CVDBTable::CVDBTable(const CVDB& db,
const char* table_name,
EMissing missing)
: m_Db(db),
m_Name(table_name)
{
DECLARE_SDK_GUARD();
if ( rc_t rc = VDatabaseOpenTableRead(db, x_InitPtr(), table_name) ) {
*x_InitPtr() = 0;
RCState rc_state = GetRCState(rc);
int rc_object = GetRCObject(rc);
if ( rc_state == rcNotFound &&
(rc_object == rcParam ||
rc_object == rcPath) ) {
// missing table in the DB
if ( missing != eMissing_Throw ) {
return;
}
NCBI_THROW2_FMT(CSraException, eNotFoundTable,
"Cannot open VDB table: "<<*this, rc);
}
else {
// other errors
NCBI_THROW2_FMT(CSraException, eOtherError,
"Cannot open VDB table: "<<*this, rc);
}
}
}
void CVPath::x_Init(const CVFSManager& mgr, const string& path, EType type)
{
VPath* vpath = 0;
if ( type == eSys ) {
if ( rc_t rc = VFSManagerMakeSysPath(mgr, &vpath, path.c_str()) ) {
*x_InitPtr() = 0;
NCBI_THROW2_FMT(CSraException, eInitFailed,
"Cannot create sys VPath: "<<path, rc);
}
}
else if ( type == eAcc ) {
if ( rc_t rc = VFSManagerMakeAccPath(mgr, &vpath, path.c_str()) ) {
*x_InitPtr() = 0;
NCBI_THROW2_FMT(CSraException, eInitFailed,
"Cannot create acc VPath: "<<path, rc);
}
}
else {
if ( rc_t rc = VFSManagerMakePath(mgr, &vpath, path.c_str()) ) {
*x_InitPtr() = 0;
NCBI_THROW2_FMT(CSraException, eInitFailed,
"Cannot create VPath: "<<path, rc);
}
}
*x_InitPtr() = vpath;
}
void CSraMgr::x_DoInit(void)
{
if ( rc_t rc = SRAMgrMakeRead(x_InitPtr()) ) {
*x_InitPtr() = 0;
NCBI_THROW2(CSraException, eInitFailed,
"Cannot open SRAMgr", rc);
}
}
CKDBManager::CKDBManager(const CVDBMgr& mgr)
{
if ( rc_t rc = VDBManagerGetKDBManagerRead(mgr, x_InitPtr()) ) {
*x_InitPtr() = 0;
NCBI_THROW2(CSraException, eInitFailed,
"Cannot get KDBManager", rc);
}
}
void CVFSManager::x_InitNew(void)
{
if ( rc_t rc = VFSManagerMake(x_InitPtr()) ) {
*x_InitPtr() = 0;
NCBI_THROW2(CSraException, eInitFailed,
"Cannot create VFSManager", rc);
}
}
CKNSManager::CKNSManager(const CVFSManager& mgr)
{
if ( rc_t rc = VFSManagerGetKNSMgr(mgr, x_InitPtr()) ) {
*x_InitPtr() = 0;
NCBI_THROW2(CSraException, eInitFailed,
"Cannot get KNSManager", rc);
}
}
CKConfig::CKConfig(const CVDBMgr& mgr)
{
*x_InitPtr() = VFSManagerGetConfig(CVFSManager(mgr));
if ( rc_t rc = KConfigAddRef(*this) ) {
*x_InitPtr() = 0;
NCBI_THROW2(CSraException, eInitFailed,
"Cannot get reference to KConfig", rc);
}
}
CVResolver::CVResolver(const CVFSManager& mgr, const CKConfig& cfg)
: m_Mgr(mgr)
{
if ( rc_t rc = VFSManagerMakeResolver(mgr, x_InitPtr(), cfg) ) {
*x_InitPtr() = 0;
NCBI_THROW2(CSraException, eInitFailed,
"Cannot create VResolver", rc);
}
}
CKConfig::CKConfig(void)
{
KConfig* cfg;
if ( rc_t rc = KConfigMake(&cfg, 0) ) {
*x_InitPtr() = 0;
NCBI_THROW2(CSraException, eInitFailed,
"Cannot create KConfig", rc);
}
*x_InitPtr() = cfg;
}
void CVDBMgr::x_Init(void)
{
if ( rc_t rc = VDBManagerMakeRead(x_InitPtr(), 0) ) {
*x_InitPtr() = 0;
NCBI_THROW2(CSraException, eInitFailed,
"Cannot open VDBManager", rc);
