Example usage for org.json.simple JSONObject writeJSONString

List of usage examples for org.json.simple JSONObject writeJSONString

  1. HOME
  2. Java
  3. org.json
  4. org.json.simple.*
  5. JSONObject
  6. writeJSONString

Introduction

In this page you can find the example usage for org.json.simple JSONObject writeJSONString.

Prototype

public void writeJSONString(Writer out) throws IOException

Source Link

Usage

From source file:edu.vt.vbi.patric.portlets.TranscriptomicsEnrichment.java

@SuppressWarnings("unchecked")
public void serveResource(ResourceRequest request, ResourceResponse response)
        throws PortletException, IOException {

    response.setContentType("text/html");
    String callType = request.getParameter("callType");

    switch (callType) {
    case "saveParams": {

        Map<String, String> key = new HashMap<>();
        key.put("feature_id", request.getParameter("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();//from  w  w w. j  a v a  2  s. co  m
        break;
    }
    case "getFeatureIds": {
        String pathwayId = request.getParameter("map");
        String featureList = request.getParameter("featureList");
        String algorithm = request.getParameter("algorithm");

        DataApiHandler dataApi = new DataApiHandler(request);

        SolrQuery query = new SolrQuery("pathway_id:(" + pathwayId.replaceAll(",", " OR ")
                + ") AND feature_id:(" + featureList.replaceAll(",", " OR ") + ")");
        query.addFilterQuery("annotation:" + algorithm).setRows(dataApi.MAX_ROWS).addField("feature_id");

        LOGGER.trace("getFeatureIds: [{}] {}", SolrCore.PATHWAY.getSolrCoreName(), query);
        String apiResponse = dataApi.solrQuery(SolrCore.PATHWAY, query);

        Map resp = jsonReader.readValue(apiResponse);
        Map respBody = (Map) resp.get("response");
        List<GenomeFeature> features = dataApi.bindDocuments((List<Map>) respBody.get("docs"),
                GenomeFeature.class);

        JSONArray featureIds = new JSONArray();
        for (GenomeFeature feature : features) {
            featureIds.add(feature.getId());
        }

        response.setContentType("application/json");
        featureIds.writeJSONString(response.getWriter());
        break;
    }
    case "getGenomeIds": {

        String featureIds = request.getParameter("feature_id");
        String pathwayId = request.getParameter("map");

        DataApiHandler dataApi = new DataApiHandler(request);

        String genomeId = "";
        if (featureIds != null && !featureIds.equals("") && pathwayId != null && !pathwayId.equals("")) {
            String[] listFeatureId = featureIds.split(",");

            SolrQuery query = new SolrQuery("pathway_id:(" + pathwayId + ") AND feature_id:("
                    + StringUtils.join(listFeatureId, " OR ") + ")");
            query.addField("genome_id").setRows(listFeatureId.length);

            String apiResponse = dataApi.solrQuery(SolrCore.PATHWAY, query);

            Map resp = jsonReader.readValue(apiResponse);
            Map respBody = (Map) resp.get("response");
            List<Map> sdl = (List<Map>) respBody.get("docs");

            Set<String> listGenomeId = new HashSet<>();
            for (Map doc : sdl) {
                listGenomeId.add(doc.get("genome_id").toString());
            }
            genomeId = StringUtils.join(listGenomeId, ",");
        }
        PrintWriter writer = response.getWriter();
        writer.write(genomeId);
        writer.close();
        break;
    }
    case "download": {

        String _filename = "PathwaySummary";
        String _fileformat = request.getParameter("fileformat");
        String pk = request.getParameter("pk");
        Map<String, String> key = jsonReader
                .readValue(SessionHandler.getInstance().get(SessionHandler.PREFIX + pk));

        if (key != null && key.containsKey("feature_id")) {
            List<String> featureIDs = Arrays.asList(key.get("feature_id").split(","));
            JSONObject jsonResult = getEnrichmentPathway(request, featureIDs);

            List<String> _tbl_header = new ArrayList<>();
            List<String> _tbl_field = new ArrayList<>();
            JSONArray _tbl_source = (JSONArray) jsonResult.get("results");

