[svn-r12482] new tool h5copy

it uses the API function H5Gcopy to copy groups and datasets from file
to file, read from a command line

note: the test script is not finished yet
tested on heping, copper, shanti

1 files changed, 355 insertions, 0 deletions

diff --git a/tools/h5copy/h5copy.c b/tools/h5copy/h5copy.c
new file mode 100644
index 0000000..604eb03
--- /dev/null
+++ b/tools/h5copy/h5copy.c
@@ -0,0 +1,355 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by the Board of Trustees of the University of Illinois.         *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the files COPYING and Copyright.html.  COPYING can be found at the root   *
+ * of the source code distribution tree; Copyright.html can be found at the  *
+ * root level of an installed copy of the electronic HDF5 document set and   *
+ * is linked from the top-level documents page.  It can also be found at     *
+ * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html.  If you do not have     *
+ * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+
+#include "hdf5.h"
+#include "h5tools.h"
+#include "H5private.h"
+#include <string.h>
+#include <stdlib.h>
+
+const char *progname="h5copy";
+int   d_status;
+
+/*-------------------------------------------------------------------------
+ * 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)
+{
+ fprintf(stderr, "\
+usage: h5copy [OPTIONS] [OBJECTS...]\n\
+   OBJECTS\n\
+      A pair of 2 HDF5 files (input and output). Each file name\n\
+      is optionally followed by a slash and an object\n\
+      name within the file (if no object is specified\n\
+      within the file then all objects are copied)\n\
+   OPTIONS\n\
+      -h               Print a usage message and exit\n\
+      -v               Print information about OBJECTS and OPTIONS\n\
+      -f               Flag type\n\n\
+      Flag type is one of the following strings:\n\n\
+      SHALLOW (Copy only immediate members for groups)\n\
+      SOFT (Expand soft links into new objects)\n\
+      EXT (Expand external links into new objects)\n\
+      REF (Copy objects that are pointed by references)\n\
+      ATTR (Copy object without copying attributes)\n\n\
+      These flag types correspond to the following API symbols\n\n\
+      H5G_COPY_SHALLOW_HIERARCHY_FLAG\n\
+      H5G_COPY_EXPAND_SOFT_LINK_FLAG\n\
+      H5G_COPY_EXPAND_EXT_LINK_FLAG\n\
+      H5G_COPY_EXPAND_OBJ_REFERENCE_FLAG\n\
+      H5G_COPY_WITHOUT_ATTR_FLAG\n");
+}
+
+
+
+/*-------------------------------------------------------------------------
+ * Function:	parse_flag
+ *
+ * Purpose:	read the flag -f STRING
+ *
+ * STRING is one of the following (API symbol and description)
+ *
+ * SHALLOW  H5G_COPY_SHALLOW_HIERARCHY_FLAG:  Copy only immediate members for groups
+ * SOFT     H5G_COPY_EXPAND_SOFT_LINK_FLAG:  Expand soft links into new objects
+ * EXT      H5G_COPY_EXPAND_EXT_LINK_FLAG: Expand external links into new objects
+ * REF      H5G_COPY_EXPAND_OBJ_REFERENCE_FLAG: Copy objects that are pointed by references
+ * ATTR     H5G_COPY_WITHOUT_ATTR_FLAG Copy object without copying attributes 
+ *
+ * Return:	Success:    SUCCEED
+ *		       Failure:    FAIL
+ *
+ * Programmer:	Pedro Vicente Nunes, 7/8/2006
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+
+
+static int parse_flag(const char* str_flag, unsigned *flag)
+{
+ unsigned fla=0;
+
+ if (strcmp(str_flag,"SHALLOW")==0)
+ {
+  fla = H5G_COPY_SHALLOW_HIERARCHY_FLAG;
+ } 
+ else  if (strcmp(str_flag,"SOFT")==0)
+ {
+  fla = H5G_COPY_EXPAND_SOFT_LINK_FLAG;
+ }
+ else  if (strcmp(str_flag,"EXT")==0)
+ {
+  fla = H5G_COPY_EXPAND_EXT_LINK_FLAG;
+ }
+ else  if (strcmp(str_flag,"REF")==0)
+ {
+  fla = H5G_COPY_EXPAND_OBJ_REFERENCE_FLAG;
+ }
+ else  if (strcmp(str_flag,"ATTR")==0)
+ {
+  fla = H5G_COPY_WITHOUT_ATTR_FLAG;
+ }
+ else
+ {
+  printf("Error in input flag\n");
+  return -1;
+ }
+
+ *flag = fla;
+
+ return 0;
+}
+
+
+
+
+/*-------------------------------------------------------------------------
+ * Function:	main
+ *
+ * Purpose:	main program
+ *
+ * Programmer:	Pedro Vicente Nunes
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int
+main (int argc, const char *argv[])
+{
+ hid_t        fid_src=-1;
+ hid_t        fid_dst=-1;
+ int          argno;
+ static char  root_name[] = "/";
+ char         *fname_src=NULL;
+ char         *fname_dst=NULL;
+ char         *oname_src=NULL;
+ char         *oname_dst=NULL;
+ char         *x;
+ unsigned     flag=0;
+ int          verbose=0;
+ hid_t        pid;	
+	char         str_flag[20];
+ 
+ /* switches come before non-switch arguments */
