In this article, I am going to explain how to merge two excel files. Some time we may need to do excel merging programmitically. If you want to do any modification by logic in merging, you can do using this program easily. To implement this program you need to download Apache POI library and have it in your build path (copy POI jars to lib folder).
There is no direct method to merge excel files using java. You have need to follow the below flow.
Click Here To Download Eclipse Project

Flow of the program

  1. Get Excel files
  2. Get Work Books of those excel files
  3. Get sheets to be merged in those excel files
  4. Read every row and add it to other sheet
  5. Read every cell and add it to the row
  6. Write merged workbook to output file

Java Code

import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;
import org.apache.poi.hssf.usermodel.HSSFCell;
import org.apache.poi.hssf.usermodel.HSSFCellStyle;
import org.apache.poi.hssf.usermodel.HSSFRow;
import org.apache.poi.ss.usermodel.Cell;
import org.apache.poi.ss.usermodel.Row;
import org.apache.poi.xssf.usermodel.XSSFCell;
import org.apache.poi.xssf.usermodel.XSSFCellStyle;
import org.apache.poi.xssf.usermodel.XSSFRow;
import org.apache.poi.xssf.usermodel.XSSFSheet;
import org.apache.poi.xssf.usermodel.XSSFWorkbook;

public class MergeExcel {

    public static void main(String[] args) {
        try {
            // excel files
            FileInputStream excellFile1 = new FileInputStream(new File(
                    "C:\\excel1.xlsx"));
            FileInputStream excellFile2 = new FileInputStream(new File(
                    "C:\\excel2.xlsx"));

            // Create Workbook instance holding reference to .xlsx file
            XSSFWorkbook workbook1 = new XSSFWorkbook(excellFile1);
            XSSFWorkbook workbook2 = new XSSFWorkbook(excellFile2);

            // Get first/desired sheet from the workbook
            XSSFSheet sheet1 = workbook1.getSheetAt(0);
            XSSFSheet sheet2 = workbook2.getSheetAt(0);

            // add sheet2 to sheet1
            addSheet(sheet1, sheet2);
            excellFile1.close();

            // save merged file
            File mergedFile = new File(
                    "C:\\merged.xlsx");
            if (!mergedFile.exists()) {
                mergedFile.createNewFile();
            }
            FileOutputStream out = new FileOutputStream(mergedFile);
            workbook1.write(out);
            out.close();
            System.out
                    .println("Files were merged succussfully");
        } catch (Exception e) {
            e.printStackTrace();
        }

    }

    public static void addSheet(XSSFSheet mergedSheet, XSSFSheet sheet) {
        // map for cell styles
        Map<Integer, XSSFCellStyle> styleMap = new HashMap<Integer, XSSFCellStyle>();
        
        // This parameter is for appending sheet rows to mergedSheet in the end
        int len = mergedSheet.getLastRowNum();
        for (int j = sheet.getFirstRowNum(); j <= sheet.getLastRowNum(); j++) {

            XSSFRow row = sheet.getRow(j);
            XSSFRow mrow = mergedSheet.createRow(len + j + 1);

            for (int k = row.getFirstCellNum(); k < row.getLastCellNum(); k++) {
                XSSFCell cell = row.getCell(k);
                XSSFCell mcell = mrow.createCell(k);

                if (cell.getSheet().getWorkbook() == mcell.getSheet()
                        .getWorkbook()) {
                    mcell.setCellStyle(cell.getCellStyle());
                } else {
                    int stHashCode = cell.getCellStyle().hashCode();
                    XSSFCellStyle newCellStyle = styleMap.get(stHashCode);
                    if (newCellStyle == null) {
                        newCellStyle = mcell.getSheet().getWorkbook()
                                .createCellStyle();
                        newCellStyle.cloneStyleFrom(cell.getCellStyle());
                        styleMap.put(stHashCode, newCellStyle);
                    }
                    mcell.setCellStyle(newCellStyle);
                }

                switch (cell.getCellType()) {
                case HSSFCell.CELL_TYPE_FORMULA:
                    mcell.setCellFormula(cell.getCellFormula());
                    break;
                case HSSFCell.CELL_TYPE_NUMERIC:
                    mcell.setCellValue(cell.getNumericCellValue());
                    break;
                case HSSFCell.CELL_TYPE_STRING:
                    mcell.setCellValue(cell.getStringCellValue());
                    break;
                case HSSFCell.CELL_TYPE_BLANK:
                    mcell.setCellType(HSSFCell.CELL_TYPE_BLANK);
                    break;
                case HSSFCell.CELL_TYPE_BOOLEAN:
                    mcell.setCellValue(cell.getBooleanCellValue());
                    break;
                case HSSFCell.CELL_TYPE_ERROR:
                    mcell.setCellErrorValue(cell.getErrorCellValue());
                    break;
                default:
                    mcell.setCellValue(cell.getStringCellValue());
                    break;
                }
            }
        }
    }
}

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