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authorAllen Byrne <byrn@hdfgroup.org>2017-05-26 14:06:51 (GMT)
committerAllen Byrne <byrn@hdfgroup.org>2017-05-26 14:06:51 (GMT)
commit79bd25fd068fc7d4764cf18f6d43019e875a99e3 (patch)
treea51595842e3e007a6821f5da5030d42303afe3a4 /tools
parentaab593f7d94748ac8e929fc0cd11f89c0431b8a4 (diff)
parentc13e0835f70b3ba9d9d706d772b5fa0f2a534cbf (diff)
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Merge pull request #543 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_8 to hdf5_1_8
* commit 'c13e0835f70b3ba9d9d706d772b5fa0f2a534cbf': Add missing creation order flag set Update usage reference file for test Remove unavailable argument Add missing variable HDFFV-8611 preserve creation order for root group
Diffstat (limited to 'tools')
-rw-r--r--tools/h5dump/h5dump.h4
-rw-r--r--tools/h5dump/h5dump_extern.h4
-rw-r--r--tools/h5repack/CMakeTests.cmake9
-rw-r--r--tools/h5repack/h5repack.c2
-rw-r--r--tools/h5repack/h5repack.sh.in8
-rw-r--r--tools/h5repack/h5repack_copy.c20
-rw-r--r--tools/h5repack/h5repack_main.c81
-rw-r--r--tools/h5repack/h5repack_verify.c7
-rw-r--r--tools/h5repack/testfiles/crtorder.tordergr.h5.ddl36
-rw-r--r--tools/h5repack/testfiles/h5repack-help.txt4
-rw-r--r--tools/lib/h5diff_attr.c2
-rw-r--r--tools/lib/h5tools.c4
-rw-r--r--tools/lib/h5tools.h4
-rw-r--r--tools/lib/h5tools_type.c32
14 files changed, 169 insertions, 48 deletions
diff --git a/tools/h5dump/h5dump.h b/tools/h5dump/h5dump.h
index 757087d..cf4c8c1 100644
--- a/tools/h5dump/h5dump.h
+++ b/tools/h5dump/h5dump.h
@@ -76,10 +76,6 @@ int disable_compact_subset= FALSE; /* disable compact form of subset no
int display_packed_bits = FALSE; /*print 1-8 byte numbers as packed bits*/
int include_attrs = TRUE; /* Display attributes */
-/* sort parameters */
-H5_index_t sort_by = H5_INDEX_NAME; /*sort_by [creation_order | name] */
-H5_iter_order_t sort_order = H5_ITER_INC; /*sort_order [ascending | descending] */
-
#define PACKED_BITS_MAX 8 /* Maximum number of packed-bits to display */
#define PACKED_BITS_SIZE_MAX (8*sizeof(long long)) /* Maximum bits size of integer types of packed-bits */
/* mask list for packed bits */
diff --git a/tools/h5dump/h5dump_extern.h b/tools/h5dump/h5dump_extern.h
index 49816ac..ae65174 100644
--- a/tools/h5dump/h5dump_extern.h
+++ b/tools/h5dump/h5dump_extern.h
@@ -75,10 +75,6 @@ extern int disable_compact_subset; /* disable compact form of subset no
extern int display_packed_bits; /*print 1-8 byte numbers as packed bits*/
extern int include_attrs; /* Display attributes */
-/* sort parameters */
-extern H5_index_t sort_by; /*sort_by [creation_order | name] */
-extern H5_iter_order_t sort_order; /*sort_order [ascending | descending] */
-
#define PACKED_BITS_MAX 8 /* Maximum number of packed-bits to display */
#define PACKED_BITS_SIZE_MAX 8*sizeof(long long) /* Maximum bits size of integer types of packed-bits */
/* mask list for packed bits */
diff --git a/tools/h5repack/CMakeTests.cmake b/tools/h5repack/CMakeTests.cmake
index 3710202..dafed86 100644
--- a/tools/h5repack/CMakeTests.cmake
+++ b/tools/h5repack/CMakeTests.cmake
@@ -88,6 +88,7 @@
${HDF5_TOOLS_SRC_DIR}/testfiles/tfamily00008.h5
${HDF5_TOOLS_SRC_DIR}/testfiles/tfamily00009.h5
${HDF5_TOOLS_SRC_DIR}/testfiles/tfamily00010.h5
+ ${HDF5_TOOLS_SRC_DIR}/testfiles/tordergr.h5
)
set (LIST_OTHER_TEST_FILES
@@ -106,6 +107,7 @@
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_layout.h5-plugin_version_test.ddl
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/plugin_version_test.h5repack_layout.h5.tst
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_layout.h5-plugin_zero.tst
+ ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/crtorder.tordergr.h5.ddl
)
foreach (h5_file ${LIST_HDF5_TEST_FILES} ${LIST_OTHER_TEST_FILES})
@@ -247,7 +249,7 @@
NAME H5REPACK_DMP-h5dump-${testname}
COMMAND "${CMAKE_COMMAND}"
-D "TEST_PROGRAM=$<TARGET_FILE:h5dump>"
- -D "TEST_ARGS:STRING=-pH;out-${testname}.${resultfile}"
+ -D "TEST_ARGS:STRING=-q;creation_order;-pH;out-${testname}.${resultfile}"
-D "TEST_FOLDER=${PROJECT_BINARY_DIR}/testfiles"
-D "TEST_OUTPUT=${resultfile}-${testname}.out"
-D "TEST_EXPECT=${resultcode}"
@@ -836,6 +838,11 @@
endif ()
ADD_H5_TEST (deflate_file ${TESTTYPE} ${arg})
+#crtorder
+ set (arg tordergr.h5 -L)
+ set (TESTTYPE "TEST")
+ ADD_H5_DMP_TEST (crtorder ${TESTTYPE} 0 ${arg})
