[svn-r13451]

h5diff bug fix, attributes differences were not being count for total
differences

Revision of H5Ocopy call in h5repack

4 files changed, 69 insertions, 852 deletions

diff --git a/tools/h5repack/h5repack.sh.in b/tools/h5repack/h5repack.sh.in
index 21cddde..4b00bc0 100755
--- a/tools/h5repack/h5repack.sh.in
+++ b/tools/h5repack/h5repack.sh.in
@@ -160,7 +160,7 @@ fi
 # copy files (these files have no filters) 
 TOOLTEST $FILE0
 TOOLTEST $FILE1
-#TOOLTEST $FILE2
+TOOLTEST $FILE2
 TOOLTEST $FILE3
 TOOLTEST $FILE4
 TOOLTEST $FILE5
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index 03faa55..e8d0f90 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -556,6 +556,10 @@ int do_copy_objects(hid_t fidin,
      /* create property to pass copy options */
      if ( (pid = H5Pcreate(H5P_OBJECT_COPY)) < 0) 
       goto error;
+
+     /* set options for object copy */
+     if(H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0) 
+      goto error;
      
      /*-------------------------------------------------------------------------
       * do the copy
@@ -573,6 +577,23 @@ int do_copy_objects(hid_t fidin,
      /* close property */
      if (H5Pclose(pid)<0)
       goto error;
+
+
+     /*-------------------------------------------------------------------------
+      * copy attrs manually
+      *-------------------------------------------------------------------------
+      */
+     if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0)
+         goto error;
+     if ((dset_out=H5Dopen(fidout,travt->objs[i].name))<0)
+         goto error;
+     if (copy_attr(dset_in,dset_out,options)<0)
+         goto error;
+     if (H5Dclose(dset_in)<0)
+         goto error;
+     if (H5Dclose(dset_out)<0)
+         goto error;
+
      
     } /* end do we have request for filter/chunking */
 
@@ -978,812 +999,3 @@ static void print_dataset_info(hid_t dcpl_id,
 
 
 
