/// <summary>
/// Read object matching the type, folder, owner, name of the given user object
/// </summary>
/// <param name="uo"></param>
/// <returns>The requested user object or null if no matching user object is found.</returns>
public static UserObject Read(UserObject uo)
{
if (ServiceFacade.UseRemoteServices)
{
_sUo = uo.SerializeBinary();
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusUserObjectService,
(int)Services.Native.ServiceOpCodes.MobiusUserObjectService.Read2,
new Services.Native.NativeMethodTransportObject(new object[] { _sUo }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
if (resultObject == null || resultObject.Value == null)
{
return(null);
}
uo = UserObject.DeserializeBinary((byte[])resultObject.Value);
return(uo);
}
else
{
return(UAL.UserObjectDao.Read(uo));
}
}
/// <summary>
/// Read object matching the type, folder, owner, name
/// </summary>
/// <param name="type">type of object</param>
/// <param name="owner">userid of object owner</param>
/// <param name="folderId">folder that it's in</param>
/// <param name="name">name of object</param>
/// <returns></returns>
public static UserObject Read(
UserObjectType type,
string owner,
string folderId,
string name)
{
if (ServiceFacade.UseRemoteServices)
{
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusUserObjectService,
(int)Services.Native.ServiceOpCodes.MobiusUserObjectService.Read3,
new Services.Native.NativeMethodTransportObject(new object[] { (int)type, owner, folderId, name }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
if (resultObject == null || resultObject.Value == null)
{
return(null);
}
_uo = UserObject.DeserializeBinary((byte[])resultObject.Value);
return(_uo);
}
else
{
return(UAL.UserObjectDao.Read(type, owner, folderId, name));
}
}
static void SetUserParameterThreadMethod(object parmArray)
{
try
{
DateTime t0 = DateTime.Now;
object[] parms = parmArray as object[];
string userId = parms[0] as string;
string parmName = parms[1] as string;
string value = parms[2] as string;
if (ServiceFacade.UseRemoteServices)
{
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusUserObjectService,
(int)Services.Native.ServiceOpCodes.MobiusUserObjectService.SetUserParameter,
new Services.Native.NativeMethodTransportObject(new object[] { userId, parmName, value }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
}
else
{
UAL.UserObjectDao.SetUserParameter(userId, parmName, value);
}
//DebugLog.TimeMessage("SetUserParameterThreadMethod " + parmName + " = " + value + ", Time(ms):", t0);
}
catch (Exception ex) // log any exception since any thrown exception for thread can't be caught
{
DebugLog.Message(ex);
}
}
/// <summary>
/// Update the update date & count columns
/// </summary>
/// <param name="objectId"></param>
/// <param name="updateDateTime"></param>
/// <param name="count"></param>
public static void UpdateUpdateDateAndCount(
int objectId,
DateTime updateDateTime,
int count)
{
if (ServiceFacade.UseRemoteServices)
{
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusUserObjectService,
(int)Services.Native.ServiceOpCodes.MobiusUserObjectService.UpdateUpdateDateAndCount,
new Services.Native.NativeMethodTransportObject(new object[] { objectId, updateDateTime, count }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
bool updateSucceeded = (bool)resultObject.Value;
if (!updateSucceeded)
{
throw new Exception("UpdateUpdateDateAndCount failed.");
}
}
else
{
UAL.UserObjectDao.UpdateUpdateDateAndCount(objectId, updateDateTime, count);
}
}
/// <summary>
/// Get a user profile parameter
/// </summary>
/// <param name="userId"></param>
/// <param name="parm"></param>
/// <param name="defaultValue"></param>
/// <returns></returns>
public static string GetUserParameter( //
string userId,
string parm,
string defaultValue)
{
if (ServiceFacade.UseRemoteServices)
{
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusUserObjectService,
(int)Services.Native.ServiceOpCodes.MobiusUserObjectService.GetUserParameter,
new Services.Native.NativeMethodTransportObject(new object[] { userId, parm, defaultValue }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
