summaryrefslogtreecommitdiffstats
path: root/java/test/TestH5OcopyOld.java
blob: e547051a50db3544c16cfb7b0d3bfae5636b4434 (plain)
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
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * Copyright by The HDF Group.                                               *
 * All rights reserved.                                                      *
 *                                                                           *
 * This file is part of HDF5.  The full HDF5 copyright notice, including     *
 * terms governing use, modification, and redistribution, is contained in    *
 * the COPYING file, which can be found at the root of the source code       *
 * distribution tree, or in https://www.hdfgroup.org/licenses.               *
 * If you do not have access to either file, you may request a copy from     *
 * help@hdfgroup.org.                                                        *
 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

package test;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;

import java.io.File;

import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
import hdf.hdf5lib.exceptions.HDF5Exception;
import hdf.hdf5lib.exceptions.HDF5LibraryException;

import org.junit.After;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.TestName;

public class TestH5OcopyOld {
    @Rule public TestName testname = new TestName();
    private static final String FILENAME = "testRefsattributeO.h5";
    private static final int DIM_X = 4;
    private static final int DIM_Y = 6;
    long H5fid = HDF5Constants.H5I_INVALID_HID;
    long H5dsid = HDF5Constants.H5I_INVALID_HID;
    long H5did1 = HDF5Constants.H5I_INVALID_HID;
    long H5did2 = HDF5Constants.H5I_INVALID_HID;
    long H5gcpl = HDF5Constants.H5I_INVALID_HID;
    long H5gid = HDF5Constants.H5I_INVALID_HID;
    long H5dsid2 = HDF5Constants.H5I_INVALID_HID;
    long[] dims = { 2 };

    private final void _deleteFile(String filename) {
        File file = new File(filename);

        if (file.exists()) {
            try {
                file.delete();
            }
            catch (Exception e) {
                e.printStackTrace();
            }
        }
    }

    private final long _createDataset(long fid, long dsid, String name, long dapl) {
        long did = HDF5Constants.H5I_INVALID_HID;
        try {
            did = H5.H5Dcreate(fid, name,
                        HDF5Constants.H5T_STD_I32BE, dsid,
                        HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, dapl);
        }
        catch (Throwable err) {
            err.printStackTrace();
            fail("H5.H5Dcreate: " + err);
        }
        assertTrue("TestH5O._createDataset: ",did >= 0);

        return did;
    }

    private final long _createGroup(long fid, String name) {
        long gid = HDF5Constants.H5I_INVALID_HID;
        try {
            H5gcpl = HDF5Constants.H5P_DEFAULT;
            gid = H5.H5Gcreate(fid, name, HDF5Constants.H5P_DEFAULT,
                    H5gcpl, HDF5Constants.H5P_DEFAULT);
        }
        catch (Throwable err) {
            err.printStackTrace();
            fail("H5.H5Gcreate: " + err);
        }
        assertTrue("TestH5O._createGroup: ",gid >= 0);

        return gid;
    }

    @Before
    public void createH5file()
            throws NullPointerException, HDF5Exception {
        assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0);
        System.out.print(testname.getMethodName());
        try {
            H5fid = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC,
                    HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
            H5dsid2 =  H5.H5Screate(HDF5Constants.H5S_SCALAR);
            H5did1 = _createDataset(H5fid, H5dsid2, "DS2", HDF5Constants.H5P_DEFAULT);
            H5dsid = H5.H5Screate_simple(1, dims, null);
            H5gid = _createGroup(H5fid, "/G1");
            H5did2 = _createDataset(H5gid, H5dsid, "DS1", HDF5Constants.H5P_DEFAULT);
        }
        catch (Throwable err) {
            err.printStackTrace();
            fail("TestH5O.createH5file: " + err);
        }
        assertTrue("TestH5O.createH5file: H5.H5Fcreate: ",H5fid >= 0);
        assertTrue("TestH5O.createH5file: H5.H5Screate_simple: ",H5dsid >= 0);
        assertTrue("TestH5O.createH5file: H5.H5Gcreate: ",H5gid >= 0);