}
uint32_t sdk_ver;
if ( rc_t rc = VDBManagerVersion(*this, &sdk_ver) ) {
NCBI_THROW2(CSraException, eInitFailed,
"Cannot get VDBManager version", rc);
}
CKNSManager kns_mgr(CVFSManager(*this));
CNcbiOstrstream str;
CNcbiApplication* app = CNcbiApplication::Instance();
if ( app ) {
str << app->GetAppName() << ": " << app->GetVersion().Print() << "; ";
}
#if NCBI_PACKAGE
str << "Package: " << NCBI_PACKAGE_NAME << ' ' <<
NCBI_PACKAGE_VERSION << "; ";
#endif
str << "C++ ";
#ifdef NCBI_PRODUCTION_VER
str << NCBI_PRODUCTION_VER << "/";
#endif
#ifdef NCBI_DEVELOPMENT_VER
str << NCBI_DEVELOPMENT_VER;
#endif
string prefix = CNcbiOstrstreamToString(str);
KNSManagerSetUserAgent(kns_mgr, "%s; SRA Toolkit %V",
prefix.c_str(),
sdk_ver);
// redirect VDB log to C++ Toolkit
if ( s_GetDiagHandler() ) {
KLogInit();
KLogLevelSet(klogDebug);
KLogLibHandlerSet(VDBLogWriter, 0);
}
if ( app ) {
string host = app->GetConfig().GetString("CONN", "HTTP_PROXY_HOST", kEmptyStr);
int port = app->GetConfig().GetInt("CONN", "HTTP_PROXY_PORT", 0);
if ( !host.empty() && port != 0 ) {
if ( rc_t rc = KNSManagerSetHTTPProxyPath(kns_mgr, "%s:%d", host.c_str(), port) ) {
NCBI_THROW2(CSraException, eInitFailed,
"Cannot set KNSManager proxy parameters", rc);
}
KNSManagerSetHTTPProxyEnabled(kns_mgr, true);
}
}
}
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);
}
}
void CSraRun::x_DoInit(CSraMgr& mgr, const string& acc)
{
if ( rc_t rc = SRAMgrOpenTableRead(mgr, x_InitPtr(),
mgr.FindAccPath(acc).c_str()) ) {
*x_InitPtr() = 0;
NCBI_THROW3(CSraException, eNotFoundDb,
"Cannot open run read", rc, acc);
}
m_Name.Init(*this, "NAME", vdb_ascii_t);
m_Read.Init(*this, "READ", insdc_fasta_t);
m_Qual.Init(*this, "QUALITY", ncbi_qual1_t);
m_SDesc.Init(*this, "SPOT_DESC", sra_spot_desc_t);
m_RDesc.Init(*this, "READ_DESC", sra_read_desc_t);
m_TrimStart.TryInitRc(*this, "TRIM_START", "INSDC:coord:zero");
}
void CSraColumn::Init(const CSraRun& run,
const char* name, const char* type)
{
if ( rc_t rc = TryInitRc(run, name, type) ) {
*x_InitPtr() = 0;
NCBI_THROW3(CSraException, eInitFailed,
"Cannot get SRA column", rc, name);
}
}
CVDB::CVDB(const CVDBMgr& mgr, const string& acc_or_path)
: m_Name(acc_or_path)
{
DECLARE_SDK_GUARD();
string path = CVPath::ConvertAccOrSysPathToPOSIX(acc_or_path);
if ( rc_t rc = VDBManagerOpenDBRead(mgr, x_InitPtr(), 0, "%.*s",
int(path.size()), path.data()) ) {
*x_InitPtr() = 0;
if ( (GetRCObject(rc) == RCObject(rcDirectory) ||
GetRCObject(rc) == RCObject(rcPath) ||
GetRCObject(rc) == RCObject(rcFile)) &&
GetRCState(rc) == rcNotFound ) {
// no SRA accession
NCBI_THROW2_FMT(CSraException, eNotFoundDb,
"Cannot open VDB: "<<acc_or_path, rc);
}
else if ( GetRCObject(rc) == rcName &&
GetRCState(rc) == rcNotFound &&
GetRCContext(rc) == rcResolving ) {
// invalid SRA database
NCBI_THROW2_FMT(CSraException, eNotFoundDb,
"Cannot open VDB: "<<acc_or_path, rc);
}
else if ( GetRCObject(rc) == RCObject(rcFile) &&
