From 2c530b054c2b0d4eb9845d294c646bd6840de082 Mon Sep 17 00:00:00 2001
From: Nathanael Jourdane <nathanael.jourdane@irap.omp.eu>
Date: Wed, 9 Mar 2016 14:38:16 +0100
Subject: [PATCH] bugFix: Parse numeric data correctly.

---
 src/main/java/eu/omp/irap/vespa/epntapclient/votable/controller/VOTableDataParser.java | 74 +++++++++++++++++++++++++++++++++++---------------------------------------
 1 file changed, 35 insertions(+), 39 deletions(-)

diff --git a/src/main/java/eu/omp/irap/vespa/epntapclient/votable/controller/VOTableDataParser.java b/src/main/java/eu/omp/irap/vespa/epntapclient/votable/controller/VOTableDataParser.java
index 6b688a7..81963c6 100644
--- a/src/main/java/eu/omp/irap/vespa/epntapclient/votable/controller/VOTableDataParser.java
+++ b/src/main/java/eu/omp/irap/vespa/epntapclient/votable/controller/VOTableDataParser.java
@@ -17,6 +17,7 @@
 package eu.omp.irap.vespa.epntapclient.votable.controller;
 
 import java.io.IOException;
+import java.nio.ByteBuffer;
 import java.util.ArrayList;
 import java.util.Base64;
 import java.util.HashMap;
@@ -53,7 +54,7 @@ public class VOTableDataParser {
 	private String[] columnsName;
 
 	/** The byte array stored in the VOTable Table stream (if any). */
-	private byte[] bytes;
+	private ByteBuffer stream;
 
 	/** The index of the current position in the bytes array. */
 	private int cursor;
@@ -178,19 +179,19 @@ public class VOTableDataParser {
 	/**
 	 * get the data on its BINARY form.
 	 * 
-	 * @param stream the data Stream in the VOTable Table.
+	 * @param voStream the data Stream in the VOTable Table.
 	 * @param fields The Fields corresponding to the Table.
 	 * @throws UnsupportedOperationException Data as arrays are not supported yet.
 	 */
-	private void parseBinaryStream(Stream stream, List<Field> fields) {
+	private void parseBinaryStream(Stream voStream, List<Field> fields) {
 		logger.info("Parsing data in BINARY stream...");
-		String strStream = stream.getValue().replaceAll("(\\r|\\n)", "");
+		String strStream = voStream.getValue().replaceAll("(\\r|\\n)", "");
 
-		bytes = Base64.getDecoder().decode(strStream);
+		stream = ByteBuffer.wrap(Base64.getDecoder().decode(strStream));
 		Object[] row = new Object[columnsName.length];
 
 		int nValue = 0;
-		while (cursor < bytes.length) {
+		while (stream.hasRemaining()) {
 			int nColumn = nValue % columnsName.length;
 			Field column = fields.get(nColumn);
 			DataType dataType = column.getDatatype();
@@ -214,39 +215,50 @@ public class VOTableDataParser {
 			if (column.getArraysize() == null) {
 				arraySize = blockSize;
 			} else if ("*".equals(column.getArraysize())) {
-				arraySize = getValue(4) * blockSize;
+				arraySize = stream.getInt() * blockSize;
 			} else {
 				arraySize = Integer.parseInt(column.getArraysize()) * blockSize;
 			}
-
 			if ((arraySize != blockSize) && !(dataType.equals(DataType.CHAR)
 					|| dataType.equals(DataType.UNICODE_CHAR))) {
-				throw new UnsupportedOperationException("Data as arrays are not supported yet.");
+				throw new UnsupportedOperationException("Numeric data as array are not supported.");
 			}
 
 			if (nColumn == 0) {
 				row = new Object[columnsName.length];
 			}
 
-			if (dataType.equals(DataType.CHAR) || dataType.equals(DataType.UNICODE_CHAR)) {
+			if (dataType.equals(DataType.BOOLEAN)) {
+				row[nColumn] = new Boolean(stream.getInt() == 0 ? false : true);
+			} else if (dataType.equals(DataType.UNSIGNED_BYTE)) {
+				row[nColumn] = stream.get();
+			} else if (dataType.equals(DataType.SHORT)) {
+				row[nColumn] = stream.getShort();
+			} else if (dataType.equals(DataType.INT)) {
+				row[nColumn] = stream.getInt();
+			} else if (dataType.equals(DataType.LONG)) {
+				row[nColumn] = stream.getLong();
+			} else if (dataType.equals(DataType.CHAR)) {
 				String value = new String();
-				for (int i = 0; i < arraySize && cursor < bytes.length; i += blockSize) {
-					value += (char) getValue(blockSize);
+				for (int i = 0; i < arraySize && cursor < stream.capacity(); i++) {
+					value += (char) stream.get();
 				}
 				row[nColumn] = value.trim();
-			} else if (dataType.equals(DataType.BOOLEAN) || dataType.equals(DataType.BIT)) {
-				row[nColumn] = new Boolean(getValue(blockSize) == 0 ? false : true);
-			} else if (dataType.equals(DataType.UNSIGNED_BYTE) || dataType.equals(DataType.SHORT)) {
-				row[nColumn] = new Short((short) getValue(blockSize));
-			} else if (dataType.equals(DataType.INT)) {
-				row[nColumn] = new Integer(getValue(blockSize));
-			} else if (dataType.equals(DataType.LONG)) {
-				row[nColumn] = new Long(getValue(blockSize));
-			} else { // float
-				row[nColumn] = new Float(getValue(blockSize));
+			} else if (dataType.equals(DataType.UNICODE_CHAR)) {
+				String value = new String();
+				for (int i = 0; i < arraySize && cursor < stream.capacity(); i += 2) {
+					value += stream.getChar();
+				}
+				row[nColumn] = value.trim();
+			} else if (dataType.equals(DataType.FLOAT)) {
+				row[nColumn] = stream.getFloat();
+			} else if (dataType.equals(DataType.DOUBLE)) {
+				row[nColumn] = stream.getDouble();
+			} else {
+				logger.warn("Data type " + dataType + " is not supprted.");
 			}
 
-			// logger.debug("**" + columnsName[nColumn] + "**: " + row[nColumn])
+			// logger.debug(columnsName[nColumn] + ": " + row[nColumn])
 
 			row[nColumn] = row[nColumn];
 			if (nColumn == columnsName.length - 1) {
@@ -283,20 +295,4 @@ public class VOTableDataParser {
 		logger.info("Parsing data in FITS stream...");
 		// TODO Implement parseFITSStream()
 	}
-
-	/**
-	 * Get the integer value of a bytes block. For example, [0x01, 0x05] returns 230, and increment
-	 * the cursor.
-	 * 
-	 * @param blockSize The size of the bytes block to get
-	 * @return The integer value of the bytes block.
-	 */
-	private int getValue(int blockSize) {
-		int intVal = 0;
-		for (int i = 0; i < blockSize; i++) {
-			intVal += 0xFF & (bytes[cursor + i] << ((blockSize - 1 - i) * 8));
-		}
-		cursor += blockSize;
-		return intVal;
-	}
 }
--
libgit2 0.21.2