Add new H5R API that abstracts object, region and attribute reference types

Also support references to external files

Add new H5T_REF type and type conversion routines

Support conversion from H5T_REF_OBJ/DSET_REG to H5T_REF

Add H5Treclaim() API to reclaim memory of vlen/reference types

Deprecate H5Dvlen_reclaim()

Fix H5T_vlen_reclaim() and H5T_reclaim() to use private callback

Add H5T_ref_reclaim()

Move previous H5R APIs to H5Rdeprec.c

Clean up H5Ocopy

Separate H5O_copy_expand_ref() to H5Ocopy_ref()

Add support for copying new reference types

Clean up deprecated routines to go through VOL and same code path

Fix return codes in existing trefer.c test

Rename trefer.c to trefer_deprec.c

trefer.c is for new references

Add performance test for trefer

Add additional obj_copy_ref test

Make use of tokens and blobs to store references

Skip blob encoding for object references

Start adding new reference examples

1 files changed, 0 insertions, 198 deletions

diff --git a/src/H5Ocopy.c b/src/H5Ocopy.c
index 9578f95..6e0db25 100644
--- a/src/H5Ocopy.c
+++ b/src/H5Ocopy.c
@@ -85,8 +85,6 @@ static herr_t H5O__copy_header(const H5O_loc_t *oloc_src, H5O_loc_t *oloc_dst /*
     hid_t ocpypl_id, hid_t lcpl_id);
 static herr_t H5O__copy_obj(H5G_loc_t *src_loc, H5G_loc_t *dst_loc,
     const char *dst_name, hid_t ocpypl_id, hid_t lcpl_id);
-static herr_t H5O__copy_obj_by_ref(H5O_loc_t *src_oloc, H5O_loc_t *dst_oloc,
-    H5G_loc_t *dst_root_loc, H5O_copy_t *cpy_info);
 static herr_t H5O__copy_free_comm_dt_cb(void *item, void *key, void *op_data);
 static int H5O__copy_comm_dt_cmp(const void *dt1, const void *dt2);
 static herr_t H5O__copy_search_comm_dt_cb(hid_t group, const char *name,
@@ -110,7 +108,6 @@ H5FL_DEFINE(H5O_copy_search_comm_dt_key_t);
 /* Declare a free list to manage haddr_t variables */
 H5FL_DEFINE(haddr_t);
 
-
 /*****************************/
 /* Library Private Variables */
 /*****************************/
@@ -1235,201 +1232,6 @@ done:
 
