Create a new branch for the September Subfiling deliverable

1 files changed, 250 insertions, 96 deletions

diff --git a/tools/src/h5diff/h5diff_common.c b/tools/src/h5diff/h5diff_common.c
index e0e6f8c..8ed2d37 100644
--- a/tools/src/h5diff/h5diff_common.c
+++ b/tools/src/h5diff/h5diff_common.c
@@ -25,7 +25,7 @@ static int check_d_input(const char*);
  * Command-line options: The user can specify short or long-named
  * parameters.
  */
-static const char *s_opts = "hVrv:qn:d:p:NcelxE:S";
+static const char *s_opts = "hVrv:qn:d:p:NcelxE:A:S";
 static struct long_options l_opts[] = {
     { "help",               no_arg, 'h' },
     { "version",            no_arg, 'V' },
@@ -41,6 +41,7 @@ static struct long_options l_opts[] = {
     { "follow-symlinks",    no_arg, 'l' },
     { "no-dangling-links",  no_arg, 'x' },
     { "exclude-path",       require_arg, 'E' },
+    { "exclude-attribute",  require_arg, 'A' },
     { "enable-error-stack", no_arg, 'S' },
     { "vol-value-1",        require_arg, '1' },
     { "vol-name-1",         require_arg, '2' },
@@ -55,7 +56,6 @@ static struct long_options l_opts[] = {
  * Function: check_options
  *
  * Purpose: parse command line input
- *
  *-------------------------------------------------------------------------
  */
 static void check_options(diff_opt_t* opts)
@@ -67,7 +67,7 @@ static void check_options(diff_opt_t* opts)
     /* check between -d , -p, --use-system-epsilon.
      * These options are mutually exclusive.
      */
-    if ((opts->d + opts->p + opts->use_system_epsilon) > 1) {
+    if ((opts->delta_bool + opts->percent_bool + opts->use_system_epsilon) > 1) {
         HDprintf("%s error: -d, -p and --use-system-epsilon options are mutually-exclusive;\n", PROGRAMNAME);
         HDprintf("use no more than one.\n");
         HDprintf("Try '-h' or '--help' option for more information or see the %s entry in the 'HDF5 Reference Manual'.\n", PROGRAMNAME);
@@ -75,27 +75,139 @@ static void check_options(diff_opt_t* opts)
     }
 }
 
