List of usage examples for org.json.simple JSONArray addAll
public boolean addAll(Collection<? extends E> c)
From source file:biomine.bmvis2.pipeline.sources.QueryGraphSource.java
@Override public JSONObject toJSON() { JSONObject ret = new JSONObject(); JSONArray queryArr = new JSONArray(); queryArr.addAll(query); ret.put("query", queryArr); ret.put("neighborhood", new Boolean(neighborhood)); return ret;// www. j a v a 2s . com }
From source file:br.bireme.prvtrm.PreviousTermServlet.java
/** * Processes requests for both HTTP//from w w w . j a v a 2 s . c o m * <code>GET</code> and * <code>POST</code> methods. * * @param request servlet request * @param response servlet response * @throws ServletException if a servlet-specific error occurs * @throws IOException if an I/O error occurs */ protected void processRequest(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { response.setContentType("application/json; charset=UTF-8"); final PrintWriter out = response.getWriter(); try { final String init = request.getParameter("init"); if (init == null) { throw new ServletException("missing 'init' parameter"); } int maxSize = previous.getMaxSize(); String maxTerms = request.getParameter("maxTerms"); if (maxTerms != null) { maxSize = Integer.parseInt(maxTerms); } List<String> fields = previous.getFields(); String fldsParam = request.getParameter("fields"); if (fldsParam != null) { fields = Arrays.asList(fldsParam.split("[,;\\-]")); } final List<String> terms; String direction = request.getParameter("direction"); if ((direction == null) || (direction.compareToIgnoreCase("next") == 0)) { terms = previous.getNextTerms(init, fields, maxSize); direction = "next"; } else { terms = previous.getPreviousTerms(init, fields, maxSize); direction = "previous"; } final JSONObject jobj = new JSONObject(); final JSONArray jlistTerms = new JSONArray(); final JSONArray jlistFields = new JSONArray(); jlistTerms.addAll(terms); jlistFields.addAll(fields); jobj.put("init", init); jobj.put("direction", direction); jobj.put("maxTerms", maxSize); jobj.put("fields", jlistFields); jobj.put("terms", jlistTerms); out.println(jobj.toJSONString()); } finally { out.close(); } }
From source file:com.p000ison.dev.simpleclans2.JSONFlags.java
@Override public String serialize() { if (data.isEmpty()) { return null; }/* ww w . ja v a2 s . co m*/ JSONObject json = new JSONObject(); for (Map.Entry<String, Object> entry : data.entrySet()) { String key = entry.getKey(); Object value = entry.getValue(); if (key == null || value == null) { continue; } if (value instanceof Collection) { Collection collection = (Collection) value; if (collection.isEmpty()) { continue; } JSONArray list = new JSONArray(); list.addAll(collection); value = list; } json.put(key, value); } return json.toJSONString(); }
From source file:ch.simas.jtoggl.TimeEntry.java
public JSONObject toJSONObject() { JSONObject object = new JSONObject(); if (billable != null) { object.put("billable", billable); }//from ww w . j a v a2 s . c om if (description != null) { object.put("description", description); } if (duration != 0) { object.put("duration", duration); } if (id != null) { object.put("id", id); } if (duronly != null) { object.put("duronly", duronly); } if (start != null) { object.put("start", DateUtil.convertDateToString(start)); } if (stop != null) { object.put("stop", DateUtil.convertDateToString(stop)); } if (created_with != null) { object.put("created_with", created_with); } if (!this.tag_names.isEmpty()) { JSONArray tag_names_arr = new JSONArray(); tag_names_arr.addAll(this.tag_names); object.put("tags", tag_names_arr); } if (project != null) { object.put("project", this.project.toJSONObject()); } if (pid != null) { object.put("pid", this.pid); } if (workspace != null) { object.put("workspace", this.workspace.toJSONObject()); } if (wid != null) { object.put("wid", this.wid); } if (tid != null) { object.put("tid", this.tid); } return object; }
From source file:com.mediaworx.intellij.opencmsplugin.connector.OpenCmsPluginConnector.java
/** * Internal utility method to convert a List of Strings into a JSON array * @param list The List of Strings to be converted * @return the list of Strings converted into a JSON array *///w w w. ja v a 2 s . c om @SuppressWarnings("unchecked") private String getJSONArrayForStringList(List<String> list) { JSONArray jsonArray = new JSONArray(); jsonArray.addAll(list); return jsonArray.toJSONString(); }