-
-#if 0
-
-
-
-/*-------------------------------------------------------------------------
- * Function: do_hardlinks
- *
- * Purpose: duplicate hard links
- *
- * Return: 0, ok, -1 no
- *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
- *
- * Date: December, 10, 2003
- *
- *-------------------------------------------------------------------------
- */
-
-static
-int do_hardlinks(hid_t fidout,trav_table_t *travt)
-{
- unsigned int i, j;
-
- for ( i = 0; i < travt->nobjs; i++)
- {
-  switch ( travt->objs[i].type )
-  {
-  case H5G_GROUP:
-
-   if (travt->objs[i].nlinks)
-   {
-    for ( j=0; j<travt->objs[i].nlinks; j++)
-    {
-      if (H5Glink(fidout,
-      H5L_TYPE_HARD,
-      travt->objs[i].name,
-      travt->objs[i].links[j].new_name)<0)
-      return -1;
-    }
-   }
-
-   break;
-
-  case H5G_DATASET:
-
-   if (travt->objs[i].nlinks)
-   {
-    for ( j=0; j<travt->objs[i].nlinks; j++){
-     if (H5Glink(fidout,
-      H5L_TYPE_HARD,
-      travt->objs[i].name,
-      travt->objs[i].links[j].new_name)<0)
-      return -1;
-    }
-   }
-
-   break;
-
-  case H5G_TYPE:
-  case H5G_LINK:
-  case H5G_UDLINK:
-
-   /*nothing to do */
-   break;
-
-  default:
-
-   break;
-  }
- }
-
- return 0;
-
-}
-
-
-/*-------------------------------------------------------------------------
- * Function: do_copy_refobjs
- *
- * Purpose: duplicate all referenced HDF5 objects in the file in a second traversal
- *
- * Return: 0, ok, -1 no
- *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
- *
- * Date: December, 10, 2003
- *
- *-------------------------------------------------------------------------
- */
-
-static
-int do_copy_refobjs(hid_t fidin,
-                    hid_t fidout,
-                    trav_table_t *travt,
-                    pack_opt_t *options) /* repack options */
-{
- hid_t     grp_in=-1;            /* read group ID */
- hid_t     grp_out=-1;           /* write group ID */
- hid_t     dset_in=-1;           /* read dataset ID */
- hid_t     dset_out=-1;          /* write dataset ID */
- hid_t     type_in=-1;           /* named type ID */
- hid_t     dcpl_id=-1;           /* dataset creation property list ID */
- hid_t     space_id=-1;          /* space ID */
- hid_t     ftype_id=-1;          /* file type ID */
- hid_t     wtype_id=-1;          /* read/write type ID */
- size_t    msize;             /* size of type */
- hsize_t   nelmts;            /* number of elements in dataset */
- int       rank;              /* rank of dataset */
- hsize_t   dims[H5S_MAX_RANK];/* dimensions of dataset */
- int       next;              /* external files */
- unsigned  i;
- int j;
-
-/*-------------------------------------------------------------------------
- * browse
- *-------------------------------------------------------------------------
- */
-
- for ( i = 0; i < travt->nobjs; i++)
- {
-  switch ( travt->objs[i].type )
-  {
-
-  case H5G_GROUP:
-
-   break;
-
-  /*-------------------------------------------------------------------------
-   * H5G_DATASET
-   *-------------------------------------------------------------------------
-   */
-  case H5G_DATASET:
-
-   if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0)
-    goto error;
-   if ((space_id=H5Dget_space(dset_in))<0)
-    goto error;
-   if ((ftype_id=H5Dget_type (dset_in))<0)
-    goto error;
-   if ((dcpl_id=H5Dget_create_plist(dset_in))<0)
-    goto error;
-   if ( (rank=H5Sget_simple_extent_ndims(space_id))<0)
-    goto error;
-   if ( H5Sget_simple_extent_dims(space_id,dims,NULL)<0)
-    goto error;
-   nelmts=1;
-   for (j=0; j<rank; j++)
-    nelmts*=dims[j];
-   
-   if (options->use_native==1)
-    wtype_id = h5tools_get_native_type(ftype_id);
-   else
-    wtype_id = H5Tcopy(ftype_id); 
-
-   if ((msize=H5Tget_size(wtype_id))==0)
-    goto error;
-
-/*-------------------------------------------------------------------------
- * check for external files
- *-------------------------------------------------------------------------
- */
-   if ((next=H5Pget_external_count (dcpl_id))<0)
-    goto error;
-/*-------------------------------------------------------------------------
- * check if the dataset creation property list has filters that
- * are not registered in the current configuration
- * 1) the external filters GZIP and SZIP might not be available
- * 2) the internal filters might be turned off
- *-------------------------------------------------------------------------
- */
-   if (next==0 && h5tools_canreadf((NULL),dcpl_id)==1)
-   {
-/*-------------------------------------------------------------------------
- * test for a valid output dataset
- *-------------------------------------------------------------------------
- */
-   dset_out = FAIL;
-
-/*-------------------------------------------------------------------------
- * object references are a special case
- * we cannot just copy the buffers, but instead we recreate the reference
- *-------------------------------------------------------------------------
- */
-   if (H5Tequal(wtype_id, H5T_STD_REF_OBJ))
-   {
-    H5G_obj_t        obj_type;
-    hid_t            refobj_id;
-    hobj_ref_t       *refbuf=NULL; /* buffer for object references */
-    hobj_ref_t       *buf=NULL;
-    const char*      refname;
-    unsigned         u;
-
-   /*-------------------------------------------------------------------------
-    * read to memory
-    *-------------------------------------------------------------------------
-    */
-
-    if (nelmts)
-    {
-     buf=(void *) HDmalloc((unsigned)(nelmts*msize));
-     if ( buf==NULL){
-      error_msg(progname, "cannot read into memory\n" );
-      goto error;
-     }
-     if (H5Dread(dset_in,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
-      goto error;
-
-     if ((obj_type = H5Rget_obj_type(dset_in,H5R_OBJECT,buf))<0)