            _tbl_header.addAll(Arrays.asList("Pathway Name", "# of Genes Selected   ", "# of Genes Annotated",
                    "% Coverage"));
            _tbl_field.addAll(Arrays.asList("pathway_name", "ocnt", "ecnt", "percentage"));

            ExcelHelper excel = new ExcelHelper("xssf", _tbl_header, _tbl_field, _tbl_source);
            excel.buildSpreadsheet();

            if (_fileformat.equalsIgnoreCase("xlsx")) {

                response.setContentType("application/octetstream");
                response.setProperty("Content-Disposition",
                        "attachment; filename=\"" + _filename + "." + _fileformat + "\"");

                excel.writeSpreadsheettoBrowser(response.getPortletOutputStream());
            } else if (_fileformat.equalsIgnoreCase("txt")) {

                response.setContentType("application/octetstream");
                response.setProperty("Content-Disposition",
                        "attachment; filename=\"" + _filename + "." + _fileformat + "\"");

                response.getWriter().write(excel.writeToTextFile());
            }
        }
        break;
    }
    case "getFeatureTable": {

        String pk = request.getParameter("pk");
        Map<String, String> key = jsonReader
                .readValue(SessionHandler.getInstance().get(SessionHandler.PREFIX + pk));

        response.setContentType("application/json");
        if (key != null && key.containsKey("feature_id")) {

            List<String> featureIDs = Arrays.asList(key.get("feature_id").split(","));
            JSONObject jsonResult = getEnrichmentPathway(request, featureIDs);

            PrintWriter writer = response.getWriter();
            jsonResult.writeJSONString(writer);
            writer.close();
        } else {
            PrintWriter writer = response.getWriter();
            writer.write("{}");
            writer.close();
        }
        break;
    }
    }
}

From source file:edu.vt.vbi.patric.portlets.PathwayTableSingle.java

@SuppressWarnings("unchecked")
public void serveResource(ResourceRequest request, ResourceResponse response)
        throws PortletException, IOException {

    response.setContentType("application/json");

    String callType = request.getParameter("callType");

    if (callType != null && callType.equals("savetopk")) {

        String cId = request.getParameter("cId");
        String cType = request.getParameter("cType");
        String map = request.getParameter("map");
        String algorithm = request.getParameter("algorithm");
        String ec_number = request.getParameter("ec_number");

        Map<String, String> key = new HashMap<>();

        if (cId != null && !cId.equals("")) {
            key.put("genomeId", cId);
        }/*  ww  w.j  av a2s  . com*/
        if (cType != null && !cType.equals("")) {
            key.put("cType", cType);
        }

        if (map != null && !map.equals("")) {
            key.put("map", map);
        }

        if (algorithm != null && !algorithm.equals("")) {
            key.put("algorithm", algorithm);
        }

        if (ec_number != null && !ec_number.equals("")) {
            key.put("ec_number", ec_number);
        }

        key.put("which", "download_from_heatmap_feature");

        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 (callType != null && callType.equals("show")) {

        JSONObject jsonResult = new JSONObject();
        JSONArray results = new JSONArray();
        String pk = request.getParameter("pk");
        Map<String, String> key = jsonReader
                .readValue(SessionHandler.getInstance().get(SessionHandler.PREFIX + pk));

        DataApiHandler dataApi = new DataApiHandler(request);
        try {
            SolrQuery query = new SolrQuery("*:*");
            List<String> joinConditions = new ArrayList<>();

            if (key.containsKey("map")) {
                joinConditions.add("pathway_id:(" + key.get("map") + ")");
            }
            if (key.containsKey("algorithm")) {
                joinConditions.add("annotation:(" + key.get("algorithm") + ")");
            }
            if (key.containsKey("ec_number")) {
                joinConditions.add("ec_number:(" + key.get("ec_number").replaceAll(",", " OR ") + ")");
            }
            if (key.containsKey("genomeId")) {
                joinConditions.add("genome_id:(" + key.get("genomeId").replace(",", " OR ") + ")");
            }

            if (!joinConditions.isEmpty()) {
                query.addFilterQuery(SolrCore.PATHWAY.getSolrCoreJoin("feature_id", "feature_id",
                        StringUtils.join(joinConditions, " AND ")));
            }
            query.setRows(10000);

