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-rw-r--r--tools/src/h5repack/h5repack.c323
-rw-r--r--tools/src/h5repack/h5repack_copy.c221
-rw-r--r--tools/src/h5repack/h5repack_main.c369
3 files changed, 507 insertions, 406 deletions
diff --git a/tools/src/h5repack/h5repack.c b/tools/src/h5repack/h5repack.c
index c18df6c..24f4e6c 100644
--- a/tools/src/h5repack/h5repack.c
+++ b/tools/src/h5repack/h5repack.c
@@ -41,7 +41,9 @@ static int have_request(pack_opt_t *options);
* Return: 0, ok, -1, fail
*-------------------------------------------------------------------------
*/
-int h5repack(const char* infile, const char* outfile, pack_opt_t *options) {
+int
+h5repack(const char* infile, const char* outfile, pack_opt_t *options)
+{
/* check input */
if (check_options(options) < 0)
return -1;
@@ -55,7 +57,7 @@ int h5repack(const char* infile, const char* outfile, pack_opt_t *options) {
return -1;
return 0;
-}
+} /* end h5repack() */
/*-------------------------------------------------------------------------
* Function: h5repack_init
@@ -86,7 +88,7 @@ h5repack_init(pack_opt_t *options, int verbose, hbool_t latest)
}
return (options_table_init(&(options->op_tbl)));
-}
+} /* end h5repack_init() */
/*-------------------------------------------------------------------------
* Function: h5repack_end
@@ -95,9 +97,11 @@ h5repack_init(pack_opt_t *options, int verbose, hbool_t latest)
*-------------------------------------------------------------------------
*/
-int h5repack_end(pack_opt_t *options) {
+int
+h5repack_end(pack_opt_t *options)
+{
return options_table_free(options->op_tbl);
-}
+} /* end h5repack_end() */
/*-------------------------------------------------------------------------
* Function: h5repack_addfilter
@@ -138,7 +142,7 @@ h5repack_addfilter(const char *str, pack_opt_t *options)
HDfree(obj_list);
return 0;
-}
+} /* end h5repack_addfilter() */
/*-------------------------------------------------------------------------
* Function: h5repack_addlayout
@@ -175,7 +179,7 @@ h5repack_addlayout(const char *str, pack_opt_t *options)
if (pack.layout == H5D_CHUNKED) {
/* -2 means the NONE option, remove chunking
and set the global layout to contiguous */
- if (pack.chunk.rank == -2)
+ if (pack.chunk.rank == -2) /* TODO: fix 'magic number' */
options->layout_g = H5D_CONTIGUOUS;
/* otherwise set the global chunking type */
else {
@@ -192,10 +196,10 @@ h5repack_addlayout(const char *str, pack_opt_t *options)
HDfree(obj_list);
ret_value = 0;
- }
+ } /* end if obj_list exists */
return ret_value;
-}
+} /* end h5repack_addlayout() */
/* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr()
* were located in h5repack_copy.c as static prior to bugfix1726.
@@ -215,8 +219,13 @@ h5repack_addlayout(const char *str, pack_opt_t *options)
* to free the stack.
*-------------------------------------------------------------------------
*/
-hid_t copy_named_datatype(hid_t type_in, hid_t fidout,
- named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options) {
+hid_t
+copy_named_datatype(hid_t type_in,
+ hid_t fidout,
+ named_dt_t **named_dt_head_p,
+ trav_table_t *travt,
+ pack_opt_t *options)
+{
named_dt_t *dt = *named_dt_head_p; /* Stack pointer */
named_dt_t *dt_ret = NULL; /* Datatype to return */
H5O_info_t oinfo; /* Object info of input dtype */
@@ -239,7 +248,8 @@ hid_t copy_named_datatype(hid_t type_in, hid_t fidout,
if (travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) {
/* Push onto the stack */
if (NULL == (dt = (named_dt_t *)HDmalloc(sizeof(named_dt_t))))
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "buffer allocation failed failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
+ "buffer allocation failed failed");
dt->next = *named_dt_head_p;
*named_dt_head_p = dt;
@@ -250,13 +260,14 @@ hid_t copy_named_datatype(hid_t type_in, hid_t fidout,
/* Check if this type is the one requested */
if (oinfo.addr == dt->addr_in) {
dt_ret = dt;
- } /* end if */
- } /* end if */
- } /* end for */
- } /* end else */
+ }
+ } /* end if named datatype */
+ } /* end for each object in traversal table */
+ } /* end else (create the stack) */
/* Handle the case that the requested datatype was not found. This is
- * possible if the datatype was committed anonymously in the input file. */
+ * possible if the datatype was committed anonymously in the input file.
+ */
if (!dt_ret) {
/* Push the new datatype onto the stack */
if (NULL == (dt_ret = (named_dt_t *)HDmalloc(sizeof(named_dt_t))))
@@ -267,31 +278,35 @@ hid_t copy_named_datatype(hid_t type_in, hid_t fidout,
/* Update the address and id */
dt_ret->addr_in = oinfo.addr;
dt_ret->id_out = -1;
- } /* end if */
+ } /* end if requested datatype not found */
/* If the requested datatype does not yet exist in the output file, copy it
- * anonymously */
+ * anonymously
+ */
if (dt_ret->id_out < 0) {
if (options->use_native == 1)
dt_ret->id_out = H5Tget_native_type(type_in, H5T_DIR_DEFAULT);
else
dt_ret->id_out = H5Tcopy(type_in);
if (dt_ret->id_out < 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_native_type-H5Tcopy failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
+ "H5Tget_native_type-H5Tcopy failed");
if (H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tcommit_anon failed");
- } /* end if */
+ } /* end if named datatype not yet in output file */
/* Set return value */
ret_value = dt_ret->id_out;
- /* Increment the ref count on id_out, because the calling function will try to close it */
- if(H5Iinc_ref(ret_value) < 0)
+ /* Increment the ref count on id_out, because the calling function will try
+ * to close it. (TODO: fix scope envy)
+ */
+ if (H5Iinc_ref(ret_value) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Iinc_ref failed");
done:
return ret_value;
-} /* end copy_named_datatype */
+} /* end copy_named_datatype() */
/*-------------------------------------------------------------------------
* Function: named_datatype_free
@@ -299,7 +314,9 @@ done:
* Purpose: Frees the stack of named datatypes.
*-------------------------------------------------------------------------
*/
-int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err) {
+int
+named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err)
+{
named_dt_t *dt = *named_dt_head_p;
int ret_value = -1;
@@ -310,13 +327,13 @@ int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err) {
dt = dt->next;
HDfree(*named_dt_head_p);
*named_dt_head_p = dt;
- } /* end while */
+ }
ret_value = 0;
done:
return (ret_value);
-} /* end named_datatype_free */
+} /* end named_datatype_free() */
/*-------------------------------------------------------------------------
* Function: copy_attr
@@ -330,8 +347,12 @@ done:
*-------------------------------------------------------------------------
*/
int
-copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
- trav_table_t *travt, pack_opt_t *options)
+copy_attr(
+ hid_t loc_in,
+ hid_t loc_out,
+ named_dt_t **named_dt_head_p,
+ trav_table_t *travt,
+ pack_opt_t *options)
{
int ret_value = 0;
hid_t attr_id = -1; /* attr ID */
@@ -361,14 +382,13 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
*/
for (u = 0; u < (unsigned) oinfo.num_attrs; u++) {
/* open attribute */
- if ((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t) u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t) u, H5P_DEFAULT, H5P_DEFAULT);
+ if (attr_id < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aopen_by_idx failed");
- /* get name */
if (H5Aget_name(attr_id, (size_t) 255, name) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- /* get the file datatype */
if ((ftype_id = H5Aget_type(attr_id)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_type failed");
@@ -385,18 +405,19 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
/* Copy named dt */
if ((wtype_id = copy_named_datatype(ftype_id, fidout, named_dt_head_p, travt, options)) < 0) {
H5Fclose(fidout);
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed");
- } /* end if */
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
+ "copy_named_datatype failed");
+ }
if (H5Fclose(fidout) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fclose failed");
- } /* end if */
+ } /* end if datatype is committed and we have a traversal table */
else {
if (options->use_native == 1)
wtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT);
else
wtype_id = H5Tcopy(ftype_id);
- } /* end else */
+ } /* end else: uncommitted datatype and/or no traversal table */
/* get the dataspace handle */
if ((space_id = H5Aget_space(attr_id)) < 0)
@@ -404,7 +425,8 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
/* get dimensions */
if ((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
+ "H5Sget_simple_extent_dims failed");
nelmts = 1;
for (j = 0; j < rank; j++)
@@ -413,12 +435,12 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
if ((msize = H5Tget_size(wtype_id)) == 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
- /*-------------------------------------------------------------------------
- * object references are a special case. We cannot just copy the buffers,
- * but instead we recreate the reference.