-      goto error;
-     refbuf=HDmalloc((unsigned)nelmts*msize);
-     if ( refbuf==NULL){
-      error_msg(progname, "cannot allocate memory\n" );
-      goto error;
-     }
-     for ( u=0; u<nelmts; u++)
-     {
-      H5E_BEGIN_TRY {
-       if ((refobj_id = H5Rdereference(dset_in,H5R_OBJECT,&buf[u]))<0)
-        continue;
-      } H5E_END_TRY;
-      /* get the name. a valid name could only occur in the
-      second traversal of the file */
-      if ((refname=MapIdToName(refobj_id,travt))!=NULL)
-      {
-       /* create the reference, -1 parameter for objects */
-       if (H5Rcreate(&refbuf[u],fidout,refname,H5R_OBJECT,-1)<0)
-        goto error;
-       if (options->verbose)
-        printf("object <%s> object reference created to <%s>\n",
-        travt->objs[i].name,
-        refname);
-      }/*refname*/
-      close_obj(obj_type,refobj_id);
-     }/*  u */
-    }/*nelmts*/
-
-    /*-------------------------------------------------------------------------
-     * create/write dataset/close
-     *-------------------------------------------------------------------------
-     */
-    if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,wtype_id,space_id,dcpl_id))<0)
-     goto error;
-    if (nelmts) {
-     if (H5Dwrite(dset_out,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
-      goto error;
-    }
-
-    if (buf)
-     free(buf);
-    if (refbuf)
-     free(refbuf);
-
-   }/*H5T_STD_REF_OBJ*/
-
-/*-------------------------------------------------------------------------
- * dataset region references
- *-------------------------------------------------------------------------
- */
-   else if (H5Tequal(wtype_id, H5T_STD_REF_DSETREG))
-   {
-    H5G_obj_t        obj_type;
-    hid_t            refobj_id;
-    hdset_reg_ref_t  *refbuf=NULL; /* input buffer for region references */
-    hdset_reg_ref_t  *buf=NULL;    /* output buffer */
-    const char*      refname;
-    unsigned         u;
-
-   /*-------------------------------------------------------------------------
-    * read input to memory
-    *-------------------------------------------------------------------------
-    */
-    if (nelmts)
-    {
-     buf=(void *) HDmalloc((unsigned)(nelmts*msize));
-     if ( buf==NULL){
-      error_msg(progname, "cannot read into memory\n" );
-      goto error;
-     }
-     if (H5Dread(dset_in,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
-      goto error;
-     if ((obj_type = H5Rget_obj_type(dset_in,H5R_DATASET_REGION,buf))<0)
-      goto error;
-
-     /*-------------------------------------------------------------------------
-      * create output
-      *-------------------------------------------------------------------------
-      */
-
-     refbuf=HDcalloc(sizeof(hdset_reg_ref_t),(size_t)nelmts); /*init to zero */
-     if ( refbuf==NULL){
-      error_msg(progname, "cannot allocate memory\n" );
-      goto error;
-     }
-     for ( u=0; u<nelmts; u++)
-     {
-      H5E_BEGIN_TRY {
-       if ((refobj_id = H5Rdereference(dset_in,H5R_DATASET_REGION,&buf[u]))<0)
-        continue;
-      } H5E_END_TRY;
-
-      /* get the name. a valid name could only occur in the
-      second traversal of the file */
-      if ((refname=MapIdToName(refobj_id,travt))!=NULL)
-      {
-       hid_t region_id;    /* region id of the referenced dataset */
-       if ((region_id = H5Rget_region(dset_in,H5R_DATASET_REGION,&buf[u]))<0)
-        goto error;
-       /* create the reference, we need the space_id */
-       if (H5Rcreate(&refbuf[u],fidout,refname,H5R_DATASET_REGION,region_id)<0)
-        goto error;
-       if (H5Sclose(region_id)<0)
-        goto error;
-       if (options->verbose)
-        printf("object <%s> region reference created to <%s>\n",
-        travt->objs[i].name,
-        refname);
-      }/*refname*/
-      close_obj(obj_type,refobj_id);
-     }/*  u */
-    }/*nelmts*/
-
-    /*-------------------------------------------------------------------------
-     * create/write dataset/close
-     *-------------------------------------------------------------------------
-     */
-    if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,wtype_id,space_id,dcpl_id))<0)
-     goto error;
-    if (nelmts) {
-     if (H5Dwrite(dset_out,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
-      goto error;
-    }
-
-    if (buf)
-     free(buf);
-    if (refbuf)
-     free(refbuf);
-   } /* H5T_STD_REF_DSETREG */
-
-
-/*-------------------------------------------------------------------------
- * not references, open previously created object in 1st traversal
- *-------------------------------------------------------------------------
- */
-   else
-   {
-    if ((dset_out=H5Dopen(fidout,travt->objs[i].name))<0)
-     goto error;
-   }
-
-   assert(dset_out!=FAIL);
-
-/*-------------------------------------------------------------------------
- * copy referenced objects in attributes
- *-------------------------------------------------------------------------
- */
-   if (copy_refs_attr(dset_in,dset_out,options,travt,fidout)<0)
-    goto error;
-
-
-
-   if (H5Dclose(dset_out)<0)
-    goto error;
-
-   }/*can_read*/
-
-   /*-------------------------------------------------------------------------
-    * close
-    *-------------------------------------------------------------------------
-    */
-
-   if (H5Tclose(ftype_id)<0)
-    goto error;
-   if (H5Tclose(wtype_id)<0)
-    goto error;
-   if (H5Pclose(dcpl_id)<0)
-    goto error;
-   if (H5Sclose(space_id)<0)
-    goto error;
-   if (H5Dclose(dset_in)<0)
-    goto error;
-
-
-   break;
-
-
-  case H5G_TYPE:
-  case H5G_LINK:
-  case H5G_UDLINK:
-
-   /*nothing to do */
-   break;
-
-  default:
-
-   break;
-  }
- }
-
-
-/*-------------------------------------------------------------------------
- * the root is a special case, we get an ID for the root group
