path: root/tools/h5copy/h5copy.c

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * 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 COPYING file, which can be found at the root of the source code       *
 * distribution tree, or in https://www.hdfgroup.org/licenses.               *
 * If you do not have access to either file, you may request a copy from     *
 * help@hdfgroup.org.                                                        *
 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

#include "H5private.h"
#include "h5tools.h"
#include "h5tools_utils.h"

/* Name of tool */
#define PROGRAMNAME "h5copy"

/* command-line options: short and long-named parameters */
static const char *        s_opts    = "d:f:hi:o:ps:vVE*";
static struct long_options l_opts[]  = {{"destination", require_arg, 'd'},
                                       {"flag", require_arg, 'f'},
                                       {"help", no_arg, 'h'},
                                       {"input", require_arg, 'i'},
                                       {"output", require_arg, 'o'},
                                       {"parents", no_arg, 'p'},
                                       {"source", require_arg, 's'},
                                       {"verbose", no_arg, 'v'},
                                       {"version", no_arg, 'V'},
                                       {"enable-error-stack", optional_arg, 'E'},
                                       {NULL, 0, '\0'}};
char *                     fname_src = NULL;
char *                     fname_dst = NULL;
char *                     oname_src = NULL;
char *                     oname_dst = NULL;
char *                     str_flag  = NULL;

/*-------------------------------------------------------------------------
 * Function:    leave
 *
 * Purpose:     Shutdown MPI & HDF5 and call exit()
 *
 * Return:      Does not return
 *
 * Programmer:  Quincey Koziol
 *              Saturday, 31. January 2004
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
static void
leave(int ret)
{
    if (fname_src)
        HDfree(fname_src);
    if (fname_dst)
        HDfree(fname_dst);
    if (oname_dst)
        HDfree(oname_dst);
    if (oname_src)
        HDfree(oname_src);
    if (str_flag)
        HDfree(str_flag);

    h5tools_close();
    HDexit(ret);
}

/*-------------------------------------------------------------------------
 * Function: usage
 *
 * Purpose: Prints a usage message on stderr and then returns.
 *
 * Return: void
 *
 * Programmer: Pedro Vicente Nunes, 7/8/2006
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
static void
usage(void)
{
    FLUSHSTREAM(rawoutstream);
    PRINTVALSTREAM(rawoutstream, "\n");
    PRINTVALSTREAM(rawoutstream, "usage: h5copy [OPTIONS] [OBJECTS...]\n");
    PRINTVALSTREAM(rawoutstream, "   OBJECTS\n");
    PRINTVALSTREAM(rawoutstream, "      -i, --input        input file name\n");
    PRINTVALSTREAM(rawoutstream, "      -o, --output       output file name\n");
    PRINTVALSTREAM(rawoutstream, "      -s, --source       source object name\n");
    PRINTVALSTREAM(rawoutstream, "      -d, --destination  destination object name\n");
    PRINTVALSTREAM(rawoutstream, "   ERROR\n");
    PRINTVALSTREAM(rawoutstream,
                   "     --enable-error-stack Prints messages from the HDF5 error stack as they occur.\n");
    PRINTVALSTREAM(rawoutstream,
                   "                          Optional value 2 also prints file open errors.\n");
    PRINTVALSTREAM(rawoutstream, "   OPTIONS\n");
    PRINTVALSTREAM(rawoutstream, "      -h, --help         Print a usage message and exit\n");
    PRINTVALSTREAM(rawoutstream,
                   "      -p, --parents      No error if existing, make parent groups as needed\n");
    PRINTVALSTREAM(rawoutstream, "      -v, --verbose      Print information about OBJECTS and OPTIONS\n");
    PRINTVALSTREAM(rawoutstream, "      -V, --version      Print version number and exit\n");
    PRINTVALSTREAM(rawoutstream, "      -f, --flag         Flag type\n\n");
    PRINTVALSTREAM(rawoutstream, "      Flag type is one of the following strings:\n\n");
    PRINTVALSTREAM(rawoutstream, "      shallow     Copy only immediate members for groups\n\n");
    PRINTVALSTREAM(rawoutstream, "      soft        Expand soft links into new objects\n\n");
    PRINTVALSTREAM(rawoutstream, "      ext         Expand external links into new objects\n\n");
    PRINTVALSTREAM(rawoutstream,
                   "      ref         Copy references and any referenced objects, i.e., objects\n");
    PRINTVALSTREAM(rawoutstream, "                  that the references point to.\n");
    PRINTVALSTREAM(rawoutstream,
                   "                    Referenced objects are copied in addition to the objects\n");
    PRINTVALSTREAM(rawoutstream,
                   "                  specified on the command line and reference datasets are\n");
    PRINTVALSTREAM(rawoutstream,
                   "                  populated with correct reference values. Copies of referenced\n");
    PRINTVALSTREAM(rawoutstream,
                   "                  datasets outside the copy range specified on the command line\n");
    PRINTVALSTREAM(rawoutstream,
                   "                  will normally have a different name from the original.\n");
    PRINTVALSTREAM(rawoutstream,
                   "                    (Default:Without this option, reference value(s) in any\n");
    PRINTVALSTREAM(rawoutstream,
                   "                  reference datasets are set to NULL and referenced objects are\n");
    PRINTVALSTREAM(rawoutstream,
                   "                  not copied unless they are otherwise within the copy range\n");
    PRINTVALSTREAM(rawoutstream, "                  specified on the command line.)\n\n");
    PRINTVALSTREAM(rawoutstream, "      noattr      Copy object without copying attributes\n\n");
    PRINTVALSTREAM(rawoutstream,
                   "      allflags    Switches all flags from the default to the non-default setting\n\n");
    PRINTVALSTREAM(rawoutstream, "      These flag types correspond to the following API symbols\n\n");
    PRINTVALSTREAM(rawoutstream, "      H5O_COPY_SHALLOW_HIERARCHY_FLAG\n");
    PRINTVALSTREAM(rawoutstream, "      H5O_COPY_EXPAND_SOFT_LINK_FLAG\n");
    PRINTVALSTREAM(rawoutstream, "      H5O_COPY_EXPAND_EXT_LINK_FLAG\n");
    PRINTVALSTREAM(rawoutstream, "      H5O_COPY_EXPAND_REFERENCE_FLAG\n");
    PRINTVALSTREAM(rawoutstream, "      H5O_COPY_WITHOUT_ATTR_FLAG\n");
    PRINTVALSTREAM(rawoutstream, "      H5O_COPY_ALL\n");
}

