rc_t make_column_namelist ( const BSTree *columns, KNamelist **names )
{
VNamelist *list;
rc_t rc = VNamelistMake ( & list, 8 );
if ( rc == 0 )
{
const String *last = NULL;
const VColumnRef *cref = ( const VColumnRef* )
BSTreeFirst ( columns );
while ( cref != NULL )
{
if ( last == NULL || ! StringEqual ( last, & cref -> name ) )
{
rc = VNamelistAppend ( list, cref -> name . addr );
if ( rc != 0 )
break;
last = & cref -> name;
}
cref = ( const VColumnRef* )
BSTNodeNext ( & cref -> n );
}
if ( rc == 0 )
rc = VNamelistToNamelist ( list, names );
VNamelistRelease ( list );
}
return rc;
}
rc_t register_temp_file( temp_registry * self, uint32_t read_id, const char * filename )
{
rc_t rc = 0;
if ( self == NULL )
rc = RC( rcVDB, rcNoTarg, rcConstructing, rcSelf, rcNull );
else if ( filename == NULL )
rc = RC( rcVDB, rcNoTarg, rcConstructing, rcParam, rcNull );
else
{
rc = KLockAcquire ( self -> lock );
if ( rc == 0 )
{
VNamelist * l = VectorGet ( &self -> lists, read_id );
if ( l == NULL )
{
rc = VNamelistMake ( &l, 12 );
if ( rc == 0 )
{
rc = VectorSet ( &self -> lists, read_id, l );
if ( rc != 0 )
VNamelistRelease ( l );
}
}
if ( rc == 0 && l != NULL )
{
rc = VNamelistAppend ( l, filename );
if ( rc == 0 )
rc = Add_File_to_Cleanup_Task ( self -> cleanup_task, filename );
}
KLockUnlock ( self -> lock );
}
}
return rc;
}
rc_t nlt_remove_names_from_namelist( const KNamelist *source,
const KNamelist **dest, const KNamelist *to_remove )
{
rc_t rc = 0;
uint32_t count;
if ( source == NULL || dest == NULL || to_remove == NULL )
return RC( rcVDB, rcNoTarg, rcConstructing, rcParam, rcNull );
*dest = NULL;
rc = KNamelistCount( source, &count );
if ( rc == 0 && count > 0 )
{
VNamelist *cleaned;
rc = VNamelistMake ( &cleaned, count );
if ( rc == 0 )
{
uint32_t idx;
for ( idx = 0; idx < count && rc == 0; ++idx )
{
const char *s;
rc = KNamelistGet( source, idx, &s );
if ( rc == 0 )
{
if ( !nlt_is_name_in_namelist( to_remove, s ) )
rc = VNamelistAppend ( cleaned, s );
}
rc = VNamelistToConstNamelist ( cleaned, dest );
}
}
}
return rc;
}
rc_t nlt_build_intersect( const KNamelist *nl1, const KNamelist *nl2, const KNamelist ** dst )
{
VNamelist *v_names;
rc_t rc = VNamelistMake ( &v_names, 5 );
if ( rc == 0 )
{
/* loop through nl1: if a entry is found in nl2 -> add it to dst */
uint32_t count;
rc = KNamelistCount( nl1, &count );
if ( rc == 0 )
{
uint32_t idx;
for ( idx = 0; idx < count && rc == 0; ++idx )
{
const char *s;
rc = KNamelistGet( nl1, idx, &s );
if ( rc == 0 && s != NULL )
{
if ( nlt_is_name_in_namelist( nl2, s ) )
rc = VNamelistAppend ( v_names, s );
}
}
}
if ( rc == 0 )
rc = VNamelistToConstNamelist ( v_names, dst );
VNamelistRelease( v_names );
}
return rc;
}
rc_t nlt_copy_namelist( const KNamelist *src, const KNamelist ** dst )
{
VNamelist *v_names;
rc_t rc = VNamelistMake ( &v_names, 5 );
if ( rc == 0 )
{
uint32_t count;
rc = KNamelistCount( src, &count );
if ( rc == 0 )
{
uint32_t idx;
for ( idx = 0; idx < count && rc == 0; ++idx )
{
const char *s;
rc = KNamelistGet( src, idx, &s );
if ( rc == 0 && s != NULL )
rc = VNamelistAppend ( v_names, s );
}
}
if ( rc == 0 )
rc = VNamelistToConstNamelist ( v_names, dst );
VNamelistRelease( v_names );
}
