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Diffstat (limited to 'tools/src/h5copy/h5copy.c')
| -rw-r--r-- | tools/src/h5copy/h5copy.c | 502 |
1 files changed, 502 insertions, 0 deletions
diff --git a/tools/src/h5copy/h5copy.c b/tools/src/h5copy/h5copy.c new file mode 100644 index 0000000..3f8f8cf --- /dev/null +++ b/tools/src/h5copy/h5copy.c @@ -0,0 +1,502 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * 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 h5_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 = H5_get_option(argc, (const char *const *)argv, s_opts, l_opts)) != EOF) { + switch ((char)opt) { + case 'd': + oname_dst = HDstrdup(H5_optarg); + break; + + case 'f': + /* validate flag */ + if (parse_flag(H5_optarg, &flag) < 0) { + usage(); + leave(EXIT_FAILURE); + } + str_flag = HDstrdup(H5_optarg); + break; + + case 'h': + usage(); + leave(EXIT_SUCCESS); + break; + + case 'i': + fname_src = HDstrdup(H5_optarg); + break; + + case 'o': + fname_dst = HDstrdup(H5_optarg); + break; + + case 'p': + parents = 1; + break; + + case 's': + oname_src = HDstrdup(H5_optarg); + break; + + case 'V': + print_version(h5tools_getprogname()); + leave(EXIT_SUCCESS); + break; + + case 'v': + verbose = 1; + break; + + case 'E': + if (H5_optarg != NULL) + enable_error_stack = HDatoi(H5_optarg); + 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); +} |