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[svn-r18614] Purpose:

Browse Source 
Fix for bug 1817 : h5copy fail to copy dangling link by specifying 
    link path directly

Tested:
    jam, amani, linew
This commit is contained in:
Jonathan Kim 2010-04-22 13:17:35 -05:00
parent 20a020a1c7
commit 249acc0355
6 changed files with 205 additions and 160 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

29
tools/h5copy/h5copy.c
View File

@ -213,6 +213,8 @@ main (int argc, const char *argv[])
hid_t lcpl_id = (-1); /* Link creation property list */
char str_flag[20];
int opt;
int li_ret;
h5tool_link_info_t linkinfo;
/* initialize h5tools lib */
h5tools_init();
@ -406,7 +408,22 @@ main (int argc, const char *argv[])
/*-------------------------------------------------------------------------
* do the copy
*-------------------------------------------------------------------------*/
/* init linkinfo struct */
memset(&linkinfo, 0, sizeof(h5tool_link_info_t));
if(verbose)
linkinfo.opt.msg_mode = 1;
li_ret = H5tools_get_link_info(fid_src, oname_src, &linkinfo);
if (li_ret == 0) /* dangling link */
{
if(H5Lcopy(fid_src, oname_src,
fid_dst, oname_dst,
H5P_DEFAULT, H5P_DEFAULT) < 0)
goto error;
}
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 */
@ -414,6 +431,11 @@ main (int argc, const char *argv[])
ocpl_id, /* Object copy property list */
lcpl_id)<0) /* Link creation property list */
goto error;
}
/* free link info path */
if (linkinfo.trg_path)
free(linkinfo.trg_path);
/* close propertis */
if(H5Pclose(ocpl_id)<0)
@ -442,6 +464,11 @@ main (int argc, const char *argv[])
error:
printf("Error in copy...Exiting\n");
/* free link info path */
if (linkinfo.trg_path)
free(linkinfo.trg_path);
H5E_BEGIN_TRY {
H5Pclose(ocpl_id);
H5Pclose(lcpl_id);

16
tools/h5copy/testfiles/h5copy_extlinks_src.out.ls
View File

@ -11,7 +11,7 @@ Opened "./testfiles/h5copy_extlinks_src.out.h5" with sec2 driver.
Storage: <details removed for portability>
Type: 32-bit little-endian integer
/copy1_group Group
Location: 1:4344
Location: 1:4696
Links: 1
/copy1_group/extlink_datatype External Link {h5copy_extlinks_trg.h5//datatype}
/copy1_group/extlink_dset External Link {h5copy_extlinks_trg.h5//simple}
@ -24,19 +24,23 @@ Opened "./testfiles/h5copy_extlinks_src.out.h5" with sec2 driver.
Storage: <details removed for portability>
Type: 32-bit little-endian integer
/copy2_group Group
Location: 1:4712
Location: 1:5128
Links: 1
/copy2_group/extlink_datatype Type
Location: 1:5912
Location: 1:6328
Links: 1
Type: shared-1:5912 32-bit little-endian integer
Type: shared-1:6328 32-bit little-endian integer
/copy2_group/extlink_dset Dataset {6/6}
Location: 1:5080
Location: 1:5496
Links: 1
Storage: <details removed for portability>
Type: 32-bit little-endian integer
/copy2_group/extlink_grp Group
Location: 1:5872
Location: 1:6288
Links: 1
/copy2_group/extlink_notyet1 External Link {h5copy_extlinks_trg.h5//notyet}
/copy2_group/extlink_notyet2 External Link {notyet_file.h5//notyet}
/copy_dangle1_1 External Link {h5copy_extlinks_trg.h5//notyet}
/copy_dangle1_2 External Link {h5copy_extlinks_trg.h5//notyet}
/copy_dangle2_1 External Link {notyet_file.h5//notyet}
/copy_dangle2_2 External Link {notyet_file.h5//notyet}

