[svn-r9019] Purpose:

Adding new 'jam' utility

Description:
New utility, plus changes to makefiles

Solution:
See http://hdf.ncsa.uiuc.edu/RFC/Jam

Platforms tested:
verbena (fortran,C++), arabica, hirdls (SGI Irix64)

Misc. update:
Manifest will be done in next checkin.

1 files changed, 314 insertions, 0 deletions

diff --git a/tools/h5jam/h5unjam.c b/tools/h5jam/h5unjam.c
new file mode 100644
index 0000000..22c190a
--- /dev/null
+++ b/tools/h5jam/h5unjam.c
@@ -0,0 +1,314 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by the Board of Trustees of the University of Illinois.         *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the files COPYING and Copyright.html.  COPYING can be found at the root   *
+ * of the source code distribution tree; Copyright.html can be found at the  *
+ * root level of an installed copy of the electronic HDF5 document set and   *
+ * is linked from the top-level documents page.  It can also be found at     *
+ * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html.  If you do not have     *
+ * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <sys/types.h>
+#include <fcntl.h>
+#include <sys/stat.h>
+#include <unistd.h>
+
+#include "hdf5.h"
+#include "h5tools_utils.h"
+
+#define TRUE 1
+#define FALSE 0
+
+hsize_t write_pad( int , hsize_t );
+hsize_t compute_pad( hsize_t );
+hsize_t copy_to_file( int , int , ssize_t, ssize_t );
+
+const char  *progname = "unjam";
+int          d_status = EXIT_SUCCESS;
+int do_delete = FALSE;
+char *output_file = NULL;
+char *input_file = NULL;
+char *ub_file = NULL;
+
+/*
+ * Command-line options: The user can specify short or long-named
+ * parameters. The long-named ones can be partially spelled. When
+ * adding more, make sure that they don't clash with each other.
+ */
+static const char *s_opts = "hu:i:o:d";
+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'},	
+    { NULL, 0, '\0' }
+};
+
+/*-------------------------------------------------------------------------
+ * Function:    usage
+ *
+ * Purpose:     Print the usage message 
+ *
+ * Return:      void
+ *
+ * Programmer:  
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+usage(const char *prog)
+{
+    fflush(stdout);
+    fprintf(stdout, "usage: %s -i h5_file -o user_block_file_out -o h5_file_out [-d | --delete]\n", prog);
+    fprintf(stdout, "           Extract user block from 'h5_file' into 'user_block_file'\n");
+    fprintf(stdout, "           and HDF5 file into 'h5_file_out'\n");
+
+    fprintf(stdout, "       %s -h\n",prog);
+    fprintf(stdout, "           Print a usage message and exit\n");
+}
+
+/*-------------------------------------------------------------------------
+ * Function:    parse_command_line
+ *
+ * Purpose:     Parse the command line for the h5dumper.
+ *
+ * Return:      Success:    
+ *
+ *              Failure:    Exits program with EXIT_FAILURE value.
+ *
+ * Programmer:  
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+
+void
+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 = strdup (opt_arg);
+	  break;
+	case 'i':
+	  input_file = strdup (opt_arg);
+	  break;
+	case 'u':
+	  ub_file = strdup (opt_arg);
+	  break;
+	case 'd':
+	  do_delete = TRUE;
+	  break;
+        case 'h':
+            usage(progname);
+            exit(EXIT_SUCCESS);
+        case '?':
+        default:
+            usage(progname);
+            exit(EXIT_FAILURE);
+        }
+    }
+
+    /* check for file name to be processed */
+/*
+    if (argc <= opt_ind+2) {
+        error_msg(progname, "missing file name\n");
+        usage(progname);
+        exit(EXIT_FAILURE);
+    }
+*/
+}
+
+/*-------------------------------------------------------------------------
+ * Function:    main
+ *
+ * Purpose:     HDF5 user block unjammer
+ *
+ * Return:      Success:    0
+ *              Failure:    1
+ *
+ * Programmer:  
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+main(int argc, const char *argv[])
+{
