ORAEXT void oraImportRDF (OCIExtProcContext *ctx,
const char *table_name, short table_name_ind,
const char *clob_col_name, short clob_col_ind,
const char *other_col_names, short other_col_ind,
const char *file_name, short file_name_ind)
{
logger.initIfClosed(log_filename);
ORABLOCK_BEGIN
{
OracleEnv env(ctx, logger);
if (table_name_ind != OCI_IND_NOTNULL)
throw BingoError("null table name");
if (clob_col_ind != OCI_IND_NOTNULL)
throw BingoError("null table name");
if (clob_col_ind != OCI_IND_NOTNULL)
throw BingoError("null file name");
if (other_col_ind != OCI_IND_NOTNULL)
other_col_names = 0;
_importRDF(env, table_name, clob_col_name, other_col_names, file_name);
}
ORABLOCK_END
}
ORAEXT void oraImportSMILES (OCIExtProcContext *ctx,
const char *table_name, short table_name_ind,
const char *smiles_col_name, short smiles_col_ind,
const char *id_col_name, short id_col_ind,
const char *file_name, short file_name_ind)
{
logger.initIfClosed(log_filename);
ORABLOCK_BEGIN
{
OracleEnv env(ctx, logger);
if (table_name_ind != OCI_IND_NOTNULL)
throw BingoError("null table name");
if (smiles_col_ind != OCI_IND_NOTNULL)
throw BingoError("null SMILES column name");
if (file_name_ind != OCI_IND_NOTNULL)
throw BingoError("null file name");
if (id_col_ind != OCI_IND_NOTNULL)
id_col_name = 0;
_importSMILES(env, table_name, smiles_col_name, id_col_name, file_name);
}
ORABLOCK_END
}
ORAEXT void oraExportSDFZip (OCIExtProcContext *ctx,
const char *table_name, short table_name_ind,
const char *clob_col_name, short clob_col_ind,
const char *other_col_names, short other_col_ind,
const char *file_name, short file_name_ind)
{
logger.initIfClosed(log_filename);
ORABLOCK_BEGIN
{
OracleEnv env(ctx, logger);
if (table_name_ind != OCI_IND_NOTNULL)
throw BingoError("null table name");
if (clob_col_ind != OCI_IND_NOTNULL)
throw BingoError("null CLOB column name");
if (file_name_ind != OCI_IND_NOTNULL)
throw BingoError("null file name");
if (other_col_ind != OCI_IND_NOTNULL)
other_col_names = 0;
FileOutput output(file_name);
GZipOutput gzoutput(output, 9);
_exportSDF(env, table_name, clob_col_name, other_col_names, gzoutput);
}
ORABLOCK_END
}
ORAEXT void oraImportSDF (OCIExtProcContext *ctx,
const char *table_name, short table_name_ind,
const char *clob_col_name, short clob_col_ind,
const char *other_col_names, short other_col_ind,
const char *file_name, short file_name_ind)
{
logger.initIfClosed(log_filename);
ORABLOCK_BEGIN
{
profTimersReset();
profTimerStart(ttotal, "total");
OracleEnv env(ctx, logger);
if (table_name_ind != OCI_IND_NOTNULL)
throw BingoError("null table name");
if (clob_col_ind != OCI_IND_NOTNULL)
throw BingoError("null table name");
if (clob_col_ind != OCI_IND_NOTNULL)
throw BingoError("null file name");
if (other_col_ind != OCI_IND_NOTNULL)
other_col_names = 0;
_importSDF(env, table_name, clob_col_name, other_col_names, file_name);
profTimerStop(ttotal);
bingoProfilingPrintStatistics(false);
}
ORABLOCK_END
}
ORAEXT OCIString * oraConfigGetString (OCIExtProcContext *ctx, int context_id,
char *key_name, short key_name_indicator,
short *return_indicator)
{
OCIString *result = NULL;
ORABLOCK_BEGIN
{
*return_indicator = OCI_IND_NULL;
OracleEnv env(ctx, logger);
if (key_name_indicator != OCI_IND_NOTNULL)
throw BingoError("Null key is given");
QS_DEF(Array<char>, value);
BingoOracleContext &context = BingoOracleContext::get(env, context_id, false, 0);
if (!context.configGetString(env, key_name, value))
throw BingoError("Key wasn't found");
env.callOCI(OCIStringAssignText(env.envhp(), env.errhp(), (text *)value.ptr(), value.size() - 1, &result));
*return_indicator = OCI_IND_NOTNULL;
}
ORABLOCK_END
return result;
}
ORAEXT OCINumber * oraConfigGetFloat (OCIExtProcContext *ctx, int context_id,
char *key_name, short key_name_indicator,
short *return_indicator)
{
OCINumber *result = NULL;
ORABLOCK_BEGIN
{
*return_indicator = OCI_IND_NULL;
OracleEnv env(ctx, logger);
if (key_name_indicator != OCI_IND_NOTNULL)
throw BingoError("Null key is given");
float value;
BingoOracleContext &context = BingoOracleContext::get(env, context_id, false, 0);
if (!context.configGetFloat(env, key_name, value))
throw BingoError("Key wasn't found");
result = (OCINumber *)OCIExtProcAllocCallMemory(ctx, sizeof(OCINumber));
if (result == NULL)
throw BingoError("can't allocate memory for number");