- * This is done on a second sweep of the file that just copies the referenced
- * objects at copy_refs_attr()
- *-------------------------------------------------------------------------
+ /*---------------------------------------------------------------------
+ * object references are a special case. We cannot just copy the
+ * buffers, but instead we recreate the reference.
+ * This is done on a second sweep of the file that just copies the
+ * referenced objects at copy_refs_attr().
+ *---------------------------------------------------------------------
*/
type_class = H5Tget_class(wtype_id);
is_ref = (type_class == H5T_REFERENCE);
@@ -429,7 +451,7 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
is_ref = (is_ref || (H5Tget_class(base_type) == H5T_REFERENCE));
if (H5Tclose(base_type) < 0)
H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose base_type failed");
- }
+ } /* end if type_class is variable length or array */
if (type_class == H5T_COMPOUND) {
int nmembers = H5Tget_nmembers(wtype_id);
@@ -444,13 +466,13 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
is_ref = 1;
break;
}
- } /* for (j=0; i<nmembers; j++) */
- } /* if (type_class == H5T_COMPOUND) */
+ } /* end for each member */
+ } /* end if type_class is H5T_COMPOUND */
if (!is_ref) {
- /*-------------------------------------------------------------------------
+ /*-----------------------------------------------------------------
* read to memory
- *-------------------------------------------------------------------------
+ *-----------------------------------------------------------------
*/
buf = (void *)HDmalloc((size_t)(nelmts * msize));
@@ -460,9 +482,9 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
if (H5Aread(attr_id, wtype_id, buf) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed");
- /*-------------------------------------------------------------------------
+ /*-----------------------------------------------------------------
* copy
- *-------------------------------------------------------------------------
+ *-----------------------------------------------------------------
*/
if ((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
@@ -485,9 +507,9 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
if (options->verbose)
HDprintf(FORMAT_OBJ_ATTR, "attr", name);
- /*-------------------------------------------------------------------------
+ /*---------------------------------------------------------------------
* close
- *-------------------------------------------------------------------------
+ *---------------------------------------------------------------------
*/
if (H5Sclose(space_id) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
@@ -501,19 +523,18 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
if (H5Aclose(attr_id) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed");
attr_id = -1;
- } /* for u */
+ } /* for u (each attribute) */
done:
H5E_BEGIN_TRY {
if (buf) {
- /* Check if we have VL data and string in the attribute's datatype that must
- * be reclaimed */
+ /* Check if we have VL data and string in the attribute's
+ * datatype that must be reclaimed
+ */
if (TRUE == h5tools_detect_vlen(wtype_id))
H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
-
- /* Free buf */
HDfree(buf);
- } /* end if */
+ }
H5Aclose(attr_out);
H5Sclose(space_id);
@@ -525,25 +546,27 @@ done:
return ret_value;
} /* end copy_attr() */
-/*-------------------------------------------------------------------------
+/*-----------------------------------------------------------------------------
* Function: check_options
*
* Purpose: print options, checks for invalid options
*
* Return: void, return -1 on error
- *-------------------------------------------------------------------------
+ *-----------------------------------------------------------------------------
*/
-static int check_options(pack_opt_t *options) {
+static int
+check_options(pack_opt_t *options)
+{
int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
unsigned int i;
int k, j, has_cp = 0, has_ck = 0;
char slayout[30];
/*-------------------------------------------------------------------------
- * objects to layout
- *-------------------------------------------------------------------------
- */
- if (options->verbose && have_request(options) /* only print if requested */) {
+ * Objects to layout
+ *-------------------------------------------------------------------------
+ */
+ if (options->verbose && have_request(options)) {
if (options->all_layout == 1) {
HDprintf("All objects to modify layout are...\n");
switch (options->layout_g) {
@@ -577,7 +600,7 @@ static int check_options(pack_opt_t *options) {
}
else
HDprintf("No all objects to modify layout\n");
- }/* verbose */
+ } /* end if verbose */
for (i = 0; i < options->op_tbl->nelems; i++) {
char* name = options->op_tbl->objs[i].path;
@@ -591,22 +614,23 @@ static int check_options(pack_opt_t *options) {
}
has_ck = 1;
}
- else if (options->op_tbl->objs[i].chunk.rank == -2) {
+ else if (options->op_tbl->objs[i].chunk.rank == -2) { /* TODO: replace 'magic number' */
if (options->verbose)
HDprintf(" <%s> %s\n", name, "NONE (contiguous)");
has_ck = 1;
}
- }
+ } /* end for each object in options */
if (options->all_layout == 1 && has_ck)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid chunking input: 'all' option is present with other objects");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
+ "invalid chunking input: 'all' option is present with other objects");
/*-------------------------------------------------------------------------
- * objects to filter
- *-------------------------------------------------------------------------
- */
+ * Objects to filter
+ *-------------------------------------------------------------------------
+ */
- if (options->verbose && have_request(options) /* only print if requested */) {
+ if (options->verbose && have_request(options)) {
if (options->all_filter == 1) {
HDprintf("All objects to apply filter are...\n");
for (k = 0; k < options->n_filter_g; k++) {
@@ -630,12 +654,12 @@ static int check_options(pack_opt_t *options) {
default:
HDprintf(" User Defined %d\n", filtn);
break;
- } /* k */
- };
- }
+ } /* end switch */
+ } /* end for each filter */
+ } /* end if options->all_filter == 1 (TODO: meaning) */
else
HDprintf("No all objects to apply filter\n");
- } /* verbose */
+ } /* end if verbose */
for (i = 0; i < options->op_tbl->nelems; i++) {
pack_info_t pack = options->op_tbl->objs[i];
@@ -643,39 +667,51 @@ static int check_options(pack_opt_t *options) {
for (j = 0; j < pack.nfilters; j++) {
if (options->verbose) {
- if(pack.filter[j].filtn >= 0) {
- if(pack.filter[j].filtn > H5Z_FILTER_SCALEOFFSET)
- HDprintf(" <%s> with %s filter %d\n", name, get_sfilter(pack.filter[j].filtn), pack.filter[j].filtn);
- else
- HDprintf(" <%s> with %s filter\n", name, get_sfilter(pack.filter[j].filtn));
+ if (pack.filter[j].filtn >= 0) {
+ if (pack.filter[j].filtn > H5Z_FILTER_SCALEOFFSET) {
+ HDprintf(" <%s> with %s filter %d\n", name,
+ get_sfilter(pack.filter[j].filtn),
+ pack.filter[j].filtn);
+ }
+ else {
+ HDprintf(" <%s> with %s filter\n",
+ name,
+ get_sfilter(pack.filter[j].filtn));
+ }
}
}
has_cp = 1;
- } /* j */
- } /* i */
+ } /* end for each filter */
+ } /* end for each object in options table */
if (options->all_filter == 1 && has_cp)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid compression input: 'all' option is present with other objects");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
+ "invalid compression input: 'all' option is present with " \
+ "other objects");
/*-------------------------------------------------------------------------
- * check options for the latest format
- *-------------------------------------------------------------------------
- */
+ * Check options for the latest format
+ *-------------------------------------------------------------------------
+ */
if (options->grp_compact < 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid maximum number of links to store as header messages");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
+ "invalid maximum number of links to store as header messages");
if (options->grp_indexed < 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid minimum number of links to store in the indexed format");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
+ "invalid minimum number of links to store in indexed format");
if (options->grp_indexed > options->grp_compact)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "minimum indexed size is greater than the maximum compact size");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
+ "minimum indexed size is greater than maximum compact size");
for (i = 0; i < 8; i++)
if (options->msg_size[i] < 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid shared message size");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
+ "invalid shared message size");
- /*--------------------------------------------------------------------------------
- * verify new user userblock options; file name must be present
- *---------------------------------------------------------------------------------
- */
+ /*------------------------------------------------------------------------
+ * Verify new user userblock options; file name must be present
+ *------------------------------------------------------------------------
+ */
if (options->ublock_filename != NULL && options->ublock_size == 0) {
if (options->verbose) {
HDprintf("Warning: user block size missing for file %s. Assigning a default size of 1024...\n", options->ublock_filename);
@@ -684,37 +720,41 @@ static int check_options(pack_opt_t *options) {
}
if (options->ublock_filename == NULL && options->ublock_size != 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file name missing for user block", options->ublock_filename);
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
+ "file name missing for user block", options->ublock_filename);
- /*--------------------------------------------------------------------------------
- * verify alignment options; threshold is zero default but alignment not
- *---------------------------------------------------------------------------------
- */
+ /*------------------------------------------------------------------------
+ * Verify alignment options; threshold is zero default but alignment not
+ *------------------------------------------------------------------------
+ */
if (options->alignment == 0 && options->threshold != 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "alignment for H5Pset_alignment missing");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
+ "alignment for H5Pset_alignment missing");
done:
return ret_value;
-}
+} /* end check_options() */
/*-------------------------------------------------------------------------
* Function: check_objects
*
- * Purpose: locate all HDF5 objects in the file and compare with user
- * supplied list
+ * Purpose: Locate all HDF5 objects in the file and compare with user-supplied
+ * list.
