object IInvokeServiceOps.InvokeServiceOperation(int opCode, object[] args)
{
MobiusQueryEngineService op = (MobiusQueryEngineService)opCode;
switch (op)
{
case MobiusQueryEngineService.Initialize:
{
Qel.QueryEngine.InitializeForSession();
return(null);
}
case MobiusQueryEngineService.CreateInstance:
{
Qel.QueryEngine instance = new Mobius.QueryEngineLibrary.QueryEngine();
return(instance.Id);
}
case MobiusQueryEngineService.DisposeInstance:
{
int instanceId = (int)args[0];
bool disposed = Qel.QueryEngine.Dispose(instanceId);
return(disposed);
}
case MobiusQueryEngineService.SetParameter:
{
string parm = "", value = "";
if (args.Length == 2)
{
parm = args[0].ToString();
value = args[1].ToString();
}
else // old form (remove when all old clients are updated)
{
parm = "DatabaseSubset";
value = args[0].ToString();
}
Qel.QueryEngine.SetParameter(parm, value);
return(null);
}
case MobiusQueryEngineService.GetSummarizationDetailQuery:
{
int instanceId = (int)args[0];
string metaTableName = (string)args[1];
string metaColumnName = (string)args[2];
int level = (int)args[3];
string resultId = (string)args[4];
//Qel.QueryEngine qe = null;
//lock (Qel.QueryEngine.IdToInstanceDict)
//{
// if (Qel.QueryEngine.IdToInstanceDict.ContainsKey(instanceId))
// {
// qe = Qel.QueryEngine.IdToInstanceDict[instanceId];
// }
//}
//if (qe != null)
//{
string queryXml = "";
Data.Query query = QueryEngine.GetSummarizationDetailQuery(metaTableName, metaColumnName, level, resultId);
if (query != null)
{
queryXml = query.Serialize(false);
}
return(queryXml);
//}
//else
//{
// throw new ArgumentException("Not a valid query engine instance id!");
//}
}
case MobiusQueryEngineService.GetDrilldownDetailQuery:
{
int instanceId = (int)args[0];
string metaTableName = (string)args[1];
string metaColumnName = (string)args[2];
int level = (int)args[3];
string resultId = (string)args[4];
//Qel.QueryEngine qe = null;
//lock (Qel.QueryEngine.IdToInstanceDict)
//{
// if (Qel.QueryEngine.IdToInstanceDict.ContainsKey(instanceId))
// {
// qe = Qel.QueryEngine.IdToInstanceDict[instanceId];
// }
//}
//if (qe != null)
//{
Mobius.Data.MetaTable metaTable = Mobius.Data.MetaTableCollection.GetExisting(metaTableName);
Mobius.Data.MetaColumn metaColumn = metaTable.GetMetaColumnByName(metaColumnName);
Data.Query query = QueryEngine.GetDrilldownDetailQuery(metaTable, metaColumn, level, resultId);
string queryXml = query.Serialize(false);
return(queryXml);
//}
//else
//{
// throw new ArgumentException("Not a valid query engine instance id!");
//}
}
case MobiusQueryEngineService.GetImage:
{
string mtMcName = null;
int instanceId = (int)args[0];
if (args[1] is string) // New "mtName.mcName" format for arg (Post Client 5.0)
{
mtMcName = (string)args[1];
}
else if (args[1] is MetaColumn) // old Mobius.Services.Types.MetaColumn format
{
MetaColumn mc = (MetaColumn)args[1];
mtMcName = mc.MetaTable.Name + "." + mc.Name;
}
else
{
return(null); // error
}
Mobius.Data.MetaColumn mobiusMC = Mobius.Data.MetaColumn.ParseMetaTableMetaColumnName(mtMcName);
string graphicsIdString = (string)args[2];
int desiredWidth = (int)args[3];
Qel.QueryEngine qe = GetQueryEngineInstance(instanceId);
