/// <summary>
/// Get a metatable from MySql catalog
/// </summary>
/// <param name="tableName">schema.table</param>
/// <returns></returns>
public static MetaTable GetMetaTableFromDatabaseDictionary(
DbConnectionMx conn,
string schema,
string tableName)
{
int t0 = TimeOfDay.Milliseconds();
MetaTable mt = new MetaTable();
mt.MetaBrokerType = MetaBrokerType.Generic;
mt.Name = tableName;
mt.Label = MetaTable.IdToLabel(tableName);
mt.TableMap = schema + "." + tableName;
List <DbColumnMetadata> cmdList = GetTableMetadataFromMySqlDictionary(conn, schema, tableName);
for (int ci = 0; ci < cmdList.Count; ci++)
{
DbColumnMetadata cmd = cmdList[ci];
MetaColumn mc = new MetaColumn();
mc.Name = cmd.Name;
mc.ColumnMap = mc.Name;
mc.Label = MetaTable.IdToLabel(cmd.Name);
if (Lex.Contains(cmd.Type, "CHAR") ||
Lex.Contains(cmd.Type, "TEXT"))
{
mc.DataType = MetaColumnType.String;
}
else if (Lex.Contains(cmd.Type, "INT") ||
Lex.Contains(cmd.Type, "ENUM"))
{
mc.DataType = MetaColumnType.Integer;
}
else if (cmd.Type == "FLOAT" ||
cmd.Type == "REAL" ||
cmd.Type == "DOUBLE" ||
cmd.Type == "DECIMAL" ||
cmd.Type == "NUMERIC")
{
mc.DataType = MetaColumnType.Number;
mc.Format = ColumnFormatEnum.Decimal;
mc.Decimals = cmd.Scale;
}
else if (cmd.Type == "DATE" ||
cmd.Type == "DATETIME" ||
cmd.Type == "TIMESTAMP")
{
mc.DataType = MetaColumnType.Date;
}
else
{
continue; // unrecognized
}
mc.InitialSelection = ColumnSelectionEnum.Selected;
mc.Width = 12;
mc.MetaTable = mt;
mc.Description = cmd.Comment;
mt.AddMetaColumn(mc);
}
t0 = TimeOfDay.Milliseconds() - t0;
return(mt);
}
public static DialogResult Show(
QueryColumn qc)
{
string tok;
if (Instance == null)
{
Instance = new DateFormatDialog();
}
DateFormatDialog dfd = Instance;
MetaColumn mc = qc.MetaColumn;
if (mc.DataType != MetaColumnType.Date)
{
XtraMessageBox.Show(mc.Label + " is not a date field");
return(DialogResult.Cancel);
}
// Setup
new JupyterGuiConverter().ConvertFormOrUserControl(Instance);
string fmt = qc.DisplayFormatString;
if (Lex.IsNullOrEmpty(fmt))
{
fmt = "d-MMM-yyyy"; // default format
}
if (Lex.Contains(fmt, "d-MMM-yyyy"))
{
dfd.d_MMM_yyyy.Checked = true;
}
else if (Lex.Contains(fmt, "d-MMM-yy"))
{
dfd.d_MMM_yy.Checked = true;
}
else if (Lex.Contains(fmt, "M/d/yyyy"))
{
dfd.M_d_yyyy.Checked = true;
}
else if (Lex.Contains(fmt, "M/d/yy"))
{
dfd.M_d_yy.Checked = true;
}
else if (Lex.Contains(fmt, "none"))
{
dfd.DateNone.Checked = true;
}
else
{
dfd.d_MMM_yyyy.Checked = true; // in case of no match
}
if (Lex.Contains(fmt, "h:mm:ss tt"))
{
dfd.h_mm_ss_tt.Checked = true; // check in reverse order to get correct hit
}
else if (Lex.Contains(fmt, "h:mm tt"))
{
dfd.h_mm_tt.Checked = true;
}
else if (Lex.Contains(fmt, "H:mm:ss"))
{
dfd.H_mm_ss.Checked = true;
}
else if (Lex.Contains(fmt, "H:mm"))
{
dfd.H_mm.Checked = true;
}
else
{
dfd.TimeNone.Checked = true;
}
// Show form & get new values
DialogResult dr = dfd.ShowDialog(SessionManager.ActiveForm);
if (dr == DialogResult.OK)
{
if (dfd.d_MMM_yyyy.Checked)
{
fmt = "d-MMM-yyyy";
}
else if (dfd.d_MMM_yy.Checked)
{
fmt = "d-MMM-yy";
}
else if (dfd.M_d_yyyy.Checked)
{
fmt = "M/d/yyyy";
}
else if (dfd.M_d_yy.Checked)
{
fmt = "M/d/yy";
}
else if (dfd.DateNone.Checked)
{
fmt = "none";
}
if (dfd.H_mm.Checked)
{
fmt += " H:mm";
}
else if (dfd.H_mm_ss.Checked)
{
fmt += " H:mm:ss";
}
else if (dfd.h_mm_tt.Checked)
{
fmt += " h:mm tt";
}
else if (dfd.h_mm_ss_tt.Checked)
{
fmt += " h:mm:ss tt";
}
else if (dfd.TimeNone.Checked)
{
}
; // nothing if no time
qc.DisplayFormatString = fmt;
}
return(dr);
}
/// <summary>
/// Get the image index corresponding to node type
/// </summary>
/// <returns></returns>
public Bitmaps16x16Enum GetImageIndexEnum()
{
MetaTreeNode mtn = this;
//if (mtn.Label == "CorpId Structures") mtn = mtn; // debug
if (IsFolderType)
{
switch (Type)
{
case MetaTreeNodeType.Root:
return(Bitmaps16x16Enum.World);
case MetaTreeNodeType.Database:
return(Bitmaps16x16Enum.Books);
case MetaTreeNodeType.Target:
