file.c

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/**
 * MOAB, a Mesh-Oriented datABase, is a software component for creating,
 * storing and accessing finite element mesh data.
 *
 * Copyright 2004 Sandia Corporation. Under the terms of Contract
 * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
 * retains certain rights in this software.
 *
 * This library is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public
 * License as published by the Free Software Foundation; either
 * version 2.1 of the License, or (at your option) any later version.
 *
 */
 
#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <H5Fpublic.h>
#include <H5Ppublic.h>
#include <H5Gpublic.h>
#include <H5Spublic.h>
#include <H5Tpublic.h>
#include <H5Apublic.h>
#ifdef MOAB_HAVE_HDF5_PARALLEL
#include <H5FDmpi.h>
#include <H5FDmpio.h>
#endif
#include "mhdf.h"
#include "status.h"
#include "names-and-paths.h"
#include "util.h"
#include "file-handle.h"
 
static int make_hdf_group( const char* path, hid_t file, size_t size, mhdf_Status* status );
 
mhdf_FileHandle mhdf_createFile( const char* filename,
 int overwrite,
 const char** elem_type_list,
 size_t elem_list_len,
 hid_t id_type,
 mhdf_Status* status )
{
 FileHandle* file_ptr;
 unsigned int flags;
 unsigned char idx;
 size_t i;
 hid_t enum_id, group_id;
 int rval;
 API_BEGIN;
 
 if( elem_list_len > 255 )
 {
 mhdf_setFail( status, "Element type list too long." );
 return NULL;
 }
 mhdf_setOkay( status );
 
 /* Create struct to hold working data */
 file_ptr = mhdf_alloc_FileHandle( 0, id_type, status );
 if( !file_ptr ) return NULL;
 
 /* Create the file */
 flags = overwrite ? H5F_ACC_TRUNC : H5F_ACC_EXCL;
 file_ptr->hdf_handle = H5Fcreate( filename, flags, H5P_DEFAULT, H5P_DEFAULT );
 if( file_ptr->hdf_handle < 0 )
 {
 mhdf_setFail( status, "Failed to create file \"%s\"", filename );
 free( file_ptr );
 return NULL;
 }
 
 /* Create file structure */
 if( !make_hdf_group( ROOT_GROUP, file_ptr->hdf_handle, 6, status ) ||
 !make_hdf_group( TAG_GROUP, file_ptr->hdf_handle, 0, status ) ||
 !make_hdf_group( ELEMENT_GROUP, file_ptr->hdf_handle, 8, status ) ||
 !make_hdf_group( NODE_GROUP, file_ptr->hdf_handle, 3, status ) ||
 !make_hdf_group( SET_GROUP, file_ptr->hdf_handle, 5, status ) ||
 !make_hdf_group( NODE_TAG_GROUP, file_ptr->hdf_handle, 0, status ) ||
 !make_hdf_group( SET_TAG_GROUP, file_ptr->hdf_handle, 0, status ) )
 {
 H5Fclose( file_ptr->hdf_handle );
 free( file_ptr );
 return NULL;
 }
 
 /* Store the max ID as an attribite on the /tstt/ group */
#if defined( H5Gopen_vers ) && H5Gopen_vers > 1
 group_id = H5Gopen2( file_ptr->hdf_handle, ROOT_GROUP, H5P_DEFAULT );
#else
 group_id = H5Gopen( file_ptr->hdf_handle, ROOT_GROUP );
#endif
 rval = mhdf_create_scalar_attrib( group_id, MAX_ID_ATTRIB, H5T_NATIVE_ULONG, &file_ptr->max_id, status );
 H5Gclose( group_id );
 if( !rval )
 {
 H5Fclose( file_ptr->hdf_handle );
 free( file_ptr );
 return NULL;
 }
 