if (resultObject == null || resultObject.Value == null)
{
return(null);
}
string result = (string)resultObject.Value;
return(result);
}
else
{
return(UAL.UserObjectDao.GetUserParameter(userId, parm, defaultValue));
}
}
/// <summary>
/// Fetch UserObject info for a list of object ids
/// </summary>
/// <param name="includeContent"></param>
/// <returns>Set of user objects ordered by folderType, parentFolder, and (case insensitively) obj name</returns>
public static List <UserObject> ReadMultiple(
List <int> uoIds,
bool includeContent)
{
if (ServiceFacade.UseRemoteServices)
{
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
int[] uoIdsArray = uoIds.ToArray(); // convert ids to array for serialization
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusUserObjectService,
(int)Services.Native.ServiceOpCodes.MobiusUserObjectService.ReadMultiple5,
new Services.Native.NativeMethodTransportObject(
new object[] { uoIdsArray, includeContent }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
if (resultObject == null || resultObject.Value == null)
{
return(null);
}
_uoList = UserObject.DeserializeListBinary((byte[])resultObject.Value);
return(_uoList);
}
else
{
return(UAL.UserObjectDao.ReadMultiple(uoIds, includeContent));
}
}
/// <summary>
/// Check that each of the numbers in the list exist in the database
/// </summary>
/// <param name="listText">String form of list as entered by user</param>
/// <param name="rootTableName">Root table to check against</param>
/// <returns></returns>
public static string ValidateList(
string listText,
string rootTableName)
{
if (ServiceFacade.UseRemoteServices)
{
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusCompoundUtilService,
(int)Services.Native.ServiceOpCodes.MobiusCompoundUtilService.ValidateList,
new Services.Native.NativeMethodTransportObject(new object[] { listText, rootTableName }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
if (resultObject == null)
{
return(null);
}
string result = (string)resultObject.Value;
return(result);
}
else
{
return(Qel.CompoundIdUtil.ValidateList(listText, rootTableName));
}
}
/// <summary>
/// Fetch info for the set of objects of a given object type visible to the specified user, optionally includes publicly visible objects as well.
/// </summary>
/// <param name="type">Object type</param>
/// <param name="userId"></param>
/// <param name="includeShared"></param>
/// <returns>Set of user objects ordered by folderType, folderId, & (case insensitively) obj name</returns>
public static List <UserObject> ReadMultiple(
UserObjectType type,
string userId,
bool includeShared,
bool includeContent)
{
if (ServiceFacade.UseRemoteServices)
{
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusUserObjectService,
(int)Services.Native.ServiceOpCodes.MobiusUserObjectService.ReadMultiple2,
new Services.Native.NativeMethodTransportObject(
new object[] { (int)type, userId, includeShared, includeContent, false }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
if (resultObject == null || resultObject.Value == null)
{
return(null);
}
_uoList = UserObject.DeserializeListBinary((byte[])resultObject.Value);
return(_uoList);
}
else
{
return(UAL.UserObjectDao.ReadMultiple(type, userId, includeShared, includeContent));
}
}
/// <summary>
/// Create a Spotfire Analysis Document displaying data for the specified
/// query using the template and other formatting info in the SpotfireParms.
/// </summary>
/// <param name="q"></param>
/// <param name="stp"></param>
/// <returns></returns>
public static string CreateSpotfireAnalysisDocument(
Query q,
TargetSummaryOptions trvp)
{
string serializedQuery = q.Serialize();
string serializedTrvp = trvp.Serialize();
if (ServiceFacade.UseRemoteServices)
{
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusTargetResultsViewerService,
(int)Services.Native.ServiceOpCodes.MobiusTargetResultsViewerService.CreateSpotfireAnalysisDocument,
new Services.Native.NativeMethodTransportObject(new object[] { serializedQuery, serializedTrvp }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
