rc_t CC KMain(int argc, char *argv[]) {
Args *args;
rc_t rc; /*, orc; */
rc = ArgsMakeAndHandle(&args, argc, argv, 0);
if (rc == 0)
{
uint32_t pcount;
rc_t orc;
/* non standard use of --quiet */
rc = ArgsOptionCount(args, OPTION_QUIET, &pcount);
if (rc)
LOGERR(klogErr, rc, "error check " OPTION_QUIET " option");
else
rc = run (pcount != 0);
orc = ArgsWhack(args);
if (rc == 0)
rc = orc;
}
return rc;
}
rc_t CC KMain(int argc, char* argv[])
{
rc_t rc = 0;
Args* args = NULL;
CmdLine cmdArgs;
LogLevelSet("info");
rc = ArgsMakeAndHandle
(&args, argc, argv, 1, Options, sizeof Options / sizeof(Options[0]));
if (rc == 0) {
rc = CmdLineInit(args, &cmdArgs);
}
if (rc == 0) {
rc = Run(&cmdArgs);
}
ArgsWhack(args);
if (rc == RC(rcVDB, rcTable, rcOpening, rcSchema, rcNotFound))
{ exit(10); }
return rc;
}
rc_t CC KMain ( int argc, char *argv [] )
{
Args * my_args;
rc_t rc;
rc = ArgsMakeAndHandle (&my_args, argc, argv, 1,
Options, sizeof (Options) / sizeof (OptDef));
if (rc == 0)
{
context *ctx;
context_init( &ctx );
rc = capture_arguments_and_options( my_args, ctx );
if ( rc == 0 )
{
if ( namelistcount( ctx->src_files ) > 0 )
{
rc = DumpSchema( ctx );
}
else
{
MiniUsage (my_args);
}
}
context_destroy( ctx );
ArgsWhack( my_args );
}
return rc;
}
/* 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;
KStsLevelSet (1);
rc = ArgsMakeAndHandle (&args, argc, argv, 1, Options,
sizeof (Options) / sizeof (Options[0]));
if (rc)
LOGERR (klogInt, rc, "failed to parse command line parameters");
else
{
uint32_t ocount;
rc = ArgsOptionCount (args, OPTION_DEC_SRA, &ocount);
if (rc)
LOGERR (klogInt, rc, "failed to examine decrypt "
"sra option");
else
{
DecryptSraFlag = (ocount > 0);
rc = CommonMain (args);
}
ArgsWhack (args);
}
if (rc)
STSMSG (1, ("exiting: %R (%u)", rc, rc));
else
STSMSG (1, ("exiting: success"));
return rc;
}
rc_t CC KMain ( int argc, char *argv [] )
{
Args * args;
rc_t rc = ArgsMakeAndHandle ( &args, argc, argv, 2,
MyOptions, sizeof MyOptions / sizeof ( OptDef ),
XMLLogger_Args, XMLLogger_ArgsQty );
KLogHandlerSetStdErr();
if ( rc != 0 )
{
LOGERR( klogErr, rc, "error creating internal structure" );
}
else
{
ld_context lctx;
lctx_init( &lctx );
rc = KDirectoryNativeDir ( &lctx.wd );
if ( rc != 0 )
{
LOGERR( klogErr, rc, "error creating internal structure" );
}
else
{
rc = XMLLogger_Make( &lctx.xml_logger, lctx.wd, args );
if ( rc != 0 )
{
LOGERR( klogErr, rc, "error creating internal structure" );
}
else
{
context ctx;
rc = ctx_init( args, &ctx );
if ( rc == 0 )
{
rc = pacbio_check_sourcefile( &ctx, &lctx );
if ( rc == 0 )
{
lctx.with_progress = ctx.with_progress;
ctx_show( &ctx );
lctx.dst_path = ctx.dst_path;
rc = pacbio_load( &ctx, &lctx, false, false );
if ( rc == 0 )
{
rc = pacbio_meta_entry( &lctx, argv[ 0 ] );
}
}
ctx_free( &ctx );
}
}
}
lctx_free( &lctx );
ArgsWhack ( args );
}
return rc;
}
static rc_t main_help_vers(int argc, char * argv[])
{
Args *args = NULL;
rc_t const rc = ArgsMakeAndHandle (&args, argc, argv, 2, Options,
sizeof Options / sizeof (OptDef), XMLLogger_Args, XMLLogger_ArgsQty);
ArgsWhack(args);
return rc;
}
static XMLLogger const *make_logger(int *argc, char *argv[])
{
XMLLogger const *rslt = NULL;
char *argf[4];
int i;
argf[0] = argv[0];
argf[1] = NULL;
argf[2] = NULL;
argf[3] = NULL;
for (i = 1; i < *argc; ++i) {
int remove = 0;
if (strcmp(argv[i], logger_options[2]) == 0) {
argf[1] = argv[i];
argf[2] = argv[i + 1];
remove = 2;
}
else {
int j;
for (j = 0; j < 2; ++j) {
if (strstr(argv[i], logger_options[j]) == argv[i]) {
int const n = strlen(logger_options[j]);
if (argv[i][n] == '\0') {
argf[1] = argv[i];
argf[2] = argv[i + 1];
remove = 2;
}
else if (argv[i][n] == '=') {
argv[i][n] = '\0';
argf[1] = argv[i];
argf[2] = argv[i] + n + 1;
remove = 1;
}
break;
}
}
}
if (argf[1] != NULL) {
Args *args = NULL;
ArgsMakeAndHandle(&args, 3, argf, 1, XMLLogger_Args, XMLLogger_ArgsQty);
if (args) {
XMLLogger_Make(&rslt, NULL, args);
ArgsWhack(args);
}
}
if (remove) {
*argc -= remove;
memmove(argv + i, argv + i + remove, (*argc + 1) * sizeof(argv[0]));
break;
}
}
return rslt;
}
/* 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 = NULL;
rc_t rc;
rc = ArgsMakeAndHandle(&args, argc, argv, 1, Options, sizeof Options / sizeof (OptDef));
if (rc)
LOGERR (klogInt, rc, "failed to parse command line parameters");
if (rc == 0)
{
uint32_t pcount;
bool force;
rc = ArgsOptionCount (args, OPTION_FORCE, &pcount);
if (rc)
LOGERR (klogInt, rc, "failed to examine force option");
else
{
force = (pcount > 0);
rc = ArgsParamCount (args, &pcount);
if (rc)
LOGERR (klogInt, rc, "failed to count parameters");
else
{
if (pcount != 2) {
MiniUsage (args);
rc = RC(rcApp, rcArgv, rcParsing, rcParam, rcInsufficient);
}
else
{
const char * src;
rc = ArgsParamValue (args, 0, (const void **)&src);
if (rc)
LOGERR (klogInt, rc, "failed to get source parameter");
else
{
const char * dst;
rc = ArgsParamValue (args, 1, (const void **)&dst);
if (rc)
LOGERR (klogInt, rc, "failed to get destination parameter");
else
{
rc = nenctool (src, dst, force);
}
}
}
}
}
ArgsWhack (args);
}
STSMSG (1, ("exiting: %R (%u)", rc, rc));
return rc;
}
rc_t CC KMain( int argc, char * argv[] )
{
Args * args;
rc_t rc = ArgsMakeAndHandle ( &args, argc, argv, 1,
MyOptions, sizeof MyOptions / sizeof ( OptDef ) );
if ( rc != 0 )