 /* Create the type name list in file */
 enum_id = H5Tenum_create( H5T_NATIVE_UCHAR );
 if( enum_id < 0 )
 {
 mhdf_setFail( status, "Failed to store elem type list." );
 H5Fclose( file_ptr->hdf_handle );
 free( file_ptr );
 return NULL;
 }
 for( i = 0; i < elem_list_len; ++i )
 {
 if( !elem_type_list[i] || !*elem_type_list[i] ) continue;
 
 idx = (unsigned char)i;
 if( H5Tenum_insert( enum_id, elem_type_list[i], &idx ) < 0 )
 {
 mhdf_setFail( status, "Failed to store elem type list." );
 H5Fclose( file_ptr->hdf_handle );
 free( file_ptr );
 return NULL;
 }
 }
#if defined( H5Tcommit_vers ) && H5Tcommit_vers > 1
 if( H5Tcommit2( file_ptr->hdf_handle, TYPE_ENUM_PATH, enum_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT ) < 0 )
#else
 if( H5Tcommit( file_ptr->hdf_handle, TYPE_ENUM_PATH, enum_id ) < 0 )
#endif
 {
 mhdf_setFail( status, "Failed to store elem type list." );
 H5Fclose( file_ptr->hdf_handle );
 free( file_ptr );
 return NULL;
 }
 H5Tclose( enum_id );
 
 API_END_H( 1 );
 return file_ptr;
}
 
mhdf_FileHandle mhdf_openFile( const char* filename,
 int writeable,
 unsigned long* max_id_out,
 hid_t id_type,
 mhdf_Status* status )
{
 return mhdf_openFileWithOpt( filename, writeable, max_id_out, id_type, H5P_DEFAULT, status );
}
 
int mhdf_countOpenHandles( mhdf_FileHandle file_handle )
{
 return H5Fget_obj_count( ( (FileHandle*)file_handle )->hdf_handle, H5F_OBJ_ALL );
}
 
static herr_t get_max_id( hid_t group_id, const char* subgroup, const char* datatable, unsigned long* data )
{
 unsigned long id;
 hid_t elem_id, conn_id, attr_id, space_id;
 herr_t rval;
 int rank;
 hsize_t dims[2];
 
#if defined( H5Gopen_vers ) && H5Gopen_vers > 1
 elem_id = H5Gopen2( group_id, subgroup, H5P_DEFAULT );
#else
 elem_id = H5Gopen( group_id, subgroup );
#endif
 if( elem_id < 0 ) return (herr_t)-1;
 
#if defined( H5Dopen_vers ) && H5Dopen_vers > 1
 conn_id = H5Dopen2( elem_id, datatable, H5P_DEFAULT );
#else
 conn_id = H5Dopen( elem_id, datatable );
#endif
 H5Gclose( elem_id );
 if( conn_id < 0 ) return (herr_t)-1;
 
 space_id = H5Dget_space( conn_id );
 if( space_id < 0 )
 {
 H5Dclose( conn_id );
 return -1;
 }
 
 rank = H5Sget_simple_extent_ndims( space_id );
 if( rank <= 0 || rank > 2 )
 {
 H5Dclose( conn_id );
 H5Sclose( space_id );
 return -1;
 }
 
 rval = H5Sget_simple_extent_dims( space_id, dims, NULL );
 H5Sclose( space_id );
 if( rval < 0 )
 {
 H5Dclose( conn_id );
 return -1;
 }
 
 attr_id = H5Aopen_name( conn_id, START_ID_ATTRIB );
 H5Dclose( conn_id );
 if( attr_id < 0 ) return (herr_t)-1;
 
 rval = H5Aread( attr_id, H5T_NATIVE_ULONG, &id );
 H5Aclose( attr_id );
 if( rval < 0 ) return rval;
 
 id += dims[0];
 if( id > *data ) *data = id;
 return 0;
}
 
static herr_t max_id_iter( hid_t group_id, const char* name, void* data )
{
 return get_max_id( group_id, name, CONNECTIVITY_NAME, (unsigned long*)data );
}
 
static int scan_for_max_id( FileHandle* file_ptr, mhdf_Status* status )
{
 hid_t group_id;
 herr_t rval;
 