+
#########################################################
# layout options (these files have no filters)
#########################################################
diff --git a/tools/h5repack/h5repack.c b/tools/h5repack/h5repack.c
index 35cf7a0..0ab5404 100644
--- a/tools/h5repack/h5repack.c
+++ b/tools/h5repack/h5repack.c
@@ -780,6 +780,8 @@ static int check_objects(const char* fname, pack_opt_t *options) {
*-------------------------------------------------------------------------
*/
+ /* Initialize indexing options */
+ h5trav_set_index(sort_by, sort_order);
/* init table */
trav_table_init(&travt);
diff --git a/tools/h5repack/h5repack.sh.in b/tools/h5repack/h5repack.sh.in
index 3b18185..3f5e013 100644
--- a/tools/h5repack/h5repack.sh.in
+++ b/tools/h5repack/h5repack.sh.in
@@ -113,6 +113,7 @@ $SRC_TOOLS_TESTFILES/tfamily00007.h5
$SRC_TOOLS_TESTFILES/tfamily00008.h5
$SRC_TOOLS_TESTFILES/tfamily00009.h5
$SRC_TOOLS_TESTFILES/tfamily00010.h5
+$SRC_TOOLS_TESTFILES/tordergr.h5
"
LIST_OTHER_TEST_FILES="
@@ -120,6 +121,7 @@ $SRC_H5REPACK_TESTFILES/h5repack-help.txt
$SRC_H5REPACK_TESTFILES/h5repack_ext.bin
$SRC_H5REPACK_TESTFILES/ublock.bin
$SRC_H5REPACK_TESTFILES/h5repack.info
+$SRC_H5REPACK_TESTFILES/crtorder.tordergr.h5.ddl
$SRC_H5REPACK_TESTFILES/deflate_limit.h5repack_layout.h5.ddl
$SRC_H5REPACK_TESTFILES/h5repack_layout.h5.ddl
$SRC_H5REPACK_TESTFILES/h5repack_filters.h5-gzip_verbose_filters.tst
@@ -531,7 +533,7 @@ TOOLTEST_DUMP()
VERIFY h5dump output $@
(
cd $TESTDIR
- $RUNSERIAL $H5DUMP_BIN -pH $outfile
+ $RUNSERIAL $H5DUMP_BIN -q creation_order -pH $outfile
) >$actual 2>$actual_err
cat $actual_err >> $actual
@@ -898,6 +900,10 @@ else
TOOLTEST deflate_file $arg
fi
+#crtorder
+arg="tordergr.h5 -L"
+TOOLTEST_DUMP crtorder $arg
+
#########################################################
# layout options (these files have no filters)
#########################################################
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index 40c3888..b41f7be 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -95,6 +95,7 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
hsize_t ub_size = 0; /* size of user block */
hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */
hid_t fapl = H5P_DEFAULT; /* file access property list ID */
+ unsigned crt_order_flags; /* group creation order flag */
/*-------------------------------------------------------------------------
* open input file
@@ -108,6 +109,8 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
/* get user block size and file space strategy/threshold */
{
hid_t fcpl_in; /* file creation property list ID for input file */
+ hid_t grp_in = -1; /* group ID */
+ hid_t gcpl_in = -1; /* group creation property list */
if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) {
error_msg("failed to retrieve file creation property list\n");
@@ -119,6 +122,18 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
+ /* open root group */
+ if ((grp_in = H5Gopen2(fidin, "/", H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");
+
+ /* get root group creation property list */
+ if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed");
+
+ /* query and set the group creation properties */
+ if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed");
+
if (H5Pclose(fcpl_in) < 0) {
error_msg("failed to close property list\n");
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
@@ -289,6 +304,9 @@ print_user_block(fnamein, fidin);
}
}
+ if(H5Pset_link_creation_order(fcpl, crt_order_flags ) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_creation_order failed");
+
/*-------------------------------------------------------------------------
* create the output file
*-------------------------------------------------------------------------
@@ -317,6 +335,8 @@ print_user_block(fnamein, fidin);
*-------------------------------------------------------------------------
*/
+ /* Initialize indexing options */
+ h5trav_set_index(sort_by, sort_order);
/* init table */
trav_table_init(&travt);
diff --git a/tools/h5repack/h5repack_main.c b/tools/h5repack/h5repack_main.c
index d14b604..e1f13fd 100644
--- a/tools/h5repack/h5repack_main.c
+++ b/tools/h5repack/h5repack_main.c
@@ -31,7 +31,7 @@ const char *outfile = NULL;
* Command-line options: The user can specify short or long-named
* parameters.