+    int   ifid;
+    int   ufid;
+    int   h5fid;
+    void               *edata;
+    hid_t               (*func)(void*);
+    hid_t               ifile;
+    off_t fsize;
+    hsize_t usize;
+    htri_t testval;
+    herr_t status;
+    hid_t plist;
+    int res;
+    struct stat sbuf;
+
+    /* Disable error reporting */
+    H5Eget_auto(H5E_DEFAULT, &func, &edata);
+    H5Eset_auto(H5E_DEFAULT, NULL, NULL);
+
+    parse_command_line(argc, argv);
+
+    testval = H5Fis_hdf5(input_file);
+
+    if (testval <= 0) {
+        error_msg(progname, "Input HDF5 file is not HDF \"%s\"\n", input_file);
+        exit(EXIT_FAILURE);
+    }
+
+    ifile = H5Fopen(input_file, H5F_ACC_RDONLY , H5P_DEFAULT);
+
+    if (ifile < 0) {
+        error_msg(progname, "Can't open input HDF5 file \"%s\"\n", input_file);
+        exit(EXIT_FAILURE);
+    }
+
+    plist = H5Fget_create_plist(ifile);
+    if (plist < 0) {
+        error_msg(progname, "Can't get file creation plist for file \"%s\"\n", input_file);
+        exit(EXIT_FAILURE);
+    }
+
+    status =  H5Pget_userblock(plist, & usize  );
+    if (status < 0) {
+        error_msg(progname, "Can't get user block for file \"%s\"\n", input_file);
+        exit(EXIT_FAILURE);
+    }
+
+    if (usize == 0) {
+	/* no user block to remove: message? */
+        error_msg(progname, "\"%s\" has no user block: no change to file\n", input_file);
+        exit(EXIT_SUCCESS);
+	
+    }
+
+    res = stat(input_file, &sbuf);
+
+    if (res < 0) {
+        error_msg(progname, "Can't stat file \"%s\"\n", input_file);
+        exit(EXIT_FAILURE);
+    }
+
+    fsize = sbuf.st_size;
+
+    ifid = open(input_file,O_RDONLY);
+
+    if (ifid < 0) {
+        error_msg(progname, "unable to open input HDF5 file \"%s\"\n", input_file);
+        exit(EXIT_FAILURE);
+    }
+
+    if (do_delete && (ub_file != NULL)) {
+            error_msg(progname, "??\"%s\"\n", ub_file);
+            exit(EXIT_FAILURE);
+    }
+
+    if (ub_file == NULL) {
+	/* write to sdtout */
+	ufid = dup(1);
+    } else {
+        ufid = open(ub_file,O_WRONLY|O_CREAT|O_TRUNC, 0644 );
+
+        if (ufid < 0) {
+            error_msg(progname, "unable to open user block file for output\"%s\"\n", ub_file);
+            exit(EXIT_FAILURE);
+        }
+    }
+
+    if (output_file == NULL) {
+        h5fid = open(input_file,O_WRONLY);
+
+        if (h5fid < 0) {
+            error_msg(progname, "unable to open output HDF5 file \"%s\"\n", input_file);
+            exit(EXIT_FAILURE);
+        }
+    } else {
+        h5fid = open(output_file,O_WRONLY|O_CREAT|O_TRUNC, 0644 );
+
+        if (h5fid < 0) {
+            error_msg(progname, "unable to open output HDF5 file \"%s\"\n", output_file);
+            exit(EXIT_FAILURE);
+        }
+    }
+
+
+    /* copy from 0 to 'usize - 1' into ufid */ 
+    if (!do_delete) {
+	    copy_to_file( ifid, ufid, 0, (ssize_t) usize);
+    }
+
+    /* copy from usize to end of file into h5fid, 
+     * starting at end of user block if present
+     */ 
+    copy_to_file( ifid, h5fid, (ssize_t) usize, (fsize - (ssize_t)usize) );
+
+
+    close(ufid);
+    close(h5fid);
+    close(ifid);
+
+    return d_status;
+}
+
+/*
+ *  Copy 'how_much' bytes from the input file to the output file, 
+ *  starting at byte 'where' in the input file.
+ *  
+ *  Returns the size of the output file.
+ */
+hsize_t 
+copy_to_file( int infid, int ofid, ssize_t where, ssize_t how_much ) {
+	char buf[1024];
+	off_t to;
+	off_t from;
+	ssize_t nchars = -1;
+
+
+	if (how_much <= 0) {
+		/* nothing to copy */
+		return(where);
+	}
+	from = where;
+	to = 0;
+
+	while( how_much > 0) {
+		lseek(infid,from,SEEK_SET);
+		if (how_much > 512) {
+			nchars = read(infid,buf,(unsigned)512);
+		} else {
+			nchars = read(infid,buf,(unsigned)how_much);
+		}
+		lseek(ofid,to,SEEK_SET);
+		write(ofid,buf,(unsigned)nchars);
+		how_much -= nchars;
+		from += nchars;
+		to += nchars;
+	}
+
+	return (where+how_much);
+}