static
rc_t CC
_AuthMake (
const char * Name,
bool NameDefaulted,
bool CanRead,
bool CanWrite,
bool CanExecute,
const struct XFSAuth ** Auth
)
{
struct XFSAuth * TheAuth;
if ( Name == NULL || Auth == NULL ) {
return XFS_RC ( rcNull );
}
* Auth = NULL;
TheAuth = calloc ( 1, sizeof ( struct XFSAuth ) );
if ( TheAuth == NULL ) {
return XFS_RC ( rcExhausted );
}
if ( ! NameDefaulted ) {
TheAuth -> Name = string_dup_measure ( Name, NULL );
if ( TheAuth -> Name == NULL ) {
_AuthDispose ( TheAuth );
return XFS_RC ( rcExhausted );
}
}
else {
TheAuth -> Name = ( char * ) Name;
}
TheAuth -> NameDefaulted = NameDefaulted;
TheAuth -> CanRead = CanRead;
TheAuth -> CanWrite = CanWrite;
TheAuth -> CanExecute = CanExecute;
* Auth = TheAuth;
return 0;
} /* _AuthMake () */
static rc_t _KConfigGetAscpRate(const KConfig *self, const char **max_rate) {
String *s = NULL;
assert(self && max_rate);
*max_rate = NULL;
s = _KConfigAscpString(self, "tools/ascp/max_rate", "Aspera max rate");
if (s != NULL) {
if (s->size == 0) {
free(s);
}
else {
*max_rate = string_dup_measure(s->addr, NULL);
free(s);
if (*max_rate == NULL) {
free((void*)*max_rate);
return RC(rcNS, rcStorage, rcAllocating, rcMemory, rcExhausted);
}
}
return 0;
}
return 0;
}
rc_t make_ref_exclude( ref_exclude *exclude, KDirectory *dir,
const char * path, bool info )
{
rc_t rc;
BSTreeInit( &exclude->ref_nodes );
BSTreeInit( &exclude->translations );
exclude->last_used_ref_node = NULL;
exclude->info = info;
rc = VDBManagerMakeUpdate ( &exclude->mgr, dir );
if ( rc != 0 )
{
LogErr( klogInt, rc, "VDBManagerMakeUpdate() in make_ref_exclude() failed\n" );
}
else
{
insert_trans_nodes( &exclude->translations );
exclude->path = string_dup_measure ( path, NULL );
}
return rc;
}
rc_t vdf_main( const p_dump_context ctx, const VDBManager * mgr, const char * acc_or_path )
{
rc_t rc = 0;
fastq_ctx fctx;
fctx.run_name = vdb_fastq_extract_run_name( acc_or_path );
ctx->path = string_dup_measure ( acc_or_path, NULL );
if ( USE_PATHTYPE_TO_DETECT_DB_OR_TAB ) /* in vdb-dump-context.h */
{
rc = vdb_fastq_by_pathtype( ctx, mgr, &fctx );
}
else
{
rc = vdb_fastq_by_probing( ctx, mgr, &fctx );
}
free( (char*)ctx->path );
free( (void*)fctx.run_name );
ctx->path = NULL;
return rc;
}
static rc_t get_user_repo_name( const Args * args, const char ** name )
{
uint32_t count;
rc_t rc = ArgsOptionCount( args, OPTION_URNAME, &count );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc,
"ArgsOptionCount( $(option) ) failed in $(func)", "option=%s,func=%s", OPTION_URNAME, __func__ ) );
}
else if ( count > 0 )
{
const char * s = NULL;
rc = ArgsOptionValue( args, OPTION_URNAME, 0, &s );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc,
"ArgsOptionValue( $(option), 0 ) failed in $(func)", "option=%s,func=%s", OPTION_URNAME, __func__ ) );
}
else if ( s != NULL )
*name = string_dup_measure ( s, NULL );
}
return rc;
}
