[svn-r23219] Description:

    Bring reviewed changes from Coverity branch back to trunk (QK & JK):

r20457:
Coverity issue 691: return of H5duo could be negative. Fixed by using
STDOUT_FILENO and redesign parse_command_line and main to cleanup file
allocations. The output_file var is null when using stdout. In cleanup do not
close output_file if NULL.

r20510:
Initialize ufid = -1 and predicate HDclose call on ufid != -1

r20511:
Purpose: Fix coverity issue 1715

Description: Free "file" and nested data on failure in H5FD_core_open.

r20512:
Initialize ifid = -1 and predicate HDclose call on ifid != -1

r20514:
Initialize h5fid = -1 and predicate HDclose call on h5fid != -1

r20516:
Added else branch to the if (ret_value < 0) check.

r20522:
Addressed coverity issues 930-933, 850, 836, 835, 1307.  All minor 
potential buffer overwrite bugs, or coverity errors.  Fixed by replacing
strcpy and sprintf with strncpy and snprintf.

r20523:
fixed coverity issues 68, 1120, 1116i

r20524:
Check  H5Z_SZIP->encoder_present < 1 assuming 0 represents absence.

r20601:
Purpose: Fix coverity issues 1703-1705

Description: Modified the cleanup code in test_free in accum.c to reset
allocated buffers to NULL after they are freed, and modified the error cleanup
code to check if these buffers are NULL before freeing them.  Also fixed some
unrelated warnings in accum.c.

r20602:
Use HDsnprintf and HDstrncat

r20603:
Purpose: Fix coverity issues 808-809

Description: Modified test_core in vfd.c to check the returns from malloc, and
keep track of whether points and check are allocated by setting them to NULL
when they are not.  Added code to free points and check on error if they are
not NULL.  Also fixed unrelated warnings in vfd.c.

r20604:
Use HDstrncpy.

r20605:
Use HDstrncpy and HDstrncat.

r20606:
Purpose: Fix coverity issue 807

Description: Modified long_compact in stab.c to keep track of whether objname is
allocated by setting it to NULL when it is not.  Added code to free objname on
error if it is not NULL.

r20607:
Changed string function calls to use versions that specify the string length
to fix coverity issues 832 and 839.


Tested on:
    Mac OSX/64 10.8.2 (amazon)
    (Too minor to require h5committest)

2 files changed, 99 insertions, 118 deletions

diff --git a/tools/h5jam/h5unjam.c b/tools/h5jam/h5unjam.c
index c304045..18b5f11 100644
--- a/tools/h5jam/h5unjam.c
+++ b/tools/h5jam/h5unjam.c
@@ -43,14 +43,14 @@ static const char *s_opts = "hu:i:o:d:V";
 static struct long_options l_opts[] = {
     { "help", no_arg, 'h' },
     { "hel", no_arg, 'h' },
-  {"i", require_arg, 'i'},  /* input file */
-  {"u", require_arg, 'u'},  /* user block file */
-  {"o", require_arg, 'o'},  /* output file */
-  {"delete", no_arg, 'd'},  /* delete ub */
-  {"delet", no_arg, 'd'},
-  {"dele", no_arg, 'd'},
-  {"del", no_arg, 'd'},
-  {"de", no_arg, 'd'},
+    {"i", require_arg, 'i'},    /* input file */
+    {"u", require_arg, 'u'},    /* user block file */
+    {"o", require_arg, 'o'},    /* output file */
+    {"delete", no_arg, 'd'},    /* delete ub */
+    {"delet", no_arg, 'd'},
+    {"dele", no_arg, 'd'},
+    {"del", no_arg, 'd'},
+    {"de", no_arg, 'd'},
     { NULL, 0, '\0' }
 };
 