LogErr( klogInt, rc, "ArgsMakeAndHandle() failed\n" );
else
{
context *ctx;
KLogHandlerSetStdErr();
rc = context_init( &ctx );
if ( rc != 0 )
LogErr( klogInt, rc, "context_init() failed\n" );
else
{
rc = context_capture_arguments_and_options( args, ctx );
if ( rc != 0 )
LogErr( klogInt, rc, "context_capture_arguments_and_options() failed\n" );
else
{
if ( ctx->usage_requested )
MiniUsage( args );
else
{
switch( ctx->output_mode[ 0 ] )
{
case 'd' :
case 't' : if ( context_schema_count( ctx ) == 0 )
{
OUTMSG(( "cannot write, schema-file is missing:\n" ));
Usage( args );
rc = RC( rcApp, rcNoTarg, rcConstructing, rcSelf, rcNull );
}
}
if ( rc == 0 )
{
/* ************************* */
rc = gater_and_write( ctx );
/* ************************* */
}
}
}
context_destroy ( ctx );
}
ArgsWhack ( args );
}
return rc;
}
rc_t CC KMain (int argc, char * argv[])
{
Args * args;
rc_t rc;
rc = ArgsMakeAndHandle (&args, argc, argv, 1, NULL, 0);
if (rc)
LOGERR (klogFatal, rc, "Could not parse command line");
else
{
rc = run();
ArgsWhack (args);
}
return rc;
}
rc_t CC KMain ( int argc, char *argv [] )
{
Args * args;
rc_t rc = ArgsMakeAndHandle ( &args, argc, argv, 1,
DumpOptions, sizeof DumpOptions / sizeof DumpOptions [ 0 ] );
if ( rc == 0 )
{
uint32_t count;
rc = ArgsParamCount( args, &count );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot detect count of program arguments" );
}
else
{
if ( count != 2 )
{
Usage ( args );
}
else
{
cg_dump_ctx cg_ctx;
const char * src;
memset( &cg_ctx, 0, sizeof cg_ctx );
rc = ArgsParamValue( args, 0, &src );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot detect source - argument" );
}
else
{
rc = ArgsParamValue( args, 1, &cg_ctx.dst );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot detect destination - argument" );
}
else
{
rc = cg_dump_src_dst( args, src, &cg_ctx ); /* <================== */
}
}
}
}
ArgsWhack ( args );
}
return rc;
}
rc_t CC KMain ( int argc, char *argv [] )
{
rc_t rc = 0;
Args * args;
rc = ArgsMakeAndHandle (&args, argc, argv, 0);
if (rc == 0)
{
do
{
uint32_t pcount;
rc = ArgsParamCount (args, &pcount);
if (rc)
break;
if (pcount == 0) {
MiniUsage(args);
rc = RC(rcExe, rcNoTarg, rcAllocating, rcParam, rcInvalid);
}
else
{
const char * pc;
rc_t exp;
uint32_t ix;
/* over rule any set log level */
rc = KLogLevelSet (klogInfo);
for (ix = 0; ix < pcount; ++ix)
{
rc = ArgsParamValue (args, ix, (const void **)&pc);
if (rc)
break;
exp = AsciiToU32 (pc, NULL, NULL);
rc = LOGERR (klogInfo, exp, pc);
}
}
} while (0);
ArgsWhack (args);
}
return rc;
}
rc_t CC KMain ( int argc, char *argv [] )
{
Args * args;
rc_t rc;
rc = ArgsMakeAndHandle (&args, argc, argv, 1,
Options, sizeof (Options) / sizeof (OptDef));
if (rc == 0)
{
do
{
uint32_t pcount;
rc = ArgsOptionCount (args, OPTION_FORCE, &pcount);
if (rc)
break;
force = (pcount > 0);
rc = ArgsOptionCount (args, OPTION_RECURSE, &pcount);
if (rc)
break;
recurse = (pcount > 0);
rc = ArgsOptionCount (args, OPTION_TEST, &pcount);
if (rc)
break;
test = (pcount > 0);
rc = ArgsOptionCount (args, OPTION_PRESERVE, &pcount);
if (rc)
break;
clobber_protections = (pcount > 0);
rc = run (args);
}while (0);
ArgsWhack (args);
}
return rc;
}
rc_t CC KMain ( int argc, char *argv [] )
{
Args * args;
rc_t rc = ArgsMakeAndHandle ( &args, argc, argv, 1,
CompressOptions, sizeof ( CompressOptions ) / sizeof ( OptDef ) );
if ( rc == 0 )
{
/* rc = compress_main( args ); */
rc = copy2_main( args );
ArgsWhack ( args );
}
else
OUTMSG( ( "ArgsMakeAndHandle() failed %R\n", rc ) );
return rc;
}
rc_t CC KMain ( int argc, char *argv [] )
{
Args * args;
rc_t rc = ArgsMakeAndHandle ( &args, argc, argv, 0 );
KLogHandlerSetStdErr();
if ( rc != 0 )
{
LOGERR( klogErr, rc, "error creating internal structure" );
}
else
{
uint32_t count;
rc = ArgsParamCount( args, &count );
if ( rc != 0 )
LOGERR( klogErr, rc, "ArgsParamCount failed" );
else
{
if ( count < 1 )
{
rc = RC( rcExe, rcNoTarg, rcAllocating, rcParam, rcInvalid );
LOGERR( klogErr, rc, "object(s) missing" );
Usage ( args );
}
else
{
uint32_t idx;
for ( idx = 0; idx < count && rc == 0; ++idx )
{
const char *obj;
rc = ArgsParamValue( args, idx, (const void **)&obj );
if ( rc != 0 )
LOGERR( klogErr, rc, "error reading commandline-parameter" );
else
rc = correct( obj ); /* ** <<<<<<<<<<<<<<<<<< ** */
}
}
}
ArgsWhack ( args );
}
return rc;
}
/***************************************************************************
Main:
* create the copy-context
* parse the commandline for arguments and options
* react to help/usage - requests ( no dump in this case )
these functions are in vdb-copy-context.c
* call copy_main() to execute the copy-operation
* destroy the copy-context
***************************************************************************/
rc_t CC KMain ( int argc, char *argv [] )
{
Args * args;
rc_t rc = ArgsMakeAndHandle ( &args, argc, argv, 1,
MyOptions, sizeof MyOptions / sizeof ( OptDef ) );
if ( rc != 0 )
{
LOGERR( klogErr, rc, "ArgsMakeAndHandle() failed" );
}
else
{
context *ctx;
KLogHandlerSetStdErr();
rc = context_init( &ctx );
if ( rc != 0 )
{
LOGERR( klogInt, rc, "KMain:context_init() failed" );
}
else
{
rc = context_capture_arguments_and_options( args, ctx );
if ( rc != 0 )
{
MiniUsage( args );
if ( argc < 2 ) rc = 0;
}
else
{
if ( ctx->usage_requested )