rc_t make_cgi_request( struct cgi_request ** request, const char * url )
{
rc_t rc = 0;
cgi_request * r = calloc( 1, sizeof * r );
if ( r == NULL )
{
rc = RC( rcVDB, rcNoTarg, rcConstructing, rcMemory, rcExhausted );
ErrMsg( "calloc( %d ) -> %R", ( sizeof * r ), rc );
}
else
{
r->url = string_dup_measure( url, NULL );
if ( r->url == NULL )
{
rc = RC( rcVDB, rcNoTarg, rcConstructing, rcMemory, rcExhausted );
ErrMsg( "string_dup_measure( '%s' ) -> %R", url, rc );
}
else
{
DBGMSG ( DBG_APP, DBG_FLAG ( DBG_APP_1 ), ( "%s\n", r -> url ) );
rc = VNamelistMake( &r->params, 10 );
if ( rc != 0 )
ErrMsg( "VNamelistMake() -> %R", rc );
else
{
rc = KNSManagerMake( &r->kns_mgr );
if ( rc != 0 )
ErrMsg( "KNSManagerMake() -> %R", rc );
else
*request = r;
}
}
if ( rc != 0 )
release_cgi_request( r );
}
return rc;
}
/* allocate a redact-value */
static p_redact_val redact_val_init( const char* name,
const uint32_t len,
const char* value )
{
p_redact_val res = NULL;
if ( name == NULL ) return res;
if ( name[0] == 0 ) return res;
res = calloc( 1, sizeof( redact_val ) );
if ( res == NULL ) return res;
res->name = string_dup_measure ( name, NULL );
res->len = len;
res->value = NULL;
if ( value != NULL )
{
if ( value[0] == '\'' && value[2] == '\'' )
{
res->value = malloc( sizeof value[0] );
if ( res->value )
{
res->len = 1;
*( ( char * )res->value ) = value[1];
}
}
else
{
char *endptr;
uint64_t x = strtou64( value, &endptr, 0 );
if ( res->len > sizeof x )
res->len = sizeof x;
res->value = malloc( len );
if ( res->value )
memcpy( res->value, &x, res->len );
}
}
return res;
}
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
rc_t CC
_SFTestMake ( const struct _SFTest ** Test, const char * Path )
{
rc_t RCt;
struct _SFTest * Ret;
struct KDirectory * Dir;
uint32_t PathType;
uint64_t Size;
RCt = 0;
Ret = NULL;
Dir = NULL;
PathType = kptNotFound;
Size = 0;
if ( Test != NULL ) {
* Test = NULL;
}
if ( Test == NULL || Path == NULL ) {
return RC ( rcExe, rcNoTarg, rcProcessing, rcParam, rcNull );
}
/* First we shoud check that file exist
*/
RCt = KDirectoryNativeDir ( & Dir );
if ( RCt == 0 ) {
PathType = KDirectoryPathType ( Dir, Path );
if ( PathType == kptFile ) {
RCt = KDirectoryFileSize ( Dir, & Size, Path );
if ( Size == 0 ) {
return RC ( rcExe, rcNoTarg, rcProcessing, rcParam, rcInvalid );
}
}
else {
return RC ( rcExe, rcNoTarg, rcProcessing, rcParam, rcInvalid );
}
KDirectoryRelease ( Dir );
}
if ( RCt == 0 ) {
Ret = calloc ( 1, sizeof ( struct _SFTest ) );
if ( Ret == NULL ) {
RCt = RC ( rcExe, rcNoTarg, rcProcessing, rcParam, rcExhausted );
}
else {
Ret -> path = string_dup_measure ( Path, NULL );
if ( Ret -> path == NULL ) {
RCt = RC ( rcExe, rcNoTarg, rcProcessing, rcParam, rcExhausted );
}
else {
Ret -> size = Size;
* Test = Ret;
}
}
}
if ( RCt != 0 ) {
* Test = NULL;
_SFTestDispose ( Ret );
}
return RCt;
} /* _SFTestMake () */
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;
}
