bool g_FixMisplacedPID(CJsonNode& stat_info, CTempString& executable_path,
const char* pid_key)
{
SIZE_TYPE misplaced_pid = NStr::Find(executable_path, "; PID: ");
if (misplaced_pid == NPOS)
return false;
SIZE_TYPE pos = misplaced_pid + sizeof("; PID: ") - 1;
stat_info.SetInteger(pid_key, NStr::StringToInt8(
CTempString(executable_path.data() + pos,
executable_path.length() - pos)));
executable_path.erase(misplaced_pid);
return true;
}
inline
TSqlString x_MakeTSqlString(const CTempString& s, EEncoding enc)
{
#if defined(UNICODE) || defined(_UNICODE) || defined(UCS2)
return CUtf8::AsBasicString<TSqlChar>(CUtf8::AsUTF8(s, enc));
#else
if (enc == eEncoding_Unknown || enc == eEncoding_UTF8) {
return CUtf8::AsSingleByteString(CUtf8::AsUTF8(s, enc),
eEncoding_ISO8859_1);
} else {
return CSqlString(s.data(), s.size());
}
#endif
}
string CDBParamVariant::MakePlainName(const CTempString& name)
{
// Do not make copy of name to process it ...
CTempString plain_name;
CTempString::const_iterator begin_str = NULL, c = name.data();
for (; c != NULL && c != name.end(); ++c) {
char ch = *c;
if (ch == ' ' || ch == '\t' || ch == '\n' || ch == '\r') {
if (begin_str == NULL) {
// Remove whitespaces ...
continue;
} else {
// Look forward for non-space characters.
bool space_chars_only = true;
for (const char* tc = c; tc != NULL && *tc != '\0'; ++tc) {
char tch = *tc;
if (tch == ' ' || tch == '\t' || tch == '\n' || tch == '\r') {
continue;
} else {
space_chars_only = false;
break;
}
}
if (space_chars_only) {
// Remove trailing whitespace ...
break;
}
}
}
// Check for leading symbol ...
if (begin_str == NULL) {
begin_str = c;
if (ch == ':' || ch == '@' || ch == '$' || ch == '%') {
// Skip leading symbol ...
++begin_str;
}
}
}
if (begin_str != NULL) {
plain_name.assign(begin_str, c - begin_str);
}
return plain_name;
}
const char * CBlastDbBlob::x_ReadRaw(int size, int * offsetp) const
{
_ASSERT(offsetp);
_ASSERT(size >= 0);
CTempString s = Str();
int begin = *offsetp;
int end = begin + size;
if (begin > end || end > (int)s.size()) {
NCBI_THROW(CSeqDBException,
eFileErr,
"CBlastDbBlob::x_ReadRaw: hit end of data");
}
*offsetp = end;
return s.data() + begin;
}
CTempString CBlastDbBlob::x_ReadString(EStringFormat fmt, int * offsetp) const
{
int sz = 0;
if (fmt == eSize4) {
sz = x_ReadIntFixed<int,4>(offsetp);
} else if (fmt == eSizeVar) {
sz = x_ReadVarInt(offsetp);
}
const char * datap = "";
if (fmt == eNUL) {
CTempString ts = Str();
int zoffset = -1;
for(size_t i = *offsetp; i < ts.size(); i++) {
if (ts[i] == (char)0) {
zoffset = i;
break;
}
}
if (zoffset == -1) {
NCBI_THROW(CSeqDBException,
eFileErr,
"CBlastDbBlob::ReadString: Unterminated string.");
}
datap = ts.data() + *offsetp;
sz = zoffset - *offsetp;
*offsetp = zoffset+1;
} else {
datap = x_ReadRaw(sz, offsetp);
}
return CTempString(datap, sz);
}
BEGIN_NCBI_SCOPE
static void NormalizeStatKeyName(CTempString& key)
{
char* begin = const_cast<char*>(key.data());
char* end = begin + key.length();
while (begin < end && !isalnum(*begin))
++begin;
while (begin < end && !isalnum(end[-1]))
--end;
if (begin == end) {
key = "_";
return;
}
key.assign(begin, end - begin);
for (; begin < end; ++begin)
*begin = isalnum(*begin) ? tolower(*begin) : '_';
