BinaryStreamParser.java
10 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
/*
* This file is a part of EpnTAPClient.
* This program aims to provide EPN-TAP support for software clients, like CASSIS spectrum analyzer.
* See draft specifications: https://voparis-confluence.obspm.fr/pages/viewpage.action?pageId=559861
* Copyright (C) 2016 Institut de Recherche en Astrophysique et Planétologie.
*
* This program is free software: you can
* redistribute it and/or modify it under the terms of the GNU General Public License as published
* by the Free Software Foundation, either version 3 of the License, or (at your option) any later
* version. This program is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details. You should have received a copy of
* the GNU General Public License along with this program. If not, see
* <http://www.gnu.org/licenses/>.
*/
package eu.omp.irap.vespa.votable.votabledata;
import java.nio.BufferUnderflowException;
import java.nio.ByteBuffer;
import java.util.ArrayList;
import java.util.List;
import java.util.StringJoiner;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.xml.bind.DatatypeConverter;
import eu.omp.irap.vespa.epntapclient.votable.model.DataType;
import eu.omp.irap.vespa.epntapclient.votable.model.Field;
import eu.omp.irap.vespa.epntapclient.votable.model.Stream;
import eu.omp.irap.vespa.votable.votable.VOTableException.CantParseVOTableException;
/**
* @author N. Jourdane
*/
public final class BinaryStreamParser implements DataParser {
/** The logger for the class BinaryStreamParser. */
private static final Logger LOGGER = Logger.getLogger(BinaryStreamParser.class.getName());
/** The index of the current position in the bytes array. */
private int cursor;
/** The XML nodes of VOTable document, containing the column names. */
private List<Field> fieldsNodes;
/** The byte array stored in the VOTable Table stream (if any). */
private int rowSize;
/** The stream to parse, containing data (column rows) stored in the VOTable. */
private ByteBuffer stream;
/**
* Constructor of BinaryStreamParser.
*
* @param voStream The stream to parse, containing data (column rows) stored in the VOTable.
* @param fieldsNodes the field XML nodes in VOTable document, containing the column names.
* @see <a href="http://www.ivoa.net/documents/REC/VOTable/VOTable-20040811.html#ToC35">The
* Binary serialization in the VOTable REC.</a>
*/
public BinaryStreamParser(Stream voStream, List<Field> fieldsNodes) {
cursor = 0;
this.fieldsNodes = fieldsNodes;
String strStream = voStream.getValue().replaceAll("(\\r|\\n)", "");
stream = ByteBuffer.wrap(DatatypeConverter.parseBase64Binary(strStream));
}
/**
* Get the size of data block according to its type.
*
* @param dataType The type of the data block, as described in the VOTable REC. See
* http://www.ivoa.net/documents/REC/VOTable/VOTable-20040811.html#ToC11
* @return The size of the block, in bytes.
*/
private static int getBlockSize(DataType dataType) {
int blockSize;
switch (dataType) {
case BOOLEAN:
case UNSIGNED_BYTE:
case CHAR:
blockSize = 1;
break;
case SHORT:
case UNICODE_CHAR:
blockSize = 2;
break;
case INT:
case FLOAT:
blockSize = 4;
break;
case LONG:
case DOUBLE:
case FLOAT_COMPLEX:
blockSize = 8;
break;
case DOUBLE_COMPLEX:
blockSize = 16;
break;
default:
blockSize = 0;
break;
}
return blockSize;
}
@Override
public List<Object[]> parse() throws CantParseVOTableException {
List<Object[]> data = new ArrayList<>();
int nbColumns = fieldsNodes.size();
BinaryStreamParser.LOGGER
.info("Parsing data (" + nbColumns + " columns) in BINARY stream...");
Object[] row = new Object[nbColumns];
int nValue = 0;
while (stream.hasRemaining()) {
int colId = nValue % nbColumns;
Field column = fieldsNodes.get(colId);
rowSize = getRowSize(column);
// May be useful: if arraySize == 0, continue
if (colId == 0) {
row = new Object[nbColumns];
}
row[colId] = processDataBlock(column.getDatatype());
if (colId == nbColumns - 1) {
data.add(row);
}
nValue++;
}
return data;
}
/**
* @param column The XML node of the VOTable data, containing informations about the column,
* like the data primitive type.
* @return The size of the row, in bytes.
* @throws BufferUnderflowException Can not get the array size because there is no bytes to read
* in the stream.
*/
private int getRowSize(Field column) {
DataType dataType = column.getDatatype();
int blockSize = getBlockSize(dataType);
int arraySize;
if (column.getArraysize() == null) {
arraySize = blockSize;
} else if ("*".equals(column.getArraysize())) {
try {
arraySize = stream.getInt() * blockSize;
} catch (BufferUnderflowException e) {
LOGGER.log(Level.SEVERE, "No space left on stream, can not get array size", e);
throw new BufferUnderflowException();
}
} else {
arraySize = Integer.parseInt(column.getArraysize()) * blockSize;
}
return arraySize;
}
/**
* @param dataType The type of the data block.