- * and copy its attributes using that ID
- * it must be done last, because the attributes might contain references to
- * objects in the object list
- *-------------------------------------------------------------------------
- */
-
- if ((grp_out = H5Gopen(fidout,"/"))<0)
-  goto error;
-
- if ((grp_in  = H5Gopen(fidin,"/"))<0)
-  goto error;
-
- if (copy_refs_attr(grp_in,grp_out,options,travt,fidout)<0)
-  goto error;
-
- if (H5Gclose(grp_out)<0)
-  goto error;
- if (H5Gclose(grp_in)<0)
-  goto error;
-
-
- return 0;
-
-error:
- H5E_BEGIN_TRY {
-  H5Gclose(grp_in);
-  H5Gclose(grp_out);
-  H5Pclose(dcpl_id);
-  H5Sclose(space_id);
-  H5Dclose(dset_in);
-  H5Dclose(dset_out);
-  H5Tclose(ftype_id);
-  H5Tclose(wtype_id);
-  H5Tclose(type_in);
- } H5E_END_TRY;
- return -1;
-
-}
-
-
-
-/*-------------------------------------------------------------------------
- * Function: copy_refs_attr
- *
- * Purpose: duplicate all referenced HDF5 objects located in attributes
- *  relative to LOC_IN, which is obtained either from
- * loc_id = H5Gopen( fid, name);
- * loc_id = H5Dopen( fid, name);
- * loc_id = H5Topen( fid, name);
- *
- * Return: 0, ok, -1 no
- *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
- *
- * Date: October, 28, 2003
- *
- *-------------------------------------------------------------------------
- */
-
-static int copy_refs_attr(hid_t loc_in,
-                          hid_t loc_out,
-                          pack_opt_t *options,
-                          trav_table_t *travt,
-                          hid_t fidout         /* for saving references */
-                          )
-{
- hid_t      attr_id=-1;      /* attr ID */
- hid_t      attr_out=-1;     /* attr ID */
- hid_t      space_id=-1;     /* space ID */
- hid_t      ftype_id=-1;     /* file type ID */
- hid_t      wtype_id=-1;     /* read/write type ID */
- size_t     msize;           /* size of type */
- hsize_t    nelmts;          /* number of elements in dataset */
- int        rank;            /* rank of dataset */
- hsize_t    dims[H5S_MAX_RANK];/* dimensions of dataset */
- char       name[255];
- int        n, j;
- unsigned   u;
-
- if ((n = H5Aget_num_attrs(loc_in))<0)
-  goto error;
-
- for ( u = 0; u < (unsigned)n; u++)
- {
-
-/*-------------------------------------------------------------------------
- * open
- *-------------------------------------------------------------------------
- */
-  /* open attribute */
-  if ((attr_id = H5Aopen_idx(loc_in, u))<0)
-   goto error;
-
-  /* get name */
-  if (H5Aget_name( attr_id, 255, name )<0)
-   goto error;
-
-  /* get the file datatype  */
-  if ((ftype_id = H5Aget_type( attr_id )) < 0 )
-   goto error;
-
-  /* get the dataspace handle  */
-  if ((space_id = H5Aget_space( attr_id )) < 0 )
-   goto error;
-
-  /* get dimensions  */
-  if ( (rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0 )
-   goto error;
-
-
-  /*-------------------------------------------------------------------------
-   * elements
-   *-------------------------------------------------------------------------
-   */
-  nelmts=1;
-  for (j=0; j<rank; j++)
-   nelmts*=dims[j];
-
-  if (options->use_native==1)
-   wtype_id = h5tools_get_native_type(ftype_id);
-  else
-   wtype_id = H5Tcopy(ftype_id); 
-
-  if ((msize=H5Tget_size(wtype_id))==0)
-   goto error;
-
-/*-------------------------------------------------------------------------
- * object references are a special case
- * we cannot just copy the buffers, but instead we recreate the reference
- *-------------------------------------------------------------------------
- */
-   if (H5Tequal(wtype_id, H5T_STD_REF_OBJ))
-   {
-    H5G_obj_t   obj_type;
-    hid_t       refobj_id;
-    hobj_ref_t  *refbuf=NULL;
-    unsigned    k;
-    const char* refname;
-    hobj_ref_t  *buf=NULL;
-
-   /*-------------------------------------------------------------------------
-    * read input to memory
-    *-------------------------------------------------------------------------
-    */
-
-    if (nelmts)
-    {
-     buf=(void *) HDmalloc((unsigned)(nelmts*msize));
-     if ( buf==NULL){
-      error_msg(progname, "cannot read into memory\n" );
-      goto error;
-     }
-     if (H5Aread(attr_id,wtype_id,buf)<0)
-      goto error;
-
-     if ((obj_type = H5Rget_obj_type(attr_id,H5R_OBJECT,buf))<0)
-      goto error;
-     refbuf=HDmalloc((unsigned)nelmts*msize);
-     if ( refbuf==NULL){
-      error_msg(progname, "cannot allocate memory\n" );
-      goto error;
-     }
-     for ( k=0; k<nelmts; k++)
-     {
-      H5E_BEGIN_TRY {
-       if ((refobj_id = H5Rdereference(attr_id,H5R_OBJECT,&buf[k]))<0)
-        goto error;
-      } H5E_END_TRY;
-      /* get the name. a valid name could only occur in the
-      second traversal of the file */
-      if ((refname=MapIdToName(refobj_id,travt))!=NULL)
-      {
-       /* create the reference */
-       if (H5Rcreate(&refbuf[k],fidout,refname,H5R_OBJECT,-1)<0)
-        goto error;
-       if (options->verbose)
-        printf("object <%s> reference created to <%s>\n",name,refname);
-      }
-      close_obj(obj_type,refobj_id);
-     }/*  k */
-    }/*nelmts*/
-
-    /*-------------------------------------------------------------------------
-     * copy
-     *-------------------------------------------------------------------------
-     */
-
-    if ((attr_out=H5Acreate(loc_out,name,ftype_id,space_id,H5P_DEFAULT))<0)
-     goto error;
-    if (nelmts) {
-     if(H5Awrite(attr_out,wtype_id,refbuf)<0)
-      goto error;
-    }
-
-    if (H5Aclose(attr_out)<0)
-     goto error;
-
-    if (refbuf)
-     free(refbuf);
-    if (buf)
-     free(buf);
-
-   }/*H5T_STD_REF_OBJ*/
-
-/*-------------------------------------------------------------------------
- * dataset region references
