/// <summary>
/// Try to get the row at the given index from the buffer or cache
/// </summary>
/// <param name="cursor"></param>
/// <returns></returns>
public bool TryToGetNextRow(
VoArrayListCursor cursor)
{
object[] vo = null;
int ri = cursor.Position + 1;
AssertMx.IsTrue(ri >= 0, "Invalid row index:" + ri);
if (ri >= TotalRowCount)
{
if (DebugCaching)
{
DebugLog.Message(string.Format("Row {0} not in cache or buffer (cacheSize: {1}, bufferSize: {2})", ri, RowsWrittenToCache, RowBuffer.Count));
}
return(false); // not in collection
}
vo = GetRow(ri);
cursor.CurrentRow = vo;
cursor.Position = ri;
return(true);
}
/// <summary>
/// Indexer into pages
/// </summary>
/// <param name="cpi"></param>
/// <returns></returns>
public ResultsPage this[int cpi]
{
get
{
AssertMx.IsTrue(cpi >= 0 && cpi < Pages.Count);
return(Pages[cpi]);
}
set
{
AssertMx.IsTrue(cpi >= 0 && cpi < Pages.Count);
Pages[cpi] = value;
}
}
/// <summary>
/// Get/set a single element in the ItemArray object array by col name
/// </summary>
/// <param name="columnName"></param>
/// <returns></returns>
public object this[string columnName]
{
get
{
int index = Table.Columns.IndexOf(columnName);
AssertMx.IsTrue(index >= 0, "Column not found: " + columnName);
return(this[index]);
}
set
{
int index = Table.Columns.IndexOf(columnName);
AssertMx.IsTrue(index >= 0, "Column not found: " + columnName);
this[index] = value;
}
}
/// <summary>
/// Read in all of the rows that have been cached
/// </summary>
/// <returns></returns>
public List <object[]> ReadCachedRows()
{
AssertMx.IsTrue(File.Exists(CacheFilePath), "CacheFilePath doesn't exist");
FileStream fs = File.Open(CacheFilePath, FileMode.Open, FileAccess.Read, FileShare.ReadWrite);
BinaryReader br = new BinaryReader(fs);
List <object[]> cachedRows = new List <object[]>(); // in-memory buffer list of rows
for (int ri = 0; ri < RowsWrittenToCache; ri++)
{
object[] vo = VoArray.ReadBinaryVoArray(br, VoaLength);
cachedRows.Add(vo);
}
br.Close(); // close reader and the underlying stream
return(cachedRows);
}
/// <summary>
/// ExecuteSearch
/// </summary>
/// <param name="queryMol"></param>
public List <StructSearchMatch> ExecuteSearch(
IAtomContainer queryMol)
{
AssertMx.IsTrue(FingerprintType == FingerprintType.MACCS || FingerprintType == FingerprintType.Circular,
"Invalid FingerprintType: " + FingerprintType);
QueryMol = queryMol;
BitSetFingerprint fp = // generate a fingerprint
CdkMol.BuildBitSetFingerprintForLargestFragment(queryMol, FingerprintType);
QueryFpCardinality = fp.cardinality();
QueryFpLongArray = fp.asBitSet().toLongArray();
MatchList = new List <StructSearchMatch>();
ThreadException = null;
foreach (string databaseName in FingerprintDbMx.Databases) // loop on all databases
{
int srcId = -1;
if (Lex.Contains(databaseName, "corp"))
{
if (!GetCorpSim)
{
continue;
}
srcId = StructSearchMatch.CorpDbId;
}
else if (Lex.Contains(databaseName, "chembl"))
{
if (!GetChemblSim)
{
continue;
}
srcId = StructSearchMatch.ChemblDbId;
}
if (Debug)
{
DebugLog.Message("Starting sim search on " + databaseName + " database");
}
FpDao = new FingerprintDao(databaseName, FingerprintType);
if (!FpDao.DataFilesExist())
{
continue; // no files for this database
}
FileStreamReaders = FpDao.OpenReaders();
FileMatchLists = new List <StructSearchMatch> [FileStreamReaders.Length];
for (int i1 = 0; i1 < FileMatchLists.Length; i1++)
{
FileMatchLists[i1] = new List <StructSearchMatch>();
}
DateTime t0 = DateTime.Now;
if (UseMultipleThreads)
{
ExecuteMultiThreadSearch();
}
else
{
ExecuteSingleThreadSearch();
}
double et = TimeOfDay.Delta(ref t0);
FpDao.CloseReaders();
