Split tools into src and test - add folders

4 files changed, 1066 insertions, 0 deletions

diff --git a/tools/src/h5jam/CMakeLists.txt b/tools/src/h5jam/CMakeLists.txt
new file mode 100644
index 0000000..cef54c2
--- /dev/null
+++ b/tools/src/h5jam/CMakeLists.txt
@@ -0,0 +1,49 @@
+cmake_minimum_required (VERSION 3.1.0)
+PROJECT (HDF5_TOOLS_SRC_H5JAM)
+
+#-----------------------------------------------------------------------------
+# Setup include Directories
+#-----------------------------------------------------------------------------
+INCLUDE_DIRECTORIES (${HDF5_TOOLS_DIR}/lib)
+
+# --------------------------------------------------------------------
+# Add the h5jam executables
+# --------------------------------------------------------------------
+add_executable (h5jam ${HDF5_TOOLS_SRC_H5JAM_SOURCE_DIR}/h5jam.c)
+TARGET_NAMING (h5jam STATIC)
+TARGET_C_PROPERTIES (h5jam STATIC " " " ")
+target_link_libraries (h5jam  ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
+set_target_properties (h5jam PROPERTIES FOLDER tools)
+set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5jam")
+
+add_executable (h5unjam ${HDF5_TOOLS_SRC_H5JAM_SOURCE_DIR}/h5unjam.c)
+TARGET_NAMING (h5unjam STATIC)
+TARGET_C_PROPERTIES (h5unjam STATIC " " " ")
+target_link_libraries (h5unjam  ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
+set_target_properties (h5unjam PROPERTIES FOLDER tools)
+set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5unjam")
+
+set (H5_DEP_EXECUTABLES
+    h5jam
+    h5unjam
+)
+
+##############################################################################
+##############################################################################
+###           I N S T A L L A T I O N                                      ###
+##############################################################################
+##############################################################################
+
+#-----------------------------------------------------------------------------
+# Rules for Installation of tools using make Install target
+#-----------------------------------------------------------------------------
+
+#INSTALL_PROGRAM_PDB (h5jam ${HDF5_INSTALL_BIN_DIR} toolsapplications)
+
+install (
+    TARGETS
+        h5jam h5unjam
+    EXPORT
+        ${HDF5_EXPORTED_TARGETS}
+    RUNTIME DESTINATION ${HDF5_INSTALL_BIN_DIR} COMPONENT toolsapplications
+)
diff --git a/tools/src/h5jam/Makefile.am b/tools/src/h5jam/Makefile.am
new file mode 100644
index 0000000..e244625
--- /dev/null
+++ b/tools/src/h5jam/Makefile.am
@@ -0,0 +1,35 @@
+#
+# Copyright by The HDF Group.
+# 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://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have
+# access to either file, you may request a copy from help@hdfgroup.org.
+##
+## Makefile.am
+## Run automake to generate a Makefile.in from this file.
+#
+# HDF5 Library Makefile(.in)
+#
+
+include $(top_srcdir)/config/commence.am
+
+# Include src and tools/lib directories
+AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
+
+bin_PROGRAMS=h5jam h5unjam
+
+# Add h5jam and h5unjam specific linker flags here
+h5jam_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
+h5unjam_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
+
+# Link against the main HDF5 library and tools library
+LDADD=$(LIBH5TOOLS) $(LIBHDF5)
+
+include $(top_srcdir)/config/conclude.am
diff --git a/tools/src/h5jam/h5jam.c b/tools/src/h5jam/h5jam.c
new file mode 100644
index 0000000..ae45714
--- /dev/null
+++ b/tools/src/h5jam/h5jam.c
@@ -0,0 +1,571 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * 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://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
+ * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+#include "hdf5.h"
+#include "H5private.h"
+#include "h5tools.h"
+#include "h5tools_utils.h"
+
+/* Name of tool */
+#define PROGRAMNAME "h5jam"
+
+herr_t write_pad(int ofile, hsize_t old_where, hsize_t *new_where);
+hsize_t compute_user_block_size (hsize_t);
