static rc_t AppCtxInit(rc_t rc, AppCtx* ctx) {
assert(ctx);
memset(ctx, 0 , sizeof *ctx);
if (rc) {
return rc;
}
if (rc == 0) {
rc = SRAMgrMakeUpdate(&ctx->s_mgr, NULL);
DISP_RC(rc, "while calling SRAMgrMakeUpdate");
}
if (rc == 0) {
rc = KXMLMgrMakeRead(&ctx->x_mgr);
DISP_RC(rc, "while calling KXMLMgrMakeRead");
}
if (rc == 0) {
rc = KDirectoryNativeDir(&ctx->dir);
DISP_RC(rc, "while calling KDirectoryNativeDir");
}
return rc;
}
static rc_t SDataInit(struct SData* self,
const char* tablePath, const SRAMgr* rdMgr, rc_t rc)
{
SRAMgr* wrMgr = NULL;
assert(self);
memset(self, 0, sizeof *self);
if (rc)
{ return rc; }
rc = SRAMgrMakeUpdate(&wrMgr, NULL);
if (rc != 0) {
logerr(klogErr, rc, "while calling SRAMgrMakeUpdate");
}
else {
plogmsg(klogInfo,
"Opening Table $(path) for read", "path=%s", tablePath);
rc = SRAMgrOpenTableRead(rdMgr, &self->_rdTbl, "%s", tablePath);
if (rc != 0) {
plogerr(klogErr, rc,
"cannot open table $(path) for read", "path=%s", tablePath);
}
}
if (rc == 0) {
plogmsg(klogInfo,
"Opening Table $(path) for update", "path=%s", tablePath);
rc = SRAMgrOpenTableUpdate(wrMgr, &self->_wrTbl, "%s", tablePath);
if (rc != 0) {
plogerr(klogErr, rc,
"cannot open table $(path) for update", "path=%s", tablePath);
}
}
SRAMgrRelease(wrMgr);
return rc;
}
rc_t KMain(int argc, char *argv[])
{
rc_t rc = 0;
Args* args = NULL;
const char* errmsg = NULL, *table_dir = NULL;
char accn[1024];
if( (rc = ArgsMakeAndHandle(&args, argc, argv, 1, MainArgs, MainArgsQty)) == 0 ) {
const char* blksz = NULL;
uint32_t count, dump = 0, gzip = 0;
if( (rc = ArgsParamCount(args, &count)) != 0 || count != 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, count > 1 ? rcExcessive : rcInsufficient);
errmsg = "table";
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_BlockSize].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_BlockSize].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_BlockSize].name, 0, (const void **)&blksz)) != 0 ) {
errmsg = MainArgs[eopt_BlockSize].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_Accession].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_Accession].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_Accession].name, 0, (const void **)&g_accession)) != 0 ) {
errmsg = MainArgs[eopt_Accession].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_DumpIndex].name, &dump)) != 0 ) {
errmsg = MainArgs[eopt_DumpIndex].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_noGzip].name, &gzip)) != 0 ) {
errmsg = MainArgs[eopt_noGzip].name;
}
while( rc == 0 ) {
long val = 0;
char* end = NULL;
if( blksz != NULL ) {
errno = 0;
val = strtol(blksz, &end, 10);
if( errno != 0 || blksz == end || *end != '\0' || val <= 0 ) {
rc = RC(rcExe, rcArgv, rcReading, rcParam, rcInvalid);
errmsg = MainArgs[eopt_BlockSize].name;
break;
} else if( val <= 128 || val > (1024 * 1024 * 1024) ) {
rc = RC(rcExe, rcArgv, rcValidating, rcParam, rcEmpty);
errmsg = "block size invalid";
break;
}
g_file_block_sz = val;
}
if( (rc = ArgsParamValue(args, 0, (const void **)&table_dir)) != 0 ) {
errmsg = "table";
break;
}
if( g_accession == NULL ) {
const char* p = strchr(table_dir, '/');
size_t l = 0;
g_accession = accn;
if( p == NULL ) {
p = strchr(table_dir, '\\');
}
strncpy(accn, p == NULL ? table_dir : p + 1, sizeof(accn) - 1);
if( accn[0] == '\0' ) {
rc = RC(rcExe, rcArgv, rcValidating, rcParam, rcEmpty);
errmsg = "accession";
}
l = strlen(accn);
if( accn[l - 1] == '/' || accn[l - 1] == '\\') {
accn[--l] = '\0';
}
if( strncmp(&accn[l - 9], ".lite.sra", 9) == 0 ) {
accn[l - 9] = '\0';
} else if( strncmp(&accn[l - 4], ".sra", 4) == 0 ) {
accn[l - 4] = '\0';
}
}
g_dump = dump > 0;
g_ungzip = gzip > 0;
break;
}
}
if( rc == 0 ) {
SRAMgr* smgr = NULL;
KDBManager* kmgr = NULL;
DEBUG_MSG(5, ("table %s, accession %s\n", table_dir, g_accession));
if( (rc = SRAMgrMakeUpdate(&smgr, NULL)) == 0 ) {
if( (rc = KDBManagerMakeUpdate(&kmgr, NULL)) == 0 ) {
bool relock = true;
if( (rc = KDBManagerUnlock(kmgr, table_dir)) != 0 ) {
relock = false;
rc = GetRCState(rc) == rcUnlocked ? 0 : rc;
} else {
PLOGMSG(klogInfo, (klogInfo, "Table $(p) locked, unlocking", PLOG_S(p), table_dir));
}
if( rc == 0 ) {
KTable* ktbl = NULL;
if( (rc = KDBManagerOpenTableUpdate(kmgr, &ktbl, table_dir)) == 0 ) {
KMetadata* meta = NULL;
if( (rc = KTableOpenMetadataUpdate(ktbl, &meta)) == 0 ) {
const SRATable* stbl = NULL;
if( (rc = SRAMgrOpenTableRead(smgr, &stbl, table_dir)) == 0 ) {
rc = MakeIndexes(stbl, ktbl, meta);
SRATableRelease(stbl);
}
}
KMetadataRelease(meta);
}
KTableRelease(ktbl);
}
if( rc == 0 && relock ) {
rc = KDBManagerLock(kmgr, table_dir);
}
KDBManagerRelease(kmgr);
}
SRAMgrRelease(smgr);
}
}
if( rc != 0 && rc != KLogLastErrorCode() ) {
if( errmsg ) {
Usage(args);
}
LOGERR(klogErr, rc, errmsg ? errmsg : "stop");
}
ArgsWhack(args);
return rc;
}
