Example usage for org.json.simple JSONArray writeJSONString

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

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Introduction

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

Prototype

public static void writeJSONString(List list, Writer out) throws IOException

Source Link

Usage

From source file:de.mpg.imeji.presentation.servlet.autocompleter.java

/**
 * Parse a JSON file from CoNE with authors, and return a JSON which can be read by imeji autocomplete
 * //from   w  w w  .  j a  v a  2s .co m
 * @param cone
 * @return
 * @throws IOException
 */
@SuppressWarnings("unchecked")
private String parseConeAuthor(String cone) throws IOException {
    Object obj = JSONValue.parse(cone);
    JSONArray array = (JSONArray) obj;
    JSONArray result = new JSONArray();
    for (int i = 0; i < array.size(); ++i) {
        JSONObject parseObject = (JSONObject) array.get(i);
        JSONObject sendObject = new JSONObject();
        sendObject.put("label", parseObject.get("http_purl_org_dc_elements_1_1_title"));
        sendObject.put("family", parseObject.get("http_xmlns_com_foaf_0_1_family_name"));
        sendObject.put("givenname", parseObject.get("http_xmlns_com_foaf_0_1_givenname"));
        sendObject.put("id", parseObject.get("id"));
        sendObject.put("orgs",
                writeJsonArrayToOneString(parseObject.get("http_purl_org_escidoc_metadata_terms_0_1_position"),
                        "http_purl_org_eprint_terms_affiliatedInstitution"));
        sendObject.put("alternatives",
                writeJsonArrayToOneString(parseObject.get("http_purl_org_dc_terms_alternative"), ""));
        result.add(sendObject);
    }
    StringWriter out = new StringWriter();
    JSONArray.writeJSONString(result, out);
    return out.toString();
}

From source file:de.mpg.imeji.presentation.servlet.autocompleter.java

private String parseCCLicense(String str) {
    str = "<licences>" + str + "</licences>";
    try {//from  ww w.j  av  a 2 s . c om
        JSONArray json = new JSONArray();
        DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
        DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
        org.w3c.dom.Document doc = dBuilder.parse(new ByteArrayInputStream(str.getBytes()));
        doc.getDocumentElement().normalize();
        NodeList nList = ((org.w3c.dom.Document) doc).getElementsByTagName("option");
        for (int i = 0; i < nList.getLength(); i++) {
            Node nNode = nList.item(i);
            if (nNode.getNodeType() == Node.ELEMENT_NODE) {
                JSONObject license = new JSONObject();
                Element eElement = (Element) nNode;
                license.put("label", eElement.getTextContent());
                license.put("value", eElement.getTextContent());
                license.put("licenseId", eElement.getAttribute("value"));
                json.add(license);
            }
        }
        StringWriter out = new StringWriter();
        JSONArray.writeJSONString(json, out);
        return out.toString();
    } catch (Exception e) {
        log("Error Parsing CC License", e);
    }
    return str;
}

From source file:at.localhost.vectorworldmap.util.FeatureJSON.java

/**
 * Writes a feature collection as GeoJSON.
 *
 * @param features The feature collection.
 * @param output The output. See {@link GeoJSONUtil#toWriter(Object)} for details.
 *//*from  w w  w .  j a  v  a  2s  . com*/
public void writeFeatureCollection(FeatureCollection features, Object output) throws IOException {
    LinkedHashMap obj = new LinkedHashMap();
    obj.put("type", "FeatureCollection");
    if (encodeFeatureCollectionBounds || encodeFeatureCollectionCRS) {
        final ReferencedEnvelope bounds = features.getBounds();

        if (encodeFeatureCollectionBounds) {
            obj.put("bbox", new JSONStreamAware() {
                public void writeJSONString(Writer out) throws IOException {
                    JSONArray.writeJSONString(Arrays.asList(bounds.getMinX(), bounds.getMinY(),
                            bounds.getMaxX(), bounds.getMaxY()), out);
                }
            });
        }

        if (encodeFeatureCollectionCRS) {
            obj.put("crs", createCRS(bounds.getCoordinateReferenceSystem()));
        }
    }
    if (encodeDistanceTolerance) {
        obj.put("tolerance", Double.toString(distanceTolerance));
    }
    obj.put("features", new FeatureCollectionEncoder(features, gjson));
    GeoJSONUtil.encode(obj, output);
}

From source file:org.mskcc.cbio.portal.servlet.ClinicalAttributesServlet.java

/**
 * Takes any sort of patient list parameter in the request
 *
 * Returns a list of clinical attributes in json format
 *
 * @param request//from   w ww  .jav a  2s.com
 * @param response
 * @throws ServletException
 */
public void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException {
    try {
        JSONArray toWrite = new JSONArray();
        response.setContentType("text/json");

        int cancerStudyId = DaoCancerStudy
                .getCancerStudyByStableId(WebserviceParserUtils.getCancerStudyId(request)).getInternalId();
        List<ClinicalAttribute> clinicalAttributes = DaoClinicalAttribute.getDataByStudy(cancerStudyId);

        for (ClinicalAttribute attr : clinicalAttributes) {
            toWrite.add(ClinicalJSON.reflectToMap(attr));
        }
        PrintWriter out = response.getWriter();
        JSONArray.writeJSONString(toWrite, out);
    } catch (DaoException e) {
        throw new ServletException(e);
    } catch (IOException e) {
        throw new ServletException(e);
    }
}