 /* Check for new format, with max_id as attrib of root group */
#if defined( H5Gopen_vers ) && H5Gopen_vers > 1
 group_id = H5Gopen2( file_ptr->hdf_handle, ROOT_GROUP, H5P_DEFAULT );
#else
 group_id = H5Gopen( file_ptr->hdf_handle, ROOT_GROUP );
#endif
 if( group_id < 0 )
 {
 mhdf_setFail( status, "Internal error - invalid file." );
 return 0;
 }
 if( mhdf_read_scalar_attrib( group_id, MAX_ID_ATTRIB, H5T_NATIVE_ULONG, &file_ptr->max_id, status ) )
 {
 H5Gclose( group_id );
 return 1;
 }
 
 /* Didn't find it, scan the elements group */
 rval = H5Giterate( group_id, ELEMENT_GROUP_NAME, 0, &max_id_iter, &file_ptr->max_id );
 if( rval )
 {
 H5Gclose( group_id );
 mhdf_setFail( status, "Internal error -- invalid file." );
 return 0;
 }
 
 /* Check node table too */
 rval = get_max_id( group_id, NODE_GROUP_NAME, "coordinates", (unsigned long*)( &file_ptr->max_id ) );
 if( rval )
 {
 H5Gclose( group_id );
 mhdf_setFail( status, "Internal error -- invalid file." );
 return 0;
 }
 
 /* Check set table, if it exists */
 rval = mhdf_is_in_group( group_id, SET_GROUP_NAME, status );
 if( rval < 1 )
 {
 H5Gclose( group_id );
 return !rval;
 }
 rval = get_max_id( group_id, SET_GROUP_NAME, SET_META_NAME, (unsigned long*)( &file_ptr->max_id ) );
 H5Gclose( group_id );
 if( rval )
 {
 mhdf_setFail( status, "Internal error -- invalid file." );
 return 0;
 }
 
 return 1;
}
 
mhdf_FileHandle mhdf_openFileWithOpt( const char* filename,
 int writable,
 unsigned long* max_id_out,
 hid_t id_type,
 hid_t access_prop,
 mhdf_Status* status )
{
 FileHandle* file_ptr;
 unsigned int flags;
 hid_t group_id;
 int check_is_hdf5 = 1;
#ifdef MOAB_HAVE_HDF5_PARALLEL
 herr_t err;
 MPI_Comm comm;
 MPI_Info info;
#endif
 API_BEGIN;
 
 /* Check if file is HDF5 */
 /* Don't do this because it can't handle MPI-IO driver code that
 passes options via prefixes on the file name. */
#ifdef MOAB_HAVE_HDF5_PARALLEL
 if( access_prop != H5P_DEFAULT )
 {
 err = H5Pget_fapl_mpio( access_prop, &comm, &info );
 if( err >= 0 )
 {
 check_is_hdf5 = 0;
 /* MPI Documentation is inconsistent with regards to whether
 or not the above call dup's these, but my testing with 1.8.3
 indicates that at least for that version they are not.
 MPI_Comm_free(&comm);
 MPI_Info_free(&info); */
 }
 }
#endif
 if( check_is_hdf5 && H5Fis_hdf5( filename ) <= 0 )
 {
 mhdf_setFail( status, "%s: File is not HDF5", filename );
 return NULL;
 }
 
 /* Create struct to hold working data */
 file_ptr = mhdf_alloc_FileHandle( 0, id_type, status );
 if( !file_ptr )
 {
 mhdf_setFail( status, "Memory allocation failed" );
 return NULL;
 }
 
 /* Create the file */
 flags = writable ? H5F_ACC_RDWR : H5F_ACC_RDONLY;
 file_ptr->hdf_handle = H5Fopen( filename, flags, access_prop );
 if( file_ptr->hdf_handle < 0 )
 {
 mhdf_setFail( status, "Failed to open file \"%s\"", filename );
 free( file_ptr );
 return NULL;
 }
 
