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-rw-r--r--release_docs/RELEASE.txt2
-rw-r--r--src/H5Ocopy.c79
-rw-r--r--src/H5T.c6
-rwxr-xr-xtest/objcopy.c165
4 files changed, 214 insertions, 38 deletions
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index d8dc6df..5fbd25d 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -210,6 +210,8 @@ Bug Fixes since HDF5-1.8.0 release
Library
-------
+ - Fixed a bug when copying objects with NULL references with the
+ H5O_COPY_EXPAND_REFERENCE_FLAG flag set. (NAF - 2010/04/08 - 1815)
- Files can now be concurrently opened more than once using the core file
driver, as long as the backing store is used. (NAF - 2010/03/09)
- Added support for H5O_COPY_EXPAND_EXT_LINK_FLAG to H5Ocopy. External
diff --git a/src/H5Ocopy.c b/src/H5Ocopy.c
index f9bf533..8896795 100644
--- a/src/H5Ocopy.c
+++ b/src/H5Ocopy.c
@@ -354,15 +354,19 @@ H5O_copy_header_real(const H5O_loc_t *oloc_src, H5O_loc_t *oloc_dst /*out */,
oh_dst->max_compact = oh_src->max_compact;
oh_dst->min_dense = oh_src->min_dense;
- /* Initialize size of chunk array. The destination always has only one
- * chunk.
+ /* Initialize size of chunk array. Start off with zero chunks so this field
+ * is consistent with the current state of the chunk array. This is
+ * important if an error occurs.
*/
- oh_dst->alloc_nchunks = oh_dst->nchunks = 1;
+ oh_dst->alloc_nchunks = oh_dst->nchunks = 0;
- /* Allocate memory for the chunk array */
- if(NULL == (oh_dst->chunk = H5FL_SEQ_MALLOC(H5O_chunk_t, oh_dst->alloc_nchunks)))
+ /* Allocate memory for the chunk array - always start with 1 chunk */
+ if(NULL == (oh_dst->chunk = H5FL_SEQ_MALLOC(H5O_chunk_t, 1)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
+ /* Update number of allocated chunks. There are still no chunks used. */
+ oh_dst->alloc_nchunks = 1;
+
/* Allocate memory for "deleted" array. This array marks the message in
* the source that shouldn't be copied to the destination.
*/
@@ -579,6 +583,9 @@ H5O_copy_header_real(const H5O_loc_t *oloc_src, H5O_loc_t *oloc_dst /*out */,
oh_dst->chunk[0].size = (size_t)dst_oh_size;
oh_dst->chunk[0].gap = dst_oh_gap;
+ /* Update size of chunk array. The destination now has one chunk. */
+ oh_dst->nchunks = 1;
+
/* Set up raw pointers and copy messages that didn't need special
* treatment. This has to happen after the destination header has been
* allocated.
@@ -1124,8 +1131,13 @@ H5O_copy_expand_ref(H5F_t *file_src, void *_src_ref, hid_t dxpl_id,
dst_oloc.addr = HADDR_UNDEF;
/* Attempt to copy object from source to destination file */
- if(H5O_copy_obj_by_ref(&src_oloc, dxpl_id, &dst_oloc, &dst_root_loc, cpy_info) < 0)
- HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object")
+ if(src_oloc.addr != (haddr_t)0) {
+ if(H5O_copy_obj_by_ref(&src_oloc, dxpl_id, &dst_oloc, &dst_root_loc, cpy_info) < 0)
+ HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object")
+ } /* end if */
+ else
+ /* Set parameters so the reference is written as all 0's */
+ HDmemset(&dst_oloc.addr, 0, sizeof(dst_oloc.addr));
/* Set the object reference info for the destination file */
p = (uint8_t *)(&dst_ref[i]);
@@ -1136,7 +1148,7 @@ H5O_copy_expand_ref(H5F_t *file_src, void *_src_ref, hid_t dxpl_id,
else if(H5R_DATASET_REGION == ref_type) {
hdset_reg_ref_t *src_ref = (hdset_reg_ref_t *)_src_ref;
hdset_reg_ref_t *dst_ref = (hdset_reg_ref_t *)_dst_ref;
- uint8_t *buf; /* Buffer to store serialized selection in */
+ uint8_t *buf = NULL; /* Buffer to store serialized selection in */
H5HG_t hobjid; /* Heap object ID */
size_t buf_size; /* Length of object in heap */