From source file:com.nubits.nubot.RPC.NuRPCClient.java
private JSONObject invokeRPC(String id, String method, List params) { DefaultHttpClient httpclient = new DefaultHttpClient(); JSONObject json = new JSONObject(); json.put("id", id); json.put("method", method); if (null != params) { JSONArray array = new JSONArray(); array.addAll(params); json.put("params", params); }//from w w w . jav a2s. c o m JSONObject responseJsonObj = null; try { httpclient.getCredentialsProvider().setCredentials(new AuthScope(this.ip, this.port), new UsernamePasswordCredentials(this.rpcUsername, this.rpcPassword)); StringEntity myEntity = new StringEntity(json.toJSONString()); if (Global.options.verbose) { LOG.info("RPC : " + json.toString()); } HttpPost httppost = new HttpPost("http://" + this.ip + ":" + this.port); httppost.setEntity(myEntity); if (Global.options.verbose) { LOG.info("RPC executing request :" + httppost.getRequestLine()); } HttpResponse response = httpclient.execute(httppost); HttpEntity entity = response.getEntity(); if (Global.options.verbose) { LOG.info("RPC----------------------------------------"); LOG.info("" + response.getStatusLine()); if (entity != null) { LOG.info("RPC : Response content length: " + entity.getContentLength()); } } JSONParser parser = new JSONParser(); String entityString = EntityUtils.toString(entity); LOG.debug("Entity = " + entityString); /* TODO In case of wrong username/pass the response would be the following .Consider parsing it. Entity = <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/1999/REC-html401-19991224/loose.dtd"> <HTML> <HEAD> <TITLE>Error</TITLE> <META HTTP-EQUIV='Content-Type' CONTENT='text/html; charset=ISO-8859-1'> </HEAD> <BODY><H1>401 Unauthorized.</H1></BODY> </HTML> */ responseJsonObj = (JSONObject) parser.parse(entityString); } catch (ClientProtocolException e) { LOG.error("Nud RPC Connection problem:" + e.toString()); this.connected = false; } catch (IOException e) { LOG.error("Nud RPC Connection problem:" + e.toString()); this.connected = false; } catch (ParseException ex) { LOG.error("Nud RPC Connection problem:" + ex.toString()); this.connected = false; } finally { // When HttpClient instance is no longer needed, // shut down the connection manager to ensure // immediate deallocation of all system resources httpclient.getConnectionManager().shutdown(); } return responseJsonObj; }
From source file:be.iminds.aiolos.ui.NodeServlet.java
@SuppressWarnings("unchecked") protected void writeJSON(final Writer w, final Locale locale) throws IOException { final Collection<NodeInfo> allNodes = this.getNodes(); final Object[] status = getStatus(allNodes); JSONObject obj = new JSONObject(); JSONArray stat = new JSONArray(); for (int i = 0; i < status.length; i++) stat.add(status[i]);/* w ww. ja v a2s . co m*/ obj.put("status", stat); JSONArray nodes = new JSONArray(); for (NodeInfo node : allNodes) { JSONObject nodeObj = new JSONObject(); JSONArray components = new JSONArray(); // TODO extend functionality nodeObj.put("id", node.getNodeId()); nodeObj.put("state", "Unknown"); // TODO hardcoded in javascript components.addAll(getComponents(node.getNodeId())); nodeObj.put("components", components); nodeObj.put("ip", node.getIP()); // nodeObj.put("proxy", node.getProxyInfoMap()); // nodeObj.put("hostname", node.getHostname()); if (node.getHttpPort() != -1) nodeObj.put("console", "http://" + node.getIP() + ":" + node.getHttpPort() + "/system/console"); // nodeObj.put("stoppable", (node.getVMInstance()!=null)); nodes.add(nodeObj); } obj.put("nodes", nodes); JSONArray components = new JSONArray(); components.addAll(getComponents()); obj.put("components", components); try { JSONArray bndruns = new JSONArray(); bndruns.addAll(cloudTracker.getService().getBndrunFiles()); obj.put("bndruns", bndruns); } catch (NullPointerException e) { } w.write(obj.toJSONString()); }
From source file:edu.vt.vbi.patric.portlets.CompareRegionViewer.java