            LOGGER.debug("[{}] {}", SolrCore.FEATURE.getSolrCoreName(), query.toString());

            String apiResponse = dataApi.solrQuery(SolrCore.FEATURE, query);

            Map resp = jsonReader.readValue(apiResponse);
            Map respBody = (Map) resp.get("response");

            int numFound = (Integer) respBody.get("numFound");
            List<GenomeFeature> features = dataApi.bindDocuments((List<Map>) respBody.get("docs"),
                    GenomeFeature.class);

            for (GenomeFeature feature : features) {

                results.add(feature.toJSONObject());
            }

            jsonResult.put("total", numFound);
            jsonResult.put("results", results);
        } catch (IOException e) {
            LOGGER.error(e.getMessage(), e);
        }

        PrintWriter writer = response.getWriter();
        jsonResult.writeJSONString(writer);
        writer.close();
    }
}

From source file:edu.vt.vbi.patric.cache.DataLandingGenerator.java

public boolean createCacheFileProteomics(String filePath) {
    boolean isSuccess = false;
    JSONObject jsonData = new JSONObject();
    JSONObject data;//from  w  w w .  j a  v a  2s  .c  om

    // from WP
    // data
    data = read(baseURL + "/tab/dlp-proteomics-data/?req=passphrase");
    if (data != null) {
        jsonData.put("data", data);
    }
    // tools
    data = read(baseURL + "/tab/dlp-proteomics-tools/?req=passphrase");
    if (data != null) {
        jsonData.put("tools", data);
    }
    // process
    data = read(baseURL + "/tab/dlp-proteomics-process/?req=passphrase");
    if (data != null) {
        jsonData.put("process", data);
    }
    // download
    data = read(baseURL + "/tab/dlp-proteomics-download/?req=passphrase");
    if (data != null) {
        jsonData.put("download", data);
    }

    // save jsonData to file
    try (PrintWriter jsonOut = new PrintWriter(
            Files.newBufferedWriter(FileSystems.getDefault().getPath(filePath), Charset.defaultCharset()));) {
        jsonData.writeJSONString(jsonOut);
        isSuccess = true;
    } catch (IOException e) {
        LOGGER.error(e.getMessage(), e);
    }
    return isSuccess;
}

From source file:edu.vt.vbi.patric.cache.DataLandingGenerator.java

public boolean createCacheFilePPInteractions(String filePath) {
    boolean isSuccess = false;
    JSONObject jsonData = new JSONObject();
    JSONObject data;//w w  w  .  jav a2 s  .co m

    // from WP
    // data
    data = read(baseURL + "/tab/dlp-ppinteractions-data/?req=passphrase");
    if (data != null) {
        jsonData.put("data", data);
    }
    // tools
    data = read(baseURL + "/tab/dlp-ppinteractions-tools/?req=passphrase");
    if (data != null) {
        jsonData.put("tools", data);
    }
    // process
    data = read(baseURL + "/tab/dlp-ppinteractions-process/?req=passphrase");
    if (data != null) {
        jsonData.put("process", data);
    }
    // download
    data = read(baseURL + "/tab/dlp-ppinteractions-download/?req=passphrase");
    if (data != null) {
        jsonData.put("download", data);
    }

    // save jsonData to file
    try (PrintWriter jsonOut = new PrintWriter(
            Files.newBufferedWriter(FileSystems.getDefault().getPath(filePath), Charset.defaultCharset()));) {
        jsonData.writeJSONString(jsonOut);
        isSuccess = true;
    } catch (IOException e) {
        LOGGER.error(e.getMessage(), e);
    }
    return isSuccess;
}

From source file:edu.vt.vbi.patric.portlets.ExperimentListPortlet.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")) {

        Map<String, String> key = new HashMap<>();