//Mobius.Data.MetaColumn mobiusMC = _transHelper.Convert<MetaColumn, Mobius.Data.MetaColumn>(metaColumn);
System.Drawing.Bitmap bitmap = qe.GetImage(mobiusMC, graphicsIdString, desiredWidth);
Types.Bitmap result = new Types.Bitmap(bitmap);
return(result);
}
case MobiusQueryEngineService.ResolveCidListReference:
{
string tok = (string)args[0];
Mobius.Data.UserObject uo = Qel.QueryEngine.ResolveCidListReference(tok);
UserObjectNode result = _transHelper.Convert <Mobius.Data.UserObject, UserObjectNode>(uo);
return(result);
}
case MobiusQueryEngineService.GetRootTable:
{
string queryString = (string)args[0];
Mobius.Data.Query mobiusQuery = Data.Query.Deserialize(queryString);
Mobius.Data.MetaTable mobiusMT = Qel.QueryEngine.GetRootTable(mobiusQuery);
string mtString = null;
if (mobiusMT != null)
{
mtString = mobiusMT.Serialize();
}
return(mtString);
}
case MobiusQueryEngineService.DoPresearchChecksAndTransforms:
{
string serializedQuery = (string)args[0];
Data.Query q = Data.Query.Deserialize(serializedQuery);
q = Qel.QueryEngine.DoPreSearchTransformations(q);
if (q == null)
{
return(null);
}
string serializedQuery2 = q.Serialize(true);
return(serializedQuery2);
}
case MobiusQueryEngineService.GetKeys:
{
int instanceId = (int)args[0];
Qel.QueryEngine qe = GetQueryEngineInstance(instanceId);
List <string> keys = qe.GetKeys();
return(keys);
}
case MobiusQueryEngineService.ExecuteQuery:
{
int instanceId = (int)args[0];
string serializedQuery = (string)args[1];
Qel.QueryEngine qe = GetQueryEngineInstance(instanceId);
Data.Query q = Data.Query.Deserialize(serializedQuery);
List <string> result = qe.ExecuteQuery(q, false, false);
return(result);
}
case MobiusQueryEngineService.TransformAndExecuteQuery:
{
int instanceId = (int)args[0];
string serializedQuery = (string)args[1];
Qel.QueryEngine qe = GetQueryEngineInstance(instanceId);
Data.Query q2;
Data.Query q = Data.Query.Deserialize(serializedQuery);
List <string> keyList = qe.TransformAndExecuteQuery(q, out q2);
object[] sa = new object[2];
sa[0] = keyList;
if (q2 != null) // any transformed query?
{
sa[1] = q2.Serialize(true, true); // serialize including metatables not previously send to client
}
return(sa);
}
case MobiusQueryEngineService.BuildSqlStatements:
{
int instanceId = (int)args[0];
string serializedQuery = (string)args[1];
Qel.QueryEngine qe = GetQueryEngineInstance(instanceId);
Data.Query q = Data.Query.Deserialize(serializedQuery);
string sqlStatements = qe.BuildSqlStatements(q);
return(sqlStatements);
}
case MobiusQueryEngineService.SaveSpotfireSql:
{
string sqlStmtName = (string)args[0];
string serializedQuery = (string)args[1];
Data.Query q = Data.Query.Deserialize(serializedQuery);
int stmtId = Mobius.QueryEngineLibrary.QueryEngine.SaveSpotfireSql(sqlStmtName, q);
return(stmtId);
}
case MobiusQueryEngineService.SaveSpotfireKeyList:
{
string keyColName, listType, keyList;
if (args.Length >= 3)
{
keyColName = (string)args[0];
listType = (string)args[1];
keyList = (string)args[2];
}
else if (args.Length == 2) // old form
{
keyColName = "CORP_ID";
listType = (string)args[0];
keyList = (string)args[1];
}
else // old form for cid list
{
keyColName = "CORP_ID";
listType = "CIDLIST";
keyList = (string)args[0];
}