+hsize_t copy_some_to_file (int, int, hsize_t, hsize_t, ssize_t);
+void parse_command_line (int, const char *[]);
+
+int do_clobber = 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 = "hi:u:o:c:V";  /* add more later ? */
+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 */
+  {"clobber", no_arg, 'c'},  /* clobber existing UB */
+  {"clobbe", no_arg, 'c'},
+  {"clobb", no_arg, 'c'},
+  {"clob", no_arg, 'c'},
+  {"clo", no_arg, 'c'},
+  {"cl", no_arg, 'c'},
+  {NULL, 0, '\0'}
+};
+
+/*-------------------------------------------------------------------------
+ * Function:    usage
+ *
+ * Purpose:     Print the usage message
+ *
+ * Return:      void
+ *
+ * Programmer:
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+usage (const char *prog)
+{
+    HDfflush (stdout);
+    HDfprintf (stdout,
+    "usage: %s -i <in_file.h5> -u <in_user_file> [-o <out_file.h5>] [--clobber]\n", prog);
+    HDfprintf (stdout, "\n");
+    HDfprintf (stdout,
+    "Adds user block to front of an HDF5 file and creates a new concatenated file.\n");
+    HDfprintf (stdout, "\n");
+    HDfprintf (stdout, 
+    "OPTIONS\n");
+    HDfprintf (stdout, 
+    "  -i in_file.h5    Specifies the input HDF5 file.\n");
+    HDfprintf (stdout, 
+    "  -u in_user_file  Specifies the file to be inserted into the user block.\n");
+    HDfprintf (stdout, 
+    "                   Can be any file format except an HDF5 format.\n");
+    HDfprintf (stdout,
+    "  -o out_file.h5   Specifies the output HDF5 file.\n");
+    HDfprintf (stdout,
+    "                   If not specified, the user block will be concatenated in\n");
+    HDfprintf (stdout,
+    "                   place to the input HDF5 file.\n");
+    HDfprintf (stdout,
+    "  --clobber        Wipes out any existing user block before concatenating\n");
+    HDfprintf (stdout,
+    "                   the given user block.\n");
+    HDfprintf (stdout,
+    "                   The size of the new user block will be the larger of;\n");
+    HDfprintf (stdout,
+    "                    - the size of existing user block in the input HDF5 file\n");
+    HDfprintf (stdout,
+    "                    - the size of user block required by new input user file\n");
+    HDfprintf (stdout,
+    "                   (size = 512 x 2N,  N is positive integer.)\n");
+    HDfprintf (stdout, "\n");
+    HDfprintf (stdout,
+    "  -h               Prints a usage message and exits.\n");
+    HDfprintf (stdout,
+    "  -V               Prints the HDF5 library version and exits.\n");
+    HDfprintf (stdout, "\n");
+    HDfprintf (stdout,
+    "Exit Status:\n");
+    HDfprintf (stdout,
+    "   0   Succeeded.\n");
+    HDfprintf (stdout,
+    "   >0  An error occurred.\n");
+}
+
+
+/*-------------------------------------------------------------------------
+ * 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:
+ *
+ *              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 = HDstrdup (opt_arg);
+          break;
+      case 'i':
+          input_file = HDstrdup (opt_arg);
+          break;
+      case 'u':
+          ub_file = HDstrdup (opt_arg);
+          break;
+      case 'c':
+          do_clobber = 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);
+      }
+    }
+}
+
+/*-------------------------------------------------------------------------
+ * Function:    main
+ *
+ * Purpose:     HDF5 user block jammer
+ *
+ * Return:      Success:    0
+ *              Failure:    1
+ *
+ * Programmer:
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+main (int argc, const char *argv[])
+{
+    int         ufid = -1;
+    int         h5fid = -1;
+    int         ofid = -1;
+    void       *edata;
+    H5E_auto2_t func;
+    hid_t       ifile = -1;
+    hid_t       plist = -1;
+    herr_t      status;
+    htri_t      testval;
+    hsize_t     usize;
+    hsize_t     h5fsize;
+    hsize_t     startub;
+    hsize_t     where;
+    hsize_t     newubsize;
+    off_t       fsize;
+    h5_stat_t   sbuf;
+    h5_stat_t   sbuf2;
