Example usage for org.json.simple JSONObject writeJSONString

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

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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.IDMapping.java

@SuppressWarnings("unchecked")
private void responseWriteFilters(ResourceResponse response) throws IOException {

    final String idGroupPATRIC = "PATRIC";
    final String idGroupOther = "Other";

    JSONObject grpPATRIC = new JSONObject();
    JSONObject grpPATRIC1 = new JSONObject();
    JSONObject grpPATRIC2 = new JSONObject();
    JSONObject grpPATRIC3 = new JSONObject();
    JSONObject grpPATRIC4 = new JSONObject();

    JSONObject grpRefSeq = new JSONObject();
    JSONObject grpRefSeq1 = new JSONObject();
    JSONObject grpRefSeq2 = new JSONObject();
    JSONObject grpRefSeq3 = new JSONObject();
    JSONObject grpRefSeq4 = new JSONObject();

    JSONObject grpOther = new JSONObject();

    // PATRIC Identifiers
    grpPATRIC.put("id", "<h5>PATRIC Identifier</h5>");
    grpPATRIC.put("value", "");

    grpPATRIC1.put("id", "PATRIC ID");
    grpPATRIC1.put("value", "patric_id");
    grpPATRIC1.put("group", idGroupPATRIC);

    grpPATRIC2.put("id", "Feature ID");
    grpPATRIC2.put("value", "feature_id");
    grpPATRIC2.put("group", idGroupPATRIC);

    grpPATRIC3.put("id", "Alt Locus Tag");
    grpPATRIC3.put("value", "alt_locus_tag");
    grpPATRIC3.put("group", idGroupPATRIC);

    grpPATRIC4.put("id", "P2 Feature ID");
    grpPATRIC4.put("value", "p2_feature_id");
    grpPATRIC4.put("group", idGroupPATRIC);

    // RefSeq Identifiers
    grpRefSeq.put("id", "<h5>RefSeq Identifiers</h5>");
    grpRefSeq.put("value", "");

    grpRefSeq1.put("id", "RefSeq");
    grpRefSeq1.put("value", "protein_id");
    grpRefSeq1.put("group", idGroupPATRIC);

    grpRefSeq2.put("id", "RefSeq Locus Tag");
    grpRefSeq2.put("value", "refseq_locus_tag");
    grpRefSeq2.put("group", idGroupPATRIC);

    grpRefSeq3.put("id", "Gene ID");
    grpRefSeq3.put("value", "gene_id");
    grpRefSeq3.put("group", idGroupPATRIC);

    grpRefSeq4.put("id", "GI");
    grpRefSeq4.put("value", "gi");
    grpRefSeq4.put("group", idGroupPATRIC);

    // Other Identifiers
    grpOther.put("id", "<h5>Other Identifiers</h5>");
    grpOther.put("value", "");

    JSONArray jsonIdTypes = new JSONArray();
    jsonIdTypes.add(grpPATRIC);//from w w  w  .j  a  va  2 s  . co  m
    jsonIdTypes.add(grpPATRIC1);
    jsonIdTypes.add(grpPATRIC2);
    jsonIdTypes.add(grpPATRIC3);
    jsonIdTypes.add(grpPATRIC4);

    jsonIdTypes.add(grpRefSeq);
    jsonIdTypes.add(grpRefSeq1);
    jsonIdTypes.add(grpRefSeq2);
    jsonIdTypes.add(grpRefSeq3);
    jsonIdTypes.add(grpRefSeq4);

    jsonIdTypes.add(grpOther);
    List<String> otherTypes = getIdTypes();
    for (String type : otherTypes) {
        JSONObject item = new JSONObject();
        item.put("id", type);
        item.put("value", type);
        item.put("group", idGroupOther);

        jsonIdTypes.add(item);
    }
    // add UniProtKB-Accession, for easier processing, treat UniProtKB-Accession as a PATRIC attribute
    JSONObject item = new JSONObject();
    item.put("id", "UniProtKB-ID");
    item.put("value", "UniProtKB-ID");
    item.put("group", idGroupOther);
    int idx = jsonIdTypes.indexOf(item);
    item.put("id", "UniProtKB-Accession");
    item.put("value", "uniprotkb_accession");
    item.put("group", idGroupPATRIC);
    jsonIdTypes.add(idx + 1, item);

