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-rw-r--r--tools/src/h5jam/CMakeLists.txt49
-rw-r--r--tools/src/h5jam/Makefile.am35
-rw-r--r--tools/src/h5jam/h5jam.c571
-rw-r--r--tools/src/h5jam/h5unjam.c411
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 */
+