*
* Return: 0, ok, -1 no
*-------------------------------------------------------------------------
*/
-static int check_objects(const char* fname, pack_opt_t *options) {
- int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+static int
+check_objects(const char* fname, pack_opt_t *options)
+{
hid_t fid = -1;
hid_t did = -1;
hid_t sid = -1;
unsigned int i;
int ifil;
trav_table_t *travt = NULL;
+ int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
/* nothing to do */
if (options->op_tbl->nelems == 0)
@@ -725,7 +765,8 @@ static int check_objects(const char* fname, pack_opt_t *options) {
*-------------------------------------------------------------------------
*/
if ((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0)) < 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_fopen failed <%s>: %s", fname, H5FOPENERROR);
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
+ "h5tools_fopen failed <%s>: %s", fname, H5FOPENERROR);
/*-------------------------------------------------------------------------
* get the list of objects in the file
@@ -734,7 +775,6 @@ 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);
/* get the list of objects in the file */
@@ -750,65 +790,74 @@ static int check_objects(const char* fname, pack_opt_t *options) {
HDprintf("Opening file. Searching %zu objects to modify ...\n", travt->nobjs);
for (i = 0; i < options->op_tbl->nelems; i++) {
- char* name = options->op_tbl->objs[i].path;
+ pack_info_t obj = options->op_tbl->objs[i];
+ char* name = obj.path;
+
if (options->verbose)
HDprintf(" <%s>", name);
/* the input object names are present in the file and are valid */
if (h5trav_getindext(name, travt) < 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "%s Could not find <%s> in file <%s>. Exiting...\n",
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
+ "%s Could not find <%s> in file <%s>. Exiting...\n",
(options->verbose ? "\n" : ""), name, fname);
if (options->verbose)
HDprintf("...Found\n");
- for (ifil = 0; ifil < options->op_tbl->objs[i].nfilters; ifil++) {
- if (options->op_tbl->objs[i].filter[ifil].filtn < 0)
+ for (ifil = 0; ifil < obj.nfilters; ifil++) {
+ if (obj.filter[ifil].filtn < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid filter");
/* check for extra filter conditions */
- switch (options->op_tbl->objs[i].filter[ifil].filtn) {
+ switch (obj.filter[ifil].filtn) {
/* chunk size must be smaller than pixels per block */
case H5Z_FILTER_SZIP:
{
int j;
hsize_t csize = 1;
- unsigned ppb = options->op_tbl->objs[i].filter[ifil].cd_values[0];
+ unsigned ppb = obj.filter[ifil].cd_values[0];
hsize_t dims[H5S_MAX_RANK];
int rank;
- if (options->op_tbl->objs[i].chunk.rank > 0) {
- rank = options->op_tbl->objs[i].chunk.rank;
+ if (obj.chunk.rank > 0) {
+ rank = obj.chunk.rank;
for (j = 0; j < rank; j++)
- csize *= options->op_tbl->objs[i].chunk.chunk_lengths[j];
+ csize *= obj.chunk.chunk_lengths[j];
}
else {
if ((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
+ "H5Dopen2 failed");
if ((sid = H5Dget_space(did)) < 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
+ "H5Dget_space failed");
if ((rank = H5Sget_simple_extent_ndims(sid)) < 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
+ "H5Sget_simple_extent_ndims failed");
HDmemset(dims, 0, sizeof dims);
if (H5Sget_simple_extent_dims(sid, dims, NULL) < 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
+ "H5Sget_simple_extent_dims failed");
for (j = 0; j < rank; j++)
csize *= dims[j];
if (H5Sclose(sid) < 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
+ "H5Sclose failed");
if (H5Dclose(did) < 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
- }
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
+ "H5Dclose failed");
+ } /* end else (chunk rank is 0) */
if (csize < ppb) {
HDprintf(" <warning: SZIP settings, chunk size is smaller than pixels per block>\n");
HGOTO_DONE(0);
}
- }
+ } /* end case SZIP */
break;
default:
break;
- }
- } /* for ifil */
- } /* for i */
+ } /* end switch */
+ } /* for ifil (each user-defined filter) */
+ } /* for i (each object in options traversal table) */
done:
H5E_BEGIN_TRY {
@@ -819,7 +868,7 @@ done:
if (travt)
trav_table_free(travt);
return ret_value;
-}
+} /* end check_objects() */
/*-------------------------------------------------------------------------
* Function: have_request
@@ -829,14 +878,15 @@ done:
* Return: 1 yes, 0 no
*-------------------------------------------------------------------------
*/
-static int have_request(pack_opt_t *options) {
+static int
+have_request(pack_opt_t *options)
+{
if (options->all_filter || options->all_layout || options->op_tbl->nelems)
return 1;
return 0;
-
-}
+} /* end have_request() */
/*-------------------------------------------------------------------------
* Function: get_sfilter
@@ -846,8 +896,9 @@ static int have_request(pack_opt_t *options) {
* Return: name of filter, exit on error
*-------------------------------------------------------------------------
*/
-
-static const char* get_sfilter(H5Z_filter_t filtn) {
+static const char *
+get_sfilter(H5Z_filter_t filtn)
+{
if (filtn < 0)
return NULL;
else if (filtn == H5Z_FILTER_NONE)
@@ -866,5 +917,5 @@ static const char* get_sfilter(H5Z_filter_t filtn) {
return "SOFF";
else
return "UD";
-}
+} /* end get_sfilter() */
diff --git a/tools/src/h5repack/h5repack_copy.c b/tools/src/h5repack/h5repack_copy.c
index 13adb7c..398d632 100644
--- a/tools/src/h5repack/h5repack_copy.c
+++ b/tools/src/h5repack/h5repack_copy.c
@@ -58,8 +58,8 @@ static void print_user_block(const char *filename, hid_t fid);
* -1 no
*-------------------------------------------------------------------------
*/
-
-int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
+int
+copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
{
int ret_value = 0;
hid_t fidin = -1;
@@ -365,7 +365,7 @@ done:
trav_table_free(travt);
return ret_value;
-}
+} /* end copy_objects() */
/*-------------------------------------------------------------------------
* Function: Get_hyperslab
@@ -521,7 +521,7 @@ Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
done:
return ret_value;
-}
+} /* end Get_hyperslab() */
/*-------------------------------------------------------------------------
* Function: do_copy_objects
@@ -577,7 +577,8 @@ done:
*-------------------------------------------------------------------------
*/
-int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
+int
+do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
pack_opt_t *options) /* repack options */
{
int ret_value = 0;
@@ -677,7 +678,11 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
}
else {
if (options->grp_compact > 0 || options->grp_indexed > 0)
- if (H5Pset_link_phase_change(gcpl_out, (unsigned) options->grp_compact, (unsigned) options->grp_indexed) < 0)
+ if (H5Pset_link_phase_change(
+ gcpl_out,
+ (unsigned) options->grp_compact,
+ (unsigned) options->grp_indexed)
+ < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_phase_change failed");
if ((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0)
@@ -777,8 +782,6 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed");
if ((dcpl_in = H5Dget_create_plist(dset_in)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed");
- if ((dcpl_out = H5Pcopy(dcpl_in)) < 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcopy failed");
if ((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
HDmemset(dims, 0, sizeof dims);
@@ -787,6 +790,20 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
if (H5Dget_space_status(dset_in, &space_status) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space_status failed");
+ /* If the input dataset has external storage, it must be contiguous.