    JSONObject json = new JSONObject();
    json.put("id_types", jsonIdTypes);

    response.setContentType("application/json");
    json.writeJSONString(response.getWriter());
}

From source file:edu.vt.vbi.patric.proteinfamily.FIGfamData.java

@SuppressWarnings("unchecked")
public void getGenomeDetails(ResourceRequest request, PrintWriter writer) throws IOException {

    String cType = request.getParameter("context_type");
    String cId = request.getParameter("context_id");
    String keyword = "";
    if (cType != null && cType.equals("taxon") && cId != null && !cId.equals("")) {
        keyword = "patric_cds:[1 TO *] AND taxon_lineage_ids:" + cId;
    } else if (request.getParameter("keyword") != null) {
        keyword = request.getParameter("keyword");
    }/*from   ww  w.  ja  va 2s . co m*/
    String fields = request.getParameter("fields");

    DataApiHandler dataApi = new DataApiHandler(request);

    SolrQuery query = new SolrQuery(keyword);
    if (fields != null && !fields.equals("")) {
        query.addField(fields);
    }
    query.setRows(DataApiHandler.MAX_ROWS).addSort("genome_name", SolrQuery.ORDER.asc);

    String pk = request.getParameter("param_key");
    Map<String, String> key = null;
    if (pk != null) {
        key = jsonReader.readValue(SessionHandler.getInstance().get(SessionHandler.PREFIX + pk));
    }

    if (key != null && key.containsKey("genomeIds") && !key.get("genomeIds").equals("")) {
        query.addFilterQuery("genome_id:(" + key.get("genomeIds").replaceAll(",", " OR ") + ")");
    }

    LOGGER.trace("getGenomeDetails(): [{}] {}", SolrCore.GENOME.getSolrCoreName(), query);

    String apiResponse = dataApi.solrQuery(SolrCore.GENOME, query);
    Map resp = jsonReader.readValue(apiResponse);
    Map respBody = (Map) resp.get("response");

    int numFound = (Integer) respBody.get("numFound");
    List<Map> sdl = (List<Map>) respBody.get("docs");

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

    JSONObject jsonResult = new JSONObject();
    jsonResult.put("results", docs);
    jsonResult.put("total", numFound);
    jsonResult.writeJSONString(writer);
}

From source file:filesscanner.MainWindow.java

private void saveToJSONBtnActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_saveToJSONBtnActionPerformed

    JSONObject object = new JSONObject();

    for (int i = 0; i < modelFiles.getSize(); i++) {

        object.put("filename" + i, modelFiles.get(i).toString());

    }//  w ww .  j a v a2  s  . c o  m

    File file = new File("C:");
    JFileChooser chooser = ShowChooser(file);
    chooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
    chooser.setDialogType(JFileChooser.SAVE_DIALOG);
    int res = chooser.showDialog(this, "  ? ??!!!");
    if (res == JFileChooser.APPROVE_OPTION) {

        try {
            Writer writer = new FileWriter(chooser.getSelectedFile());
            object.writeJSONString(writer);
            JOptionPane.showMessageDialog(rootPane, "SAVED SUCCESFULLY!!!");
            writer.flush();
            writer.close();
        } catch (IOException ex) {
            Logger.getLogger(MainWindow.class.getName()).log(Level.SEVERE, null, ex);
            JOptionPane.showMessageDialog(rootPane, "Something bad!!!");
        }