@@ -123,86 +123,69 @@ usage(const char *prog)
 }
 
 /*-------------------------------------------------------------------------
- * Function:    leave
- *
- * Purpose:     Shutdown and call exit()
- *
- * Return:      Does not return
- *
- *-------------------------------------------------------------------------
- */
-static void
-leave(int ret)
-{
-    if (ub_file)
-        HDfree (ub_file);
-    if (input_file)
-        HDfree (input_file);
-    if (output_file)
-        HDfree (output_file);
-
-    h5tools_close();
-
-    HDexit(ret);
-}
-
-/*-------------------------------------------------------------------------
  * Function:    parse_command_line
  *
  * Purpose:     Parse the command line for the h5dumper.
  *
- * Return:      Success:
+ * Return:      Success:    EXIT_SUCCESS;
  *
- *              Failure:    Exits program with EXIT_FAILURE value.
- *
- * Programmer:
- *
- * Modifications:
+ *              Failure:    Exits function with EXIT_FAILURE value.
  *
  *-------------------------------------------------------------------------
  */
-
-static void
+static int
 parse_command_line(int argc, const char *argv[])
 {
     int opt = FALSE;
 
     /* parse command line options */
     while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
-        switch ((char) opt) {
-        case 'o':
-            output_file = HDstrdup (opt_arg);
-            break;
-        case 'i':
-            input_file = HDstrdup (opt_arg);
-            break;
-        case 'u':
-            ub_file = HDstrdup (opt_arg);
-            break;
-        case 'd':
-            do_delete = TRUE;
-            break;
-        case 'h':
-            usage(h5tools_getprogname());
-            leave(EXIT_SUCCESS);
-        case 'V':
-            print_version(h5tools_getprogname());
-            leave(EXIT_SUCCESS);
-        case '?':
-        default:
-            usage(h5tools_getprogname());
-            leave(EXIT_FAILURE);
+        switch((char)opt) {
+            case 'o':
+                output_file = HDstrdup(opt_arg);
+                break;
+
+            case 'i':
+                input_file = HDstrdup(opt_arg);
+                break;
+
+            case 'u':
+                ub_file = HDstrdup(opt_arg);
+                break;
+
+            case 'd':
+                do_delete = TRUE;
+                break;
+
+            case 'h':
+                usage(h5tools_getprogname());
+                h5tools_setstatus(EXIT_SUCCESS);
+                goto done;
+
+            case 'V':
+                print_version (h5tools_getprogname());
+                h5tools_setstatus(EXIT_SUCCESS);
+                goto done;
+
+            case '?':
+            default:
+                usage(h5tools_getprogname());
+                h5tools_setstatus(EXIT_FAILURE);
+                goto done;
         }
     }
 
-    /* check for file name to be processed */
-/*
-    if (argc <= opt_ind+2) {
-        error_msg("missing file name\n");
-        usage(h5tools_getprogname());
-        HDexit(EXIT_FAILURE);
-    }
-*/
+    return EXIT_SUCCESS;
+    
+done:
+    if(input_file)
+        HDfree(input_file);
+    if(output_file)
+        HDfree(output_file);
+    if(ub_file)
+        HDfree(ub_file);
+
+    return EXIT_FAILURE;
 }
 
 /*-------------------------------------------------------------------------
@@ -246,13 +229,15 @@ main(int argc, const char *argv[])
     /* Initialize h5tools lib */
     h5tools_init();
 
-    parse_command_line(argc, argv);
+    if(EXIT_FAILURE == parse_command_line(argc, argv))
+        goto done;
 
     if (input_file == NULL) {
         /* no user block */
         error_msg("missing arguemnt for HDF5 file input.\n");
         help_ref_msg(stderr);
-        leave (EXIT_FAILURE);
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
     }
 
     testval = H5Fis_hdf5(input_file);
@@ -286,8 +271,10 @@ main(int argc, const char *argv[])
         goto done;
     }
 