+#if TRILABS-227
+/*-------------------------------------------------------------------------
+ * Function:    parse_hsize_list
+ *
+ * Purpose:     Parse a list of comma or space separated integers and return
+ *              them in a list. The string being passed into this function
+ *              should be at the start of the list you want to parse. You are
+ *              responsible for freeing the array returned from here.
+ *
+ *              Lists in the so-called "terse" syntax are separated by
+ *              semicolons (;). The lists themselves can be separated by
+ *              either commas (,) or white spaces.
+ *
+ * Return:      <none>
+ *-------------------------------------------------------------------------
+ */
+static void
+parse_hsize_list(const char *h_list, subset_d *d)
+{
+    hsize_t        *p_list;
+    const char     *ptr;
+    unsigned int    size_count = 0;
+    unsigned int    i = 0;
+    unsigned int    last_digit = 0;
+
+    if (!h_list || !*h_list || *h_list == ';')
+        return;
+
+    H5TOOLS_START_DEBUG(" - h_list:%s", h_list);
+    /* count how many integers do we have */
+    for (ptr = h_list; ptr && *ptr && *ptr != ';' && *ptr != ']'; ptr++)
+        if (HDisdigit(*ptr)) {
+            if (!last_digit)
+                /* the last read character wasn't a digit */
+                size_count++;
+
+            last_digit = 1;
+        }
+        else
+            last_digit = 0;
+
+    if (size_count == 0) {
+        /* there aren't any integers to read */
+        H5TOOLS_ENDDEBUG("No integers to read");
+        return;
+    }
+    H5TOOLS_DEBUG("Number integers to read=%ld", size_count);
+
+    /* allocate an array for the integers in the list */
+    if((p_list = (hsize_t *)HDcalloc(size_count, sizeof(hsize_t))) == NULL)
+        H5TOOLS_INFO("Unable to allocate space for subset data");
+
+    for (ptr = h_list; i < size_count && ptr && *ptr && *ptr != ';' && *ptr != ']'; ptr++)
+        if(HDisdigit(*ptr)) {
+            /* we should have an integer now */
+            p_list[i++] = (hsize_t)HDstrtoull(ptr, NULL, 0);
+
+            while (HDisdigit(*ptr))
+                /* scroll to end of integer */
+                ptr++;
+        }
+    d->data = p_list;
+    d->len = size_count;
+    H5TOOLS_ENDDEBUG("");
+}
+
+/*-------------------------------------------------------------------------
+ * Function:    parse_subset_params
+ *
+ * Purpose:     Parse the so-called "terse" syntax for specifying subsetting parameters.
+ *
+ * Return:      Success:    struct subset_t object
+ *              Failure:    NULL
+ *-------------------------------------------------------------------------
+ */
+static struct subset_t *
+parse_subset_params(const char *dset)
+{
+    struct subset_t *s = NULL;
+    char   *brace;
+
+    H5TOOLS_START_DEBUG(" - dset:%s", dset);
+    if ((brace = HDstrrchr(dset, '[')) != NULL) {
+        *brace++ = '\0';
+
+        s = (struct subset_t *)HDcalloc(1, sizeof(struct subset_t));
+        parse_hsize_list(brace, &s->start);
+
+        while (*brace && *brace != ';')
+            brace++;
+
+        if (*brace)
+            brace++;
+
+        parse_hsize_list(brace, &s->stride);
+
+        while (*brace && *brace != ';')
+            brace++;
+
+        if (*brace)
+            brace++;
+
+        parse_hsize_list(brace, &s->count);
+
+        while (*brace && *brace != ';')
+            brace++;
+
+        if (*brace)
+            brace++;
+
+        parse_hsize_list(brace, &s->block);
+    }
+    H5TOOLS_ENDDEBUG("");
+
+    return s;
+}
+#endif
 
 /*-------------------------------------------------------------------------
  * Function: parse_command_line
  *
  * Purpose: parse command line input
- *
  *-------------------------------------------------------------------------
  */
 
-void parse_command_line(int argc,
-                        const char* argv[],
-                        const char** fname1,
-                        const char** fname2,
-                        const char** objname1,
-                        const char** objname2,
-                        diff_opt_t* opts)
+void parse_command_line(int argc, const char* argv[], const char** fname1, const char** fname2, const char** objname1, const char** objname2, diff_opt_t* opts)
 {
     int i;
     int opt;
     struct exclude_path_list *exclude_head, *exclude_prev, *exclude_node;
+    struct exclude_path_list *exclude_attr_head, *exclude_attr_prev, *exclude_attr_node;
 
+    H5TOOLS_START_DEBUG("");
     /* process the command-line */
     HDmemset(opts, 0, sizeof (diff_opt_t));
 
@@ -106,15 +218,18 @@ void parse_command_line(int argc,
     opts->do_nans = 1;
 
     /* not Listing objects that are not comparable */
-    opts->m_list_not_cmp = 0;
+    opts->mode_list_not_cmp = 0;
 
     /* initially no not-comparable. */
     /**this is bad in mixing option with results**/
-    opts->not_cmp=0;
+    opts->not_cmp = 0;
 
     /* init for exclude-path option */
     exclude_head = NULL;
 
+    /* init for exclude-attribute option */
+    exclude_attr_head = NULL;
+
     /* parse command line options */
     while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
         switch ((char)opt) {
@@ -134,7 +249,7 @@ void parse_command_line(int argc,
             break;
 
         case 'v':
-            opts->m_verbose = 1;
+            opts->mode_verbose = 1;
             /* This for loop is for handling style like
              * -v, -v1, --verbose, --verbose=1.
              */
@@ -144,11 +259,11 @@ void parse_command_line(int argc,
                  */
                 if (!strcmp (argv[i], "-v")) {  /* no arg */
                     opt_ind--;
-                    opts->m_verbose_level = 0;
+                    opts->mode_verbose_level = 0;
                     break;
                 }
                 else if (!strncmp (argv[i], "-v", (size_t)2)) {
-                    opts->m_verbose_level = atoi(&argv[i][2]);
+                    opts->mode_verbose_level = atoi(&argv[i][2]);
                     break;
                 }
 