+ for (argno=1; argno<argc && '-'==argv[argno][0]; argno++) 
+ {
+  if (strcmp(argv[argno], "-h") == 0) 
+  {
+   usage();
+  }
+  else if (strcmp(argv[argno], "-v") == 0) 
+  {
+   verbose = 1;
+  }
+  else if (strcmp(argv[argno], "-f") == 0) 
+  {
+   /* parse flag */
+   if (parse_flag(argv[argno+1],&flag)<0)
+   {
+    usage();
+    exit(1);
+   }
+   strcpy(str_flag,argv[argno+1]);
+   
+   /* jump to next */
+   ++argno;
+  }
+ }
+
+
+ /* no more arguments remain */
+ if (argno>=argc) 
+ {
+  usage();
+  exit(1);
+ }
+
+/*-------------------------------------------------------------------------
+ * 
+ * each remaining argument is an hdf5 file name followed by an optional slash
+ * and object name.
+ *
+ * Example: test1.h5/bar/baz
+ *          \______/\______/
+ *            file     obj
+ *
+ * The dichotomy is determined by calling H5Fopen() repeatedly until it
+ * succeeds. The first call uses the entire name and each subsequent call
+ * chops off the last component. If we reach the beginning of the name
+ * then there must have been something wrong with the file (perhaps it
+ * doesn't exist). 
+ *
+ *-------------------------------------------------------------------------*/
+
+ fname_src = HDstrdup(argv[argno++]);
+
+ while (fname_src && *fname_src) 
+ {
+  fid_src = h5tools_fopen(fname_src, NULL, NULL, 0, argc, argv);
+  
+  if (fid_src>=0) 
+   break; /*success*/
+  
+  /* shorten the file name; lengthen the object name */
+  x = oname_src;
+  oname_src = strrchr(fname_src, '/');
+  if (x) 
+   *x = '/';
+  if (!oname_src) 
+   break;
+  *oname_src = '\0';
+ }
+ if (oname_src) 
+  oname_src++;
+ if (!oname_src || !*oname_src) 
+  oname_src = root_name;
+
+
+/*-------------------------------------------------------------------------
+ * last argument, same logic, but the file does not exist, so we attempt to
+ * create one instead
+ *-------------------------------------------------------------------------*/
+
+ fname_dst = HDstrdup(argv[argno]);
+
+ while (fname_dst && *fname_dst) 
+ {
+  H5E_BEGIN_TRY {
+   fid_dst = H5Fcreate(fname_dst, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+  } H5E_END_TRY;
+  
+  if (fid_dst>=0) 
+   break; /*success*/
+  
+  /* shorten the file name; lengthen the object name */
+  x = oname_dst;
+  oname_dst = strrchr(fname_dst, '/');
+  if (x) 
+   *x = '/';
+  if (!oname_dst) 
+   break;
+  *oname_dst = '\0';
+ }
+ if (oname_dst) 
+  oname_dst++;
+ if (!oname_dst || !*oname_dst) 
+  oname_dst = NULL;
+
+ 
+/*-------------------------------------------------------------------------
+ * check destination name
+ *-------------------------------------------------------------------------*/
+
+ if (oname_dst==NULL) 
+ {
+  printf("Destination object name missing\n");
+  usage();
+  goto error;
+ }
+
+ 
+/*-------------------------------------------------------------------------
+ * print some info
+ *-------------------------------------------------------------------------*/
+ 
+ if (verbose)
+ {
+  printf("Copying file <%s> and object <%s> to file <%s> and object <%s>\n",
+   fname_src,
+   oname_src,
+   fname_dst,
+   oname_dst);
+  if (flag)
+   printf("Using %s flag\n", str_flag);
+ }
+
+ 
+/*-------------------------------------------------------------------------
+ * create a property list for copy
+ *-------------------------------------------------------------------------*/
+ 
+ /* create property to pass copy options */
+ if ( (pid = H5Pcreate(H5P_OBJECT_COPY)) < 0) 
+  goto error;
+ 
+ /* set options for object copy */
+ if (flag)
+ {
+  if ( H5Pset_copy_object(pid, flag) < 0) 
+   goto error;
+ }
+
+
+/*-------------------------------------------------------------------------
+ * do the copy
+ *-------------------------------------------------------------------------*/
+
+  if (H5Gcopy(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  */
+              pid,            /* Properties which apply to the copy   */
+              H5P_DEFAULT)<0) /* Properties which apply to the new hard link */              
+              goto error;
+
+  
+ 
+ /* close property */
+ if (H5Pclose(pid)<0)
+  goto error;
+
+ if (fid_src>0)
+  H5Fclose(fid_src);
+ if (fid_dst>0)
+  H5Fclose(fid_dst);
+
+ if (fname_src)
+  free(fname_src);
+ if (fname_dst)
+  free(fname_dst);
+ 
+
+ return 0;
+
+error:
+ printf("Error in copy...Exiting\n");
+ H5E_BEGIN_TRY {
+  H5Pclose(pid);
+  H5Fclose(fid_src);
+  H5Fclose(fid_dst);
+  } H5E_END_TRY;
+ if (fname_src)
+  free(fname_src);
+ if (fname_dst)
+  free(fname_dst);
+ 
+ 
+ return 1;
+}
+