string keyListName = Mobius.QueryEngineLibrary.QueryEngine.SaveSpotfireKeyList(keyColName, listType, keyList);
return(keyListName);
}
case MobiusQueryEngineService.ReadSpotfireSql:
{
string sqlStmtName = args[0] as string;
int version = (int)args[1];
string sql = Mobius.QueryEngineLibrary.QueryEngine.ReadSpotfireSql(sqlStmtName, version);
return(sql);
}
case MobiusQueryEngineService.RemapTablesForRetrieval: // DoPreRetrievalTransformation
{
int instanceId = (int)args[0];
Qel.QueryEngine qe = GetQueryEngineInstance(instanceId);
Mobius.Data.Query q = qe.DoPreRetrievalTableExpansions();
if (q == null)
{
return(null);
}
string serializedQuery = q.Serialize(true); // serialize including metatables not previously included
return(serializedQuery);
}
case MobiusQueryEngineService.NextRowsSerialized:
{
int minRows = 1;
bool returnQeStats = false;
List <Mobius.Data.MetaBrokerStats> mbStats = null;
int instanceId = (int)args[0];
int ai = 1;
if (args.Length >= 4) // newer version with minRows arg
{
minRows = (int)args[ai++];
}
int maxRows = (int)args[ai++];
int maxTime = (int)args[ai++];
if (ai < args.Length) // newer version with returnQeStats arg
{
returnQeStats = (bool)args[ai++];
}
Qel.QueryEngine qe = GetQueryEngineInstance(instanceId);
if (returnQeStats)
{
mbStats = new List <Mobius.Data.MetaBrokerStats>();
}
byte[] serializedRows = qe.NextRowsSerialized(minRows, maxRows, maxTime, mbStats);
if (!returnQeStats)
{
return(serializedRows);
}
else // return serialized rows and stats in a two-element object array
{
object[] oa = new object[2];
oa[0] = serializedRows;
oa[1] = Mobius.Data.MetaBrokerStats.SerializeList(mbStats);
return(oa);
}
}
case MobiusQueryEngineService.NextRows:
{
int minRows = 1;
int instanceId = (int)args[0];
int ai = 1;
if (args.Length >= 4) // newer version with minRows arg
{
minRows = (int)args[ai++];
}
int maxRows = (int)args[ai++];
int maxTime = (int)args[ai++];
Qel.QueryEngine qe = GetQueryEngineInstance(instanceId);
List <object[]> rows = qe.NextRows(minRows, maxRows, maxTime);
DataRow dataRow = null;
List <DataRow> dataRows = new List <DataRow>();
if (rows == null)
{
return(dataRows);
}
for (int ri = 0; ri < rows.Count; ri++) // convert each row
{
object[] row = rows[ri];
if (row != null)
{
dataRow = new DataRow();
object[] convertedRow = new object[row.Length];
for (int i = 0; i < row.Length; i++)
{
convertedRow[i] = _transHelper.ConvertObject(row[i]);
}
dataRow.Data = convertedRow;
}
dataRows.Add(dataRow);
}
return(dataRows);
}
case MobiusQueryEngineService.NextRow:
{
int instanceId = (int)args[0];
Qel.QueryEngine qe = GetQueryEngineInstance(instanceId);
object[] row = qe.NextRow();
DataRow dataRow = null;
if (row != null)
{
dataRow = new DataRow();
object[] convertedRow = new object[row.Length];
for (int i = 0; i < row.Length; i++)
{
convertedRow[i] = _transHelper.ConvertObject(row[i]);
}
dataRow.Data = convertedRow;
}
return(dataRow);
}
case MobiusQueryEngineService.Close:
{
int instanceId = (int)args[0];
Qel.QueryEngine qe = GetQueryEngineInstance(instanceId);
qe.Close();
return(true);
}
case MobiusQueryEngineService.Cancel:
{
int instanceId = (int)args[0];
Qel.QueryEngine qe = GetQueryEngineInstance(instanceId);
qe.Cancel(false);