@@ -156,11 +271,11 @@ void parse_command_line(int argc,
                  * long opt
                  */
                 if (!strcmp (argv[i], "--verbose")) {  /* no arg */
-                    opts->m_verbose_level = 0;
+                    opts->mode_verbose_level = 0;
                     break;
                 }
-                else if ( !strncmp (argv[i], "--verbose", (size_t)9) && argv[i][9]=='=') {
-                    opts->m_verbose_level = atoi(&argv[i][10]);
+                else if (!strncmp (argv[i], "--verbose", (size_t)9) && argv[i][9]=='=') {
+                    opts->mode_verbose_level = atoi(&argv[i][10]);
                     break;
                 }
             }
@@ -168,11 +283,11 @@ void parse_command_line(int argc,
 
         case 'q':
             /* use quiet mode; supress the message "0 differences found" */
-            opts->m_quiet = 1;
+            opts->mode_quiet = 1;
             break;
 
         case 'r':
-            opts->m_report = 1;
+            opts->mode_report = 1;
             break;
 
         case 'l':
@@ -214,23 +329,47 @@ void parse_command_line(int argc,
             }
             break;
 
+        case 'A':
+            opts->exclude_attr_path = 1;
+
+            /* create linked list of excluding objects */
+            if( (exclude_attr_node = (struct exclude_path_list*) HDmalloc(sizeof(struct exclude_path_list))) == NULL) {
+                HDprintf("Error: lack of memory!\n");
+                h5diff_exit(EXIT_FAILURE);
+            }
+
+            /* init */
+            exclude_attr_node->obj_path = opt_arg;
+            exclude_attr_node->obj_type = H5TRAV_TYPE_UNKNOWN;
+            exclude_attr_prev = exclude_attr_head;
+
+            if (NULL == exclude_attr_head) {
+                exclude_attr_head = exclude_attr_node;
+                exclude_attr_head->next = NULL;
+            }
+            else {
+                while(NULL != exclude_attr_prev->next)
+                    exclude_attr_prev = exclude_attr_prev->next;
+
+                exclude_attr_node->next = NULL;
+                exclude_attr_prev->next = exclude_attr_node;
+            }
+            break;
+
         case 'd':
-            opts->d = 1;
+            opts->delta_bool = 1;
 
-            if (check_d_input(opt_arg) == - 1) {
+            if (check_d_input(opt_arg) == -1) {
                 HDprintf("<-d %s> is not a valid option\n", opt_arg);
                 usage();
                 h5diff_exit(EXIT_FAILURE);
             }
             opts->delta = HDatof(opt_arg);
-
-            /* -d 0 is the same as default */
-            if (H5_DBL_ABS_EQUAL(opts->delta, (double)0.0F))
-                opts->d=0;
+            /* do not check against default, the DBL_EPSILON is being replaced by user */
             break;
 
         case 'p':
-            opts->p = 1;
+            opts->percent_bool = 1;
             if (check_p_input(opt_arg) == -1) {
                 HDprintf("<-p %s> is not a valid option\n", opt_arg);
                 usage();
@@ -240,12 +379,12 @@ void parse_command_line(int argc,
 
