com.novartis.opensource.yada.io.YADABufferedReader.java Source code

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Here is the source code for com.novartis.opensource.yada.io.YADABufferedReader.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.io;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.Reader;

import org.apache.log4j.Logger;
import org.json.JSONException;
import org.json.JSONObject;

/**
 * A subclass of {@link java.io.BufferedReader} which contains methods for returning a line of input 
 * as a {@link JSONObject}
 * @author David Varon
 *
 */
public class YADABufferedReader extends BufferedReader {

    /**
     * Local logger handle
     */
    private static Logger l = Logger.getLogger(YADABufferedReader.class);

    /**
     * Instance variable.  The {@link FileHelper} enables functionality essential to {@link #readLine2JSON()} 
     * such as access to the index of column headers which are required to be used as json keys.
     */
    private FileHelper helper;

    /**
     * Override of super-constructor with additional {@code helper} argument.
     * @param reader a java i/o object
     * @param helper a YADA FileHelper to handle headers
     * @throws YADAIOException when the {@code helper} can't be set
     */
    public YADABufferedReader(Reader reader, FileHelper helper) throws YADAIOException {
        super(reader);
        setFileHelper(helper);
    }

    /**
     * Override of super-constructor with additional {@code helper} argument.
     * @param reader java i/o component
     * @param bufferSize the size of the internal buffer to store processed content
     * @param helper the YADA FileHelper for handling headers
     * @throws YADAIOException when the {@code helper} can't be set
     */
    public YADABufferedReader(Reader reader, int bufferSize, FileHelper helper) throws YADAIOException {
        super(reader, bufferSize);
        setFileHelper(helper);
    }

    /**
     * Called by the constructor to set the instance variable, this method also, in turn sets the 
     * the current object (a subclass of {@link java.io.Reader}) as an instance variable in the {@code helper}
     * (via {@link FileHelper#setReader(Reader)}). It also calls {@link FileHelper#setHeaders()} 
     * @param helper the FileHelper subclass to handle headers
     * @throws YADAIOException when helper can't set the headers
     * @see FileHelper
     */
    private void setFileHelper(FileHelper helper) throws YADAIOException {
        this.helper = helper;
        helper.setReader(this);
        helper.setHeaders();
    }

    /**
     * Alternative to {@link java.io.BufferedReader#readLine()} which will wrap content of a line in JSON using corresponding 
     * indexed column headers as keys.
     * @return a json object containing a line of content with corresponding column headers as keys and column values as values.
     * @throws YADAIOException when the content can't be read, or wrapped in JSON successfully
     */
    public JSONObject readLine2JSON() throws YADAIOException {
        JSONObject result = null;
        try {
            String orig = this.readLine();
            l.debug(orig);
            if (null != orig) {
                String[] line = orig.split(this.helper.getDelimiter());
                String[] head = this.helper.getColHeaderArray();
                if (line.length == head.length) {
                    result = new JSONObject();
                    for (int i = 0; i < line.length; i++) {
                        result.put(head[i], line[i]);
                    }
                    l.debug(result);
                } else {
                    String msg = "Header/Line of different lengths: " + head.length + "/" + line.length;
                    throw new YADAIOException(msg);
                }
            }
        } catch (IOException e) {
            l.error(e.getMessage());
            e.printStackTrace();
            throw new YADAIOException(e.getMessage(), e);
        } catch (JSONException e) {
            l.error(e.getMessage());
            e.printStackTrace();
            throw new YADAIOException(e.getMessage(), e);
        }
        return result;
    }

}