+ * Accordingly, there would be no filter or chunk properties to preserve,
+ * so create a new DCPL.
+ * Otherwise, copy dcpl_in.
+ */
+ if (H5Pget_external_count(dcpl_in)) {
+ if ((dcpl_out = H5Pcreate(H5P_DATASET_CREATE)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed");
+ }
+ else
+ if ((dcpl_out = H5Pcopy(dcpl_in)) < 0) {
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcopy failed");
+ }
+
nelmts = 1;
for (j = 0; j < rank; j++)
nelmts *= dims[j];
@@ -797,7 +814,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
wtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT);
else
wtype_id = H5Tcopy(ftype_id);
- } /* end if */
+ }
if ((msize = H5Tget_size(wtype_id)) == 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
@@ -830,18 +847,29 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
* changing to COMPACT. For the reference, COMPACT is limited
* by size 64K by library.
*/
- if (options->layout_g != H5D_COMPACT)
- if (size_dset < options->min_comp)
+ if (options->layout_g != H5D_COMPACT) {
+ if (size_dset < options->min_comp) {
apply_s = 0;
+ }
+ }
/* apply the filter */
- if (apply_s)
- if (apply_filters(travt->objs[i].name, rank, dims, msize, dcpl_out, options, &has_filter) < 0)
+ if (apply_s) {
+ if (apply_filters(
+ travt->objs[i].name,
+ rank,
+ dims,
+ msize,
+ dcpl_out,
+ options,
+ &has_filter)
+ < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "apply_filters failed");
+ }
/* only if layout change requested for entire file or
* individual obj */
- if (options->all_layout > 0 || req_obj_layout == 1)
+ if (options->all_layout > 0 || req_obj_layout == 1) {
/*-------------------------------------------------
* Unset the unlimited max dims if convert to other
* than chunk layouts, because unlimited max dims
@@ -861,14 +889,14 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
/* if convert to COMPACT */
if (options->layout_g == H5D_COMPACT)
- /* should be smaller than 64K */
if (size_dset > MAX_COMPACT_DSIZE)
limit_maxdims = FALSE;
/* unset unlimited max dims */
if (limit_maxdims)
H5Sset_extent_simple(f_space_id, rank, dims, NULL);
- }
+ } /* end if not chunked */
+ } /* end if layout change requested for entire file or individual object */
/*-------------------------------------------------------------------------
* create the output dataset;
@@ -876,16 +904,39 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
* modified dcpl; in that case use the original instead
*-------------------------------------------------------------------------
*/
- dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_out, H5P_DEFAULT);
- if (dset_out == FAIL) {
- H5Epush2(H5tools_ERR_STACK_g, __FILE__, FUNC, __LINE__, H5tools_ERR_CLS_g, H5E_tools_g, H5E_tools_min_id_g, "H5Dcreate2 failed");
- if (options->verbose)
- HDprintf(" warning: could not create dataset <%s>. Applying original settings\n", travt->objs[i].name);
-
- if ((dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0)
+ dset_out = H5Dcreate2(fidout,
+ travt->objs[i].name,
+ wtype_id,
+ f_space_id,
+ H5P_DEFAULT,
+ dcpl_out,
+ H5P_DEFAULT);
+ /* if unable to create, retry with original DCPL */
+ if (dset_out < 0) {
+ H5Epush2(H5tools_ERR_STACK_g,
+ __FILE__,
+ FUNC,
+ __LINE__,
+ H5tools_ERR_CLS_g,
+ H5E_tools_g,
+ H5E_tools_min_id_g,
+ "H5Dcreate2 failed");
+ if (options->verbose) {
+ HDprintf(" warning: could not create dataset <%s>. Applying original settings\n",
+ travt->objs[i].name);
+ }
+ dset_out = H5Dcreate2(
+ fidout,
+ travt->objs[i].name,
+ wtype_id,
+ f_space_id,
+ H5P_DEFAULT,
+ dcpl_in,
+ H5P_DEFAULT);
+ if (dset_out < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed");
apply_f = 0;
- }
+ } /* end if retry dataset create */
/*-------------------------------------------------------------------------
* read/write
@@ -909,8 +960,8 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
if (TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
if (H5Dvlen_reclaim(wtype_id, f_space_id, H5P_DEFAULT, buf) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dvlen_reclaim failed");
- /* free */
- if (buf != NULL) {
+
+ if (buf != NULL) { /* TODO: is buf potentially released by H5Dvlen_reclaim()? */
HDfree(buf);
buf = NULL;
}
@@ -946,17 +997,25 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
dset_layout = H5Pget_layout(dcpl_out);
if (dset_layout == H5D_CHUNKED)
dcpl_tmp = dcpl_out; /* writing dataset */
- else { /* if reading dataset is chunked */
+ else {
dset_layout = H5Pget_layout(dcpl_in);
if (dset_layout == H5D_CHUNKED)
dcpl_tmp = dcpl_in; /* reading dataset */
}
- /* get hyperslab dims and size in byte */
- if (Get_hyperslab(dcpl_tmp, rank, dims, p_type_nbytes, hslab_dims, &hslab_nbytes) < 0)
+ if (Get_hyperslab(
+ dcpl_tmp,
+ rank,
+ dims,
+ p_type_nbytes,
+ hslab_dims,
+ &hslab_nbytes)
+ < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Get_hyperslab failed");
hslab_buf = HDmalloc((size_t)hslab_nbytes);
+ if (hslab_buf == NULL)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "can't allocate space for hyperslab");
hslab_nelmts = hslab_nbytes / p_type_nbytes;
hslab_space = H5Screate_simple(1, &hslab_nelmts, NULL);
@@ -974,28 +1033,57 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
*/
for (k = 0, hs_select_nelmts = 1; k < rank; k++) {
/* MIN() is used to get the remaining edge portion if exist.
- * "dims[k] - hs_sel_offset[k]" is remaining edge portion that is smaller then the hyperslab.*/
+ * "dims[k] - hs_sel_offset[k]" is remaining edge portion that is
+ * smaller then the hyperslab.