@@ -1147,30 +1159,35 @@ H5O_copy_expand_ref(H5F_t *file_src, void *_src_ref, hid_t dxpl_id,
H5F_addr_decode(src_oloc.file, (const uint8_t **)&p, &(hobjid.addr));
INT32DECODE(p, hobjid.idx);
- /* Get the dataset region from the heap (allocate inside routine) */
- if((buf = (uint8_t *)H5HG_read(src_oloc.file, dxpl_id, &hobjid, NULL, &buf_size)) == NULL)
- HGOTO_ERROR(H5E_REFERENCE, H5E_READERROR, FAIL, "Unable to read dataset region information")
-
- /* Get the object oid for the dataset */
- p = (uint8_t *)buf;
- H5F_addr_decode(src_oloc.file, (const uint8_t **)&p, &(src_oloc.addr));
- dst_oloc.addr = HADDR_UNDEF;
-
- /* copy the object pointed by the ref to the destination */
- if(H5O_copy_obj_by_ref(&src_oloc, dxpl_id, &dst_oloc, &dst_root_loc, cpy_info) < 0) {
- H5MM_xfree(buf);
- HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object")
- } /* end if */
-
- /* Serialize object ID */
- p = (uint8_t *)buf;
- H5F_addr_encode(dst_oloc.file, &p, dst_oloc.addr);
-
- /* Save the serialized buffer to the destination */
- if(H5HG_insert(dst_oloc.file, dxpl_id, buf_size, buf, &hobjid) < 0) {
- H5MM_xfree(buf);
- HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "Unable to write dataset region information")
+ if(hobjid.addr != (haddr_t)0) {
+ /* Get the dataset region from the heap (allocate inside routine) */
+ if((buf = (uint8_t *)H5HG_read(src_oloc.file, dxpl_id, &hobjid, NULL, &buf_size)) == NULL)
+ HGOTO_ERROR(H5E_REFERENCE, H5E_READERROR, FAIL, "Unable to read dataset region information")
+
+ /* Get the object oid for the dataset */
+ p = (uint8_t *)buf;
+ H5F_addr_decode(src_oloc.file, (const uint8_t **)&p, &(src_oloc.addr));
+ dst_oloc.addr = HADDR_UNDEF;
+
+ /* copy the object pointed by the ref to the destination */
+ if(H5O_copy_obj_by_ref(&src_oloc, dxpl_id, &dst_oloc, &dst_root_loc, cpy_info) < 0) {
+ H5MM_xfree(buf);
+ HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object")
+ } /* end if */
+
+ /* Serialize object ID */
+ p = (uint8_t *)buf;
+ H5F_addr_encode(dst_oloc.file, &p, dst_oloc.addr);
+
+ /* Save the serialized buffer to the destination */
+ if(H5HG_insert(dst_oloc.file, dxpl_id, buf_size, buf, &hobjid) < 0) {
+ H5MM_xfree(buf);
+ HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "Unable to write dataset region information")
+ } /* end if */
} /* end if */
+ else
+ /* Set parameters so the reference is written as all 0's */
+ HDmemset(&hobjid, 0, sizeof(hobjid));
/* Set the dataset region reference info for the destination file */
p = (uint8_t *)(&dst_ref[i]);
diff --git a/src/H5T.c b/src/H5T.c
index 4b77559..7dfe0f2 100644
--- a/src/H5T.c
+++ b/src/H5T.c
@@ -1863,12 +1863,6 @@ H5T_get_class(const H5T_t *dt, htri_t internal)
assert(dt);
- /* Lie to the user if they have a VL string and tell them it's in the string class */
- if(dt->shared->type==H5T_VLEN && dt->shared->u.vlen.type==H5T_VLEN_STRING)
- ret_value=H5T_STRING;
- else
- ret_value=dt->shared->type;
-
/* Externally, a VL string is a string; internally, a VL string is a VL. */
if(internal) {
ret_value=dt->shared->type;
diff --git a/test/objcopy.c b/test/objcopy.c
index 439cfb1..8f92a01 100755
--- a/test/objcopy.c
+++ b/test/objcopy.c
@@ -7783,6 +7783,168 @@ error:
/*-------------------------------------------------------------------------
+ * Function: test_copy_null_ref
+ *
+ * Purpose: Creates 2 datasets with references, one with object and
+ * the other with region references. Copies these datasets
+ * to a new file without expanding references, causing them
+ * to become NULL. Next, copies these references to a third
+ * file with expanding references, to verify that NULL
+ * references are handled correctly.