List <StructSearchMatch> matchList = MergeIndividualFileMatchLists();
if (KeysToExclude != null || SearchKeySubset != null) // filter by any allowed/disallowed keys
{
List <StructSearchMatch> matchList2 = new List <StructSearchMatch>();
foreach (StructSearchMatch m0 in matchList)
{
if (KeysToExclude != null && KeysToExclude.Contains(m0.SrcCid))
{
continue;
}
if (SearchKeySubset != null && !SearchKeySubset.Contains(m0.SrcCid))
{
continue;
}
matchList2.Add(m0);
}
matchList = matchList2;
}
matchList.Sort(StructSearchMatch.CompareByMatchQuality);
//int removeCount = matchList.Count - MaxHits; // limit to maxhits per database
//if (removeCount > 0)
// matchList.RemoveRange(MaxHits, removeCount);
//foreach (StructSearchMatch ssm0 in matchList)
// if (ssm0.SrcId != srcId) ssm0.SrcId = srcId; // debug
MatchList.AddRange(matchList);
double et2 = TimeOfDay.Delta(ref t0);
string msg =
string.Format("Search complete (" + databaseName + ").Time : {0:0.00} ", et) +
string.Format("{0} Hits: ", FileMatchLists[0].Count);
if (Debug)
{
DebugLog.Message(msg);
}
for (int hi = 0; hi < 5 && hi < FileMatchLists[0].Count; hi++)
{
StructSearchMatch sm = FileMatchLists[0][hi];
msg += sm.SrcCid + string.Format(" = {0:0.00}, ", sm.MatchScore);
}
} // database loop
if (ThreadException != null)
{
throw new Exception(ThreadException.Message, ThreadException);
}
MatchList.Sort( // sort by decreasing sim value
delegate(StructSearchMatch p1, StructSearchMatch p2)
{ return(p2.MatchScore.CompareTo(p1.MatchScore)); });
if (MaxHits > 0 && MatchList.Count > MaxHits) // remove hits beyond maximum if defined
{
MatchList.RemoveRange(MaxHits, MatchList.Count - MaxHits);
}
//ShowProgress(msg);
//Thread.Sleep(10000000);
return(MatchList);
}
/// <summary>
/// GetFpFileName
/// </summary>
/// <param name="fi"></param>
/// <returns></returns>
public string GetFpFileName(int fi)
{
AssertMx.IsTrue(FingerprintType == FingerprintType.MACCS || FingerprintType == FingerprintType.Circular);
return(ServicesDirs.BinaryDataDir + @"\Fingerprints\" + DatabaseName + FingerprintFileNameToken + string.Format(@"Fingerprints{0:00}", fi));
}
/// <summary>
/// Run the query
/// </summary>
/// <param name="browseExistingResults">If true browse existing results</param>
/// <returns></returns>
public string RunQuery3(
ResultsFormat rf,
bool saveHitlist,
bool browseExistingResults)
{
Query modifiedQuery;
QueryTable qt;
QueryColumn qc;
ResultsTable rt;
ResultsField rfld;
MetaTable mt;
MetaColumn mc;
string txt, msg;
DialogResult dr;
bool success;
CellGraphic cg;
Lex lex = new Lex();
string tempfile, tok, command, unrecognizedCommand, response;
int ti, gi, rc, i1, i2;
// Begin execution
if (rf == null)
{
throw new Exception("QueryExec.Run - Null ResultsFormat");
}
if (ResultsFormatter == null)
{
throw new Exception("QueryExec.Run - Null ResultsFormatter");
}
if (rf.Segments == null)
{
throw new Exception("QueryExec.Run - Null ResultsFormat.Segments");
}
if (Query == null)
{
throw new Exception("QueryExec.Run - Null Rf.Query");
}
if (Query.Tables == null || Query.Tables.Count <= 0)
{
throw new QueryException("QueryExec.Run - No Query Tables");
}
QueryManager qm = QueryManager;
ReturnMsg = "";
//bool useExistingQueryEngine = Rf.ParentQe != null;
//bool useExistingDataTable = Query.BrowseExistingResultsWhenOpened && Query.SerializeResults &&
// qm.DataTable != null && qm.DataTable.Rows.Count > 0;
try
{
//if (Math.Sqrt(4) == 2) throw new Exception("test"); // debug
if (!browseExistingResults) // normal open of search
{
Progress.Show("Analyzing query..."); // put up a status message to the user as soon as possible to let them know something is happening...