MiniUsage( args );
else
rc = ref_seq_load_main( ctx ); /* <====================== */
}
context_destroy( ctx );
}
ArgsWhack ( args );
}
return rc;
}
rc_t CC KMain ( int argc, char *argv [] )
{
Args * args;
rc_t rc;
rc = ArgsMakeAndHandle ( &args, argc, argv, 1, NULL, 0 );
if ( rc == 0 )
{
rc = call_zlib();
OUTMSG (( "calling zlib : %R\n", rc ));
rc = call_bz2();
OUTMSG (( "calling bz2 : %R\n", rc ));
ArgsWhack ( args );
}
else
OUTMSG( ( "ArgsMakeAndHandle() failed %R\n", rc ) );
return rc;
}
rc_t CC KMain ( int argc, char *argv [] )
{
Args * args;
rc_t rc = ArgsMakeAndHandle ( &args, argc, argv, 1,
sra_seq_count_options,
( sizeof sra_seq_count_options / sizeof sra_seq_count_options [ 0 ] ) );
if ( rc == 0 )
{
struct sra_seq_count_options options;
rc = gather_options( args, &options );
if ( rc == 0 && options.valid )
{
rc = report_options( &options );
if ( rc == 0 )
{
rc = matching( &options ); /* here we are calling into C++ */
}
}
ArgsWhack ( args );
}
return rc;
}
rc_t CC KMain (int argc, char * argv[])
{
Args * args;
rc_t rc;
unsigned n_aligned = 0;
unsigned n_unalgnd = 0;
char *aligned[256];
char *unalgnd[256];
char *name_buffer = NULL;
unsigned next_name = 0;
unsigned nbsz = 0;
char const *value;
char *dummy;
const XMLLogger* xml_logger = NULL;
memset(&G, 0, sizeof(G));
G.mode = mode_Archive;
G.maxSeqLen = TableWriterRefSeq_MAX_SEQ_LEN;
G.schemaPath = SCHEMAFILE;
G.omit_aligned_reads = true;
G.omit_reference_reads = true;
G.minMapQual = 0; /* accept all */
G.tmpfs = "/tmp";
#if _ARCH_BITS == 32
G.cache_size = ( size_t ) 1 << 30;
#else
G.cache_size = ( size_t ) 10 << 30;
#endif
G.maxErrCount = 1000;
G.minMatchCount = 10;
set_pid();
rc = ArgsMakeAndHandle (&args, argc, argv, 2, Options,
sizeof Options / sizeof (OptDef), XMLLogger_Args, XMLLogger_ArgsQty);
while (rc == 0) {
uint32_t pcount;
if( (rc = XMLLogger_Make(&xml_logger, NULL, args)) != 0 ) {
break;
}
rc = ArgsOptionCount(args, option_only_verify, &pcount);
if (rc)
break;
G.onlyVerifyReferences = (pcount > 0);
rc = ArgsOptionCount(args, option_no_verify, &pcount);
if (rc)
break;
G.noVerifyReferences = (pcount > 0);
rc = ArgsOptionCount(args, option_use_qual, &pcount);
if (rc)
break;
G.useQUAL = (pcount > 0);
rc = ArgsOptionCount(args, option_ref_config, &pcount);
if (rc)
break;
G.limit2config = (pcount > 0);
rc = ArgsOptionCount(args, OPTION_REF_FILE, &pcount);
if (rc)
break;
G.refFiles = calloc(pcount + 1, sizeof(*(G.refFiles)));
if( !G.refFiles ) {
rc = RC(rcApp, rcArgv, rcAccessing, rcMemory, rcExhausted);
break;
}
while(pcount-- > 0) {
rc = ArgsOptionValue(args, OPTION_REF_FILE, pcount, &G.refFiles[pcount]);
if (rc)
break;
}
rc = ArgsOptionCount (args, OPTION_TMPFS, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_TMPFS, 0, &G.tmpfs);
if (rc)
break;
}
else if (pcount > 1)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
OUTMSG (("Single parameter required\n"));
MiniUsage (args);
break;
}
rc = ArgsOptionCount (args, OPTION_INPUT, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_INPUT, 0, &G.inpath);
if (rc)
break;
}
else if (pcount > 1)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
OUTMSG (("Single input parameter required\n"));
MiniUsage (args);
break;
}
rc = ArgsOptionCount (args, option_ref_filter, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, option_ref_filter, 0, &G.refFilter);
if (rc)
break;
}
else if (pcount > 1)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
OUTMSG (("Single parameter required\n"));
MiniUsage (args);
break;
}
rc = ArgsOptionCount (args, OPTION_CONFIG, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_CONFIG, 0, &G.refXRefPath);
if (rc)
break;
}
else if (pcount > 1)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
OUTMSG (("Single input parameter required\n"));
MiniUsage (args);
break;
}
rc = ArgsOptionCount (args, OPTION_OUTPUT, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_OUTPUT, 0, &G.outpath);
if (rc)
break;
}
else if (pcount > 1)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
OUTMSG (("Single output parameter required\n"));
MiniUsage (args);
break;
}
else if (!G.onlyVerifyReferences) {
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcInsufficient);
OUTMSG (("Output parameter required\n"));
MiniUsage (args);
break;
}
rc = ArgsOptionCount (args, OPTION_MINMAPQ, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_MINMAPQ, 0, &value);
if (rc)
break;
G.minMapQual = strtoul(value, &dummy, 0);
}
rc = ArgsOptionCount (args, OPTION_QCOMP, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_QCOMP, 0, &G.QualQuantizer);
if (rc)
break;
}
rc = ArgsOptionCount (args, option_edit_aligned_qual, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, option_edit_aligned_qual, 0, &value);
if (rc)
break;
G.alignedQualValue = strtoul(value, &dummy, 0);
if (G.alignedQualValue == 0) {
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcIncorrect);
OUTMSG (("edit-aligned-qual: bad value\n"));
MiniUsage (args);
break;
}
G.editAlignedQual = true;
}
rc = ArgsOptionCount (args, OPTION_CACHE_SIZE, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_CACHE_SIZE, 0, &value);
if (rc)
break;
G.cache_size = strtoul(value, &dummy, 0) * 1024UL * 1024UL;
if (G.cache_size == 0) {
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcIncorrect);
OUTMSG (("cache-size: bad value\n"));