if (resultObject == null || resultObject.Value == null)
{
return(null);
}
string path = resultObject.Value.ToString();
return(path);
}
else
{
q = Query.Deserialize(serializedQuery);
trvp = TargetSummaryOptions.Deserialize(serializedTrvp);
string path = Mobius.ToolServices.TargetResultsViewerService.CreateSpotfireAnalysisDocument(q, trvp);
return(path);
}
}
/// <summary>
/// Build MetaTable
/// </summary>
/// <param name="name"></param>
/// <returns></returns>
public MetaTable GetMetaTable(string name)
{
MetaTable mt;
if (ServiceFacade.UseRemoteServices)
{
Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject = ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusMetaTableService,
(int)Services.Native.ServiceOpCodes.MobiusMetaTableService.GetMetaTable,
new Services.Native.NativeMethodTransportObject(new object[] { name }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
if (resultObject == null || resultObject.Value == null)
{
return(null);
}
string serializedMt = resultObject.Value.ToString();
mt = MetaTable.Deserialize(serializedMt);
return(mt);
}
else
{
int t0 = TimeOfDay.Milliseconds();
mt = MetaTableFactoryInstance.GetMetaTable(name);
//DebugLog.TimeMessage("MetaTableFactory.GetMetaTable " + name + ", time = ", t0);
return(mt);
}
}
/// <summary>
/// Select a list of molecule strings MoleculeMx objects for a compound id
/// </summary>
/// <param name="cid"></param>
/// <param name="mt">MetaTable used to get root table to select structures from</param>
/// <returns></returns>
public static Dictionary <string, MoleculeMx> SelectChemicalStructuresForCidList(
List <string> cidList,
MetaTable mt = null)
{
Dictionary <string, MoleculeMx> csDict = null;
Stopwatch sw = Stopwatch.StartNew();
if (ServiceFacade.UseRemoteServices)
{
string mtName = mt?.Name;
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusCompoundUtilService,
(int)Services.Native.ServiceOpCodes.MobiusCompoundUtilService.SelectMoleculesForCidList,
new Services.Native.NativeMethodTransportObject(new object[] { cidList, mtName }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
csDict = (resultObject != null) ? (Dictionary <string, MoleculeMx>)resultObject.Value : null;
}
else // local
{
csDict = QEL.MoleculeUtil.SelectMoleculesForCidList(cidList, mt);
}
long ms = sw.ElapsedMilliseconds;
return(csDict);
}
/// <summary>
/// Read the list of ids for a compound library
/// </summary>
/// <param name="libId"></param>
/// <returns></returns>
public static CidList ReadLibrary(
int libId)
{
if (ServiceFacade.UseRemoteServices)
{
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusCidListService,
(int)Services.Native.ServiceOpCodes.MobiusCidListService.ReadLibrary,
new Services.Native.NativeMethodTransportObject(new object[] { libId }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
if (resultObject == null || resultObject.Value == null)
{
return(null);
}
UserObject uo = UserObject.DeserializeBinary((byte[])resultObject.Value);
MetaTable mt = MetaTableCollection.Get(MetaTable.PrimaryRootTable);
CidList cidList = CidList.Deserialize(uo, mt);
return(cidList);
}
else
{
return(UAL.CidListDao.ReadLibrary(libId));
}
}
/// <summary>
/// Get image & coordinates file from KEGG FTP
/// </summary>
/// <param name="pathwayId"></param>
/// <returns></returns>
public static TargetMap GetKeggPathway(
string pathwayId)
{
if (ServiceFacade.UseRemoteServices)
{
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusTargetMapService,
(int)Services.Native.ServiceOpCodes.MobiusTargetMapService.GetKeggPathway,
new Services.Native.NativeMethodTransportObject(new object[] { pathwayId }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
if (resultObject == null)
{
return(null);
}
ServiceTypes.TargetMap serviceTargetMap = (ServiceTypes.TargetMap)resultObject.Value;
TargetMap targetMap =
ServiceFacade.TypeConversionHelper.Convert <ServiceTypes.TargetMap, TargetMap>(serviceTargetMap);
return(targetMap);
}
else
{
return(UAL.TargetMapDao.GetKeggPathway(pathwayId));
}
}
/// <summary>
/// Select row for specified result id
/// </summary>
/// <param name="rsltId"></param>
/// <returns></returns>
public AnnotationVo Select(
long rsltId)
{
if (ServiceFacade.UseRemoteServices)
{
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusAnnotationService,
(int)Services.Native.ServiceOpCodes.MobiusAnnotationService.SelectByResultId,
new Services.Native.NativeMethodTransportObject(new object[] { instanceId, rsltId }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
if (resultObject == null)
{
return(null);
}
ServiceTypes.AnnotationVo serviceAnnotationVo =
(ServiceTypes.AnnotationVo)resultObject.Value;
AnnotationVo annotationVo =
ServiceFacade.TypeConversionHelper.Convert <ServiceTypes.AnnotationVo, AnnotationVo>(serviceAnnotationVo);
return(annotationVo);
}
else
{
return(Instance.Select(rsltId));
}
}
/// <summary>
/// Select all rows for a method and compoundId
/// </summary>
/// <param name="mthdVrsnId"></param>
/// <param name="cmpndId"></param>
/// <returns></returns>
public List <AnnotationVo> Select(
int mthdVrsnId,
string cmpndId)
{
if (ServiceFacade.UseRemoteServices)
{
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusAnnotationService,
(int)Services.Native.ServiceOpCodes.MobiusAnnotationService.Select,
new Services.Native.NativeMethodTransportObject(new object[] { instanceId, mthdVrsnId, cmpndId }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
if (resultObject == null)
{
return(null);
}
List <ServiceTypes.AnnotationVo> serviceAnnotationVos =
(List <ServiceTypes.AnnotationVo>)resultObject.Value;
List <AnnotationVo> annotationVos =
ServiceFacade.TypeConversionHelper.Convert <List <ServiceTypes.AnnotationVo>, List <AnnotationVo> >(serviceAnnotationVos);
return(annotationVos);
}
else
{
return(Instance.Select(mthdVrsnId, cmpndId));
}
}
/// <summary>
/// Perform a deep clone of an annotation table UserObject including the underlying data
/// </summary>
/// <param name="uo"></param>
/// <returns></returns>
public static UserObject DeepClone(UserObject uo)
{
if (ServiceFacade.UseRemoteServices)
{
ServiceTypes.UserObjectNode serviceUONode =
ServiceFacade.TypeConversionHelper.Convert <UserObject, ServiceTypes.UserObjectNode>(uo);
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusAnnotationService,
(int)Services.Native.ServiceOpCodes.MobiusAnnotationService.DeepClone,
new Services.Native.NativeMethodTransportObject(new object[] { serviceUONode }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
if (resultObject == null)
{
return(null);
}
ServiceTypes.UserObjectNode uoNode = (ServiceTypes.UserObjectNode)resultObject.Value;
UserObject uo2 = ServiceFacade.TypeConversionHelper.Convert <ServiceTypes.UserObjectNode, UserObject>(uoNode);
return(uo2);
}
else
{
return(UAL.AnnotationDao.DeepClone(uo));
}
}
/// <summary>
/// Get list of related structures using the supplied compound id for the query structure
/// </summary>
/// <param name="cid"></param>
/// <param name="type"></param>
/// <returns></returns>
public static string GetRelatedMatchCounts(
string cid,
string mtName,
string chime,
StructureSearchType searchTypes,
int searchId)
{
if (ServiceFacade.UseRemoteServices)
{
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusCompoundUtilService,
(int)Services.Native.ServiceOpCodes.MobiusCompoundUtilService.GetRelatedCompoundIds,
//new Services.Native.NativeMethodTransportObject(new object[] { cid, mtName, chime, (int)searchTypes, searchId }));
new Services.Native.NativeMethodTransportObject(new object[] { cid, mtName, chime, searchId }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
string result = (resultObject != null) ? (string)resultObject.Value : null;
return(result);
}
else
{
return(QEL.MoleculeUtil.GetRelatedMatchCounts(cid, mtName, chime, searchTypes, searchId));
}
}
/// <summary>
/// Select the header information for all of the databases owned by a user
/// </summary>
/// <param name="ownerUserName"></param>
/// <returns></returns>
public UcdbDatabase[] SelectDatabaseHeaders(
string ownerUserName)
{
if (ServiceFacade.UseRemoteServices)
{
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusUserCmpndDbService,
(int)Services.Native.ServiceOpCodes.MobiusUserCmpndDbService.SelectDatabaseHeadersByOwner,
