LIB_EXPORT rc_t CC KNSManagerVSetHTTPProxyPath ( KNSManager * self, const char * fmt, va_list args )
{
rc_t rc = 0;
if ( self == NULL )
rc = RC ( rcNS, rcMgr, rcUpdating, rcSelf, rcNull );
else
{
uint16_t proxy_port = 0;
const String * proxy = NULL;
if ( fmt != NULL && fmt [ 0 ] != 0 )
{
size_t psize;
char path [ 4096 ];
rc = string_vprintf ( path, sizeof path, & psize, fmt, args );
if ( rc == 0 && psize != 0 )
{
char * colon = string_rchr ( path, psize, ':' );
if ( colon != NULL )
{
char * end;
const char * port_spec = colon + 1;
/* it is true that some day we might read symbolic port names... */
long port_num = strtol ( port_spec, & end, 10 );
if ( port_num <= 0 || port_num >= 0x10000 || end [ 0 ] != 0 )
rc = RC ( rcNS, rcMgr, rcUpdating, rcPath, rcInvalid );
else
{
proxy_port = ( uint64_t ) port_num;
psize = colon - path;
}
}
if ( rc == 0 )
{
String tmp;
StringInit ( & tmp, path, psize, string_len ( path, psize ) );
rc = StringCopy ( & proxy, & tmp );
}
}
}
if ( rc == 0 )
{
if ( self -> http_proxy != NULL )
{
StringWhack ( self -> http_proxy );
self -> http_proxy_port = 0;
}
self -> http_proxy = proxy;
self -> http_proxy_enabled = ( proxy != NULL );
self -> http_proxy_port = proxy_port;
}
}
return rc;
}
int KDBPathType ( const KDirectory *dir, bool *pHasZombies, const char *path )
{
const char *leaf, *parent;
rc_t rc;
int type = KDirectoryPathType ( dir, "%s", path );
if (pHasZombies)
*pHasZombies = false;
switch ( type )
{
case kptDir:
case kptDir | kptAlias:
type = KDBPathTypeDir (dir, type, pHasZombies, path);
break;
case kptFile:
case kptFile | kptAlias:
{
/* if we hit a file first try it as an archive */
const KDirectory * ldir;
rc = KDirectoryOpenSraArchiveRead_silent ( dir, &ldir, false, "%s", path );
#if SUPPORT_KDB_TAR
if ( rc != 0 )
rc = KDirectoryOpenTarArchiveRead_silent ( dir, &ldir, false, "%s", path );
#endif
/* it was an archive so recur */
if ( rc == 0 )
{
/* recheck this newly opened directory for KDB/KFS type */
int type2;
type2 = KDBPathType ( ldir, NULL, "." );
if ((type2 != kptDir) || (type != (kptDir|kptAlias)))
type = type2;
KDirectoryRelease (ldir);
}
/* it was not an archive so see if it it's an idx file */
else
{
leaf = strrchr ( path, '/' );
if ( leaf != NULL )
{
parent = string_rchr ( path, leaf - path, '/' );
if ( parent ++ == NULL )
parent = path;
if ( memcmp ( parent, "idx/", 4 ) == 0 )
type += kptIndex - kptFile;
}
}
break;
}
}
return type;
}
static char * vdb_fastq_extract_run_name( const char * acc_or_path )
{
char * delim = string_rchr ( acc_or_path, string_size( acc_or_path ), '/' );
if ( delim == NULL )
return string_dup_measure ( acc_or_path, NULL );
else
return string_dup_measure ( delim + 1, NULL );
}
/* KMain - EXTERN
* executable entrypoint "main" is implemented by
* an OS-specific wrapper that takes care of establishing
* signal handlers, logging, etc.
*
* in turn, OS-specific "main" will invoke "KMain" as
* platform independent main entrypoint.
*
* "argc" [ IN ] - the number of textual parameters in "argv"
* should never be < 0, but has been left as a signed int
* for reasons of tradition.
*
* "argv" [ IN ] - array of NUL terminated strings expected
* to be in the shell-native character set: ASCII or UTF-8
* element 0 is expected to be executable identity or path.