-    H5Pclose(plist);
-    H5Fclose(ifile);
+    status = H5Pclose(plist);
+    HDassert(status >= 0);
+    status = H5Fclose(ifile);
+    HDassert(status >= 0);
 
     if (usize == 0) {
   /* no user block to remove: message? */
@@ -320,7 +307,7 @@ main(int argc, const char *argv[])
 
     if (ub_file == NULL) {
         /* write to sdtout */
-        ufid = HDdup(1);
+        ufid = STDOUT_FILENO;
     } 
     else {
         ufid = HDopen(ub_file,O_WRONLY|O_CREAT|O_TRUNC, 0644 );
@@ -371,17 +358,25 @@ main(int argc, const char *argv[])
     }
 
 done:
-    if (ub_file) {
-        HDfree (ub_file);
-        if (ufid >= 0) HDclose(ufid);
+    if(input_file)
+        HDfree(input_file);
+    if(output_file)
+        HDfree(output_file);
+    if(ub_file) {
+        HDfree(ub_file);
+        if(ufid >= 0)
+            status = HDclose(ufid);
+            HDassert(status >= 0);
     }
-    if (input_file)
-        HDfree (input_file);
-    if (output_file)
-        HDfree (output_file);
 
-    if (h5fid >= 0) HDclose(h5fid);
-    if (ifid >= 0) HDclose(ifid);
+    if(h5fid >= 0) {
+        status = HDclose(h5fid);
+        HDassert(status >= 0);
+    }
+    if(ifid >= 0) {
+        status = HDclose(ifid);
+        HDassert(status >= 0);
+    }
 
     return h5tools_getstatus();
 }
diff --git a/tools/lib/h5tools.c b/tools/lib/h5tools.c
index 66c0e64..0d9bc15 100644
--- a/tools/lib/h5tools.c
+++ b/tools/lib/h5tools.c
@@ -30,10 +30,6 @@
 #include "h5tools_utils.h"
 #include "H5private.h"
 
-#define SANITY_CHECK
-
-#define ALIGN(A,Z)  ((((A) + (Z) - 1) / (Z)) * (Z))
-
 /* global variables */
 hid_t H5tools_ERR_STACK_g = 0;
 hid_t H5tools_ERR_CLS_g = -1;
@@ -1122,7 +1118,6 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem,  hsize_t
             while(block_index > 0) {
                 size_t bytes_in        = 0;    /* # of bytes to write  */
                 size_t bytes_wrote     = 0;    /* # of bytes written   */
-                size_t item_size       = size;    /* size of items in bytes */
 
                 if(block_index > sizeof(size_t))
                     bytes_in = sizeof(size_t);
@@ -1168,16 +1163,21 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem,  hsize_t
             break;
         case H5T_COMPOUND:
             {
-                unsigned j;
-                hid_t    memb;
+                int snmembs;
                 unsigned nmembs;
-                size_t   offset;
 
-                nmembs = H5Tget_nmembers(tid);
+                if((snmembs = H5Tget_nmembers(tid)) < 0)
+                    H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_nmembers of compound failed");
+                nmembs = (unsigned)snmembs;
 
                 for (block_index = 0; block_index < block_nelmts; block_index++) {
+                    unsigned j;
+
                     mem = ((unsigned char*)_mem) + block_index * size;
                     for (j = 0; j < nmembs; j++) {
+                        hid_t    memb;
+                        size_t   offset;
+
                         offset = H5Tget_member_offset(tid, j);
                         memb   = H5Tget_member_type(tid, j);
 
@@ -1192,7 +1192,7 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem,  hsize_t
         case H5T_ARRAY:
             {
                 int     k, ndims;
-                hsize_t i, dims[H5S_MAX_RANK], temp_nelmts, nelmts;
+                hsize_t dims[H5S_MAX_RANK], temp_nelmts, nelmts;
                 hid_t   memb;
 
                 /* get the array's base datatype for each element */
@@ -1219,7 +1219,6 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem,  hsize_t
             break;
         case H5T_VLEN:
             {
-                unsigned int i;
                 hsize_t      nelmts;
                 hid_t        memb;
 
