[svn-r18454] Purpose:

    Fix for the bug1726 - NPOESS: h5repack loses attributes for datasets of 
    type H5T_REFERENCE.

Description:
    include test cases.
    also test cases for attribute with object and region reference.

Tested:
    jam, amani, linew

1 files changed, 331 insertions, 0 deletions

diff --git a/tools/h5repack/h5repack.c b/tools/h5repack/h5repack.c
index db0b158..96b8369 100644
--- a/tools/h5repack/h5repack.c
+++ b/tools/h5repack/h5repack.c
@@ -240,6 +240,337 @@ int h5repack_addlayout(const char* str,
     return 0;
 }
 
+/* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr() 
+ * were located in h5repack_copy.c as static prior to bugfix1726. 
+ * Made shared functions as copy_attr() was needed in h5repack_refs.c. 
+ * However copy_attr() may be obsoleted when H5Acopy is available and put back
+ * others to static in h5repack_copy.c.
+ */
+/*-------------------------------------------------------------------------
+* Function: copy_named_datatype
+*
+* Purpose: Copies the specified datatype anonymously, and returns an open
+*          id for that datatype in the output file.  The first time this
+*          is called it scans every named datatype in travt into a
+*          private stack, afterwards it simply scans that stack.  The id
+*          returned must be closed after it is no longer needed.
+*          named_datatype_free must be called before the program exits
+*          to free the stack.
+*
+* Programmer: Neil Fortner
+*
+* Date: April 14, 2009
+*
+*-------------------------------------------------------------------------
+*/
+hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options)
+{
+    named_dt_t  *dt = *named_dt_head_p; /* Stack pointer */
+    named_dt_t  *dt_ret = NULL;     /* Datatype to return */
+    H5O_info_t  oinfo;              /* Object info of input dtype */
+    hid_t       ret_value = -1;     /* The identifier of the named dtype in the out file */
+
+    if(H5Oget_info(type_in, &oinfo) < 0)
+        goto error;
+
+    if(*named_dt_head_p) 
+    {
+        /* Stack already exists, search for the datatype */
+        while(dt && dt->addr_in != oinfo.addr)
+            dt = dt->next;
+
+        dt_ret = dt;
+    } 
+    else 
+    {
+        /* Create the stack */
+        size_t  i;
+
+        for(i=0; i<travt->nobjs; i++)
+            if(travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) 
+            {
+                /* Push onto the stack */
+                if(NULL == (dt = (named_dt_t *) HDmalloc(sizeof(named_dt_t))))
+                    goto error;
+                dt->next = *named_dt_head_p;
+                *named_dt_head_p = dt;
+
+                /* Update the address and id */
+                dt->addr_in = travt->objs[i].objno;
+                dt->id_out = -1;
+
+                /* Check if this type is the one requested */
+                if(oinfo.addr == dt->addr_in) 
+                {
+                    HDassert(!dt_ret);
+                    dt_ret = dt;
+                } /* end if */
+            } /* end if */
+    } /* end else */
+
+    /* Handle the case that the requested datatype was not found.  This is
+     * possible if the datatype was committed anonymously in the input file. */
+    if(!dt_ret) 
+    {
+        /* Push the new datatype onto the stack */
+        if(NULL == (dt_ret = (named_dt_t *) HDmalloc(sizeof(named_dt_t))))
+            goto error;
+        dt_ret->next = *named_dt_head_p;
+        *named_dt_head_p = dt_ret;
+
+        /* Update the address and id */
+        dt_ret->addr_in = oinfo.addr;
+        dt_ret->id_out = -1;
+    } /* end if */
+
+    /* If the requested datatype does not yet exist in the output file, copy it
+     * anonymously */
+    if(dt_ret->id_out < 0) 
+    {
+        if (options->use_native==1)
+            dt_ret->id_out = h5tools_get_native_type(type_in);
+        else
+            dt_ret->id_out = H5Tcopy(type_in);
+        if(dt_ret->id_out < 0)
+            goto error;
+        if(H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0)
+            goto error;
+    } /* end if */
+
+    /* Set return value */
+    ret_value = dt_ret->id_out;
+
+    /* Increment the ref count on id_out, because the calling function will try
+     * to close it */
+    if(H5Iinc_ref(ret_value) < 0)
+        goto error;
+
+    return(ret_value);
+
+error:
+    return(-1);
+} /* end copy_named_datatype */
+
+
+/*-------------------------------------------------------------------------
+* Function: named_datatype_free
+*
+* Purpose: Frees the stack of named datatypes.
+*
+* Programmer: Neil Fortner
+*
+* Date: April 14, 2009
+*
+*-------------------------------------------------------------------------
+*/
+int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err)
+{
+    named_dt_t *dt = *named_dt_head_p;
+
+    while(dt) 
+    {
+        /* Pop the datatype off the stack and free it */
+        if(H5Tclose(dt->id_out) < 0 && !ignore_err)
+            goto error;
+        dt = dt->next;
+        HDfree(*named_dt_head_p);