        String genomeId = request.getParameter("genomeId");
        String taxonId = "";
        String cType = request.getParameter("context_type");
        String cId = request.getParameter("context_id");
        if (cType != null && cId != null && cType.equals("taxon") && !cId.equals("")) {
            taxonId = cId;//from   w w w. j av a  2s  .c o  m
        }
        String keyword = request.getParameter("keyword");
        String state = request.getParameter("state");
        String ncbi_taxon_id = request.getParameter("ncbi_taxon_id");

        if (genomeId != null && !genomeId.equalsIgnoreCase("")) {
            key.put("genomeId", genomeId);
        }
        if (!taxonId.equalsIgnoreCase("")) {
            key.put("taxonId", taxonId);
        }
        if (keyword != null) {
            key.put("keyword", keyword.trim());
        }
        if (ncbi_taxon_id != null) {
            key.put("ncbi_taxon_id", ncbi_taxon_id);
        }
        if (state != null) {
            key.put("state", state);
        }
        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");
        JSONObject jsonResult = new JSONObject();

        switch (need) {
        case "0": {
            // Experiments
            String pk = request.getParameter("pk");
            Map data = processExperimentTab(request);

            Map<String, String> key = (Map) data.get("key");
            int numFound = (Integer) data.get("numFound");
            List<Map> experiments = (List<Map>) data.get("experiments");

            JSONArray docs = new JSONArray();
            for (Map item : experiments) {
                JSONObject doc = new JSONObject();
                doc.putAll(item);
                docs.add(doc);
            }

            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();
            writer.write(jsonResult.toString());
            writer.close();

            break;
        }
        case "1": {
            // Comparisons
            Map data = processComparisonTab(request);

            int numFound = (Integer) data.get("numFound");
            List<Map> comparisons = (List<Map>) data.get("comparisons");

            JSONArray docs = new JSONArray();
            for (Map item : comparisons) {
                JSONObject doc = new JSONObject();
                doc.putAll(item);
                docs.add(doc);
            }

            //            key.put("keyword", orig_keyword);

            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");
            Map<String, String> key = jsonReader
                    .readValue(SessionHandler.getInstance().get(SessionHandler.PREFIX + pk));
            String state;

            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").equals("{}")) {

                    JSONObject facet_fields = (JSONObject) new JSONParser().parse(key.get("facets"));
                    DataApiHandler dataApi = new DataApiHandler(request);
                    tree = FacetHelper.processStateAndTree(dataApi, SolrCore.TRANSCRIPTOMICS_EXPERIMENT, key,
                            need, facet_fields, key.get("facet"), state, null, 4);
                }
            } catch (ParseException e) {
                LOGGER.error(e.getMessage(), e);
            }

            response.setContentType("application/json");
            PrintWriter writer = response.getWriter();
            tree.writeJSONString(writer);
            writer.close();
            break;
        }
        case "download": {
            List<String> tableHeader = new ArrayList<>();
            List<String> tableField = new ArrayList<>();
            JSONArray tableSource = new JSONArray();

            String fileName = "Transcriptomics";
            String fileFormat = request.getParameter("fileformat");

            String aT = request.getParameter("aT");

            switch (aT) {
            case "0": {
                // experiments
                Map data = processExperimentTab(request);
                List<Map> experiments = (List<Map>) data.get("experiments");

                for (Map item : experiments) {
                    JSONObject doc = new JSONObject();
                    doc.putAll(item);
                    tableSource.add(doc);
                }

                tableHeader.addAll(DownloadHelper.getHeaderForTranscriptomicsExperiment());
                tableField.addAll(DownloadHelper.getFieldsForTranscriptomicsExperiment());
                break;
            }
            case "1": {
                // comparisons
                Map data = processComparisonTab(request);
                List<Map> comparisons = (List<Map>) data.get("comparisons");

                for (Map item : comparisons) {
                    JSONObject doc = new JSONObject();
                    doc.putAll(item);
                    tableSource.add(doc);
                }

                tableHeader.addAll(DownloadHelper.getHeaderForTranscriptomicsComparison());
                tableField.addAll(DownloadHelper.getFieldsForTranscriptomicsComparison());
                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());
            }
            break;
        }
        }
    }
}