double value_double = value;
env.callOCI(OCINumberFromReal(env.errhp(), &value_double, sizeof(value_double), result));
*return_indicator = OCI_IND_NOTNULL;
}
ORABLOCK_END
return result;
}
static void _ringoIndexStart (OracleEnv &env, RingoFetchContext &context,
const char *oper, const Array<char> &query_buf,
OCINumber *p_strt, OCINumber *p_stop, const char *params)
{
RingoShadowFetch &shadow_fetch = context.shadow_fetch.ref();
RingoFastIndex &fast_index = context.fast_index.ref();
if (strcasecmp(oper, "RSUB") == 0)
{
if (!context.substructure.parse(params))
throw BingoError("can not parse parameters: %s", params);
context.substructure.loadQuery(query_buf);
int right = bingoGetExactRightPart(env, p_strt, p_stop, 64);
if (right == 1)
{
fast_index.prepareSubstructure(env);
context.fetch_engine = &fast_index;
}
else // right == 0
{
shadow_fetch.prepareNonSubstructure(env);
context.fetch_engine = &shadow_fetch;
}
}
else if (strcasecmp(oper, "RSMARTS") == 0)
{
context.substructure.loadSMARTS(query_buf);
int right = bingoGetExactRightPart(env, p_strt, p_stop, 64);
if (right == 1)
{
fast_index.prepareSubstructure(env);
context.fetch_engine = &fast_index;
}
else // right == 0
{
shadow_fetch.prepareNonSubstructure(env);
context.fetch_engine = &shadow_fetch;
}
}
else if (strcasecmp(oper, "REXACT") == 0)
{
context.exact.setParameters(params);
context.exact.loadQuery(query_buf);
int right = bingoGetExactRightPart(env, p_strt, p_stop, 64);
shadow_fetch.prepareExact(env, right);
context.fetch_engine = &shadow_fetch;
}
else
throw BingoError("unknown operator: %s", oper);
}
ORAEXT OCILobLocator *oraLoadFileToBLOB (OCIExtProcContext *ctx, char *filename,
short filename_indicator, short *return_indicator)
{
OCILobLocator *result = 0;
ORABLOCK_BEGIN
{
*return_indicator = OCI_IND_NULL;
OracleEnv env(ctx, logger);
if (filename_indicator != OCI_IND_NOTNULL)
throw BingoError("Null filename given");
FileScanner scanner(filename);
QS_DEF(Array<char>, buf);
scanner.readAll(buf);
OracleLOB lob(env);
lob.createTemporaryBLOB();
lob.write(0, buf.ptr(), buf.size());
*return_indicator = OCI_IND_NOTNULL;
lob.doNotDelete();
result = lob.get();
}
ORABLOCK_END
return result;
}
void _parseFieldList (const char *str, StringPool &props, StringPool &columns)
{
QS_DEF(Array<char>, prop);
QS_DEF(Array<char>, column);
BufferScanner scanner(str);
props.clear();
columns.clear();
scanner.skipSpace();
while (!scanner.isEOF())
{
scanner.readWord(prop, " ,");
scanner.skipSpace();
scanner.readWord(column, " ,");
scanner.skipSpace();
props.add(prop.ptr());
columns.add(column.ptr());
if (scanner.isEOF())
break;
if (scanner.readChar() != ',')
throw BingoError("_parseFieldList(): comma expected");
scanner.skipSpace();
}
}
ORAEXT OCIString *oraLoadFileToString (OCIExtProcContext *ctx, char *filename,
short filename_indicator, short *return_indicator)
{
OCIString *result = 0;
ORABLOCK_BEGIN
{
OracleEnv env(ctx, logger);
*return_indicator = OCI_IND_NULL;
if (filename_indicator != OCI_IND_NOTNULL)
throw BingoError("Null filename given");
FileScanner scanner(filename);
QS_DEF(Array<char>, buf);
scanner.readAll(buf);
env.callOCI(OCIStringAssignText(env.envhp(), env.errhp(), (text *)buf.ptr(), buf.size(), &result));
*return_indicator = OCI_IND_NOTNULL;
}
ORABLOCK_END
return result;
}
ORAEXT OCINumber * oraRingoSub (OCIExtProcContext *ctx, int context_id,
OCILobLocator *target_loc, short target_ind,
OCILobLocator *query_loc, short query_ind,
const char *params, short params_ind,
short *return_ind)
{
OCINumber *result = NULL;
ORABLOCK_BEGIN
{
OracleEnv env(ctx, logger);
*return_ind = OCI_IND_NULL;
if (query_ind != OCI_IND_NOTNULL)
throw BingoError("Null query given");
if (target_ind != OCI_IND_NOTNULL)
throw BingoError("Null target given");
if (params_ind != OCI_IND_NOTNULL)
params = 0;
RingoOracleContext &context = RingoOracleContext::get(env, context_id, false);
QS_DEF(Array<char>, query_buf);
QS_DEF(Array<char>, target_buf);
OracleLOB target_lob(env, target_loc);
OracleLOB query_lob(env, query_loc);
target_lob.readAll(target_buf, false);
query_lob.readAll(query_buf, false);
if (!context.substructure.parse(params))
throw BingoError("can not parse parameters: %s", params);
result = _ringoSub(env, context, query_buf, target_buf, params);
if (result == 0)
// This is needed for Oracle 9. Returning NULL drops the extproc.