return(Bitmaps16x16Enum.Target);
case MetaTreeNodeType.UserFolder:
if (Lex.Eq(mtn.Label, "Queries"))
{
return(Bitmaps16x16Enum.QueryFolder);
}
else if (Lex.Eq(mtn.Label, "Lists"))
{
return(Bitmaps16x16Enum.ListFolder);
}
else if (Lex.Eq(mtn.Label, "Annotations"))
{
return(Bitmaps16x16Enum.AnnotationFolder);
}
else if (Lex.Eq(mtn.Label, "Calculated Fields"))
{
return(Bitmaps16x16Enum.CalcFieldFolder);
}
else if (Lex.StartsWith(mtn.Label, "Shared ") || Lex.StartsWith(mtn.Label, "Public "))
{
return(Bitmaps16x16Enum.People);
}
else
{
return(Bitmaps16x16Enum.Folder);
}
case MetaTreeNodeType.Project:
return(Bitmaps16x16Enum.Project);
default:
return(Bitmaps16x16Enum.Folder);
}
}
// Leaf-type nodes
switch (Type)
{
case MetaTreeNodeType.Url:
if (Lex.Contains(Target, "Spotfire")) // link to Spotfire webplayer
{
return(Bitmaps16x16Enum.Spotfire);
}
else if (Lex.Contains(Target, "Show") && Lex.Contains(Target, "Description")) // use help image for showing descriptions
{
return(Bitmaps16x16Enum.Info);
}
else
{
return(Bitmaps16x16Enum.URL); // generic URL
}
case MetaTreeNodeType.Action:
return(Bitmaps16x16Enum.Action);
case MetaTreeNodeType.CnList:
if (Shared)
{
return(Bitmaps16x16Enum.CidListPublic);
}
else
{
return(Bitmaps16x16Enum.CidList);
}
case MetaTreeNodeType.Query:
if (Lex.StartsWith(Name, "MULTITABLE_")) // use tables icon for multitable
{
return(Bitmaps16x16Enum.Tables);
}
else
{
if (Shared)
{
return(Bitmaps16x16Enum.QueryPublic);
}
else
{
return(Bitmaps16x16Enum.SarTable);
}
}
case MetaTreeNodeType.CalcField:
if (Shared)
{
return(Bitmaps16x16Enum.CalcFieldPublic);
}
else
{
return(Bitmaps16x16Enum.CalcField);
}
case MetaTreeNodeType.Annotation:
if (Lex.Contains(Label, "STRUCTURES")) // special case for structure annotation in user databases
{
return(Bitmaps16x16Enum.Structure);
}
else
{
if (Shared)
{
return(Bitmaps16x16Enum.AnnotationPublic);
}
else
{
return(Bitmaps16x16Enum.AnnotationTable);
}
}
case MetaTreeNodeType.CondFormat:
return(Bitmaps16x16Enum.CondFormat);
case MetaTreeNodeType.MetaTable: // must be metatable
if (Lex.Contains(Name, "_STRUCTURE2") && // special case for struct "plus"
!Lex.StartsWith(Name, "ORACLE")) // but not in direct Oracle references
{
return(Bitmaps16x16Enum.StructurePlus);
}
else if (Lex.Contains(Name, "_STRUCTURE") && // special case for struct
!Lex.StartsWith(Name, "ORACLE")) // but not in direct Oracle references
{
return(Bitmaps16x16Enum.Structure);
}
else if (Lex.Eq(Name, MetaTable.SmallWorldMetaTableName))
{
return(Bitmaps16x16Enum.Structure);
}
else
{
return(Bitmaps16x16Enum.DataTable);
}
case MetaTreeNodeType.Library:
return(Bitmaps16x16Enum.Library);
case MetaTreeNodeType.ResultsView:
return(Bitmaps16x16Enum.Spotfire);
default:
return(Bitmaps16x16Enum.World);
}
}
/// <summary>
/// Scan all loaded assemblies and get list of those that contain Mobius types
/// </summary>
static void GetMobiusAssemblies()
{
HashSet <Assembly> aDict = new HashSet <Assembly>();
HashSet <string> aNamesTriedDict = new HashSet <string>();
Assembly serviceFacadeAssembly = null; // assembly that contains the ServiceFacade classes
HashSet <string> serviceFacadeClassNames = new HashSet <string>(); // names of classes in ServiceFacade
Type[] types;
Assembly[] initialAssemblies = AppDomain.CurrentDomain.GetAssemblies();
foreach (Assembly a in initialAssemblies) // Get all Mobius assemblies from initial set
{
aNamesTriedDict.Add(a.FullName);
if (!IsMobiusAssembly(a))
{
continue;
}
aDict.Add(a);
}
MobiusAssemblies = new List <Assembly>(aDict); // initial set of Mobius assemblies
foreach (Assembly a in MobiusAssemblies) // Check referenced assemblies not initially loaded
{
CheckReferencedAssemblies(a, aDict, aNamesTriedDict);
}
MobiusAssemblies = new List <Assembly>(aDict); // get full set of Mobius assemblies
foreach (Assembly a in MobiusAssemblies) // look for ServiceFacade assembly
{
if (Lex.Contains(a.FullName, "ServiceFacade"))
{
serviceFacadeAssembly = a;