new Services.Native.NativeMethodTransportObject(new object[] { ownerUserName }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
if (resultObject == null)
{
return(null);
}
ServiceTypes.UcdbDatabase[] serviceUcdbDatabases =
(ServiceTypes.UcdbDatabase[])resultObject.Value;
UcdbDatabase[] ucdbDatabases =
ServiceFacade.TypeConversionHelper.Convert <ServiceTypes.UcdbDatabase[], UcdbDatabase[]>(serviceUcdbDatabases);
return(ucdbDatabases);
}
else
{
return(Instance.SelectDatabaseHeaders(ownerUserName));
}
}
/// <summary>
/// Read user object given the object id
/// </summary>
/// <param name="objectId">id of item to read</param>
/// <returns>The requested user object or null if no matching user object is found.</returns>
public static UserObject ReadQueryWithMetaTables(int objectId)
{
if (ServiceFacade.UseRemoteServices)
{
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusUserObjectService,
(int)Services.Native.ServiceOpCodes.MobiusUserObjectService.ReadQueryWithMetaTables1,
new Services.Native.NativeMethodTransportObject(new object[] { objectId }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
if (resultObject == null || resultObject.Value == null)
{
return(null);
}
UserObject uo = UserObject.DeserializeBinary((byte[])resultObject.Value);
return(uo);
}
else
{
return(Mobius.QueryEngineLibrary.QueryUserObjectReader.ReadQueryWithMetaTables(objectId));
}
}
/// <summary>
/// Calculate metatable statistics for each broker type
/// </summary>
/// <param name="factoryName"></param>
/// <returns></returns>
public static int UpdateStats(
string factoryName)
{
if (ServiceFacade.UseRemoteServices)
{
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusMetaTableService,
(int)Services.Native.ServiceOpCodes.MobiusMetaTableService.UpdateStats,
new Services.Native.NativeMethodTransportObject(new object[] { factoryName }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
if (resultObject == null || resultObject.Value == null)
{
return(-1);
}
else
{
return((int)resultObject.Value);
}
}
else
{
return(Mobius.MetaFactoryNamespace.MetaTableFactory.UpdateStats(factoryName));
}
}
/// <summary>
/// Write entry to specified file
/// </summary>
/// <param name="msg"></param>
/// <param name="logFileName"></param>
public static void Message(
string msg,
string logFileName)
{
if (ServiceFacade.UseRemoteServices)
{
if (!msg.StartsWith("[")) // include local method info if needed
{
string prefix = DebugLog.GetCallingClassAndMethodPrefix();
msg = prefix + msg;
}
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusServerLogFileService,
(int)Services.Native.ServiceOpCodes.MobiusServerLogFileService.LogMessage,
new Services.Native.NativeMethodTransportObject(new object[] { msg, logFileName }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
}
else // just log locally
{
if (Lex.IsNullOrEmpty(logFileName)) // assign default name
{
logFileName = CommonConfigInfo.ServicesLogFileName;
}
logFileName = Path.GetFileName(logFileName);
//if (!logFileName.Contains(":") && !logFileName.StartsWith(@"\\")) // include directory if none defined
logFileName = ServicesDirs.LogDir + @"\" + logFileName;
DebugLog.MessageDirect(msg, logFileName);
}
}
/// <summary>
/// Build MetaTable from a dictionary in oracle
/// </summary>
/// <param name="name"></param>
/// <returns></returns>
public static MetaTable GetMetaTableFromDatabaseDictionary(string mtName)
{
MetaTable mt;
if (ServiceFacade.UseRemoteServices)
{
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusMetaTableService,
(int)Services.Native.ServiceOpCodes.MobiusMetaTableService.GetMetaTableFromDatabaseDictionary,
new Services.Native.NativeMethodTransportObject(new object[] { mtName }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
if (resultObject == null || resultObject.Value == null)
{
return(null);
}
string serializedMt = resultObject.Value.ToString();
mt = MetaTable.Deserialize(serializedMt);
return(mt);
}
else
{
return(Mobius.MetaFactoryNamespace.MetaTableFactory.GetMetaTableFromDatabaseDictionary(mtName));
}
}
/// <summary>
/// Read database header for a database id
/// </summary>