GetRCState(rc) == rcUnauthorized ) {
// invalid SRA database
NCBI_THROW2_FMT(CSraException, eProtectedDb,
"Cannot open VDB: "<<acc_or_path, rc);
}
else if ( GetRCObject(rc) == RCObject(rcDatabase) &&
GetRCState(rc) == rcIncorrect ) {
// invalid SRA database
NCBI_THROW2_FMT(CSraException, eDataError,
"Cannot open VDB: "<<acc_or_path, rc);
}
else {
// other errors
NCBI_THROW2_FMT(CSraException, eOtherError,
"Cannot open VDB: "<<acc_or_path, rc);
}
}
}
CVDBTable::CVDBTable(const CVDBMgr& mgr,
const string& acc_or_path,
EMissing missing)
: m_Name(acc_or_path)
{
*x_InitPtr() = 0;
VSchema *schema;
DECLARE_SDK_GUARD();
if ( rc_t rc = SRASchemaMake(&schema, mgr) ) {
NCBI_THROW2(CSraException, eInitFailed,
"Cannot make default SRA schema", rc);
}
string path = CVPath::ConvertAccOrSysPathToPOSIX(acc_or_path);
if ( rc_t rc = VDBManagerOpenTableRead(mgr, x_InitPtr(), schema, "%.*s",
int(path.size()), path.data()) ) {
*x_InitPtr() = 0;
VSchemaRelease(schema);
if ( (GetRCObject(rc) == RCObject(rcDirectory) ||
GetRCObject(rc) == RCObject(rcPath)) &&
GetRCState(rc) == rcNotFound ) {
// no SRA accession
if ( missing != eMissing_Throw ) {
return;
}
NCBI_THROW2_FMT(CSraException, eNotFoundTable,
"Cannot open SRA table: "<<acc_or_path, rc);
}
else if ( GetRCObject(rc) == RCObject(rcDatabase) &&
GetRCState(rc) == rcIncorrect ) {
// invalid SRA database
NCBI_THROW2_FMT(CSraException, eDataError,
"Cannot open SRA table: "<<acc_or_path, rc);
}
else {
// other errors
NCBI_THROW2_FMT(CSraException, eOtherError,
"Cannot open SRA table: "<<acc_or_path, rc);
}
}
VSchemaRelease(schema);
}
void CVDBCursor::Init(const CVDBTable& table)
{
if ( *this ) {
NCBI_THROW2(CSraException, eInvalidState,
"Cannot init VDB cursor again",
RC(rcApp, rcCursor, rcConstructing, rcSelf, rcOpen));
}
if ( rc_t rc = VTableCreateCursorRead(table, x_InitPtr()) ) {
*x_InitPtr() = 0;
NCBI_THROW2(CSraException, eInitFailed,
"Cannot create VDB cursor", rc);
}
if ( rc_t rc = VCursorPermitPostOpenAdd(*this) ) {
NCBI_THROW2(CSraException, eInitFailed,
"Cannot allow VDB cursor post open column add", rc);
}
if ( rc_t rc = VCursorOpen(*this) ) {
NCBI_THROW2(CSraException, eInitFailed,
"Cannot open VDB cursor", rc);
}
m_Table = table;
}
CVDBTableIndex::CVDBTableIndex(const CVDBTable& table,
const char* index_name,
EMissing missing)
: m_Table(table),
m_Name(index_name)
{
if ( rc_t rc = VTableOpenIndexRead(table, x_InitPtr(), index_name) ) {
*x_InitPtr() = 0;
if ( GetRCObject(rc) == RCObject(rcIndex) &&
GetRCState(rc) == rcNotFound ) {
// no such index
if ( missing != eMissing_Throw ) {
return;
}
NCBI_THROW2_FMT(CSraException, eNotFoundIndex,
"Cannot open VDB table index: "<<*this, rc);
}
else {
NCBI_THROW2_FMT(CSraException, eOtherError,
"Cannot open VDB table index: "<<*this, rc);
}
}
}
rc_t CSraColumn::TryInitRc(const CSraRun& run,
const char* name, const char* type)
{
return SRATableOpenColumnRead(run, x_InitPtr(), name, type);
}