continue;
}
}
ServiceAssemblyNames = new HashSet <string>();
if (serviceFacadeAssembly == null)
{
return; // just return if no serviceFacadeAssembly
}
MobiusAssemblies.Remove(serviceFacadeAssembly);
// Get list of assemblies that are primarily service assemblies
serviceFacadeClassNames = new HashSet <string>(); // build hash set of service facade class names
types = serviceFacadeAssembly.GetTypes();
for (int ti = 0; ti < types.Length; ti++)
{
Type t = types[ti];
serviceFacadeClassNames.Add(t.Name);
}
foreach (Assembly a in MobiusAssemblies) // see if any class in assemble matches a class name in the service facade
{
types = a.GetTypes();
for (int ti = 0; ti < types.Length; ti++)
{
Type t = types[ti];
if (serviceFacadeClassNames.Contains(t.Name))
{
ServiceAssemblyNames.Add(a.FullName);
break;
}
}
}
// Put ServiceFacade assembly last so non-facade classes are found first first
MobiusAssemblies.Add(serviceFacadeAssembly);
return;
}
/// <summary>
/// Deserialize an alert header in a user object
/// </summary>
/// <param name="uo"></param>
/// <returns></returns>
private static Alert DeserializeHeader(
UserObject uo)
{
Alert alert = new Alert();
alert.Id = uo.Id;
string serializedForm = uo.Description;
if (String.IsNullOrEmpty(serializedForm))
{
return(alert);
}
if (!Lex.Contains(serializedForm, "<Alert"))
{
return(DeserializeHeaderOld(uo));
}
XmlMemoryStreamTextReader mstr = new XmlMemoryStreamTextReader(serializedForm);
XmlTextReader tr = mstr.Reader;
tr.Read(); // get CondFormat element
tr.MoveToContent();
if (!Lex.Eq(tr.Name, "Alert"))
{
throw new Exception("\"Alert\" element not found");
}
XmlUtil.GetStringAttribute(tr, "Owner", ref alert.Owner);
XmlUtil.GetIntAttribute(tr, "QueryObjId", ref alert.QueryObjId);
XmlUtil.GetIntAttribute(tr, "Interval", ref alert.Interval);
XmlUtil.GetStringAttribute(tr, "MailTo", ref alert.MailTo);
XmlUtil.GetDateAttribute(tr, "LastCheck", ref alert.LastCheck);
XmlUtil.GetIntAttribute(tr, "LastCheckElapsedTime", ref alert.LastCheckExecutionTime);
XmlUtil.GetIntAttribute(tr, "NewCompounds", ref alert.NewCompounds);
XmlUtil.GetIntAttribute(tr, "ChangedCompounds", ref alert.ChangedCompounds);
XmlUtil.GetIntAttribute(tr, "NewRows", ref alert.NewRows);
XmlUtil.GetIntAttribute(tr, "TotalRows", ref alert.TotalRows);
XmlUtil.GetIntAttribute(tr, "TotalCompounds", ref alert.TotalCompounds);
XmlUtil.GetBoolAttribute(tr, "CheckTablesWithCriteriaOnly", ref alert.CheckTablesWithCriteriaOnly);
XmlUtil.GetDateAttribute(tr, "LastNewData", ref alert.LastNewData);
XmlUtil.GetBoolAttribute(tr, "HighlightChangedCompounds", ref alert.HighlightChangedCompounds);
XmlUtil.GetBoolAttribute(tr, "RunImmediately", ref alert.RunImmediately);
XmlUtil.GetStringAttribute(tr, "Days", ref alert.Days);
XmlUtil.GetIntAttribute(tr, "DayInterval", ref alert.DayInterval);
XmlUtil.GetDateAttribute(tr, "StartTime", ref alert.StartTime);
alert.StartTime = GetLocalFromEasternStandardTime(alert.StartTime);
XmlUtil.GetStringAttribute(tr, "Pattern", ref alert.Pattern);
if (string.IsNullOrEmpty(alert.Pattern))
{
alert.Pattern = PatternEnum.Daily.ToString();
}
if (!tr.IsEmptyElement)
{
tr.Read(); // move to Export options or end of Alert element
tr.MoveToContent();
if (tr.NodeType == XmlNodeType.Element && Lex.Eq(tr.Name, "ResultsFormat"))
{
alert.ExportParms = ResultsFormat.Deserialize(tr);
tr.Read(); // get Alert end element
tr.MoveToContent();
}
if (!Lex.Eq(tr.Name, "Alert") || tr.NodeType != XmlNodeType.EndElement)
{
throw new Exception("Alert.Deserialize - Expected Alert end element");
}
}
mstr.Close();
double daysSinceLastCheckwithDecimal = (alert.LastCheck == DateTime.MinValue) ? alert.Interval : (DateTime.Now - alert.LastCheck).TotalDays;
double daysSinceNewDatawithDecimal = (alert.LastNewData == DateTime.MinValue) ? 0 : (DateTime.Now - alert.LastNewData).TotalDays;
//Round these calculations so .5 days will become 1 day, effectively 12 hours or more will count as a whole day.
