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authorJonathan Kim <jkm@hdfgroup.org>2010-03-25 17:29:51 (GMT)
committerJonathan Kim <jkm@hdfgroup.org>2010-03-25 17:29:51 (GMT)
commit20fd1f47b757873e6e8e9b7e283f4264ad9c4f1f (patch)
treeca9f4be0e25512350917c72215a698f75044a3f0 /tools/h5repack/h5repack.c
parent1267cda98921c760bcca9d90767f83248ad28314 (diff)
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[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
Diffstat (limited to 'tools/h5repack/h5repack.c')
-rw-r--r--tools/h5repack/h5repack.c331
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