*/
-static const char *s_opts = "hVvf:l:m:e:nLc:d:s:u:b:M:t:a:i:o:E";
+static const char *s_opts = "hVvf:l:m:e:nLc:d:s:u:b:M:t:a:i:o:q:z:E";
static struct long_options l_opts[] = {
{ "help", no_arg, 'h' },
{ "version", no_arg, 'V' },
@@ -52,6 +52,8 @@ static struct long_options l_opts[] = {
{ "alignment", require_arg, 'a' },
{ "infile", require_arg, 'i' }, /* -i for backward compability */
{ "outfile", require_arg, 'o' }, /* -o for backward compability */
+ { "sort_by", require_arg, 'q' },
+ { "sort_order", require_arg, 'z' },
{ "enable-error-stack", no_arg, 'E' },
{ NULL, 0, '\0' }
};
@@ -86,6 +88,8 @@ static void usage(const char *prog) {
PRINTVALSTREAM(rawoutstream, " -M A, --metadata_block_size=A Metadata block size for H5Pset_meta_block_size\n");
PRINTVALSTREAM(rawoutstream, " -t T, --threshold=T Threshold value for H5Pset_alignment\n");
PRINTVALSTREAM(rawoutstream, " -a A, --alignment=A Alignment value for H5Pset_alignment\n");
+ PRINTVALSTREAM(rawoutstream, " -q Q, --sort_by=Q Sort groups and attributes by index Q\n");
+ PRINTVALSTREAM(rawoutstream, " -z Z, --sort_order=Z Sort groups and attributes by order Z\n");
PRINTVALSTREAM(rawoutstream, " -f FILT, --filter=FILT Filter type\n");
PRINTVALSTREAM(rawoutstream, " -l LAYT, --layout=LAYT Layout type\n");
PRINTVALSTREAM(rawoutstream, "\n");
@@ -95,6 +99,8 @@ static void usage(const char *prog) {
PRINTVALSTREAM(rawoutstream, " U - is a filename.\n");
PRINTVALSTREAM(rawoutstream, " T - is an integer\n");
PRINTVALSTREAM(rawoutstream, " A - is an integer greater than zero\n");
+ PRINTVALSTREAM(rawoutstream, " Q - is the sort index type for the input file. It can be \"name\" or \"creation_order\" (default)\n");
+ PRINTVALSTREAM(rawoutstream, " Z - is the sort order type for the input file. It can be \"descending\" or \"ascending\" (default)\n");
PRINTVALSTREAM(rawoutstream, " B - is the user block size, any value that is 512 or greater and is\n");
PRINTVALSTREAM(rawoutstream, " a power of 2 (1024 default)\n");
PRINTVALSTREAM(rawoutstream, " F - is the shared object header message type, any of <dspace|dtype|fill|\n");
@@ -340,6 +346,52 @@ done:
}
/*-------------------------------------------------------------------------
+ * Function: set_sort_by
+ *
+ * Purpose: set the "by" form of sorting by translating from a string input
+ * parameter to a H5_index_t return value
+ * current sort values are [creation_order | name]
+ *
+ * Return: H5_index_t form of sort or H5_INDEX_UNKNOWN if none found
+ *-------------------------------------------------------------------------
+ */
+static H5_index_t
+set_sort_by(const char *form)
+{
+ H5_index_t idx_type = H5_INDEX_UNKNOWN;
+
+ if (HDstrcmp(form,"name")==0) /* H5_INDEX_NAME */
+ idx_type = H5_INDEX_NAME;
+ else if (HDstrcmp(form,"creation_order")==0) /* H5_INDEX_CRT_ORDER */
+ idx_type = H5_INDEX_CRT_ORDER;
+
+ return idx_type;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: set_sort_order
+ *
+ * Purpose: set the order of sorting by translating from a string input
+ * parameter to a H5_iter_order_t return value
+ * current order values are [ascending | descending ]
+ *
+ * Return: H5_iter_order_t form of order or H5_ITER_UNKNOWN if none found
+ *-------------------------------------------------------------------------
+ */
+static H5_iter_order_t
+set_sort_order(const char *form)
+{
+ H5_iter_order_t iter_order = H5_ITER_UNKNOWN;
+
+ if (HDstrcmp(form,"ascending")==0) /* H5_ITER_INC */
+ iter_order = H5_ITER_INC;