             /* -p 0 is the same as default */
             if (H5_DBL_ABS_EQUAL(opts->percent, (double)0.0F))
-                opts->p = 0;
+                opts->percent_bool = 0;
             break;
 
         case 'n':
-            opts->n = 1;
-            if ( check_n_input(opt_arg) == -1) {
+            opts->count_bool = 1;
+            if (check_n_input(opt_arg) == -1) {
                 HDprintf("<-n %s> is not a valid option\n", opt_arg);
                 usage();
                 h5diff_exit(EXIT_FAILURE);
@@ -258,7 +397,7 @@ void parse_command_line(int argc,
             break;
 
         case 'c':
-            opts->m_list_not_cmp = 1;
+            opts->mode_list_not_cmp = 1;
             break;
 
         case 'e':
@@ -266,35 +405,35 @@ void parse_command_line(int argc,
             break;
 
         case '1':
-            opts->vol_info_1.type = VOL_BY_VALUE;
-            opts->vol_info_1.u.value = (H5VL_class_value_t)HDatoi(opt_arg);
-            opts->custom_vol_1 = TRUE;
+            opts->vol_info[0].type = VOL_BY_VALUE;
+            opts->vol_info[0].u.value = (H5VL_class_value_t)HDatoi(opt_arg);
+            opts->custom_vol[0] = TRUE;
             break;
 
         case '2':
-            opts->vol_info_1.type = VOL_BY_NAME;
-            opts->vol_info_1.u.name = opt_arg;
-            opts->custom_vol_1 = TRUE;
+            opts->vol_info[0].type = VOL_BY_NAME;
+            opts->vol_info[0].u.name = opt_arg;
+            opts->custom_vol[0] = TRUE;
             break;
 
         case '3':
-            opts->vol_info_1.info_string = opt_arg;
+            opts->vol_info[0].info_string = opt_arg;
             break;
 
         case '4':
-            opts->vol_info_2.type = VOL_BY_VALUE;
-            opts->vol_info_2.u.value = (H5VL_class_value_t)HDatoi(opt_arg);
-            opts->custom_vol_2 = TRUE;
+            opts->vol_info[1].type = VOL_BY_VALUE;
+            opts->vol_info[1].u.value = (H5VL_class_value_t)HDatoi(opt_arg);
+            opts->custom_vol[1] = TRUE;
             break;
 
         case '5':
-            opts->vol_info_2.type = VOL_BY_NAME;
-            opts->vol_info_2.u.name = opt_arg;
-            opts->custom_vol_2 = TRUE;
+            opts->vol_info[1].type = VOL_BY_NAME;
+            opts->vol_info[1].u.name = opt_arg;
+            opts->custom_vol[1] = TRUE;
             break;
 
         case '6':
-            opts->vol_info_2.info_string = opt_arg;
+            opts->vol_info[1].info_string = opt_arg;
             break;
         }
     }
@@ -306,30 +445,49 @@ void parse_command_line(int argc,
     if (opts->exclude_path)
         opts->exclude = exclude_head;
 
+    /* if exclude-attribute option is used, keep the exclude attr list */
+    if (opts->exclude_attr_path)
+        opts->exclude_attr = exclude_attr_head;
+
     /* check for file names to be processed */
-    if (argc <= opt_ind || argv[ opt_ind + 1 ] == NULL) {
+    if (argc <= opt_ind || argv[opt_ind + 1] == NULL) {
         error_msg("missing file names\n");
         usage();
         h5diff_exit(EXIT_FAILURE);
     }
 
-    *fname1 = argv[ opt_ind ];
-    *fname2 = argv[ opt_ind + 1 ];
-    *objname1 = argv[ opt_ind + 2 ];
+    *fname1 = argv[opt_ind];
+    *fname2 = argv[opt_ind + 1];
+    *objname1 = argv[opt_ind + 2];
+    H5TOOLS_DEBUG("file1 = %s", *fname1);
+    H5TOOLS_DEBUG("file2 = %s", *fname2);
 
     if (*objname1 == NULL) {
         *objname2 = NULL;
+        H5TOOLS_ENDDEBUG("No obj names");
         return;
     }
+    H5TOOLS_DEBUG("objname1 = %s", *objname1);
 