- *-------------------------------------------------------------------------
- */
-   else if (H5Tequal(wtype_id, H5T_STD_REF_DSETREG))
-   {
-    H5G_obj_t        obj_type;
-    hid_t            refobj_id;
-    hdset_reg_ref_t  *refbuf=NULL; /* input buffer for region references */
-    hdset_reg_ref_t  *buf=NULL;    /* output buffer */
-    const char*      refname;
-    unsigned         k;
-
-   /*-------------------------------------------------------------------------
-    * read input to memory
-    *-------------------------------------------------------------------------
-    */
-
-    if (nelmts)
-    {
-     buf=(void *) HDmalloc((unsigned)(nelmts*msize));
-     if ( buf==NULL){
-      error_msg(progname, "cannot read into memory\n" );
-      goto error;
-     }
-     if (H5Aread(attr_id,wtype_id,buf)<0)
-      goto error;
-     if ((obj_type = H5Rget_obj_type(attr_id,H5R_DATASET_REGION,buf))<0)
-      goto error;
-
-    /*-------------------------------------------------------------------------
-     * create output
-     *-------------------------------------------------------------------------
-     */
-
-     refbuf=HDcalloc(sizeof(hdset_reg_ref_t),(size_t)nelmts); /*init to zero */
-     if ( refbuf==NULL){
-      error_msg(progname, "cannot allocate memory\n" );
-      goto error;
-     }
-     for ( k=0; k<nelmts; k++)
-     {
-      H5E_BEGIN_TRY {
-       if ((refobj_id = H5Rdereference(attr_id,H5R_DATASET_REGION,&buf[k]))<0)
-        continue;
-      } H5E_END_TRY;
-      /* get the name. a valid name could only occur in the
-      second traversal of the file */
-      if ((refname=MapIdToName(refobj_id,travt))!=NULL)
-      {
-       hid_t region_id;    /* region id of the referenced dataset */
-       if ((region_id = H5Rget_region(attr_id,H5R_DATASET_REGION,&buf[k]))<0)
-        goto error;
-       /* create the reference, we need the space_id */
-       if (H5Rcreate(&refbuf[k],fidout,refname,H5R_DATASET_REGION,region_id)<0)
-        goto error;
-       if (H5Sclose(region_id)<0)
-        goto error;
-       if (options->verbose)
-        printf("object <%s> region reference created to <%s>\n",name,refname);
-      }
-      close_obj(obj_type,refobj_id);
-     }/*  k */
-    }/*nelmts */
-
-    /*-------------------------------------------------------------------------
-     * copy
-     *-------------------------------------------------------------------------
-     */
-
-    if ((attr_out=H5Acreate(loc_out,name,ftype_id,space_id,H5P_DEFAULT))<0)
-     goto error;
-    if (nelmts) {
-     if(H5Awrite(attr_out,wtype_id,refbuf)<0)
-      goto error;
-    }
-    if (H5Aclose(attr_out)<0)
-     goto error;
-    if (refbuf)
-     free(refbuf);
-    if (buf)
-     free(buf);
-   } /* H5T_STD_REF_DSETREG */
-
-/*-------------------------------------------------------------------------
- * close
- *-------------------------------------------------------------------------
- */
-
-  if (H5Tclose(ftype_id)<0) goto error;
-  if (H5Tclose(wtype_id)<0) goto error;
-  if (H5Sclose(space_id)<0) goto error;
-  if (H5Aclose(attr_id)<0) goto error;
- } /* u */
-
-  return 0;
-
-error:
- H5E_BEGIN_TRY {
-  H5Tclose(ftype_id);
-  H5Tclose(wtype_id);
-  H5Sclose(space_id);
-  H5Aclose(attr_id);
-  H5Aclose(attr_out);
- } H5E_END_TRY;
- return -1;
-}
-
-/*-------------------------------------------------------------------------
- * Function: close_obj
- *
- * Purpose: Auxiliary function to close an object
- *
- *-------------------------------------------------------------------------
- */
-
-static void close_obj(H5G_obj_t obj_type, hid_t obj_id)
-{
- H5E_BEGIN_TRY
- {
-  switch (obj_type)
-  {
-  case H5G_GROUP:
-   H5Gclose(obj_id);
-   break;
-  case H5G_DATASET:
-   H5Dclose(obj_id);
-   break;
-  case H5G_TYPE:
-   H5Tclose(obj_id);
-   break;
-  default:
-   break;
-  }
- } H5E_END_TRY;
-}
-
-/*-------------------------------------------------------------------------
- * Function: MapIdToName
- *
- * Purpose: map an object ID to a name
- *
- *-------------------------------------------------------------------------
- */
-
-static const char* MapIdToName(hid_t refobj_id,
-                               trav_table_t *travt)
-{
- hid_t id;
- hid_t fid;
- H5G_stat_t refstat;    /* Stat for the refobj id */
- H5G_stat_t objstat;    /* Stat for objects in the file */
- unsigned int   i;
-
- /* obtain information to identify the referenced object uniquely */
- if(H5Gget_objinfo(refobj_id, ".", 0, &refstat) <0)
-  return NULL;
-
- /* obtains the file ID given an object ID.  This ID must be closed */
- if ((fid = H5Iget_file_id(refobj_id))<0)
- {
-  return NULL;
- }
-
- /* linear search */
- for ( i=0; i<travt->nobjs; i++)
- {
-  switch ( travt->objs[i].type )
-  {
-  default:
-   break;
-
-  /*-------------------------------------------------------------------------
-   * H5G_DATASET
-   *-------------------------------------------------------------------------
-   */
-
-  case H5G_DATASET:
-
-   if ((id = H5Dopen(fid,travt->objs[i].name))<0)
-    return NULL;
-   if(H5Gget_objinfo(id, ".", 0, &objstat) <0)
-    return NULL;
-   if (H5Dclose(id)<0)
-    return NULL;
-   if (!HDmemcmp(&refstat.fileno, &objstat.fileno, sizeof(refstat.fileno)) && !HDmemcmp(&refstat.objno, &objstat.objno, sizeof(refstat.objno)))
-   {
-    H5Fclose(fid);
-    return travt->objs[i].name;
-   }
-   break;
-  }  /* switch */
- } /* i */
-
- if (H5Fclose(fid)<0)
-  return NULL;
-
- return NULL;
-}
-
-
-#endif
-
diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c
index 0fc9dc3..e29769a 100644
--- a/tools/h5repack/h5repack_refs.c
+++ b/tools/h5repack/h5repack_refs.c
@@ -1,3 +1,4 @@
+
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
  * Copyright by the Board of Trustees of the University of Illinois.         *
@@ -20,18 +21,14 @@
 #include "H5private.h"
 #include "h5repack.h"
 