12
tools/h5copy/testh5copy.sh
View File

@ -353,20 +353,16 @@ COPY_EXT_LINKS()
TOOLTEST -f ext -i $TESTFILE -o $FILEOUT -v -s /group_ext/extlink_dset -d /copy2_dset
echo "Test copying dangling external link (no obj) directly without -f ext"
#TOOLTEST -i $TESTFILE -o $FILEOUT -v -s /copy2_group/extlink_notyet1 -d /copy2_dangle1
SKIP -s /copy2_group/extlink_notyet1 -d /copy2_dangle1
TOOLTEST -i $TESTFILE -o $FILEOUT -v -s /group_ext/extlink_notyet1 -d /copy_dangle1_1
echo "Test copying dangling external link (no obj) directly with -f ext"
#TOOLTEST -f ext -i $TESTFILE -o $FILEOUT -v -s /copy2_group/extlink_notyet1 -d /copy2_dangle1
SKIP -f ext -s /copy2_group/extlink_notyet1 -d /copy2_dangle1
TOOLTEST -f ext -i $TESTFILE -o $FILEOUT -v -s /group_ext/extlink_notyet1 -d /copy_dangle1_2
echo "Test copying dangling external link (no file) directly without -f ext"
#TOOLTEST -i $TESTFILE -o $FILEOUT -v -s /copy2_group/extlink_notyet2 -d /copy2_dangle2
SKIP -s /copy2_group/extlink_notyet2 -d /copy2_dangle2
TOOLTEST -i $TESTFILE -o $FILEOUT -v -s /group_ext/extlink_notyet2 -d /copy_dangle2_1
echo "Test copying dangling external link (no file) directly with -f ext"
#TOOLTEST -f ext -i $TESTFILE -o $FILEOUT -v -s /copy2_group/extlink_notyet2 -d /copy2_dangle2
SKIP -f ext -s /copy2_group/extlink_notyet2 -d /copy2_dangle2
TOOLTEST -f ext -i $TESTFILE -o $FILEOUT -v -s /group_ext/extlink_notyet2 -d /copy_dangle2_2
echo "Test copying a group contains external links without -f ext"
TOOLTEST -v -i $TESTFILE -o $FILEOUT -s /group_ext -d /copy1_group