 /* Check for TSTT data in file */
#if defined( H5Gopen_vers ) && H5Gopen_vers > 1
 group_id = H5Gopen2( file_ptr->hdf_handle, ROOT_GROUP, H5P_DEFAULT );
#else
 group_id = H5Gopen( file_ptr->hdf_handle, ROOT_GROUP );
#endif
 if( group_id < 0 )
 {
 mhdf_setFail( status, "Invalid file \"%s\"\n", filename );
 H5Fclose( file_ptr->hdf_handle );
 free( file_ptr );
 return NULL;
 }
 H5Gclose( group_id );
 
 /* Get max id */
 if( !scan_for_max_id( file_ptr, status ) )
 {
 H5Fclose( file_ptr->hdf_handle );
 mhdf_setFail( status, "Internal error reading file" );
 free( file_ptr );
 return NULL;
 }
 
 if( max_id_out ) *max_id_out = file_ptr->max_id;
 
 mhdf_setOkay( status );
 API_END_H( 1 );
 return file_ptr;
}
 
void mhdf_getElemName( mhdf_FileHandle file_handle,
 unsigned int type_index,
 char* buffer,
 size_t buf_size,
 mhdf_Status* status )
{
 FileHandle* file_ptr;
 herr_t rval;
 hid_t enum_id;
 API_BEGIN;
 
 if( type_index > 255 )
 {
 mhdf_setFail( status, "Type index out of bounds." );
 return;
 }
 
 file_ptr = (FileHandle*)( file_handle );
 if( !mhdf_check_valid_file( file_ptr, status ) ) return;
 
 enum_id = get_elem_type_enum( file_ptr, status );
 if( enum_id < 0 ) return;
 
 rval = H5Tconvert( H5T_NATIVE_UINT, H5Tget_super( enum_id ), 1, &type_index, NULL, H5P_DEFAULT );
 if( rval < 0 )
 {
 H5Tclose( enum_id );
 mhdf_setFail( status, "Internal error converting to enum type." );
 return;
 }
 
 rval = H5Tenum_nameof( enum_id, &type_index, buffer, buf_size );
 H5Tclose( enum_id );
 if( rval < 0 )
 mhdf_setFail( status, "H5Tenum_nameof failed. Invalid type index?" );
 else
 mhdf_setOkay( status );
 
 API_END;
}
 
int mhdf_checkOpenHandles( mhdf_FileHandle handle, mhdf_Status* status )
{
 FileHandle* file_ptr;
 int result;
 API_BEGIN;
 
 file_ptr = (FileHandle*)( handle );
 if( !mhdf_check_valid_file( file_ptr, status ) ) return -1;
 
 /* Check for open handles. HDF5 will not actually close the
 file until all handles are closed. */
 result = H5Fget_obj_count( file_ptr->hdf_handle, H5F_OBJ_ALL );
 if( result != 1 )
 {
 mhdf_setFail( status,
 "Cannot close file with open handles: "
 "%d file, %d data, %d group, %d type, %d attr\n",
 H5Fget_obj_count( file_ptr->hdf_handle, H5F_OBJ_FILE ) - 1,
 H5Fget_obj_count( file_ptr->hdf_handle, H5F_OBJ_DATASET ),
 H5Fget_obj_count( file_ptr->hdf_handle, H5F_OBJ_GROUP ),
 H5Fget_obj_count( file_ptr->hdf_handle, H5F_OBJ_DATATYPE ),
 H5Fget_obj_count( file_ptr->hdf_handle, H5F_OBJ_ATTR ) );
 return result - 1;
 }
 