* @return An object representing the data. It can be any of the primitive type defined in the
* VOtableREC. See http://www.ivoa.net/documents/REC/VOTable/VOTable-20040811.html#ToC11
*/
private Object processDataBlock(DataType dataType) {
Object dataBlock;
int blockSize = getBlockSize(dataType);
if (dataType.equals(DataType.BOOLEAN)) {
if (rowSize != blockSize) {
int nb = rowSize / blockSize;
if (nb == 0) { dataBlock = ""; }
else {
StringJoiner sj = new StringJoiner(" ", "", "");
for (int i = 0; i < nb; i++) {
sj.add(String.valueOf(new Boolean(stream.getInt() == 0 ? false : true)));
}
dataBlock = sj.toString();
}
} else {
dataBlock = new Boolean(stream.getInt() == 0 ? false : true);
}
} else if (dataType.equals(DataType.UNSIGNED_BYTE)) {
if (rowSize != blockSize) {
int nb = rowSize / blockSize;
if (nb == 0) { dataBlock = ""; }
else {
StringJoiner sj = new StringJoiner(" ", "", "");
for (int i = 0; i < nb; i++) {
sj.add(String.valueOf(stream.get()));
}
dataBlock = sj.toString();
}
} else {
dataBlock = stream.get();
}
} else if (dataType.equals(DataType.SHORT)) {
if (rowSize != blockSize) {
int nb = rowSize / blockSize;
if (nb == 0) { dataBlock = ""; }
else {
StringJoiner sj = new StringJoiner(" ", "", "");
for (int i = 0; i < nb; i++) {
sj.add(String.valueOf(stream.getShort()));
}
dataBlock = sj.toString();
}
} else {
dataBlock = stream.getShort();
}
} else if (dataType.equals(DataType.INT)) {
if (rowSize != blockSize) {
int nb = rowSize / blockSize;
if (nb == 0) { dataBlock = ""; }
else {
StringJoiner sj = new StringJoiner(" ", "", "");
for (int i = 0; i < nb; i++) {
sj.add(String.valueOf(stream.getInt()));
}
dataBlock = sj.toString();
}
} else {
dataBlock = stream.getInt();
}
} else if (dataType.equals(DataType.LONG)) {
if (rowSize != blockSize) {
int nb = rowSize / blockSize;
if (nb == 0) { dataBlock = ""; }
else {
StringJoiner sj = new StringJoiner(" ", "", "");
for (int i = 0; i < nb; i++) {
sj.add(String.valueOf(stream.getLong()));
}
dataBlock = sj.toString();
}
} else {
dataBlock = stream.getLong();
}
} else if (dataType.equals(DataType.CHAR)) {
String value = new String();
for (int i = 0; i < rowSize && cursor < stream.capacity()
&& stream.position() < stream.limit(); i++) {
value += (char) stream.get();
}
dataBlock = value.trim();
} else if (dataType.equals(DataType.UNICODE_CHAR)) {
String value = new String();
for (int i = 0; i < rowSize && cursor < stream.capacity(); i += 2) {
value += stream.getChar();
}
dataBlock = value.trim();
} else if (dataType.equals(DataType.FLOAT)) {
if (rowSize != blockSize) {
int nb = rowSize / blockSize;
if (nb == 0) { dataBlock = ""; }
else {
StringJoiner sj = new StringJoiner(" ", "", "");
for (int i = 0; i < nb; i++) {
sj.add(String.valueOf(stream.getFloat()));
}
dataBlock = sj.toString();
}
} else {
dataBlock = stream.getFloat();
}
} else if (dataType.equals(DataType.DOUBLE)) {
if (rowSize != blockSize) {
int nb = rowSize / blockSize;
if (nb == 0) { dataBlock = ""; }
else {
StringJoiner sj = new StringJoiner(" ", "", "");
for (int i = 0; i < nb; i++) {
sj.add(String.valueOf(stream.getDouble()));
}
dataBlock = sj.toString();
}
} else {
dataBlock = stream.getDouble();
}
} else if (dataType.equals(DataType.FLOAT_COMPLEX)) {
if (rowSize != blockSize) {
int nb = rowSize / blockSize;
if (nb == 0) { dataBlock = ""; }
else {
StringJoiner sj = new StringJoiner(" ", "", "");
for (int i = 0; i < nb; i++) {
sj.add(String.valueOf(stream.getFloat()));
sj.add(String.valueOf(stream.getFloat()));
}
dataBlock = sj.toString();
}
} else {
StringJoiner sj = new StringJoiner(" ", "", "");
sj.add(String.valueOf(stream.getFloat()));
sj.add(String.valueOf(stream.getFloat()));
dataBlock = sj.toString();
}
} else if (dataType.equals(DataType.DOUBLE_COMPLEX)) {
if (rowSize != blockSize) {
int nb = rowSize / blockSize;
if (nb == 0) { dataBlock = ""; }
else {
StringJoiner sj = new StringJoiner(" ", "", "");
for (int i = 0; i < nb; i++) {
sj.add(String.valueOf(stream.getDouble()));
sj.add(String.valueOf(stream.getDouble()));
}
dataBlock = sj.toString();
}
} else {
StringJoiner sj = new StringJoiner(" ", "", "");
sj.add(String.valueOf(stream.getDouble()));
sj.add(String.valueOf(stream.getDouble()));
dataBlock = sj.toString();
}
} else {
BinaryStreamParser.LOGGER.warning("Data type " + dataType + " is not supported.");
dataBlock = null;
}
return dataBlock;
}
}