+ *
+ * Return: Success: 0
+ * Failure: number of errors
+ *
+ * Programmer: Neil Fortner
+ * Wednesday, March 31, 2005
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+test_copy_null_ref(hid_t fcpl_src, hid_t fcpl_dst, hid_t fapl)
+{
+ hid_t fid1 = -1, fid2 = -1; /* File IDs */
+ hid_t sid = -1; /* Dataspace ID */
+ hid_t pid = -1; /* Object copy property list ID */
+ hid_t did1 = -1, did2 = -1; /* Dataset IDs */
+ hsize_t dim1d[1] = {2}; /* Dataset dimensions */
+ hobj_ref_t obj_buf[2]; /* Buffer for object refs */
+ hdset_reg_ref_t reg_buf[2]; /* Buffer for region refs */
+ char zeros[MAX(sizeof(obj_buf),sizeof(reg_buf))]; /* Array of zeros, for memcmp */
+ char src_filename[NAME_BUF_SIZE];
+ char mid_filename[NAME_BUF_SIZE];
+ char dst_filename[NAME_BUF_SIZE];
+
+ TESTING("H5Ocopy(): NULL references");
+
+ /* Initialize "zeros" array */
+ HDmemset(zeros, 0, sizeof(zeros));
+
+ /* Initialize the filenames */
+ h5_fixname(FILENAME[0], fapl, src_filename, sizeof src_filename);
+ h5_fixname(FILENAME[1], fapl, mid_filename, sizeof mid_filename);
+ h5_fixname(FILENAME[2], fapl, dst_filename, sizeof dst_filename);
+
+ /* Reset file address checking info */
+ addr_reset();
+
+ /* Create source file */
+ if((fid1 = H5Fcreate(src_filename, H5F_ACC_TRUNC, fcpl_src, fapl)) < 0)
+ TEST_ERROR
+
+ /* Create dataspace */
+ if((sid = H5Screate_simple(1, dim1d, NULL)) < 0) TEST_ERROR
+
+ /* Create object reference dataset at SRC file */
+ if((did1 = H5Dcreate2(fid1, "obj_ref_dset", H5T_STD_REF_OBJ, sid,
+ H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR
+
+ /* Create region reference dataset at SRC file */
+ if((did2 = H5Dcreate2(fid1, "reg_ref_dset", H5T_STD_REF_DSETREG,
+ sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR
+
+ /* Create references */
+ if(H5Rcreate(&obj_buf[0], did1, ".", H5R_OBJECT, -1) < 0) TEST_ERROR
+ if(H5Rcreate(&obj_buf[1], did2, ".", H5R_OBJECT, -1) < 0) TEST_ERROR
+ if(H5Rcreate(&reg_buf[0], did1, ".", H5R_DATASET_REGION, sid) < 0)
+ TEST_ERROR
+ if(H5Rcreate(&reg_buf[1], did2, ".", H5R_DATASET_REGION, sid) < 0)
+ TEST_ERROR
+
+ /* Write data into file */
+ if(H5Dwrite(did1, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, obj_buf)
+ < 0) TEST_ERROR
+ if(H5Dwrite(did2, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL, H5P_DEFAULT,
+ reg_buf) < 0) TEST_ERROR
+
+ /* Close datasets */
+ if(H5Dclose(did1) < 0) TEST_ERROR
+ if(H5Dclose(did2) < 0) TEST_ERROR
+
+ /* Create middle file */
+ if((fid2 = H5Fcreate(mid_filename, H5F_ACC_TRUNC, fcpl_src, fapl)) < 0)
+ TEST_ERROR
+
+ /* Copy the source file to the middle file. Note the expand references
+ * flag is not set. */
+ if(H5Ocopy(fid1, "/", fid2, "/A", H5P_DEFAULT, H5P_DEFAULT) < 0) TEST_ERROR
+
+ /* Close source file */
+ if(H5Fclose(fid1) < 0) TEST_ERROR
+
+ /* Open copied datasets */