dr = ValidateQuery(Query);
if (dr == DialogResult.Cancel)
{
return("");
}
WriteCurrentListToServerIfNeeded(Query);
if (rf.OutputDestination == OutputDest.WinForms) // update access stats if grid
{
UpdateTableUsageStatistics(Query);
}
Query.ResultsDataTable = null; // be sure to get new results
qm = BuildQueryManager(Query, rf);
Query.ResetViewStates(); // reset state of views for proper operation
if (Rf.ParentQe == null) // open search unless using existing query engine
{
if (!ExecuteSearch(saveHitlist)) // returns false if cancelled by user
{
Progress.Hide();
return("");
}
}
if ((ResultsKeys == null || ResultsKeys.Count == 0) && // nothing for search
!Query.Preview &&
!MqlUtil.SingleStepExecution(Query) &&
qm.DataTable.Rows.Count == 0 &&
Query.RetrievesDataFromQueryEngine)
{
// if (!Rf.PopupDisplay)
Progress.Hide();
if (qm.StatusBarManager != null)
{
qm.StatusBarManager.DisplayStatusMessage("");
}
// if (QueryEngine.Cancelled) return ""; // cancelled by user
msg = "No data have been found that matches your query.";
if (ResultsFormat.PopupOutputFormContext && !ResultsFormat.SuppressNoDataMessage)
{
MessageBoxMx.Show(msg, "Search Result",
MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
return("Command EditQuery"); // return to edit query menu
}
else
{
return(msg);
}
}
//if (ResultsFormat.PopupDisplay)
// SessionManager.DisplayStatusMessage("Retrieving data...");
//else Progress.Show("Retrieving data...", UmlautMobius.Value, true, "Cancelling Retrieval...");
//Progress.Show("Retrieving data...", UmlautMobius.String, true, "Cancelling Retrieval...");
Progress.Hide(); // hide progress - "Retrieving data..." message now appears as bottom line of grid
if (ResultsFormat.Grid)
{
if (ResultsFormat.SessionOutputFormContext) // if normal main session form grid display, set browse mode & view state
{
Query.ResetViewStates(); // reset view state for all views
QbUtil.SetMode(QueryMode.Browse, Query);
if (ResultsFormat.Query.LogicType == QueryLogicType.And) // log grid query by logic type
{
UsageDao.LogEvent("QueryGridAnd", "");
}
else if (ResultsFormat.Query.LogicType == QueryLogicType.Or)
{
UsageDao.LogEvent("QueryGridOr", "");
}
else if (ResultsFormat.Query.LogicType == QueryLogicType.Complex)
{
UsageDao.LogEvent("QueryGridComplex", "");
}
}
else if (ResultsFormat.PopupOutputFormContext) // create popup window & configure
{
PopupResults.Show(qm);
//MoleculeGridPanel.ConfigureAndShow(qm, null);
}
else if (ResultsFormat.ToolOutputFormContext)
{
ContainerControl cc;
QueryResultsControl qrc = ResultsFormat.OutputContainerControl as QueryResultsControl;
AssertMx.IsTrue(qrc != null, "ResultsFormat.OutputContainerControl must be a QueryResultsControl");
if (!WindowsHelper.FindContainerControl(qrc, typeof(ToolResultsContainer), out cc))
{
throw new Exception("ToolResultsContainer not found");
}
ToolResultsContainer trc = cc as ToolResultsContainer;
trc.SetupQueryResultsControlForResultsDisplay(qm);
}
else
{
throw new Exception("Invalid OutputformContext: " + ResultsFormat.OutputFormContext);
}
}
}
else // reentering display switch to browse tab
{
QbUtil.SetMode(QueryMode.Browse, Query);
}
response = ResultsFormatter.BeginFormatting(browseExistingResults); // format the data
if (ResultsFormat.SessionOutputFormContext) // normal display
{
if (MqlUtil.SingleStepExecution(Query))
{ // be sure hit count display is up to date
if (ResultsKeys != null)
{
if (qm.StatusBarManager != null)
{
qm.StatusBarManager.DisplayCurrentCount();
}
}
}
if (saveHitlist)
{
CidList hitList = new CidList(ResultsKeys);
rc = CidListCommand.WriteCurrentList(hitList);
SessionManager.DisplayCurrentCount();