+    int         res;
+
+    h5tools_setprogname(PROGRAMNAME);
+    h5tools_setstatus(EXIT_SUCCESS);
+
+    /* Disable error reporting */
+    H5Eget_auto2(H5E_DEFAULT, &func, &edata);
+    H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
+
+    /* Initialize h5tools lib */
+    h5tools_init();
+
+    parse_command_line (argc, argv);
+
+    if (ub_file == NULL) {
+        /* no user block */
+        error_msg("missing arguemnt for -u <user_file>.\n");
+        help_ref_msg(stderr);
+        leave (EXIT_FAILURE);
+    }
+
+    testval = H5Fis_hdf5 (ub_file);
+
+    if (testval > 0) {
+        error_msg("-u <user_file> cannot be HDF5 file, but it appears to be an HDF5 file.\n");
+        help_ref_msg(stderr);
+        leave (EXIT_FAILURE);
+    }
+
+    if (input_file == NULL) {
+        error_msg("missing arguemnt for -i <HDF5 file>.\n");
+        help_ref_msg(stderr);
+        leave (EXIT_FAILURE);
+    }
+
+    testval = H5Fis_hdf5 (input_file);
+
+    if (testval <= 0) {
+        error_msg("Input HDF5 file \"%s\" is not HDF5 format.\n", input_file);
+        help_ref_msg(stderr);
+        leave (EXIT_FAILURE);
+    }
+
+    ifile = H5Fopen (input_file, H5F_ACC_RDONLY, H5P_DEFAULT);
+
+    if (ifile < 0) {
+        error_msg("Can't open input HDF5 file \"%s\"\n", input_file);
+        leave (EXIT_FAILURE);
+    }
+
+    plist = H5Fget_create_plist (ifile);
+    if (plist < 0) {
+        error_msg("Can't get file creation plist for file \"%s\"\n", input_file);
+        H5Fclose(ifile);
+        leave (EXIT_FAILURE);
+    }
+
+    status = H5Pget_userblock (plist, &usize);
+    if (status < 0) {
+        error_msg("Can't get user block for file \"%s\"\n", input_file);
+        H5Pclose(plist);
+        H5Fclose(ifile);
+        leave (EXIT_FAILURE);
+    }
+
+    H5Pclose(plist);
+    H5Fclose(ifile);
+
+    ufid = HDopen(ub_file, O_RDONLY, 0);
+    if(ufid < 0) {
+        error_msg("unable to open user block file \"%s\"\n", ub_file);
+        leave (EXIT_FAILURE);
+    }
+
+    res = HDfstat(ufid, &sbuf);
+    if(res < 0) {
+        error_msg("Can't stat file \"%s\"\n", ub_file);
+        HDclose (ufid);
+        leave (EXIT_FAILURE);
+    }
+
+    fsize = (off_t)sbuf.st_size;
+
+    h5fid = HDopen(input_file, O_RDONLY, 0);
+    if(h5fid < 0) {
+        error_msg("unable to open HDF5 file for read \"%s\"\n", input_file);
+        HDclose (ufid);
+        leave (EXIT_FAILURE);
+    }
+
+    res = HDfstat(h5fid, &sbuf2);
+    if(res < 0) {
+        error_msg("Can't stat file \"%s\"\n", input_file);
+        HDclose (h5fid);
+        HDclose (ufid);
+        leave (EXIT_FAILURE);
+    }
+
+    h5fsize = (hsize_t)sbuf2.st_size;
+
+    if (output_file == NULL) {
+        ofid = HDopen (input_file, O_WRONLY, 0);
+
+        if (ofid < 0) {
+            error_msg("unable to open output file \"%s\"\n", output_file);
+            HDclose (h5fid);
+            HDclose (ufid);
+            leave (EXIT_FAILURE);
+        }
+    }
+    else {
+        ofid = HDopen (output_file, O_WRONLY | O_CREAT | O_TRUNC, 0644);
+
+        if (ofid < 0) {
+            error_msg("unable to create output file \"%s\"\n", output_file);
+            HDclose (h5fid);
+            HDclose (ufid);
+            leave (EXIT_FAILURE);
+        }
+    }
+
+    newubsize = compute_user_block_size ((hsize_t) fsize);
+
+    startub = usize;
+
+    if (usize > 0) {
+        if (do_clobber == TRUE) {
+            /* where is max of the current size or the new UB */
+            if (usize > newubsize) {
+                newubsize = usize;
+            }
+            startub = 0;    /*blast the old */
+        }
+        else {
+            /* add new ub to current ublock, pad to new offset */
+            newubsize += usize;
+            newubsize = compute_user_block_size ((hsize_t) newubsize);
+        }
+    }
+
+    /* copy the HDF5 from starting at usize to starting at newubsize:
+     *  makes room at 'from' for new ub */
+    /* if no current ub, usize is 0 */