result = OracleExtproc::createInt(env, 0);
else
*return_ind = OCI_IND_NOTNULL;
}
ORABLOCK_END
return result;
}
int bingoGetExactRightPart (OracleEnv &env, OCINumber *p_strt, OCINumber *p_stop, int flags)
{
if ((flags & 64) == 0)
throw BingoError("only exact match allowed");
if (p_strt == 0 || p_stop == 0)
throw BingoError("only exact match allowed");
int strt = OracleUtil::numberToInt(env, p_strt);
int stop = OracleUtil::numberToInt(env, p_stop);
if (strt != stop)
throw BingoError("only exact match allowed");
if (strt != 0 && strt != 1)
throw BingoError("only =0 and =1 allowed");
return strt;
}
ORAEXT OCINumber * oraProfilingGetTime (OCIExtProcContext *ctx, char *key_name, short key_name_indicator,
short *return_indicator)
{
OCINumber *result = NULL;
ORABLOCK_BEGIN
{
*return_indicator = OCI_IND_NULL;
OracleEnv env(ctx, logger);
if (key_name_indicator != OCI_IND_NOTNULL)
throw BingoError("Null key is given");
float value;
// Try to find in profiling data
ProfilingSystem &inst = ProfilingSystem::getInstance();
if (inst.hasLabel(key_name))
//throw BingoError("Key wasn't found");
value = inst.getLabelExecTime(key_name);
else
value = 0;
result = (OCINumber *)OCIExtProcAllocCallMemory(ctx, sizeof(OCINumber));
if (result == NULL)
throw BingoError("can't allocate memory for number");
double value_double = value;
env.callOCI(OCINumberFromReal(env.errhp(), &value_double, sizeof(value_double), result));
*return_indicator = OCI_IND_NOTNULL;
}
ORABLOCK_END
return result;
}
void bingoGetTauCondition (const char *list_ptr, int &aromaticity, Array<int> &label_list)
{
if (isdigit(*list_ptr))
{
if (*list_ptr == '1')
aromaticity = 1;
else if (*list_ptr == '0')
aromaticity = 0;
else
throw BingoError("Bad tautomer configuration string format");
list_ptr++;
} else {
aromaticity = -1;
}
label_list.clear();
QS_DEF(Array<char>, buf);
buf.clear();
while (*list_ptr != 0)
{
if (isalpha((unsigned)*list_ptr))
buf.push(*list_ptr);
else if (*list_ptr == ',')
{
buf.push(0);
label_list.push(Element::fromString(buf.ptr()));
buf.clear();
} else
throw BingoError("Bad label list format");
list_ptr++;
}
buf.push(0);
label_list.push(Element::fromString(buf.ptr()));
}
ORAEXT OCIString *oraBingoGetName (OCIExtProcContext *ctx,
OCILobLocator *source_locator, short source_indicator,
short *return_indicator)
{
OCIString *result = NULL;
ORABLOCK_BEGIN
{
OracleEnv env(ctx, logger);
if (source_indicator == OCI_IND_NULL)
throw BingoError("null source given");
QS_DEF(Array<char>, source);
QS_DEF(Array<char>, name);
OracleLOB source_lob(env, source_locator);
source_lob.readAll(source, false);
BufferScanner scanner(source);
bingoGetName(scanner, name);
if (name.size() < 1)
{
// This is needed for Oracle 9. Returning NULL drops the extproc.