return rc;
}
rc_t add_cgi_request_param( struct cgi_request * request, const char * fmt, ... )
{
rc_t rc;
if ( request == NULL || fmt == NULL )
rc = RC( rcVDB, rcNoTarg, rcConstructing, rcParam, rcNull );
else
{
va_list args;
char buffer[ 4096 ];
size_t num_writ;
va_start ( args, fmt );
rc = string_vprintf( buffer, sizeof buffer, &num_writ, fmt, args );
if ( rc != 0 )
ErrMsg( "string_vprintf( '%s' ) -> %R", fmt, rc );
else
{
DBGMSG ( DBG_APP, DBG_FLAG ( DBG_APP_1 ), ( "\t%s\n", buffer ) );
rc = VNamelistAppend( request->params, buffer );
if ( rc != 0 )
ErrMsg( "VNamelistAppend( '%s' ) -> %R", buffer, rc );
}
va_end ( args );
}
return rc;
}
rc_t ref_walker_add_source( struct ref_walker * self, const char * src )
{
rc_t rc = 0;
if ( self == NULL )
rc = RC( rcApp, rcNoTarg, rcConstructing, rcParam, rcNull );
else
rc = VNamelistAppend ( self->sources, src );
return rc;
}
static rc_t add_tool_options_path( tool_options * options, const char * path )
{
rc_t rc = VNamelistAppend ( options->paths, path );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc,
"VNamelistAppend( $(name) ) failed in $(func)", "name=%s, func=%s", path, __func__ ) );
}
if ( rc == 0 )
options->path_count++;
return rc;
}
static
bool CC list_dylib ( void *item, void *data )
{
size_t bytes;
char utf8 [ 4096 ], *p;
list_dylib_param *pb = data;
const KDylib *lib = ( const void* ) item;
/* "lib" was created with KDylibMake
which creates a NUL terminated path.
of course, this could seg-fault if bad... */
assert ( lib -> path . addr [ lib -> path . len ] == 0 );
/* convert wide-character to UTF-8 */
bytes = wchar_cvt_string_copy ( utf8, sizeof utf8, lib -> path . addr, lib -> path . size );
if ( bytes < sizeof utf8 )
{
pb -> rc = VNamelistAppend ( pb -> list, utf8 );
return pb -> rc != 0;
}
p = malloc ( 16 * 1024 );
if ( p == NULL )
{
pb -> rc = RC ( rcFS, rcDylib, rcListing, rcMemory, rcExhausted );
return true;
}
bytes = wchar_cvt_string_copy ( p, 16 * 1024, lib -> path . addr, lib -> path . size );
if ( bytes >= 16 * 1024 )
pb -> rc = RC ( rcFS, rcDylib, rcListing, rcPath, rcTooLong );
else
pb -> rc = VNamelistAppend ( pb -> list, p );
free ( p );
return pb -> rc != 0;
}
rc_t report_set_columns( p_report self, size_t count, ... )
{
rc_t rc;
if ( self != NULL )
{
VNamelistRelease ( self->columns ); /* ignores NULL */
rc = VNamelistMake ( &self->columns, count );
if ( rc == 0 )
{
self->col_count = count;
if ( self->max_width != NULL )
free( self->max_width );
self->max_width = malloc( count * sizeof( *self->max_width ) );
if ( self->max_width == NULL )
rc = RC( rcExe, rcNoTarg, rcConstructing, rcMemory, rcExhausted );
if ( rc == 0 )
{
size_t idx;
va_list args;
va_start ( args, count );
for ( idx = 0; idx < count && rc == 0; ++idx )
{
const char * s = va_arg( args, const char * );
if ( s != NULL )
{
rc = VNamelistAppend ( self->columns, s );
self->max_width[ idx ] = string_size( s );
}
else
{
rc = VNamelistAppend ( self->columns, "." );
self->max_width[ idx ] = 1;
}
}
va_end ( args );
}
static
bool CC list_dylib ( void *item, void *data )
{
list_dylib_param *pb = data;
const KDylib *lib = ( const void* ) item;
/* "lib" was created with KDylibMake
which creates a NUL terminated path.
