarks/101/onto.rdf"; //String onto2 = "http://oaei.ontologymatching.org/2011/benchmarks/248/onto.rdf"; String onto1 = filenameSource;// oaeiDirectoryEqualsConceptsOnly + fileSeparator + source + fileSeparator + "onto.rdf";; String onto2 = filenameTarget;// oaeiDirectoryEqualsConceptsOnly + fileSeparator + target + fileSeparator + "onto.rdf";;; onto1 = new File(onto1).toURI().toString(); onto2 = new File(onto2).toURI().toString(); String outputPath = System.getProperty("user.dir") + fileSeparator; // System.out.println(outputPath + "refalign.rdf"); /* ResultsStorage storePrecisionCSR = new ResultsStorage("precisionCSR.txt"); ResultsStorage storeRecalCSR = new ResultsStorage("recallCSR.txt"); ResultsStorage storePrecisionVSM = new ResultsStorage("precisionVSM.txt"); ResultsStorage storeRecalVSM = new ResultsStorage("recallVSM.txt"); ResultsStorage storePrecisionCSRFactor = new ResultsStorage("precisionCSRFactor.txt"); ResultsStorage storeRecalCSRFactor = new ResultsStorage("recallCSRFactor.txt"); ResultsStorage storePrecisionVSMFactor = new ResultsStorage("precisionVSMFactor.txt"); ResultsStorage storeRecalVSMFactor = new ResultsStorage("recallVSMFactor.txt"); ResultsStorage storePrecisionCocluFactor = new ResultsStorage("precisionCocluFactor.txt"); ResultsStorage storeRecalCocluFactor = new ResultsStorage("recallCocluFactor.txt"); ResultsStorage storePrecisionCoclu = new ResultsStorage("precisionCoclu.txt"); ResultsStorage storeRecalCoclu = new ResultsStorage("recallCoclu.txt"); ResultsStorage storeCorrectCSR = new ResultsStorage("correctCSR.txt"); ResultsStorage storeErrorCSR = new ResultsStorage("errorCSR.txt"); ResultsStorage storeCorrectCoclu = new ResultsStorage("correctCoclu.txt"); ResultsStorage storeErrorCoclu = new ResultsStorage("errorCoclu.txt"); ResultsStorage storeCorrectCocluFactor = new ResultsStorage("correctCocluFactor.txt"); ResultsStorage storeErrorCocluFactor = new ResultsStorage("errorCocluFactor.txt"); ResultsStorage storeConfuzedEqualsForSubsCoclu = new ResultsStorage("ConfuzedEqualsForSubsCoclu.txt"); ResultsStorage storeConfuzedEqualsForSubsCocluFactor = new ResultsStorage("ConfuzedEqualsForSubsCocluFactor.txt"); ResultsStorage storeCorrectVSM = new ResultsStorage("correctVSM.txt"); ResultsStorage storeErrorVSM = new ResultsStorage("errorVSM.txt"); ResultsStorage storeCorrectCSRFactor = new ResultsStorage("correctCSRFactor.txt"); ResultsStorage storeErrorCSRFactor = new ResultsStorage("errorCSRFactor.txt"); ResultsStorage storeCorrectVSMFactor = new ResultsStorage("correctVSMFactor.txt"); ResultsStorage storeErrorVSMFactor = new ResultsStorage("errorVSMFactor.txt"); ResultsStorage storeConfuzedEqualsForSubsVSM = new ResultsStorage("ConfuzedEqualsForSubsVSM.txt"); ResultsStorage storeConfuzedEqualsForSubsVSMFactor = new ResultsStorage("ConfuzedEqualsForSubsVSMFactor.txt"); ResultsStorage storeConflictsEquals = new ResultsStorage("ConflictsEquals.txt"); ResultsStorage storeConflictsSubs = new ResultsStorage("ConflictsSubs.txt"); ResultsStorage storeMessages = new ResultsStorage("Messages.txt"); ResultsStorage timeDuration = new ResultsStorage("timeDuration.txt"); try { RunCoclouVsmCsrFactorGraphs synthesis = new RunCoclouVsmCsrFactorGraphs(onto1, onto2, outputPath, outputPath + "refalign.rdf", outputPath + "refalign.rdf", false, false, true, true, 1, false, false, 0, 0.3, true, false, "over", "j48", false, false, 10000, false, storePrecisionCSR, storeRecalCSR, storePrecisionVSM, storeRecalVSM, storePrecisionCSRFactor, storeRecalCSRFactor, storePrecisionVSMFactor, storeRecalVSMFactor, storeCorrectCSR, storeErrorCSR, storeCorrectVSM, storeErrorVSM, storeCorrectCSRFactor, storeErrorCSRFactor, storeCorrectVSMFactor, storeErrorVSMFactor, storeConfuzedEqualsForSubsVSM, storeConfuzedEqualsForSubsVSMFactor, storePrecisionCoclu, storeRecalCoclu, storeCorrectCoclu, storeErrorCoclu, storeConfuzedEqualsForSubsCoclu, storePrecisionCocluFactor, storeRecalCocluFactor, storeCorrectCocluFactor, storeErrorCocluFactor, storeConfuzedEqualsForSubsCocluFactor, timeDuration, storeConflictsEquals, storeConflictsSubs, storeMessages, true); synthesis.run(); System.out.println(filenameTarget + " finished..."); } catch (Exception e) { e.printStackTrace(); } storePrecisionCSR.exportToFile(); storeRecalCSR.exportToFile(); storePrecisionVSM.exportToFile(); storeRecalVSM.exportToFile(); storePrecisionCSRFactor.exportToFile(); storeRecalCSRFactor.exportToFile(); storePrecisionVSMFactor.exportToFile(); storeRecalVSMFactor.exportToFile(); storeCorrectCSR.exportToFile(); storeErrorCSR.exportToFile(); storeCorrectVSM.exportToFile(); storeErrorVSM.exportToFile(); storeCorrectCSRFactor.exportToFile(); storeErrorCSRFactor.exportToFile(); storeCorrectVSMFactor.exportToFile(); storeErrorVSMFactor.exportToFile(); storeConfuzedEqualsForSubsVSM.exportToFile(); storeConfuzedEqualsForSubsVSMFactor.exportToFile(); storePrecisionCoclu.exportToFile(); storeRecalCoclu.exportToFile(); storeCorrectCoclu.exportToFile(); storeErrorCoclu.exportToFile(); storeConfuzedEqualsForSubsCoclu.exportToFile(); storePrecisionCocluFactor.exportToFile(); storeRecalCocluFactor.exportToFile(); storeCorrectCocluFactor.exportToFile(); storeErrorCocluFactor.exportToFile(); storeConfuzedEqualsForSubsCocluFactor.exportToFile(); timeDuration.exportToFile(); storeConflictsEquals.exportToFile(); storeConflictsSubs.exportToFile(); storeMessages.exportToFile(); storePrecisionCSR.close(); storeRecalCSR.close(); storePrecisionVSM.close(); storeRecalVSM.close(); storePrecisionCSRFactor.close(); storeRecalCSRFactor.close(); storePrecisionVSMFactor.close(); storeRecalVSMFactor.close(); storeCorrectCSR.close(); storeErrorCSR.close(); storeCorrectVSM.close(); storeErrorVSM.close(); storeCorrectCSRFactor.close(); storeErrorCSRFactor.close(); storeCorrectVSMFactor.close(); storeErrorVSMFactor.close(); storeConfuzedEqualsForSubsVSM.close(); storeConfuzedEqualsForSubsVSMFactor.close(); storePrecisionCoclu.close(); storeRecalCoclu.close(); storeCorrectCoclu.close(); storeErrorCoclu.close(); storeConfuzedEqualsForSubsCoclu.close(); storePrecisionCocluFactor.close(); storeRecalCocluFactor.close(); storeCorrectCocluFactor.close(); storeErrorCocluFactor.close(); storeConfuzedEqualsForSubsCocluFactor.close(); timeDuration.close(); storeConflictsEquals.close(); storeConflictsSubs.close(); storeMessages.close();*/ DocumentBuilderFactory builderFactory = DocumentBuilderFactory.newInstance(); DocumentBuilder builder = null; Document document = null; try { builder = builderFactory.newDocumentBuilder(); document = (Document) builder.parse(new FileInputStream(outputPath + "alignment.rdf")); } catch (ParserConfigurationException e) { e.printStackTrace(); } document.getDocumentElement().normalize(); System.out.println("Root element :" + document.getDocumentElement().getNodeName()); NodeList nl = document.getElementsByTagName("Cell"); System.out.println("----------------------------"); for (int temp = 0; temp < nl.getLength(); temp++) { Node nNode = nl.item(temp); System.out.println("\nCurrent Element :" + nNode.getNodeName()); if (nNode.getNodeType() == Node.ELEMENT_NODE) { Element eElement = (Element) nNode; Element ent1 = (Element) eElement.getElementsByTagName("entity1").item(0); Element ent2 = (Element) eElement.getElementsByTagName("entity2").item(0); System.out.println(ent1.getAttribute("rdf:resource").split("#")[1]); System.out.println(ent2.getAttribute("rdf:resource").split("#")[1]); // System.out.println("Staff id : " + eElement.getAttribute("rdf:resource")); System.out.println( "relation : " + eElement.getElementsByTagName("relation").item(0).getTextContent()); System.out .println("measure : " + eElement.getElementsByTagName("measure").item(0).getTextContent()); if (eElement.getElementsByTagName("relation").item(0).getTextContent().equalsIgnoreCase("=")) { Queries q = new Queries(this.conn); q.Insert(ent1.getAttribute("rdf:resource").split("#")[1], ent2.getAttribute("rdf:resource").split("#")[1], eElement.getElementsByTagName("measure").item(0).getTextContent()); } } } // String expression = "//Alignment//Cell"; // XPath xPath = XPathFactory.newInstance().newXPath(); // XPathExpression expr = xPath.compile(expression); // NodeList nl = (NodeList) expr.evaluate(document, XPathConstants.NODESET); // for (Node n : nl) { // System.out.println(n.getNodeName()); // } // Object[] idsNode = node.evaluateXPath("//Alignment/Cell"); //read a string value // Node node = (Node) xPath.compile(expression).evaluate(document, XPathConstants.NODE); /* BufferedReader in = new BufferedReader(new FileReader(outputPath + "alignment.rdf")); String line; while ((line = in.readLine()) != null) { }*/ return new HashSet<String>(); }
From source file:net.openkoncept.vroom.VroomController.java
private void processRequestInvoke(HttpServletRequest request, HttpServletResponse response) throws ServletException { String method = request.getParameter(METHOD); String beanClass = request.getParameter(BEAN_CLASS); String var = request.getParameter(VAR); if (var == null || var.trim().length() == 0) { var = beanClass; }/*w w w . java 2s . c om*/ String scope = request.getParameter(SCOPE); if (scope == null || scope.trim().length() == 0) { if (var.equals(beanClass)) { scope = SCOPE_APPLICATION; } else { scope = SCOPE_SESSION; } } Object beanObject; Object object = null; try { Class clazz = Class.forName(beanClass); if (SCOPE_APPLICATION.equals(scope)) { beanObject = appBeanMap.get(var); if (beanObject == null) { beanObject = clazz.newInstance(); appBeanMap.put(var, beanObject); } } else if (SCOPE_SESSION.equals(scope)) { beanObject = request.getSession().getAttribute(var); if (beanObject == null) { beanObject = clazz.newInstance(); request.getSession().setAttribute(var, beanObject); } } else if (SCOPE_REQUEST.equals(scope)) { beanObject = request.getAttribute(var); if (beanObject == null) { beanObject = clazz.newInstance(); request.setAttribute(var, beanObject); } } else { beanObject = clazz.newInstance(); } String output; if ("getProperties".equals(method)) { object = beanObject; } else { Class[] signature = new Class[] { HttpServletRequest.class, HttpServletResponse.class }; Method m; try { m = clazz.getMethod(method, signature); object = m.invoke(beanObject, new Object[] { request, response }); } catch (Exception ex) { try { m = clazz.getMethod(method, null); object = m.invoke(beanObject, null); } catch (Exception ex2) { try { signature = new Class[] { HttpServletRequest.class }; m = clazz.getMethod(method, signature); object = m.invoke(beanObject, new Object[] { request }); } catch (NoSuchMethodException ex3) { throw new ServletException("Invocation Failed for method [" + method + "]", ex); } catch (InvocationTargetException ex3) { throw new ServletException("Invocation Failed for method [" + method + "]", ex); } } } if (object == null) { object = ""; } } JSONObject jo = VroomUtilities.convertObjectToJSONObject(object); jo.put("contextPath", request.getContextPath()); jo.put("sessionId", request.getSession().getId()); jo.put("locale", VroomUtilities.convertObjectToJSONObject(request.getLocale())); output = jo.toString(); String encoding = request.getHeader("response-encoding"); if (encoding == null || encoding.trim().length() == 0) { encoding = request.getCharacterEncoding(); } response.setContentType(JSON_MIME_TYPE); if (encoding != null) { VroomUtilities.safeCall(response, "setCharacterEncoding", new Class[] { String.class }, new Object[] { encoding }); // response.setCharacterEncoding(encoding); } PrintWriter out = null; try { out = response.getWriter(); out.write(output); } catch (IOException e) { throw new ServletException(e); } finally { if (out != null) { out.close(); } } } catch (ClassNotFoundException ex) { throw new ServletException("Invocation Failed for method [" + method + "]", ex); } catch (InstantiationException ex) { throw new ServletException("Invocation Failed for method [" + method + "]", ex); } catch (IllegalAccessException ex) { throw new ServletException("Invocation Failed for method [" + method + "]", ex); } catch (JSONException ex) { throw new ServletException("Invalid JSON Object [" + object + "]", ex); } }