+        *named_dt_head_p = dt;
+    } /* end while */
+
+    return 0;
+
+error:
+    return -1;
+} /* end named_datatype_free */
+
+/*-------------------------------------------------------------------------
+* Function: copy_attr
+*
+* Purpose: copy attributes located in LOC_IN, which is obtained either from
+* loc_id = H5Gopen2( fid, name);
+* loc_id = H5Dopen2( fid, name);
+* loc_id = H5Topen2( fid, name);
+*
+* Return: 0, ok, -1 no
+*
+* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+*
+* Date: October, 28, 2003
+*
+*-------------------------------------------------------------------------
+*/
+int copy_attr(hid_t loc_in,
+              hid_t loc_out,
+              named_dt_t **named_dt_head_p,
+              trav_table_t *travt,
+              pack_opt_t *options)
+{
+    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 */
+    void       *buf=NULL;         /* data buffer */
+    hsize_t    nelmts;            /* number of elements in dataset */
+    int        rank;              /* rank of dataset */
+    htri_t     is_named;          /* Whether the datatype is named */
+    hsize_t    dims[H5S_MAX_RANK];/* dimensions of dataset */
+    char       name[255];
+    H5O_info_t oinfo;             /* object info */
+    int        j;
+    unsigned   u;
+
+    if(H5Oget_info(loc_in, &oinfo) < 0)
+        goto error;
+
+    /*-------------------------------------------------------------------------
+    * copy all attributes
+    *-------------------------------------------------------------------------
+    */
+
+    for ( u = 0; u < (unsigned)oinfo.num_attrs; u++)
+    {
+        buf=NULL;
+
+        /* open attribute */
+        if((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+            goto error;
+
+        /* get name */
+        if (H5Aget_name( attr_id, (size_t)255, name ) < 0)
+            goto error;
+
+        /* get the file datatype  */
+        if ((ftype_id = H5Aget_type( attr_id )) < 0 )
+            goto error;
+
+        /* Check if the datatype is committed */
+        if((is_named = H5Tcommitted(ftype_id)) < 0)
+            goto error;
+        if(is_named) 
+        {
+            hid_t fidout;
+
+            /* Create out file id */
+            if((fidout = H5Iget_file_id(loc_out)) < 0)
+                goto error;
+
+            /* Copy named dt */
+            if((wtype_id = copy_named_datatype(ftype_id, fidout, named_dt_head_p,
+                    travt, options)) < 0) 
+            {
+                H5Fclose(fidout);
+                goto error;
+            } /* end if */
+
+            if(H5Fclose(fidout) < 0)
+                goto error;
+        } /* end if */
+
+        /* 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;
+
+        nelmts=1;
+        for (j=0; j<rank; j++)
+            nelmts*=dims[j];
+
+        /* wtype_id will have already been set if using a named dtype */
+        if(!is_named) 
+        {
+            if (options->use_native==1)
+                wtype_id = h5tools_get_native_type(ftype_id);
+            else
+                wtype_id = H5Tcopy(ftype_id);
+        } /* end if */
+
+        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
+        * this is done on a second sweep of the file that just copies
+        * the referenced objects
+        *-------------------------------------------------------------------------
+        */
+
+        if (H5T_REFERENCE==H5Tget_class(wtype_id))
+        {
+            ;
+        }
+        else
+        {
+            /*-------------------------------------------------------------------------
+            * read to memory
+            *-------------------------------------------------------------------------
+            */
+
+            buf = (void *)HDmalloc((size_t)(nelmts * msize));
+            if(buf == NULL) 
+            {
+                error_msg("h5repack", "cannot read into memory\n" );
+                goto error;
+            }
+            if(H5Aread(attr_id, wtype_id, buf) < 0)
+                goto error;
+
+            /*-------------------------------------------------------------------------
+            * copy
+            *-------------------------------------------------------------------------
+            */
+
+            if((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+                goto error;
+            if(H5Awrite(attr_out, wtype_id, buf) < 0)
+                goto error;
+
+            /*close*/
+            if(H5Aclose(attr_out) < 0)
+                goto error;
+
+
+            if(buf)
+                free(buf);
+
+        } /*H5T_REFERENCE*/
+
+
+        if(options->verbose)
+            printf(FORMAT_OBJ_ATTR, "attr", name);
+
+        /*-------------------------------------------------------------------------
+        * 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);
+        if (buf)
+            free(buf);
+    } H5E_END_TRY;
+    return -1;
+}
 
 /*-------------------------------------------------------------------------
 * Function: check_options