static char *translate_accession( SRAPath *my_sra_path,
const char *accession,
const size_t bufsize )
{
rc_t rc;
char * res = calloc( 1, bufsize );
if ( res == NULL ) return NULL;
rc = SRAPathFind( my_sra_path, accession, res, bufsize );
if ( GetRCState( rc ) == rcNotFound )
{
free( res );
return NULL;
}
else if ( GetRCState( rc ) == rcInsufficient )
{
free( res );
return translate_accession( my_sra_path, accession, bufsize * 2 );
}
else if ( rc != 0 )
{
free( res );
return NULL;
}
return res;
}
string CSraPath::FindAccPath(const string& acc) const
{
string ret;
ret.resize(128);
for ( ;; ) {
rc_t rc;
{{
CFastMutexGuard guard(sx_PathMutex);
rc = SRAPathFind(*this, acc.c_str(), &ret[0], ret.size());
}}
if ( !rc ) {
break;
}
if ( GetRCState(rc) == rcInsufficient ) {
// buffer too small, realloc and repeat
ret.resize(ret.size()*2);
}
else {
NCBI_THROW3(CSraException, eNotFound,
"Cannot find acc path", rc, acc);
}
}
SIZE_TYPE eol_pos = ret.find('\0');
if ( eol_pos != NPOS ) {
ret.resize(eol_pos);
}
return ret;
}
/* ResolveTablePath
* takes either an accession or path
* substitutes any arguments
* resolves via SRAPath mgr if present
*/
rc_t ResolveTablePath ( const SRAMgr *mgr,
char *path, size_t psize, const char *spec, va_list args )
{
int len;
char tblpath [ 4096 ];
const SRAPath *pmgr = mgr -> pmgr;
/* if no path manager or if the spec string has embedded path separators,
then this can't be an accession - just print it out */
if ( mgr -> pmgr == NULL || strchr( spec, '/' ) != NULL )
{
len = vsnprintf ( path, psize, spec, args );
if ( len < 0 || ( size_t ) len >= psize )
return RC ( rcSRA, rcTable, rcOpening, rcPath, rcExcessive );
return 0;
}
/* create a copy - not likely to be too large */
len = vsnprintf ( tblpath, sizeof tblpath, spec, args );
if ( len < 0 || ( size_t ) len >= sizeof tblpath )
return RC ( rcSRA, rcTable, rcOpening, rcPath, rcExcessive );
/* test if the path exists in current directory, i.e. with assumed dot */
if ( ! SRAPathTest ( pmgr, tblpath ) )
{
rc_t rc = SRAPathFind ( pmgr, tblpath, path, psize );
if ( rc == 0 )
return 0;
}
/* use the path given */
if ( ( size_t ) len >= psize )
return RC ( rcSRA, rcTable, rcOpening, rcBuffer, rcInsufficient );
strcpy ( path, tblpath );
return 0;
}
rc_t CC KMain ( int argc, char *argv [] )
{
Args *args;
rc_t rc = ArgsMakeAndHandle ( & args, argc, argv, 0 );
if ( rc != 0 )
LogErr ( klogErr, rc, "failed to parse arguments" );
else
{
uint32_t paramc;
rc = ArgsParamCount ( args, & paramc );
if ( rc != 0 )
LogErr ( klogInt, rc, "failed to obtain param count" );
else
{
if ( paramc == 0 )
{
rc = RC ( rcExe, rcArgv, rcParsing, rcParam, rcInsufficient );
LogErr ( klogErr, rc, "missing target object" );
MiniUsage ( args );
}
else if ( paramc > 1 )
{
rc = RC ( rcExe, rcArgv, rcParsing, rcParam, rcExcessive );
LogErr ( klogErr, rc, "expected single target object" );
MiniUsage ( args );
}
else
{
const char *target;
rc = ArgsParamValue ( args, 0, & target );
if ( rc != 0 )
LogErr ( klogInt, rc, "failed to obtain param value" );
else
{
VDBManager *mgr;