 API_END_H( 0 );
 return 0;
}
 
void mhdf_closeFile( mhdf_FileHandle handle, mhdf_Status* status )
{
 FileHandle* file_ptr;
 API_BEGIN;
 
 file_ptr = (FileHandle*)( handle );
 if( !mhdf_check_valid_file( file_ptr, status ) ) return;
 /*
 if (file_ptr->open_handle_count)
 {
 mhdf_setError( status, "Cannot close file with %d open data handles.",
 file_ptr->open_handle_count );
 return;
 }
 */
 
 /* Check for open handles. HDF5 will not actually close the
 file until all handles are closed. */
 if( mhdf_checkOpenHandles( handle, status ) ) return;
 
 if( 0 > H5Fclose( file_ptr->hdf_handle ) )
 {
 mhdf_setFail( status, "H5FClose failed. Invalid handle?" );
 return;
 }
 
 memset( file_ptr, 0, sizeof( FileHandle ) );
 free( file_ptr );
 mhdf_setOkay( status );
 API_END_H( -1 );
}
 
void mhdf_closeData( mhdf_FileHandle file, hid_t handle, mhdf_Status* status )
{
 FileHandle* file_ptr;
 herr_t rval = -1;
 
 file_ptr = (FileHandle*)( file );
 if( !mhdf_check_valid_file( file_ptr, status ) ) return;
 
 switch( H5Iget_type( handle ) )
 {
 case H5I_GROUP:
 rval = H5Gclose( handle );
 break;
 case H5I_DATATYPE:
 rval = H5Tclose( handle );
 break;
 case H5I_DATASPACE:
 rval = H5Sclose( handle );
 break;
 case H5I_DATASET:
 rval = H5Dclose( handle );
 break;
 default:
 rval = -1;
 }
 
 if( rval < 0 )
 {
 mhdf_setFail( status, "H5Xclose failed. Invalid handle?\n" );
 }
 else
 {
 file_ptr->open_handle_count--;
 mhdf_setOkay( status );
 }
}
 
void mhdf_addElement( mhdf_FileHandle file_handle, const char* name, unsigned int elem_type, mhdf_Status* status )
{
 FileHandle* file_ptr = (FileHandle*)file_handle;
 hid_t group_id, tag_id, enum_id;
 char *path, *ptr;
 size_t name_len;
 herr_t rval;
 API_BEGIN;
 
 if( !mhdf_check_valid_file( file_ptr, status ) ) return;
 
 name_len = mhdf_name_to_path( name, NULL, 0 );
 name_len += strlen( ELEMENT_GROUP ) + 1;
 path = (char*)mhdf_malloc( name_len, status );
 if( !path ) return;
 
 strcpy( path, ELEMENT_GROUP );
 ptr = path + strlen( ELEMENT_GROUP );
 if( !mhdf_path_to_name( name, ptr ) )
 {
 mhdf_setFail( status, "Invalid character string in internal file path: \"%s\"\n", name );
 return;
 }
 
#if defined( H5Gcreate_vers ) && H5Gcreate_vers > 1
 group_id = H5Gcreate2( file_ptr->hdf_handle, path, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT );
#else
 group_id = H5Gcreate( file_ptr->hdf_handle, path, 3 );
#endif
 if( group_id < 0 )
 {
 mhdf_setFail( status, "Creation of \"%s\" group failed.\n", path );
 free( path );
 return;
 }
 free( path );
 
#if defined( H5Gcreate_vers ) && H5Gcreate_vers > 1
 tag_id = H5Gcreate2( group_id, DENSE_TAG_SUBGROUP, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT );
#else
 tag_id = H5Gcreate( group_id, DENSE_TAG_SUBGROUP, 0 );
#endif
 if( tag_id < 0 )
 {
 H5Gclose( group_id );
 mhdf_setFail( status, "Creation of tag subgroup failed.\n" );
 return;
 }
 H5Gclose( tag_id );
 
 enum_id = get_elem_type_enum( file_ptr, status );
 if( enum_id < 0 )
 {
 H5Gclose( group_id );
 return;
 }
 
 rval = H5Tconvert( H5T_NATIVE_UINT, H5Tget_super( enum_id ), 1, &elem_type, NULL, H5P_DEFAULT );
 if( rval < 0 )
 {
 H5Gclose( group_id );
 H5Tclose( enum_id );
 mhdf_setFail( status, "Internal error converting to enum type." );
 return;
 }
 
 rval = mhdf_create_scalar_attrib( group_id, ELEM_TYPE_ATTRIB, enum_id, &elem_type, status );
 H5Tclose( enum_id );
 if( rval < 0 )
 {
 H5Gclose( group_id );
 return;
 }
 