From source file:org.mskcc.cbio.portal.servlet.ClinicalJSON.java

/**
 * Using post request to increase URL length, actually this should not be a POST request
 *
 * @param request//from   w ww  . j  a v a  2  s.c o m
 * @param response
 * @throws ServletException
 * @throws IOException
 */
@Override
public void doPost(HttpServletRequest request, HttpServletResponse response)
        throws ServletException, IOException {

    String query = request.getParameter("q");
    String type = request.getParameter("t");

    String samples = request.getParameter("samples");
    String cancerStudyId = request.getParameter("cancer_study_id");

    List<ClinicalData> clinicals;
    JSONArray maps = null;

    try {
        if (samples == null || samples.equals(ALL)) {
            clinicals = DaoClinicalData.getData(cancerStudyId);
            maps = clinicals2JSONArray(clinicals);
        } else {
            clinicals = DaoClinicalData.getData(cancerStudyId,
                    Arrays.asList(samples.trim().split(SAMPLES_DELIMITER)));
            maps = clinicals2JSONArray(clinicals);
        }
    } catch (DaoException e) {
        throw new ServletException(e);
    }

    for (ClinicalData c : clinicals) {
        maps.add(reflectToMap(c));
    }

    response.setContentType("application/json");
    PrintWriter out = response.getWriter();
    JSONArray.writeJSONString(maps, out);
}

From source file:org.mskcc.cbio.portal.servlet.GeneDataJSON.java

/**
 *
 * @param request/*  w ww . j av a  2 s.  com*/
 * @param response
 * @throws ServletException
 * @throws IOException
 */
@Override
public void doPost(HttpServletRequest request, HttpServletResponse response)
        throws ServletException, IOException {

    // OncoQuery Language string
    String oql = request.getParameter("oql");

    if (request instanceof XssRequestWrapper) {
        oql = ((XssRequestWrapper) request).getRawParameter("oql");
    }

    oql = oql.replaceAll("\n", " \n ");

    List<String> sampleIdList;
    try {
        sampleIdList = WebserviceParserUtils.getSampleIds(request);
    } catch (ProtocolException e) {
        throw new ServletException(e);
    } catch (DaoException e) {
        throw new ServletException(e);
    }

    String _geneticProfileIds = request.getParameter("geneticProfileIds");
    // list of geneticProfileIds separated by a space
    // e.g. gbm_mutations, gbm_cna_consensus

    HashSet<String> geneticProfileIdSet = new HashSet<String>(
            Arrays.asList(_geneticProfileIds.trim().split(" ")));

    // map geneticProfileIds -> geneticProfiles
    Iterator<String> gpSetIterator = geneticProfileIdSet.iterator();
    ArrayList<GeneticProfile> profileList = new ArrayList<GeneticProfile>();
    while (gpSetIterator.hasNext()) {
        String gp_str = gpSetIterator.next();

        GeneticProfile gp = DaoGeneticProfile.getGeneticProfileByStableId(gp_str);
        profileList.add(gp);
        // pointer to gp is local, but gets added to profileList which is outside
    }

    double zScoreThreshold = Double.valueOf(request.getParameter("z_score_threshold"));
    double rppaScoreThreshold = Double.valueOf(request.getParameter("rppa_score_threshold"));

    // todo: this is code duplication!
    // this is a duplication of work that is being done in QueryBuilder.
    // For now, we cannot remove it from QueryBuilder because other parts use it...for now
    // ...this is a temporary solution
    ParserOutput theOncoPrintSpecParserOutput = OncoPrintSpecificationDriver.callOncoPrintSpecParserDriver(oql,
            geneticProfileIdSet, profileList, zScoreThreshold, rppaScoreThreshold);

    ArrayList<String> listOfGenes = theOncoPrintSpecParserOutput.getTheOncoPrintSpecification().listOfGenes();

    String[] listOfGeneNames = new String[listOfGenes.size()];
    listOfGeneNames = listOfGenes.toArray(listOfGeneNames);

    ArrayList<ProfileData> profileDataList = new ArrayList<ProfileData>();
    Iterator<String> profileIterator = geneticProfileIdSet.iterator();

    XDebug xdebug = new XDebug(request);
    while (profileIterator.hasNext()) {
        String profileId = profileIterator.next();
        GeneticProfile profile = GeneticProfileUtil.getProfile(profileId, profileList);
        if (null == profile) {
            continue;
        }

        xdebug.logMsg(this, "Getting data for:  " + profile.getProfileName());