MiniUsage (args);
break;
}
}
rc = ArgsOptionCount (args, OPTION_MAX_WARN_DUP_FLAG, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_MAX_WARN_DUP_FLAG, 0, &value);
if (rc)
break;
G.maxWarnCount_DupConflict = strtoul(value, &dummy, 0);
}
rc = ArgsOptionCount (args, option_unsorted, &pcount);
if (rc)
break;
G.expectUnsorted = pcount > 0;
rc = ArgsOptionCount (args, OPTION_MAX_REC_COUNT, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_MAX_REC_COUNT, 0, &value);
if (rc)
break;
G.maxAlignCount = strtoul(value, &dummy, 0);
}
rc = ArgsOptionCount (args, OPTION_MAX_ERR_COUNT, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_MAX_ERR_COUNT, 0, &value);
if (rc)
break;
G.maxErrCount = strtoul(value, &dummy, 0);
}
rc = ArgsOptionCount (args, OPTION_MIN_MATCH, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_MIN_MATCH, 0, &value);
if (rc)
break;
G.minMatchCount = strtoul(value, &dummy, 0);
}
rc = ArgsOptionCount (args, OPTION_ACCEPT_DUP, &pcount);
if (rc)
break;
G.acceptBadDups = pcount > 0;
rc = ArgsOptionCount (args, OPTION_ACCEPT_NOMATCH, &pcount);
if (rc)
break;
G.acceptNoMatch = pcount > 0;
rc = ArgsOptionCount (args, option_keep_mismatch_qual, &pcount);
if (rc)
break;
G.keepMismatchQual = pcount > 0;
rc = ArgsOptionCount (args, OPTION_NO_CS, &pcount);
if (rc)
break;
G.noColorSpace = pcount > 0;
rc = ArgsOptionCount (args, OPTION_NO_SECONDARY, &pcount);
if (rc)
break;
G.noSecondary = pcount > 0;
rc = ArgsOptionCount (args, OPTION_TI, &pcount);
if (rc)
break;
G.hasTI = pcount > 0;
rc = ArgsOptionCount (args, OPTION_ACCEPT_HARD_CLIP, &pcount);
if (rc)
break;
G.acceptHardClip = pcount > 0;
rc = ArgsOptionCount (args, OPTION_NOMATCH_LOG, &pcount);
if (rc)
break;
if (pcount == 1)
{
KDirectory *dir;
rc = ArgsOptionValue (args, OPTION_NOMATCH_LOG, 0, &value);
if (rc) break;
rc = KDirectoryNativeDir(&dir);
if (rc) break;
rc = KDirectoryCreateFile(dir, &G.noMatchLog, 0, 0664, kcmInit, value);
KDirectoryRelease(dir);
if (rc) break;
}
rc = ArgsOptionCount (args, OPTION_HEADER, &pcount);
if (rc)
break;
if (pcount == 1) {
rc = ArgsOptionValue (args, OPTION_HEADER, 0, &value);
if (rc) break;
rc = LoadHeader(&G.headerText, value, G.inpath);
if (rc) break;
}
rc = ArgsParamCount (args, &pcount);
if (rc) break;
if (pcount == 0)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcInsufficient);
MiniUsage (args);
break;
}
else if (pcount > sizeof(aligned)/sizeof(aligned[0])) {
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
(void)PLOGERR(klogErr, (klogErr, rc, "$(count) input files is too many, $(max) is the limit",
"count=%u,max=%u", (unsigned)pcount, (unsigned)(sizeof(aligned)/sizeof(aligned[0]))));
break;
}
else {
unsigned need = G.inpath ? (strlen(G.inpath) + 1) * pcount : 0;
unsigned i;
for (i = 0; i < pcount; ++i) {
rc = ArgsParamValue(args, i, &value);
if (rc) break;
need += strlen(value) + 1;
}
nbsz = need;
}
rc = ArgsOptionCount (args, OPTION_UNALIGNED, &pcount);
if (rc)
break;
if (pcount > 0)
{
unsigned need = G.inpath ? (strlen(G.inpath) + 1) * pcount : 0;
unsigned i;
for (i = 0; i < pcount; ++i) {
rc = ArgsOptionValue(args, OPTION_UNALIGNED, i, &value);
if (rc) break;
need += strlen(value) + 1;
}
if (rc) break;
nbsz += need;
}
name_buffer = malloc(nbsz);
if (name_buffer == NULL) {
rc = RC(rcApp, rcArgv, rcAccessing, rcMemory, rcExhausted);
break;
}
rc = ArgsOptionCount (args, OPTION_UNALIGNED, &pcount);
if (rc == 0) {
unsigned i;
for (i = 0; i < pcount; ++i) {
rc = ArgsOptionValue(args, OPTION_UNALIGNED, i, &value);
if (rc) break;
unalgnd[n_unalgnd++] = name_buffer + next_name;
rc = PathWithBasePath(name_buffer + next_name, nbsz - next_name, value, G.inpath);
if (rc) break;
next_name += strlen(name_buffer + next_name) + 1;
}
if (rc) break;
}
else
break;
rc = ArgsParamCount (args, &pcount);
if (rc == 0) {
unsigned i;
for (i = 0; i < pcount; ++i) {
rc = ArgsParamValue(args, i, &value);
if (rc) break;
aligned[n_aligned++] = name_buffer + next_name;
rc = PathWithBasePath(name_buffer + next_name, nbsz - next_name, value, G.inpath);
if (rc) break;
next_name += strlen(name_buffer + next_name) + 1;
}
}
else
break;
rc = run(argv[0], n_aligned, (char const **)aligned, n_unalgnd, (char const **)unalgnd);
break;
}
free(name_buffer);
free((void *)G.headerText);
free(G.refFiles);
value = G.outpath ? strrchr(G.outpath, '/') : "/???";
if( value == NULL ) {
value = G.outpath;
} else {
value++;
}
if (rc) {
(void)PLOGERR(klogErr, (klogErr, rc, "load failed",
"severity=total,status=failure,accession=%s,errors=%u", value, G.errCount));
} else {
(void)PLOGMSG(klogInfo, (klogInfo, "loaded",
"severity=total,status=success,accession=%s,errors=%u", value, G.errCount));
}
ArgsWhack(args);
XMLLogger_Release(xml_logger);
return rc;
}
static rc_t argsHandler(int argc, char* argv[]) {
Args* args = NULL;
rc_t rc = ArgsMakeAndHandle(&args, argc, argv, 0, NULL, 0);
ArgsWhack(args);
return rc;
}
rc_t CC KMain( int argc, char *argv [] )
{
Args * args;
rc_t rc = ArgsMakeAndHandle( &args, argc, argv, 1, options, sizeof options / sizeof options [ 0 ] );
if ( rc == 0 )
{
try
{
NGS_Pileup::Settings settings;
uint32_t pcount;
rc = ArgsOptionCount ( args, OPTION_REF, &pcount );
if ( pcount > 1 )
{
throw ngs :: ErrorMsg ( "multiple positions are not supported at this point" );
}
if ( pcount == 1 )
{