-static const char* MapIdToName(hid_t refobj_id,
-                               trav_table_t *travt);
-
-static void close_obj(H5G_obj_t obj_type, hid_t obj_id);
+/*-------------------------------------------------------------------------
+ * local functions
+ *-------------------------------------------------------------------------
+ */
 
-
-static int copy_refs_attr(hid_t loc_in,
-                          hid_t loc_out,
-                          pack_opt_t *options,
-                          trav_table_t *travt,
-                          hid_t fidout         /* for saving references */
-                          );
+static const char* MapIdToName(hid_t refobj_id,trav_table_t *travt);
+static void close_obj(H5G_obj_t1 obj_type, hid_t obj_id);
+static int copy_refs_attr(hid_t loc_in,hid_t loc_out,pack_opt_t *options,trav_table_t *travt,hid_t fidout);
 
 /*-------------------------------------------------------------------------
  * Function: do_copy_refobjs
@@ -62,12 +59,13 @@ int do_copy_refobjs(hid_t fidin,
  hid_t     space_id=(-1);          /* space ID */
  hid_t     ftype_id=(-1);          /* file data type ID */
  hid_t     mtype_id=(-1);          /* memory data type ID */
- size_t    msize;             /* memory size of memory type */
- hsize_t   nelmts;            /* number of elements in dataset */
- int       rank;              /* rank of dataset */
- hsize_t   dims[H5S_MAX_RANK];/* dimensions of dataset */
- int       next;              /* external files */
- unsigned  i, j;
+ size_t    msize;                  /* memory size of memory type */
+ hsize_t   nelmts;                 /* number of elements in dataset */
+ int       rank;                   /* rank of dataset */
+ hsize_t   dims[H5S_MAX_RANK];     /* dimensions of dataset */
+ int       next;                   /* external files */
+ unsigned int i, j;
+ int       k;
 