        GetProfileData remoteCall;
        List<Sample.Type> excludes = new ArrayList<Sample.Type>();
        excludes.add(Sample.Type.SOLID_NORMAL);
        excludes.add(Sample.Type.BLOOD_NORMAL);
        String sampleIds = StringUtils.join(sampleIdList, " ");

        try {
            remoteCall = new GetProfileData(profile, listOfGenes, sampleIds);
        } catch (DaoException e) {
            throw new ServletException(e);
        }
        ProfileData pData = remoteCall.getProfileData();
        if (pData == null) {
            System.err.println("pData == null");
        } else {
            if (pData.getGeneList() == null) {
                System.err.println("pData.getValidGeneList() == null");
            }
            if (pData.getCaseIdList().size() == 0) {
                System.err.println("pData.length == 0");
            }
        }
        if (pData != null) {
            xdebug.logMsg(this, "Got number of genes:  " + pData.getGeneList().size());
            xdebug.logMsg(this, "Got number of cases:  " + pData.getCaseIdList().size());
        }
        xdebug.logMsg(this, "Number of warnings received:  " + remoteCall.getWarnings().size());
        profileDataList.add(pData);
    }

    xdebug.logMsg(this, "Merging Profile Data");
    ProfileMerger merger = new ProfileMerger(profileDataList);
    ProfileData mergedProfile = merger.getMergedProfile();

    ProfileDataSummary dataSummary = new ProfileDataSummary(mergedProfile,
            theOncoPrintSpecParserOutput.getTheOncoPrintSpecification(), zScoreThreshold, rppaScoreThreshold);

    GeneticEvent geneticEvents[][] = ConvertProfileDataToGeneticEvents.convert(dataSummary, listOfGeneNames,
            theOncoPrintSpecParserOutput.getTheOncoPrintSpecification(), zScoreThreshold, rppaScoreThreshold);

    // out.write the matrix

    response.setContentType("application/json");
    PrintWriter out = response.getWriter();

    JSONArray jsonArray = mapGeneticEventMatrix(geneticEvents);
    JSONArray.writeJSONString(jsonArray, out);
}

From source file:org.mskcc.cbio.portal.servlet.PancancerMutationsJSON.java

/**
 * the request requires a parameter "mutation_keys" which is a JSON list of strings.
 *
 * @param request/* ww  w.ja v a2 s  .c  o m*/
 * @param response
 * @throws ServletException
 * @throws IOException
 */
@Override
public void doGet(HttpServletRequest request, HttpServletResponse response)
        throws ServletException, IOException {

    Collection<Map<String, Object>> data = null;
    PrintWriter writer = response.getWriter();
    response.setContentType("application/json");

    String cmd = request.getParameter("cmd");
    String query = request.getParameter("q");

    if (query == null || query.equals("")) {
        throw new ServletException("no q parameter provided");
    }
    List<String> queryTerms = Arrays.asList(query.split(","));

    if (cmd.equals("byKeywords")) {
        try {
            data = byKeywords(queryTerms);
        } catch (DaoException e) {
            throw new ServletException(e);
        } catch (ProtocolException e) {
            throw new ServletException(e);
        }
    } else if (cmd.equals("byHugos")) {
        try {
            data = byHugos(queryTerms);
        } catch (DaoException e) {
            throw new ServletException(e);
        } catch (ProtocolException e) {
            throw new ServletException(e);
        }
    } else if (cmd.equals("byMutations")) {
        try {
            data = byProteinChanges(queryTerms);
        } catch (DaoException e) {
            throw new ServletException(e);
        } catch (ProtocolException e) {
            throw new ServletException(e);
        }
    } else if (cmd.equals("byProteinPos")) {
        try {
            data = byProteinPosStarts(queryTerms);
        } catch (DaoException e) {
            throw new ServletException(e);
        } catch (ProtocolException e) {
            throw new ServletException(e);
        }
    } else {
        throw new ServletException("cmd not found");
    }

    JSONArray.writeJSONString((List) data, writer);
}

From source file:uk.co.didz.hypersignsbukkit.HyperSignsBukkit.java

/**
 * Attempt to save signs. If the data file doesn't exist, create it.
 *///from www. j a va 2  s .  co  m
protected void saveSignsData() {
    File signsFile = new File(getDataFolder(), "signs.json");
    FileWriter fileWriter;
    try {
        fileWriter = new FileWriter(signsFile);
    } catch (IOException e) {
        log.severe("Unable to open signs.json for writing.");
        e.printStackTrace();
        return;
    }

    List<Map<String, Object>> signsList = new ArrayList<Map<String, Object>>();

    for (Entry<Location, URL> entry : loadedSigns.entrySet()) {
        Location location = entry.getKey();
        URL url = entry.getValue();

        // Using LinkedHashMap for the insertion-order retention
        Map<String, Object> obj = new LinkedHashMap<String, Object>();
        obj.put("world", location.getWorld().getName());
        obj.put("x", (int) location.getX());
        obj.put("y", (int) location.getY());
        obj.put("z", (int) location.getZ());
        obj.put("url", url.toString());
        signsList.add(obj);
    }

    try {
        // Save the file
        JSONArray.writeJSONString(signsList, fileWriter);
        fileWriter.close();
    } catch (IOException e) {
        log.severe("Unable to open signs.json for writing.");
        e.printStackTrace();
        return;
    }
}