@SuppressWarnings("unchecked") private void printTrackInfo(ResourceRequest request, ResourceResponse response) throws IOException { String _rowID = request.getParameter("rowId"); String pk = request.getParameter("key"); Gson gson = new Gson(); String pin_strand = null;/*from w ww . ja v a 2s . c o m*/ CRTrack crTrack = null; String pseed_ids = null; try { CRResultSet crRS = gson.fromJson(SessionHandler.getInstance().get(SessionHandler.PREFIX + pk), CRResultSet.class); pin_strand = crRS.getPinStrand(); crTrack = crRS.getTrackMap().get(Integer.parseInt(_rowID)); pseed_ids = crTrack.getSeedIds(); } catch (Exception e) { LOGGER.error(e.getMessage()); LOGGER.debug("{}", SessionHandler.getInstance().get(SessionHandler.PREFIX + pk)); } int _window_size = 0; try { _window_size = Integer .parseInt(SessionHandler.getInstance().get(SessionHandler.PREFIX + "_windowsize" + pk)); } catch (Exception e) { LOGGER.error(e.getMessage()); LOGGER.debug("pk:{}, {}", SessionHandler.getInstance().get(SessionHandler.PREFIX + "_windowsize" + pk)); } int features_count = 0; try { crTrack.relocateFeatures(_window_size, pin_strand); Collections.sort(crTrack.getFeatureList()); features_count = crTrack.getFeatureList().size(); } catch (Exception ex) { LOGGER.error(ex.getMessage(), ex); } Map<String, GenomeFeature> pseedMap = getPSeedMapping(request, pseed_ids); // formatting JSONArray nclist = new JSONArray(); CRFeature feature; GenomeFeature feature_patric; for (int i = 0; i < features_count; i++) { feature = crTrack.getFeatureList().get(i); feature_patric = pseedMap.get(feature.getfeatureID()); if (feature_patric != null) { JSONArray alist = new JSONArray(); alist.addAll(Arrays.asList(0, feature.getStartPosition(), feature.getStartString(), feature.getEndPosition(), (feature.getStrand().equals("+") ? 1 : -1), feature.getStrand(), feature_patric.getId(), feature_patric.getPatricId(), feature_patric.getRefseqLocusTag(), feature_patric.getAltLocusTag(), "PATRIC", feature_patric.getFeatureType(), feature_patric.getProduct(), feature_patric.getGene(), feature_patric.getGenomeName(), feature_patric.getAccession(), feature.getPhase())); nclist.add(alist); } } // formatter.close(); JSONObject track = new JSONObject(); track.put("featureCount", features_count); track.put("formatVersion", 1); track.put("histograms", new JSONObject()); JSONObject intervals = new JSONObject(); JSONArray _clses = new JSONArray(); JSONObject _cls = new JSONObject(); _cls.put("attributes", Arrays.asList("Start", "Start_str", "End", "Strand", "strand_str", "id", "patric_id", "refseq_locus_tag", "alt_locus_tag", "source", "type", "product", "gene", "genome_name", "accession", "phase")); _cls.put("isArrayAttr", new JSONObject()); _clses.add(_cls); intervals.put("classes", _clses); intervals.put("lazyClass", 5); intervals.put("minStart", 1); intervals.put("maxEnd", 20000); intervals.put("urlTemplate", "lf-{Chunk}.json"); intervals.put("nclist", nclist); track.put("intervals", intervals); response.setContentType("application/json"); track.writeJSONString(response.getWriter()); response.getWriter().close(); }
From source file:edu.vt.vbi.patric.portlets.CompareRegionViewer.java
@SuppressWarnings("unchecked") private void printTrackList(ResourceRequest request, ResourceResponse response) throws IOException { String contextType = request.getParameter("cType"); String contextId = request.getParameter("cId"); String pinFeatureSeedId = request.getParameter("feature"); // pin feature String windowSize = request.getParameter("window"); // window size int _numRegion = Integer.parseInt(request.getParameter("regions")); // number of genomes to compare int _numRegion_buffer = 10; // number of genomes to use as a buffer in case that PATRIC has no genome data, // which was retrieved from API String _key = ""; DataApiHandler dataApi = new DataApiHandler(request); // if pin feature is not given, retrieve from the database based on na_feature_id if (pinFeatureSeedId == null && (contextType != null && contextType.equals("feature") && contextId != null)) { GenomeFeature feature = dataApi.getFeature(contextId); pinFeatureSeedId = feature.getPatricId(); }/*w w w . j av a 2 s . c o m*/ if (pinFeatureSeedId != null && !pinFeatureSeedId.equals("") && windowSize != null) { CRResultSet crRS = null; try { SAPserver sapling = new SAPserver("http://servers.nmpdr.org/pseed/sapling/server.cgi"); crRS = new CRResultSet(pinFeatureSeedId, sapling.compared_regions(pinFeatureSeedId, _numRegion + _numRegion_buffer, Integer.parseInt(windowSize) / 2)); long pk = (new Random()).nextLong(); _key = "" + pk; Gson gson = new Gson(); SessionHandler.getInstance().set(SessionHandler.PREFIX + pk, gson.toJson(crRS, CRResultSet.class)); SessionHandler.getInstance().set(SessionHandler.PREFIX + "_windowsize" + pk, windowSize); } catch (Exception ex) { LOGGER.error(ex.getMessage(), ex); } JSONObject trackList = new JSONObject(); JSONArray tracks = new JSONArray(); JSONObject trStyle = new JSONObject(); trStyle.put("className", "feature5"); trStyle.put("showLabels", false); trStyle.put("label", "function( feature ) { return feature.get('patric_id'); }"); JSONObject trHooks = new JSONObject(); trHooks.put("modify", "function(track, feature, div) { div.style.backgroundColor = ['red','#1F497D','#938953','#4F81BD','#9BBB59','#806482','#4BACC6','#F79646'][feature.get('phase')];}"); // query genome metadata SolrQuery query = new SolrQuery("genome_id:(" + StringUtils.join(crRS.getGenomeIds(), " OR ") + ")"); query.setFields( "genome_id,genome_name,isolation_country,host_name,disease,collection_date,completion_date"); query.setRows(_numRegion + _numRegion_buffer); String apiResponse = dataApi.solrQuery(SolrCore.GENOME, query); Map resp = jsonReader.readValue(apiResponse); Map respBody = (Map) resp.get("response"); List<Genome> patricGenomes = dataApi.bindDocuments((List<Map>) respBody.get("docs"), Genome.class); int count_genomes = 1; if (crRS.getGenomeNames().size() > 0) { for (Integer idx : crRS.getTrackMap().keySet()) { if (count_genomes > _numRegion) { break; } CRTrack crTrack = crRS.getTrackMap().get(idx); Genome currentGenome = null; for (Genome genome : patricGenomes) { if (genome.getId().equals(crTrack.getGenomeID())) { currentGenome = genome; } } if (currentGenome != null) { count_genomes++; crRS.addToDefaultTracks(crTrack); JSONObject tr = new JSONObject(); tr.put("style", trStyle); tr.put("hooks", trHooks); tr.put("type", "FeatureTrack"); tr.put("tooltip", "<div style='line-height:1.7em'><b>{patric_id}</b> | {refseq_locus_tag} | {alt_locus_tag} | {gene}<br>{product}<br>{type}:{start}...{end} ({strand_str})<br> <i>Click for detail information</i></div>"); tr.put("urlTemplate", "/portal/portal/patric/CompareRegionViewer/CRWindow?action=b&cacheability=PAGE&mode=getTrackInfo&key=" + _key + "&rowId=" + crTrack.getRowID() + "&format=.json"); tr.put("key", crTrack.getGenomeName()); tr.put("label", "CR" + idx); tr.put("dataKey", _key); JSONObject metaData = new JSONObject(); if (currentGenome.getIsolationCountry() != null) { metaData.put("Isolation Country", currentGenome.getIsolationCountry()); } if (currentGenome.getHostName() != null) { metaData.put("Host Name", currentGenome.getHostName()); } if (currentGenome.getDisease() != null) { metaData.put("Disease", currentGenome.getDisease()); } if (currentGenome.getCollectionDate() != null) { metaData.put("Collection Date", currentGenome.getCollectionDate()); } if (currentGenome.getCompletionDate() != null) { metaData.put("Completion Date", currentGenome.getCompletionDate()); } tr.put("metadata", metaData); tracks.add(tr); } } } trackList.put("tracks", tracks); JSONObject facetedTL = new JSONObject(); JSONArray dpColumns = new JSONArray(); dpColumns.addAll(Arrays.asList("key", "Isolation Country", "Host Name", "Disease", "Collection Date", "Completion Date")); facetedTL.put("displayColumns", dpColumns); facetedTL.put("type", "Faceted"); facetedTL.put("escapeHTMLInData", false); trackList.put("trackSelector", facetedTL); trackList.put("defaultTracks", crRS.getDefaultTracks()); response.setContentType("application/json"); trackList.writeJSONString(response.getWriter()); response.getWriter().close(); } else { response.getWriter().write("{}"); } }
From source file:com.googlecode.fascinator.common.JsonSimpleConfig.java
@SuppressWarnings(value = { "unchecked" })
private void mergeConfig(Map targetMap, Map srcMap) {
for (Object key : srcMap.keySet()) {
Object src = srcMap.get(key);
Object target = targetMap.get(key);
if (target == null) {
targetMap.put(key, src);/* w ww . j a v a 2s .c o m*/
} else {
if (src instanceof Map && target instanceof Map) {
mergeConfig((Map) target, (Map) src);
} else if (src instanceof JSONArray && target instanceof JSONArray) {
JSONArray srcArray = (JSONArray) src;
JSONArray targetArray = (JSONArray) target;
targetArray.addAll(srcArray);
} else {
targetMap.put(key, src);
}
}
}
}