-    if (argv[ opt_ind + 3 ] != NULL) {
-        *objname2 = argv[ opt_ind + 3 ];
+    if (argv[opt_ind + 3] != NULL) {
+        *objname2 = argv[opt_ind + 3];
     }
     else {
         *objname2 = *objname1;
     }
+    H5TOOLS_DEBUG("objname2 = %s", *objname2);
+
+    /*
+     * TRILABS-227 is complete except for an issue with printing indices
+     * the following calls will enable subsetting
+    */
+#if TRILABS-227
+    opts->sset[0] = parse_subset_params(*objname1);
 
+    opts->sset[1] = parse_subset_params(*objname2);
+#endif
 
+    H5TOOLS_ENDDEBUG("");
 }
 
 
@@ -337,26 +495,25 @@ void parse_command_line(int argc,
  * Function: print_info
  *
  * Purpose: print several information messages after h5diff call
- *
  *-------------------------------------------------------------------------
  */
 void print_info(diff_opt_t* opts)
 {
-    if (opts->m_quiet || opts->err_stat)
+    if (opts->mode_quiet || opts->err_stat)
         return;
 
     if (opts->cmn_objs == 0) {
         HDprintf("No common objects found. Files are not comparable.\n");
-        if (!opts->m_verbose)
+        if (!opts->mode_verbose)
             HDprintf("Use -v for a list of objects.\n");
     }
 
     if (opts->not_cmp == 1) {
-        if (opts->m_list_not_cmp == 0) {
+        if (opts->mode_list_not_cmp == 0) {
             HDprintf("--------------------------------\n");
             HDprintf("Some objects are not comparable\n");
             HDprintf("--------------------------------\n");
-            if (opts->m_verbose)
+            if (opts->mode_verbose)
                 HDprintf("Use -c for a list of objects without details of differences.\n");
             else
                 HDprintf("Use -c for a list of objects.\n");
@@ -370,19 +527,10 @@ void print_info(diff_opt_t* opts)
  * Purpose: check for valid input
  *
  * Return: 1 for ok, -1 for fail
- *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
- *
- * Date: May 9, 2003
- *
- * Comments:
- *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
 H5_ATTR_PURE static int
-check_n_input( const char *str )
+check_n_input(const char *str)
 {
     unsigned i;
     char c;
@@ -406,24 +554,17 @@ check_n_input( const char *str )
  * Purpose: check for a valid p option input
  *
  * Return: 1 for ok, -1 for fail
- *
- * Date: May 9, 2003
- *
- * Comments:
- *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
 static int
-check_p_input( const char *str )
+check_p_input(const char *str)
 {
     double x;
 
     /*
-    the atof return value on a hexadecimal input is different
-    on some systems; we do a character check for this
-    */
+     * the atof return value on a hexadecimal input is different
+     * on some systems; we do a character check for this
+     */
     if (HDstrlen(str) > 2 && str[0] == '0' && str[1] == 'x')
         return -1;
 
@@ -440,24 +581,17 @@ check_p_input( const char *str )
  * Purpose: check for a valid d option input
  *
  * Return: 1 for ok, -1 for fail
- *
- * Date: November 11, 2007
- *
- * Comments:
- *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
 static int
-check_d_input( const char *str )
+check_d_input(const char *str)
 {
     double x;
 
     /*
-    the atof return value on a hexadecimal input is different
-    on some systems; we do a character check for this
-    */
+     * the atof return value on a hexadecimal input is different
+     * on some systems; we do a character check for this
+     */
     if (HDstrlen(str) > 2 && str[0] == '0' && str[1] == 'x')
         return -1;
 
@@ -474,7 +608,6 @@ check_d_input( const char *str )
  * Purpose: print a usage message
  *
  * Return: void
- *
  *-------------------------------------------------------------------------
  */
 