+ */
hs_sel_count[k] = MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]);
hs_select_nelmts *= hs_sel_count[k];
}
- if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_sel_offset, NULL, hs_sel_count, NULL) < 0)
+ if (H5Sselect_hyperslab(
+ f_space_id,
+ H5S_SELECT_SET,
+ hs_sel_offset,
+ NULL,
+ hs_sel_count,
+ NULL)
+ < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed");
- if (H5Sselect_hyperslab(hslab_space, H5S_SELECT_SET, zero, NULL, &hs_select_nelmts, NULL) < 0)
+ if (H5Sselect_hyperslab(
+ hslab_space,
+ H5S_SELECT_SET,
+ zero,
+ NULL,
+ &hs_select_nelmts,
+ NULL)
+ < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed");
- }
+ } /* end if rank > 0 */
else {
H5Sselect_all(f_space_id);
H5Sselect_all(hslab_space);
hs_select_nelmts = 1;
- } /* rank */
-
- if(H5Dread(dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf) < 0)
+ } /* end (else) rank == 0 */
+
+ if (H5Dread(
+ dset_in,
+ wtype_id,
+ hslab_space,
+ f_space_id,
+ H5P_DEFAULT,
+ hslab_buf)
+ < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
- if(H5Dwrite(dset_out, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf) < 0)
+ if (H5Dwrite(
+ dset_out,
+ wtype_id,
+ hslab_space,
+ f_space_id,
+ H5P_DEFAULT,
+ hslab_buf)
+ < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dwrite failed");
- /* reclaim any VL memory, if necessary */
if (vl_data)
H5Dvlen_reclaim(wtype_id, hslab_space, H5P_DEFAULT, hslab_buf);
@@ -1007,20 +1095,19 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
hs_sel_offset[k - 1] = 0;
else
carry = 0;
- } /* k */
- } /* elmtno */
+ }
+ } /* end for (hyperslab selection loop) */
H5Sclose(hslab_space);
- /* free */
if (hslab_buf != NULL) {
HDfree(hslab_buf);
hslab_buf = NULL;
}
- } /* hyperslab read */
- } /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */
+ } /* end if reading/writing by hyperslab */
+ } /* end if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) */
/*-------------------------------------------------------------------------
- * amount of compression used
+ * print amount of compression used
*-------------------------------------------------------------------------
*/
if (options->verbose) {
@@ -1040,14 +1127,17 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
print_dataset_info(dcpl_in, travt->objs[i].name, ratio, 0);
/* print a message that the filter was not applied
- (in case there was a filter)
+ * (in case there was a filter)
*/
- if (has_filter && apply_s == 0)
- HDprintf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n", travt->objs[i].name, (int) options->min_comp);
+ if (has_filter && apply_s == 0) {
+ HDprintf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n",
+ travt->objs[i].name,
+ (int) options->min_comp);
+ }
if (has_filter && apply_f == 0)
HDprintf(" <warning: could not apply the filter to %s>\n", travt->objs[i].name);
- } /* verbose */
+ } /* end if verbose (print compression) */
/*-------------------------------------------------------------------------
* copy attrs
@@ -1056,14 +1146,13 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");
- /*close */
if (H5Dclose(dset_out) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
- }/*!H5T_REFERENCE*/
- }/*h5tools_canreadf*/
+ } /* end if not a reference */
+ } /* end if h5tools_canreadf (filter availability check) */
/*-------------------------------------------------------------------------
- * close
+ * Close
*-------------------------------------------------------------------------
*/
if (H5Tclose(ftype_id) < 0)
@@ -1080,7 +1169,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
}
/*-------------------------------------------------------------------------
- * we do not have request for filter/chunking use H5Ocopy instead
+ * We do not have request for filter/chunking; use H5Ocopy instead
*-------------------------------------------------------------------------
*/
else {
@@ -1094,11 +1183,6 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
if (H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_copy_object failed");
- /*-------------------------------------------------------------------------
- * do the copy
- *-------------------------------------------------------------------------
- */
-
if (H5Ocopy(fidin, /* Source file or group identifier */
travt->objs[i].name, /* Name of the source object to be copied */
fidout, /* Destination file or group identifier */
@@ -1107,12 +1191,11 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
H5P_DEFAULT) < 0) /* Properties which apply to the new hard link */
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Ocopy failed");
- /* close property */
if (H5Pclose(pid) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
/*-------------------------------------------------------------------------
- * copy attrs manually
+ * Copy attrs manually
*-------------------------------------------------------------------------
*/
if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
@@ -1129,7 +1212,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
if (options->verbose)
HDprintf(FORMAT_OBJ, "dset", travt->objs[i].name);
- } /* end do we have request for filter/chunking */
+ } /* end whether we have request for filter/chunking */
break;
/*-------------------------------------------------------------------------
@@ -1189,8 +1272,8 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
default:
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Object type not found");
} /* switch */
- } /* end for */
- } /* end if */
+ } /* end for each object to traverse */
+ } /* end if there are objects */
done:
@@ -1228,7 +1311,7 @@ done:
HDfree(hslab_buf);
return ret_value;
-}
+} /* end do_copy_objects() */
/*-------------------------------------------------------------------------
* Function: print_dataset_info
@@ -1322,8 +1405,8 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr)
default:
HDstrcat(strfilter, "UD ");
break;
- } /* switch */
- }/*i*/
+ } /* end switch */
+ } /* end for each filter */
if (!pr)
HDprintf(FORMAT_OBJ, "dset", objname);
@@ -1336,7 +1419,7 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr)
HDstrcat(str, temp);
HDprintf(FORMAT_OBJ, str, objname);
}
-}
+} /* end print_dataset_info() */
/*-------------------------------------------------------------------------
* Function: copy_user_block
@@ -1406,7 +1489,7 @@ done:
HDclose(outfid);
return ret_value;
-}
+} /* end copy_user_block() */
/*-------------------------------------------------------------------------
* Function: print_user_block
@@ -1479,6 +1562,6 @@ done:
HDclose(fh);
return;
-}
+} /* end print_user_block() */
#endif
diff --git a/tools/src/h5repack/h5repack_main.c b/tools/src/h5repack/h5repack_main.c
index b961765..8c887a2 100644
--- a/tools/src/h5repack/h5repack_main.c
+++ b/tools/src/h5repack/h5repack_main.c
@@ -23,7 +23,8 @@ static void leave(int ret) H5_ATTR_NORETURN;
/* module-scoped variables */
-static int has_i_o = 0;
+static int has_i = 0;
+static int has_o = 0;
const char *infile = NULL;
const char *outfile = NULL;
@@ -33,34 +34,34 @@ const char *outfile = NULL;
*/
static const char *s_opts = "hVvf:l:m:e:nLj:k:c:d:s:u:b:M:t:a:i:o:S:P:T:G:q:z:E";
static struct long_options l_opts[] = {
- { "help", no_arg, 'h' },
- { "version", no_arg, 'V' },
- { "verbose", no_arg, 'v' },
- { "filter", require_arg, 'f' },
- { "layout", require_arg, 'l' },
- { "minimum", require_arg, 'm' },
- { "file", require_arg, 'e' },
- { "native", no_arg, 'n' },
- { "latest", no_arg, 'L' },
- { "low", require_arg, 'j' },
- { "high", require_arg, 'k' },
- { "compact", require_arg, 'c' },
- { "indexed", require_arg, 'd' },
- { "ssize", require_arg, 's' },
- { "ublock", require_arg, 'u' },
- { "block", require_arg, 'b' },