        H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
    }

    @After
    public void deleteH5file() throws HDF5LibraryException {
        if (H5gid > 0)
            try {H5.H5Gclose(H5gid);} catch (Exception ex) {}
        if (H5did2 > 0)
            try {H5.H5Dclose(H5did2);} catch (Exception ex) {}
        if (H5dsid > 0)
            try {H5.H5Sclose(H5dsid);} catch (Exception ex) {}
        if (H5dsid2 > 0)
            try {H5.H5Sclose(H5dsid2);} catch (Exception ex) {}
        if (H5did1 > 0)
            try {H5.H5Dclose(H5did1);} catch (Exception ex) {}
        if (H5fid > 0)
            try {H5.H5Fclose(H5fid);} catch (Exception ex) {}

        _deleteFile(FILENAME);
        System.out.println();
    }

    @Test
    public void testH5OcopyRefsAttr() {
        long ocp_plist_id = HDF5Constants.H5I_INVALID_HID;
        byte rbuf0[]=null , rbuf1[] = null;
        byte[] dset_data = new byte[16];
        long attribute_id = HDF5Constants.H5I_INVALID_HID;

        try {
            rbuf0 = H5.H5Rcreate(H5fid, "/G1", HDF5Constants.H5R_OBJECT, -1);
            rbuf1 = H5.H5Rcreate(H5fid, "DS2", HDF5Constants.H5R_OBJECT, -1);
            //System.arraycopy(rbuf0, 0, dset_data, 0, 8);
            System.arraycopy(rbuf1, 0, dset_data, 8, 8);
        }
        catch (Exception ex) {
            fail("testH5OcopyRefsAttr: H5Rcreate failed");
        }

        try {
            attribute_id = H5.H5Acreate(H5did2, "A1", HDF5Constants.H5T_STD_REF_OBJ, H5dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
            assertTrue("testH5OcopyRefsAttr.H5Acreate: ", attribute_id >= 0);
            H5.H5Awrite(attribute_id, HDF5Constants.H5T_STD_REF_OBJ, dset_data);

            H5.H5Aclose(attribute_id);
        }
        catch (Exception ex) {
            fail("testH5OcopyRefsAttr: H5Awrite failed");
        }
        finally {
            try {H5.H5Aclose(attribute_id);} catch (Exception exx) {}
        }

        try {
            ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY);
            assertTrue("testH5OcopyRefsAttr.H5Pcreate: ", ocp_plist_id >= 0);
            H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG);
            H5.H5Ocopy(H5fid, ".", H5fid, "CPYREF", ocp_plist_id, HDF5Constants.H5P_DEFAULT);
        }
        catch (Exception ex) {
             fail("testH5OcopyRefsAttr: H5Ocopy failed");
        }
        finally {
            try {H5.H5Pclose(ocp_plist_id);} catch (Exception ex) {}
        }
    }

    @Test
    public void testH5OcopyRefsDatasettodiffFile() {
        byte rbuf1[] = null;
        byte[] dset_data = new byte[16];
        long ocp_plist_id = HDF5Constants.H5I_INVALID_HID;
        long dataset_id = HDF5Constants.H5I_INVALID_HID;
        long H5fid2 = HDF5Constants.H5I_INVALID_HID;

        try {
            rbuf1 = H5.H5Rcreate(H5fid, "DS2", HDF5Constants.H5R_OBJECT, -1);
            System.arraycopy(rbuf1, 0, dset_data, 8, 8);

            dataset_id = H5.H5Dcreate(H5fid, "DSREF",
                    HDF5Constants.H5T_STD_REF_OBJ, H5dsid,
                    HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
            assertTrue("testH5OcopyRefsDatasettodiffFile.H5Dcreate: ", dataset_id >= 0);
            H5.H5Dwrite(dataset_id, HDF5Constants.H5T_STD_REF_OBJ,
                    HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
                    HDF5Constants.H5P_DEFAULT, dset_data);
            H5.H5Dclose(dataset_id);
        }
        catch (Exception ex) {
            fail("testH5OcopyRefsDatasettodiffFile: create dataset failed");
        }
        finally {
            try {H5.H5Dclose(dataset_id);} catch (Exception exx) {}
        }

        try {
            //create new file
            H5fid2 = H5.H5Fcreate("copy.h5", HDF5Constants.H5F_ACC_TRUNC,
                    HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
            assertTrue("testH5OcopyRefsDatasettodiffFile.H5Fcreate: ", H5fid2 >= 0);
            H5.H5Fflush(H5fid2, HDF5Constants.H5F_SCOPE_LOCAL);
        }
        catch (Exception ex) {
            try {H5.H5Fclose(H5fid2);} catch (Exception exx) {}
            fail("testH5OcopyRefsDatasettodiffFile: H5Fcreate failed");
        }

        try {
            //create object copy property list id and set the flags.
            ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY);
            assertTrue("testH5OcopyRefsDatasettodiffFile.H5Pcreate: ", ocp_plist_id >= 0);
            H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG);