    }

}

From source file:cc.siara.csv_ml_demo.MainActivity.java

/**
 * Transforms csv_ml to JSON Object/*from  w w  w.j  a va  2s  .c  om*/
 */
void toJSON() {
    EditText etInput = (EditText) findViewById(R.id.etInput);
    CheckBox cbPretty = (CheckBox) findViewById(R.id.cbPretty);
    MultiLevelCSVParser parser = new MultiLevelCSVParser();
    try {
        JSONObject jo = parser.parseToJSO(new StringReader(etInput.getText().toString()), false);
        String ex_str = parser.getEx().get_all_exceptions();
        if (ex_str.length() > 0) {
            Toast.makeText(getApplicationContext(), ex_str, Toast.LENGTH_LONG).show();
            if (parser.getEx().getErrorCode() > 0)
                return;
        }
        String outStr = null;
        if (cbPretty.isChecked()) {
            JSONWriter jw = new JSONWriter();
            try {
                jo.writeJSONString(jw);
            } catch (IOException e) {
                e.printStackTrace();
            }
            outStr = jw.toString();
        } else
            outStr = jo.toJSONString();
        EditText etOutput = (EditText) findViewById(R.id.etOutput);
        etOutput.setText(outStr);
        // tfOutputSize.setText(String.valueOf(outStr.length()));
    } catch (IOException e) {
        Toast.makeText(getApplicationContext(), e.getMessage(), Toast.LENGTH_LONG).show();
    }
}

From source file:edu.vt.vbi.patric.portlets.IDMapping.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 keyword = request.getParameter("keyword");
        String from = request.getParameter("from");
        String fromGroup = request.getParameter("fromGroup");
        String to = request.getParameter("to");
        String toGroup = request.getParameter("toGroup");

        if (!keyword.equals("")) {
            key.put("keyword", keyword.replaceAll("\n", " OR ").replaceAll(",", " OR "));
        }/*ww w  . ja  va 2  s . c  o  m*/

        key.put("from", from);
        key.put("to", to);
        key.put("fromGroup", fromGroup);
        key.put("toGroup", toGroup);

        // random
        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 != null && sraction.equals("filters")) {
        // this.responseWriteFilters(response);
        this.responseWriteFiltersStatic(response);
    } else if (sraction != null && sraction.equals("download")) {
        processDownload(request, response);
    } else {

        DataApiHandler dataApi = new DataApiHandler(request);

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

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

        LOGGER.debug("id mapping param: {}", key);

        JSONObject jsonResult = processIDMapping(dataApi, key.get("from"), key.get("fromGroup"), key.get("to"),
                key.get("toGroup"), key.get("keyword"));

        response.setContentType("application/json");
        jsonResult.writeJSONString(response.getWriter());
    }
}

From source file:de.jaide.courier.email.SmtpConfiguration.java

/**
 * Returns the SMTP configuration as a JSON string.
 * //from  w w w. j ava  2  s .  c o m
 * @return The SMTP configuration as a JSON string.
 */
@SuppressWarnings("unchecked")
@Override
public String toJSONString() {
    JSONObject entry = new JSONObject();

    Map<String, Object> configuration = new LinkedHashMap<String, Object>();
    configuration.put("smtpHostname", smtpHostname);
    configuration.put("smtpPort", new Integer(smtpPort));
    configuration.put("tls", tls);
    configuration.put("ssl", ssl);
    configuration.put("username", username);
    configuration.put("password", password);
    configuration.put("fromEMail", fromEMail);
    configuration.put("fromSenderName", fromSenderName);

    entry.put(configurationName, configuration);

    /*
     * The JSONWriter will pretty-print the output
     */
    Writer jsonWriter = new JSONWriter();
    try {
        entry.writeJSONString(jsonWriter);
    } catch (IOException ioe) {
        throw new RuntimeException(ioe);
    }

    return jsonWriter.toString();
}

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

public void serveResource(ResourceRequest request, ResourceResponse response)
        throws PortletException, IOException {

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

    DataApiHandler dataApi = new DataApiHandler(request);

    String pathwayClass = request.getParameter("pathway_class");
    String pathwayId = request.getParameter("pathway_id");
    String ecNumber = request.getParameter("ec_number");
    String annotation = request.getParameter("algorithm");
    String contextId = request.getParameter("cId");
    String contextType = request.getParameter("cType");

