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authorAllen Byrne <byrn@hdfgroup.org>2019-12-04 22:36:32 (GMT)
committerAllen Byrne <byrn@hdfgroup.org>2019-12-04 22:36:32 (GMT)
commitd552e97eae59408f210d7d7909b8b71811fbd930 (patch)
tree0a1269e15fdf7ba08126917d6236d53493202a9e /tools/src
parentcc2407257af31cca253e2c42c1d69c0f205e271b (diff)
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Update h5ls help and rework dump_mem routines for attrs
Diffstat (limited to 'tools/src')
-rw-r--r--tools/src/h5dump/h5dump.c2
-rw-r--r--tools/src/h5dump/h5dump_xml.c42
-rw-r--r--tools/src/h5ls/h5ls.c109
3 files changed, 57 insertions, 96 deletions
diff --git a/tools/src/h5dump/h5dump.c b/tools/src/h5dump/h5dump.c
index 507a62f..0222c8b 100644
--- a/tools/src/h5dump/h5dump.c
+++ b/tools/src/h5dump/h5dump.c
@@ -1703,6 +1703,8 @@ main(int argc, const char *argv[])
/* To Do: clean up XML table */
+ H5Eset_auto2(H5E_DEFAULT, func, edata);
+
leave(h5tools_getstatus());
done:
diff --git a/tools/src/h5dump/h5dump_xml.c b/tools/src/h5dump/h5dump_xml.c
index 0868467..b78cf00 100644
--- a/tools/src/h5dump/h5dump_xml.c
+++ b/tools/src/h5dump/h5dump_xml.c
@@ -1880,47 +1880,17 @@ xml_dump_data(hid_t obj_id, int obj_data, struct subset_t H5_ATTR_UNUSED *sset,
status = xml_print_strs(obj_id, ATTRIBUTE_DATA);
}
else { /* all other data */
- /* VL data special information */
- unsigned int vl_data = 0; /* contains VL datatypes */
-
- p_type = H5Tget_native_type(type, H5T_DIR_DEFAULT);
-
- /* Check if we have VL data in the dataset's datatype */
- if (h5tools_detect_vlen(p_type) == TRUE)
- vl_data = TRUE;
-
- H5Tclose(type);
-
space = H5Aget_space(obj_id);
if(space == H5S_NULL || space == H5S_NO_CLASS) {
status = SUCCEED;
}
else {
- ndims = H5Sget_simple_extent_dims(space, size, NULL);
-
- for (i = 0; i < ndims; i++)
- nelmts *= size[i];
-
- if((buf = HDmalloc((size_t)(nelmts * MAX(H5Tget_size(type), H5Tget_size(p_type))))) == NULL) {
- error_msg("unable to allocate buffer\n");
- h5tools_setstatus(EXIT_FAILURE);
- status = FAIL;
- }
- else {
- if (H5Aread(obj_id, p_type, buf) >= 0) {
- h5tools_context_t datactx;
- HDmemset(&datactx, 0, sizeof(datactx));
- datactx.need_prefix = TRUE;
- datactx.indent_level = ctx.indent_level;
- datactx.cur_column = ctx.cur_column;
- status = h5tools_dump_mem(rawoutstream, outputformat, &datactx, obj_id, p_type, space, buf);
- }
- /* Reclaim any VL memory, if necessary */
- if (vl_data)
- H5Treclaim(p_type, space, H5P_DEFAULT, buf);
-
- HDfree(buf);
- }
+ h5tools_context_t datactx;
+ HDmemset(&datactx, 0, sizeof(datactx));
+ datactx.need_prefix = TRUE;
+ datactx.indent_level = ctx.indent_level;
+ datactx.cur_column = ctx.cur_column;
+ status = h5tools_dump_mem(rawoutstream, outputformat, &datactx, obj_id);
}
H5Tclose(p_type);
H5Sclose(space);
diff --git a/tools/src/h5ls/h5ls.c b/tools/src/h5ls/h5ls.c
index 876b59e..416d5d2 100644
--- a/tools/src/h5ls/h5ls.c
+++ b/tools/src/h5ls/h5ls.c
@@ -132,7 +132,6 @@ static hbool_t no_dangling_link_g = FALSE; /* treat dangling link is error */
static hbool_t follow_elink_g = FALSE; /* follow external links */
static hbool_t grp_literal_g = FALSE; /* list group, not contents */
static hbool_t hexdump_g = FALSE; /* show data as raw hexadecimal */
-static hbool_t show_errors_g = FALSE; /* print HDF5 error messages */
static hbool_t simple_output_g = FALSE; /* make output more machine-readable */
static hbool_t show_file_name_g = FALSE; /* show file name for full names */
static hbool_t no_line_wrap_g = FALSE; /* show data content without line wrap */