alert.DaysSinceLastCheck = (int)Math.Round(daysSinceLastCheckwithDecimal, MidpointRounding.AwayFromZero);
alert.DaysSinceNewData = (int)Math.Round(daysSinceNewDatawithDecimal, MidpointRounding.AwayFromZero);
//DebugLog.Message("Alert: " + alert.Id + " daysSinceLastCheckwithDecimal: " + daysSinceLastCheckwithDecimal);
//DebugLog.Message("Alert: " + alert.Id + " new DaysSinceLastCheck: " + alert.DaysSinceLastCheck);
//DebugLog.Message("Alert: " + alert.Id + " daysSinceNewDatawithDecimal: " + daysSinceNewDatawithDecimal);
//DebugLog.Message("Alert: " + alert.Id + " DaysSinceNewData: " + alert.DaysSinceNewData);
return(alert);
}
static bool ContainsPriv(string content, string s)
{
s = "<" + s + ">";
return(Lex.Contains(content, s));
}
/// <summary>
/// Do setup in preparation for decompose
/// </summary>
/// <param name="qt"></param>
/// <param name="q"></param>
public void PrepareForDecompose(
QueryTable qt,
Query q)
{
throw new NotImplementedException();
#if false
Stopwatch sw = Stopwatch.StartNew();
MetaTable mt = qt.MetaTable;
QueryColumn qc = qt.GetQueryColumnByName("core");
if (qc == null)
{
throw new UserQueryException("Core column not defined in rgroup_decomposition table");
}
string molfile = qc.MolString;
if (molfile == null || molfile == "")
{ // core not defined in Rgroup decomposition table, try to get from structure search in rest of query
foreach (QueryTable qt3 in q.Tables)
{
if (!qt3.MetaTable.IsRootTable)
{
continue;
}
MetaColumn mc3 = qt3.MetaTable.FirstStructureMetaColumn;
if (mc3 != null)
{
QueryColumn qc3 = qt3.GetQueryColumnByName(mc3.Name);
molfile = qc3.MolString;
break;
}
}
}
if (molfile == null || molfile == "")
{
throw new UserQueryException("R-group decomposition core structure is not defined");
}
bool allowHydrogenSubstituents = true;
qc = qt.GetQueryColumnByName("AllowHydrogenSubstituents");
if (Lex.Contains(qc?.Criteria, "'N'"))
{
allowHydrogenSubstituents = false; // set to false if "no" criteria specified
}
TerminateOptionString = "First mapping";
bool allowMultipleCoreMappings = false;
qc = qt.GetQueryColumnByName("Terminate_Option");
if (qc != null && qc.Criteria != "")
{
ParsedSingleCriteria psc = MqlUtil.ParseSingleCriteria(qc.Criteria);
TerminateOptionString = psc.Value;
allowMultipleCoreMappings = Lex.Contains(TerminateOptionString, "All");
}
MoleculeMx cs = new MoleculeMx(MoleculeFormat.Molfile, molfile);
cs.GetCoreRGroupInfo(out RgCounts, out RgTotalCount); // need to redefine these
RGroupDecomp.Initialize();
RGroupDecomp.SetAlignStructuresToCore(true);
RGroupDecomp.SetAllowMultipleCoreMappings(allowMultipleCoreMappings);
RGroupDecomp.SetIncludeHydrogenFragments(allowHydrogenSubstituents);
if (DebugMx.True) // debug
{
String coreSmiles = "[R1]c1cn2c3c(c1= O)cc(c(c3SC(C2)[R4])[R3])[R2]";
string coreChime = "CYAAFQwAUewQeV58YHemfM^EQqPRfIYlJGEkx6M7e4db95jjK5HrNFVP2e1qHphWPL98KvcvrsF7bP9bRcW4QH$si9PXkkuwre6Q5UkHZjciQqeAKVLSHNAeQTAMlkiXEBD$BePpbNQCPD3BkklFEaQqwokeI$FwUoS5cAixQXkMbLTWDaAK7t7cOkSmt3RhwQedbrba6OHKBq3OF4Dhlz$0BfLeKCUUo8ixle176M2aIzXUccTOU8Xy8ARwE3bTyMfjuI3UunZceJf4iZELvsj3PX2MHZG73baUvQGS4DaxUaBGps81PPiDljfvxwFv8OfdOyIRlOBeuEAvk2rT9SRT6oMZIV6UtLFvmCHdwKnu9WtrfV1rEctydNUVxW4qKVlV0rZtpK1oZXuKcv6WVdl6r2hrjVLxBhblTVKO7w1qGRoziquOnPQkKd9H4EQfV0rP6mzI8Au8ulti2fu3YKB94lPXftPGbwr5yA";
IMolLib coreMol = MolLibFactory.NewMolLib(MoleculeFormat.Molfile, molfile);
coreChime = MoleculeMx.MolfileStringToChimeString(molfile);
molfile = coreMol.MolfileString;
}
CoreMolecule = CdkMol.Util.MolfileStringToMolecule(molfile);