}
void Reset(const CTempString& line)
{
const char* line_buf = line.data();
Reset(line_buf, line_buf + line.size());
}
inline
CLightString::CLightString(const CTempString& str)
: m_String(str.data()), m_Length(str.length())
{
}
CRef<CSeq_entry>
CShortReadFastaInputSource::x_ReadFastqOneSeq(CRef<ILineReader> line_reader)
{
CTempString line;
CTempString id;
CRef<CSeq_entry> retval;
// first read defline
++(*line_reader);
line = **line_reader;
// skip empty lines
while (!line_reader->AtEOF() && line.empty()) {
++(*line_reader);
line = **line_reader;
}
if (line[0] != '@') {
NCBI_THROW(CInputException, eInvalidInput, (string)"FASTQ parse error:"
" defline expected at line: " +
NStr::IntToString(line_reader->GetLineNumber()));
}
id = x_ParseDefline(line);
CRef<CSeq_id> seqid(new CSeq_id);
seqid->Set(CSeq_id::e_Local, id);
// read sequence
++(*line_reader);
line = **line_reader;
// skip empty lines
while (!line_reader->AtEOF() && line.empty()) {
++(*line_reader);
line = **line_reader;
}
// set up sequence
if (line.length() > 0) {
CRef<CSeq_entry> seq_entry(new CSeq_entry);
CBioseq& bioseq = seq_entry->SetSeq();
bioseq.SetInst().SetMol(CSeq_inst::eMol_na);
bioseq.SetInst().SetRepr(CSeq_inst::eRepr_raw);
bioseq.SetId().clear();
bioseq.SetId().push_back(seqid);
bioseq.SetInst().SetLength(line.length());
bioseq.SetInst().SetSeq_data().SetIupacna(CIUPACna(line.data()));
bioseq.SetDescr();
m_BasesAdded += line.length();
retval = seq_entry;
}
// read and skip second defline
++(*line_reader);
line = **line_reader;
// skip empty lines
while (!line_reader->AtEOF() && line.empty()) {
++(*line_reader);
line = **line_reader;
}
if (line[0] != '+') {
NCBI_THROW(CInputException, eInvalidInput, (string)"FASTQ parse error:"
" defline expected at line: " +
NStr::IntToString(line_reader->GetLineNumber()));
}
// read and skip quality scores
++(*line_reader);
line = **line_reader;
// skip empty lines
while (!line_reader->AtEOF() && line.empty()) {
++(*line_reader);
line = **line_reader;
}
return retval;
}
CTempString CDBParamVariant::MakeName(const CTempString& name,
CDBParamVariant::ENameFormat& format)
{
// Do not make copy of name to process it ...
CTempString new_name;
CTempString::const_iterator begin_str = NULL, c = name.data();
format = ePlainName;
for (; c != NULL && c != name.end(); ++c) {
char ch = *c;
if (ch == ' ' || ch == '\t' || ch == '\n' || ch == '\r') {
if (begin_str == NULL) {
// Remove whitespace ...
continue;
} else {
// Look forward for non-space characters.
bool space_chars_only = true;
for (const char* tc = c; tc != NULL && *tc != '\0'; ++tc) {
char tch = *tc;
if (tch == ' ' || tch == '\t' || tch == '\n' || tch == '\r') {
continue;
} else {
space_chars_only = false;
break;
}
}
if (space_chars_only) {
// Remove trailing whitespace ...
break;
}
}
}
// Check for leading symbol ...
if (begin_str == NULL) {
begin_str = c;
switch (ch) {
case '?' :
format = eQMarkName;
break;
case ':' :
if (*(c + 1)) {
if (isdigit(*(c + 1))) {
format = eNumericName;
} else {
format = eNamedName;
}
} else {
DATABASE_DRIVER_ERROR("Invalid parameter format.", 1);
}
break;
case '@' :
format = eSQLServerName;
break;
case '%' :
format = eFormatName;
break;
case '$' :
// !!!!