@@ -1305,10 +1304,9 @@ render_bin_output_region_data_blocks(hid_t region_id, FILE *stream,
     hsize_t     *start = NULL;
     hsize_t     *count = NULL;
     hsize_t      numelem;
-    hsize_t      numindex;
     hsize_t      total_size[H5S_MAX_RANK];
     int          jndx;
-    int          type_size;
+    size_t       type_size;
     hid_t        mem_space = -1;
     void        *region_buf = NULL;
     int          blkndx;
@@ -1399,15 +1397,17 @@ render_bin_output_region_blocks(hid_t region_space, hid_t region_id,
         FILE *stream, hid_t container)
 {
     HERR_INIT(hbool_t, TRUE)
-    hssize_t     nblocks;
+    hssize_t     snblocks;
+    hsize_t      nblocks;
     hsize_t      alloc_size;
-    hsize_t     *ptdata = NULL;
+    hsize_t     *ptdata;
     int          ndims;
     hid_t        dtype;
     hid_t        type_id;
 
-    if((nblocks = H5Sget_select_hyper_nblocks(region_space)) <= 0)
+    if((snblocks = H5Sget_select_hyper_nblocks(region_space)) <= 0)
         H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_select_hyper_nblocks failed");
+    nblocks = (hsize_t)snblocks;
 
     /* Print block information */
     if((ndims = H5Sget_simple_extent_ndims(region_space)) < 0)
@@ -1463,13 +1463,12 @@ render_bin_output_region_blocks(hid_t region_space, hid_t region_id,
  *      hssize_t npoints is the number of points in the region
  *-------------------------------------------------------------------------
  */
-int
+static int
 render_bin_output_region_data_points(hid_t region_space, hid_t region_id,
         FILE *stream, hid_t container,
-        int ndims, hid_t type_id, hssize_t npoints, hsize_t *ptdata)
+        int ndims, hid_t type_id, hssize_t npoints)
 {
     hsize_t *dims1 = NULL;
-    int      jndx;
     int      type_size;
     hid_t    mem_space = -1;
     void    *region_buf = NULL;
@@ -1525,8 +1524,6 @@ render_bin_output_region_points(hid_t region_space, hid_t region_id,
 {
     HERR_INIT(hbool_t, TRUE)
     hssize_t npoints;
-    hsize_t  alloc_size;
-    hsize_t *ptdata;
     int      ndims;
     hid_t    dtype;
     hid_t    type_id;
@@ -1538,15 +1535,6 @@ render_bin_output_region_points(hid_t region_space, hid_t region_id,
     if((ndims = H5Sget_simple_extent_ndims(region_space)) < 0)
         H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
 
-    alloc_size = npoints * ndims * sizeof(ptdata[0]);
-    HDassert(alloc_size == (hsize_t) ((size_t) alloc_size)); /*check for overflow*/
-    if(NULL == (ptdata = (hsize_t *)HDmalloc((size_t) alloc_size)))
-        HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "Could not allocate buffer for ptdata");
-
-    H5_CHECK_OVERFLOW(npoints, hssize_t, hsize_t);
-    if(H5Sget_select_elem_pointlist(region_space, (hsize_t) 0, (hsize_t) npoints, ptdata) < 0)
-        HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Sget_select_elem_pointlist failed");
-
     if((dtype = H5Dget_type(region_id)) < 0)
         HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Dget_type failed");
 
@@ -1554,11 +1542,9 @@ render_bin_output_region_points(hid_t region_space, hid_t region_id,
         HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Tget_native_type failed");
 
     render_bin_output_region_data_points(region_space, region_id,
-            stream, container, ndims, type_id, npoints, ptdata);
+            stream, container, ndims, type_id, npoints);
 
  done:
-    HDfree(ptdata);
-
     if(H5Tclose(type_id) < 0)
         HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed");