bool mangoPrepareMolecule (OracleEnv &env, const char *rowid,
const Array<char> &molfile_buf,
MangoOracleContext &context,
MangoIndex &index,
Array<char> &data,
OsLock *lock_for_exclusive_access)
{
profTimerStart(tall, "moleculeIndex.prepare");
ArrayOutput output(data);
output.writeChar(0); // 0 -- present, 1 -- removed from index
QS_DEF(Array<char>, compressed_rowid);
ArrayOutput rid_output(compressed_rowid);
{
// RowIDSaver modifies context.context().rid_dict and
// requires exclusive access for this
OsLockerNullable locker(lock_for_exclusive_access);
RowIDSaver rid_saver(context.context().rid_dict, rid_output);
rid_saver.saveRowID(rowid);
}
output.writeByte((byte)compressed_rowid.size());
output.writeArray(compressed_rowid);
TRY_READ_TARGET_MOL
{
BufferScanner scanner(molfile_buf);
try
{
index.prepare(scanner, output, lock_for_exclusive_access);
}
catch (CmfSaver::Error &e)
{
OsLockerNullable locker(lock_for_exclusive_access);
env.dbgPrintf(bad_molecule_warning_rowid, rowid, e.message());
return false;
}
}
CATCH_READ_TARGET_MOL_ROWID(rowid, return false);
// some magic: round it up to avoid ora-22282
if (data.size() % 2 == 1)
output.writeChar(0);
return true;
}
bool _ringoRegisterReaction (OracleEnv &env, const char *rowid,
const Array<char> &reaction_buf,
RingoOracleContext &context,
RingoIndex &index,
BingoFingerprints &fingerprints)
{
QS_DEF(Array<char>, data);
QS_DEF(Array<char>, compressed_rowid);
ArrayOutput output(data);
output.writeChar(0); // 0 -- present, 1 -- removed from index
ArrayOutput rid_output(compressed_rowid);
RowIDSaver rid_saver(context.context().rid_dict, rid_output);
rid_saver.saveRowID(rowid);
output.writeByte((byte)compressed_rowid.size());
output.writeArray(compressed_rowid);
TRY_READ_TARGET_RXN
{
BufferScanner scanner(reaction_buf);
try
{
index.prepare(scanner, output, NULL);
}
catch (CmfSaver::Error &e)
{
if (context.context().reject_invalid_structures)
throw; // Rethrow this exception further
env.dbgPrintf(bad_reaction_warning_rowid, rowid, e.message());
return false;
}
catch (CrfSaver::Error &e)
{
if (context.context().reject_invalid_structures)
throw; // Rethrow this exception further
env.dbgPrintf(bad_reaction_warning_rowid, rowid, e.message());
return false;
}
}
CATCH_READ_TARGET_RXN_ROWID(rowid, {
if (context.context().reject_invalid_structures)
throw; // Rethrow this exception further
return false;
});
bool _ringoRegisterReaction (OracleEnv &env, const char *rowid,
const Array<char> &reaction_buf,
RingoOracleContext &context,
RingoIndex &index,
BingoFingerprints &fingerprints)
{
QS_DEF(Array<char>, data);
QS_DEF(Array<char>, compressed_rowid);
ArrayOutput output(data);
output.writeChar(0); // 0 -- present, 1 -- removed from index
ArrayOutput rid_output(compressed_rowid);
RowIDSaver rid_saver(context.context().rid_dict, rid_output);
rid_saver.saveRowID(rowid);
output.writeByte((byte)compressed_rowid.size());
output.writeArray(compressed_rowid);
TRY_READ_TARGET_RXN
{
BufferScanner scanner(reaction_buf);
try
{
index.prepare(scanner, output, NULL);
}
catch (CmfSaver::Error &e) { env.dbgPrintf(bad_reaction_warning_rowid, rowid, e.message()); return false;}
catch (CrfSaver::Error &e) { env.dbgPrintf(bad_reaction_warning_rowid, rowid, e.message()); return false;}
}
CATCH_READ_TARGET_RXN_ROWID(rowid, return false);
// some magic: round it up to avoid ora-22282
if (data.size() % 2 == 1)
output.writeChar(0);
int blockno, offset;
context.context().storage.add(env, data, blockno, offset);
fingerprints.addFingerprint(env, index.getFingerprint());
context.shadow_table.addReaction(env, index, rowid, blockno + 1, offset);
return true;
}