const void * value;
rc = ArgsOptionValue ( args, OPTION_REF, 0, & value );
if ( rc != 0 )
{
throw ngs :: ErrorMsg ( "ArgsOptionValue (" OPTION_REF ") failed" );
}
settings . AddReference ( static_cast <char const*> (value) );
}
rc = ArgsParamCount ( args, &pcount );
if ( rc == 0 )
{
if ( pcount > 1 )
{
throw ngs :: ErrorMsg ( "multiple accessions are not supported at this point" );
}
settings . output = & std::cout;
void const *value;
rc = ArgsParamValue ( args, 0, &value );
if ( rc == 0 )
{
settings . AddInput ( static_cast <char const*> (value) );
NGS_Pileup ( settings ) . Run ();
}
else
{
throw ngs :: ErrorMsg ( "ArgsParamValue failed" );
}
}
}
catch (ngs :: ErrorMsg& ex)
{
std :: cerr << "Program aborted: " << ex.what() << std::endl;
exit ( -1 );
}
ArgsWhack( args );
}
return 0;
}
/* KMain
*/
rc_t CC KMain ( int argc, char *argv [] )
{
Args * args;
rc_t rc;
rc = ArgsMakeAndHandle (&args, argc, argv, 0);
if (rc)
LOGERR (klogInt, rc, "failed to parse arguments");
else do
{
uint32_t acount;
rc = ArgsParamCount (args, &acount);
if (rc)
{
LOGERR (klogInt, rc, "failed to count parameters");
break;
}
if (acount == 0)
{
rc = MiniUsage (args);
break;
}
else
{
VFSManager* mgr;
rc = VFSManagerMake(&mgr);
if (rc)
LOGERR ( klogErr, rc, "failed to create VFSManager object" );
else
{
VResolver * resolver;
rc = VFSManagerGetResolver (mgr, &resolver);
if (rc == 0)
{
uint32_t ix;
for ( ix = 0; ix < acount; ++ ix )
{
const char * pc;
rc = ArgsParamValue (args, ix, &pc );
if (rc)
LOGERR (klogInt, rc,
"failed to retrieve parameter value");
else
{
const VPath * upath = NULL;
rc = VFSManagerMakePath ( mgr, (VPath**)&upath, "%s", pc);
if (rc == 0)
{
const VPath * local;
const VPath * remote;
rc = VResolverQuery (resolver, eProtocolHttp, upath, &local, &remote, NULL);
if (rc == 0)
{
const String * s;
if (local != NULL)
rc = VPathMakeString (local, &s);
else
rc = VPathMakeString (remote, &s);
if (rc == 0)
{
OUTMSG (("%S\n", s));
free ((void*)s);
}
VPathRelease (local);
VPathRelease (remote);
}
else
{
KDirectory * cwd;
rc_t orc = VFSManagerGetCWD (mgr, &cwd);
if (orc == 0)
{
KPathType kpt
= KDirectoryPathType(cwd, "%s", pc);
switch (kpt &= ~kptAlias)
{
case kptNotFound:
STSMSG(1, ("'%s': not found while "
"searching the file system",
pc));
break;
case kptBadPath:
STSMSG(1, ("'%s': bad path while "
"searching the file system",
pc));
break;
default:
STSMSG(1, ("'%s': "
"found in the file system",
pc));
rc = 0;
break;
}
}
if (orc == 0 && rc == 0) {
if (rc != 0) {
PLOGMSG(klogErr, (klogErr,
"'$(name)': not found",
"name=%s", pc));
}
else {
char resolved[PATH_MAX] = "";
rc = KDirectoryResolvePath(cwd, true,
resolved, sizeof resolved, "%s", pc);
if (rc == 0) {
STSMSG(1, ("'%s': found in "
"the current directory at '%s'",
pc, resolved));
OUTMSG (("%s\n", resolved));
}
else {
STSMSG(1, ("'%s': cannot resolve "
"in the current directory",
pc));
OUTMSG (("./%s\n", pc));
}
}
}
KDirectoryRelease(cwd);
}
}
RELEASE(VPath, upath);
}
}
VResolverRelease (resolver);
}
VFSManagerRelease(mgr);
}
}
ArgsWhack (args);
} while (0);
return rc;
}
rc_t CC KMain (int argc, char * argv[])
{
Args * args;
uint32_t pcount;
rc_t rc = ArgsMakeAndHandle (&args, argc, argv, 1, Options, sizeof Options / sizeof (OptDef));
if ( rc == 0 )
{
rc = ArgsParamCount (args, &pcount);
if ( rc == 0 )
{
if ( pcount != 0 )
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
MiniUsage (args);
}
else
{
const KStream *std_in;
rc = KStreamMakeStdIn ( & std_in );
if ( rc == 0 )
{
KStream* buffered;
rc = KStreamMakeBuffered ( &buffered, std_in, 0 /*input-only*/, 0 /*use default size*/ );
if ( rc == 0 )
{
GeneralLoader loader ( *buffered );
rc = ArgsOptionCount (args, OPTION_INCLUDE_PATHS, &pcount);
if ( rc == 0 )
{
for ( uint32_t i = 0 ; i < pcount; ++i )
{
const char* value;
rc = ArgsOptionValue (args, OPTION_INCLUDE_PATHS, i, &value);
if ( rc != 0 )
{
break;
}
loader . AddSchemaIncludePath ( value );
}
}
rc = ArgsOptionCount (args, OPTION_SCHEMAS, &pcount);
if ( rc == 0 )
{
for ( uint32_t i = 0 ; i < pcount; ++i )
{
const char* value;
rc = ArgsOptionValue (args, OPTION_SCHEMAS, i, &value);
if ( rc != 0 )
{
break;
}
loader . AddSchemaFile( value );
}
}
rc = ArgsOptionCount (args, OPTION_TARGET, &pcount);
if ( rc == 0 && pcount == 1 )
{
const char* value;
rc = ArgsOptionValue (args, OPTION_TARGET, 0, &value);
if ( rc == 0 )
{
loader . SetTargetOverride ( value );
}
}
if ( rc == 0 )
{
rc = loader . Run();
}
KStreamRelease ( buffered );
}
KStreamRelease ( std_in );
}
}
}
}
if ( rc != 0)
{
LOGERR ( klogErr, rc, "load failed" );
}
ArgsWhack(args);
return rc;
}
rc_t CC KMain( int argc, char* argv[] )
{
rc_t rc = 0;
Args* args = NULL;
const char* errmsg = NULL, *refseq_chunk = NULL, *min_mapq = NULL, *cluster_size = NULL;
const XMLLogger* xml_logger = NULL;
SParam params;
memset(¶ms, 0, sizeof(params));
params.schema = "align/align.vschema";
params.argv0 = argv[0];
if( (rc = ArgsMakeAndHandle(&args, argc, argv, 2, MainArgs, MainArgsQty, XMLLogger_Args, XMLLogger_ArgsQty)) == 0 ) {
uint32_t count;
if( (rc = ArgsParamCount (args, &count)) != 0 || count != 0 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
ArgsParamValue(args, 0, &errmsg);
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_Output].name, &count)) != 0 || count != 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, count ? rcExcessive : rcInsufficient);