 /*-------------------------------------------------------------------------
  * browse
@@ -143,8 +141,8 @@ int do_copy_refobjs(hid_t fidin,
    if ( H5Sget_simple_extent_dims(space_id,dims,NULL)<0)
     goto error;
    nelmts=1;
-   for (j=0; j<rank; j++)
-    nelmts*=dims[j];
+   for (k=0; k<rank; k++)
+    nelmts*=dims[k];
 
    if ((mtype_id=h5tools_get_native_type(ftype_id))<0)
     goto error;
@@ -180,7 +178,7 @@ int do_copy_refobjs(hid_t fidin,
  */
    if (H5Tequal(mtype_id, H5T_STD_REF_OBJ))
    {
-    H5G_obj_t       obj_type;
+    H5G_obj_t1       obj_type;
     hid_t            refobj_id;
     hobj_ref_t       *refbuf=NULL; /* buffer for object references */
     hobj_ref_t       *buf=NULL;
@@ -255,7 +253,7 @@ int do_copy_refobjs(hid_t fidin,
  */
    else if (H5Tequal(mtype_id, H5T_STD_REF_DSETREG))
    {
-    H5G_obj_t       obj_type;
+    H5G_obj_t1       obj_type;
     hid_t            refobj_id;
     hdset_reg_ref_t  *refbuf=NULL; /* input buffer for region references */
     hdset_reg_ref_t  *buf=NULL;    /* output buffer */
@@ -350,8 +348,10 @@ int do_copy_refobjs(hid_t fidin,
  * copy referenced objects in attributes
  *-------------------------------------------------------------------------
  */
+#if 1
    if (copy_refs_attr(dset_in,dset_out,options,travt,fidout)<0)
     goto error;
+#endif
 