+    copy_some_to_file (h5fid, ofid, usize, newubsize, (ssize_t) (h5fsize - usize));
+
+    /* copy the old ub to the beginning of the new file */
+    if (!do_clobber) {
+        where = copy_some_to_file (h5fid, ofid, (hsize_t) 0, (hsize_t) 0, (ssize_t) usize);
+    }
+
+    /* copy the new ub to the end of the ub */
+    where = copy_some_to_file (ufid, ofid, (hsize_t) 0, startub, (ssize_t) - 1);
+
+    /* pad the ub */
+    if(write_pad(ofid, where, &where) < 0) {
+        error_msg("Can't pad file \"%s\"\n", output_file);
+        HDclose (h5fid);
+        HDclose (ufid);
+        HDclose (ofid);
+        leave (EXIT_FAILURE);
+    } /* end if */
+
+    if(ub_file)
+        HDfree (ub_file);
+    if(input_file)
+        HDfree (input_file);
+    if(output_file)
+        HDfree (output_file);
+    
+    if(ufid >= 0)
+        HDclose (ufid);
+    if(h5fid >= 0)
+        HDclose (h5fid);
+    if(ofid >= 0)
+        HDclose (ofid);
+
+    return h5tools_getstatus();
+}
+
+/*-------------------------------------------------------------------------
+ * Function:    copy_some_to_file
+ *
+ * Purpose:     Copy part of the input file to output.
+ *      infid: fd of file to read
+ *      outfid: fd of file to write
+ *      startin: offset of where to read from infid
+ *      startout: offset of where to write to outfid
+ *      limit: bytes to read/write
+ *
+ *    If limit is < 0, the entire input file is copied.
+ *
+ *    Note: this routine can be used to copy within
+ *    the same file, i.e., infid and outfid can be the
+ *    same file.
+ *
+ * Return:      Success:    last byte written in the output.
+ *              Failure:    Exits program with EXIT_FAILURE value.
+ *
+ *-------------------------------------------------------------------------
+ */
+hsize_t
+copy_some_to_file(int infid, int outfid, hsize_t startin, hsize_t startout,
+       ssize_t limit)
+{
+    char buf[1024];
+    h5_stat_t sbuf;
+    int res;
+    ssize_t tot = 0;
+    ssize_t howmuch = 0;
+    ssize_t nchars = -1;
+    ssize_t to;
+    ssize_t from;
+    ssize_t toend;
+    ssize_t fromend;
+
+    if(startin > startout) {
+        /* this case is prohibited */
+        error_msg("copy_some_to_file: panic: startin > startout?\n");
+        exit (EXIT_FAILURE);
+    } /* end if */
+
+    if(limit < 0) {
+        res = HDfstat(infid, &sbuf);
+        if(res < 0) {
+            error_msg("Can't stat file \n");
+            HDexit(EXIT_FAILURE);
+        } /* end if */
+
+        howmuch = (ssize_t)sbuf.st_size;
+    } else {
+        howmuch = limit;
+    } /* end if */
+
+    if(0 == howmuch)
+        return 0;
+
+    toend = (ssize_t) startout + howmuch;
+    fromend = (ssize_t) startin + howmuch;
+
+    if (howmuch > 512) {
+        to = toend - 512;
+        from = fromend - 512;
+    } else {
+        to = toend - howmuch;
+        from = fromend - howmuch;
+    } /* end if */
+
+    while (howmuch > 0) {
+        HDlseek(outfid, (off_t) to, SEEK_SET);
+        HDlseek(infid, (off_t) from, SEEK_SET);
+
+        if (howmuch > 512) {
+            nchars = HDread(infid, buf, (unsigned) 512);
+        } else {
+            nchars = HDread(infid, buf, (unsigned)howmuch);
+        } /* end if */
+
+        if (nchars <= 0) {
+            error_msg("Read error \n");
+            HDexit(EXIT_FAILURE);
+        } /* end if */
+
+        if(HDwrite (outfid, buf, (unsigned) nchars) < 0) {
+            error_msg("Write error \n");
+            HDexit(EXIT_FAILURE);
+        }
+
+        tot += nchars;
+        howmuch -= nchars;
+        if(howmuch > 512) {
+            to -= nchars;
+            from -= nchars;
+        } else {
+            to -= howmuch;
+            from -= howmuch;
+        } /* end if */
+    } /* end while */
+
+    return (hsize_t)tot + (hsize_t)startout;
+} /* end copy_some_to_file() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:    compute_user_block_size
+ *
+ * Purpose:     Find the offset of the HDF5 header after the user block:
+ *                 align at 0, 512, 1024, etc.