#if TOOLS_USE_SRAPATH != 0
char full [ 4096 ];
SRAPath *sra_path;
rc = SRAPathMake ( & sra_path, NULL );
if ( rc == 0 )
{
if ( ! SRAPathTest ( sra_path, target ) )
{
rc = SRAPathFind ( sra_path, target, full, sizeof full );
if ( rc == 0 )
target = full;
}
SRAPathRelease ( sra_path );
}
#endif
rc = VDBManagerMakeUpdate ( & mgr, NULL );
if ( rc != 0 )
LogErr ( klogInt, rc, "failed to open VDB manager" );
else
{
rc = VDBManagerLock ( mgr, target );
if ( rc == 0 )
pLogMsg ( klogInfo, "locked '$(target)'", "target=%s", target );
else switch ( GetRCState ( rc ) )
{
case rcLocked:
pLogMsg ( klogInfo, "'$(target)' was already locked", "target=%s", target );
break;
default:
pLogErr ( klogErr, rc, "failed to lock '$(target)'", "target=%s", target );
}
VDBManagerRelease ( mgr );
}
}
}
}
ArgsWhack ( args );
}
return rc;
}
/* Find
* finds location of run within rep-server/volume matrix
*
* "accession" [ IN ] - NUL terminated run accession,
* e.g. "SRR000001"
*
* "path" [ OUT ] and "path_max" [ IN ] - return buffer for
* NUL-terminated full path to accession.
*
* returns 0 if path exists, rc state rcNotFound if
* path cannot be found, and rcInsufficient if buffer is
* too small.
*/
inline rc_t Find ( const char *accession, char *path,
size_t path_max ) const throw()
{
return SRAPathFind ( this, accession, path, path_max );
}
/* ResolveTablePath
* takes either an accession or path
* substitutes any arguments
* resolves via SRAPath mgr if present
*/
rc_t ResolveTablePath ( const SRAMgr *mgr,
char *path, size_t psize, const char *spec, va_list args )
{
#if OLD_SRAPATH_MGR
int len;
char tblpath [ 4096 ];
const SRAPath *pmgr = mgr -> _pmgr;
/* if no path manager or if the spec string has embedded path separators,
then this can't be an accession - just print it out */
if ( mgr -> _pmgr == NULL || strchr( spec, '/' ) != NULL )
{
len = vsnprintf ( path, psize, spec, args );
if ( len < 0 || ( size_t ) len >= psize )
return RC ( rcSRA, rcTable, rcOpening, rcPath, rcExcessive );
return 0;
}
/* create a copy - not likely to be too large */
len = vsnprintf ( tblpath, sizeof tblpath, spec, args );
if ( len < 0 || ( size_t ) len >= sizeof tblpath )
return RC ( rcSRA, rcTable, rcOpening, rcPath, rcExcessive );
/* test if the path exists in current directory, i.e. with assumed dot */
if ( ! SRAPathTest ( pmgr, tblpath ) )
{
rc_t rc = SRAPathFind ( pmgr, tblpath, path, psize );
if ( rc == 0 )
return 0;
}
/* use the path given */
if ( ( size_t ) len >= psize )
return RC ( rcSRA, rcTable, rcOpening, rcBuffer, rcInsufficient );
strcpy ( path, tblpath );
return 0;
#else
VFSManager *vfs;
rc_t rc = VFSManagerMake ( & vfs );
if ( rc == 0 )
{
VPath *accession;
const VPath *tblpath = NULL;
rc = VFSManagerVMakePath ( vfs, & accession, spec, args );
if ( rc == 0 )
{
rc = VResolverLocal ( ( const VResolver* ) mgr -> _pmgr, accession, & tblpath );
if ( rc == 0 )
{
size_t size;
rc = VPathReadPath ( tblpath, path, psize, & size );
VPathRelease ( tblpath );
}
VPathRelease ( accession );
}
VFSManagerRelease ( vfs );
}
return rc;
#endif
}