*/
rc_t CC KMain ( int argc, char *argv [] )
{
Args * args;
rc_t rc;
default_log_level = KLogLevelGet();
rc = ArgsMakeAndHandle (&args, argc, argv, 1, Options, sizeof Options / sizeof (OptDef));
if (rc == 0)
{
do
{
srakar_parms pb;
KDirectory * pwd;
const char * name;
uint32_t pcount;
char archive_name [256];
rc = KDirectoryNativeDir (&pwd);
if (rc)
break;
pb.lite = false;
pb.force = false;
pb.dir = pwd;
rc = ArgsOptionCount (args, OPTION_LITE, &pcount);
if (rc)
break;
if (pcount == 1)
{
STSMSG (1, ("Using lite option"));
pb.lite = true;
}
#if USE_FORCE
rc = ArgsOptionCount (args, OPTION_FORCE, &pcount);
if (rc)
break;
if (pcount == 1)
{
STSMSG (1, ("Using force option"));
pb.force = true;
}
#endif
rc = ArgsParamCount (args, &pcount);
if (rc)
break;
if (pcount == 0)
{
KOutMsg ("missing source table\n");
rc = MiniUsage (args);
break;
}
else if (pcount > 2)
{
KOutMsg ("Too many parameters\n");
rc = MiniUsage (args);
break;
}
rc = ArgsParamValue (args, 0, &pb.src_path);
if (rc)
{
KOutMsg ("failure to get source path/name\n");
break;
}
pb.dst_path = archive_name;
name = string_rchr (pb.src_path, string_size (pb.src_path), '/');
if (name == NULL)
name = pb.src_path;
if (pcount == 1)
{
size_t size;
rc = string_printf (archive_name, sizeof (archive_name), & size,
"%s%s", name, pb.lite ? ".lite.sra" : ".sra");
if ( rc != 0 )
{
rc = RC (rcExe, rcArgv, rcParsing, rcPath, rcInsufficient);
PLOGERR (klogFatal, (klogFatal, rc, "Failure building archive name $(P)", "P=%s", archive_name));
break;
}
}
else
{
rc = ArgsParamValue (args, 1, &pb.dst_path);
if (rc)
{
LOGERR (klogInt, rc, "failure to get destination path");
break;
}
}
if (rc == 0)
{
KPathType kpt;
kpt = KDirectoryPathType (pwd, "%s", pb.dst_path);
switch (kpt & ~kptAlias)
{
case kptNotFound:
/* found nothing so assume its a valid new file name
* not gonna tweak extensions at this point but that can be upgraded */
break;
case kptFile:
/* got a file name, use it - would need force... */
if (pb.force == false)
{
rc = RC (rcExe, rcArgv, rcParsing, rcPath, rcBusy);
PLOGERR (klogFatal, (klogFatal, rc,
"Output file already exists $(P)",
"P=%s", archive_name));
}
break;
case kptDir:
{
size_t size;
rc = string_printf (archive_name, sizeof (archive_name), & size,
"%s/%s%s", pb.dst_path, name, pb.lite ? ".lite.sra" : ".sra");
if ( rc != 0 )
{
rc = RC (rcExe, rcArgv, rcParsing, rcPath, rcInsufficient);
PLOGERR (klogFatal, (klogFatal, rc, "Failure building archive name $(P)", "P=%s", archive_name));
break;
}
pb.dst_path = archive_name;
break;
}
default:
rc = RC (rcExe, rcArgv, rcParsing, rcPath, rcInvalid);
break;
}
if (rc == 0)
{
STSMSG (1,("Creating archive (%s) from table (%s)\n", pb.dst_path, pb.src_path));
rc = run (&pb);
STSMSG (5, ("Run exits with %d %R\n", rc, rc));
}
}
} while (0);
}
STSMSG (1, ("Exit status %u %R", rc, rc));
return rc;
}
/* ----------------------------------------------------------------------
*/
static
rc_t walk_path_file (char * path, size_t z, uint64_t * offset, KPathType kpt)
{
uint64_t this_offset;
char * pc;
rc_t rc;
assert (path);
assert (offset);
this_offset = 0;
rc = 0;
if (kpt == kptFile)
{
rc = KDirectoryFileLocator (options.base, &this_offset, "%s", path);
if (rc)
PLOGERR (klogErr,
(klogErr, rc, "failure walking path '$(P)'",
"P=%s", path));