From source file:edu.vt.vbi.patric.cache.DataLandingGenerator.java

public boolean createCacheFileSpecialtyGenes(String filePath) {
    boolean isSuccess = false;
    JSONObject jsonData = new JSONObject();
    JSONObject data;/*  w w w  .  ja v  a  2s .  c  o  m*/

    // from WP
    // data
    data = read(baseURL + "/tab/dlp-specialtygenes-data/?req=passphrase");
    if (data != null) {
        jsonData.put("data", data);
    }
    // popular genomes
    data = getPopularGenomesForSpecialtyGene();
    if (data != null) {
        jsonData.put("popularGenomes", data);
    }
    // tools
    data = read(baseURL + "/tab/dlp-specialtygenes-tools/?req=passphrase");
    if (data != null) {
        jsonData.put("tools", data);
    }
    // process
    data = read(baseURL + "/tab/dlp-specialtygenes-process/?req=passphrase");
    if (data != null) {
        jsonData.put("process", data);
    }
    // download
    data = read(baseURL + "/tab/dlp-specialtygenes-download/?req=passphrase");
    if (data != null) {
        jsonData.put("download", data);
    }

    // save jsonData to file
    try (PrintWriter jsonOut = new PrintWriter(
            Files.newBufferedWriter(FileSystems.getDefault().getPath(filePath), Charset.defaultCharset()));) {
        jsonData.writeJSONString(jsonOut);
        isSuccess = true;
    } catch (IOException e) {
        LOGGER.error(e.getMessage(), e);
    }
    return isSuccess;
}

From source file:edu.vt.vbi.patric.cache.DataLandingGenerator.java

public boolean createCacheFileGenomicFeatures(String filePath) {
    boolean isSuccess = false;
    JSONObject jsonData = new JSONObject();
    JSONObject data;//  w ww .  j ava 2  s . c  o m

    // from WP
    // data
    data = read(baseURL + "/tab/dlp-genomicfeatures-data/?req=passphrase");
    if (data != null) {
        jsonData.put("data", data);
    }
    // popular genomes
    data = getPopularGenomesForGenomicFeature();
    if (data != null) {
        jsonData.put("popularGenomes", data);
    }
    // tools
    data = read(baseURL + "/tab/dlp-genomicfeatures-tools/?req=passphrase");
    if (data != null) {
        jsonData.put("tools", data);
    }
    // process
    data = read(baseURL + "/tab/dlp-genomicfeatures-process/?req=passphrase");
    if (data != null) {
        jsonData.put("process", data);
    }
    // download
    data = read(baseURL + "/tab/dlp-genomicfeatures-download/?req=passphrase");
    if (data != null) {
        jsonData.put("download", data);
    }

    // save jsonData to file
    try (PrintWriter jsonOut = new PrintWriter(
            Files.newBufferedWriter(FileSystems.getDefault().getPath(filePath), Charset.defaultCharset()));) {
        jsonData.writeJSONString(jsonOut);
        isSuccess = true;
    } catch (IOException e) {
        LOGGER.error(e.getMessage(), e);
    }
    return isSuccess;
}

From source file:edu.vt.vbi.patric.cache.DataLandingGenerator.java

public boolean createCacheFileAntibioticResistanceGenes(String filePath) {
    boolean isSuccess = false;
    JSONObject jsonData = new JSONObject();
    JSONObject data;/*from  ww  w.  j  a  v  a2 s.c  o  m*/

    // from WP
    // data
    data = read(baseURL + "/tab/dlp-antibioticresistance-data/?req=passphrase");
    if (data != null) {
        jsonData.put("data", data);
    }
    // popular genomes
    data = this.getPopularGenomesForAntibioticResistanceGene();
    if (data != null) {
        jsonData.put("popularGenomes", data);
    }
    // tools
    data = read(baseURL + "/tab/dlp-antibioticresistance-tools/?req=passphrase");
    if (data != null) {
        jsonData.put("tools", data);
    }
    // process
    data = read(baseURL + "/tab/dlp-antibioticresistance-process/?req=passphrase");
    if (data != null) {
        jsonData.put("process", data);
    }
    // download
    data = read(baseURL + "/tab/dlp-antibioticresistance-download/?req=passphrase");
    if (data != null) {
        jsonData.put("download", data);
    }