 
 /*-------------------------------------------------------------------------
- * Function:    H5O__copy_obj_by_ref
- *
- * Purpose:     Copy the object pointed by _src_ref.
- *
- * Return:      Non-negative on success/Negative on failure
- *
- * Programmer:  Peter Cao
- *              Aug 7 2006
- *
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5O__copy_obj_by_ref(H5O_loc_t *src_oloc, H5O_loc_t *dst_oloc,
-    H5G_loc_t *dst_root_loc, H5O_copy_t *cpy_info)
-{
-    herr_t  ret_value = SUCCEED;
-
-    FUNC_ENTER_STATIC
-
-    HDassert(src_oloc);
-    HDassert(dst_oloc);
-
-    /* Perform the copy, or look up existing copy */
-    if((ret_value = H5O_copy_header_map(src_oloc, dst_oloc, cpy_info, FALSE, NULL, NULL)) < 0)
-        HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object")
-
-    /* Check if a new valid object is copied to the destination */
-    if(H5F_addr_defined(dst_oloc->addr) && (ret_value > SUCCEED)) {
-        char    tmp_obj_name[80];
-        H5G_name_t      new_path;
-        H5O_loc_t       new_oloc;
-        H5G_loc_t       new_loc;
-
-        /* Set up group location for new object */
-        new_loc.oloc = &new_oloc;
-        new_loc.path = &new_path;
-        H5G_loc_reset(&new_loc);
-        new_oloc.file = dst_oloc->file;
-        new_oloc.addr = dst_oloc->addr;
-
-        /* Pick a default name for the new object */
-        HDsnprintf(tmp_obj_name, sizeof(tmp_obj_name), "~obj_pointed_by_%llu", (unsigned long long)dst_oloc->addr);
-
-        /* Create a link to the newly copied object */
-        /* Note: since H5O_copy_header_map actually copied the target object, it
-         * must exist either in cache or on disk, therefore it is is safe to not
-         * pass the obj_type and udata fields returned by H5O_copy_header_map.
-         * This could be changed in the future to slightly improve performance
-         * --NAF */
-        if(H5L_link(dst_root_loc, tmp_obj_name, &new_loc, cpy_info->lcpl_id) < 0)
-            HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to insert link")
-
-        H5G_loc_free(&new_loc);
-    } /* if (H5F_addr_defined(dst_oloc.addr)) */
-
-done:
-    FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5O__copy_obj_by_ref() */
-
-
-/*-------------------------------------------------------------------------
- * Function:	H5O_copy_expand_ref
- *
- * Purpose:	Copy the object pointed by _src_ref.
- *
- * Return:	Non-negative on success/Negative on failure
- *
- * Programmer:  Peter Cao
- *		Aug 7 2006
- *
- *-------------------------------------------------------------------------
- */
-herr_t
-H5O_copy_expand_ref(H5F_t *file_src, void *_src_ref, H5F_t *file_dst,
-    void *_dst_ref, size_t ref_count, H5R_type_t ref_type, H5O_copy_t *cpy_info)
-{
-    H5O_loc_t 	dst_oloc;         	/* Copied object object location */
-    H5O_loc_t	src_oloc;          	/* Temporary object location for source object */
-    H5G_loc_t   dst_root_loc;           /* The location of root group of the destination file */
-    const uint8_t *q;                   /* Pointer to source OID to store */
-    uint8_t     *p;                     /* Pointer to destination OID to store */
-    size_t      i;                      /* Local index variable */
-    herr_t	ret_value = SUCCEED;
-
-    FUNC_ENTER_NOAPI(FAIL)
-
-    /* Sanity checks */
-    HDassert(file_src);
-    HDassert(_src_ref);
-    HDassert(file_dst);
-    HDassert(_dst_ref);
-    HDassert(ref_count);
-    HDassert(cpy_info);
-
-    /* Initialize object locations */
-    H5O_loc_reset(&src_oloc);
-    H5O_loc_reset(&dst_oloc);
-    src_oloc.file = file_src;
-    dst_oloc.file = file_dst;
-
-    /* Set up the root group in the destination file */
-    if(NULL == (dst_root_loc.oloc = H5G_oloc(H5G_rootof(file_dst))))
-        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "unable to get object location for root group")
-    if(NULL == (dst_root_loc.path = H5G_nameof(H5G_rootof(file_dst))))
-        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "unable to get path for root group")
-
-    /* Copy object references */
-    if(H5R_OBJECT == ref_type) {
-        hobj_ref_t *src_ref = (hobj_ref_t *)_src_ref;
-        hobj_ref_t *dst_ref = (hobj_ref_t *)_dst_ref;
-
-        /* Making equivalent references in the destination file */
-        for(i = 0; i < ref_count; i++) {
-            /* Set up for the object copy for the reference */
-            q = (uint8_t *)(&src_ref[i]);
-            H5F_addr_decode(src_oloc.file, (const uint8_t **)&q, &(src_oloc.addr));
-            dst_oloc.addr = HADDR_UNDEF;
-
-            /* Attempt to copy object from source to destination file */
-            if(src_oloc.addr != (haddr_t)0) {
-                if(H5O__copy_obj_by_ref(&src_oloc, &dst_oloc, &dst_root_loc, cpy_info) < 0)
-                    HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object")
-            } /* end if */
-            else
-                /* Set parameters so the reference is written as all 0's */
-                HDmemset(&dst_oloc.addr, 0, sizeof(dst_oloc.addr));
-
-            /* Set the object reference info for the destination file */
-            p = (uint8_t *)(&dst_ref[i]);
-            H5F_addr_encode(dst_oloc.file, &p, dst_oloc.addr);
-	} /* end for */
-    }  /* end if */
-    /* Copy region references */
-    else if(H5R_DATASET_REGION == ref_type) {
-        hdset_reg_ref_t *src_ref = (hdset_reg_ref_t *)_src_ref;
-        hdset_reg_ref_t *dst_ref = (hdset_reg_ref_t *)_dst_ref;
-        uint8_t *buf = NULL;    /* Buffer to store serialized selection in */
-        H5HG_t hobjid;          /* Heap object ID */
-        size_t buf_size;        /* Length of object in heap */
-
-        /* Making equivalent references in the destination file */
-        for(i = 0; i < ref_count; i++) {
-            /* Get the heap ID for the dataset region */
-            q = (const uint8_t *)(&src_ref[i]);
-            H5F_addr_decode(src_oloc.file, (const uint8_t **)&q, &(hobjid.addr));
-            UINT32DECODE(q, hobjid.idx);
-
-            if(hobjid.addr != (haddr_t)0) {
-                /* Get the dataset region from the heap (allocate inside routine) */
-                if((buf = (uint8_t *)H5HG_read(src_oloc.file, &hobjid, NULL, &buf_size)) == NULL)
-                    HGOTO_ERROR(H5E_REFERENCE, H5E_READERROR, FAIL, "Unable to read dataset region information")
-
-                /* Get the object oid for the dataset */
-                q = (const uint8_t *)buf;
-                H5F_addr_decode(src_oloc.file, (const uint8_t **)&q, &(src_oloc.addr));
-                dst_oloc.addr = HADDR_UNDEF;
-
-                /* copy the object pointed by the ref to the destination */
-                if(H5O__copy_obj_by_ref(&src_oloc, &dst_oloc, &dst_root_loc, cpy_info) < 0) {
-                    H5MM_xfree(buf);
-                    HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object")
-                } /* end if */
-
-                /* Serialize object ID */
-                p = (uint8_t *)buf;
-                H5F_addr_encode(dst_oloc.file, &p, dst_oloc.addr);
-
-                /* Save the serialized buffer to the destination */
-                if(H5HG_insert(dst_oloc.file, buf_size, buf, &hobjid) < 0) {
-                    H5MM_xfree(buf);
-                    HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "Unable to write dataset region information")
-                } /* end if */
-            } /* end if */
-            else
-                /* Set parameters so the reference is written as all 0's */
-                HDmemset(&hobjid, 0, sizeof(hobjid));
-
-            /* Set the dataset region reference info for the destination file */
-            p = (uint8_t *)(&dst_ref[i]);
-            H5F_addr_encode(dst_oloc.file, &p, hobjid.addr);
-            UINT32ENCODE(p, hobjid.idx);
-
-            /* Free the buffer allocated in H5HG_read() */
-            H5MM_xfree(buf);
-        } /* end for */
-    } /* end if */
-    else
-        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid reference type")
-
-done:
-    FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5O_copy_expand_ref() */
-
-
-/*-------------------------------------------------------------------------
  * Function:    H5O__copy_free_comm_dt_cb
  *
  * Purpose:     Frees the merge committed dt skip list key and object.