+ else if (HDstrcmp(form,"descending")==0) /* H5_ITER_DEC */
+ iter_order = H5_ITER_DEC;
+
+ return iter_order;
+}
+
+/*-------------------------------------------------------------------------
* Function: parse_command_line
*
* Purpose: parse command line input
@@ -497,9 +549,27 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
}
break;
- case 'E':
- enable_error_stack = TRUE;
- break;
+ case 'q':
+ if((sort_by = set_sort_by(opt_arg)) < 0) {
+ error_msg(" failed to set sort by form <%s>\n", opt_arg);
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = -1;
+ goto done;
+ }
+ break;
+
+ case 'z':
+ if((sort_order = set_sort_order(opt_arg)) < 0) {
+ error_msg(" failed to set sort order form <%s>\n", opt_arg);
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = -1;
+ goto done;
+ }
+ break;
+
+ case 'E':
+ enable_error_stack = TRUE;
+ break;
default:
break;
@@ -568,6 +638,9 @@ int main(int argc, const char **argv)
/* initialize options */
h5repack_init(&options, 0);
+ /* Initialize default indexing options */
+ sort_by = H5_INDEX_CRT_ORDER;
+
if (parse_command_line(argc, argv, &options) < 0)
goto done;
diff --git a/tools/h5repack/h5repack_verify.c b/tools/h5repack/h5repack_verify.c
index 3905842..003875d 100644
--- a/tools/h5repack/h5repack_verify.c
+++ b/tools/h5repack/h5repack_verify.c
@@ -115,6 +115,8 @@ h5repack_verify(const char *out_fname, pack_opt_t *options)
if(options->all_filter == 1 || options->all_layout == 1)
{
+ /* Initialize indexing options */
+ h5trav_set_index(sort_by, sort_order);
/* init table */
trav_table_init(&travt);
@@ -329,6 +331,9 @@ int h5repack_cmp_pl(const char *fname1,
* get file table list of objects
*-------------------------------------------------------------------------
*/
+ /* Initialize indexing options */
+ h5trav_set_index(sort_by, sort_order);
+ /* init table */
trav_table_init(&trav);
if(h5trav_gettable(fid1, trav) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5trav_gettable failed");
@@ -517,7 +522,7 @@ int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter)
{
case H5Z_FILTER_NONE:
- break;
+ break;
case H5Z_FILTER_SHUFFLE:
/* 1 private client value is returned by DCPL */
diff --git a/tools/h5repack/testfiles/crtorder.tordergr.h5.ddl b/tools/h5repack/testfiles/crtorder.tordergr.h5.ddl
new file mode 100644
index 0000000..870d154
--- /dev/null
+++ b/tools/h5repack/testfiles/crtorder.tordergr.h5.ddl
@@ -0,0 +1,36 @@
+HDF5 "out-crtorder.tordergr.h5" {
+GROUP "/" {
+ GROUP "2" {
+ GROUP "a" {
+ GROUP "a1" {
+ }
+ GROUP "a2" {
+ GROUP "a21" {
+ }
+ GROUP "a22" {
+ }
+ }
+ }
+ GROUP "b" {
+ }
+ GROUP "c" {
+ }
+ }
+ GROUP "1" {
+ GROUP "c" {
+ }
+ GROUP "b" {
+ }
+ GROUP "a" {
+ GROUP "a1" {
+ }
+ GROUP "a2" {
+ GROUP "a22" {
+ }
+ GROUP "a21" {
+ }
+ }
+ }
+ }
+}
+}
diff --git a/tools/h5repack/testfiles/h5repack-help.txt b/tools/h5repack/testfiles/h5repack-help.txt
index 5c30ce8..b9157d7 100644
--- a/tools/h5repack/testfiles/h5repack-help.txt
+++ b/tools/h5repack/testfiles/h5repack-help.txt
@@ -17,6 +17,8 @@ usage: h5repack [OPTIONS] file1 file2
-M A, --metadata_block_size=A Metadata block size for H5Pset_meta_block_size
-t T, --threshold=T Threshold value for H5Pset_alignment
-a A, --alignment=A Alignment value for H5Pset_alignment
+ -q Q, --sort_by=Q Sort groups and attributes by index Q
+ -z Z, --sort_order=Z Sort groups and attributes by order Z
-f FILT, --filter=FILT Filter type
-l LAYT, --layout=LAYT Layout type
@@ -26,6 +28,8 @@ usage: h5repack [OPTIONS] file1 file2
U - is a filename.