@@ -499,10 +632,9 @@ void usage(void)
  PRINTVALSTREAM(rawoutstream, "         Verbose mode with level. Print differences and list of objects.\n");
  PRINTVALSTREAM(rawoutstream, "         Level of detail depends on value of N:\n");
  PRINTVALSTREAM(rawoutstream, "          0 : Identical to '-v' or '--verbose'.\n");
- PRINTVALSTREAM(rawoutstream, "          1 : All level 0 information plus one-line attribute\n");
- PRINTVALSTREAM(rawoutstream, "              status summary.\n");
- PRINTVALSTREAM(rawoutstream, "          2 : All level 1 information plus extended attribute\n");
- PRINTVALSTREAM(rawoutstream, "              status report.\n");
+ PRINTVALSTREAM(rawoutstream, "          1 : All level 0 information plus one-line attribute status summary.\n");
+ PRINTVALSTREAM(rawoutstream, "          2 : All level 1 information plus extended attribute status report.\n");
+ PRINTVALSTREAM(rawoutstream, "          3 : All level 2 information plus file names.\n");
  PRINTVALSTREAM(rawoutstream, "   -q, --quiet\n");
  PRINTVALSTREAM(rawoutstream, "         Quiet mode. Do not produce output.\n");
  PRINTVALSTREAM(rawoutstream, "   --enable-error-stack\n");
@@ -591,7 +723,14 @@ void usage(void)
  PRINTVALSTREAM(rawoutstream, "         excluded.\n");
  PRINTVALSTREAM(rawoutstream, "         This option can be used repeatedly to exclude multiple paths.\n");
  PRINTVALSTREAM(rawoutstream, "\n");
-
+ PRINTVALSTREAM(rawoutstream, "   --exclude-attribute \"path/to/object/with/attribute\"\n");
+ PRINTVALSTREAM(rawoutstream, "         Exclude attributes on the specified path to an object when comparing files or groups.\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, "         If there are multiple paths to an object, only the specified path(s)\n");
+ PRINTVALSTREAM(rawoutstream, "         will be excluded; the comparison will include any path not explicitly\n");
+ PRINTVALSTREAM(rawoutstream, "         excluded.\n");
+ PRINTVALSTREAM(rawoutstream, "         This option can be used repeatedly to exclude multiple paths.\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
  PRINTVALSTREAM(rawoutstream, " Modes of output:\n");
  PRINTVALSTREAM(rawoutstream, "  Default mode: print the number of differences found and where they occured\n");
  PRINTVALSTREAM(rawoutstream, "  -r Report mode: print the above plus the differences\n");
@@ -622,7 +761,22 @@ void usage(void)
  PRINTVALSTREAM(rawoutstream, "      (The option --follow-symlinks overrides the default behavior when\n");
  PRINTVALSTREAM(rawoutstream, "       symbolic links are compared.).\n");
  PRINTVALSTREAM(rawoutstream, "\n");
-
+ /*
+  * TRILABS-227 is complete except for an issue with printing indices
+  * the following will be needed for subsetting
+ PRINTVALSTREAM(rawoutstream, " Subsetting options:\n");
+ PRINTVALSTREAM(rawoutstream, "  Subsetting is available by using the fcompact form of subsetting, as follows:\n");
+ PRINTVALSTREAM(rawoutstream, "    obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]\n");
+ PRINTVALSTREAM(rawoutstream, "  It is not required to use all parameters, but until the last parameter value used,\n");
+ PRINTVALSTREAM(rawoutstream, "  all of the semicolons (;) are required, even when a parameter value is not specified. Example:\n");
+ PRINTVALSTREAM(rawoutstream, "    obj1 /foo/mydataset[START;;COUNT;BLOCK]\n");
+ PRINTVALSTREAM(rawoutstream, "    obj1 /foo/mydataset[START]\n");
+ PRINTVALSTREAM(rawoutstream, "  The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in\n");
+ PRINTVALSTREAM(rawoutstream, "  each dimension. START is optional and will default to 0 in each dimension.\n");
+ PRINTVALSTREAM(rawoutstream, "  Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with\n");
+ PRINTVALSTREAM(rawoutstream, "  one integer for each dimension of the dataset.\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+*/
  PRINTVALSTREAM(rawoutstream, " Exit code:\n");
  PRINTVALSTREAM(rawoutstream, "  0 if no differences, 1 if differences found, 2 if error\n");
  PRINTVALSTREAM(rawoutstream, "\n");