    JSONObject jsonResult;

    switch (need) {
    case "0":
        jsonResult = this.processPathwayTab(dataApi, pathwayClass, pathwayId, ecNumber, annotation, contextType,
                contextId);//from w w  w. ja va2s.co  m
        response.setContentType("application/json");
        jsonResult.writeJSONString(response.getWriter());
        break;
    case "1":
        jsonResult = this.processEcNumberTab(dataApi, pathwayClass, pathwayId, ecNumber, annotation,
                contextType, contextId);
        response.setContentType("application/json");
        jsonResult.writeJSONString(response.getWriter());
        break;
    case "2":
        jsonResult = this.processGeneTab(dataApi, pathwayClass, pathwayId, ecNumber, annotation, contextType,
                contextId);
        response.setContentType("application/json");
        jsonResult.writeJSONString(response.getWriter());
        break;
    case "filter":
        getFilterData(request, response);
        break;
    case "download":
        this.processDownload(request, response);
        break;
    case "getFeatureIds":
        this.processFeatureIds(request, response);
        break;
    }
}

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  .  ja  v  a 2  s . c  om*/
        }
        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:cc.siara.csv_ml_demo.MultiLevelCSVSwingDemo.java

/**
 * Parses csv_ml from input box to JSON object and sets to output text box
 *//* w w  w. j  ava 2 s  .  c o m*/
void toJSON() {

    try {
        JSONObject jo = parser.parseToJSO(new StringReader(taInput.getText()), false);
        String ex_str = parser.getEx().get_all_exceptions();
        if (ex_str.length() > 0) {
            JOptionPane.showMessageDialog(null, ex_str);
            if (parser.getEx().getErrorCode() > 0)
                return;
        }
        String outStr;
        if (cbPretty.isSelected()) {
            JSONWriter jw = new JSONWriter();
            try {
                jo.writeJSONString(jw);
            } catch (IOException e) {
                e.printStackTrace();
            }
            outStr = jw.toString();
        } else
            outStr = jo.toJSONString();
        taOutput.setText(outStr);
        tfOutputSize.setText(String.valueOf(outStr.length()));
        taOutput.setCaretPosition(0);
    } catch (Exception e) {
        JOptionPane.showMessageDialog(null, e.getMessage());
        e.printStackTrace();
    }

}

From source file:com.intel.genomicsdb.GenomicsDBImporter.java

/**
 * Setup the importer after all the buffer streams are added, but before any
 * data is inserted into any stream//from w ww.  j  ava 2  s .  co m
 * No more buffer streams can be added once setupGenomicsDBImporter() is called
 * @throws IOException throws IOException if modified callsets JSON cannot be written
 */
public void setupGenomicsDBImporter() throws IOException {
    if (mIsLoaderSetupDone)
        return;
    //Callset mapping JSON - convert to string
    JSONObject topCallsetJSON = new JSONObject();
    topCallsetJSON.put("callsets", mCallsetMappingJSON);
    StringWriter stringWriter = new StringWriter();
    topCallsetJSON.writeJSONString(stringWriter);
    //Call native setupGenomicsDBImporter()
    mMaxBufferStreamIdentifiers = jniSetupGenomicsDBLoader(mGenomicsDBImporterObjectHandle,
            stringWriter.toString());
    //Why 2* - each identifier is a pair<buffer_stream_idx, partition_idx>
    //Why +1 - the last element will contain the number of exhausted stream identifiers
    //when importBatch() is called
    mExhaustedBufferStreamIdentifiers = new long[2 * ((int) mMaxBufferStreamIdentifiers) + 1];
    //Set all streams to empty
    //Add all streams to mExhaustedBufferStreamIdentifiers - this way when importBatch is
    //called the first time all streams' data are written
    for (int i = 0, idx = 0; i < mBufferStreamWrapperVector.size(); ++i, idx += 2) {
        SilentByteBufferStream currStream = mBufferStreamWrapperVector.get(i).mStream;
        currStream.setNumValidBytes(0);
        mExhaustedBufferStreamIdentifiers[idx] = i;
        mExhaustedBufferStreamIdentifiers[idx + 1] = 0;
    }
    //Set number of exhausted buffer streams - all streams are exhausted the first time
    mNumExhaustedBufferStreams = mBufferStreamWrapperVector.size();
    mExhaustedBufferStreamIdentifiers[(int) (2 * mMaxBufferStreamIdentifiers)] = mNumExhaustedBufferStreams;
    mIsLoaderSetupDone = true;
}