RGroupDecomp.SetCoreStructure(CoreMolecule, false);
CoreChemicalStructure = new MoleculeMx(MoleculeFormat.Molfile, molfile);
StrMatcher = null;
int msTime = (int)sw.ElapsedMilliseconds;
if (RGroupDecomp.Debug)
{
DebugLog.Message("Time(ms): " + msTime);
}
return;
#endif
}
/// <summary>
/// Open the specified target
/// </summary>
/// <param name="mtn"></param>
public static void OpenMetaTreeNode(
MetaTreeNode mtn)
{
UserObject uo;
string tok;
int i1;
if (mtn == null)
{
return;
}
MetaTreeNodeType nodeType = mtn.Type;
string target = mtn.Target;
//if (!Permissions.UserHasReadAccess(SS.I.UserName, target))
//{
// MessageBoxMx.ShowError("You are not authorized to open: " + mtn.Label);
// return;
//}
if (nodeType == MetaTreeNodeType.MetaTable || // data table types
nodeType == MetaTreeNodeType.CalcField ||
nodeType == MetaTreeNodeType.CondFormat ||
nodeType == MetaTreeNodeType.Annotation ||
nodeType == MetaTreeNodeType.ResultsView)
{
QbUtil.CallCurrentProcessTreeItemOperationMethod("Open", target);
}
else if (MetaTreeNode.IsFolderNodeType(nodeType))
{
if (Lex.StartsWith(target, "USERDATABASE_")) // edit a user compound database
{
uo = ParseAndReadUserObject(target);
if (uo == null)
{
return;
}
UserData.OpenExistingUserDatabase(uo);
}
}
else if (nodeType == MetaTreeNodeType.Url)
{ // open url or execute click function
if ((i1 = Lex.IndexOf(target, "ClickFunction")) >= 0)
{
string cmd = target.Substring(i1 + "ClickFunction".Length + 1); // get function name
ClickFunctions.Process(cmd, null);
}
else if (Lex.Contains(target, "SpotfireWeb")) // link to Spotfire webplayer
{
SpotfireLinkUI.OpenLink(target);
}
else
{
SystemUtil.StartProcess(target); // open in default user browser
}
}
else if (nodeType == MetaTreeNodeType.Action)
{ // execute action
return; // CommandLineControl.Execute(mtn.Target);
}
else if (nodeType == MetaTreeNodeType.CnList) // open list
{
uo = ParseAndReadUserObject(target);
if (uo == null)
{
return;
}
tok = uo.InternalName;
CidListEditor.Edit(tok);
}
else if (nodeType == MetaTreeNodeType.Query) // open query
{
uo = ParseAndReadUserObject(target);
if (uo == null)
{
return;
}
if (uo.Type == UserObjectType.Query) // normal query
{
tok = uo.InternalName;
string nextCommand = QbUtil.OpenQuery(tok);
while (!(String.IsNullOrEmpty(nextCommand)))
{
nextCommand = CommandExec.ExecuteCommand(nextCommand);
}
}
else if (uo.Type == UserObjectType.MultiTable) // multitable query
{
QbUtil.AddAndRenderTables(target);
}
}
else if (nodeType == MetaTreeNodeType.Library)
{
CommandExec.ExecuteCommandAsynch("ContentsViewLibAsList " + mtn.Name);
}
}
/// <summary>
/// Handle a click on a link to a 3D structure & open in Vida
/// If clicked from an XtraGrid give the user a range of options for the data
/// to be exported. If clicked from a HTML page give limited options.
/// </summary>
/// <param name="mtName"></param>
/// <param name="mcName"></param>
/// <param name="url"></param>
public void ClickFunction(
string mtName,
string mcName,
string url)
{
ResultsFormatter fmtr = null;
ResultsField rfld = null;
//DataRowMx dr;
StringMx sx;
StreamWriter sw;
int markedCount = 0;
string densityMapUrl = null;
string target = null;
_currentMetaTable = mtName;
_currentPdbColumnName = mcName;
IncludeElectronDensityPyMol.Checked = false;
MetaTable mt = MetaTableCollection.Get(mtName);
if (mt == null)
{
return;
}
MetaColumn mc = mt.GetMetaColumnByName(mcName);
if (mc == null)
{
return;
}
_xRay2Request = Lex.Contains(mtName, "XRay2"); // newer XRay2 database table?
