/* Make
*/
static
rc_t SRAMgrInitPath ( SRAMgr *mgr, const KDirectory *wd )
{
#if OLD_SRAPATH_MGR
/* try to make the path manager */
rc_t rc = SRAPathMake ( & mgr -> _pmgr, wd );
if ( GetRCState ( rc ) == rcNotFound && GetRCTarget ( rc ) == rcDylib )
{
/* we are operating outside of the archive */
assert ( mgr -> _pmgr == NULL );
rc = 0;
}
return rc;
#else
KConfig *kfg;
rc_t rc = KConfigMake ( & kfg, NULL );
if ( rc == 0 )
{
VFSManager *vfs;
rc = VFSManagerMake ( & vfs );
if ( rc == 0 )
{
rc = VFSManagerMakeResolver ( vfs, ( VResolver** ) & mgr -> _pmgr, kfg );
VFSManagerRelease ( vfs );
}
KConfigRelease ( kfg );
}
if ( rc != 0 )
mgr -> _pmgr = NULL;
return 0;
#endif
}
static bool CanResolveAccessions( void )
{
bool res = false;
SRAPath *sra_path;
rc_t rc = SRAPathMake( &sra_path, NULL );
if ( rc == 0 )
{
res = true;
SRAPathRelease( sra_path );
}
return res;
}
void CSraPath::x_Init(void)
{
CSraMgr::RegisterFunctions();
if ( rc_t rc = SRAPathMake(x_InitPtr(), 0) ) {
*x_InitPtr() = 0;
NCBI_THROW2(CSraException, eInitFailed,
"Cannot make SRAPath", rc);
}
if ( rc_t rc = SRAPathClear(*this) ) {
NCBI_THROW2(CSraException, eInitFailed,
"Cannot clear SRAPath", rc);
}
}
static rc_t resolve_accession( const KDirectory *my_dir, char ** path )
{
SRAPath *my_sra_path;
rc_t rc = 0;
if ( strchr ( *path, '/' ) != NULL )
return 0;
rc = SRAPathMake( &my_sra_path, my_dir );
if ( rc != 0 )
{
if ( GetRCState ( rc ) != rcNotFound || GetRCTarget ( rc ) != rcDylib )
{
if ( rc != 0 )
{
LOGERR( klogInt, rc, "SRAPathMake() failed" );
}
}
else
rc = 0;
}
else
{
if ( !SRAPathTest( my_sra_path, *path ) )
{
char *buf = translate_accession( my_sra_path, *path, 64 );
if ( buf != NULL )
{
free( (char*)(*path) );
*path = buf;
}
}
SRAPathRelease( my_sra_path );
}
return rc;
}
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;
}
/* Make
* create path manager
*
* the path manager should already be configured with
* standard search paths, but can be augmented by using
* the Add*Path messages.
*
* "dir" [ IN, NULL OKAY ] - optional root directory to use
* attaches a new reference
*/
static inline rc_t Make ( SRAPath **pm,
struct KDirectory const *dir = NULL ) throw()
{
return SRAPathMake ( pm, dir );
}