return(true);
}
case MobiusQueryEngineService.GetQueryEngineState:
{
int instanceId = (int)args[0];
Qel.QueryEngine qe = GetQueryEngineInstance(instanceId);
Mobius.Data.QueryEngineState state = qe.State;
QueryEngineState result = _transHelper.Convert <Mobius.Data.QueryEngineState, QueryEngineState>(state);
return(result);
}
case MobiusQueryEngineService.LogExceptionAndSerializedQuery:
{
string exMsg = (string)args[0];
string serializedQuery = (string)args[1];
Data.Query query = Data.Query.Deserialize(serializedQuery);
return(Qel.QueryEngine.LogExceptionAndSerializedQuery(exMsg, query));
}
case MobiusQueryEngineService.LogQueryExecutionStatistics:
{
Qel.QueryEngine.LogQueryExecutionStatistics();
return(null);
}
case MobiusQueryEngineService.ValidateCalculatedFieldExpression:
{
string advExpr = (string)args[0];
return(Qel.QueryEngine.ValidateCalculatedFieldExpression(advExpr));
}
case MobiusQueryEngineService.CreateQueryFromMQL:
{
string mql = (string)args[0];
Mobius.Data.Query mobiusQuery = Mobius.Data.MqlUtil.ConvertMqlToQuery(mql);
Query result = _transHelper.Convert <Mobius.Data.Query, Query>(mobiusQuery); //translate the result
return(result);
}
case MobiusQueryEngineService.ExecuteMQLQuery:
{
Mobius.Data.Query q2;
int instanceId = (int)args[0];
string mql = (string)args[1];
Qel.QueryEngine qe = GetQueryEngineInstance(instanceId);
Mobius.Data.Query q = Mobius.Data.MqlUtil.ConvertMqlToQuery(mql);
List <string> result = qe.TransformAndExecuteQuery(q, out q2);
return(result);
}
case MobiusQueryEngineService.GetSelectAllDataQuery:
{
string mtName = (string)args[0];
string cn = (string)args[1];
string queryXml = "";
Mobius.Data.Query q = QueryEngineLibrary.QueryEngine.GetSelectAllDataQuery(mtName, cn);
if (q != null)
{
queryXml = q.Serialize(false);
}
return(queryXml);
}
case MobiusQueryEngineService.GetStandardMobileQueries:
{
Data.Query[] mobileQueries = QueryEngineLibrary.QueryEngine.GetStandardMobileQueries();
List <Query> queries = new List <Query>();
foreach (Data.Query query in mobileQueries)
{
Query typesQuery = _transHelper.Convert <Mobius.Data.Query, Query>(query);
queries.Add(typesQuery);
}
return(queries.ToArray());
}
case MobiusQueryEngineService.GetMobileQueriesByOwner:
{
string user = (string)args[0];
Data.Query[] mobileQueries = QueryEngineLibrary.QueryEngine.GetMobileQueriesByOwner(user);
List <Query> queries = new List <Query>();
foreach (Data.Query query in mobileQueries)
{
Query typesQuery = _transHelper.Convert <Mobius.Data.Query, Query>(query);
queries.Add(typesQuery);
}
return(queries.ToArray());
}
case MobiusQueryEngineService.GetAdditionalData:
{
int instanceId = (int)args[0];
string command = (string)args[1];
Qel.QueryEngine qe = GetQueryEngineInstance(instanceId);
object o = qe.GetAdditionalData(command);
return(o);
}
case MobiusQueryEngineService.ExportDataToSpotfireFiles:
{
int instanceId = (int)args[0];
Qel.QueryEngine qe = GetQueryEngineInstance(instanceId);
ExportParms ep = ExportParms.Deserialize(args[1] as string);
QueryEngineStats qeStats = qe.ExportDataToSpotfireFiles(ep);
return(qeStats != null ? qeStats.Serialize() : null);
}
case MobiusQueryEngineService.CompleteRowRetrieval:
{
int instanceId = (int)args[0];