+ if((did1 = H5Dopen2(fid2, "/A/obj_ref_dset", H5P_DEFAULT)) < 0) TEST_ERROR
+ if((did2 = H5Dopen2(fid2, "/A/reg_ref_dset", H5P_DEFAULT)) < 0) TEST_ERROR
+
+ /* Read copied datasets */
+ if(H5Dread(did1, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, obj_buf)
+ < 0) TEST_ERROR
+ if(H5Dread(did2, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL, H5P_DEFAULT,
+ reg_buf) < 0) TEST_ERROR
+
+ /* Verify that the references contain only "0" bytes */
+ if(HDmemcmp(obj_buf, zeros, sizeof(obj_buf))) TEST_ERROR
+ if(HDmemcmp(reg_buf, zeros, sizeof(reg_buf))) TEST_ERROR
+
+ /* Close datasets */
+ if(H5Dclose(did1) < 0) TEST_ERROR
+ if(H5Dclose(did2) < 0) TEST_ERROR
+
+ /* Create destination file */
+ if((fid1 = H5Fcreate(dst_filename, H5F_ACC_TRUNC, fcpl_dst, fapl)) < 0)
+ TEST_ERROR
+
+ /* Create object copy property list */
+ if((pid = H5Pcreate(H5P_OBJECT_COPY)) < 0) TEST_ERROR
+
+ /* Set the "expand references" flag */
+ if(H5Pset_copy_object(pid, H5O_COPY_EXPAND_REFERENCE_FLAG) < 0) TEST_ERROR
+
+ /* Copy the middle file to the destination file. Note the expand references
+ * flag *is* set, even though the references are now NULL. */
+ if(H5Ocopy(fid2, "/", fid1, "/AA", pid, H5P_DEFAULT) < 0) TEST_ERROR
+
+ /* Close source file */
+ if(H5Fclose(fid2) < 0) TEST_ERROR
+
+ /* Open copied datasets */
+ if((did1 = H5Dopen2(fid1, "/AA/A/obj_ref_dset", H5P_DEFAULT)) < 0) TEST_ERROR
+ if((did2 = H5Dopen2(fid1, "/AA/A/reg_ref_dset", H5P_DEFAULT)) < 0) TEST_ERROR
+
+ /* Read copied datasets */
+ if(H5Dread(did1, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, obj_buf)
+ < 0) TEST_ERROR
+ if(H5Dread(did2, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL, H5P_DEFAULT,
+ reg_buf) < 0) TEST_ERROR
+
+ /* Verify that the references contain only "0" bytes */
+ if(HDmemcmp(obj_buf, zeros, sizeof(obj_buf))) TEST_ERROR
+ if(HDmemcmp(reg_buf, zeros, sizeof(reg_buf))) TEST_ERROR
+
+ /* Close */
+ if(H5Pclose(pid) < 0) TEST_ERROR
+ if(H5Dclose(did1) < 0) TEST_ERROR
+ if(H5Dclose(did2) < 0) TEST_ERROR
+ if(H5Fclose(fid1) < 0) TEST_ERROR
+ if(H5Sclose(sid) < 0) TEST_ERROR
+
+ PASSED();
+ return 0;
+
+error:
+ H5E_BEGIN_TRY {
+ H5Pclose(pid);
+ H5Dclose(did1);
+ H5Dclose(did2);
+ H5Fclose(fid1);
+ H5Fclose(fid2);
+ H5Sclose(sid);
+ } H5E_END_TRY;
+ return 1;
+} /* end test_copy_null_ref */
+
+
+/*-------------------------------------------------------------------------
* Function: test_copy_option
*
* Purpose: Create a group in SRC file and copy it to DST file
@@ -8251,7 +8413,8 @@ main(void)
nerrors += test_copy_same_file_named_datatype(fcpl_src, my_fapl);
nerrors += test_copy_old_layout(fcpl_dst, my_fapl);
- }
+ nerrors += test_copy_null_ref(fcpl_src, fcpl_dst, my_fapl);
+ }
/* TODO: not implemented
nerrors += test_copy_mount(my_fapl);
generated by cgit v0.12 at 2024-07-23 07:35:52 (GMT)