void RingoFastIndex::_decompressRowid (const Array<char> &stored, OraRowidText &rid)
{
BufferScanner scanner(stored.ptr() + 2, stored[1]);
RowIDLoader loader(_context.context().context().rid_dict, scanner);
QS_DEF(Array<char>, rowid);
loader.loadRowID(rowid);
if (rowid.size() != 18)
throw Error("rowid size=%d?", rowid.size());
memcpy(rid.ptr(), rowid.ptr(), 18);
rid.ptr()[18] = 0;
}
void mangoRegisterTable (OracleEnv &env, MangoOracleContext &context,
const char *source_table, const char *source_column,
const char *target_datatype)
{
profTimerStart(tall, "total");
QS_DEF(Array<char>, molfile_buf);
OracleStatement statement(env);
AutoPtr<OracleLOB> molfile_lob;
OraRowidText rowid;
char varchar2_text[4001];
// Oracle's BLOB and CLOB types always come uppercase
bool blob = (strcmp(target_datatype, "BLOB") == 0);
bool clob = (strcmp(target_datatype, "CLOB") == 0);
int total_count = 0;
OracleStatement::executeSingleInt(total_count, env,
"SELECT COUNT(*) FROM %s WHERE %s IS NOT NULL AND LENGTH(%s) > 0",
source_table, source_column, source_column);
context.context().longOpInit(env, total_count, "Building molecule index",
source_table, "molecules");
statement.append("SELECT %s, RowidToChar(rowid) FROM %s WHERE %s IS NOT NULL AND LENGTH(%s) > 0",
source_column, source_table, source_column, source_column);
//"ORDER BY dbms_rowid.rowid_block_number(rowid), dbms_rowid.rowid_row_number(rowid)",
statement.prepare();
if (blob)
{
molfile_lob.reset(new OracleLOB(env));
statement.defineBlobByPos(1, molfile_lob.ref());
}
else if (clob)
{
molfile_lob.reset(new OracleLOB(env));
statement.defineClobByPos(1, molfile_lob.ref());
}
else
statement.defineStringByPos(1, varchar2_text, sizeof(varchar2_text));
statement.defineStringByPos(2, rowid.ptr(), sizeof(rowid));
BingoFingerprints &fingerprints = context.fingerprints;
fingerprints.validateForUpdate(env);
if (context.context().nthreads == 1)
{
int n = 0;
QS_DEF(MangoIndex, index);
index.init(context.context());
if (statement.executeAllowNoData()) do
{
env.dbgPrintf("inserting molecule #%d with rowid %s\n", n, rowid.ptr());
if (blob || clob)
molfile_lob->readAll(molfile_buf, false);
else
molfile_buf.readString(varchar2_text, false);
try
{
mangoPrepareAndRegisterMolecule(env, rowid.ptr(),
molfile_buf, context, index, fingerprints, true);
}
catch (Exception &ex)
{
char buf[4096];
snprintf(buf, NELEM(buf), "Failed on record with rowid=%s. Error message is '%s'",
rowid.ptr(), ex.message());
throw Exception(buf);
}
n++;
if ((n % 50) == 0)
context.context().longOpUpdate(env, n);
if ((n % 1000) == 0)
{
env.dbgPrintf("done %d molecules; flushing\n", n);
context.context().storage.flush(env);
}
} while (statement.fetch());
}
else
{
if (statement.executeAllowNoData())
{
MangoRegisterDispatcher dispatcher(context, env, rowid.ptr());
dispatcher.setup(&statement, molfile_lob.get(),
varchar2_text, blob || clob);
int nthreads = context.context().nthreads;
if (nthreads <= 0)
dispatcher.run();
else
dispatcher.run(nthreads);
}
}
fingerprints.flush(env);
context.shadow_table.flush(env);
}
void ringoRegisterTable (OracleEnv &env, RingoOracleContext &context,
const char *source_table, const char *source_column,
const char *target_datatype)
{
QS_DEF(Array<char>, reaction_buf);
OracleStatement statement(env);
AutoPtr<OracleLOB> reaction_lob;
OraRowidText rowid;
char varchar2_text[4001];