}
}
return(response);
} // end of surrounding try
catch (Exception ex)
{
Progress.Hide();
if (ex is UserQueryException) // exception that can occur from user error
{
throw new UserQueryException(ex.Message, ex);
}
else
{
msg = DebugLog.FormatExceptionMessage(ex);
if (!Lex.Contains(msg, "QueryLogged:")) // exception & query
{
QueryEngine.LogExceptionAndSerializedQuery(msg, Query);
}
else
{
ServicesLog.Message(msg); // just log exception
}
throw new Exception(ex.Message, ex); // pass it up
}
}
}
/// <summary>
/// Try to get the row at the given index from the buffer or cache
/// </summary>
/// <param name="ri"></param>
/// <returns></returns>
///
public object[] GetRow(
int ri)
{
object[] vo = null;
if (ri < 0 || ri >= TotalRowCount)
{
string msg = string.Format("Row {0} not in cache or buffer (cacheSize: {1}, bufferSize: {2})", ri, RowsWrittenToCache, RowBuffer.Count);
throw new InvalidDataException(msg);
}
// See if in buffer
if (ri >= RowsWrittenToCache)
{
vo = (object[])RowBuffer[ri - RowsWrittenToCache];
if (DebugCaching)
{
DebugLog.Message(string.Format("Row: {0} in Buffer (cacheSize: {1}, bufferSize: {2})", ri, RowsWrittenToCache, RowBuffer.Count));
}
return(vo);
}
// Get from cache
if (ri < CacheReaderPosition + 1) // if already read past this then close current cursor
{
CloseCacheReader();
}
if (CacheReader == null) // need to open reader?
{
AssertMx.IsNotNull(CacheWriter, "CacheWriter");
AssertMx.IsTrue(File.Exists(CacheFilePath), "CacheFilePath doesn't exist");
FileStream fs = File.Open(CacheFilePath, FileMode.Open, FileAccess.Read, FileShare.ReadWrite);
CacheReader = new BinaryReader(fs);
CacheReaderPosition = -1;
if (DebugCaching)
{
DebugLog.Message("Opening cache reader");
}
}
while (CacheReaderPosition + 1 <= ri) // read rows until we get the one we want
{
vo = VoArray.ReadBinaryVoArray(CacheReader, VoaLength);
CacheReaderPosition++;
}
CacheReaderPosition = ri;
if (DebugCaching)
{
DebugLog.Message(string.Format("Row: {0} in Cache (cacheSize: {1}, bufferSize: {2})", ri, RowsWrittenToCache, RowBuffer.Count));
}
return(vo);
}
/// <summary>
/// Get the next value for the sequence (MySQL)
/// </summary>
/// <param name="seqName"></param>
/// <returns></returns>
public static long NextValLongMySQL(
string seqName)
{
string sql;
long nextVal;
SequenceDao seqDao = Lookup(seqName);
Queue <long> seqQueue = seqDao.Queue;
if (seqQueue.Count > 0)
{
nextVal = seqQueue.Dequeue();
return(nextVal);
}
int count = (seqDao.CacheSize > 0 ? seqDao.CacheSize : 1);
int t0 = TimeOfDay.Milliseconds();
DbCommandMx seqCmd = new DbCommandMx();
seqCmd.MxConn = DbConnectionMx.GetConnection("MySql_Mobius"); // "MySql_Mobius_Sequences"
sql = String.Format(
@"update mbs_owner.mbs_sequences
set value = last_insert_id(value) + {0}
where name = '{1}'" , count, seqName.ToUpper());
seqCmd.PrepareUsingDefinedConnection(sql);
int updCount = seqCmd.ExecuteNonReader();
if (updCount <= 0)
{
throw new Exception("Error updating sequence (may not exist): " + seqName);
}
sql = "select last_insert_id()"; // gets value before update above
seqCmd.PrepareUsingDefinedConnection(sql, null);
DbDataReader rdr = seqCmd.ExecuteReader();
bool readOk = rdr.Read();
AssertMx.IsTrue(readOk, "readOk");
long value = rdr.GetInt64(0);
rdr.Close();
seqCmd.CloseReader();
nextVal = value + 1; // return this one now
long v2 = value + 2; // next value
long vn = value + count; // last value
for (long vi = v2; vi <= vn; vi++)
{
seqQueue.Enqueue(vi);
}
t0 = TimeOfDay.Milliseconds() - t0;
// DebugLog.Message("Read sequence, set size = " + seqQueue.Count.ToString() + ", Time(ms) = " + t0.ToString());
return(nextVal);
}
