UploadBatchExcelReader.java

/* File:        col7a1/model/UploadBatch.java
 * Copyright:   GBIC 2000-2010, all rights reserved
 * Date:        August 11, 2010
 * 
 * generator:   org.molgenis.generators.excel.ExcelReaderGen 3.3.2-testing
 *
 * 
 * THIS FILE HAS BEEN GENERATED, PLEASE DO NOT EDIT!
 */

package org.molgenis.mutation.excel;

import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;

import jxl.Cell;
import jxl.Sheet;

import org.apache.log4j.Logger;
import org.molgenis.framework.db.CsvToDatabase;
import org.molgenis.framework.db.Database;
import org.molgenis.framework.db.Database.DatabaseAction;
import org.molgenis.framework.db.DatabaseException;
import org.molgenis.util.CsvWriter;
import org.molgenis.util.Entity;
import org.molgenis.util.SimpleTuple;
import org.molgenis.util.Tuple;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;

/**
 * Reads UploadBatch from Excel file.
 */
@Component
public class UploadBatchExcelReader
{
	public final transient Logger logger = Logger.getLogger(UploadBatchExcelReader.class);

	@Autowired
	private CsvToDatabase<Entity> uploadBatchCsvReader;

	/**
	 * Imports UploadBatch from a workbook sheet.
	 */
	public int importSheet(final Database db, Sheet sheet, final Tuple defaults, final DatabaseAction dbAction,
			final String missingValue) throws DatabaseException, IOException, Exception
	{
		File tmpUploadBatch = new File(System.getProperty("java.io.tmpdir") + File.separator + "tmpUploadBatch.txt");
		if (tmpUploadBatch.exists())
		{
			boolean deleteSuccess = tmpUploadBatch.delete();
			if (!deleteSuccess)
			{
				throw new Exception("Deletion of tmp file 'tmpUploadBatch.txt' failed, cannot proceed.");
			}
		}
		boolean createSuccess = tmpUploadBatch.createNewFile();
		if (!createSuccess)
		{
			throw new Exception("Creation of tmp file 'tmpUploadBatch.txt' failed, cannot proceed.");
		}
		boolean fileHasHeaders = writeSheetToFile(sheet, tmpUploadBatch);
		if (fileHasHeaders)
		{
			int count = this.uploadBatchCsvReader.importCsv(db, tmpUploadBatch, defaults, dbAction, missingValue);
			tmpUploadBatch.delete();
			return count;
		}
		else
		{
			tmpUploadBatch.delete();
			return 0;
		}
	}

	public List<String> getNonEmptyHeaders(Sheet sheet)
	{
		List<String> headers = new ArrayList<String>();
		Cell[] headerCells = sheet.getRow(0); // assume headers are on first
												// line
		for (int i = 0; i < headerCells.length; i++)
		{
			if (!headerCells[i].getContents().equals(""))
			{
				headers.add(headerCells[i].getContents());
			}
		}
		return headers;
	}

	private boolean writeSheetToFile(Sheet sheet, File file) throws IOException
	{
		List<String> headers = new ArrayList<String>();
		Cell[] headerCells = sheet.getRow(0); // assume headers are on first
												// line
		if (headerCells.length == 0)
		{
			return false;
		}
		ArrayList<Integer> namelessHeaderLocations = new ArrayList<Integer>(); // allow
																				// for
																				// empty
																				// columns,
																				// also
																				// column
																				// order
																				// does
																				// not
																				// matter
		for (int i = 0; i < headerCells.length; i++)
		{
			if (!headerCells[i].getContents().equals(""))
			{
				headers.add(headerCells[i].getContents());
			}
			else
			{
				headers.add("nameless" + i);
				namelessHeaderLocations.add(i);
			}
		}
		PrintWriter pw = new PrintWriter(file);
		CsvWriter cw = new CsvWriter(pw, headers);
		cw.setMissingValue("");
		cw.writeHeader();
		for (int rowIndex = 1; rowIndex < sheet.getRows(); rowIndex++)
		{
			Tuple t = new SimpleTuple();
			int colIndex = 0;
			for (Cell c : sheet.getRow(rowIndex))
			{
				if (!namelessHeaderLocations.contains(colIndex))
				{
					t.set(headers.get(colIndex), c.getContents());
				}
				colIndex++;
			}
			cw.writeRow(t);
		}
		cw.close();
		return true;
	}

	public void setUploadBatchCsvReader(CsvToDatabase<Entity> uploadBatchCsvReader)
	{
		this.uploadBatchCsvReader = uploadBatchCsvReader;
	}
}