}
if (rc == 0)
{
pc = string_rchr (path, z, '/');
if (pc)
{
uint64_t that_offset;
KPathType lkpt;
*pc = '\0';
lkpt = KDirectoryPathType (options.base, "%s", path);
switch (lkpt)
{
default:
rc = RC (rcExe, rcPath, rcAccessing, rcPath, rcInvalid);
break;
case kptNotFound:
case kptZombieFile:
rc = RC (rcExe, rcPath, rcAccessing, rcPath, rcNotFound);
break;
case kptBadPath:
rc = RC (rcExe, rcPath, rcAccessing, rcPath, rcInvalid);
break;
case kptFile:
case kptDir:
/* we should always hit here */
rc = walk_path_file (path, z, &that_offset, lkpt);
if (rc == 0)
{
this_offset += that_offset;
}
break;
case kptCharDev:
case kptBlockDev:
case kptFIFO:
rc = RC (rcExe, rcPath, rcAccessing, rcPath, rcIncorrect);
break;
}
*pc = '/';
}
}
*offset = this_offset;
return rc;
}
int KDBPathTypeDir (const KDirectory * dir, int type, bool * pHasZombies, const char * path)
{
const char * leaf, * parent;
uint32_t bits;
rc_t rc;
bits = 0;
assert ((type == kptDir) || (type == (kptDir|kptAlias)));
rc = KDirectoryVVisit ( dir, false, scan_dbdir, & bits, path, NULL );
if ( rc == 0 ) do
{
if ( ( bits & scan_zombie ) != 0 ) {
bits &= ~scan_zombie;
if (pHasZombies)
*pHasZombies = true;
}
/* look for a column */
if ( ( bits & scan_idxN ) != 0 &&
( bits & ( scan_data | scan_dataN ) ) != 0 )
{
if ( ( bits & ( scan_db | scan_tbl | scan_idx | scan_col ) ) == 0 )
type += kptColumn - kptDir;
break;
}
/* look for a table */
if ( ( bits & scan_col ) != 0 )
{
/* can't have sub-tables or a db */
if ( ( bits & ( scan_db | scan_tbl ) ) == 0 )
{
/* look for an old-structure table */
if ( ( bits & ( scan_meta | scan_md ) ) == scan_meta ||
( bits & ( scan_skey | scan_idx ) ) == scan_skey )
type += kptPrereleaseTbl - kptDir;
else
type += kptTable - kptDir;
}
break;
}
/* look for metadata */
if ( ( bits & ( scan_cur | scan_rNNN ) ) != 0 )
{
if ( ( bits & ( scan_db | scan_tbl | scan_idx | scan_col ) ) == 0 )
type += kptMetadata - kptDir;
break;
}
/* look for a database */
if ( ( bits & scan_tbl ) != 0 )
{
if ( ( bits & scan_col ) == 0 )
type += kptDatabase - kptDir;
break;
}
/* look for a structured column */
if ( ( bits & scan_odir ) != 0 )
{
leaf = strrchr ( path, '/' );
if ( leaf != NULL )
{
parent = string_rchr ( path, leaf - path, '/' );
if ( parent ++ == NULL )
parent = path;
if ( memcmp ( parent, "col/", 4 ) != 0 )
break;
bits = 0;
if ( KDirectoryVVisit ( dir, 1, scan_dbdir, & bits, path, NULL ) == 0 )
{
if ( ( bits & scan_idxN ) != 0 &&
( bits & ( scan_data | scan_dataN ) ) != 0 )
{
if ( ( bits & ( scan_db | scan_tbl | scan_idx | scan_col ) ) == 0 )
type += kptColumn - kptDir;
break;
}
}
}
}
} while (0);
return type;
}
/* LoadSchema
* looks in metadata for stored schema
*/
static
rc_t CC VPhysicalLoadV1Schema ( VPhysical *self,
VTypedecl *td, VSchema *schema, const KMDataNode *node )
{
rc_t rc;
KMDataNodeSchemaFillData pb;
pb . node = node;
pb . pos = 0;
pb . add_v0 = true;
/* add stored declaration to cursor schema */
rc = VSchemaParseTextCallback ( schema,
"VPhysicalLoadV1Schema", KMDataNodeFillSchema, & pb );
if ( rc == 0 )
{
size_t size;
char type_expr [ 256 ];
/* retrieve and resolve "type" attribute */
rc = KMDataNodeReadAttr ( node, "type",
type_expr, sizeof type_expr, & size );
if ( rc == 0 )
rc = VSchemaResolveTypedecl ( schema, td, type_expr );