+ *      ublock_size: the size of the user block (bytes).
+ *
+ * Return:      Success:    the location of the header == the size of the
+ *        padded user block.
+ *              Failure:    none
+ *
+ * Return:      Success:    last byte written in the output.
+ *              Failure:    Exits program with EXIT_FAILURE value.
+ *-------------------------------------------------------------------------
+ */
+H5_ATTR_CONST hsize_t
+compute_user_block_size(hsize_t ublock_size)
+{
+    hsize_t where = 512;
+
+    if(0 == ublock_size)
+        return 0;
+
+    while(where < ublock_size)
+        where *= 2;
+
+    return where;
+} /* end compute_user_block_size() */
+
+/*
+ *  Write zeroes to fill the file from 'where' to 512, 1024, etc. bytes.
+ *
+ *  Sets new_where to the size of the padded file and
+ *  returns SUCCEED/FAIL.
+ */
+herr_t
+write_pad(int ofile, hsize_t old_where, hsize_t *new_where)
+{
+    unsigned int i;
+    char buf[1];
+    hsize_t psize;
+
+    HDassert(new_where);
+
+    buf[0] = '\0';
+
+    HDlseek(ofile, (off_t)old_where, SEEK_SET);
+
+    psize = compute_user_block_size(old_where);
+    psize -= old_where;
+
+    for(i = 0; i < psize; i++)
+        if(HDwrite(ofile, buf, 1) < 0)
+            return FAIL;
+
+    /* Set the new size of the file. */
+    *new_where = old_where + psize;
+
+    return SUCCEED;
+} /* end write_pad() */
+
diff --git a/tools/src/h5jam/h5unjam.c b/tools/src/h5jam/h5unjam.c
new file mode 100644
index 0000000..8f88398
--- /dev/null
+++ b/tools/src/h5jam/h5unjam.c
@@ -0,0 +1,411 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * 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://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
+ * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+#include "hdf5.h"
+#include "H5private.h"
+#include "h5tools.h"
+#include "h5tools_utils.h"
+
+/* Name of tool */
+#define PROGRAMNAME "h5unjam"
+
+#define COPY_BUF_SIZE 1024
+
+hsize_t write_pad( int , hsize_t );
+hsize_t compute_pad( hsize_t );
+herr_t copy_to_file( FILE *, FILE * , ssize_t, ssize_t );
+
+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: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'},
+    { NULL, 0, '\0' }
+};
+
+/*-------------------------------------------------------------------------
+ * Function:    usage
+ *
+ * Purpose:     Print the usage message
+ *
+ * Return:      void
+ *
+ * Programmer:
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+usage(const char *prog)
+{
+    HDfflush(stdout);
+    HDfprintf(stdout,
+    "usage: %s -i <in_file.h5>  [-o <out_file.h5> ] [-u <out_user_file> | --delete]\n", prog);
+    HDfprintf(stdout, "\n");
+    HDfprintf(stdout,
+    "Splits user file and HDF5 file into two files: user block data and HDF5 data.\n");
+    HDfprintf(stdout, "\n");
+    HDfprintf(stdout,
+    "OPTIONS\n");
+    HDfprintf(stdout,
+    "  -i in_file.h5   Specifies the HDF5 as input.  If the input HDF5 file\n");
+    HDfprintf(stdout,
+    "                  contains no user block, exit with an error message.\n");
+    HDfprintf(stdout,
+    "  -o out_file.h5  Specifies output HDF5 file without a user block.\n");
+    HDfprintf(stdout,
+    "                  If not specified, the user block will be removed from the\n");
+    HDfprintf(stdout,
+    "                  input HDF5 file.\n");
+    HDfprintf(stdout,
+    "  -u out_user_file\n");
+    HDfprintf(stdout,
+    "                  Specifies the output file containing the data from the\n");
+    HDfprintf(stdout,
+    "                  user block.\n");
+    HDfprintf(stdout,
+    "                  Cannot be used with --delete option.\n");
+    HDfprintf(stdout,
+    "  --delete        Remove the user block from the input HDF5 file. The content\n");