            //Perform copy function.
            H5.H5Ocopy(H5fid, ".", H5fid2, "CPYREFD", ocp_plist_id, HDF5Constants.H5P_DEFAULT);
        }
        catch (Exception ex){
            ex.printStackTrace();
            fail("testH5OcopyRefsDatasettodiffFile: H5Ocopy failed");
        }
        finally {
            try {H5.H5Pclose(ocp_plist_id);} catch (Exception ex) {}
            try {H5.H5Fclose(H5fid2);} catch (Exception ex) {}
        }
        _deleteFile("copy.h5");
    }

    @Test
    public void testH5OcopyRefsDatasettosameFile() {
        byte rbuf0[]=null , rbuf1[] = null;
        byte[] dset_data = new byte[16];
        long ocp_plist_id = HDF5Constants.H5I_INVALID_HID;
        long dataset_id = HDF5Constants.H5I_INVALID_HID;
        long did = HDF5Constants.H5I_INVALID_HID;
        int obj_type = -1;
        byte[] read_data = new byte[16];

        try {
            rbuf0 = H5.H5Rcreate(H5fid, "/G1", HDF5Constants.H5R_OBJECT, -1);
            rbuf1 = H5.H5Rcreate(H5fid, "DS2", HDF5Constants.H5R_OBJECT, -1);
            System.arraycopy(rbuf0, 0, dset_data, 0, 8);
            System.arraycopy(rbuf1, 0, dset_data, 8, 8);

            //Create a dataset and write object references to it.
            dataset_id = H5.H5Dcreate(H5fid, "DSREF",
                    HDF5Constants.H5T_STD_REF_OBJ, H5dsid,
                    HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
            assertTrue("testH5OcopyRefsDatasettosameFile.H5Dcreate: ", dataset_id >= 0);
            H5.H5Dwrite(dataset_id, HDF5Constants.H5T_STD_REF_OBJ,
                    HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
                    HDF5Constants.H5P_DEFAULT, dset_data);
            //Close the dataset.
            H5.H5Dclose(dataset_id);
        }
        catch (Exception ex) {
            try {H5.H5Dclose(dataset_id);} catch (Exception exx) {}
            fail("testH5OcopyRefsDatasettosameFile: create dataset failed");
        }

        try {
            ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY);
            assertTrue("testH5OcopyRefsDatasettosameFile.H5Pcreate: ", ocp_plist_id >= 0);
            H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG);
        }
        catch (Exception ex) {
            try {H5.H5Pclose(ocp_plist_id);} catch (Exception exx) {}
            fail("testH5OcopyRefsDatasettosameFile: H5Pset_copy_object failed");
        }

        //Perform copy function.
        try {
            H5.H5Ocopy(H5fid, "DSREF", H5fid, "CPYREFD", ocp_plist_id, HDF5Constants.H5P_DEFAULT);
        }
        catch(Exception ex) {
            try {H5.H5Pclose(ocp_plist_id);} catch (Exception exx) {}
            fail("testH5OcopyRefsDatasettosameFile: H5Ocopy failed");
        }

        //Open the dataset that has been copied
        try {
            did = H5.H5Dopen(H5fid, "DSREF", HDF5Constants.H5P_DEFAULT);
            assertTrue("testH5OcopyRefsDatasettosameFile.H5Dopen: ", did >= 0);
        }
        catch (Exception e) {
            try {H5.H5Dclose(did);} catch (Exception exx) {}
            e.printStackTrace();
            fail("testH5OcopyRefsDatasettosameFile: H5Dopen failed");
        }

        try {
            //Read the dataset object references in the read_data buffer.
            H5.H5Dread(did, HDF5Constants.H5T_STD_REF_OBJ, HDF5Constants.H5S_ALL,HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, read_data);
            System.arraycopy(read_data, 0, rbuf0, 0, 8);
            System.arraycopy(read_data, 8, rbuf1, 0, 8);

