com.novartis.opensource.yada.format.RESTResultDelimitedConverter.java Source code

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Here is the source code for com.novartis.opensource.yada.format.RESTResultDelimitedConverter.java

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/**
 * Copyright 2016 Novartis Institutes for BioMedical Research Inc.
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 * http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
/**
 * 
 */
package com.novartis.opensource.yada.format;

import java.io.IOException;
import java.io.LineNumberReader;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

import org.json.JSONException;
import org.json.JSONObject;

import com.novartis.opensource.yada.YADAQueryResult;
import com.novartis.opensource.yada.YADARequest;
import com.novartis.opensource.yada.YADAResourceException;
import com.novartis.opensource.yada.io.YADAIOException;

/**
 * @author David Varon
 * @since 4.0.0
 */
public class RESTResultDelimitedConverter extends AbstractConverter {

    /**
     * Default constructor
     * @throws YADAResourceException when the path to {@code r.js} or {@code harmony.js} is corrupt
     * @throws YADAIOException when the path to {@code r.js} or {@code harmony.js} can't be read
     * @throws YADAConverterException when the Rhino javascript engine throws an error
     */
    public RESTResultDelimitedConverter() throws YADAResourceException, YADAIOException, YADAConverterException {
        // default constructor
        setHarmonizer(new Harmonizer());
    }

    /**
     * Constructor with {@link YADAQueryResult}
     * @param yqr the container for result processing artifacts
     * @throws YADAResourceException when the path to {@code r.js} or {@code harmony.js} is corrupt
     * @throws YADAIOException when the path to {@code r.js} or {@code harmony.js} can't be read
     * @throws YADAConverterException when the Rhino javascript engine throws an error
     */
    public RESTResultDelimitedConverter(YADAQueryResult yqr)
            throws YADAResourceException, YADAIOException, YADAConverterException {
        this.setYADAQueryResult(yqr);
        setHarmonizer(new Harmonizer());
    }

    /**
     * Creates a delimited result object using {@code newColSep} as a column
     * separator and {@code newRecSep} as a row separator.
     * 
     * @see com.novartis.opensource.yada.format.AbstractConverter#convert(java.lang.Object,
     *      java.lang.String, java.lang.String)
     */
    @Override
    public Object convert(Object o, String newColSep, String newRecSep) throws YADAConverterException {

        StringBuffer result = new StringBuffer();
        this.colsep = newColSep;
        this.recsep = newRecSep;

        try {
            getDelimitedRows(o);
        } catch (JSONException e) {
            String msg = "Unable to read Harmony Map";
            throw new YADAConverterException(msg, e);
        }
        return result;
    }

    /**
     * Parses global harmony map for duplicate values, and removes key/value pairs that
     * are not present in local harmony map.
     * @return the parsed global harmony map
     * @since 6.1.0
     */
    @Override
    public Object getHarmonyMap() {
        JSONObject globMap = (JSONObject) this.harmonyMap;
        JSONObject local = new JSONObject(getYADAQueryResult().getYADAQueryParamValue(YADARequest.PS_HARMONYMAP));
        ArrayList<Object> locVals = new ArrayList<>();
        ArrayList<String> omit = new ArrayList<>();
        for (Object k : local.keySet()) {
            locVals.add(local.get((String) k));
        }
        for (Object globalKey : globMap.keySet()) {
            String gk = (String) globalKey;
            Object gv = globMap.get(gk);
            if (locVals.contains(gv) && !local.has(gk)) // the value is associated to a different key in the local map
            {
                omit.add(gk);
            }
        }
        for (String k : omit) {
            globMap.remove(k);
        }
        return globMap;
    }

    /**
     * Converts hierarchical data in a JSON result to a
     * {@link java.lang.StringBuffer} containing tabular data delimited
     * accordingly per request parameters
     * 
     * @param rs
     *          the result set to convert
     * @throws YADAConverterException 
     * @throws SQLException
     *           when {@link ResultSet} or {@link ResultSetMetaData} iteration
     *           fails
     */
    protected void getDelimitedRows(Object result) throws YADAConverterException {
        String harm = (String) result;
        List<List<String>> convertedResults = new ArrayList<>();
        Harmonizer harmonizer = getHarmonizer();
        Object map = getHarmonyMap().toString();
        Object[] o = new Object[] { result, map };
        if (map != null) {
            harm = harmonizer.call(HARMONIZE, o);
        }
        o = new Object[] { harm };
        String delimited = harmonizer.call(FLATTEN, o), s = "";
        try (LineNumberReader lnr = new LineNumberReader(new StringReader(delimited))) {
            while ((s = lnr.readLine()) != null) {
                if (lnr.getLineNumber() == 1)
                    this.yqr.setConvertedHeader(Arrays.asList(s.split(",")));
                else
                    convertedResults.add(Arrays.asList(s.split(",")));
            }
        } catch (IOException e) {
            String msg = "Rhino javascript result could not be parsed.";
            throw new YADAConverterException(msg, e);
        }
        this.yqr.getConvertedResults().add(convertedResults);
    }
}