 H5Gclose( group_id );
 mhdf_setOkay( status );
 API_END;
}
 
char** mhdf_getElemHandles( mhdf_FileHandle file_handle, unsigned int* count_out, mhdf_Status* status )
{
 hsize_t count, length, i;
 char** buffer;
 char* current;
 hid_t group_id;
 herr_t rval;
 ssize_t rlen = 0;
 size_t remaining;
 FileHandle* file_ptr = (FileHandle*)file_handle;
 if( !mhdf_check_valid_file( file_ptr, status ) ) return NULL;
 
#if defined( H5Gopen_vers ) && H5Gopen_vers > 1
 group_id = H5Gopen2( file_ptr->hdf_handle, ELEMENT_GROUP, H5P_DEFAULT );
#else
 group_id = H5Gopen( file_ptr->hdf_handle, ELEMENT_GROUP );
#endif
 if( group_id < 0 )
 {
 mhdf_setFail( status, "Invalid file -- element group does not exist." );
 return NULL;
 }
 
 rval = H5Gget_num_objs( group_id, &count );
 if( rval < 0 )
 {
 H5Gclose( group_id );
 mhdf_setFail( status, "Internal error calling H5Gget_num_objs." );
 return NULL;
 }
 *count_out = count;
 
 for( i = 0; i < count; ++i )
 {
 rlen += H5Gget_objname_by_idx( group_id, i, NULL, 0 ) + 1;
 }
 
 length = count * sizeof( char* ) + rlen;
 buffer = (char**)mhdf_malloc( length, status );
 if( !buffer )
 {
 H5Gclose( group_id );
 return NULL;
 }
 current = (char*)( buffer + count );
 remaining = rlen;
 
 for( i = 0; i < count; ++i )
 {
 buffer[i] = current;
 rlen = H5Gget_objname_by_idx( group_id, i, current, remaining ) + 1;
 if( rlen < 0 )
 {
 H5Gclose( group_id );
 free( buffer );
 mhdf_setFail( status, "Internal error calling H5Gget_objname_by_idx." );
 return NULL;
 }
 
 mhdf_path_to_name( current, current );
 remaining -= rlen;
 current += rlen;
 }
 
 H5Gclose( group_id );
 mhdf_setOkay( status );
 return buffer;
}
 
void mhdf_getElemTypeName( mhdf_FileHandle file_handle,
 const char* elem_handle,
 char* buffer,
 size_t buf_len,
 mhdf_Status* status )
{
 FileHandle* file_ptr;
 hid_t elem_id, type_id, attr_id;
 char bytes[16];
 herr_t rval;
 API_BEGIN;
 
 if( NULL == buffer || buf_len < 2 )
 {
 mhdf_setFail( status, "invalid input" );
 return;
 }
 buffer[0] = '\0';
 
 file_ptr = (FileHandle*)( file_handle );
 if( !mhdf_check_valid_file( file_ptr, status ) ) return;
 
 elem_id = mhdf_elem_group_from_handle( file_ptr, elem_handle, status );
 if( elem_id < 0 ) return;
 
 attr_id = H5Aopen_name( elem_id, ELEM_TYPE_ATTRIB );
 H5Gclose( elem_id );
 if( attr_id < 0 )
 {
 mhdf_setFail( status, "Missing element type attribute. Invalid file." );
 return;
 }
 