145
tools/lib/h5diff.c
View File

@ -20,28 +20,6 @@
#include "h5tools.h"
#include "h5tools_utils.h"
/* This code is layout for common code among tools */
typedef enum toolname_t {
TOOL_H5DIFF, TOOL_H5LS, TOOL__H5DUMP /* add as necessary */
} h5tool_toolname_t;
/* this struct can be used to differntiate among tools if necessary */
typedef struct {
h5tool_toolname_t toolname;
int msg_mode;
} h5tool_opt_t;
/* To return link info
* Functions:
* H5tools_get_link_info()
* Note: this may be move to h5tools code if used by other tools
*/
typedef struct {
H5O_type_t trg_type; /* OUT: target type */
const char *trg_path; /* OUT: target obj path. This must be freed
* when used with H5tools_get_link_info() */
H5L_info_t linfo; /* OUT: link info */
h5tool_opt_t opt; /* IN: options */
} h5tool_link_info_t;
/*
* Debug printf macros. The prefix allows output filtering by test scripts.
*/
@ -254,129 +232,6 @@ out:
}
/*-------------------------------------------------------------------------
* Function: H5tools_get_link_info
*
* Purpose: Get link (soft, external) info and its target object type
(dataset, group, named datatype) and path, if exist
*
* Patameters:
* - [IN] fileid : link file id
* - [IN] linkpath : link path
* - [OUT] h5li : link's info (H5L_info_t)
* - [OUT] link_info: returning target object info (h5tool_link_info_t)
*
* Return:
* 1 : Succed to get link info.
* 0 : Detected as a dangling link
* -1 : H5 API failed.
*
* NOTE:
* link_info->trg_path must be freed out of this function
*
* Programmer: Jonathan Kim
*
* Date: Feb 8, 2010
*-------------------------------------------------------------------------*/
static int H5tools_get_link_info(hid_t file_id, const char * linkpath, h5tool_link_info_t *link_info)
{
int Ret = -1; /* init to fail */
htri_t l_ret;
H5O_info_t trg_oinfo;
hid_t fapl;
hid_t lapl = H5P_DEFAULT;
/* init */
link_info->trg_type = H5O_TYPE_UNKNOWN;
/* check if link itself exist */
if((H5Lexists(file_id, linkpath, H5P_DEFAULT) <= 0))
{
if(link_info->opt.msg_mode==1)
parallel_print("Warning: link <%s> doesn't exist \n",linkpath);
goto out;
}
/* get info from link */
if(H5Lget_info(file_id, linkpath, &(link_info->linfo), H5P_DEFAULT) < 0)
{
if(link_info->opt.msg_mode==1)
parallel_print("Warning: unable to get link info from <%s>\n",linkpath);
goto out;
}
/* trg_path must be freed out of this function when finished using */
link_info->trg_path = (char*)HDcalloc(link_info->linfo.u.val_size, sizeof(char));
HDassert(link_info->trg_path);
/* get link value */
if(H5Lget_val(file_id, linkpath, link_info->trg_path, link_info->linfo.u.val_size, H5P_DEFAULT) < 0)
{
if(link_info->opt.msg_mode==1)
parallel_print("Warning: unable to get link value from <%s>\n",linkpath);
goto out;
}
/*-----------------------------------------------------
* if link type is external link use different lapl to
* follow object in other file
*/
if (link_info->linfo.type == H5L_TYPE_EXTERNAL)
{
fapl = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_sec2(fapl);
lapl = H5Pcreate(H5P_LINK_ACCESS);
H5Pset_elink_fapl(lapl, fapl);
}
/*--------------------------------------------------------------
* if link's target object exist, get type
*/
/* check if target object exist */
l_ret = H5Oexists_by_name(file_id, linkpath, lapl);
/* detect dangling link */
if(l_ret == FALSE)
{
Ret = 0;
goto out;
}
/* function failed */
else if (l_ret < 0)
{
goto out;
}
/* get target object info */
if(H5Oget_info_by_name(file_id, linkpath, &trg_oinfo, lapl) < 0)
{
if(link_info->opt.msg_mode==1)
parallel_print("Warning: unable to get object information for <%s>\n", linkpath);
goto out;
}
/* check unknown type */
if (trg_oinfo.type < H5O_TYPE_GROUP || trg_oinfo.type >=H5O_TYPE_NTYPES)
{
if(link_info->opt.msg_mode==1)
parallel_print("Warning: target object of <%s> is unknown type\n", linkpath);
goto out;
}
/* set target obj type to return */
link_info->trg_type = trg_oinfo.type;
/* succeed */
Ret = 1;
out:
if (link_info->linfo.type == H5L_TYPE_EXTERNAL)
{
H5Pclose(fapl);
H5Pclose(lapl);
}
return Ret;
}
/*-------------------------------------------------------------------------
* Function: h5diff