/*-------------------------------------------------------------------------
 * Function: parse_flag
 *
 * Purpose: read the flag -f STRING
 *
 * STRING is one of the following (API symbol and description)
 *
 * shallow  H5O_COPY_SHALLOW_HIERARCHY_FLAG:  Copy only immediate members for groups
 * soft     H5O_COPY_EXPAND_SOFT_LINK_FLAG:  Expand soft links into new objects
 * ext      H5O_COPY_EXPAND_EXT_LINK_FLAG: Expand external links into new objects
 * ref      H5O_COPY_EXPAND_OBJ_REFERENCE_FLAG: Copy objects that are pointed by references
 * noattr   H5O_COPY_WITHOUT_ATTR_FLAG Copy object without copying attributes
 * allflags Switches all flags from the default to the non-default setting
 *
 * Return: Success:    SUCCEED
 *         Failure:    FAIL
 *
 * Programmer: Pedro Vicente Nunes, 7/8/2006
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */

static int
parse_flag(const char *s_flag, unsigned *flag)
{
    unsigned fla = 0;

    if (HDstrcmp(s_flag, "shallow") == 0) {
        fla = H5O_COPY_SHALLOW_HIERARCHY_FLAG;
    }
    else if (HDstrcmp(s_flag, "soft") == 0) {
        fla = H5O_COPY_EXPAND_SOFT_LINK_FLAG;
    }
    else if (HDstrcmp(s_flag, "ext") == 0) {
        fla = H5O_COPY_EXPAND_EXT_LINK_FLAG;
    }
    else if (HDstrcmp(s_flag, "ref") == 0) {
        fla = H5O_COPY_EXPAND_REFERENCE_FLAG;
    }
    else if (HDstrcmp(s_flag, "noattr") == 0) {
        fla = H5O_COPY_WITHOUT_ATTR_FLAG;
    }
    else if (HDstrcmp(s_flag, "allflags") == 0) {
        fla = H5O_COPY_ALL;
    }
    else if (HDstrcmp(s_flag, "nullmsg") == 0) {
        fla = H5O_COPY_PRESERVE_NULL_FLAG;
    }
    else {
        error_msg("Error in input flag\n");
        return -1;
    }

    *flag = (*flag) | fla;

    return 0;
}

/*-------------------------------------------------------------------------
 * Function: main
 *
 * Purpose: main program
 *
 * Programmer: Pedro Vicente Nunes
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */

int
main(int argc, char *argv[])
{
    hid_t              fid_src = H5I_INVALID_HID;
    hid_t              fid_dst = H5I_INVALID_HID;
    unsigned           flag    = 0;
    unsigned           verbose = 0;
    unsigned           parents = 0;
    hid_t              ocpl_id = H5I_INVALID_HID; /* Object copy property list */
    hid_t              lcpl_id = H5I_INVALID_HID; /* Link creation property list */
    int                opt;
    int                li_ret;
    h5tool_link_info_t linkinfo;
    int                ret_value = 0;

    h5tools_setprogname(PROGRAMNAME);
    h5tools_setstatus(EXIT_SUCCESS);