_urlFileName = Path.GetFileName(url); // extract file name from url
QueryManager qm = ClickFunctions.CurrentClickQueryManager;
if (qm != null)
{
Query q = qm.Query;
ResultsFormat rf = qm.ResultsFormat;
fmtr = qm.ResultsFormatter;
rfld = rf.GetResultsField(mc);
if (rfld == null)
{
return;
}
QueryTable qt = q.GetQueryTableByNameWithException(mtName);
_qcProtein = qt.GetQueryColumnByNameWithException(mcName);
if (_xRay2Request) // newer XRay2 database
{
string mapUrl = "";
if (mcName == "ALIGNED_SPLIT_COMPLEX_URL")
{
mapUrl = "ALIGNED_SPLIT_MAP_URL";
}
else if (mcName == "ALIGNED_FULL_COMPLEX_URL")
{
mapUrl = "ALIGNED_FULL_MAP_URL";
}
else if (mcName == "ORIGINAL_PDB_URL")
{
mapUrl = "ORIGINAL_MAP_URL";
} //{ mapUrl = "ORIGINAL_MAP_URL"; }
_qcDensity = qt.GetQueryColumnByName(mapUrl); //("ALIGNED_SPLIT_MAP_URL");
if (_qcDensity != null && !_qcDensity.Selected)
{
_qcDensity = null;
}
_qcTarget = qt.GetQueryColumnByName("primary_gene_name_alias");
if (_qcTarget != null && !_qcTarget.Selected)
{
_qcTarget = null;
}
}
if (_qcDensity != null)
{
// if there is a density map url located in the density column, enable the PyMol CheckEdit
DataRowMx dr = qm.DataTable.Rows[qm.MoleculeGrid.LastMouseDownCellInfo.DataRowIndex];
densityMapUrl = Lex.ToString(dr[_qcDensity.VoPosition]);
}
else
{
// user did not select the map column, try to retrieve the XRay1 or Xray2 density map url fromt he metatable
densityMapUrl = _xRay2Request ? GetXray2DensityMapUrl(url, qt.MetaTable.Name, mcName) : GetXray1DensityMapUrl(url, qt.MetaTable.Name);
}
// default checkbox to false so user does not load electron density maps everytime, since these take
// extra time to load.
IncludeElectronDensityPyMol.Checked = false;
IncludeElectronDensityPyMol.Enabled = !string.IsNullOrEmpty(densityMapUrl);
if (_qcProtein == null && _qcDensity == null)
{
throw new Exception("Neither the PDB nor the MAP column is selected in the query");
}
markedCount = fmtr.MarkedRowCount;
int unmarkedCount = fmtr.UnmarkedRowCount;
if (markedCount == 0 || unmarkedCount == 0) // if no specific selection assume user wants single structure
{
ExportSingle.Checked = true;
FileName.Text = _urlFileName;
}
else
{
ExportMarked.Checked = true; // assume wants marked structures
}
ExportMarked.Enabled = true;
}
else // simple setup for click from HTML display
{
ExportSingle.Checked = true;
ExportMarked.Enabled = false;
FileName.Text = _urlFileName;
densityMapUrl = GetXray2DensityMapUrl(url, _currentMetaTable, mcName);
target = GetTarget(url, _currentMetaTable, mcName);
////IncludeProtein.Enabled = IncludeElectronDensityEnabled = false;
////if (Lex.Eq(mcName, "bsl_xray_cmplx_url"))
//// IncludeProtein.Checked = true;
////else if (Lex.Eq(mcName, "bsl_xray_edensity_url"))
//// IncludeElectronDensityChecked = true;
}
if (mcName == "ALIGNED_SPLIT_MAP_URL" || mcName == "ALIGNED_FULL_MAP_URL" || mcName == "ORIGINAL_MAP_URL") // not viewable fileds
{
DisablePymol();
DisableMoe();
ExportToFile.Enabled = ExportToFile.Checked = true;
}
else if (mcName == "ALIGNED_FULL_COMPLEX_URL" || mcName == "ORIGINAL_PDB_URL" || mcName == "ALIGNED_SPLIT_COMPLEX_URL") // viewable by PyMol
{
EnableMoe();
EnablePymol();
ExportToFile.Enabled = true;
ExportToFile.Checked = false;
}
else //everything else should be viewable by MOE
{
EnableMoe();
DisablePymol();
ExportToFile.Enabled = true;
ExportToFile.Checked = false;
}
DialogResult dlgRslt = ShowDialog(SessionManager.ActiveForm);
if (dlgRslt == DialogResult.Cancel)
{
return;
}
bool exportSingle = ExportSingle.Checked;
bool exportMarked = !exportSingle;
if (!IncludeElectronDensityPyMol.Checked)
{
densityMapUrl = null;
}
if (exportMarked) // see if reasonable count if exporting marked rows
{
string msg;
if (markedCount == 0)
{
msg = "No rows have been marked for export";
MessageBoxMx.Show(msg, "Mobius", MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
return;
}
if (markedCount > 10)
{
msg =
markedCount + " structures have been selected out export.\n" +
"Are you sure these are the structures you want to export?";
dlgRslt = MessageBoxMx.Show(msg, "Mobius", MessageBoxButtons.YesNoCancel, MessageBoxIcon.Question);
if (dlgRslt != DialogResult.Yes)
{
return;
}
}
}
// Export to PyMol (Schrodinger) - Collab with Paul Sprengeler and Ken Schwinn
// Relavant Files:
// 1. Plugin: CorpView.py (in Mobius config dir)
// 2. Script: CorpView.pml - Runs the plugin and then passes in the .csv file (in Mobius config dir)
// Expected content (note: <csv-file-name> gets replaced):