format = eFormatName;
break;
}
}
}
if (begin_str != NULL) {
new_name.assign(begin_str, c - begin_str);
}
return new_name;
}
bool CODBC_BCPInCmd::x_AssignParams(void* pb)
{
RETCODE r;
if (!m_WasBound) {
for (unsigned int i = 0; i < GetBindParamsImpl().NofParams(); ++i) {
if (GetBindParamsImpl().GetParamStatus(i) == 0) {
r = bcp_bind(GetHandle(), (BYTE*) pb, 0, SQL_VARLEN_DATA, 0, 0, 0, i + 1);
}
else {
CDB_Object& param = *GetBindParamsImpl().GetParam(i);
EDB_Type data_type = param.GetType();
r = bcp_bind(GetHandle(),
static_cast<LPCBYTE>(const_cast<void*>(x_GetDataPtr(data_type, pb))),
0,
static_cast<DBINT>(x_GetBCPDataSize(data_type)),
static_cast<LPCBYTE>(x_GetDataTerminator(data_type)),
static_cast<INT>(x_GetDataTermSize(data_type)),
x_GetBCPDataType(data_type),
i + 1);
m_HasTextImage = m_HasTextImage || (data_type == eDB_Image || data_type == eDB_Text);
}
if (r != SUCCEED) {
ReportErrors();
return false;
}
}
GetBindParamsImpl().LockBinding();
m_WasBound = true;
}
for (unsigned int i = 0; i < GetBindParamsImpl().NofParams(); i++) {
if (GetBindParamsImpl().GetParamStatus(i) == 0) {
r = bcp_collen(GetHandle(), SQL_NULL_DATA, i + 1);
}
else {
CDB_Object& param = *GetBindParamsImpl().GetParam(i);
switch ( param.GetType() ) {
case eDB_Bit:
DATABASE_DRIVER_ERROR("Bit data type is not supported", 10005);
break;
case eDB_Int: {
CDB_Int& val = dynamic_cast<CDB_Int&> (param);
r = bcp_colptr(GetHandle(), (BYTE*) val.BindVal(), i + 1)
== SUCCEED &&
bcp_collen(GetHandle(), val.IsNULL() ? SQL_NULL_DATA : sizeof(Int4), i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
break;
case eDB_SmallInt: {
CDB_SmallInt& val = dynamic_cast<CDB_SmallInt&> (param);
// DBSMALLINT v = (DBSMALLINT) val.Value();
r = bcp_colptr(GetHandle(), (BYTE*) val.BindVal(), i + 1)
== SUCCEED &&
bcp_collen(GetHandle(), val.IsNULL() ? SQL_NULL_DATA : sizeof(Int2), i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
break;
case eDB_TinyInt: {
CDB_TinyInt& val = dynamic_cast<CDB_TinyInt&> (param);
// DBTINYINT v = (DBTINYINT) val.Value();
r = bcp_colptr(GetHandle(), (BYTE*) val.BindVal(), i + 1)
== SUCCEED &&
bcp_collen(GetHandle(), val.IsNULL() ? SQL_NULL_DATA : sizeof(Uint1), i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
break;
case eDB_BigInt: {
CDB_BigInt& val = dynamic_cast<CDB_BigInt&> (param);
r = bcp_colptr(GetHandle(), (BYTE*) val.BindVal(), i + 1)
== SUCCEED &&
bcp_collen(GetHandle(), val.IsNULL() ? SQL_NULL_DATA : sizeof(Int8), i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
break;
case eDB_Char:
case eDB_VarChar:
case eDB_LongChar: {
CDB_String& val = dynamic_cast<CDB_String&> (param);
CTempString data;
if (val.IsNULL()) {
data.assign(static_cast<char*>(pb), 0);
} else {
if (IsMultibyteClientEncoding()) {
const wstring& ws = val.AsWString(GetClientEncoding());
// hack
data.assign((const char*)(ws.data()),
ws.size() * sizeof(wchar_t));
} else {
data = val.Value();
}
}
DBINT length;
INT dummy; // Can't just supply NULL
if (val.IsNULL()) {
length = SQL_NULL_DATA;
} else if (bcp_getcolfmt(GetHandle(), i + 1, BCP_FMT_DATA_LEN,
&length, sizeof(length), &dummy)
== FAIL || length < 0) {
length = SQL_VARLEN_DATA; // Be conservative.