@@ -193,7 +192,7 @@ usage (void)
PRINTVALSTREAM(rawoutstream, " --no-dangling-links\n");
PRINTVALSTREAM(rawoutstream, " Must be used with --follow-symlinks option;\n");
PRINTVALSTREAM(rawoutstream, " otherwise, h5ls shows error message and returns an exit\n");
- PRINTVALSTREAM(rawoutstream, " code of 1. \n");
+ PRINTVALSTREAM(rawoutstream, " code of 1.\n");
PRINTVALSTREAM(rawoutstream, " Check for any symbolic links (soft links or external links)\n");
PRINTVALSTREAM(rawoutstream, " that do not resolve to an existing object (dataset, group,\n");
PRINTVALSTREAM(rawoutstream, " or named datatype).\n");
@@ -228,11 +227,8 @@ usage (void)
PRINTVALSTREAM(rawoutstream, " \"%%05d\" to open a file family.\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, " Deprecated Options\n");
- PRINTVALSTREAM(rawoutstream, " The following options have been deprecated in HDF5. While they remain\n");
- PRINTVALSTREAM(rawoutstream, " available, they have been superseded as indicated and may be removed\n");
- PRINTVALSTREAM(rawoutstream, " from HDF5 in the future. Use the indicated replacement option in all\n");
- PRINTVALSTREAM(rawoutstream, " new work; where possible, existing scripts, et cetera, should also be\n");
- PRINTVALSTREAM(rawoutstream, " updated to use the replacement option.\n");
+ PRINTVALSTREAM(rawoutstream, " The following options have been removed in HDF5 1.12. Use the indicated\n");
+ PRINTVALSTREAM(rawoutstream, " replacement option in all work.\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, " -E or --external Follow external links.\n");
PRINTVALSTREAM(rawoutstream, " Replaced by --follow-symlinks.\n");
@@ -1530,6 +1526,7 @@ dump_dataset_values(hid_t dset)
{
H5TOOLS_ERR_INIT(herr_t, SUCCEED)
hid_t f_type = H5I_INVALID_HID;
+ hid_t space = H5I_INVALID_HID;
hid_t new_obj_id = H5I_INVALID_HID;
hid_t new_obj_sid = H5I_INVALID_HID;
hsize_t total_size[H5S_MAX_RANK];
@@ -1537,7 +1534,6 @@ dump_dataset_values(hid_t dset)
hsize_t elmt_counter = 0; /*counts the # elements printed. */
int ndims;
size_t i;
- size_t size;
char string_prefix[64];
static char fmt_double[16];
static char fmt_float[16];
@@ -1553,7 +1549,7 @@ dump_dataset_values(hid_t dset)
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "enter");
f_type = H5Dget_type(dset);
- size = H5Tget_size(f_type);
+ space = H5Dget_space(dset);
HDmemset(&ctx, 0, sizeof(ctx));
HDmemset(&buffer, 0, sizeof(h5tools_str_t));
@@ -1623,7 +1619,7 @@ dump_dataset_values(hid_t dset)
* command line switch was given. */
outputformat.raw = TRUE;
}
- else if (string_g && 1 == size && H5T_INTEGER == H5Tget_class(f_type)) {
+ else if (string_g && H5Tget_size(f_type) == 1 && (H5Tget_class(f_type) == H5T_INTEGER)) {
/* Print 1-byte integer data as an ASCI character string instead of
* integers if the `-s' or `--string' command-line option was given. */
outputformat.ascii = TRUE;
@@ -1640,11 +1636,12 @@ dump_dataset_values(hid_t dset)
/* Print all the values. */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, " Data:\n");
+
h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0);
+
ctx.need_prefix = TRUE;
ctx.cur_column = (size_t)curr_pos;
if (H5Tget_class(f_type) == H5T_REFERENCE) {
- hid_t space = H5Dget_space(dset);
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "reference class type");
if (!H5Tequal(f_type, H5T_STD_REF) && !H5Tequal(f_type, H5T_STD_REF_DSETREG) && !H5Tequal(f_type, H5T_STD_REF_OBJ)) {
HGOTO_DONE(SUCCEED);
@@ -1659,13 +1656,12 @@ dump_dataset_values(hid_t dset)
ctx.p_min_idx[i] = 0;
H5Sget_simple_extent_dims(space, total_size, NULL);
- H5Sclose(space);