+ { "help", no_arg, 'h' },
+ { "version", no_arg, 'V' },
+ { "verbose", no_arg, 'v' },
+ { "filter", require_arg, 'f' },
+ { "layout", require_arg, 'l' },
+ { "minimum", require_arg, 'm' },
+ { "file", require_arg, 'e' },
+ { "native", no_arg, 'n' },
+ { "latest", no_arg, 'L' },
+ { "low", require_arg, 'j' },
+ { "high", require_arg, 'k' },
+ { "compact", require_arg, 'c' },
+ { "indexed", require_arg, 'd' },
+ { "ssize", require_arg, 's' },
+ { "ublock", require_arg, 'u' },
+ { "block", require_arg, 'b' },
{ "metadata_block_size", require_arg, 'M' },
- { "threshold", require_arg, 't' },
- { "alignment", require_arg, 'a' },
- { "infile", require_arg, 'i' }, /* -i for backward compability */
- { "outfile", require_arg, 'o' }, /* -o for backward compability */
- { "fs_strategy", require_arg, 'S' },
- { "fs_persist", require_arg, 'P' },
- { "fs_threshold", require_arg, 'T' },
- { "fs_pagesize", require_arg, 'G' },
- { "sort_by", require_arg, 'q' },
- { "sort_order", require_arg, 'z' },
- { "enable-error-stack", no_arg, 'E' },
+ { "threshold", require_arg, 't' },
+ { "alignment", require_arg, 'a' },
+ { "infile", require_arg, 'i' }, /* for backward compability */
+ { "outfile", require_arg, 'o' }, /* for backward compability */
+ { "fs_strategy", require_arg, 'S' },
+ { "fs_persist", require_arg, 'P' },
+ { "fs_threshold", require_arg, 'T' },
+ { "fs_pagesize", require_arg, 'G' },
+ { "sort_by", require_arg, 'q' },
+ { "sort_order", require_arg, 'z' },
+ { "enable-error-stack", no_arg, 'E' },
{ NULL, 0, '\0' }
};
@@ -83,13 +84,17 @@ static void usage(const char *prog) {
PRINTVALSTREAM(rawoutstream, " -v, --verbose Verbose mode, print object information\n");
PRINTVALSTREAM(rawoutstream, " -V, --version Print version number and exit\n");
PRINTVALSTREAM(rawoutstream, " -n, --native Use a native HDF5 type when repacking\n");
- PRINTVALSTREAM(rawoutstream, " --enable-error-stack Prints messages from the HDF5 error stack as they occur\n");
+ PRINTVALSTREAM(rawoutstream, " --enable-error-stack Prints messages from the HDF5 error stack as they\n");
+ PRINTVALSTREAM(rawoutstream, " occur\n");
PRINTVALSTREAM(rawoutstream, " -L, --latest Use latest version of file format\n");
- PRINTVALSTREAM(rawoutstream, " This option will take precedence over the -j and -k options\n");
- PRINTVALSTREAM(rawoutstream, " --low=BOUND The low bound for library release versions to use when creating\n");
- PRINTVALSTREAM(rawoutstream, " objects in the file (default is H5F_LIBVER_EARLIEST)\n");
- PRINTVALSTREAM(rawoutstream, " --high=BOUND The high bound for library release versions to use when creating\n");
- PRINTVALSTREAM(rawoutstream, " objects in the file (default is H5F_LIBVER_LATEST)\n");
+ PRINTVALSTREAM(rawoutstream, " This option will take precedence over the options\n");
+ PRINTVALSTREAM(rawoutstream, " --low and --high\n");
+ PRINTVALSTREAM(rawoutstream, " --low=BOUND The low bound for library release versions to use\n");
+ PRINTVALSTREAM(rawoutstream, " when creating objects in the file\n");
+ PRINTVALSTREAM(rawoutstream, " (default is H5F_LIBVER_EARLIEST)\n");
+ PRINTVALSTREAM(rawoutstream, " --high=BOUND The high bound for library release versions to use\n");
+ PRINTVALSTREAM(rawoutstream, " when creating objects in the file\n");
+ PRINTVALSTREAM(rawoutstream, " (default is H5F_LIBVER_LATEST)\n");
PRINTVALSTREAM(rawoutstream, " -c L1, --compact=L1 Maximum number of links in header messages\n");
PRINTVALSTREAM(rawoutstream, " -d L2, --indexed=L2 Minimum number of links in the indexed format\n");
PRINTVALSTREAM(rawoutstream, " -s S[:F], --ssize=S[:F] Shared object header message minimum size\n");
@@ -104,10 +109,14 @@ static void usage(const char *prog) {
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, " -S FS_STRATEGY, --fs_strategy=FS_STRATEGY File space management strategy for H5Pset_file_space_strategy\n");
- PRINTVALSTREAM(rawoutstream, " -P FS_PERSIST, --fs_persist=FS_PERSIST Persisting or not persisting free-space for H5Pset_file_space_strategy\n");
- PRINTVALSTREAM(rawoutstream, " -T FS_THRESHOLD, --fs_threshold=FS_THRESHOLD Free-space section threshold for H5Pset_file_space_strategy\n");
- PRINTVALSTREAM(rawoutstream, " -G FS_PAGESIZE, --fs_pagesize=FS_PAGESIZE File space page size for H5Pset_file_space_page_size\n");
+ PRINTVALSTREAM(rawoutstream, " -S FS_STRATEGY, --fs_strategy=FS_STRATEGY File space management strategy for\n");
+ PRINTVALSTREAM(rawoutstream, " H5Pset_file_space_strategy\n");
+ PRINTVALSTREAM(rawoutstream, " -P FS_PERSIST, --fs_persist=FS_PERSIST Persisting or not persisting free-\n");
+ PRINTVALSTREAM(rawoutstream, " space for H5Pset_file_space_strategy\n");
+ PRINTVALSTREAM(rawoutstream, " -T FS_THRESHOLD, --fs_threshold=FS_THRESHOLD Free-space section threshold\n");
+ PRINTVALSTREAM(rawoutstream, " for H5Pset_file_space_strategy\n");
+ PRINTVALSTREAM(rawoutstream, " -G FS_PAGESIZE, --fs_pagesize=FS_PAGESIZE File space page size for\n");
+ PRINTVALSTREAM(rawoutstream, " H5Pset_file_space_page_size\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, " M - is an integer greater than 1, size of dataset in bytes (default is 0)\n");
PRINTVALSTREAM(rawoutstream, " E - is a filename.\n");
@@ -115,15 +124,17 @@ 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, " Q - is the sort index type for the input file. It can be \"name\" or\n");
+ PRINTVALSTREAM(rawoutstream, " \"creation_order\" (default)\n");
+ PRINTVALSTREAM(rawoutstream, " Z - is the sort order type for the input file. It can be \"descending\" or\n");
+ PRINTVALSTREAM(rawoutstream, " \"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");
PRINTVALSTREAM(rawoutstream, " pline|attr>. If F is not specified, S applies to all messages\n");
PRINTVALSTREAM(rawoutstream, "\n");
- PRINTVALSTREAM(rawoutstream, " BOUND is an integer indicating the library release versions to use when creating\n");
- PRINTVALSTREAM(rawoutstream, " objects in the file (see H5Pset_libver_bounds()):\n");
+ PRINTVALSTREAM(rawoutstream, " BOUND is an integer indicating the library release versions to use when\n");
+ PRINTVALSTREAM(rawoutstream, " creating objects in the file (see H5Pset_libver_bounds()):\n");
PRINTVALSTREAM(rawoutstream, " 0: This is H5F_LIBVER_EARLIEST in H5F_libver_t struct\n");
PRINTVALSTREAM(rawoutstream, " 1: This is H5F_LIBVER_V18 in H5F_libver_t struct\n");
PRINTVALSTREAM(rawoutstream, " 2: This is H5F_LIBVER_V110 in H5F_libver_t struct\n");
@@ -132,24 +143,31 @@ static void usage(const char *prog) {
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, " FS_STRATEGY is a string indicating the file space strategy used:\n");
PRINTVALSTREAM(rawoutstream, " FSM_AGGR:\n");
- PRINTVALSTREAM(rawoutstream, " The mechanisms used in managing file space are free-space managers, aggregators and virtual file driver.\n");
+ PRINTVALSTREAM(rawoutstream, " The mechanisms used in managing file space are free-space\n");
+ PRINTVALSTREAM(rawoutstream, " managers, aggregators and virtual file driver.\n");
PRINTVALSTREAM(rawoutstream, " PAGE:\n");
- PRINTVALSTREAM(rawoutstream, " The mechanisms used in managing file space are free-space managers with embedded paged aggregation and virtual file driver.\n");
+ PRINTVALSTREAM(rawoutstream, " The mechanisms used in managing file space are free-space\n");
+ PRINTVALSTREAM(rawoutstream, " managers with embedded paged aggregation and virtual file driver.\n");
PRINTVALSTREAM(rawoutstream, " AGGR:\n");
- PRINTVALSTREAM(rawoutstream, " The mechanisms used in managing file space are aggregators and virtual file driver.\n");
+ PRINTVALSTREAM(rawoutstream, " The mechanisms used in managing file space are aggregators and\n");