of course, this could seg-fault if bad... */
assert ( lib -> path . addr [ lib -> path . size ] == 0 );
pb -> rc = VNamelistAppend ( pb -> list, lib -> path . addr );
return pb -> rc != 0;
}
static void append_str_arguments( const Args *my_args, VNamelist *dst )
{
uint32_t count;
rc_t rc = ArgsParamCount( my_args, &count );
if ( ( rc == 0 )&&( count > 0 ) )
{
uint32_t idx;
for ( idx=0; idx<count; ++idx )
{
const char* s;
if ( ArgsParamValue( my_args, idx, (const void **)&s ) == 0 )
VNamelistAppend( dst, s );
}
}
}
static void append_str_options( const Args *my_args, const char *name, VNamelist *dst )
{
uint32_t count;
rc_t rc = ArgsOptionCount( my_args, name, &count );
if ( ( rc == 0 )&&( count > 0 ) )
{
uint32_t idx;
for ( idx=0; idx<count; ++idx )
{
const char* s;
if ( ArgsOptionValue( my_args, name, idx, (const void **)&s ) == 0 )
VNamelistAppend( dst, s );
}
}
}
static
rc_t CC
_AddTrimStringToList_ZHR ( struct VNamelist * List, char * String )
{
/*))
(( We suppose that String is null terminated and editable
)) ... i.e. it could be called by Tokenizer only
((*/
char * BG, * EN;
if ( String == NULL ) {
return 0;
}
if ( List == NULL ) {
return XFS_RC ( rcNull );
}
BG = String;
EN = BG + strlen ( String );
/*) Trim from front (*/
while ( BG < EN ) {
if ( isspace ( * BG ) ) {
BG ++;
}
else {
break;
}
}
/*) Trim from end (*/
while ( BG < EN ) {
if ( isspace ( * EN ) || * EN == 0 ) {
* EN = 0;
EN --;
}
else {
break;
}
}
if ( 0 < EN - BG ) {
return VNamelistAppend ( List, BG );
}
return 0;
} /* _AddTrimStringToList_ZHR () */
rc_t make_column_typelist ( const BSTree *columns,
const char *col, uint32_t *dflt_idx, KNamelist **typedecls )
{
VNamelist *list;
rc_t rc = VNamelistMake ( & list, 8 );
if ( rc == 0 )
{
uint32_t idx;
const VColumnRef *first;
String col_name;
StringInitCString ( & col_name, col );
first = ( const VColumnRef* )
BSTreeFind ( columns, & col_name, VColumnRefCmpString );
if ( first != NULL )
{
const VColumnRef *cref = ( const VColumnRef* ) BSTNodePrev ( & first -> n );
while ( cref != NULL && StringEqual ( & first -> name, & cref -> name ) )
{
first = cref;
cref = ( const VColumnRef* ) BSTNodePrev ( & cref -> n );
}
for ( cref = first, idx = 0; ; ++ idx )
{
rc = VNamelistAppend ( list, cref -> typedecl );
if ( rc != 0 )
break;
if ( cref -> dflt )
* dflt_idx = idx;
cref = ( const VColumnRef* ) BSTNodeNext ( & cref -> n );
if ( cref == NULL || ! StringEqual ( & first -> name, & cref -> name ) )
break;
}
}
if ( rc == 0 )
rc = VNamelistToNamelist ( list, typedecls );
VNamelistRelease ( list );
}
return rc;
}
static
void
_ListKeysCallback ( BSTNode * Node, void * Data )
{
struct VNamelist * List;
struct XFSOwpEntry * TheNode;
List = NULL;
TheNode = NULL;
if ( Node != NULL && Data != NULL ) {
List = ( struct VNamelist * ) Data;
TheNode = ( struct XFSOwpEntry * ) Node;
VNamelistAppend ( List, TheNode -> Key );
}
} /* _ListKeysCallback () */
static rc_t extract_spotgroups_from_stats( VNamelist * spotgroups, input_database * id, const KMetadata * meta )
{
const KMDataNode * node;
rc_t rc = KMetadataOpenNodeRead( meta, &node, "STATS/SPOT_GROUP" );
if ( rc != 0 )
(void)PLOGERR( klogErr, ( klogErr, rc, "cannot open meta-node 'STATS/SPOT_GROUP' from '$(t)'", "t=%s", id->path ) );
else
{
KNamelist * node_childs;
rc = KMDataNodeListChildren( node, &node_childs );
if ( rc != 0 )
(void)PLOGERR( klogErr, ( klogErr, rc, "cannot list children of SPOT_GROUP-node in '$(t)'", "t=%s", id->path ) );
else
{
uint32_t n_count;