OCIStringAssignText(env.envhp(), env.errhp(), (text *)"nil", 3, &result);
*return_indicator = OCI_IND_NULL;
}
else
{
name.push(0);
OCIStringAssignText(env.envhp(), env.errhp(), (text *)name.ptr(), strlen(name.ptr()), &result);
*return_indicator = OCI_IND_NOTNULL;
}
}
ORABLOCK_END
return result;
}
static void _mangoIndexStart (OracleEnv &env, MangoFetchContext &context,
const char *oper, const Array<char> &query_buf,
OCINumber *p_strt, OCINumber *p_stop,
int flags, const char *params)
{
MangoShadowFetch &shadow_fetch = context.shadow_fetch.ref();
MangoFastIndex &fast_index = context.fast_index.ref();
if (strcasecmp(oper, "SUB") == 0)
{
if (context.substructure.parse(params))
{
context.substructure.loadQuery(query_buf);
int right = bingoGetExactRightPart(env, p_strt, p_stop, flags);
if (right == 1)
{
fast_index.prepareSubstructure(env);
context.fetch_engine = &fast_index;
}
else // right == 0
{
shadow_fetch.prepareNonSubstructure(env);
context.fetch_engine = &shadow_fetch;
}
}
else if (context.tautomer.parseSub(params))
{
context.tautomer.loadQuery(query_buf);
int right = bingoGetExactRightPart(env, p_strt, p_stop, flags);
if (right == 1)
{
fast_index.prepareTautomerSubstructure(env);
context.fetch_engine = &fast_index;
}
else // right == 0
{
shadow_fetch.prepareNonTautomerSubstructure(env);
context.fetch_engine = &shadow_fetch;
}
}
else
throw BingoError("can't parse parameters: '%s'", params);
}
else if (strcasecmp(oper, "SMARTS") == 0)
{
context.substructure.loadSMARTS(query_buf);
int right = bingoGetExactRightPart(env, p_strt, p_stop, flags);
if (right == 1)
{
fast_index.prepareSubstructure(env);
context.fetch_engine = &fast_index;
}
else // right == 0
{
shadow_fetch.prepareNonSubstructure(env);
context.fetch_engine = &shadow_fetch;
}
}
else if (strcasecmp(oper, "EXACT") == 0)
{
if (context.tautomer.parseExact(params))
{
context.tautomer.loadQuery(query_buf);
int right = bingoGetExactRightPart(env, p_strt, p_stop, flags);
shadow_fetch.prepareTautomer(env, right);
context.fetch_engine = &shadow_fetch;
}
else if (context.exact.parse(params))
{
context.exact.loadQuery(query_buf);
int right = bingoGetExactRightPart(env, p_strt, p_stop, flags);
shadow_fetch.prepareExact(env, right);
context.fetch_engine = &shadow_fetch;
}
else
throw BingoError("can't parse parameters: '%s'", params);
}
else if (strcasecmp(oper, "SIM") == 0)
{
context.similarity.setMetrics(params);
context.similarity.loadQuery(query_buf);
float bottom = -0.1f;
float top = 1.1f;
if (p_strt == 0 && p_stop == 0)
throw BingoError("no bounds for similarity search");
if (p_strt != 0)
bottom = OracleUtil::numberToFloat(env, p_strt);
if (p_stop != 0)
top = OracleUtil::numberToFloat(env, p_stop);
if (flags & 64)
throw BingoError("exact match not allowed");
context.similarity.include_bottom = ((flags & 16) != 0);
context.similarity.include_top = ((flags & 32) != 0);
context.similarity.bottom = bottom;
context.similarity.top = top;
fast_index.prepareSimilarity(env);
context.fetch_engine = &fast_index;
}
else if (strcasecmp(oper, "GROSS") == 0)
{
int right = bingoGetExactRightPart(env, p_strt, p_stop, flags);
MangoGross &instance = context.gross;
instance.parseQuery(query_buf);
shadow_fetch.prepareGross(env, right);
context.fetch_engine = &shadow_fetch;
}
else if (strcasecmp(oper, "MASS") == 0)
{
float bottom = 0;
float top = 1e10;
if (p_strt == 0 && p_stop == 0)
throw BingoError("no bounds for molecular mass search");
if (p_strt != 0)
bottom = OracleUtil::numberToFloat(env, p_strt);
if (p_stop != 0)
top = OracleUtil::numberToFloat(env, p_stop);
context.mass.bottom = bottom;
context.mass.top = top;
shadow_fetch.prepareMass(env);
context.fetch_engine = &shadow_fetch;
}
else
throw BingoError("unknown operator: %s", oper);
}