/// <param name="databaseId"></param>
/// <returns></returns>
public UcdbDatabase SelectDatabaseHeader(
long databaseId)
{
if (ServiceFacade.UseRemoteServices)
{
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusUserCmpndDbService,
(int)Services.Native.ServiceOpCodes.MobiusUserCmpndDbService.SelectDatabaseHeaderByDatabaseId,
new Services.Native.NativeMethodTransportObject(new object[] { databaseId }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
if (resultObject == null)
{
return(null);
}
ServiceTypes.UcdbDatabase serviceUcdbDatabase =
(ServiceTypes.UcdbDatabase)resultObject.Value;
UcdbDatabase ucdbDatabase =
ServiceFacade.TypeConversionHelper.Convert <ServiceTypes.UcdbDatabase, UcdbDatabase>(serviceUcdbDatabase);
return(ucdbDatabase);
}
else
{
return(Instance.SelectDatabaseHeader(databaseId));
}
}
/// <summary>
/// Build query to fetch all summarized (by target) assay data for a target
/// </summary>
/// <param name="geneSymbol"></param>
/// <returns></returns>
public static Query BuildTargetAssaySummarizedDataQuery(
string geneSymbol)
{
if (ServiceFacade.UseRemoteServices)
{
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusTargetAssayService,
(int)Services.Native.ServiceOpCodes.MobiusTargetAssayService.BuildTargetAssaySummarizedDataQuery,
new Services.Native.NativeMethodTransportObject(new object[] { geneSymbol }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
if (resultObject == null)
{
return(null);
}
string serializedQuery = (string)resultObject.Value;
Query query = Query.Deserialize(serializedQuery);
return(query);
}
else
{
return(Qel.MultiDbAssayMetaBroker.BuildTargetAssaySummarizedDataQuery(geneSymbol));
}
}
/// <summary>
/// Update the compounds for a database
/// </summary>
/// <param name="ucdb"></param>
/// <param name="cpds"></param>
/// <returns>New number of compounds in database</returns>
public void UpdateDatabaseCompounds(
UcdbDatabase ucdb,
UcdbCompound[] cpds)
{
if (ServiceFacade.UseRemoteServices)
{
ServiceTypes.UcdbDatabase serviceUcdbDatabase =
ServiceFacade.TypeConversionHelper.Convert <UcdbDatabase, ServiceTypes.UcdbDatabase>(ucdb);
ServiceTypes.UcdbCompound[] serviceUcdbCompounds =
ServiceFacade.TypeConversionHelper.Convert <UcdbCompound[], ServiceTypes.UcdbCompound[]>(cpds);
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusUserCmpndDbService,
(int)Services.Native.ServiceOpCodes.MobiusUserCmpndDbService.UpdateDatabaseCompounds,
new Services.Native.NativeMethodTransportObject(new object[] { serviceUcdbDatabase, serviceUcdbCompounds }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
UpdateUcdb(resultObject, ucdb);
}
else
{
Instance.UpdateDatabaseCompounds(ucdb, cpds);
}
}
/// <summary>
/// Select database compound data for a databaseId and expCmpndIdTxt
/// </summary>
/// <param name="databaseId"></param>
/// <param name="extCmpndIdTxt"></param>
/// <returns></returns>
public UcdbCompound SelectDatabaseCompound(
long databaseId,
string extCmpndIdTxt)
{
if (ServiceFacade.UseRemoteServices)
{
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusUserCmpndDbService,
(int)Services.Native.ServiceOpCodes.MobiusUserCmpndDbService.SelectDatabaseCompound,
new Services.Native.NativeMethodTransportObject(new object[] { databaseId, extCmpndIdTxt }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
if (resultObject == null)
{
return(null);
}
ServiceTypes.UcdbCompound serviceUcdbCompound =
(ServiceTypes.UcdbCompound)resultObject.Value;
UcdbCompound ucdbCompound =
ServiceFacade.TypeConversionHelper.Convert <ServiceTypes.UcdbCompound, UcdbCompound>(serviceUcdbCompound);
return(ucdbCompound);
}
else
{
return(Instance.SelectDatabaseCompound(databaseId, extCmpndIdTxt));
}
}
/// <summary>
/// Get list of database string compound ids
/// </summary>
/// <param name="databaseId"></param>
/// <returns></returns>
public string[] SelectDatabaseExtStringCids(
long databaseId)
{
if (ServiceFacade.UseRemoteServices)
{
string[] sa;
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusUserCmpndDbService,
(int)Services.Native.ServiceOpCodes.MobiusUserCmpndDbService.SelectDatabaseExtStringCids,
