static rc_t vdb_info_1( VSchema * schema, dump_format_t format, const VDBManager *mgr,
const char * acc_or_path, const char * table_name )
{
rc_t rc = 0;
vdb_info_data data;
memset( &data, 0, sizeof data );
data.s_platform = PT_NONE;
data.acc = acc_or_path;
/* #1 get path-type */
data.s_path_type = get_path_type( mgr, acc_or_path );
if ( data.s_path_type[ 0 ] == 'D' || data.s_path_type[ 0 ] == 'T' )
{
rc_t rc1;
/* #2 fork by table or database */
switch ( data.s_path_type[ 0 ] )
{
case 'D' : vdb_info_db( &data, schema, mgr ); break;
case 'T' : vdb_info_tab( &data, schema, mgr ); break;
}
/* try to resolve the path locally */
rc1 = resolve_accession( acc_or_path, data.path, sizeof data.path, false ); /* vdb-dump-helper.c */
if ( rc1 == 0 )
data.file_size = get_file_size( data.path, false );
else
{
/* try to resolve the path remotely */
rc1 = resolve_accession( acc_or_path, data.path, sizeof data.path, true ); /* vdb-dump-helper.c */
if ( rc1 == 0 )
{
data.file_size = get_file_size( data.path, true );
/* try to find out the cache-file */
rc1 = resolve_cache( acc_or_path, data.cache, sizeof data.cache ); /* vdb-dump-helper.c */
if ( rc1 == 0 )
{
/* try to find out cache completeness */
check_cache_comleteness( data.cache, &data.cache_percent, &data.bytes_in_cache );
}
}
}
switch ( format )
{
case df_xml : rc = vdb_info_print_xml( &data ); break;
case df_json : rc = vdb_info_print_json( &data ); break;
case df_csv : rc = vdb_info_print_sep( &data, ',' ); break;
case df_tab : rc = vdb_info_print_sep( &data, '\t' ); break;
case df_sql : rc = vdb_info_print_sql( table_name, &data ); break;
default : rc = vdb_info_print_dflt( &data ); break;
}
}
return rc;
}
static rc_t report_references( const VDBManager *vdb_mgr, VFSManager * vfs_mgr,
const char * spec, bool extended )
{
const String * resolved = NULL;
rc_t rc = resolve_accession( vfs_mgr, spec, &resolved );
if ( rc == 0 && resolved != NULL )
{
rc = KOutMsg( "resolved into '%S'\n", resolved );
if ( rc == 0 )
{
int path_type = ( VDBManagerPathType ( vdb_mgr, "%s", spec ) & ~ kptAlias );
switch( path_type )
{
case kptDatabase :
rc = report_ref_database( vdb_mgr, vfs_mgr, spec, extended );
break;
case kptTable :
KOutMsg( "cannot report references on a table-object\n" );
rc = RC ( rcApp, rcNoTarg, rcAccessing, rcParam, rcInvalid );
(void)LOGERR( klogErr, rc, "cannot report references on a table-object" );
break;
default :
KOutMsg( "the given object is not a vdb-database\n" );
rc = RC ( rcApp, rcNoTarg, rcAccessing, rcParam, rcInvalid );
(void)LOGERR( klogErr, rc, "the given object is not a vdb-database" );
break;
}
}
StringWhack ( resolved );
}
return rc;
}
static rc_t report_ref_loc( const VDBManager *vdb_mgr, VFSManager * vfs_mgr, const char * seq_id )
{
const String * path;
rc_t rc = resolve_accession( vfs_mgr, seq_id, &path );
if ( rc == 0 )
{
rc = KOutMsg( "location:\t%S\n", path );
if ( rc == 0 )
{
uint32_t pt = VDBManagerPathType ( vdb_mgr, "%S", path );
const char * spt = path_type_2_str( pt );
rc = KOutMsg( "pathtype:\t%s\n", spt );
}
free ( (void*) path );
}
return rc;
}
static rc_t vdb_info_1( VSchema * schema, dump_format_t format, const VDBManager *mgr,
const char * acc_or_path, const char * table_name )
{
rc_t rc = 0;
vdb_info_data data;
memset( &data, 0, sizeof data );
data.s_platform = PT_NONE;
data.acc = acc_or_path;
/* #1 get path-type */
data.s_path_type = get_path_type( mgr, acc_or_path );
if ( data.s_path_type[ 0 ] == 'D' || data.s_path_type[ 0 ] == 'T' )
{
rc_t rc1;
/* #2 fork by table or database */
switch ( data.s_path_type[ 0 ] )
{
case 'D' : vdb_info_db( &data, schema, mgr ); break;
case 'T' : vdb_info_tab( &data, schema, mgr ); break;
}
rc1 = resolve_accession( acc_or_path, data.path, sizeof data.path, false );
if ( rc1 == 0 )
data.file_size = get_file_size( data.path );
switch ( format )
{
case df_xml : rc = vdb_info_print_xml( &data ); break;
case df_json : rc = vdb_info_print_json( &data ); break;
case df_csv : rc = vdb_info_print_sep( &data, ',' ); break;
case df_tab : rc = vdb_info_print_sep( &data, '\t' ); break;
case df_sql : rc = vdb_info_print_sql( table_name, &data ); break;
default : rc = vdb_info_print_dflt( &data ); break;
}
}
return rc;
}
rc_t foreach_argument( Args * args, KDirectory *dir, bool div_by_spotgrp, bool * empty,
rc_t ( CC * on_argument ) ( const char * path, const char * spot_group, void * data ), void * data )
{
uint32_t count;
rc_t rc = ArgsParamCount( args, &count );
if ( rc != 0 )
{
LOGERR( klogInt, rc, "ArgsParamCount() failed" );
}
else
{
uint32_t idx;
if ( empty != NULL )
{
*empty = ( count == 0 );
}
for ( idx = 0; idx < count && rc == 0; ++idx )
{
const char *param = NULL;
rc = ArgsParamValue( args, idx, ¶m );
if ( rc != 0 )
{
LOGERR( klogInt, rc, "ArgsParamvalue() failed" );
}
else
{
char * path = NULL;
char * spot_group = NULL;
rc = split_argument_into_path_and_readgroup( param, &path, &spot_group );
if ( rc == 0 && path != NULL )
{
/* in case there is no spotgroup-override from the commandline AND
the option to divide by spot-group is set, let spot_group point
to an empty string ---> divide by original spot-group! */
if ( spot_group == NULL && div_by_spotgrp )
{
spot_group = calloc( 1, 1 );
}
#if TOOLS_USE_SRAPATH != 0
if ( !is_this_a_filesystem_path( path ) )
{
rc = resolve_accession( dir, &path );
}
#endif
if ( rc == 0 )
{
rc = on_argument( path, spot_group, data );
}
free( path );
if ( spot_group != NULL )
free( spot_group );
}
}
}
}
return rc;
}
