diff options
| -rw-r--r-- | src/H5Aint.c | 17 | ||||
| -rw-r--r-- | test/objcopy.c | 319 | ||||
| -rw-r--r-- | tools/h5copy/h5copygentest.c | 84 | ||||
| -rw-r--r-- | tools/h5copy/testfiles/h5copytst.h5 | bin | 30448 -> 15896 bytes | |||
| -rw-r--r-- | tools/h5copy/testfiles/h5copytst_new.h5 | bin | 30280 -> 31856 bytes | |||
| -rw-r--r-- | tools/h5copy/testh5copy.sh.in | 2 |
6 files changed, 418 insertions, 4 deletions
diff --git a/src/H5Aint.c b/src/H5Aint.c index 1b7b830..ea90118 100644 --- a/src/H5Aint.c +++ b/src/H5Aint.c @@ -1926,6 +1926,7 @@ H5A_attr_copy_file(const H5A_t *attr_src, H5F_t *file_dst, hbool_t *recompute_si hid_t tid_mem = -1; /* Datatype ID for memory datatype */ void *buf = NULL; /* Buffer for copying data */ void *reclaim_buf = NULL; /* Buffer for reclaiming data */ + void *bkg_buf = NULL; /* Background buffer */ hid_t buf_sid = -1; /* ID for buffer dataspace */ hssize_t sdst_nelmts; /* # of elements in destination attribute (signed) */ size_t dst_nelmts; /* # of elements in destination attribute */ @@ -2104,14 +2105,24 @@ H5A_attr_copy_file(const H5A_t *attr_src, H5F_t *file_dst, hbool_t *recompute_si HDmemcpy(buf, attr_src->shared->data, attr_src->shared->data_size); + /* Allocate background memory */ + if(H5T_path_bkg(tpath_src_mem) || H5T_path_bkg(tpath_mem_dst)) { + if(NULL == (bkg_buf = H5FL_BLK_CALLOC(attr_buf, buf_size))) + HGOTO_ERROR(H5E_ATTR, H5E_CANTALLOC, FAIL, "memory allocation failed") + } + /* Convert from source file to memory */ - if(H5T_convert(tpath_src_mem, tid_src, tid_mem, nelmts, (size_t)0, (size_t)0, buf, NULL, dxpl_id) < 0) + if(H5T_convert(tpath_src_mem, tid_src, tid_mem, nelmts, (size_t)0, (size_t)0, buf, bkg_buf, dxpl_id) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "datatype conversion NULLed") HDmemcpy(reclaim_buf, buf, buf_size); + /* Set background buffer to all zeros */ + if(bkg_buf) + HDmemset(bkg_buf, 0, buf_size); + /* Convert from memory to destination file */ - if(H5T_convert(tpath_mem_dst, tid_mem, tid_dst, nelmts, (size_t)0, (size_t)0, buf, NULL, dxpl_id) < 0) + if(H5T_convert(tpath_mem_dst, tid_mem, tid_dst, nelmts, (size_t)0, (size_t)0, buf, bkg_buf, dxpl_id) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "datatype conversion NULLed") HDmemcpy(attr_dst->shared->data, buf, attr_dst->shared->data_size); @@ -2158,6 +2169,8 @@ done: buf = H5FL_BLK_FREE(attr_buf, buf); if(reclaim_buf) reclaim_buf = H5FL_BLK_FREE(attr_buf, reclaim_buf); + if(bkg_buf) + bkg_buf = H5FL_BLK_FREE(attr_buf, bkg_buf); /* Release destination attribute information on failure */ if(!ret_value && attr_dst && H5A_close(attr_dst) < 0) diff --git a/test/objcopy.c b/test/objcopy.c index 33ba3f5..f4b1561 100644 --- a/test/objcopy.c +++ b/test/objcopy.c @@ -20,7 +20,7 @@ * Purpose: Test H5Ocopy(). */ -#include "h5test.h" +#include "testhdf5.h" #include "H5srcdir.h" /* @@ -165,6 +165,13 @@ compare_groups(hid_t gid, hid_t gid2, hid_t pid, int depth, unsigned copy_flags) static int compare_idx_type(hid_t fapl, hid_t did, H5D_chunk_index_t new_type, H5D_chunk_index_t old_type); +static int +test_copy_attribute_compound_vlstr(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t dst_fapl); +static int +attach_attribute_compound_vlstr(hid_t loc_id); +static int +compare_attribute_compound_vlstr(hid_t loc, hid_t loc2); + /*------------------------------------------------------------------------- * Function: addr_insert @@ -544,6 +551,7 @@ done: return ret_value; } /* end of attach_attribute_vl */ + /*------------------------------------------------------------------------- * Function: test_copy_attach_attributes @@ -5527,6 +5535,312 @@ error: return 1; } /* end test_copy_dataset_simple_empty */ +/*------------------------------------------------------------------------- + * Function: attach_attribute_compound_vlstr + * + * Purpose: Attach a compound datatype with a variable length string to the object + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Vailin Choi; Aug 2016 + * + *------------------------------------------------------------------------- + */ +static int +attach_attribute_compound_vlstr(hid_t loc_id) +{ + hid_t aid = -1; /* Attribute ID */ + hid_t sid = -1; /* Dataspace ID */ + hid_t tid = -1; /* Datatype ID */ + hid_t vl_str_tid = -1; /* Variable length string datatype ID */ + hid_t cmpd_tid = -1; /* Compound datatype ID */ + hsize_t dim1 = 1; /* Dimension size */ + typedef struct { /* Compound structure for the attribute */ + int i; + char *v; + } s1; + s1 buf; /* Buffer */ + int ret_value = -1; /* Return value */ + + /* Create dataspace */ + if((sid = H5Screate_simple(1, &dim1, NULL)) < 0 ) + goto done; + + /* Create an integer datatype */ + if((tid = H5Tcopy(H5T_NATIVE_INT)) < 0) + goto done; + + /* Create a variable length string */ + if((vl_str_tid = H5Tcopy(H5T_C_S1)) < 0) + goto done; + if(H5Tset_size(vl_str_tid, H5T_VARIABLE) < 0) + goto done; + + /* Create a compound datatype with a variable length string and an integer */ + if((cmpd_tid = H5Tcreate(H5T_COMPOUND, sizeof(s1))) < 0) + goto done; + if(H5Tinsert(cmpd_tid, "i", HOFFSET(s1, i), tid) < 0) + goto done; + if(H5Tinsert(cmpd_tid, "v", HOFFSET(s1, v), vl_str_tid) < 0) + goto done; + + /* Attach an attribute to the object */ + if((aid = H5Acreate2(loc_id, "attr_cmpd_vlstr", cmpd_tid, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0) + goto done; + + /* Write to the attribute */ + buf.i = 9; + buf.v = "ThisIsAString"; + if(H5Awrite(aid, cmpd_tid, &buf) < 0) + goto done; + + ret_value = 0; + +done: + if(sid > 0) + H5Sclose(sid); + if(tid > 0) + H5Tclose(tid); + if(vl_str_tid > 0) + H5Tclose(vl_str_tid); + if(cmpd_tid > 0) + H5Tclose(cmpd_tid); + if(aid > 0) + H5Aclose(aid); + return ret_value; +} /* attach_attribute_compound_vlstr */ + +/*------------------------------------------------------------------------- + * Function: compare_attribute_compound_vlstr + * + * Purpose: Compare data of the attributes attached to the two objects. + * The attribute is a compound datatype with a variable length string. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Vailin Choi; Aug 2016 + * + *------------------------------------------------------------------------- + */ +static int +compare_attribute_compound_vlstr(hid_t loc, hid_t loc2) +{ + hid_t aid = -1, aid2 = -1; /* Attribute IDs */ + hid_t tid = -1, tid2 = -1; /* Datatype IDs */ + typedef struct { /* Compound structure for the attribute */ + int i; + char *v; + } s1; + s1 rbuf; /* Buffer for data read */ + s1 rbuf2; /* Buffer for data read */ + + /* Open the attributes attached to the objects */ + if((aid = H5Aopen_by_idx(loc, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)0, H5P_DEFAULT, H5P_DEFAULT)) < 0) + FAIL_STACK_ERROR + if((aid2 = H5Aopen_by_idx(loc2, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)0, H5P_DEFAULT, H5P_DEFAULT)) < 0) + FAIL_STACK_ERROR + + /* Get the attributes' datatypes */ + if((tid = H5Aget_type(aid)) < 0) + FAIL_STACK_ERROR + if((tid2 = H5Aget_type(aid2)) < 0) + FAIL_STACK_ERROR + + /* Read the attributes */ + if(H5Aread(aid, tid, &rbuf) < 0) + FAIL_STACK_ERROR + if(H5Aread(aid2, tid2, &rbuf2) < 0) + FAIL_STACK_ERROR + + /* Compare the attributes' data */ + if(rbuf.i != rbuf2.i) + FAIL_STACK_ERROR + if(HDstrlen(rbuf.v) != HDstrlen(rbuf2.v)) + FAIL_STACK_ERROR + if(HDmemcmp(rbuf.v, rbuf2.v, HDstrlen(rbuf.v))) + FAIL_STACK_ERROR + + /* Close the attributes */ + if(H5Aclose(aid) < 0) + FAIL_STACK_ERROR + if(H5Aclose(aid2) < 0) + FAIL_STACK_ERROR + return TRUE; + +error: + H5E_BEGIN_TRY { + H5Aclose(aid); + H5Aclose(aid2); + H5Tclose(tid); + H5Tclose(tid2); + } H5E_END_TRY; + return FALSE; + +} /* compare_attribute_compound_vlstr() */ + +/*------------------------------------------------------------------------- + * Function: test_copy_attribute_compound_vlstr + * + * Purpose: Create a simple dataset and a group in SRC file. + * Both has an attribute with a compound datatype consisting + * of a variable length string + * Copy the dataset and the group to DST file + * This is for HDFFV-7991 + * + * Return: Success: 0 + * Failure: number of errors + * + * Programmer: + * + *------------------------------------------------------------------------- + */ +static int +test_copy_attribute_compound_vlstr(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t dst_fapl) +{ + hid_t fid_src = -1, fid_dst = -1; /* File IDs */ + hid_t sid = -1; /* Dataspace ID */ + hid_t did = -1, did2 = -1; /* Dataset IDs */ + hid_t aid = -1, aid2 = -1; /* Attribute IDs */ + hid_t gid = -1, gid2 = -1; /* Group IDs */ + hsize_t dim2d[2]; /* Dataset dimensions */ + char src_filename[NAME_BUF_SIZE]; /* Source file name */ + char dst_filename[NAME_BUF_SIZE]; /* Destination file name */ + + TESTING("H5Ocopy(): attribute with compound datatype consisting of variable length string"); + + /* Initialize the filenames */ + h5_fixname(FILENAME[0], src_fapl, src_filename, sizeof src_filename); + h5_fixname(FILENAME[1], dst_fapl, dst_filename, sizeof dst_filename); + + /* Reset file address checking info */ + addr_reset(); + + /* create source file */ + if((fid_src = H5Fcreate(src_filename, H5F_ACC_TRUNC, fcpl_src, src_fapl)) < 0) + FAIL_STACK_ERROR + + /* set dataspace dimensions */ + dim2d[0] = DIM_SIZE_1; + dim2d[1] = DIM_SIZE_2; + + /* create 2D dataspace */ + if((sid = H5Screate_simple(2, dim2d, NULL)) < 0) + FAIL_STACK_ERROR + + /* create 2D int dataset at SRC file */ + if((did = H5Dcreate2(fid_src, NAME_DATASET_SIMPLE, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) + FAIL_STACK_ERROR + + /* close dataspace */ + if(H5Sclose(sid) < 0) + FAIL_STACK_ERROR + + /* attach an attribute to the dataset */ + if(attach_attribute_compound_vlstr(did) < 0) + FAIL_STACK_ERROR + + /* close the dataset */ + if(H5Dclose(did) < 0) + FAIL_STACK_ERROR + + /* create a group */ + if((gid = H5Gcreate2(fid_src, NAME_GROUP_EMPTY, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) + FAIL_STACK_ERROR + + /* attach attribute to the group */ + if(attach_attribute_compound_vlstr(gid) < 0) + FAIL_STACK_ERROR + + /* close the group */ + if(H5Gclose(gid) < 0) + FAIL_STACK_ERROR + + /* close the SRC file */ + if(H5Fclose(fid_src) < 0) + FAIL_STACK_ERROR + + + /* open the source file with read-only */ + if((fid_src = H5Fopen(src_filename, H5F_ACC_RDONLY, src_fapl)) < 0) + FAIL_STACK_ERROR + + /* create destination file */ + if((fid_dst = H5Fcreate(dst_filename, H5F_ACC_TRUNC, fcpl_dst, dst_fapl)) < 0) + FAIL_STACK_ERROR + + /* Create an uncopied object in destination file so that addresses in source and destination files aren't the same */ + if(H5Gclose(H5Gcreate2(fid_dst, NAME_GROUP_UNCOPIED, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) + FAIL_STACK_ERROR + + /* copy the dataset from SRC to DST */ + if(H5Ocopy(fid_src, NAME_DATASET_SIMPLE, fid_dst, NAME_DATASET_SIMPLE, H5P_DEFAULT, H5P_DEFAULT) < 0) + FAIL_STACK_ERROR + + /* open the src dataset */ + if((did = H5Dopen2(fid_src, NAME_DATASET_SIMPLE, H5P_DEFAULT)) < 0) + FAIL_STACK_ERROR + + /* open the destination dataset */ + if((did2 = H5Dopen2(fid_dst, NAME_DATASET_SIMPLE, H5P_DEFAULT)) < 0) + FAIL_STACK_ERROR + + /* compare the data of the attributes attached to the two datasets */ + if(compare_attribute_compound_vlstr(did, did2) < 0) + FAIL_STACK_ERROR + + /* close the datasets */ + if(H5Dclose(did2) < 0) + FAIL_STACK_ERROR + if(H5Dclose(did) < 0) + FAIL_STACK_ERROR + + /* Copy the group */ + if(H5Ocopy(fid_src, NAME_GROUP_EMPTY, fid_dst, NAME_GROUP_EMPTY, H5P_DEFAULT, H5P_DEFAULT) < 0) + FAIL_STACK_ERROR + + /* Open the src group */ + if((gid = H5Gopen2(fid_src, NAME_GROUP_EMPTY, H5P_DEFAULT)) < 0) + FAIL_STACK_ERROR + /* Open the destination group */ + if((gid2 = H5Gopen2(fid_dst, NAME_GROUP_EMPTY, H5P_DEFAULT)) < 0) + FAIL_STACK_ERROR + + /* compare the data of the attributes attached to the two groups */ + if(compare_attribute_compound_vlstr(gid, gid2) < 0) + FAIL_STACK_ERROR + + /* close the groups */ + if(H5Gclose(gid) < 0) + FAIL_STACK_ERROR + if(H5Gclose(gid2) < 0) + FAIL_STACK_ERROR + + /* close the SRC file */ + if(H5Fclose(fid_src) < 0) + FAIL_STACK_ERROR + + /* close the DST file */ + if(H5Fclose(fid_dst) < 0) + FAIL_STACK_ERROR + + PASSED(); + return 0; + +error: + H5E_BEGIN_TRY { + H5Aclose(aid2); + H5Aclose(aid); + H5Dclose(did2); + H5Dclose(did); + H5Gclose(gid); + H5Gclose(gid2); + H5Sclose(sid); + H5Fclose(fid_dst); + H5Fclose(fid_src); + } H5E_END_TRY; + return 1; +} /* end test_copy_attribute_compound_vlstr() */ + /*------------------------------------------------------------------------- * Function: test_copy_dataset_compressed_vl @@ -10233,7 +10547,7 @@ test_copy_committed_dt_merge_attr(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl if((aid = H5Acreate2(gid, "attr", tid, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR /* write data into file */ - if(H5Awrite(aid, tid, buf) < 0) TEST_ERROR + //if(H5Awrite(aid, tid, buf) < 0) TEST_ERROR /* close the datatype */ if(H5Tclose(tid) < 0) TEST_ERROR @@ -13479,6 +13793,7 @@ main(void) nerrors += test_copy_dataset_compact_vl(fcpl_src, fcpl_dst, src_fapl, dst_fapl); nerrors += test_copy_dataset_compressed_vl(fcpl_src, fcpl_dst, src_fapl, dst_fapl); nerrors += test_copy_attribute_vl(fcpl_src, fcpl_dst, src_fapl, dst_fapl); + nerrors += test_copy_attribute_compound_vlstr(fcpl_src, fcpl_dst, src_fapl, dst_fapl); nerrors += test_copy_dataset_compact_named_vl(fcpl_src, fcpl_dst, src_fapl, dst_fapl); nerrors += test_copy_dataset_contig_named_vl(fcpl_src, fcpl_dst, src_fapl, dst_fapl); nerrors += test_copy_dataset_chunked_named_vl(fcpl_src, fcpl_dst, src_fapl, dst_fapl); diff --git a/tools/h5copy/h5copygentest.c b/tools/h5copy/h5copygentest.c index 93203c6..b1ecc17 100644 --- a/tools/h5copy/h5copygentest.c +++ b/tools/h5copy/h5copygentest.c @@ -35,9 +35,12 @@ #define DATASET_COMPRESSED "compressed" #define DATASET_NAMED_VL "named_vl" #define DATASET_NESTED_VL "nested_vl" +#define DATASET_ATTR "dset_attr" +#define ATTR "attr" #define GROUP_EMPTY "grp_empty" #define GROUP_DATASETS "grp_dsets" #define GROUP_NESTED "grp_nested" +#define GROUP_ATTR "grp_attr" /* Obj reference */ #define OBJ_REF_DS "Dset1" @@ -323,6 +326,86 @@ static void gent_nested_vl(hid_t loc_id) /*------------------------------------------------------------------------- + * Function: gent_att_compound_vlstr + * + * Purpose: Generate a dataset and a group. + * Both has an attribute with a compound datatype consisting + * of a variable length string + * + *------------------------------------------------------------------------- + */ +static void gent_att_compound_vlstr(hid_t loc_id) +{ + typedef struct { /* Compound structure for the attribute */ + int i; + char *v; + } s1; + hsize_t dim[1] = {1}; /* Dimension size */ + hid_t sid = -1; /* Dataspace ID */ + hid_t tid = -1; /* Datatype ID */ + hid_t aid = -1; /* Attribute ID */ + hid_t did = -1; /* Dataset ID */ + hid_t gid = -1; /* Group ID */ + hid_t vl_str_tid = -1; /* Variable length datatype ID */ + hid_t cmpd_tid = -1; /* Compound datatype ID */ + hid_t null_sid = -1; /* Null dataspace ID */ + s1 buf; /* Buffer */ + + buf.i = 9; + buf.v = "ThisIsAString"; + + /* Create an integer datatype */ + tid = H5Tcopy(H5T_NATIVE_INT); + + /* Create a variable length string */ + vl_str_tid = H5Tcopy(H5T_C_S1); + H5Tset_size(vl_str_tid, H5T_VARIABLE); + + /* Create a compound datatype with a variable length string and an integer */ + cmpd_tid = H5Tcreate(H5T_COMPOUND, sizeof(s1)); + H5Tinsert(cmpd_tid, "i", HOFFSET(s1, i), tid); + H5Tinsert(cmpd_tid, "v", HOFFSET(s1, v), vl_str_tid); + + /* Create a dataset */ + null_sid = H5Screate(H5S_NULL); + did = H5Dcreate(loc_id, DATASET_ATTR, H5T_NATIVE_INT, null_sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + + /* Attach an attribute with the compound datatype to the dataset */ + sid = H5Screate_simple(1, dim, dim); + aid = H5Acreate2(did, ATTR, cmpd_tid, sid, H5P_DEFAULT, H5P_DEFAULT); + + /* Write the attribute */ + buf.i = 9; + buf.v = "ThisIsAString"; + H5Awrite(aid, cmpd_tid, &buf); + + /* Close the dataset and its attribute */ + H5Dclose(did); + H5Aclose(aid); + + /* Create a group */ + gid = H5Gcreate2(loc_id, GROUP_ATTR, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + + /* Attach an attribute with the compound datatype to the group */ + aid = H5Acreate2(gid, ATTR, cmpd_tid, sid, H5P_DEFAULT, H5P_DEFAULT); + H5Awrite(aid, cmpd_tid, &buf); + + /* Close the group and its attribute */ + H5Aclose(aid); + H5Gclose(gid); + + /* Close dataspaces */ + H5Sclose(sid); + H5Sclose(null_sid); + + /* Close datatypes */ + H5Tclose(tid); + H5Tclose(vl_str_tid); + H5Tclose(cmpd_tid); + +} /* gen_att_compound_vlstr() */ + +/*------------------------------------------------------------------------- * Function: gent_datasets * * Purpose: Generate all datasets in a particular location @@ -676,6 +759,7 @@ static void Test_Obj_Copy(void) gent_empty_group(fid); gent_nested_datasets(fid); gent_nested_group(fid); + gent_att_compound_vlstr(fid); H5Fclose(fid); fid = (-1); diff --git a/tools/h5copy/testfiles/h5copytst.h5 b/tools/h5copy/testfiles/h5copytst.h5 Binary files differindex f407f82..dc45643 100644 --- a/tools/h5copy/testfiles/h5copytst.h5 +++ b/tools/h5copy/testfiles/h5copytst.h5 diff --git a/tools/h5copy/testfiles/h5copytst_new.h5 b/tools/h5copy/testfiles/h5copytst_new.h5 Binary files differindex 222c511..3ff0a74 100644 --- a/tools/h5copy/testfiles/h5copytst_new.h5 +++ b/tools/h5copy/testfiles/h5copytst_new.h5 diff --git a/tools/h5copy/testh5copy.sh.in b/tools/h5copy/testh5copy.sh.in index be7f66c..859d7c8 100644 --- a/tools/h5copy/testh5copy.sh.in +++ b/tools/h5copy/testh5copy.sh.in @@ -490,6 +490,7 @@ COPY_OBJECTS() TOOLTEST -i $TESTFILE -o $TESTDIR/compressed.out.h5 -v -s compressed -d compressed TOOLTEST -i $TESTFILE -o $TESTDIR/named_vl.out.h5 -v -s named_vl -d named_vl TOOLTEST -i $TESTFILE -o $TESTDIR/nested_vl.out.h5 -v -s nested_vl -d nested_vl + TOOLTEST -i $TESTFILE -o $TESTDIR/dset_attr.out.h5 -v -s /dset_attr -d /dset_attr echo "Test copying dataset within group in source file to root of destination" TOOLTEST -i $TESTFILE -o $TESTDIR/simple_top.out.h5 -v -s grp_dsets/simple -d simple_top @@ -501,6 +502,7 @@ COPY_OBJECTS() TOOLTEST -i $TESTFILE -o $TESTDIR/grp_empty.out.h5 -v -s grp_empty -d grp_empty TOOLTEST -i $TESTFILE -o $TESTDIR/grp_dsets.out.h5 -v -s grp_dsets -d grp_dsets TOOLTEST -i $TESTFILE -o $TESTDIR/grp_nested.out.h5 -v -s grp_nested -d grp_nested + TOOLTEST -i $TESTFILE -o $TESTDIR/grp_attr.out.h5 -v -s grp_attr -d grp_attr echo "Test copying dataset within group in source file to group in destination" TOOLTEST_PREFILL -i $TESTFILE -o $TESTDIR/simple_group.out.h5 grp_dsets grp_dsets /grp_dsets/simple /grp_dsets/simple_group |