_csvDecode.java

public List<String> decodeCSV(List<String> lines) {
        return decode(lines.get(0));
    }

    public List<String> decode(String line) {
        List<String> result = new ArrayList<>();
        StringBuilder sb = new StringBuilder();
        boolean pendingWrap = false;
        int len = line.length();
        for (int i = 0; i < len; i++) {
            char c = line.charAt(i);
            if (c == ',') {
                if (pendingWrap) {
                    sb.append(',');
                } else {
                    result.add(sb.toString());
                    sb.setLength(0); // clear
                }
            } else if (c == '\"') {
                if (pendingWrap && i + 1 < len && line.charAt(i + 1) == '\"') {
                    sb.append('\"');
                    i++;
                } else {
                    pendingWrap = !pendingWrap;
                }
            } else {
                sb.append(c);
            }
        }
        if (sb.length() > 0) {
            result.add(sb.toString());
        }
        return result;
    }

_csvEncode.java

public String encodeCSV(List<String> lines) {
        StringBuilder sb = new StringBuilder();
        for (String line : lines) {
            sb.append(encode(line)).append(',');
        }
        sb.setLength(sb.length() - 1);
        return sb.toString();
    }

    public String encode (String line){
        boolean wrap = false;
        StringBuilder sb = new StringBuilder();
        for (int i = 0; i < line.length(); i++) {
            char c = line.charAt(i);
            if (c == ',') {
                wrap = true;
                sb.append(c);
            } else if (c == '\"') {
                wrap = true;
                sb.append('\"').append('\"');
            } else {
                sb.append(c);
            }
        }
        return wrap ? "\"" + sb.toString() + "\"" : sb.toString();
    }

CSV.java

import org.junit.Assert;
import org.junit.Test;

import java.io.*;
import java.util.*;

public class CSV {
    class InputValues {
        String cmd;
        int n;
        List<String> lines;
        public InputValues(String cmd, int n, List<String> lines) {
            this.cmd = cmd;
            this.n = n;
            this.lines = lines;
        }
        @Override
        public String toString() {
            String res = "cmd: " + cmd + "\nn: " + n;
            for (String line : lines) {
                res += "\n" + line;
            }
            return res;
        }
    }

    @Test
    public void testAll() {
        File[] files = readFolder("src/input/CSV");
        for (int i = 0; i < files.length; i+=2) {
            CSV.InputValues testEncode = readFile(files[i]);
            CSV.InputValues testDecode = readFile(files[i+1]);
            String  encodeResult = encodeCSV(testEncode.lines);
            Assert.assertEquals(encodeResult, testDecode.lines.get(0));
            List<String> decodeResult = decodeCSV(testDecode.lines);
            Assert.assertEquals(decodeResult, testEncode.lines);
        }
    }

    @Test
    public void generateOutput() throws IOException {
        File[] files = readFolder("src/input/CSV");
        for (int i = 0; i < files.length; i++) {
            File file = files[i];
            CSV.InputValues test = readFile(file);
            String outfileName = "src/output/CSV/" + file.getName().replace(".in", ".out");
            File outfile = new File(outfileName);
            outfile.getParentFile().mkdirs();
            outfile.createNewFile();
            PrintWriter printWriter = new PrintWriter(new FileWriter(outfileName));
            if ("encode".equals(test.cmd)) {
                String encodeResult = encodeCSV(test.lines);
                printWriter.println(encodeResult);
            } else if ("decode".equals(test.cmd)) {
                List<String> decodeResult = decodeCSV(test.lines);
                for (String line : decodeResult) {
                    printWriter.println(line);
                }
            }
            printWriter.close();
        }
    }

    public String encodeCSV(List<String> lines) {
        StringBuilder sb = new StringBuilder();
        for (String line : lines) {
            sb.append(encode(line)).append(',');
        }
        sb.setLength(sb.length() - 1);
        return sb.toString();
    }

    public String encode (String line){
        boolean wrap = false;
        StringBuilder sb = new StringBuilder();
        for (int i = 0; i < line.length(); i++) {
            char c = line.charAt(i);
            if (c == ',') {
                wrap = true;
                sb.append(c);
            } else if (c == '\"') {
                wrap = true;
                sb.append('\"').append('\"');
            } else {
                sb.append(c);
            }
        }
        return wrap ? "\"" + sb.toString() + "\"" : sb.toString();
    }

    public List<String> decodeCSV(List<String> lines) {
        return decode(lines.get(0));
    }

    public List<String> decode(String line) {
        List<String> result = new ArrayList<>();
        StringBuilder sb = new StringBuilder();
        boolean pendingWrap = false;
        int len = line.length();
        for (int i = 0; i < len; i++) {
            char c = line.charAt(i);
            if (c == ',') {
                if (pendingWrap) {
                    sb.append(',');
                } else {
                    result.add(sb.toString());
                    sb.setLength(0); // clear
                }
            } else if (c == '\"') {
                if (pendingWrap && i + 1 < len && line.charAt(i + 1) == '\"') {
                    sb.append('\"');
                    i++;
                } else {
                    pendingWrap = !pendingWrap;
                }
            } else {
                sb.append(c);
            }
        }
        if (sb.length() > 0) {
            result.add(sb.toString());
        }
        return result;
    }

    private int getInt(String name) {
        return Integer.parseInt(name.replaceAll("\\D", ""));
    }

    private File[] readFolder(String path) {
        File folder = new File(path);
        File[] files = folder.listFiles();
        Arrays.sort(files, (a, b) -> getInt(a.getName()) - getInt(b.getName()));
        return files;
    }

    private CSV.InputValues readFile(File file) {
        try {
            // assume the input file is always valid
            Scanner sc = new Scanner(file);
            String cmd = sc.nextLine().trim();
            int n = -1;
            if ("encode".equals(cmd)) {
                n = Integer.parseInt(sc.nextLine().trim());
            }
            List<String> lines = new ArrayList<>();
            while(sc.hasNextLine()){
                lines.add(sc.nextLine());
            }
            return new CSV.InputValues(cmd, n, lines);
        } catch (FileNotFoundException e) {
            System.out.println(file.getName() + " not exist");
        }
        return null;
    }

}