Qel.QueryEngine qe = GetQueryEngineInstance(instanceId);
QueryEngineStats qeStats = qe.CompleteRowRetrieval();
return(qeStats != null ? qeStats.Serialize() : null);
}
default:
throw new InvalidOperationException("Unrecognized operation: " + (int)op);
}
}
/// <summary>
/// Read input data from database
/// </summary>
/// <param name="smp">
/// <returns></returns>
List<CompoundStructureActivityData> ReadData(
SasMapParms smp)
{
MetaColumn activityMc = smp.EndpointMc;
QueryColumn keyCriteriaQc = smp.KeyCriteriaQc;
AssertMx.IsNotNull(activityMc, "mc");
AssertMx.IsNotNull(keyCriteriaQc, "keyCriteriaQc");
MetaTable mt, mt2;
MetaColumn mc2 = null;
Query q = new Query();
mt = activityMc.MetaTable;
QueryTable qt = new QueryTable(mt);
if (mt.SummarizedExists && !mt.UseSummarizedData)
{ // retrieve summarized data if exists
mt2 = MetaTableCollection.Get(mt.Name + MetaTable.SummarySuffix);
if (mt2 != null)
{
mc2 = mt2.GetMetaColumnByName(activityMc.Name);
if (mc2 == null) mc2 = mt2.GetMetaColumnByLabel(activityMc.Label);
}
if (mc2 != null) // same column available in summarized?
{
mt = mt2;
activityMc = mc2;
}
}
SMP.KeyCriteriaQc.CopyCriteriaToQueryKeyCritera(q);
q.KeyCriteriaDisplay = SMP.KeyCriteriaQc.CriteriaDisplay;
qt.SelectKeyOnly();
QueryColumn qc = qt.GetQueryColumnByName(activityMc.Name);
qc.Selected = true;
q.AddQueryTable(qt);
QueryEngine qe = new QueryEngine();
List<string> keyList = qe.ExecuteQuery(q); // note that keylist may be empty if single-step query
HashSet<string> keySet = new HashSet<string>(StringComparer.OrdinalIgnoreCase);
List<CompoundStructureActivityData> data = new List<CompoundStructureActivityData>();
int rowCount = 0;
while (true)
{
object[] vo = qe.NextRow();
if (vo == null) break;
CompoundStructureActivityData cd = new CompoundStructureActivityData();
string cid = (string)vo[0];
cd.Cid = cid;
keySet.Add(cid); // accumulate keys
object val = vo[2];
if (NullValue.IsNull(val)) continue;
if (val is double)
cd.Activity = (double)val;
else if (val is Int32)
cd.Activity = (Int32)val;
else if (val is NumberMx)
{
NumberMx nex = val as NumberMx;
cd.Activity = nex.Value;
}
else if (val is QualifiedNumber)
{
QualifiedNumber qn = val as QualifiedNumber;
cd.Activity = qn.NumberValue;
//if (qn.Qualifier != null && qn.Qualifier != "" && qn.Qualifier != "=")
// continue; // (don't want to do this since may filter out good data (e.g. IC50 <0.0001))
}
else continue;
if (cd.Activity == NullValue.NullNumber) continue;
data.Add(cd);
rowCount++;
}
// Retrieve structures
keyList = new List<string>(keySet);
Dictionary<string, MoleculeMx> csDict = MoleculeUtil.SelectMoleculesForCidList(keyList, qt.MetaTable); // get the structures in a single step
// Add structures and build/store fingerprints to data
DebugLog.Message("========== Fingerprints ============");
foreach (CompoundStructureActivityData cd in data)
{
if (!csDict.ContainsKey(cd.Cid) || csDict[cd.Cid] == null) continue;
if (cd.Cid == "111" || cd.Cid == "222") csDict = csDict; // debug
MoleculeMx cs = csDict[cd.Cid];
cd.Structure = cs;
FingerprintType fpType = FingerprintType.Circular;
int fpSubtype = -1;
if (SMP.SimilarityType == SimilaritySearchType.ECFP4) // some issue with ECFP4?