if (ctx.ndims > 0)
init_acc_pos(&ctx, total_size);
ctx.need_prefix = TRUE;
if (NULL != (ref_buf = (H5R_ref_t *)HDcalloc(MAX(sizeof(unsigned), sizeof(H5R_ref_t)), ndims))) {
- H5TOOLS_GOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread reference read");
+ H5TOOLS_DEBUG(H5E_tools_min_id_g, "H5Dread reference read");
if(H5Dread(dset, H5T_STD_REF, H5S_ALL, H5S_ALL, H5P_DEFAULT, ref_buf) < 0) {
HDfree(ref_buf);
H5TOOLS_GOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread reference failed");
@@ -1682,6 +1678,7 @@ dump_dataset_values(hid_t dset)
}
}
done:
+ H5Sclose(space);
H5Tclose(f_type);
h5tools_str_close(&buffer);
@@ -1843,10 +1840,11 @@ dump_attribute_values(hid_t attr, const char *attr_name)
H5Sget_simple_extent_dims(space, total_size, NULL);
if (ctx.ndims > 0)
init_acc_pos(&ctx, total_size);
+ ctx.need_prefix = TRUE;
if (NULL != (ref_buf = (H5R_ref_t *)HDcalloc(MAX(sizeof(unsigned), sizeof(H5R_ref_t)), ndims))) {
- H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "Attribute reference read");
- if(H5Aread(attr, H5T_STD_REF, ref_buf) >= 0) {
+ H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "H5Aread reference read");
+ if(H5Aread(attr, H5T_STD_REF, ref_buf) < 0) {
HDfree(ref_buf);
H5TOOLS_GOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread reference failed");
}
@@ -1858,40 +1856,13 @@ dump_attribute_values(hid_t attr, const char *attr_name)
}
else {
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "Attribute data read");
- if (hexdump_g)
- p_type = H5Tcopy(f_type);
- else
- p_type = H5Tget_native_type(f_type, H5T_DIR_DEFAULT);
-
- if (p_type >= 0) {
- /* VL data special information */
- unsigned int vl_data = 0; /* contains VL datatypes */
-
- /* Check if we have VL data in the dataset's datatype */
- if (h5tools_detect_vlen(p_type) == TRUE)
- vl_data = TRUE;
-
- temp_need = nelmts * MAX(H5Tget_size(f_type), H5Tget_size(p_type));
- need = (size_t)temp_need;
- if((buf = HDmalloc(need)) != NULL) {
- if(H5Aread(attr, p_type, buf) >= 0) {
- ctx.indent_level++;
- if (h5tools_dump_mem(rawoutstream, info, &ctx, attr, p_type, space, buf) < 0) {
- h5tools_str_reset(&buffer);
- h5tools_str_append(&buffer, " Unable to print data.");
- h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0);
- }
- ctx.indent_level--;
- }
-
- /* Reclaim any VL memory, if necessary */
- if (vl_data)
- H5Treclaim(p_type, space, H5P_DEFAULT, buf);
-
- HDfree(buf);
- }
- H5Tclose(p_type);
- } /* end if */
+ ctx.indent_level++;
+ if (h5tools_dump_mem(rawoutstream, info, &ctx, attr) < 0) {
+ h5tools_str_reset(&buffer);
+ h5tools_str_append(&buffer, " Unable to print data.");
+ h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0);
+ }
+ ctx.indent_level--;
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "Attribute data read complete");
}
done:
@@ -1919,7 +1890,7 @@ static herr_t
list_attr(hid_t obj, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *ainfo,
void H5_ATTR_UNUSED *op_data)
{
- H5TOOLS_ERR_INIT(herr_t, SUCCEED);
+ H5TOOLS_ERR_INIT(herr_t, SUCCEED)
hid_t attr = H5I_INVALID_HID;
hid_t space = H5I_INVALID_HID;
hid_t type = H5I_INVALID_HID;
@@ -1952,7 +1923,7 @@ list_attr(hid_t obj, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *ain
print_string(&buffer, attr_name, TRUE);
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "Attribute name:%s", attr_name);
- if ((attr = H5Aopen(obj, attr_name, H5P_DEFAULT)) < 0) {
+ if ((attr = H5Aopen(obj, attr_name, H5P_DEFAULT)) >= 0) {
space = H5Aget_space(attr);
type = H5Aget_type(attr);
@@ -2344,7 +2315,7 @@ datatype_list2(hid_t type, const char H5_ATTR_UNUSED *name)