 
 /*-------------------------------------------------------------------------
@@ -489,14 +489,14 @@ static int copy_refs_attr(hid_t loc_in,
                           hid_t fidout         /* for saving references */
                           )
 {
- hid_t      attr_id=-1;      /* attr ID */
- hid_t      attr_out=-1;     /* attr ID */
- hid_t      space_id=-1;     /* space ID */
- hid_t      ftype_id=-1;     /* file data type ID */
- hid_t      mtype_id=-1;     /* memory data type ID */
- size_t     msize;        /* memory size of type */
- hsize_t    nelmts;       /* number of elements in dataset */
- int        rank;         /* rank of dataset */
+ hid_t      attr_id=-1;        /* attr ID */
+ hid_t      attr_out=-1;       /* attr ID */
+ hid_t      space_id=-1;       /* space ID */
+ hid_t      ftype_id=-1;       /* file data type ID */
+ hid_t      mtype_id=-1;       /* memory data type ID */
+ size_t     msize;             /* memory size of type */
+ hsize_t    nelmts;            /* number of elements in dataset */
+ int        rank;              /* rank of dataset */
  hsize_t    dims[H5S_MAX_RANK];/* dimensions of dataset */
  char       name[255];
  int        n, j;
@@ -554,7 +554,7 @@ static int copy_refs_attr(hid_t loc_in,
  */
    if (H5Tequal(mtype_id, H5T_STD_REF_OBJ))
    {
-    H5G_obj_t  obj_type;
+    H5G_obj_t1  obj_type;
     hid_t       refobj_id;
     hobj_ref_t  *refbuf=NULL;
     unsigned    k;
@@ -631,7 +631,7 @@ static int copy_refs_attr(hid_t loc_in,
  */
    else if (H5Tequal(mtype_id, H5T_STD_REF_DSETREG))
    {
-    H5G_obj_t       obj_type;
+    H5G_obj_t1       obj_type;
     hid_t            refobj_id;
     hdset_reg_ref_t  *refbuf=NULL; /* input buffer for region references */
     hdset_reg_ref_t  *buf=NULL;    /* output buffer */
@@ -734,14 +734,14 @@ error:
 }
 
 /*-------------------------------------------------------------------------
- * Function: close_obj
+ * Function:	close_obj
  *
- * Purpose: Auxiliary function to close an object
+ * Purpose:	Auxiliary function to close an object
  *
  *-------------------------------------------------------------------------
  */
 
-static void close_obj(H5G_obj_t obj_type, hid_t obj_id)
+static void close_obj(H5G_obj_t1 obj_type, hid_t obj_id)
 {
  H5E_BEGIN_TRY
  {
@@ -761,6 +761,7 @@ static void close_obj(H5G_obj_t obj_type, hid_t obj_id)
   }
  } H5E_END_TRY;
 }
+
 /*-------------------------------------------------------------------------
  * Function:	MapIdToName
  *
@@ -772,11 +773,11 @@ static void close_obj(H5G_obj_t obj_type, hid_t obj_id)
 static const char* MapIdToName(hid_t refobj_id,
                                trav_table_t *travt)
 {
- hid_t id;
- hid_t fid;
- H5G_stat_t refstat;    /* Stat for the refobj id */
- H5G_stat_t objstat;    /* Stat for objects in the file */
- int   i;
+ hid_t        id;
+ hid_t        fid;
+ H5G_stat_t   refstat;    /* Stat for the refobj id */
+ H5G_stat_t   objstat;    /* Stat for objects in the file */
+ unsigned int i;
 
  /* obtain information to identify the referenced object uniquely */
  if(H5Gget_objinfo(refobj_id, ".", 0, &refstat) <0)
@@ -825,3 +826,5 @@ static const char* MapIdToName(hid_t refobj_id,
  return NULL;
 }
 
+
+
diff --git a/tools/h5repack/h5repacktst.c b/tools/h5repack/h5repacktst.c
index 6d58abc..098d6d8 100644
--- a/tools/h5repack/h5repacktst.c
+++ b/tools/h5repack/h5repacktst.c
@@ -160,6 +160,8 @@ int main (void)
  *-------------------------------------------------------------------------
  */
 
+#if 0
+
 /*-------------------------------------------------------------------------
  * file with fill values
  *-------------------------------------------------------------------------
@@ -198,11 +200,12 @@ int main (void)
   GOERROR;
  PASSED();
 
+#endif
+
 /*-------------------------------------------------------------------------
  * file with attributes
  *-------------------------------------------------------------------------
  */
-#if 0
  TESTING("    copy of datasets (attributes)");
  if (h5repack_init (&pack_options, 0)<0)
   GOERROR;
@@ -217,7 +220,6 @@ int main (void)
  if (h5repack_end (&pack_options)<0)
   GOERROR;
  PASSED();
-#endif
 
 /*-------------------------------------------------------------------------
  * file with hardlinks
@@ -3541,7 +3543,7 @@ void write_attr_in(hid_t loc_id,
  {
   status=H5Rcreate(&buf4[0],fid,dset_name,H5R_OBJECT,-1);
   status=H5Rcreate(&buf4[1],fid,dset_name,H5R_OBJECT,-1);
-  make_attr(loc_id,1,dims,"reference to object",H5T_STD_REF_OBJ,buf4);
+  make_attr(loc_id,1,dims,"reference",H5T_STD_REF_OBJ,buf4);
  }