errmsg = MainArgs[eopt_Output].name;
} else if( (rc = ArgsOptionValue(args, MainArgs[eopt_Output].name, 0, ¶ms.out)) != 0 ) {
errmsg = MainArgs[eopt_Output].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_MapInput].name, &count)) != 0 || count != 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, count ? rcExcessive : rcInsufficient);
errmsg = MainArgs[eopt_MapInput].name;
} else if( (rc = ArgsOptionValue(args, MainArgs[eopt_MapInput].name, 0, ¶ms.map_path)) != 0 ) {
errmsg = MainArgs[eopt_MapInput].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_Schema].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, count ? rcExcessive : rcInsufficient);
errmsg = MainArgs[eopt_Schema].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_Schema].name, 0, ¶ms.schema)) != 0 ) {
errmsg = MainArgs[eopt_Schema].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_AsmInput].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_AsmInput].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_AsmInput].name, 0, ¶ms.asm_path)) != 0 ) {
errmsg = MainArgs[eopt_AsmInput].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_RefSeqConfig].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_RefSeqConfig].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_RefSeqConfig].name, 0, ¶ms.refseqcfg)) != 0 ) {
errmsg = MainArgs[eopt_RefSeqConfig].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_RefSeqPath].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_RefSeqPath].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_RefSeqPath].name, 0, ¶ms.refseqpath)) != 0 ) {
errmsg = MainArgs[eopt_RefSeqPath].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_Library].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_Library].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_Library].name, 0, ¶ms.library)) != 0 ) {
errmsg = MainArgs[eopt_Library].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_RefSeqChunk].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_RefSeqChunk].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_RefSeqChunk].name, 0, &refseq_chunk)) != 0 ) {
errmsg = MainArgs[eopt_RefSeqChunk].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_Force].name, ¶ms.force)) != 0 ) {
errmsg = MainArgs[eopt_Force].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_ForceRef].name, ¶ms.force_refw)) != 0 ) {
errmsg = MainArgs[eopt_ForceRef].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_ForceRead].name, ¶ms.force_readw)) != 0 ) {
errmsg = MainArgs[eopt_ForceRead].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_noReadAhead].name, ¶ms.no_read_ahead)) != 0 ) {
errmsg = MainArgs[eopt_noReadAhead].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_NoSpotGroup].name, ¶ms.no_spot_group)) != 0 ) {
errmsg = MainArgs[eopt_NoSpotGroup].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_No2nd_ary].name, ¶ms.min_mapq)) != 0 ) {
errmsg = MainArgs[eopt_No2nd_ary].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_QualQuantization].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_QualQuantization].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_QualQuantization].name, 0, ¶ms.qual_quant)) != 0 ) {
errmsg = MainArgs[eopt_QualQuantization].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_MinMapQ].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_MinMapQ].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_MinMapQ].name, 0, &min_mapq)) != 0 ) {
errmsg = MainArgs[eopt_MinMapQ].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_ClusterSize].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_ClusterSize].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_ClusterSize].name, 0, &cluster_size)) != 0 ) {
errmsg = MainArgs[eopt_ClusterSize].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_SingleMate].name, ¶ms.single_mate)) != 0 ) {
errmsg = MainArgs[eopt_SingleMate].name;
} else {
do {
long val = 0;
char* end = NULL;
uint32_t count;
if( (rc = ArgsOptionCount(args, MainArgs[eopt_RefFile].name, &count)) != 0 ) {
break;
} else {
params.refFiles = calloc(count + 1, sizeof(*(params.refFiles)));
if( params.refFiles == NULL ) {
rc = RC(rcApp, rcArgv, rcReading, rcMemory, rcExhausted);
break;
}
while(rc == 0 && count-- > 0) {
rc = ArgsOptionValue(args, MainArgs[eopt_RefFile].name, count, ¶ms.refFiles[count]);
}
}
if( refseq_chunk != NULL ) {
errno = 0;
val = strtol(refseq_chunk, &end, 10);
if( errno != 0 || refseq_chunk == end || *end != '\0' || val < 0 || val > UINT32_MAX ) {
rc = RC(rcExe, rcArgv, rcReading, rcParam, rcInvalid);
break;
}
params.refseq_chunk = val;
}
if( params.min_mapq > 0 ) {
params.min_mapq = ~0;
} else if( min_mapq != NULL ) {
errno = 0;
val = strtol(min_mapq, &end, 10);
if( errno != 0 || min_mapq == end || *end != '\0' || val < 0 || val > 255 ) {
rc = RC(rcExe, rcArgv, rcReading, rcParam, rcInvalid);
break;
}
params.min_mapq = val;
}
if ( cluster_size )
params.cluster_size = atoi( cluster_size );
else
params.cluster_size = 0;
rc = KDirectoryNativeDir( ¶ms.input_dir );
if ( rc != 0 )
errmsg = "current directory";
else
{
rc = XMLLogger_Make( &xml_logger, params.input_dir, args );
if ( rc != 0 )
errmsg = "XML logging";
else
rc = Load( ¶ms );
}
} while( false );