new Services.Native.NativeMethodTransportObject(new object[] { databaseId }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
if (resultObject == null)
{
return(null);
}
string[] extStringIds = resultObject.ToStringArray();
return(extStringIds);
}
else
{
return(Instance.SelectDatabaseExtStringCids(databaseId));
}
}
/// <summary>
/// Insert a list of rows
/// </summary>
/// <param name="vo"></param>
/// <returns></returns>
public bool Insert(List <AnnotationVo> voList)
{
if (voList == null || voList.Count == 0)
{
return(true); // nothing to do
}
if (ServiceFacade.UseRemoteServices)
{
List <ServiceTypes.AnnotationVo> serviceVoList =
ServiceFacade.TypeConversionHelper.Convert <List <AnnotationVo>, List <ServiceTypes.AnnotationVo> >(voList);
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusAnnotationService,
(int)Services.Native.ServiceOpCodes.MobiusAnnotationService.Insert,
new Services.Native.NativeMethodTransportObject(new object[] { instanceId, serviceVoList }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
bool succeeded = (bool)resultObject.Value;
return(succeeded);
}
else
{
return(Instance.Insert(voList));
}
}
/// <summary>
/// Select a MoleculeMx object for a compound id
/// </summary>
/// <param name="cid"></param>
/// <param name="mt"></param>
/// <returns></returns>
public static MoleculeMx SelectMoleculeForCid(
string cid,
MetaTable mt = null)
{
MoleculeMx mol = null;
Stopwatch sw = Stopwatch.StartNew();
mol = MoleculeCache.Get(cid); // see if molecule in cache
if (mol != null)
{
return(mol);
}
if (ServiceFacade.UseRemoteServices)
{
string mtName = mt?.Name;
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusCompoundUtilService,
(int)Services.Native.ServiceOpCodes.MobiusCompoundUtilService.SelectMoleculeFromCid,
new Services.Native.NativeMethodTransportObject(new object[] { cid, mtName })); // , setStereoChemistryComments
((System.ServiceModel.IClientChannel)nativeClient).Close();
if (resultObject == null)
{
return(null);
}
byte[] ba = resultObject.Value as byte[];
if (ba != null && ba.Length > 0)
{
MobiusDataType mdt = MobiusDataType.DeserializeBinarySingle(ba);
mol = mdt as MoleculeMx;
}
}
else
{
mol = QEL.MoleculeUtil.SelectMoleculeForCid(cid, mt);
}
if (MoleculeMx.IsDefined(mol))
{
bool isUcdb = (mt != null && mt.Root.IsUserDatabaseStructureTable); // user compound database
if (!isUcdb)
{
MoleculeCache.AddMolecule(cid, mol); // add to cache
}
}
long ms = sw.ElapsedMilliseconds;
return(mol);
}
/// <summary>
/// Delete a user object by id.
/// Optionally calls IUDUserObject.UserObjectDeleted to trigger content tree updates
/// </summary>
/// <param name="objectId">id of user object</param>
/// <param name="notifyUi">if true notify any associated UI of change</param>
/// <returns>True if successful, false otherwise.</returns>
public static bool Delete(
int objectId,
bool notifyUi)
{
if (ServiceFacade.UseRemoteServices)
{
bool deleteSucceeded = false;
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusUserObjectService,
(int)Services.Native.ServiceOpCodes.MobiusUserObjectService.ReadHeader1,
new Services.Native.NativeMethodTransportObject(new object[] { objectId }));
_sUo = (byte[])resultObject.Value;
if (_sUo != null)
{
_uo = UserObject.DeserializeBinary(_sUo);
if (_uo != null)
{
resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusUserObjectService,
(int)Services.Native.ServiceOpCodes.MobiusUserObjectService.Delete,
new Services.Native.NativeMethodTransportObject(new object[] { objectId }));
deleteSucceeded = (bool)resultObject.Value;
}
if (deleteSucceeded && notifyUi && IUserObjectIUD != null && _uo.ParentFolderType != 0) // notify other object of change
{
IUserObjectIUD.UserObjectDeleted(_uo);
}
}
((System.ServiceModel.IClientChannel)nativeClient).Close();
return(deleteSucceeded);
}
else // non-service mode
{
UserObject uo = ReadHeader(objectId);
if (uo == null)
{
return(false);
}
bool result = UAL.UserObjectDao.Delete(objectId);
if (notifyUi && IUserObjectIUD != null && uo.ParentFolderType != 0) // notify other object of change
{
IUserObjectIUD.UserObjectDeleted(uo);
}
return(result);
}
}