rc = KNamelistCount( node_childs, &n_count );
if ( rc == 0 && n_count > 0 )
{
uint32_t n_idx;
for ( n_idx = 0; n_idx < n_count && rc == 0; ++n_idx )
{
const char * spotgroup;
rc = KNamelistGet( node_childs, n_idx, &spotgroup );
if ( rc == 0 && spotgroup != NULL )
{
uint32_t found;
rc_t rc1 = VNamelistIndexOf( spotgroups, spotgroup, &found );
if ( GetRCState( rc1 ) == rcNotFound )
rc = VNamelistAppend( spotgroups, spotgroup );
}
}
}
KNamelistRelease( node_childs );
}
KMDataNodeRelease( node );
}
return rc;
}
rc_t nlt_make_namelist_from_string( const KNamelist **list, const char * src )
{
VNamelist *v_names;
rc_t rc = VNamelistMake ( &v_names, 5 );
if ( rc == 0 )
{
char * s = string_dup_measure ( src, NULL );
if ( s )
{
uint32_t str_begin = 0;
uint32_t str_end = 0;
char c;
do
{
c = s[ str_end ];
if ( c == ',' || c == 0 )
{
if ( str_begin < str_end )
{
char c_temp = c;
s[ str_end ] = 0;
rc = VNamelistAppend ( v_names, &(s[str_begin]) );
s[ str_end ] = c_temp;
}
str_begin = str_end + 1;
}
str_end++;
} while ( c != 0 && rc == 0 );
free( s );
}
if ( rc == 0 )
rc = VNamelistToConstNamelist ( v_names, list );
VNamelistRelease( v_names );
}
return rc;
}
static void LoadFromBuffer( VNamelist * nl, buffer_range * range )
{
uint32_t idx;
const char * p = range->start;
String S;
S.addr = p;
S.len = S.size = range->processed;
for ( idx = range->processed; idx < range->count; ++idx )
{
switch( p[ idx ] )
{
case 0x0A :
switch( range->state )
{
case STATE_ALPHA : /* ALPHA --> LF */
VNamelistAppendString ( nl, &S );
range->state = STATE_LF;
break;
case STATE_LF : /* LF --> LF */
VNamelistAppend ( nl, empty_str );
break;
case STATE_NL : /* NL --> LF */
VNamelistAppend ( nl, empty_str );
range->state = STATE_LF;
break;
}
break;
case 0x0D :
switch( range->state )
{
case STATE_ALPHA : /* ALPHA --> NL */
VNamelistAppendString ( nl, &S );
range->state = STATE_NL;
break;
case STATE_LF : /* LF --> NL */
range->state = STATE_NL;
break;
case STATE_NL : /* NL --> NL */
VNamelistAppend ( nl, empty_str );
break;
}
break;
default :
switch( range->state )
{
case STATE_ALPHA : /* ALPHA --> ALPHA */
S.len++;
S.size++;
break;
case STATE_LF : /* LF --> ALPHA */
S.addr = &p[ idx ];
S.len = S.size = 1;
range->state = STATE_ALPHA;
break;
case STATE_NL : /* NL --> ALPHA */
S.addr = &p[ idx ];
S.len = S.size = 1;
range->state = STATE_ALPHA;
break;
}
break;
}
}
if ( range->state == STATE_ALPHA )
{
range->start = S.addr;
range->count = S.len;
}
else
range->count = 0;
}
static rc_t gather_string_options( Args * args, samdump_opts * opts )
{
const char * s;
uint32_t count;
rc_t rc = get_str_option( args, OPT_PREFIX, &s );
if ( rc == 0 && s != NULL )
{
opts->qname_prefix = string_dup_measure( s, NULL );
if ( opts->qname_prefix == NULL )
{
rc = RC( rcExe, rcNoTarg, rcValidating, rcMemory, rcExhausted );
(void)LOGERR( klogErr, rc, "error storing QNAME-PREFIX" );
}
}
if ( rc == 0 )
{
rc = get_str_option( args, OPT_Q_QUANT, &s );
if ( rc == 0 && s != NULL )
{
opts->qual_quant = string_dup_measure( s, NULL );
if ( opts->qual_quant == NULL )
{
rc = RC( rcExe, rcNoTarg, rcValidating, rcMemory, rcExhausted );
(void)LOGERR( klogErr, rc, "error storing QUAL-QUANT" );
}
else
{
bool bres = QualityQuantizerInitMatrix( opts->qual_quant_matrix, opts->qual_quant );
if ( !bres )
{
rc = RC( rcExe, rcNoTarg, rcValidating, rcParam, rcInvalid );
(void)LOGERR( klogErr, rc, "error initializing quality-quantizer-matrix" );
}
}
}
}
if ( rc == 0 )
{
rc = get_str_option( args, OPT_OUTPUTFILE, &s );