+    HDfprintf(stdout,
+    "                  of the user block is discarded.\n");
+    HDfprintf(stdout,
+    "                  Cannot be used with the -u option.\n");
+    HDfprintf(stdout, "\n");
+    HDfprintf(stdout,
+    "  -h              Prints a usage message and exits.\n");
+    HDfprintf(stdout,
+    "  -V              Prints the HDF5 library version and exits.\n");
+    HDfprintf(stdout, "\n");
+    HDfprintf(stdout,
+    "  If neither --delete nor -u is specified, the user block from the input file\n");
+    HDfprintf(stdout,
+    "  will be displayed to stdout.\n");
+    HDfprintf(stdout, "\n");
+    HDfprintf(stdout,
+    "Exit Status:\n");
+    HDfprintf(stdout,
+    "  0      Succeeded.\n");
+    HDfprintf(stdout,
+    "  >0    An error occurred.\n");
+}
+
+/*-------------------------------------------------------------------------
+ * Function:    parse_command_line
+ *
+ * Purpose:     Parse the command line for the h5dumper.
+ *
+ * Return:      Success:    EXIT_SUCCESS;
+ *
+ *              Failure:    Exits function with EXIT_FAILURE value.
+ *
+ *-------------------------------------------------------------------------
+ */
+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);
+				if (output_file)
+				    h5tools_set_data_output_file(output_file, 1);
+	            break;
+
+            case 'i':
+                input_file = HDstrdup(opt_arg);
+				if (input_file)
+   				    h5tools_set_input_file(input_file, 1);
+	            break;;
+
+            case 'u':
+                ub_file = HDstrdup(opt_arg);
+				if (ub_file)
+				    h5tools_set_output_file(ub_file, 1);
+				else 
+				    rawoutstream = stdout;			
+                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;
+        }
+    }
+
+    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;
+}
+
+/*-------------------------------------------------------------------------
+ * Function:    main
+ *
+ * Purpose:     HDF5 user block unjammer
+ *
+ * Return:      Success:    0
+ *              Failure:    1
+ *
+ * Programmer:
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+main(int argc, const char *argv[])
+{
+    void               *edata;
+    H5E_auto2_t         func;
+    hid_t               ifile = -1;
+    hid_t               plist = -1;
+    off_t               fsize;
+    hsize_t             usize;
+    htri_t              testval;
+    herr_t              status;
+    int                 res;
+    h5_stat_t           sbuf;
+
+    h5tools_setprogname(PROGRAMNAME);
+    h5tools_setstatus(EXIT_SUCCESS);
+
+    /* Disable error reporting  */
+    H5Eget_auto2(H5E_DEFAULT, &func, &edata);
+    H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
+
+    /* Initialize h5tools lib  */
+    h5tools_init();
+
+    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);
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
+    }
+  
+    testval = H5Fis_hdf5(input_file);
+
+    if (testval <= 0) {
+        error_msg("Input HDF5 file \"%s\" is not HDF\n", input_file);
+        help_ref_msg (stderr);
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
+    }
+
+    ifile = H5Fopen(input_file, H5F_ACC_RDONLY , H5P_DEFAULT);
+
+    if (ifile < 0) {
+        error_msg("Can't open input HDF5 file \"%s\"\n", input_file);
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
+    }
+
+    plist = H5Fget_create_plist(ifile);
+    if (plist < 0) {
+        error_msg("Can't get file creation plist for file \"%s\"\n", input_file);
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
+    }
+
+    status = H5Pget_userblock(plist, & usize);
+    if (status < 0) {
+        error_msg("Can't get user block for file \"%s\"\n", input_file);
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
+    }
+