// Oracle's BLOB and CLOB types always come uppercase
bool blob = (strcmp(target_datatype, "BLOB") == 0);
bool clob = (strcmp(target_datatype, "CLOB") == 0);
int total_count = 0;
OracleStatement::executeSingleInt(total_count, env,
"SELECT COUNT(*) FROM %s WHERE %s IS NOT NULL AND LENGTH(%s) > 0",
source_table, source_column, source_column);
context.context().longOpInit(env, total_count, "Building reaction index",
source_table, "reactions");
statement.append("SELECT %s, RowidToChar(rowid) FROM %s WHERE %s IS NOT NULL AND LENGTH(%s) > 0",
source_column, source_table, source_column, source_column);
statement.prepare();
if (blob)
{
reaction_lob.reset(new OracleLOB(env));
statement.defineBlobByPos(1, reaction_lob.ref());
}
else if (clob)
{
reaction_lob.reset(new OracleLOB(env));
statement.defineClobByPos(1, reaction_lob.ref());
}
else
statement.defineStringByPos(1, varchar2_text, sizeof(varchar2_text));
statement.defineStringByPos(2, rowid.ptr(), sizeof(rowid));
BingoFingerprints &fingerprints = context.fingerprints;
int nthreads = 0;
fingerprints.validateForUpdate(env);
context.context().configGetInt(env, "NTHREADS", nthreads);
nthreads = 1;
//if (nthreads == 1)
{
int n = 0;
QS_DEF(RingoIndex, index);
index.init(context.context());
if (statement.executeAllowNoData()) do
{
env.dbgPrintf("inserting reaction #%d with rowid %s\n", n, rowid.ptr());
if (blob || clob)
reaction_lob->readAll(reaction_buf, false);
else
reaction_buf.readString(varchar2_text, false);
try
{
if (_ringoRegisterReaction(env, rowid.ptr(), reaction_buf, context, index, fingerprints))
n++;
}
catch (Exception &ex)
{
char buf[4096];
snprintf(buf, NELEM(buf), "Failed on record with rowid=%s. Error message is '%s'",
rowid.ptr(), ex.message());
throw Exception(buf);
}
if ((n % 50) == 0)
context.context().longOpUpdate(env, n);
if ((n % 1000) == 0)
{
env.dbgPrintfTS("done %d reactions ; flushing\n", n);
context.context().storage.flush(env);
}
} while (statement.fetch());
fingerprints.flush(env);
}
}
void MangoFastIndex::_match (OracleEnv &env, int idx)
{
_last_id = idx;
BingoStorage &storage = this->_context.context().context().storage;
QS_DEF(Array<char>, stored);
storage.get(idx, stored);
if (stored[0] != 0)
return; // molecule was removed from index
BufferScanner scanner(stored);
scanner.skip(1); // skip the deletion mark
scanner.skip(scanner.readByte()); // skip the compessed rowid
scanner.skip(2); // skip 'ord' bits count
bool res = false;
profTimerStart(tall, "match");
if (_fetch_type == _SUBSTRUCTURE)
{
QS_DEF(Array<char>, xyz_buf);
if (_context.substructure.needCoords())
{
OraRowidText rid;
_decompressRowid(stored, rid);
if (_loadCoords(env, rid.ptr(), xyz_buf))
{
BufferScanner xyz_scanner(xyz_buf);
res = _context.substructure.matchBinary(scanner, &xyz_scanner);
}
else
// no XYZ --> skip the molecule
res = false;
}
else
res = _context.substructure.matchBinary(scanner, 0);
}
else if (_fetch_type == _TAUTOMER_SUBSTRUCTURE)
res = _context.tautomer.matchBinary(scanner);
else // _fetch_type == _SIMILARITY
res = _context.similarity.matchBinary(scanner);
profTimerStop(tall);
if (res)
{
OraRowidText & rid = matched.at(matched.add());
_decompressRowid(stored, rid);
profIncTimer("match.found", profTimerGetTime(tall));
_matched++;
}
else
{
profIncTimer("match.not_found", profTimerGetTime(tall));
_unmatched++;
}
}