if ( rc == 0 && s != NULL )
{
opts->outputfile = string_dup_measure( s, NULL );
if ( opts->outputfile == NULL )
{
rc = RC( rcExe, rcNoTarg, rcValidating, rcMemory, rcExhausted );
(void)LOGERR( klogErr, rc, "error storing OUTPUTFILE" );
}
}
}
if ( rc == 0 )
{
rc = ArgsOptionCount( args, OPT_HDR_COMMENT, &count );
if ( rc == 0 && count > 0 )
{
uint32_t i;
rc = VNamelistMake( &opts->hdr_comments, 10 );
for ( i = 0; i < count && rc == 0; ++i )
{
const char * src;
rc = ArgsOptionValue( args, OPT_HDR_COMMENT, i, &src );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "error retrieving comandline option '$(t)' #$(n)",
"t=%s,n=%u", OPT_HDR_COMMENT, i ) );
}
else
{
rc = VNamelistAppend( opts->hdr_comments, src );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "error appending hdr-comment '$(t)'",
"t=%s", src ) );
}
}
}
if ( rc != 0 )
{
VNamelistRelease( opts->hdr_comments );
opts->hdr_comments = NULL;
}
}
}
if ( rc == 0 )
{
rc = ArgsParamCount( args, &count );
if ( rc == 0 && count > 0 )
{
uint32_t i;
rc = VNamelistMake( &opts->input_files, 10 );
for ( i = 0; i < count && rc == 0; ++i )
{
const char * src;
rc = ArgsParamValue( args, i, &src );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "error retrieving comandline param #$(n)",
"n=%u", i ) );
}
else
{
rc = VNamelistAppend( opts->input_files, src );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "error appending input_file '$(t)'",
"t=%s", src ) );
}
}
}
if ( rc != 0 )
{
VNamelistRelease( opts->input_files );
opts->input_files = NULL;
}
}
opts->input_file_count = count;
}
rc = get_str_option( args, OPT_CIGAR_TEST, &s );
if ( rc == 0 && s != NULL )
{
opts->cigar_test = string_dup_measure( s, NULL );
if ( opts->cigar_test == NULL )
{
rc = RC( rcExe, rcNoTarg, rcValidating, rcMemory, rcExhausted );
(void)LOGERR( klogErr, rc, "error storing CIGAR-TEST" );
}
}
return rc;
}
/* ListPhysColumns
* avail: 2.4
*/
LIB_EXPORT rc_t CC VTableListPhysColumns ( const VTable *self, KNamelist **names )
{
rc_t rc;
if ( names == NULL )
rc = RC ( rcVDB, rcTable, rcListing, rcParam, rcNull );
else
{
* names = NULL;
if ( self == NULL )
rc = RC ( rcVDB, rcTable, rcListing, rcSelf, rcNull );
else
{
KNamelist *kcol_names;
rc = KTableListCol ( self -> ktbl, & kcol_names );
if ( rc == 0 )
{
uint32_t kcol_count;
rc = KNamelistCount ( kcol_names, & kcol_count );
if ( rc == 0 )
{
uint32_t scol_count = 0;
KNamelist *scol_names = NULL;
const KMDataNode *col_node = self -> col_node;
#if LAZY_OPEN_COL_NODE
if ( col_node == NULL )
{
rc = KMetadataOpenNodeRead ( self -> meta, & ( ( VTable* ) self ) -> col_node, "col" );
if ( rc == 0 || GetRCState ( rc ) != rcNotFound )
col_node = self -> col_node;
}
#endif
if ( col_node != NULL )
{
rc = KMDataNodeListChildren ( col_node, & scol_names );
if ( rc == 0 )
rc = KNamelistCount ( scol_names, & scol_count );
}
if ( rc == 0 )
{
VNamelist *vnames;
rc = VNamelistMake ( & vnames, kcol_count + scol_count );
if ( rc == 0 )
{
uint32_t i;
const char *name;
for ( i = 0; i < kcol_count && rc == 0; ++ i )
{
rc = KNamelistGet ( kcol_names, i, & name );
if ( rc == 0 )
rc = VNamelistAppend ( vnames, name );
}
for ( i = 0; i < scol_count && rc == 0; ++ i )
{
rc = KNamelistGet ( scol_names, i, & name );
if ( rc == 0 )
rc = VNamelistAppend ( vnames, name );
}
if ( rc == 0 )
{
rc = VNamelistToNamelist ( vnames, names );
if ( rc == 0 )
VNamelistReorder ( vnames, false );
}
}
VNamelistRelease ( vnames );
}
KNamelistRelease ( scol_names );
}
KNamelistRelease ( kcol_names );
}
}
}
return rc;
}