From source file:com.ephesoft.gxt.admin.server.ImportDocumentTypeUploadServlet.java
/** * This API is used to write content in temp file. * /*from ww w . j a v a 2s . co m*/ * @param item {@link FileItem} uploaded file item. * @param filePath {@link String} to create temporary file. * @param printWriter {@link PrintWriter}. * @return {@link File} temporary file. */ private File copyItemContentInFile(final FileItem item, final String filePath, final PrintWriter printWriter) { File tempZipFile = null; OutputStream out = null; InputStream instream = null; try { instream = item.getInputStream(); tempZipFile = new File(filePath); if (tempZipFile.exists()) { tempZipFile.delete(); } out = new FileOutputStream(tempZipFile); final byte buf[] = new byte[1024]; int len; while ((len = instream.read(buf)) > 0) { out.write(buf, 0, len); } } catch (final FileNotFoundException e) { printWriter.write("Unable to create the export folder.Please try again."); } catch (final IOException e) { printWriter.write("Unable to read the file.Please try again."); } finally { if (out != null) { try { out.close(); } catch (final IOException ioe) { log.error("Could not close stream for file." + tempZipFile); } } if (instream != null) { try { instream.close(); } catch (final IOException ioe) { log.error("Could not close stream for file." + filePath); } } } return tempZipFile; }
From source file:au.com.gaiaresources.bdrs.controller.theme.ThemeControllerTest.java
private byte[] createMemoryFile(String content) throws IOException { ByteArrayOutputStream bos = new ByteArrayOutputStream(); PrintWriter writer = new PrintWriter(bos); writer.write(content); writer.flush();/*from w w w . j av a 2s .c om*/ writer.close(); byte[] data = bos.toByteArray(); bos.close(); return data; }
From source file:edu.ku.brc.af.core.db.DBTableIdMgr.java
/** * //from w ww . j av a 2 s . c o m */ public void dumpTablesAsCSV() { boolean checkMM = true; try { PrintWriter pw = new PrintWriter("TablesAndField.csv"); for (DBTableInfo ti : getTables()) { pw.write("\"" + ti.getName() + "\",,\"" + ti.getTitle() + "\",\"" + ti.getDescription() + "\"," + (checkMM ? "Mismatch" : "") + "\n"); for (DBFieldInfo fi : ti.getFields()) { pw.write(",\"" + fi.getName() + "\",\"" + fi.getTitle() + "\",\"" + (StringUtils.isNotEmpty(fi.getDescription()) ? fi.getDescription() : "") + "\",\"" + fi.getType() + "\""); if (checkMM) { if (fi.getColumn().startsWith("Number")) { if (StringUtils.contains(fi.getType(), "Byte") || StringUtils.contains(fi.getType(), "Short") || StringUtils.contains(fi.getType(), "Integer") || StringUtils.contains(fi.getType(), "Long") || StringUtils.contains(fi.getType(), "Float") || StringUtils.contains(fi.getType(), "Double")) { //pw.write(", OK"); } else { pw.write(",*"); } } else if (fi.getColumn().startsWith("Text")) { if (StringUtils.contains(fi.getType(), "String")) { //pw.write(", OK"); } else { pw.write(",*"); } } else if (fi.getColumn().startsWith("Yes")) { if (StringUtils.contains(fi.getType(), "Boolean")) { //pw.write(", OK"); } else { pw.write(",*"); } } else if (fi.getColumn().startsWith("Remark")) { if (StringUtils.contains(fi.getType(), "text")) { //pw.write(", OK"); } else { pw.write(",*"); } } } pw.write("\n"); } for (DBRelationshipInfo ri : ti.getRelationships()) { pw.write(",\"" + ri.getName() + "\",\"" + ri.getTitle() + "\",\"" + (StringUtils.isNotEmpty(ri.getDescription()) ? ri.getDescription() : "") + "\",\"" + ri.getType() + "\"\n"); } } pw.close(); } catch (IOException ex) { ex.printStackTrace(); } }