static herr_t
list_obj(const char *name, const H5O_info_t *oinfo, const char *first_seen, void *_iter)
{
- H5TOOLS_ERR_INIT(herr_t, SUCCEED);
+ H5TOOLS_ERR_INIT(herr_t, SUCCEED)
H5O_type_t obj_type = oinfo->type; /* Type of the object */
iter_t *iter = (iter_t*)_iter;
hsize_t curr_pos = 0; /* total data element position */
@@ -2892,6 +2863,10 @@ main(int argc, const char *argv[])
const char *preferred_driver = NULL;
int err_exit = 0;
hid_t fapl_id = H5P_DEFAULT;
+ H5E_auto2_t func;
+ H5E_auto2_t tools_func;
+ void *edata;
+ void *tools_edata;
#ifdef H5_HAVE_ROS3_VFD
/* default "anonymous" s3 configuration */
@@ -2919,9 +2894,17 @@ main(int argc, const char *argv[])
h5tools_setprogname(PROGRAMNAME);
h5tools_setstatus(EXIT_SUCCESS);
+ /* Disable error reporting */
+ H5Eget_auto2(H5E_DEFAULT, &func, &edata);
+ H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
+
/* Initialize h5tools lib */
h5tools_init();
+ /* Disable tools error reporting */
+ H5Eget_auto2(H5tools_ERR_STACK_g, &tools_func, &tools_edata);
+ H5Eset_auto2(H5tools_ERR_STACK_g, NULL, NULL);
+
/* Build object display table */
DISPATCH(H5O_TYPE_GROUP, "Group", NULL, NULL);
DISPATCH(H5O_TYPE_DATASET, "Dataset", dataset_list1, dataset_list2);
@@ -2948,11 +2931,11 @@ main(int argc, const char *argv[])
data_g = TRUE;
}
else if (!HDstrcmp(argv[argno], "--enable-error-stack")) {
- show_errors_g = TRUE;
+ enable_error_stack = 1;
/* deprecated --errors */
}
else if (!HDstrcmp(argv[argno], "--errors")) {
- show_errors_g = TRUE;
+ enable_error_stack = 1;
}
else if (!HDstrcmp(argv[argno], "--follow-symlinks")) {
follow_symlink_g = TRUE;
@@ -3201,7 +3184,7 @@ main(int argc, const char *argv[])
/* deprecated -e */
case 'e': /* --errors */
- show_errors_g = TRUE;
+ enable_error_stack = 1;
break;
case 'E': /* --external */
@@ -3309,10 +3292,10 @@ main(int argc, const char *argv[])
}
} /* preferred_driver defined */
- /* Turn off HDF5's automatic error printing unless you're debugging h5ls */
- if(!show_errors_g)
- H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
-
+ if (enable_error_stack > 0) {
+ H5Eset_auto2(H5E_DEFAULT, func, edata);
+ H5Eset_auto2(H5tools_ERR_STACK_g, tools_func, tools_edata);
+ }
/* Each remaining argument is an hdf5 file followed by an optional slash
* and object name.
@@ -3376,6 +3359,7 @@ main(int argc, const char *argv[])
x = oname;
if (NULL == (oname = HDstrdup(oname))) {
HDfprintf(rawerrorstream, "memory allocation failed\n");
+ H5Eset_auto2(H5E_DEFAULT, func, edata);
leave(EXIT_FAILURE);
}
*x = '\0';
@@ -3420,6 +3404,7 @@ main(int argc, const char *argv[])
h5tools_str_reset(&buffer);
print_obj_name(&buffer, &iter, oname, "**NOT FOUND**");
h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0);
+ H5Eset_auto2(H5E_DEFAULT, func, edata);
leave(EXIT_FAILURE);
} /* end if */
} /* end if */
@@ -3428,8 +3413,10 @@ main(int argc, const char *argv[])
/* Open the object and display it's information */
if (li.type == H5L_TYPE_HARD) {
- if (visit_obj(file, oname, &iter) < 0)
+ if (visit_obj(file, oname, &iter) < 0) {
+ H5Eset_auto2(H5E_DEFAULT, func, edata);
leave(EXIT_FAILURE);
+ }
} /* end if(li.type == H5L_TYPE_HARD) */
else {
/* Specified name is not for object -- list that link */
@@ -3458,10 +3445,12 @@ main(int argc, const char *argv[])
if (fapl_id != H5P_DEFAULT) {
if (0 < H5Pclose(fapl_id)) {
HDfprintf(rawerrorstream, "Error: Unable to set close fapl entry\n\n");
+ H5Eset_auto2(H5E_DEFAULT, func, edata);
leave(EXIT_FAILURE);
}
}
+ H5Eset_auto2(H5E_DEFAULT, func, edata);
if (err_exit)
leave(EXIT_FAILURE);
else