+    status = H5Pclose(plist);
+    HDassert(status >= 0);
+    status = H5Fclose(ifile);
+    HDassert(status >= 0);
+
+    if (usize == 0) {
+  /* no user block to remove: message? */
+        error_msg("\"%s\" has no user block: no change to file\n", input_file);
+        h5tools_setstatus(EXIT_SUCCESS);
+        goto done;
+    }
+
+    res = HDfstat(HDfileno(rawinstream), &sbuf);
+    if(res < 0) {
+        error_msg("Can't stat file \"%s\"\n", input_file);
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
+    }
+
+    fsize = sbuf.st_size;
+
+    if (do_delete && (ub_file != NULL)) {
+        error_msg("??\"%s\"\n", ub_file);
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
+    }
+
+    if (output_file == NULL) {
+            error_msg("unable to open output HDF5 file \"%s\"\n", input_file);
+            h5tools_setstatus(EXIT_FAILURE);
+            goto done;
+    } 
+
+    /* copy from 0 to 'usize - 1' into ufid  */
+    if (!do_delete) {
+        if(copy_to_file(rawinstream, rawoutstream, 0, (ssize_t) usize) < 0) {
+            error_msg("unable to copy user block to output file \"%s\"\n", ub_file);
+            h5tools_setstatus(EXIT_FAILURE);
+            goto done;
+        }
+    }
+
+    /* copy from usize to end of file into h5fid,
+     * starting at end of user block if present */
+   if(copy_to_file(rawinstream, rawdatastream, (ssize_t) usize, (ssize_t)(fsize - (ssize_t)usize)) < 0) {
+        error_msg("unable to copy hdf5 data to output file \"%s\"\n", output_file);
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
+    }
+ 
+done:
+    if(input_file)
+        HDfree(input_file);
+		
+    if(output_file)
+        HDfree(output_file);
+		
+    if(ub_file) {
+        HDfree(ub_file);
+    }
+	   
+    h5tools_close();
+
+    return h5tools_getstatus();
+}
+
+/*
+ *  Copy 'how_much' bytes from the input file to the output file,
+ *  starting at byte 'where' in the input file.
+ *
+ *  Returns 0 on success, -1 on failure.
+ */
+herr_t
+copy_to_file( FILE *infid, FILE *ofid, ssize_t _where, ssize_t show_much )
+{
+    static char buf[COPY_BUF_SIZE];
+    size_t how_much;
+    off_t where = (off_t)_where;
+    off_t to;
+    off_t from;
+    herr_t ret_value = 0;
+
+    /* nothing to copy */
+    if(show_much <= 0)
+        goto done;
+    how_much = (size_t)show_much;
+
+    /* rewind */
+    HDfseek(infid, 0L, 0);
+
+    from = where;
+    to = 0;
+    while(how_much > 0) {
+        size_t bytes_in        = 0;    /* # of bytes to read       */
+        size_t bytes_read      = 0;    /* # of bytes actually read */
+        size_t bytes_wrote     = 0;    /* # of bytes written   */
+
+        if (how_much > COPY_BUF_SIZE)
+            bytes_in = COPY_BUF_SIZE;
+        else
+            bytes_in = how_much;
+
+			/* Seek to correct position in input file */
+        HDfseek(infid, from, SEEK_SET);
+
+        /* Read data to buffer */
+        bytes_read = HDfread(buf, (size_t)1, bytes_in, infid);
+        if(0 == bytes_read && HDferror(infid)) {
+            ret_value = -1;
+            goto done;
+        } /* end if */
+        if(0 == bytes_read && HDfeof(infid)) {
+            goto done;
+        } /* end if */
+
+        /* Seek to correct position in output file */
+        HDfseek(ofid, to, SEEK_SET);
+
+        /* Update positions/size */
+        how_much -= bytes_read;
+        from += (off_t)bytes_read;
+        to += (off_t)bytes_read;
+
+       /* Write nchars bytes to output file */
+		bytes_wrote = HDfwrite(buf, (size_t)1, bytes_read, ofid);
+		if(bytes_wrote != bytes_read || (0 == bytes_wrote && HDferror(ofid))) { /* error */
+			ret_value = -1;
+			goto done;
+		} /* end if */
+    } /* end while */
+
+done:
+    return ret_value;
+}  /* end copy_to_file */
+