// import pymol
// pluginLocation = 'C:\Progra~1\PyMOL\PyMOL\modules\pmg_tk\startup\CorpView.py'
// cmd.do('run ' + pluginLocation)
// cmd.do('lv_create_environment')
// cmd.do('lv_import_mobius <csv-file-name>')
// cmd.do('lv_destroy_environment')
// 3. Csv file: PyMolBatchLoad.csv - Csv file in format expected by plugin (in Mobius temp dir)
if (ExportToPyMol.Checked)
{
ExportToPyMolMethod(url, densityMapUrl, target, qm);
}
else if (ExportToMOE.Checked) // Export to MOE
{
ExportToMOEMethod(url, qm, fmtr, rfld);
}
else
{
ExportToFilesMethod(url, qm, fmtr, rfld);
}
}
/// <summary>
/// ExportToPyMolMethod
/// </summary>
/// <param name="url"></param>
/// <param name="qm"></param>
void ExportToPyMolMethod(
string url,
string densityMapUrl,
string target,
QueryManager qm)
{
StreamWriter sw;
string rec, msg, scriptSourceFile, pluginSourceFile, script;
bool includeProtein = true; // always include protein
//bool includeElectronDensity = IncludeElectronDensityPyMol.Checked;
if (!IncludeElectronDensityPyMol.Checked)
{
_qcDensity = null;
}
pluginSourceFile = CommonConfigInfo.MiscConfigDir + @"\CorpView.py"; // the PyMOL plugin
CopyToReadLockedFile(pluginSourceFile, CommonConfigInfo.MiscConfigDir + @"\CorpView2.py"); // move CorpView2.py to CorpView.py
if (!File.Exists(pluginSourceFile))
{
throw new Exception("Plugin file not found: " + pluginSourceFile);
}
scriptSourceFile = CommonConfigInfo.MiscConfigDir + @"\CorpView.pml"; // the script that starts pymol & hands it the .csv file
CopyToReadLockedFile(scriptSourceFile, CommonConfigInfo.MiscConfigDir + @"\CorpView2.pml");
if (!File.Exists(scriptSourceFile))
{
throw new Exception("Script file not found: " + scriptSourceFile);
}
string csvFile = ClientDirs.TempDir + @"\PyMolBatchLoad.csv"; // the .csv file to write
WriteCsvFile(csvFile, ExportSingle.Checked, _qcProtein, _qcDensity, _qcTarget, qm, url, densityMapUrl, target);
//qm.Query.Tables[0].MetaTable.Name
try // Read the CorpView2.pml that gets edited.
{
StreamReader sr = new StreamReader(scriptSourceFile);
script = sr.ReadToEnd();
sr.Close();
}
catch (Exception ex)
{ throw new Exception("Error reading " + scriptSourceFile + ": " + ex.Message); }
// Get the path to the plugin file
string pluginFile = null;
Lex lex = new Lex("=");
lex.OpenString(script);
while (true)
{
string tok = lex.Get();
if (tok == "")
{
break;
}
if (Lex.Ne(tok, "pluginLocation"))
{
continue;
}
pluginFile = lex.Get();
if (pluginFile == "=")
{
pluginFile = lex.Get();
}
pluginFile = Lex.RemoveSingleQuotes(pluginFile);
}
if (pluginFile == null)
{
throw new Exception("Can't find definition of plugin location");
}
// Get the proper plugin directory
string pluginFolder = Path.GetDirectoryName(pluginFile);
if (!Directory.Exists(pluginFolder))
{
string pluginFile2 = pluginFile;
pluginFile2 = Lex.Replace(pluginFile2, "Progra~1", "Progra~2"); // Win7 x86 folder using 8.3 names
pluginFile2 = Lex.Replace(pluginFile2, "Program Files", "Program Files (x86)"); // Win7 x86 folder with regular names
string pluginFolder2 = Path.GetDirectoryName(pluginFile2);
if (!Directory.Exists(pluginFolder2))
{
DebugLog.Message("Can't find PyMOL plugin folder: " + pluginFolder);
MessageBox.Show("Can't find PyMol plugin folder " + pluginFolder + ".\rContact Pymol Support team.");
Progress.Hide();
return;
}
script = Lex.Replace(script, pluginFile, pluginFile2); // substitute proper plugin file name in script
pluginFile = pluginFile2;
}
bool update = false;
bool pyMolInstalled = File.Exists(pluginFile);
ClientLog.Message("Checking for PyMol installation...");
if (pyMolInstalled)
{
DateTime dt1 = File.GetLastWriteTime(pluginSourceFile);
DateTime dt2 = File.GetLastWriteTime(pluginFile);
if (DateTime.Compare(dt1, dt2) > 0)
{
ClientLog.Message(" PyMol file is older than the Mobius version.");
update = true;
}
}
else
{
ClientLog.Message(" Could not find PyMol file: " + pluginFile);
update = true;
}
// Be sure the plugin is up to date
if (update)
{
try
{
File.Copy(pluginSourceFile, pluginFile, true); // copy CorpView.py to Pymol startup dir
}
catch (Exception ex)
{
ClientLog.Message(" Error copying CorpView.py to: " + pluginFile + ", " + ex.Message);
if (!pyMolInstalled)
{
MessageBox.Show("Unable to find Corp Plugin (CorpView.py) for Pymol.\rWindows 7 will not allow Mobius access to copy the plugin to your machine.\rContact Pymol Support team.");
Progress.Hide();
return;
}
}
}
DebugLog.Message("Error copying CorpView.py to: " + pluginFile);
// Plug the csv file name into the script
string csvFileNameParm = "<csv-file-name>";
if (!Lex.Contains(script, csvFileNameParm))
{
throw new Exception("<csv-file-name> not found in script");
}
string csvFileNameForScript = csvFile.Replace(@"\", "/"); // translate backslashes so they aren't interpreted as escapes
script = Lex.Replace(script, csvFileNameParm, csvFileNameForScript);
string scriptFile = ClientDirs.TempDir + @"\CorpView.pml";
sw = new StreamWriter(scriptFile);
sw.Write(script);
sw.Close();
Progress.Show("Passing data to PyMOL...");
try
{
//DebugLog.Message("startFile: " + startFile);
//DebugLog.Message("startArgs: " + startArgs);
Process p = Process.Start(scriptFile);
}
catch (Exception ex)
{
MessageBoxMx.ShowError("Failed to start PyMOL");
Progress.Hide();
return;
}
System.Threading.Thread.Sleep(3000); // leave message up a bit while PyMOL is starting/being activated
Progress.Hide();
}
/// <summary>
/// Execute query in preparation for retrieving rows
/// </summary>
/// <param name="parms"></param>
public override void ExecuteQuery(
ExecuteQueryParms eqp)
{
BufferedRows = new List <UnpivotedAssayResult>();
MultiTablePivotBrokerTypeData mpd = null;
MetaTable mt;
List <MultiDbAssayMetaBroker> mbList = null;
MultiDbAssayMetaBroker mb, mb2 = null;
UnpivotedAssayResult rr, rr2;
List <UnpivotedAssayResult> rrList = new List <UnpivotedAssayResult>(); // list of results summarized by target & result type
bool unpivotedTableIsFirst;
object[] vo;
string mtName = null;
int t0 = TimeOfDay.Milliseconds();
mt = eqp.QueryTable.MetaTable;
Dictionary <string, MultiTablePivotBrokerTypeData> mbsi = eqp.Qe.MetaBrokerStateInfo;
if (PivotInCode)
{
mpd = mbsi[MpGroupKey];
if (PivotInCode && mpd.MbInstances.Count == 1 && UnpivotedAssayResult.IsUnpivotedSummarizedMdbAssayTable(mt.Name))
{
PivotInCode = false; // don't multipivot if single unpivoted summary table
}
}
if (!PivotInCode) // if not multipivot then call generic broker
{
base.ExecuteQuery(eqp);
return;
}
if (mpd.FirstTableName != Qt.MetaTable.Name)
{
return; // retrieve data for all tables when we see first table
}
SetupSecondaryMetaBroker(eqp, mpd, out unpivotedTableIsFirst);
mb2 = SecondaryMetaBroker;
mpd.ClearBuffers();
// Retrieve data & store for associated metabrokers
if (mb2 == this)
{
base.ExecuteQuery(eqp); // execute with the base generic broker
}
else
{
mb2.ExecuteQuery(Eqp2); // use the secondary broker that was created
}
AssayDict dict = new AssayDict();
rr = new UnpivotedAssayResult();
int readCnt = 0;
bool includeResultDetail = MdbAssayVoMap.ResultDetailId.Voi >= 0;
while (true)
{
if (mb2 == this)
{
vo = base.NextRow(); // get data via generic broker
}
else
{
vo = mb2.NextRow(); // get data with secondary broker
}
if (vo == null)
{
break;
}
rr.FromValueObject(vo, mb2.MdbAssayVoMap); // parse values into a UnpivotedAssayResult
int rowsFetched = 0, vosCreated = 0;
for (int pup = 0; pup < 2; pup++) // first pass for unpivoted table, 2nd for pivoted by gene
{
//try
//{
if (pup == 0)
{
if (!unpivotedTableIsFirst)
{
continue; // if no unpivoted first table skip this
}
mtName = mpd.FirstTableName; // unpivoted table should be first
}
else // pivoted table
{
if (Lex.IsNullOrEmpty(rr.GeneSymbol))
{
continue; // skip if no target symbol
}
if (Lex.Contains(mpd.FirstTableName, "CORP")) // mapped to pivoted corp only table
{
mtName = MultiDbAssayDataNames.BasePivotTablePrefix + rr.GeneSymbol.ToUpper(); // name of table mapped to
}
else // combined tables
{
mtName = MultiDbAssayDataNames.CombinedPivotTablePrefix + rr.GeneSymbol.ToUpper();
}
}
//}
//catch (Exception ex) { ex = ex; }
mt = MetaTableCollection.Get(mtName);
if (mt == null)
{
continue;
}
if (!mpd.MbInstances.ContainsKey(mt.Name))
{
continue; // have row hash for broker?
}
int mbIdx = 0;
if (mpd.MbInstances[mtName] is MultiDbAssayMetaBroker)
{
mb = (MultiDbAssayMetaBroker)mpd.MbInstances[mtName]; // broker assoc w/table
}
else
{
mbList = (List <MultiDbAssayMetaBroker>)mpd.MbInstances[mtName];
mb = (MultiDbAssayMetaBroker)mbList[0];
}
while (true) // copy out for each metabroker for metatable
{
UnpivotedAssayResultFieldPositionMap voMap = mb.MdbAssayVoMap;
vo = rr.ToValueObject(mb.Qt.SelectedCount, voMap);
if (mb.MultipivotRowList == null)
{
mb.MultipivotRowList = new List <object[]>();
}
mb.MultipivotRowList.Add(vo);
if (mbList == null)
{
break; // single broker
}
mbIdx++; // go to next broker
if (mbIdx >= mbList.Count)
{
break; // at end of brokers?
}
mb = (MultiDbAssayMetaBroker)mbList[mbIdx];
}
} // tables to copy data to loop
} // row fetch loop
return;
}