132
tools/lib/h5tools_utils.c
View File

@ -626,3 +626,135 @@ tmpfile(void)
}
#endif
/*-------------------------------------------------------------------------
* Function: H5tools_get_link_info
*
* Purpose: Get link (soft, external) info and its target object type
(dataset, group, named datatype) and path, if exist
*
* Patameters:
* - [IN] fileid : link file id
* - [IN] linkpath : link path
* - [OUT] h5li : link's info (H5L_info_t)
* - [OUT] link_info: returning target object info (h5tool_link_info_t)
*
* Return:
* 2 : given pathname is object
* 1 : Succed to get link info.
* 0 : Detected as a dangling link
* -1 : H5 API failed.
*
* NOTE:
* link_info->trg_path must be freed out of this function
*
* Programmer: Jonathan Kim
*
* Date: Feb 8, 2010
*-------------------------------------------------------------------------*/
int H5tools_get_link_info(hid_t file_id, const char * linkpath, h5tool_link_info_t *link_info)
{
int Ret = -1; /* init to fail */
htri_t l_ret;
H5O_info_t trg_oinfo;
hid_t fapl;
hid_t lapl = H5P_DEFAULT;
/* init */
link_info->trg_type = H5O_TYPE_UNKNOWN;
/* check if link itself exist */
if((H5Lexists(file_id, linkpath, H5P_DEFAULT) <= 0))
{
if(link_info->opt.msg_mode==1)
parallel_print("Warning: link <%s> doesn't exist \n",linkpath);
goto out;
}
/* get info from link */
if(H5Lget_info(file_id, linkpath, &(link_info->linfo), H5P_DEFAULT) < 0)
{
if(link_info->opt.msg_mode==1)
parallel_print("Warning: unable to get link info from <%s>\n",linkpath);
goto out;
}
/* given path is hard link (object) */
if (link_info->linfo.type == H5L_TYPE_HARD)
{
Ret = 2;
goto out;
}
/* trg_path must be freed out of this function when finished using */
link_info->trg_path = (char*)HDcalloc(link_info->linfo.u.val_size, sizeof(char));
HDassert(link_info->trg_path);
/* get link value */
if(H5Lget_val(file_id, linkpath, link_info->trg_path, link_info->linfo.u.val_size, H5P_DEFAULT) < 0)
{
if(link_info->opt.msg_mode==1)
parallel_print("Warning: unable to get link value from <%s>\n",linkpath);
goto out;
}
/*-----------------------------------------------------
* if link type is external link use different lapl to
* follow object in other file
*/
if (link_info->linfo.type == H5L_TYPE_EXTERNAL)
{
fapl = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_sec2(fapl);
lapl = H5Pcreate(H5P_LINK_ACCESS);
H5Pset_elink_fapl(lapl, fapl);
}
/*--------------------------------------------------------------
* if link's target object exist, get type
*/
/* check if target object exist */
l_ret = H5Oexists_by_name(file_id, linkpath, lapl);
/* detect dangling link */
if(l_ret == FALSE)
{
Ret = 0;
goto out;
}
/* function failed */
else if (l_ret < 0)
{
goto out;
}
/* get target object info */
if(H5Oget_info_by_name(file_id, linkpath, &trg_oinfo, lapl) < 0)
{
if(link_info->opt.msg_mode==1)
parallel_print("Warning: unable to get object information for <%s>\n", linkpath);
goto out;
}
/* check unknown type */
if (trg_oinfo.type < H5O_TYPE_GROUP || trg_oinfo.type >=H5O_TYPE_NTYPES)
{
if(link_info->opt.msg_mode==1)
parallel_print("Warning: target object of <%s> is unknown type\n", linkpath);
goto out;
}
/* set target obj type to return */
link_info->trg_type = trg_oinfo.type;
/* succeed */
Ret = 1;
out:
if (link_info->linfo.type == H5L_TYPE_EXTERNAL)
{
H5Pclose(fapl);
H5Pclose(lapl);
}
return Ret;
}

31
tools/lib/h5tools_utils.h
View File

@ -119,4 +119,35 @@ extern obj_t *search_obj(table_t *temp, haddr_t objno);
extern FILE * tmpfile(void);
#endif
/*************************************************************
*
* candidate functions to be public
*
*************************************************************/
/* This code is layout for common code among tools */
typedef enum toolname_t {
TOOL_H5DIFF, TOOL_H5LS, TOOL__H5DUMP /* add as necessary */
} h5tool_toolname_t;
/* this struct can be used to differntiate among tools */
typedef struct {
h5tool_toolname_t toolname;
int msg_mode;
} h5tool_opt_t;
/* obtain link info from H5tools_get_link_info() */
typedef struct {
H5O_type_t trg_type; /* OUT: target type */
const char *trg_path; /* OUT: target obj path. This must be freed
* when used with H5tools_get_link_info() */
H5L_info_t linfo; /* OUT: link info */
h5tool_opt_t opt; /* IN: options */
} h5tool_link_info_t;
/* Definitions of routines */
extern int H5tools_get_link_info(hid_t file_id, const char * linkpath, h5tool_link_info_t *link_info);
#endif /* H5TOOLS_UTILS_H__ */