T - is an integer
A - is an integer greater than zero
+ Q - is the sort index type for the input file. It can be "name" or "creation_order" (default)
+ Z - is the sort order type for the input file. It can be "descending" or "ascending" (default)
B - is the user block size, any value that is 512 or greater and is
a power of 2 (1024 default)
F - is the shared object header message type, any of <dspace|dtype|fill|
diff --git a/tools/lib/h5diff_attr.c b/tools/lib/h5diff_attr.c
index 004672e..3018f18 100644
--- a/tools/lib/h5diff_attr.c
+++ b/tools/lib/h5diff_attr.c
@@ -91,7 +91,7 @@ static void table_attrs_free( table_attrs_t *table )
/*-------------------------------------------------------------------------
* Function: table_attr_mark_exist
*
- * Purpose: mark given attribute name to table as sign of exsit
+ * Purpose: mark given attribute name to table as sign of exist
*
* Parameter:
* - exist [IN]
diff --git a/tools/lib/h5tools.c b/tools/lib/h5tools.c
index 9a7dc9e..159349a 100644
--- a/tools/lib/h5tools.c
+++ b/tools/lib/h5tools.c
@@ -51,6 +51,10 @@ unsigned packed_data_length; /* length of packed bits to display */
unsigned long long packed_data_mask; /* mask in which packed bits to display */
int enable_error_stack= FALSE; /* re-enable error stack */
+/* sort parameters */
+H5_index_t sort_by = H5_INDEX_NAME; /*sort_by [creation_order | name] */
+H5_iter_order_t sort_order = H5_ITER_INC; /*sort_order [ascending | descending] */
+
/* module-scoped variables */
static int h5tools_init_g; /* if h5tools lib has been initialized */
diff --git a/tools/lib/h5tools.h b/tools/lib/h5tools.h
index 2e01ad2..09ec527 100644
--- a/tools/lib/h5tools.h
+++ b/tools/lib/h5tools.h
@@ -540,6 +540,10 @@ H5TOOLS_DLLVAR int oid_output; /* oid output */
H5TOOLS_DLLVAR int data_output; /* data output */
H5TOOLS_DLLVAR int attr_data_output; /* attribute data output */
+/* sort parameters */
+H5TOOLS_DLLVAR H5_index_t sort_by; /*sort_by [creation_order | name] */
+H5TOOLS_DLLVAR H5_iter_order_t sort_order; /*sort_order [ascending | descending] */
+
/* things to display or which are set via command line parameters */
H5TOOLS_DLLVAR int enable_error_stack; /* re-enable error stack */
diff --git a/tools/lib/h5tools_type.c b/tools/lib/h5tools_type.c
index b57e274..ae7160b 100644
--- a/tools/lib/h5tools_type.c
+++ b/tools/lib/h5tools_type.c
@@ -15,38 +15,6 @@
#include "h5tools.h"
/*-------------------------------------------------------------------------
- * Function: h5tools_get_native_type
- *
- * Purpose: Wrapper around H5Tget_native_type() to work around
- * Problems with bitfields.
- *
- * Return: Success: datatype ID
- *
- * Failure: FAIL
- *
- * Programmer: Quincey Koziol
- * Tuesday, October 5, 2004
- *
- * Modifications:
- *
- *-------------------------------------------------------------------------
- */
-hid_t
-h5tools_get_native_type(hid_t type)
-{
- hid_t p_type;
- H5T_class_t type_class;
-
- type_class = H5Tget_class(type);
- if(type_class==H5T_BITFIELD)
- p_type=H5Tcopy(type);
- else
- p_type = H5Tget_native_type(type,H5T_DIR_DEFAULT);
-
- return(p_type);
-}
-
-/*-------------------------------------------------------------------------
* Function: h5tools_get_little_endian_type
*
* Purpose: Get a little endian type from a file type