private static void _DropIndexData(SqlConnection conn, string bingo_schema,
BingoIndexID id, bool throw_if_not_exists)
{
BingoIndexData data = _extractIndexData(conn, bingo_schema, id, throw_if_not_exists);
if (data != null)
{
data.DropTables(conn);
data.DropTriggers(conn);
}
BingoSqlUtils.ExecNonQueryNoThrow(conn, "DELETE FROM {0} WHERE obj_id = '{1}'",
_contextTable(bingo_schema), id.table_id);
for (int i = index_data_list.Count - 1; i >= 0; i--)
{
BingoIndexDataRefs refs = (BingoIndexDataRefs)index_data_list[i];
if (refs.index_data.id.Equals(id))
{
index_data_list.RemoveAt(i);
BingoLog.logMessage("Sessions for table {0} have been released", id.InformationName(conn));
}
}
if (data != null)
{
BingoLog.logMessage("Bingo index for table {0} has been dropped", id.InformationName(conn));
}
}
private static BingoIndexData GetIndexDataById(SqlConnection conn, string bingo_schema,
BingoIndexID id, int spid)
{
lock (index_data_list_lock)
{
foreach (BingoIndexDataRefs index_data_refs in index_data_list)
{
if (index_data_refs.index_data.id.Equals(id))
{
if (!index_data_refs.session_ids.Contains(spid))
{
BingoLog.logMessage("Existing BingoIndexData added for spid={0} table={1}",
spid, id.FullTableName(conn));
index_data_refs.session_ids.Add(spid);
}
return(index_data_refs.index_data);
}
}
BingoLog.logMessage("Extracting new BingoIndexData for spid={0} table={1}",
spid, id.FullTableName(conn));
BingoIndexData data = _extractIndexData(conn, bingo_schema, id, true);
_AddIndexDataToList(spid, data);
return(data);
}
}
private static void _AddIndexDataToList(int spid, BingoIndexData data)
{
BingoIndexDataRefs new_refs = new BingoIndexDataRefs();
new_refs.index_data = data;
new_refs.session_ids = new List <int>();
new_refs.session_ids.Add(spid);
index_data_list.Add(new_refs);
}
private static BingoIndexData _extractIndexData(SqlConnection conn, string bingo_schema,
BingoIndexID id, bool throw_if_not_exists)
{
BingoIndexData data = null;
using (SqlCommand cmd = new SqlCommand(String.Format(
"SELECT id_column, data_column, type FROM {0} WHERE obj_id = '{1}'",
_contextTable(bingo_schema), id.table_id), conn))
{
using (SqlDataReader reader = cmd.ExecuteReader())
{
if (!reader.Read())
{
if (throw_if_not_exists)
{
throw new Exception("Cannot find Bingo index for table with id=" + id.table_id);
}
else
{
return(null);
}
}
string id_column = Convert.ToString(reader[0]);
string data_column = Convert.ToString(reader[1]);
string type = Convert.ToString(reader[2]);
if (type.ToLower().Equals("molecule"))
{
data = new MangoIndexData(id, id_column, data_column, bingo_schema);
}
if (type.ToLower().Equals("reaction"))
{
data = new RingoIndexData(id, id_column, data_column, bingo_schema);
}
if (data == null)
{
throw new Exception("unknown type: " + type);
}
}
}
data.keep_cache =
(BingoConfig.getInt(conn, bingo_schema, "KEEP_CACHE", id.table_id) != 0);
return(data);
}
private static IEnumerable<FetchedData> _Fetch (SqlString query, string search_type,
bool highlighting, object[] ext_options, SqlConnection conn,
BingoIndexData index_data, string options_str, int? id_next_from)
{
int? storage_id_next_from = null;
if (id_next_from.HasValue)
{
// -1 means start of the iterations
if (id_next_from.Value != -1)
{
storage_id_next_from = index_data.getStorageIdById(conn, id_next_from.Value);
if (!storage_id_next_from.HasValue)
throw new Exception(String.Format("Cannot find record with id={0}", id_next_from));
}
else
storage_id_next_from = -1;
}
IEnumerable<FetchedData> fetched;
if (search_type == "SUB" || search_type == "SMARTS")
{
MangoFastIndexFetch fetch_sub = new MangoFastIndexFetch((MangoIndexData)index_data);
fetch_sub.prepareSub(query.Value, options_str, highlighting, search_type == "SMARTS");
fetch_sub.nextAfterStorageId = storage_id_next_from;
fetched = fetch_sub.fetch(conn);
}
else if (search_type == "EXACT")
{
MangoShadowFetch fetch_exact = new MangoShadowFetch((MangoIndexData)index_data);
fetch_exact.prepareExact(query.Value, options_str);
fetch_exact.nextAfterStorageId = storage_id_next_from;
