Handle BINARY(16) as UUID in Downloads

src/main/java/org/genesys2/server/service/impl/CSVResultSetHelper.java

+package org.genesys2.server.service.impl;
+
+import java.io.IOException;
+import java.io.Reader;
+import java.math.BigDecimal;
+import java.sql.Clob;
+import java.sql.ResultSet;
+import java.sql.ResultSetMetaData;
+import java.sql.SQLException;
+import java.sql.Time;
+import java.sql.Timestamp;
+import java.sql.Types;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.UUID;
+
+import org.genesys2.util.NumberUtils;
+
+import au.com.bytecode.opencsv.ResultSetHelperService;
+
+/**
+ * This class extends {@link ResultSetHelperService} by adding support for UUID.
+ * Copied straigth from superclass.
+ */
+public class CSVResultSetHelper extends ResultSetHelperService {
+
+	public static final int CLOBBUFFERSIZE = 2048;
+
+	// note: we want to maintain compatibility with Java 5 VM's
+	// These types don't exist in Java 5
+	private static final int NVARCHAR = -9;
+	private static final int NCHAR = -15;
+	private static final int LONGNVARCHAR = -16;
+	private static final int NCLOB = 2011;
+
+	/// Copied straight from superclass
+	@Override
+	public String[] getColumnValues(ResultSet rs) throws SQLException, IOException {
+
+		List<String> values = new ArrayList<String>();
+		ResultSetMetaData metadata = rs.getMetaData();
+
+		for (int i = 0; i < metadata.getColumnCount(); i++) {
+			values.add(getColumnValue(rs, metadata.getColumnType(i + 1), i + 1));
+		}
+
+		String[] valueArray = new String[values.size()];
+		return values.toArray(valueArray);
+	}
+
+	private String handleObject(Object obj) {
+		return obj == null ? "" : String.valueOf(obj);
+	}
+
+	private String handleBigDecimal(BigDecimal decimal) {
+		return decimal == null ? "" : decimal.toString();
+	}
+
+	private String handleLong(ResultSet rs, int columnIndex) throws SQLException {
+		long lv = rs.getLong(columnIndex);
+		return rs.wasNull() ? "" : Long.toString(lv);
+	}
+
+	private String handleInteger(ResultSet rs, int columnIndex) throws SQLException {
+		int i = rs.getInt(columnIndex);
+		return rs.wasNull() ? "" : Integer.toString(i);
+	}
+
+	private String handleDate(ResultSet rs, int columnIndex) throws SQLException {
+		java.sql.Date date = rs.getDate(columnIndex);
+		String value = null;
+		if (date != null) {
+			SimpleDateFormat dateFormat = new SimpleDateFormat("dd-MMM-yyyy");
+			value = dateFormat.format(date);
+		}
+		return value;
+	}
+
+	private String handleBinary(ResultSet rs, int colIndex) throws SQLException {
+		byte[] bs = rs.getBytes(colIndex);
+
+		if (bs == null) {
+			return null;
+		}
+		
+		if (bs.length == 16) {
+			// UUID?
+			UUID uuid = NumberUtils.toUUID(bs);
+			return uuid.toString();
+		} else {
+			// TODO FIXME What to do with other binary?
+			return "";
+		}
+	}
+
+	private String handleTime(Time time) {
+		return time == null ? null : time.toString();
+	}
+
+	private String handleTimestamp(Timestamp timestamp) {
+		SimpleDateFormat timeFormat = new SimpleDateFormat("dd-MMM-yyyy HH:mm:ss");
+		return timestamp == null ? null : timeFormat.format(timestamp);
+	}
+
+	private String getColumnValue(ResultSet rs, int colType, int colIndex) throws SQLException, IOException {
+
+		String value = "";
+
+		switch (colType) {
+		case Types.BIT:
+		case Types.JAVA_OBJECT:
+			value = handleObject(rs.getObject(colIndex));
+			break;
+		case Types.BOOLEAN:
+			boolean b = rs.getBoolean(colIndex);
+			value = Boolean.valueOf(b).toString();
+			break;
+		case NCLOB: // todo : use rs.getNClob
+		case Types.CLOB:
+			Clob c = rs.getClob(colIndex);
+			if (c != null) {
+				value = read(c);
+			}
+			break;
+		case Types.BIGINT:
+			value = handleLong(rs, colIndex);
+			break;
+		case Types.DECIMAL:
+		case Types.DOUBLE:
+		case Types.FLOAT:
+		case Types.REAL:
+		case Types.NUMERIC:
+			value = handleBigDecimal(rs.getBigDecimal(colIndex));
+			break;
+		case Types.INTEGER:
+		case Types.TINYINT:
+		case Types.SMALLINT:
+			value = handleInteger(rs, colIndex);
+			break;
+		case Types.DATE:
+			value = handleDate(rs, colIndex);
+			break;
+		case Types.TIME:
+			value = handleTime(rs.getTime(colIndex));
+			break;
+		case Types.TIMESTAMP:
+			value = handleTimestamp(rs.getTimestamp(colIndex));
+			break;
+		case NVARCHAR: // todo : use rs.getNString
+		case NCHAR: // todo : use rs.getNString
+		case LONGNVARCHAR: // todo : use rs.getNString
+		case Types.LONGVARCHAR:
+		case Types.VARCHAR:
+		case Types.CHAR:
+			value = rs.getString(colIndex);
+			break;
+		case Types.BINARY:
+			value = handleBinary(rs, colIndex);
+			break;
+		default:
+//			System.err.println("SQLType not handled " + colType);
+			value = "";
+		}
+
+		if (value == null) {
+			value = "";
+		}
+
+		return value;
+
+	}
+
+	private static String read(Clob c) throws SQLException, IOException {
+		StringBuilder sb = new StringBuilder((int) c.length());
+		Reader r = c.getCharacterStream();
+		char[] cbuf = new char[CLOBBUFFERSIZE];
+		int n;
+		while ((n = r.read(cbuf, 0, cbuf.length)) != -1) {
+			sb.append(cbuf, 0, n);
+		}
+		return sb.toString();
+	}
+}

src/main/java/org/genesys2/server/service/impl/GenesysServiceImpl.java

@@ -1209,7 +1209,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 		csv.writeNext(new String[] { "genesysId", "uuid", "instCode", "acceNumb", "genus", "species", "fullTaxa", "orgCty", "acqSrc", "acqDate", "mlsStat",
 				"available", "historic", "storage", "sampStat", "duplSite", "createdBy", "createdDate", "lastModifiedBy", "lastModifiedDate" });
 
-		final ResultSetHelper csvResultsetHelper = new ResultSetHelperService();
+		final ResultSetHelper csvResultsetHelper = new CSVResultSetHelper();
 
 		// Write accession information
 		genesysLowlevelRepository.listAccessions(filters, new RowCallbackHandler() {

src/main/java/org/genesys2/util/NumberUtils.java

@@ -16,6 +16,7 @@
 
 package org.genesys2.util;
 
+import java.util.UUID;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
@@ -96,7 +97,21 @@ public abstract class NumberUtils {
 			}
 			v += d;
 		}
-		
+
 		return v;
 	}
+
+	/**
+	 * UUID from byte[]
+	 */
+	public static UUID toUUID(byte[] data) {
+		long msb = 0;
+		long lsb = 0;
+		assert data.length == 16 : "data must be 16 bytes in length";
+		for (int i = 0; i < 8; i++)
+			msb = (msb << 8) | (data[i] & 0xff);
+		for (int i = 8; i < 16; i++)
+			lsb = (lsb << 8) | (data[i] & 0xff);
+		return new UUID(msb, lsb);
+	}
 }