} else if (static_cast<SIZE_TYPE>(length) > data.size()) {
// Retain automatic truncation, which blindly supplying
// data.size() could lose.
length = data.size();
}
r = bcp_colptr(GetHandle(),
(BYTE*) data.data(),
i + 1)
== SUCCEED &&
bcp_collen(GetHandle(),
length,
i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
break;
case eDB_Binary: {
CDB_Binary& val = dynamic_cast<CDB_Binary&> (param);
r = bcp_colptr(GetHandle(), (!val.IsNULL())? ((BYTE*) val.Value()) : (BYTE*)pb, i + 1)
== SUCCEED &&
bcp_collen(GetHandle(),
val.IsNULL() ? SQL_NULL_DATA : (Int4) val.Size(), i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
break;
case eDB_VarBinary: {
CDB_VarBinary& val = dynamic_cast<CDB_VarBinary&> (param);
r = bcp_colptr(GetHandle(), (!val.IsNULL())? ((BYTE*) val.Value()) : (BYTE*)pb, i + 1)
== SUCCEED &&
bcp_collen(GetHandle(),
val.IsNULL() ? SQL_NULL_DATA : (Int4) val.Size(), i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
break;
case eDB_LongBinary: {
CDB_LongBinary& val = dynamic_cast<CDB_LongBinary&> (param);
r = bcp_colptr(GetHandle(), (!val.IsNULL())? ((BYTE*) val.Value()) : (BYTE*)pb, i + 1)
== SUCCEED &&
bcp_collen(GetHandle(),
val.IsNULL() ? SQL_NULL_DATA : (Int4) val.DataSize(), i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
break;
case eDB_Float: {
CDB_Float& val = dynamic_cast<CDB_Float&> (param);
//DBREAL v = (DBREAL) val.Value();
r = bcp_colptr(GetHandle(), (BYTE*) val.BindVal(), i + 1)
== SUCCEED &&
bcp_collen(GetHandle(), val.IsNULL() ? SQL_NULL_DATA : sizeof(float), i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
break;
case eDB_Double: {
CDB_Double& val = dynamic_cast<CDB_Double&> (param);
//DBFLT8 v = (DBFLT8) val.Value();
r = bcp_colptr(GetHandle(), (BYTE*) val.BindVal(), i + 1)
== SUCCEED &&
bcp_collen(GetHandle(), val.IsNULL() ? SQL_NULL_DATA : sizeof(double), i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
break;
case eDB_SmallDateTime: {
CDB_SmallDateTime& val =
dynamic_cast<CDB_SmallDateTime&> (param);
DBDATETIM4* dt = (DBDATETIM4*) pb;
DBDATETIME4_days(dt) = val.GetDays();
DBDATETIME4_mins(dt) = val.GetMinutes();
r = bcp_colptr(GetHandle(), (BYTE*) dt, i + 1)
== SUCCEED &&
bcp_collen(GetHandle(), val.IsNULL() ? SQL_NULL_DATA : sizeof(DBDATETIM4), i + 1)
== SUCCEED ? SUCCEED : FAIL;
pb = (void*) (dt + 1);
}
break;
case eDB_DateTime: {
CDB_DateTime& val = dynamic_cast<CDB_DateTime&> (param);
DBDATETIME* dt = (DBDATETIME*) pb;
if (val.IsNULL()) {
r = bcp_colptr(GetHandle(), (BYTE*) dt, i + 1)
== SUCCEED &&
bcp_collen(GetHandle(), SQL_NULL_DATA, i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
else {
dt->dtdays = val.GetDays();
dt->dttime = val.Get300Secs();
r = bcp_colptr(GetHandle(), (BYTE*) dt, i + 1)
== SUCCEED &&
bcp_collen(GetHandle(), sizeof(DBDATETIME), i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
pb = (void*) (dt + 1);
}
break;
case eDB_Text: {
CDB_Text& val = dynamic_cast<CDB_Text&> (param);
if (val.IsNULL()) {
r = bcp_colptr(GetHandle(), (BYTE*) pb, i + 1)
== SUCCEED &&
bcp_collen(GetHandle(), SQL_NULL_DATA, i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
else {
r = bcp_bind(GetHandle(), (BYTE*) NULL, 0, (DBINT) val.Size(),
static_cast<LPCBYTE>(x_GetDataTerminator(eDB_Text)),
static_cast<INT>(x_GetDataTermSize(eDB_Text)),
x_GetBCPDataType(eDB_Text),
i + 1);
}
}
break;
case eDB_Image: {
CDB_Image& val = dynamic_cast<CDB_Image&> (param);
// Null images doesn't work in odbc
// (at least in those tests that exists in dbapi_unit_test)
r = bcp_collen(GetHandle(), (DBINT) val.Size(), i + 1);
}
break;
default:
return false;
}
}
if (r != SUCCEED) {
ReportErrors();
return false;
}
}
return true;
}