    // save jsonData to file
    try (PrintWriter jsonOut = new PrintWriter(
            Files.newBufferedWriter(FileSystems.getDefault().getPath(filePath), Charset.defaultCharset()));) {
        jsonData.writeJSONString(jsonOut);
        isSuccess = true;
    } catch (IOException e) {
        LOGGER.error(e.getMessage(), e);
    }
    return isSuccess;
}

From source file:edu.vt.vbi.patric.cache.DataLandingGenerator.java

public boolean createCacheFilePathways(String filePath) {
    boolean isSuccess = false;
    JSONObject jsonData = new JSONObject();
    JSONObject data;/*from w  w  w  .j av a  2 s . c  o m*/

    // from WP
    // data
    data = read(baseURL + "/tab/dlp-pathways-data/?req=passphrase");
    if (data != null) {
        jsonData.put("data", data);
    }
    // conservation
    data = getPathwayECDist();
    if (data != null) {
        jsonData.put("conservation", data);
    }
    // popular genomes
    data = getPopularGenomesForPathways();
    if (data != null) {
        jsonData.put("popularGenomes", data);
    }
    // tools
    data = read(baseURL + "/tab/dlp-pathways-tools/?req=passphrase");
    if (data != null) {
        jsonData.put("tools", data);
    }
    // process
    data = read(baseURL + "/tab/dlp-pathways-process/?req=passphrase");
    if (data != null) {
        jsonData.put("process", data);
    }
    // download
    data = read(baseURL + "/tab/dlp-pathways-download/?req=passphrase");
    if (data != null) {
        jsonData.put("download", data);
    }

    // save jsonData to file
    try (PrintWriter jsonOut = new PrintWriter(
            Files.newBufferedWriter(FileSystems.getDefault().getPath(filePath), Charset.defaultCharset()));) {
        jsonData.writeJSONString(jsonOut);
        isSuccess = true;
    } catch (IOException e) {
        LOGGER.error(e.getMessage(), e);
    }
    return isSuccess;
}

From source file:edu.vt.vbi.patric.cache.DataLandingGenerator.java

public boolean createCacheFileProteinFamilies(String filePath) {
    boolean isSuccess = false;
    JSONObject jsonData = new JSONObject();
    JSONObject data;/*www. ja va2  s  .  co m*/

    // from WP
    // data
    data = read(baseURL + "/tab/dlp-proteinfamilies-data/?req=passphrase");
    if (data != null) {
        jsonData.put("data", data);
    }
    // tools
    data = read(baseURL + "/tab/dlp-proteinfamilies-tools/?req=passphrase");
    if (data != null) {
        jsonData.put("tools", data);
    }
    // process
    data = read(baseURL + "/tab/dlp-proteinfamilies-process/?req=passphrase");
    if (data != null) {
        jsonData.put("process", data);
    }
    // download
    data = read(baseURL + "/tab/dlp-proteinfamilies-download/?req=passphrase");
    if (data != null) {
        jsonData.put("download", data);
    }
    //
    // add popularGenra
    data = getPopularGeneraFigfam();
    if (data != null) {
        jsonData.put("popularGenomes", data);
    }
    // add figfam graph data
    data = getProteinFamilies();
    if (data != null) {
        jsonData.put("FIGfams", data);
    }

    // save jsonData to file
    try (PrintWriter jsonOut = new PrintWriter(
            Files.newBufferedWriter(FileSystems.getDefault().getPath(filePath), Charset.defaultCharset()));) {
        jsonData.writeJSONString(jsonOut);
        isSuccess = true;
    } catch (IOException e) {
        LOGGER.error(e.getMessage(), e);
    }
    return isSuccess;
}