+ PRINTVALSTREAM(rawoutstream, " virtual file driver.\n");
PRINTVALSTREAM(rawoutstream, " NONE:\n");
- PRINTVALSTREAM(rawoutstream, " The mechanisms used in managing file space are virtual file driver.\n");
- PRINTVALSTREAM(rawoutstream, " The default strategy when not set is FSM_AGGR without persisting free-space.\n");
+ PRINTVALSTREAM(rawoutstream, " The mechanisms used in managing file space are virtual file\n");
+ PRINTVALSTREAM(rawoutstream, " driver.\n");
+ PRINTVALSTREAM(rawoutstream, " The default strategy when not set is FSM_AGGR without persisting free-\n");
+ PRINTVALSTREAM(rawoutstream, " space.\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, " FS_PERSIST is 1 to persisting free-space or 0 to not persisting free-space.\n");
PRINTVALSTREAM(rawoutstream, " The default when not set is not persisting free-space.\n");
PRINTVALSTREAM(rawoutstream, " The value is ignored for AGGR and NONE strategies.\n");
PRINTVALSTREAM(rawoutstream, "\n");
- PRINTVALSTREAM(rawoutstream, " FS_THRESHOLD is the minimum size (in bytes) of free-space sections to be tracked by the library.\n");
+ PRINTVALSTREAM(rawoutstream, " FS_THRESHOLD is the minimum size (in bytes) of free-space sections to be\n");
+ PRINTVALSTREAM(rawoutstream, " tracked by the library.\n");
PRINTVALSTREAM(rawoutstream, " The default when not set is 1.\n");
PRINTVALSTREAM(rawoutstream, " The value is ignored for AGGR and NONE strategies.\n");
PRINTVALSTREAM(rawoutstream, "\n");
- PRINTVALSTREAM(rawoutstream, " FS_PAGESIZE is the size (in bytes) >=512 that is used by the library when the file space strategy PAGE is used.\n");
+ PRINTVALSTREAM(rawoutstream, " FS_PAGESIZE is the size (in bytes) >=512 that is used by the library when\n");
+ PRINTVALSTREAM(rawoutstream, " the file space strategy PAGE is used.\n");
PRINTVALSTREAM(rawoutstream, " The default when not set is 4096.\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, " FILT - is a string with the format:\n");
@@ -177,9 +195,9 @@ static void usage(const char *prog) {
PRINTVALSTREAM(rawoutstream, " NBIT (no parameter)\n");
PRINTVALSTREAM(rawoutstream, " SOFF=<scale_factor,scale_type> scale_factor is an integer and scale_type\n");
PRINTVALSTREAM(rawoutstream, " is either IN or DS\n");
- PRINTVALSTREAM(rawoutstream, " UD=<filter_number,filter_flag,cd_value_count,value_1[,value_2,...,value_N]>\n");
- PRINTVALSTREAM(rawoutstream, " required values for filter_number,filter_flag,cd_value_count,value_1\n");
- PRINTVALSTREAM(rawoutstream, " optional values for value_2 to value_N\n");
+ PRINTVALSTREAM(rawoutstream, " UD=<filter_number,filter_flag,cd_value_count,value1[,value2,...,valueN]>\n");
+ PRINTVALSTREAM(rawoutstream, " Required values: filter_number, filter_flag, cd_value_count, value1\n");
+ PRINTVALSTREAM(rawoutstream, " Optional values: value2 to valueN\n");
PRINTVALSTREAM(rawoutstream, " NONE (no parameter)\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, " LAYT - is a string with the format:\n");
@@ -216,12 +234,12 @@ static void usage(const char *prog) {
PRINTVALSTREAM(rawoutstream, "4) h5repack -L -c 10 -s 20:dtype file1 file2\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, " Using latest file format with maximum compact group size of 10 and\n");
- PRINTVALSTREAM(rawoutstream, " and minimum shared datatype size of 20\n");
+ PRINTVALSTREAM(rawoutstream, " minimum shared datatype size of 20\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, "5) h5repack --low=0 --high=1 file1 file2\n");
PRINTVALSTREAM(rawoutstream, "\n");
- PRINTVALSTREAM(rawoutstream, " Set low=H5F_LIBVER_EARLIEST and high=H5F_LIBVER_V18 via H5Pset_libver_bounds() when\n");
- PRINTVALSTREAM(rawoutstream, " creating the repacked file: file2\n");
+ PRINTVALSTREAM(rawoutstream, " Set low=H5F_LIBVER_EARLIEST and high=H5F_LIBVER_V18 via\n");
+ PRINTVALSTREAM(rawoutstream, " H5Pset_libver_bounds() when creating the repacked file, file2\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, "5) h5repack -f SHUF -f GZIP=1 file1 file2\n");
PRINTVALSTREAM(rawoutstream, "\n");
@@ -265,7 +283,7 @@ int read_info(const char *filename, pack_opt_t *options)
int i, rc = 1;
int ret_value = EXIT_SUCCESS;
- if ((fp = HDfopen(filename, "r")) == (FILE *) NULL) {
+ if (NULL == (fp = HDfopen(filename, "r"))) {
error_msg("cannot open options file %s\n", filename);
h5tools_setstatus(EXIT_FAILURE);
ret_value = EXIT_FAILURE;
@@ -274,90 +292,46 @@ int read_info(const char *filename, pack_opt_t *options)
/* cycle until end of file reached */
while (1) {
- rc = fscanf(fp, "%s", stype);
- if (rc == -1)
- break;
-
- /*-------------------------------------------------------------------------
- * filter
- *-------------------------------------------------------------------------
- */
- if (HDstrcmp(stype,"-f") == 0) {
- /* find begining of info */
- i = 0;
- c = '0';
- while (c != ' ') {
- if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
- error_msg("fscanf error\n");
- h5tools_setstatus(EXIT_FAILURE);
- ret_value = EXIT_FAILURE;
- goto done;
- } /* end if */
- if (HDfeof(fp))
- break;
- }
- c = '0';
- /* go until end */
- while (c != ' ') {
- if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
- error_msg("fscanf error\n");
- h5tools_setstatus(EXIT_FAILURE);
- ret_value = EXIT_FAILURE;
- goto done;
- } /* end if */
- comp_info[i] = c;
- i++;
- if (HDfeof(fp))
- break;
- if (c == 10 /*eol*/)
- break;
- }
- comp_info[i - 1] = '\0'; /*cut the last " */
- if (h5repack_addfilter(comp_info, options) == -1) {
- error_msg("could not add compression option\n");
+ /* Info indicator must be for layout or filter */
+ if (HDstrcmp(stype,"-l") && HDstrcmp(stype, "-f")) {
+ error_msg("bad file format for %s", filename);
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = EXIT_FAILURE;
+ goto done;
+ }
+
+ /* find begining of info */
+ i = 0;
+ c = '0';
+ while (c != ' ') {
+ if (fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
+ error_msg("fscanf error\n");
h5tools_setstatus(EXIT_FAILURE);
ret_value = EXIT_FAILURE;
goto done;
}
+ if (HDfeof(fp))
+ break;
}
- /*-------------------------------------------------------------------------
- * layout
- *-------------------------------------------------------------------------
- */
- else if (HDstrcmp(stype,"-l") == 0) {
-
- /* find begining of info */
- i = 0;
- c = '0';
- while (c != ' ') {
- if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
- error_msg("fscanf error\n");
- h5tools_setstatus(EXIT_FAILURE);
- ret_value = EXIT_FAILURE;
- goto done;
- } /* end if */
- if (HDfeof(fp))
- break;
- }
- c = '0';
- /* go until end */
- while (c != ' ') {
- if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
- error_msg("fscanf error\n");
- h5tools_setstatus(EXIT_FAILURE);
- ret_value = EXIT_FAILURE;
- goto done;
- } /* end if */
- comp_info[i] = c;
- i++;
- if (HDfeof(fp))
- break;
- if (c == 10 /*eol*/)
- break;
+ c = '0';
+ /* go until end */
+ while (c != ' ') {
+ if (fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
+ error_msg("fscanf error\n");
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = EXIT_FAILURE;
+ goto done;
}
- comp_info[i - 1] = '\0'; /*cut the last " */
+ comp_info[i++] = c;
+ if (HDfeof(fp))
+ break;
+ if (c == 10 /*eol*/)
+ break;
+ }
+ comp_info[i - 1] = '\0'; /*cut the last " */
+ if (!HDstrcmp(stype, "-l")) {
if (h5repack_addlayout(comp_info, options) == -1) {
error_msg("could not add chunck option\n");
h5tools_setstatus(EXIT_FAILURE);
@@ -365,17 +339,15 @@ int read_info(const char *filename, pack_opt_t *options)
goto done;
}
}
- /*-------------------------------------------------------------------------
- * not valid
- *-------------------------------------------------------------------------