/* if a decoding schema exists */
if ( rc == 0 && pb . pos != 0 )
{
char sphysical_name [ 512 ];
/* preserve schema function expression */
size_t decoding_xsize;
char decoding_expr [ 256 ];
rc = KMDataNodeReadAttr ( node, "schema",
decoding_expr, sizeof decoding_expr, & decoding_xsize );
if ( rc == 0 )
{
/* look for "encoding" */
const KMDataNode *enc;
rc = KMetadataOpenNodeRead ( self -> meta, & enc, "encoding" );
if ( rc == 0 )
{
#if ALLOW_V1_UPDATE
if ( ! self -> read_only )
{
/* add stored declaration to cursor schema */
pb . node = enc;
pb . pos = 0;
pb . add_v0 = true;
rc = VSchemaParseTextCallback ( schema,
"VPhysicalLoadV1Schema", KMDataNodeFillSchema, & pb );
}
if ( rc == 0 )
#endif
{
/* preserve schema function expression */
size_t encoding_xsize;
char encoding_expr [ 256 ], enc_type [ 256 ];
rc = KMDataNodeReadAttr ( enc, "schema",
encoding_expr, sizeof encoding_expr, & encoding_xsize );
if ( rc == 0 )
{
rc = KMDataNodeReadAttr ( enc, "type",
enc_type, sizeof enc_type, & size );
}
if ( rc == 0 )
{
#if ALLOW_V1_UPDATE
if ( self -> read_only )
{
#endif
/* build sphysical name */
sprintf ( sphysical_name, "%s_only", decoding_expr );
/* build physical decl */
pb . pos = sprintf ( pb . buff, "version 1;"
"physical %s %s:phys#1"
"{decode{%s k=@;return %s(k);}}"
, type_expr
, sphysical_name
, enc_type
, decoding_expr
);
#if ALLOW_V1_UPDATE
}
else
{
/* strip off common namespace */
size_t i, ns_size;
string_match ( decoding_expr, decoding_xsize,
encoding_expr, encoding_xsize, -1, & ns_size );
if ( ns_size != 0 )
{
char *p = string_rchr ( decoding_expr, ns_size, ':' );
ns_size = ( p == NULL ) ? 0U : ( uint32_t ) ( p - decoding_expr ) + 1U;
}
/* build sphysical name */
sprintf ( sphysical_name, "%s_%s", decoding_expr, & encoding_expr [ ns_size ] );
for ( i = ns_size; sphysical_name [ i ] != 0; ++ i )
{
if ( sphysical_name [ i ] == ':' )
sphysical_name [ i ] = '_';
}
/* build physical decl */
pb . pos = sprintf ( pb . buff, "version 1;"
"physical %s %s:phys#1"
"{encode{return %s(@);}"
"decode{%s k=@;return %s(k);}}"
, type_expr
, sphysical_name
, encoding_expr
, enc_type
, decoding_expr
);
}
#endif
}
}
KMDataNodeRelease ( enc );
}
else if ( GetRCState ( rc ) == rcNotFound )
{
/* build sphysical name */
sprintf ( sphysical_name, "%s_only", decoding_expr );
/* build decode-only physical decl */
pb . pos = sprintf ( pb . buff, "version 1;"
"physical %s %s:phys#1"
"{decode{opaque k=@;return %s(k);}}"
, type_expr
, sphysical_name
, decoding_expr
);
rc = 0;
}
if ( rc == 0 )
{
/* parse synthesized schema into cursor VSchema */
rc = VSchemaParseText ( schema,
"VPhysicalLoadV1Schema", pb . buff, pb . pos );
if ( rc == 0 )
{
VTypedecl etd;
/* create a new expression object */
sprintf ( pb . buff, "%s:phys#1", sphysical_name );
rc = VSchemaImplicitPhysEncExpr ( schema, & etd,
& self -> enc, pb . buff, "VPhysicalLoadV1Schema" );
if ( rc != 0 )
{
PLOGERR ( klogInt, ( klogInt, rc, "failed to establish column type from '$(expr)'",
"expr=%s", pb . buff ));
}
else if ( self -> smbr != NULL && self -> smbr -> type == NULL )
{
/* back-patch schema */
( ( SPhysMember* ) self -> smbr ) -> type = self -> enc;
atomic32_inc ( & ( ( SExpression* ) self -> enc ) -> refcount );
}
}
}
}
}
}
KMDataNodeRelease ( node );
return rc;
}