{
fpType = FingerprintType.Circular;
fpSubtype = CircularFingerprintType.ECFP4;
}
else if (SMP.SimilarityType == SimilaritySearchType.Normal)
{
fpType = FingerprintType.MACCS;
}
cd.BitsetFingerprint = cs.BuildBitSetFingerprint(fpType, fpSubtype);
if (cd.BitsetFingerprint == null) continue; // couldn't build fingerprint (e.g. no structure)
if (Debug) DebugLog.Message(cd.Cid + ": " + Lex.Join(CdkMolUtil.GetBitSet(cd.BitsetFingerprint), ", "));
}
return data;
}
/// <summary>
/// Convert a multipivot table into a set of tables where data exists for
/// one or more of the compound identifiers in the list.
/// </summary>
/// <param name="qt">Current form of query table</param>
/// <param name="q">Query to add transformed tables to</param>
/// <param name="ResultKeys">Keys data will be retrieved for</param>
public override void ExpandToMultipleTables(
QueryTable qt,
Query q,
List <string> resultKeys)
{
MetaTable mt2;
QueryTable qt2;
QueryColumn qc2;
HashSet <string> geneDict = new HashSet <string>();
string sql;
string geneSymbol;
int t0 = TimeOfDay.Milliseconds();
// Build query & get set of gene symbols
Query q2 = new Query();
q2.SingleStepExecution = true;
q2.KeyCriteria = q2.KeyCriteriaDisplay = // keylist to return (may want to include all target summary option criteria)
" in (" + MqlUtil.FormatValueListString(resultKeys, true) + ")";
qt2 = qt.Clone();
qt2.SelectKeyOnly();
qc2 = qt2.GetQueryColumnByNameWithException("gene_symbol");
qc2.Selected = true;
q2.AddQueryTable(qt2);
QueryEngine qe2 = new QueryEngine();
qe2.ExecuteQuery(q2);
while (true)
{
object[] vo = qe2.NextRow();
if (vo == null)
{
qe2.Close();
break;
}
if (qe2.Cancelled)
{
qe2.Close();
return;
}
geneSymbol = vo[2] as string;
if (Lex.IsNullOrEmpty(geneSymbol))
{
continue;
}
geneDict.Add(geneSymbol.ToUpper());
}
string[] sa = new string[geneDict.Count];
geneDict.CopyTo(sa);
Array.Sort(sa);
foreach (string s0 in sa)
{
geneSymbol = s0;
string mt2Name = MultiDbAssayDataNames.BasePivotTablePrefix + geneSymbol;
//if (QueryEngine.FilterAllDataQueriesByDatabaseContents &&
// !MetaTableCollection.IsMetaTableInContents(mtName)) continue; // metatable must be in contents
mt2 = MetaTableCollection.Get(mt2Name);
if (mt2 == null)
{
continue; // in case can't allocate for some reason
}
qt2 = q.GetQueryTableByName(mt2.Name); // see if already in query
if (qt2 != null)
{
continue; // ignore if already there
}
qt2 = new QueryTable(q, mt2); // allocate new query table & add to query
qt2.DeselectAll();
foreach (QueryColumn qc0 in qt.QueryColumns) // set selected columns to match those in the source qt
{
if (qc0.Selected && qt2.GetQueryColumnByName(qc0.MetaColumn.Name) != null)
{
qt2.GetQueryColumnByName(qc0.MetaColumn.Name).Selected = true;
}
}
if (qt.HeaderBackgroundColor != Color.Empty)
{
qt2.HeaderBackgroundColor = qt.HeaderBackgroundColor;
}
}
t0 = TimeOfDay.Milliseconds() - t0;
return;
}