- */
else {
- error_msg("bad file format for %s", filename);
- h5tools_setstatus(EXIT_FAILURE);
- ret_value = EXIT_FAILURE;
- goto done;
+ if (h5repack_addfilter(comp_info, options) == -1) {
+ error_msg("could not add compression option\n");
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = EXIT_FAILURE;
+ goto done;
+ }
}
- }
+ } /* end while info-read cycling */
done:
if (fp)
@@ -399,9 +371,9 @@ set_sort_by(const char *form)
{
H5_index_t idx_type = H5_INDEX_UNKNOWN;
- if (HDstrcmp(form,"name")==0) /* H5_INDEX_NAME */
+ if (!HDstrcmp(form, "name"))
idx_type = H5_INDEX_NAME;
- else if (HDstrcmp(form,"creation_order")==0) /* H5_INDEX_CRT_ORDER */
+ else if (!HDstrcmp(form, "creation_order"))
idx_type = H5_INDEX_CRT_ORDER;
return idx_type;
@@ -422,9 +394,9 @@ set_sort_order(const char *form)
{
H5_iter_order_t iter_order = H5_ITER_UNKNOWN;
- if (HDstrcmp(form,"ascending")==0) /* H5_ITER_INC */
+ if (!HDstrcmp(form, "ascending"))
iter_order = H5_ITER_INC;
- else if (HDstrcmp(form,"descending")==0) /* H5_ITER_DEC */
+ else if (!HDstrcmp(form, "descending"))
iter_order = H5_ITER_DEC;
return iter_order;
@@ -443,19 +415,19 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
int ret_value = 0;
/* parse command line options */
- while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+ while (EOF != (opt = get_option(argc, argv, s_opts, l_opts))) {
switch ((char) opt) {
/* -i for backward compatibility */
case 'i':
infile = opt_arg;
- has_i_o = 1;
+ has_i++;
break;
/* -o for backward compatibility */
case 'o':
outfile = opt_arg;
- has_i_o = 1;
+ has_o++;
break;
case 'h':
@@ -520,7 +492,7 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
case 'j':
options->low_bound = (H5F_libver_t)HDatoi(opt_arg);
- if(options->low_bound < H5F_LIBVER_EARLIEST || options->low_bound > H5F_LIBVER_LATEST) {
+ if (options->low_bound < H5F_LIBVER_EARLIEST || options->low_bound > H5F_LIBVER_LATEST) {
error_msg("in parsing low bound\n");
goto done;
}
@@ -528,7 +500,7 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
case 'k':
options->high_bound = (H5F_libver_t)HDatoi(opt_arg);
- if(options->high_bound < H5F_LIBVER_EARLIEST || options->high_bound > H5F_LIBVER_LATEST) {
+ if (options->high_bound < H5F_LIBVER_EARLIEST || options->high_bound > H5F_LIBVER_LATEST) {
error_msg("in parsing high bound\n");
goto done;
}
@@ -550,10 +522,10 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
{
int idx = 0;
int ssize = 0;
- char *msgPtr = HDstrchr( opt_arg, ':');
+ char *msgPtr = HDstrchr(opt_arg, ':');
options->latest = TRUE; /* must use latest format */
if (msgPtr == NULL) {
- ssize = HDatoi( opt_arg );
+ ssize = HDatoi(opt_arg);
for (idx = 0; idx < 5; idx++)
options->msg_size[idx] = ssize;
}
@@ -563,15 +535,15 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
HDstrcpy(msgType, msgPtr + 1);
msgPtr[0] = '\0';
ssize = HDatoi( opt_arg );
- if (HDstrncmp(msgType, "dspace",6) == 0)
+ if (!HDstrncmp(msgType, "dspace", 6))
options->msg_size[0] = ssize;
- else if (HDstrncmp(msgType, "dtype", 5) == 0)
+ else if (!HDstrncmp(msgType, "dtype", 5))
options->msg_size[1] = ssize;
- else if (HDstrncmp(msgType, "fill", 4) == 0)
+ else if (!HDstrncmp(msgType, "fill", 4))
options->msg_size[2] = ssize;
- else if (HDstrncmp(msgType, "pline", 5) == 0)
+ else if (!HDstrncmp(msgType, "pline", 5))
options->msg_size[3] = ssize;
- else if (HDstrncmp(msgType, "attr", 4) == 0)
+ else if (!HDstrncmp(msgType, "attr", 4))
options->msg_size[4] = ssize;
}
}
@@ -608,13 +580,13 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
char strategy[MAX_NC_NAME];
HDstrcpy(strategy, opt_arg);
- if(!HDstrcmp(strategy, "FSM_AGGR"))
+ if (!HDstrcmp(strategy, "FSM_AGGR"))
options->fs_strategy = H5F_FSPACE_STRATEGY_FSM_AGGR;
- else if(!HDstrcmp(strategy, "PAGE"))
+ else if (!HDstrcmp(strategy, "PAGE"))
options->fs_strategy = H5F_FSPACE_STRATEGY_PAGE;
- else if(!HDstrcmp(strategy, "AGGR"))
+ else if (!HDstrcmp(strategy, "AGGR"))
options->fs_strategy = H5F_FSPACE_STRATEGY_AGGR;
- else if(!HDstrcmp(strategy, "NONE"))
+ else if (!HDstrcmp(strategy, "NONE"))
options->fs_strategy = H5F_FSPACE_STRATEGY_NONE;
else {
error_msg("invalid file space management strategy\n", opt_arg);
@@ -622,7 +594,7 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
ret_value = -1;
goto done;
}
- if(options->fs_strategy == (H5F_fspace_strategy_t)0)
+ if (options->fs_strategy == (H5F_fspace_strategy_t)0)
/* To distinguish the "specified" zero value */
options->fs_strategy = (H5F_fspace_strategy_t)-1;
}
@@ -630,27 +602,27 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
case 'P':
options->fs_persist = HDatoi(opt_arg);
- if(options->fs_persist == 0)
+ if (options->fs_persist == 0)
/* To distinguish the "specified" zero value */
options->fs_persist = -1;
break;
case 'T':
options->fs_threshold = HDatol(opt_arg);
- if(options->fs_threshold == 0)
+ if (options->fs_threshold == 0)
/* To distinguish the "specified" zero value */
options->fs_threshold = -1;
break;
case 'G':
options->fs_pagesize = HDstrtoll(opt_arg, NULL, 0);
- if(options->fs_pagesize == 0)
+ if (options->fs_pagesize == 0)
/* To distinguish the "specified" zero value */
options->fs_pagesize = -1;
break;
case 'q':
- if((sort_by = set_sort_by(opt_arg)) < 0) {
+ if (H5_INDEX_UNKNOWN == set_sort_by(opt_arg)) {
error_msg(" failed to set sort by form <%s>\n", opt_arg);
h5tools_setstatus(EXIT_FAILURE);
ret_value = -1;
@@ -659,7 +631,7 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
break;
case 'z':
- if((sort_order = set_sort_order(opt_arg)) < 0) {
+ if (set_sort_order(opt_arg) == H5_ITER_UNKNOWN) {
error_msg(" failed to set sort order form <%s>\n", opt_arg);
h5tools_setstatus(EXIT_FAILURE);
ret_value = -1;
@@ -673,18 +645,35 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
default:
break;
- } /* switch */
- } /* while */
-
- if (has_i_o == 0) {
- /* check for file names to be processed */
- if (argc <= opt_ind || argv[opt_ind + 1] == NULL) {
- error_msg("missing file names\n");
- usage(h5tools_getprogname());
- h5tools_setstatus(EXIT_FAILURE);
- ret_value = -1;
- }
- }
+ } /* end switch */
+ } /* end while there are more options to parse */
+
+ /* If neither -i nor -o given, get in and out files positionally */
+ if (0 == (has_i + has_o)) {
+ if (argv[opt_ind] != NULL && argv[opt_ind + 1] != NULL) {
+ infile = argv[opt_ind];
+ outfile = argv[opt_ind + 1];
+
+ if (!HDstrcmp(infile, outfile)) {
+ error_msg("file names cannot be the same\n");
+ usage(h5tools_getprogname());
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = -1;
+ }
+ }
+ else {
+ error_msg("file names missing\n");
+ usage(h5tools_getprogname());
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = -1;
+ }
+ }
+ else if (has_i != 1 || has_o != 1) {
+ error_msg("filenames must be either both -i -o or both positional\n");
+ usage(h5tools_getprogname());
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = -1;
+ }
done:
return ret_value;
@@ -741,28 +730,6 @@ int main(int argc, const char **argv)
if (parse_command_line(argc, argv, &options) < 0)
goto done;
- /* get file names if they were not yet got */
- if (has_i_o == 0) {
-
- if (argv[opt_ind] != NULL && argv[opt_ind + 1] != NULL) {
- infile = argv[opt_ind];
- outfile = argv[opt_ind + 1];
-
- if ( HDstrcmp( infile, outfile ) == 0) {
- error_msg("file names cannot be the same\n");
- usage(h5tools_getprogname());
- h5tools_setstatus(EXIT_FAILURE);
- goto done;
- }
- }
- else {
- error_msg("file names missing\n");
- usage(h5tools_getprogname());
- h5tools_setstatus(EXIT_FAILURE);
- goto done;
- }
- }
-
if (enable_error_stack > 0) {
H5Eset_auto2(H5E_DEFAULT, func, edata);
H5Eset_auto2(H5tools_ERR_STACK_g, tools_func, tools_edata);