KDirectoryRelease( params.input_dir );
}
}
/* find accession as last part of path for internal XML logging */
refseq_chunk = params.out ? strrchr(params.out, '/') : "/???";
if( refseq_chunk ++ == NULL )
refseq_chunk = params.out;
if( argc < 2 )
MiniUsage(args);
else if( rc != 0 )
{
if( errmsg )
{
MiniUsage(args);
LOGERR(klogErr, rc, errmsg);
}
else
{
PLOGERR(klogErr, (klogErr, rc, "load failed: $(reason_short)",
"severity=total,status=failure,accession=%s", refseq_chunk));
}
}
else
{
PLOGMSG(klogInfo, (klogInfo, "loaded",
"severity=total,status=success,accession=%s", refseq_chunk));
}
ArgsWhack(args);
XMLLogger_Release(xml_logger);
return rc;
}
rc_t CC KMain ( int argc, char *argv [] )
{
Args * args;
rc_t rc = ArgsMakeAndHandle ( &args, argc, argv, 1,
QfileTestOptions, sizeof ( QfileTestOptions ) / sizeof ( OptDef ) );
if ( rc != 0 )
{
OUTMSG(( "ArgsMakeAndHandle( ... ) failed: %R\n", rc ));
}
else
{
uint32_t arg_count = 0;
rc = ArgsParamCount ( args, &arg_count );
if ( rc != 0 )
{
OUTMSG(( "ArgsParamCount( ... ) failed: %R\n", rc ));
}
else
{
KDirectory *dir = NULL;
uint64_t position = get_uint64_option( args, OPTION_POS, 0 );
uint64_t count = get_uint64_option( args, OPTION_COUNT, 0 );
uint32_t qsize = get_uint32_option( args, OPTION_QSIZE, 1024 );
uint32_t bsize = get_uint32_option( args, OPTION_BSIZE, 0 );
uint32_t csize = get_uint32_option( args, OPTION_CSIZE, 1024 );
uint64_t pos2 = get_uint64_option( args, OPTION_POS2, 0 );
OUTMSG(( "start-position : %lu\n", position ));
if ( pos2 > 0 )
{
OUTMSG(( "2nd position : %lu\n", pos2 ));
}
if ( count > 0 )
{
OUTMSG(( "count : %lu\n", count ));
}
OUTMSG(( "queue-size : %u\n", qsize ));
OUTMSG(( "block-size : %u\n", bsize ));
OUTMSG(( "chunk-size : %u\n", csize ));
rc = KDirectoryNativeDir( &dir );
if ( rc != 0 )
{
OUTMSG(( "KDirectoryNativeDir( ... ) failed: %R\n", rc ));
}
else
{
uint32_t i;
for ( i = 0; i < arg_count && rc == 0; ++i )
{
const char * filename;
rc = ArgsParamValue ( args, i, &filename );
if ( rc != 0 )
{
OUTMSG(( "ArgsParamValue( %d ) failed: %R\n", i, rc ));
}
else
{
OUTMSG(( "file to read : '%s'\n", filename ));
rc = perform_test( dir, filename, position, pos2,
count, qsize, bsize, csize );
}
}
KDirectoryRelease( dir );
}
}
ArgsWhack ( args );
}
return rc;
}
rc_t CC KMain ( int argc, char *argv [] )
{
Args *args;
rc_t rc;
do {
uint32_t paramc;
bool requireAmd64 = false;
uint64_t requireRam = 0;
rc = ArgsMakeAndHandle ( & args, argc, argv, 1,
Options, sizeof Options / sizeof (OptDef) );
if ( rc != 0 )
{
LogErr ( klogErr, rc, "failed to parse arguments" );
break;
}
// TODO: cehck if we need it
rc = ArgsParamCount ( args, & paramc );
if ( rc != 0 ) {
LogErr ( klogInt, rc, "failed to obtain param count" );
break;
}
{ // OPTION_AMD64
rc = ArgsOptionCount( args, OPTION_AMD64, & paramc );
if ( rc ) {
LOGERR( klogErr, rc, "Failure to get '" OPTION_AMD64 "' argument" );
break;
}
if ( paramc ) {
requireAmd64 = true;
}
}
{
// OPTION_RAM
rc = ArgsOptionCount ( args, OPTION_RAM, & paramc );
if ( rc ) {
LOGERR ( klogErr, rc, "Failure to get '" OPTION_RAM "' argument" );
break;
}
if ( paramc ) {
const char* dummy = NULL;
rc = ArgsOptionValue(args, OPTION_RAM, 0, (const void **)&dummy);
if ( rc ) {
LOGERR(klogErr, rc, "Failure to get '" OPTION_RAM "' argument");
break;
}
rc = sscanf(dummy, "%llu", &requireRam);
if ( rc != 1)
{
LOGMSG(klogErr, "Failure to parse '" OPTION_RAM "' argument value");
break;
}
}
}
{
rc = KAppCheckEnvironment(requireAmd64, requireRam);
if (rc != 0 )
printf("Invalid environment\n");
else
printf("Enviroment is fine!\n");
}
} while (false);
ArgsWhack ( args );
return rc;
}
rc_t CC KMain ( int argc, char *argv[] )
{
rc_t rc = 0;
Args * args;
rc = ArgsMakeStandardOptions (&args);
if (rc == 0)
{
do
{
uint32_t pcount;
rc = ArgsAddOptionArray (args, MyOptions, sizeof MyOptions / sizeof (OptDef));
if (rc)
break;
rc = ArgsParse (args, argc, argv);
if (rc)
break;
/* quirky way default path is generated means this comes
* before standard argument handling */
rc = ArgsOptionCount (args, OPTION_TABLE, &pcount);
if (rc)
break;
if (pcount == 0)
{
static char * default_name = "RowWriteTestOutTable";
char * user;
user = getenv ("USER");
if (user)
snprintf (tablePath, sizeof (tablePath),
"/home/%s/%s", user, default_name);
else
strncpy (tablePath, default_name, sizeof (tablePath));
}
else
{
const char * pc;
ArgsOptionValue (args, OPTION_TABLE, 0, &pc);
strncpy (tablePath, pc, sizeof (tablePath));
}
rc = ArgsHandleStandardOptions (args);
if (rc)
break;
rc = ArgsParamCount (args, &pcount);
if (rc)
break;
if (pcount)
{
const char * pc;
rc = ArgsArgvValue (args, 0, &pc);
if (rc)
break;
rc = RC (rcExe, rcNoTarg, rcParsing, rcParam, rcExcessive);
PLOGERR (klogFatal, (klogFatal, rc, "$(P) takes no parameters", PLOG_S(P), pc));
break;
}
rc = ArgsOptionCount (args, OPTION_ROW, &pcount);
if (rc == 0)
{
uint64_t row_count;
if (pcount)
{
const char * pc;
rc = ArgsOptionValue (args, OPTION_ROW, 0, &pc);
if (rc)
break;
row_count = AsciiToU32 (pc, NULL, NULL);
}
else
row_count = ROWS;
rc = run (tablePath, row_count);
}
} while (0);
ArgsWhack (args);
}
return rc;
}
rc_t CC KMain ( int argc, char *argv [] )
{
Args * args;
rc_t rc;
rc = ArgsMakeAndHandle (&args, argc, argv, 1, MyOptions, sizeof MyOptions / sizeof (OptDef));
if (rc)