            //Get the type of object the reference points to.
            obj_type = H5.H5Rget_obj_type(H5fid, HDF5Constants.H5R_OBJECT, rbuf1);
            assertEquals(obj_type, HDF5Constants.H5O_TYPE_DATASET);

            obj_type = H5.H5Rget_obj_type(H5fid, HDF5Constants.H5R_OBJECT, rbuf0);
            assertEquals(obj_type, HDF5Constants.H5O_TYPE_GROUP);
        }
        catch (Exception ex) {
            ex.printStackTrace();
        }
        finally {
            try {H5.H5Dclose(did);} catch (Exception ex) {}
            try {H5.H5Pclose(ocp_plist_id);} catch (Exception ex) {}
        }
     }
    
    @Test
    public void testH5OcopyNullRef() throws Throwable {
        final long _pid_ = HDF5Constants.H5P_DEFAULT;
        long sid = HDF5Constants.H5I_INVALID_HID;
        long did = HDF5Constants.H5I_INVALID_HID;
        long aid = HDF5Constants.H5I_INVALID_HID;

        try {
            sid = H5.H5Screate_simple(1, new long[] {1}, null);
            assertTrue("testH5OcopyNullRef.H5Screate_simple: ", sid >= 0);
            did = H5.H5Dcreate(H5fid, "Dataset_with_null_Ref", HDF5Constants.H5T_NATIVE_INT, sid, _pid_, _pid_, _pid_);
            assertTrue("testH5OcopyNullRef.H5Dcreate: ", did > 0);
            aid = H5.H5Acreate(did, "Null_Ref", HDF5Constants.H5T_STD_REF_OBJ, sid, _pid_, _pid_);
            assertTrue("testH5OcopyNullRef.H5Acreate: ", aid > 0);
        }
        catch (Exception ex) {
            ex.printStackTrace();
        }
        finally {
            try {H5.H5Dclose(did);} catch (Exception exx) {}
            try {H5.H5Aclose(aid);} catch (Exception exx) {}
            try {H5.H5Sclose(sid);} catch (Exception exx) {}
        }

        long ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY);
        assertTrue("testH5OcopyNullRef.H5Pcreate: ", ocp_plist_id >= 0);
        H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG);
        try {
            H5.H5Ocopy(H5fid, "/Dataset_with_null_Ref", H5fid, "/Dataset_with_null_Ref_cp", ocp_plist_id, _pid_);
        }
        finally {
            try {H5.H5Pclose(ocp_plist_id);} catch (Exception exx) {}
        }
    }

//    @Ignore because of JIRA HDF5-9547
//    @Test(expected = HDF5LibraryException.class)
//    public void testH5OcopyInvalidRef() throws Throwable {
//        final long _pid_ = HDF5Constants.H5P_DEFAULT;
//        long sid = HDF5Constants.H5I_INVALID_HID;
//        long did = HDF5Constants.H5I_INVALID_HID;
//        long aid = HDF5Constants.H5I_INVALID_HID;
//
//        try {
//            sid = H5.H5Screate_simple(1, new long[] {1}, null);
//            assertTrue("testH5OcopyInvalidRef.H5Screate_simple: ", sid >= 0);
//            did = H5.H5Dcreate(H5fid, "Dataset_with_invalid_Ref", HDF5Constants.H5T_NATIVE_INT, sid, _pid_, _pid_, _pid_);
//            assertTrue("testH5OcopyInvalidRef.H5Dcreate: ", did > 0);
//            aid = H5.H5Acreate(did, "Invalid_Ref", HDF5Constants.H5T_STD_REF_OBJ, sid, _pid_, _pid_);
//            assertTrue("testH5OcopyInvalidRef.H5Acreate: ", aid > 0);
//            H5.H5Awrite(aid, HDF5Constants.H5T_STD_REF_OBJ, new long[]{-1});
//        }
//        catch (Exception ex) {
//            ex.printStackTrace();
//        }
//        finally {
//            try {H5.H5Dclose(did);} catch (Exception exx) {}
//            try {H5.H5Aclose(aid);} catch (Exception exx) {}
//            try {H5.H5Sclose(sid);} catch (Exception exx) {}
//        }
//
//        long ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY);
//        assertTrue("testH5OcopyInvalidRef.H5Pcreate: ", ocp_plist_id >= 0);
//        H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG);
//        try {
//            H5.H5Ocopy(H5fid, "/Dataset_with_invalid_Ref", H5fid, "/Dataset_with_invalid_Ref_cp", ocp_plist_id, _pid_);
//        }
//        finally {
//            try {H5.H5Pclose(ocp_plist_id);} catch (Exception exx) {}
//        }
//    }

}