 type_id = H5Aget_type( attr_id );
 assert( type_id > 0 );
 
 rval = H5Aread( attr_id, type_id, bytes );
 H5Aclose( attr_id );
 if( rval < 0 )
 {
 H5Tclose( type_id );
 mhdf_setFail( status, "Failed to read element type attribute. Invalid file." );
 return;
 }
 
 rval = H5Tenum_nameof( type_id, bytes, buffer, buf_len );
 H5Tclose( type_id );
 if( rval < 0 )
 {
 mhdf_setFail( status, "Invalid datatype for element type attribute. Invalid file." );
 return;
 }
 
 mhdf_setOkay( status );
 API_END;
 return;
}
 
static int make_hdf_group( const char* path, hid_t file, size_t sz, mhdf_Status* status )
{
#if defined( H5Gcreate_vers ) && H5Gcreate_vers > 1
 hid_t handle = H5Gcreate2( file, path, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT );
 /* empty statement to avoid compiler warning */
 if( sz )
 {
 }
#else
 hid_t handle = H5Gcreate( file, path, sz );
#endif
 if( handle < 0 )
 {
 mhdf_setFail( status, "Failed to create \"%s\" group.", path );
 return 0;
 }
 else
 {
 H5Gclose( handle );
 return 1;
 }
}
 
const char* mhdf_node_type_handle( void )
{
 static const char rval[] = "nodes";
 return rval;
}
 
const char* mhdf_set_type_handle( void )
{
 static const char rval[] = "sets";
 return rval;
}
 
int mhdf_isPolyElement( mhdf_FileHandle file_handle, const char* elem_handle, mhdf_Status* status )
{
 FileHandle* file_ptr;
 hid_t elem_id;
 int rval;
 API_BEGIN;
 
 file_ptr = (FileHandle*)( file_handle );
 if( !mhdf_check_valid_file( file_ptr, status ) ) return -1;
 
 elem_id = mhdf_elem_group_from_handle( file_ptr, elem_handle, status );
 if( elem_id < 0 ) return -1;
 
 mhdf_setOkay( status );
 rval = mhdf_is_in_group( elem_id, POLY_INDEX_NAME, status );
 H5Gclose( elem_id );
 API_END;
 return rval;
}
 
void mhdf_writeHistory( mhdf_FileHandle file_handle, const char** strings, int num_strings, mhdf_Status* status )
{
 FileHandle* file_ptr;
 hid_t data_id, type_id, space_id;
 hsize_t dim = (hsize_t)num_strings;
 herr_t rval;
 API_BEGIN;
 
 file_ptr = (FileHandle*)( file_handle );
 if( !mhdf_check_valid_file( file_ptr, status ) ) return;
 
 type_id = H5Tcopy( H5T_C_S1 );
 if( type_id < 0 || H5Tset_size( type_id, H5T_VARIABLE ) < 0 )
 {
 if( type_id >= 0 ) H5Tclose( type_id );
 mhdf_setFail( status, "Could not create variable length string type." );
 return;
 }
 
 space_id = H5Screate_simple( 1, &dim, NULL );
 if( space_id < 0 )
 {
 H5Tclose( type_id );
 mhdf_setFail( status, "H5Screate_simple failed." );
 return;
 }
 
#if defined( H5Dcreate_vers ) && H5Dcreate_vers > 1
 data_id =
 H5Dcreate2( file_ptr->hdf_handle, HISTORY_PATH, type_id, space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT );
#else
 data_id = H5Dcreate( file_ptr->hdf_handle, HISTORY_PATH, type_id, space_id, H5P_DEFAULT );
#endif
 H5Sclose( space_id );
 if( data_id < 0 )
 {
 H5Tclose( type_id );
 mhdf_setFail( status, "Failed to create \"%s\".", HISTORY_PATH );
 return;
 }
 