LOGERR (klogInt, rc, "failed to parse arguments");
else
{
do
{
KDyld *dl;
uint32_t num_libs;
rc = ArgsParamCount (args, &num_libs);
if (rc)
{
LOGERR ( klogInt, rc, "Failure to count parameters" );
break;
}
if (num_libs == 0)
{
rc = MiniUsage(args);
break;
}
/* create loader */
rc = KDyldMake (&dl);
if (rc)
{
LOGERR ( klogInt, rc, "failed to create dynamic loader" );
break;
}
else
{
do
{
KDlset *libs;
const char * path;
uint32_t ix;
uint32_t num_paths;
rc = ArgsOptionCount (args, OPTION_LOAD, &num_paths);
if (rc)
{
LOGERR (klogInt, rc, "failed to count paths");
break;
}
for (ix = 0; ix < num_paths; ix++)
{
rc = ArgsOptionValue (args, OPTION_LOAD, ix, (const void **)&path);
if (rc)
{
LOGERR (klogInt, rc, "failed to access a path option");
break;
}
testld_update_libpath (dl, path);
}
if (rc)
break;
/* append contents of LD_LIBRARY_PATH */
path = getenv ( "LD_LIBRARY_PATH" );
if (path)
testld_update_libpath (dl, path);
/* create libset */
rc = KDyldMakeSet (dl, & libs);
if (rc)
{
LOGERR (klogInt, rc, "failed to create dl library set");
break;
}
else
{
/* test it */
for (ix = 0; ix < num_libs; ++ ix )
{
rc = ArgsParamValue (args, ix, (const void **)&path);
if (rc)
break;
testld_load_library (dl, libs, path);
}
KDlsetRelease ( libs );
}
} while (0);
KDyldRelease ( dl );
}
} while (0);
ArgsWhack (args);
}
return rc;
}
rc_t CC KMain ( int argc, char *argv [] )
{
Args * args;
rc_t rc;
rc = ArgsMakeAndHandle (&args, argc, argv, 1, Options, sizeof Options / sizeof (OptDef));
if (rc == 0)
{
uint32_t pcount;
const char * pc;
const char * directory;
const char * archive;
do
{
op_mode mode;
uint32_t ix;
BSTreeInit (&pnames);
rc = ArgsParamCount (args, &pcount);
if (rc)
break;
for (ix = 0; ix < pcount; ++ix)
{
rc = ArgsParamValue (args, ix, (const void **)&pc);
if (rc)
break;
rc = pnamesInsert (pc);
if (rc)
{
PLOGERR (klogInt, (klogInt, rc, "failure to process filter parameter [%s]", pc));
break;
}
}
if (rc)
break;
rc = ArgsOptionCount (args, OPTION_ALIGN, &pcount);
if (rc)
break;
if (pcount == 0)
pc = NULL;
else
{
rc = ArgsOptionValue (args, OPTION_ALIGN, 0, (const void **)&pc);
if (rc)
break;
}
alignment = get_alignment (pc);
if (alignment == sraAlignInvalid)
{
rc = RC (rcExe, rcArgv, rcParsing, rcParam, rcInvalid);
PLOGERR (klogFatal, (klogFatal, rc,
"Parameter for alignment [$(A)] is invalid: must be a power of two bytes",
PLOG_S(A), pc));
break;
}
rc = ArgsOptionCount (args, OPTION_LONGLIST, &pcount);
if (rc)
break;
long_list = (pcount != 0);
rc = ArgsOptionCount (args, OPTION_FORCE, &pcount);
if (rc)
break;
force = (pcount != 0);
mode = OM_NONE;
rc = ArgsOptionCount (args, OPTION_DIRECTORY, &pcount);
if (rc)
break;
if (pcount)
{
rc = ArgsOptionValue (args, OPTION_DIRECTORY, 0, (const void **)&directory);
if (rc)
break;
}
else
directory = NULL;
rc = ArgsOptionCount (args, OPTION_CREATE, &pcount);
if (rc)
break;
if (pcount)
{
rc = ArgsOptionValue (args, OPTION_CREATE, 0, (const void **)&archive);
if (rc)
break;
mode = OM_CREATE;
}
rc = ArgsOptionCount (args, OPTION_TEST, &pcount);
if (rc)
break;
if (pcount)
{
if (mode == OM_NONE)
{
mode = OM_TEST;
rc = ArgsOptionValue (args, OPTION_TEST, 0, (const void **)&archive);
if (rc)
break;
}
else
mode = OM_ERROR;
}
rc = ArgsOptionCount (args, OPTION_LIST, &pcount);
if (rc)
break;
if (pcount)
{
if (mode == OM_NONE)
{
mode = OM_TEST;
rc = ArgsOptionValue (args, OPTION_LIST, 0, (const void **)&archive);
if (rc)
break;
}
else
mode = OM_ERROR;
}
rc = ArgsOptionCount (args, OPTION_EXTRACT, &pcount);
if (rc)
break;
if (pcount)
{
if (mode == OM_NONE)
{
mode = OM_EXTRACT;
rc = ArgsOptionValue (args, OPTION_EXTRACT, 0, (const void **)&archive);
if (rc)
break;
}
else
mode = OM_ERROR;
}
if (mode == OM_NONE)
{
MiniUsage(args);
rc = RC(rcApp, rcArgv, rcParsing, rcParam, rcInsufficient);
break;
}
/* -----
* Mount the native filesystem as root
*/
rc = KDirectoryNativeDir (&kdir);
if (rc != 0)
{
LOGMSG (klogFatal, "Failed to open native KDirectory");
}
else
{
switch (mode)
{
default: /* OM_NONE presumably */
/* assert (mode == OM_NONE); */
/* rc = RC (rcExe, rcNoTarg, rcParsing, rcParam, rcEmpty); */
/* LOGERR (klogFatal, rc, "Must provide a single operating mode and archive: Create, Test (list) or eXtract"); */
pc = NULL;
break;
case OM_ERROR:
rc = RC (rcExe, rcNoTarg, rcParsing, rcParam, rcAmbiguous);
LOGERR (klogFatal, rc, "Must provide a single operating mode and archive: Create, Test (list) or eXtract");
break;
case OM_CREATE:
STSMSG (2, ("Create Mode %s %s", archive, directory));
if (directory == NULL)
{
rc = RC (rcExe, rcNoTarg, rcParsing, rcParam, rcNull);
LOGERR (klogFatal, rc, "Must provide a directory for create mode");
}
else
rc = run_kar_create (archive, directory);
break;
case OM_TEST:
STSMSG (2, ("Test Mode %s", archive));
rc = run_kar_test (archive);
break;
case OM_EXTRACT:
STSMSG (2, ("Extract Mode %s %s", archive, directory));
if (directory == NULL)
{
rc = RC (rcExe, rcNoTarg, rcParsing, rcParam, rcNull);
LOGERR (klogFatal, rc, "Must provide a directory for extract mode");
}
else
rc = run_kar_extract (archive, directory);
break;
}
KDirectoryRelease (kdir);
}
} while (0);
ArgsWhack (args);
}
if (rc)
LOGERR (klogWarn, rc, "Failure exiting kar");
else
STSMSG (1, ("Success: Exiting kar\n"));
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;
}