Example usage for javax.json JsonException getMessage

Introduction

In this page you can find the example usage for javax.json JsonException getMessage.

Prototype

public String getMessage() 

Source Link

Document

Returns the detail message string of this throwable.

Usage

From source file:edu.harvard.hms.dbmi.bd2k.irct.ri.i2b2transmart.I2B2TranSMARTResourceImplementation.java

@Override
public Result runQuery(SecureSession session, Query query, Result result) throws ResourceInterfaceException {
    result = super.runQuery(session, query, result);

    if (result.getResultStatus() != ResultStatus.ERROR) {
        String resultInstanceId = result.getResourceActionId();
        String resultId = resultInstanceId.split("\\|")[2];
        try {//from   www. j av  a  2 s  .c  om
            // Wait for it to be either ready or fail
            result = checkForResult(session, result);
            while ((result.getResultStatus() != ResultStatus.ERROR)
                    && (result.getResultStatus() != ResultStatus.COMPLETE)) {
                Thread.sleep(3000);
                result = checkForResult(session, result);
            }
            if (result.getResultStatus() == ResultStatus.ERROR) {
                return result;
            }
            result.setResultStatus(ResultStatus.RUNNING);
            // Loop through the select clauses to build up the select string
            String gatherAllEncounterFacts = "false";
            Map<String, String> aliasMap = new HashMap<String, String>();

            for (ClauseAbstract clause : query.getClauses().values()) {
                if (clause instanceof SelectClause) {
                    SelectClause selectClause = (SelectClause) clause;
                    String pui = convertPUItoI2B2Path(selectClause.getParameter().getPui());
                    aliasMap.put(pui, selectClause.getAlias());

                } else if (clause instanceof WhereClause) {
                    WhereClause whereClause = (WhereClause) clause;
                    String encounter = whereClause.getStringValues().get("ENCOUNTER");
                    if ((encounter != null) && (encounter.equalsIgnoreCase("yes"))) {
                        gatherAllEncounterFacts = "true";
                    }
                }

            }

            if (!aliasMap.isEmpty()) {

                ResultSet rs = (ResultSet) result.getData();
                if (rs.getSize() == 0) {
                    rs = createInitialDataset(result, aliasMap, gatherAllEncounterFacts);
                    result.setData(rs);
                }

                // Loop through the columns submitting and appending to the
                // rows every 10
                List<String> parameterList = new ArrayList<String>();
                int counter = 0;
                String parameters = "";
                for (String param : aliasMap.keySet()) {
                    if (counter == 10) {
                        parameterList.add(parameters);
                        counter = 0;
                        parameters = "";
                    }
                    if (!parameters.equals("")) {
                        parameters += "|";
                    }
                    parameters += param;
                }
                if (!parameters.equals("")) {
                    parameterList.add(parameters);
                }

                for (String parameter : parameterList) {
                    // Call the tranSMART API to get the dataset
                    String url = this.transmartURL + "/ClinicalData/retrieveClinicalData?rid=" + resultId
                            + "&conceptPaths=" + URLEncoder.encode(parameter, "UTF-8")
                            + "&gatherAllEncounterFacts=" + gatherAllEncounterFacts;
                    HttpClient client = createClient(session);
                    HttpGet get = new HttpGet(url);
                    try {
                        HttpResponse response = client.execute(get);
                        JsonReader reader = Json.createReader(response.getEntity().getContent());
                        JsonArray arrayResults = reader.readArray();
                        // Convert the dataset to Tabular format
                        result = convertJsonToResultSet(result, arrayResults, aliasMap,
                                gatherAllEncounterFacts);
                    } catch (JsonException e) {
                    }
                }

            }
            // Set the status to complete
            result.setResultStatus(ResultStatus.COMPLETE);
        } catch (InterruptedException | UnsupportedOperationException | IOException | ResultSetException
                | PersistableException e) {
            result.setResultStatus(ResultStatus.ERROR);
            result.setMessage(e.getMessage());
        }
    }
    return result;
}

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