 rval = H5Dwrite( data_id, type_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, strings );
 H5Dclose( data_id );
 H5Tclose( type_id );
 if( rval < 0 )
 {
 H5Gunlink( file_ptr->hdf_handle, HISTORY_PATH );
 mhdf_setFail( status, "Failed to write history data." );
 return;
 }
 
 mhdf_setOkay( status );
 API_END;
}
 
char** mhdf_readHistory( mhdf_FileHandle file_handle, int* num_strings, mhdf_Status* status )
{
 FileHandle* file_ptr;
 hid_t data_id, type_id, space_id, group_id;
 hsize_t dim;
 herr_t rval;
 char** array;
 API_BEGIN;
 
 file_ptr = (FileHandle*)( file_handle );
 if( !mhdf_check_valid_file( file_ptr, status ) ) return NULL;
 
 /* check if file contains history data */
#if defined( H5Gopen_vers ) && H5Gopen_vers > 1
 group_id = H5Gopen2( file_ptr->hdf_handle, ROOT_GROUP, H5P_DEFAULT );
#else
 group_id = H5Gopen( file_ptr->hdf_handle, ROOT_GROUP );
#endif
 if( group_id < 0 )
 {
 mhdf_setFail( status, "Could not open root group. Invalid file." );
 return NULL;
 }
 
 rval = mhdf_is_in_group( group_id, HISTORY_NAME, status );
 if( rval < 1 )
 {
 H5Gclose( group_id );
 *num_strings = 0;
 if( 0 == rval ) mhdf_setOkay( status );
 return NULL;
 }
 
#if defined( H5Dopen_vers ) && H5Dopen_vers > 1
 data_id = H5Dopen2( group_id, HISTORY_NAME, H5P_DEFAULT );
#else
 data_id = H5Dopen( group_id, HISTORY_NAME );
#endif
 H5Gclose( group_id );
 if( data_id < 0 )
 {
 mhdf_setFail( status, "Failed to open \"%s\".", HISTORY_PATH );
 return NULL;
 }
 
 space_id = H5Dget_space( data_id );
 if( space_id < 0 )
 {
 H5Dclose( data_id );
 mhdf_setFail( status, "Internal error calling H5Dget_space." );
 return NULL;
 }
 
 if( 1 != H5Sget_simple_extent_ndims( space_id ) || 1 != H5Sget_simple_extent_dims( space_id, &dim, NULL ) )
 {
 H5Dclose( data_id );
 mhdf_setFail( status, "Invalid dimension for \"%s\".", HISTORY_PATH );
 return NULL;
 }
 H5Sclose( space_id );
 
 if( 0 == dim )
 {
 H5Dclose( data_id );
 *num_strings = 0;
 mhdf_setOkay( status );
 return NULL;
 }
 
 array = (char**)mhdf_malloc( dim * sizeof( char* ), status );
 if( !array )
 {
 H5Dclose( data_id );
 return NULL;
 }
 
 type_id = H5Tcopy( H5T_C_S1 );
 if( type_id < 0 || H5Tset_size( type_id, H5T_VARIABLE ) < 0 )
 {
 H5Dclose( data_id );
 if( type_id >= 0 ) H5Tclose( type_id );
 mhdf_setFail( status, "Could not create variable length string type." );
 free( array );
 return NULL;
 }
 
 rval = H5Dread( data_id, type_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, array );
 H5Tclose( type_id );
 H5Dclose( data_id );
 if( rval < 0 )
 {
 free( array );
 mhdf_setFail( status, "H5Dread failed." );
 return NULL;
 }
 
 *num_strings = dim;
 mhdf_setOkay( status );
 API_END;
 return array;
}
 
void mhdf_getNextStartId( mhdf_FileHandle file, mhdf_index_t* start_id_out, mhdf_Status* status )
{
 FileHandle* file_ptr = (FileHandle*)file;
 API_BEGIN;
 
 mhdf_setOkay( status );
 if( mhdf_check_valid_file( file_ptr, status ) ) *start_id_out = file_ptr->max_id + 1;
 
 API_END;
}