fetched = fetch_exact.fetch(conn);
}
else if (search_type == "SIM")
{
MangoFastIndexFetch fetch_sim = new MangoFastIndexFetch((MangoIndexData)index_data);
float min = (float)ext_options[0];
float max = (float)ext_options[1];
fetch_sim.prepareSimilarity(query.Value, options_str, min, max);
fetch_sim.nextAfterStorageId = storage_id_next_from;
fetched = fetch_sim.fetch(conn);
}
else if (search_type == "MASS")
{
MangoShadowFetch fetch_mass = new MangoShadowFetch((MangoIndexData)index_data);
float? min = (float?)ext_options[0];
float? max = (float?)ext_options[1];
fetch_mass.prepareMass(min, max);
fetch_mass.nextAfterStorageId = storage_id_next_from;
fetched = fetch_mass.fetch(conn);
}
else if (search_type == "GROSS")
{
MangoShadowFetch fetch_gross = new MangoShadowFetch((MangoIndexData)index_data);
fetch_gross.prepareGross(query.Value);
fetch_gross.nextAfterStorageId = storage_id_next_from;
fetched = fetch_gross.fetch(conn);
}
else if (search_type == "RSUB" || search_type == "RSMARTS")
{
RingoFastIndexFetch fetch_sub = new RingoFastIndexFetch((RingoIndexData)index_data);
fetch_sub.prepareSub(query.Value, options_str, highlighting, search_type == "RSMARTS");
fetch_sub.nextAfterStorageId = storage_id_next_from;
fetched = fetch_sub.fetch(conn);
}
else if (search_type == "REXACT")
{
RingoShadowFetch fetch_exact = new RingoShadowFetch((RingoIndexData)index_data);
fetch_exact.prepareExact(query.Value, options_str);
fetch_exact.nextAfterStorageId = storage_id_next_from;
fetched = fetch_exact.fetch(conn);
}
else
throw new Exception("Unknown search type: " + search_type);
return fetched;
}
private static bool _AddReactionToIndex (SqlConnection conn, BingoIndexData bingo_data)
{
RingoIndexData data = (RingoIndexData)bingo_data;
int id;
RingoIndex index = new RingoIndex();
if (!index.readPrepared(out id))
{
string message =
String.Format("Reaction with ID={0} wasn't added to the index: {1}",
id, BingoCore.lib.bingoGetWarning());
SqlContext.Pipe.Send(message);
BingoLog.logMessage(message);
return false;
}
byte[] new_data = new byte[index.crf.Length + 4];
index.crf.CopyTo(new_data, 4);
MemoryStream stream = new MemoryStream(new_data, 0, 4, true);
BinaryWriter writer = new BinaryWriter(stream);
writer.Write(id);
int storage_id = data.storage.add(new_data, conn);
data.fingerprints.addFingerprint(conn, index.fingerprint, storage_id);
data.addToShadowTable(conn, index, id, storage_id);
return false;
}
private static bool _AddMoleculeToIndex (SqlConnection conn, BingoIndexData bingo_data)
{
MangoIndexData data = (MangoIndexData)bingo_data;
MangoIndex index = new MangoIndex();
int id;
if (!index.readPrepared(out id))
{
string message =
String.Format("Molecule with ID={0} wasn't added to the index: {1}",
id, BingoCore.lib.bingoGetWarning());
SqlContext.Pipe.Send(message);
BingoLog.logMessage(message);
return false;
}
// 4 bytes for Id, 2 bytes for similarity fingerprints bits counts
byte[] new_data = new byte[index.cmf.Length + 4 + 2];
index.cmf.CopyTo(new_data, 6);
MemoryStream stream = new MemoryStream(new_data, 0, 6, true);
BinaryWriter writer = new BinaryWriter(stream);
writer.Write(id);
writer.Write((short)index.sim_fp_bits_count);
int storage_id = data.storage.add(new_data, conn);
data.fingerprints.addFingerprint(conn, index.fingerprint, storage_id);
data.addToShadowTable(conn, index, id, storage_id);
return true;
}
public BingoStorage(BingoIndexData index_data)
{
_index_data = index_data;
}
public BingoStorage (BingoIndexData index_data)
{
_index_data = index_data;
}
public BingoFingerprints (BingoIndexData index_data)
{
_index_data = index_data;
_fp_bytes = -1;
_chunk_bytes = 8000;
}
public BingoFingerprints(BingoIndexData index_data)
{
_index_data = index_data;
_fp_bytes = -1;
_chunk_bytes = 8000;
}
private static void _AddIndexDataToList (int spid, BingoIndexData data)
{
BingoIndexDataRefs new_refs = new BingoIndexDataRefs();
new_refs.index_data = data;
new_refs.session_ids = new List<int>();
new_refs.session_ids.Add(spid);
index_data_list.Add(new_refs);
}