    /* Initialize h5tools lib */
    h5tools_init();

    /* init linkinfo struct */
    HDmemset(&linkinfo, 0, sizeof(h5tool_link_info_t));

    /* Check for no command line parameters */
    if (argc == 1) {
        usage();
        leave(EXIT_FAILURE);
    } /* end if */

    /* parse command line options */
    while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
        switch ((char)opt) {
            case 'd':
                oname_dst = HDstrdup(opt_arg);
                break;

            case 'f':
                /* validate flag */
                if (parse_flag(opt_arg, &flag) < 0) {
                    usage();
                    leave(EXIT_FAILURE);
                }
                str_flag = HDstrdup(opt_arg);
                break;

            case 'h':
                usage();
                leave(EXIT_SUCCESS);
                break;

            case 'i':
                fname_src = HDstrdup(opt_arg);
                break;

            case 'o':
                fname_dst = HDstrdup(opt_arg);
                break;

            case 'p':
                parents = 1;
                break;

            case 's':
                oname_src = HDstrdup(opt_arg);
                break;

            case 'V':
                print_version(h5tools_getprogname());
                leave(EXIT_SUCCESS);
                break;

            case 'v':
                verbose = 1;
                break;

            case 'E':
                if (opt_arg != NULL)
                    enable_error_stack = HDatoi(opt_arg);
                else
                    enable_error_stack = 1;
                break;

            default:
                usage();
                leave(EXIT_FAILURE);
        }
    } /* end of while */

    /*-------------------------------------------------------------------------
     * check for missing file/object names
     *-------------------------------------------------------------------------*/

    if (fname_src == NULL) {
        error_msg("Input file name missing\n");
        usage();
        leave(EXIT_FAILURE);
    }

    if (fname_dst == NULL) {
        error_msg("Output file name missing\n");
        usage();
        leave(EXIT_FAILURE);
    }

    if (oname_src == NULL) {
        error_msg("Source object name missing\n");
        usage();
        leave(EXIT_FAILURE);
    }

    if (oname_dst == NULL) {
        error_msg("Destination object name missing\n");
        usage();
        leave(EXIT_FAILURE);
    }

    /* enable error reporting if command line option */
    h5tools_error_report();

    /*-------------------------------------------------------------------------
     * open output file
     *-------------------------------------------------------------------------*/

    /* Attempt to open an existing HDF5 file first. Need to open the dst file
       before the src file just in case that the dst and src are the same file
     */
    fid_dst = h5tools_fopen(fname_dst, H5F_ACC_RDWR, H5P_DEFAULT, FALSE, NULL, 0);

    /*-------------------------------------------------------------------------
     * open input file
     *-------------------------------------------------------------------------*/

    fid_src = h5tools_fopen(fname_src, H5F_ACC_RDONLY, H5P_DEFAULT, FALSE, NULL, 0);

    /*-------------------------------------------------------------------------
     * test for error in opening input file
     *-------------------------------------------------------------------------*/
    if (fid_src == -1) {
        error_msg("Could not open input file <%s>...Exiting\n", fname_src);
        leave(EXIT_FAILURE);
    }

    /*-------------------------------------------------------------------------
     * create an output file when failed to open it
     *-------------------------------------------------------------------------*/

    /* If we couldn't open an existing file, try creating file */
    /* (use "EXCL" instead of "TRUNC", so we don't blow away existing non-HDF5 file) */
    if (fid_dst < 0)
        fid_dst = H5Fcreate(fname_dst, H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);

    /*-------------------------------------------------------------------------
     * test for error in opening output file
     *-------------------------------------------------------------------------*/
    if (fid_dst == -1) {
        error_msg("Could not open output file <%s>...Exiting\n", fname_dst);
        leave(EXIT_FAILURE);
    }

    /*-------------------------------------------------------------------------
     * print some info
     *-------------------------------------------------------------------------*/

    if (verbose) {
        HDprintf("Copying file <%s> and object <%s> to file <%s> and object <%s>\n", fname_src, oname_src,
                 fname_dst, oname_dst);
        if (flag) {
            HDprintf("Using %s flag\n", str_flag);
        }
    }

    /*-------------------------------------------------------------------------
     * create property lists for copy
     *-------------------------------------------------------------------------*/

    /* create property to pass copy options */
    if ((ocpl_id = H5Pcreate(H5P_OBJECT_COPY)) < 0)
        H5TOOLS_GOTO_ERROR(EXIT_FAILURE, "H5Pcreate failed");

    /* set options for object copy */
    if (flag) {
        if (H5Pset_copy_object(ocpl_id, flag) < 0)
            H5TOOLS_GOTO_ERROR(EXIT_FAILURE, "H5Pset_copy_object failed");
    }

    /* Create link creation property list */
    if ((lcpl_id = H5Pcreate(H5P_LINK_CREATE)) < 0) {
        error_msg("Could not create link creation property list\n");
        H5TOOLS_GOTO_ERROR(EXIT_FAILURE, "H5Pcreate failed");
    } /* end if */

    /* Check for creating intermediate groups */
    if (parents) {
        /* Set the intermediate group creation property */
        if (H5Pset_create_intermediate_group(lcpl_id, 1) < 0) {
            error_msg("Could not set property for creating parent groups\n");
            H5TOOLS_GOTO_ERROR(EXIT_FAILURE, "H5Pset_create_intermediate_group failed");
        } /* end if */

        /* Display some output if requested */
        if (verbose)
            HDprintf("%s: Creating parent groups\n", h5tools_getprogname());
    } /* end if */
    else {
        /* error, if parent groups doesn't already exist in destination file */
        size_t i, len;

        len = HDstrlen(oname_dst);

        /* check if all the parents groups exist. skip root group */
        for (i = 1; i < len; i++) {
            if ('/' == oname_dst[i]) {
                char *str_ptr;

                str_ptr = (char *)HDcalloc(i + 1, sizeof(char));
                HDstrncpy(str_ptr, oname_dst, i);
                str_ptr[i] = '\0';
                if (H5Lexists(fid_dst, str_ptr, H5P_DEFAULT) <= 0) {
                    error_msg("group <%s> doesn't exist. Use -p to create parent groups.\n", str_ptr);
                    HDfree(str_ptr);
                    H5TOOLS_GOTO_ERROR(EXIT_FAILURE, "H5Lexists failed");
                }
                HDfree(str_ptr);
            }
        }
    }

    /*-------------------------------------------------------------------------
     * do the copy
     *-------------------------------------------------------------------------*/

    if (verbose)
        linkinfo.opt.msg_mode = 1;

    li_ret = H5tools_get_symlink_info(fid_src, oname_src, &linkinfo, 1);
    if (li_ret == 0) {
        /* dangling link */
        if (H5Lcopy(fid_src, oname_src, fid_dst, oname_dst, H5P_DEFAULT, H5P_DEFAULT) < 0)
            H5TOOLS_GOTO_ERROR(EXIT_FAILURE, "H5Lcopy failed");
    }
    else {
        /* valid link */
        if (H5Ocopy(fid_src,      /* Source file or group identifier */
                    oname_src,    /* Name of the source object to be copied */
                    fid_dst,      /* Destination file or group identifier  */
                    oname_dst,    /* Name of the destination object  */
                    ocpl_id,      /* Object copy property list */
                    lcpl_id) < 0) /* Link creation property list */
            H5TOOLS_GOTO_ERROR(EXIT_FAILURE, "H5Ocopy failed");
    }

    /* free link info path */
    if (linkinfo.trg_path)
        HDfree(linkinfo.trg_path);

    /* close propertis */
    if (H5Pclose(ocpl_id) < 0)
        H5TOOLS_GOTO_ERROR(EXIT_FAILURE, "H5Pclose failed");
    if (H5Pclose(lcpl_id) < 0)
        H5TOOLS_GOTO_ERROR(EXIT_FAILURE, "H5Pclose failed");

    /* close files */
    if (H5Fclose(fid_src) < 0)
        H5TOOLS_GOTO_ERROR(EXIT_FAILURE, "H5Fclose failed");
    if (H5Fclose(fid_dst) < 0)
        H5TOOLS_GOTO_ERROR(EXIT_FAILURE, "H5Fclose failed");

    leave(EXIT_SUCCESS);

done:
    HDprintf("Error in copy...Exiting\n");

    /* free link info path */
    if (linkinfo.trg_path)
        HDfree(linkinfo.trg_path);

    H5E_BEGIN_TRY
    {
        H5Pclose(ocpl_id);
        H5Pclose(lcpl_id);
        H5Fclose(fid_src);
        H5Fclose(fid_dst);
    }
    H5E_END_TRY;

    leave(ret_value);
}