bool Save(bool prompt)
{
UserObject uo2;
if (!IsValidCalcField())
{
return(false);
}
if (!GetCalcFieldForm())
{
return(false);
}
if (prompt)
{
uo2 = UserObjectSaveDialog.Show("Save Calculated Field Definition", UoIn);
if (uo2 == null)
{
return(false);
}
}
else
{
uo2 = UoIn.Clone();
}
if (!UserObjectUtil.UserHasWriteAccess(uo2))
{ // is the user authorized to save this?
MessageBoxMx.ShowError("You are not authorized to save this calculated field");
return(false);
}
SessionManager.DisplayStatusMessage("Saving calculated field...");
string content = CalcField.Serialize();
uo2.Content = content;
//need the name of the folder to which the object will be saved
MetaTreeNode targetFolder = UserObjectTree.GetValidUserObjectTypeFolder(uo2);
if (targetFolder == null)
{
MessageBoxMx.ShowError("Failed to save your calculated field.");
return(false);
}
UserObjectDao.Write(uo2);
string tName = "CALCFIELD_" + uo2.Id.ToString();
QbUtil.UpdateMetaTableCollection(tName);
MainMenuControl.UpdateMruList(tName);
string title = "Edit Calculated Field - " + uo2.Name;
Text = title;
UoIn = uo2.Clone(); // now becomes input object
SessionManager.DisplayStatusMessage("");
return(true);
}
/// <summary>
/// Setup the form
/// </summary>
void Setup()
{
// Temporary surrogates for current and other temp lists that gets added to the preferred project
TempNodes = new List <MetaTreeNode>();
foreach (TempCidList tcl in SS.I.TempCidLists)
{
UserObject uo = new UserObject(UserObjectType.CnList);
uo.ParentFolder = SS.I.PreferredProjectId;
uo.ParentFolderType = (uo.ParentFolder.ToUpper().StartsWith("FOLDER_")) ? FolderTypeEnum.User : FolderTypeEnum.System;
uo.Id = tcl.Id;
uo.Name = "*" + tcl.Name;
uo.AccessLevel = UserObjectAccess.Private;
uo.Count = tcl.Count;
MetaTreeNode mtn = UserObjectTree.GetValidUserObjectTypeFolder(uo);
mtn = UserObjectTree.AddObjectToTree(uo);
ParentFolder = uo.ParentFolder;
TempNodes.Add(mtn);
}
ListTree1.FillTree(UserObjectType.CnList);
ListTree2.FillTree(UserObjectType.CnList);
StatusMessage.Caption = "";
return;
}
/// <summary>
/// Change the owner of a UserObject
/// </summary>
/// <param name="args"></param>
/// <returns></returns>
public static string ChangeOwner(
int objId,
string newOwner)
{
newOwner = newOwner.ToUpper();
UserObject uo = UserObjectDao.ReadHeader(objId);
if (uo == null)
{
return("User object not found: " + objId);
}
if (uo.Owner == newOwner)
{
return("This user object is already owned by " + newOwner);
}
if (!Security.IsAdministrator(SS.I.UserName) && Lex.Ne(uo.Owner, SS.I.UserName))
{
return("You're not authorized to change the owner of this user object");
}
if (!Security.CanLogon(newOwner))
{
return("Not a valid userId: " + newOwner);
}
UserInfo ui = Security.GetUserInfo(newOwner);
string msg = "Are you sure you want to transfer ownership of " + Lex.AddDoubleQuotes(uo.Name) + "\n" +
"to " + ui.FullName + "?";
DialogResult dr = MessageBoxMx.Show(msg, "Change Owner", MessageBoxButtons.YesNoCancel, MessageBoxIcon.Question);
if (dr != DialogResult.Yes)
{
return("");
}
UserObject uo2 = uo.Clone();
uo2.Owner = newOwner;
UserObjectTree.GetValidUserObjectTypeFolder(uo2); // set valid parent folder
Permissions.UpdateAclForNewOwner(uo2, uo.Owner, newOwner); // Set the ACL to give us r/w access
uo2.Content = "ChangeOwner"; // indicate changing owner
if (UserObjectDao.ReadHeader(uo2) != null)
{
return("A user object with that name already exists for the specified new user");
}
UserObjectDao.UpdateHeader(uo2, false, false);
if (Data.InterfaceRefs.IUserObjectIUD != null)
{
Data.InterfaceRefs.IUserObjectIUD.UserObjectDeleted(uo); // remove from view
}
string newOwnerName = SecurityUtil.GetPersonNameReversed(newOwner);
return("Ownership of \"" + uo2.Name + "\" has been changed to " + newOwnerName);
}
/// <summary>
/// Save the SpotfireLink UserObject
/// </summary>
/// <param name="prompt"></param>
/// <returns></returns>
bool Save(bool prompt)
{
UserObject uo2;
if (!IsValidSpotfireLink())
{
return(false);
}
if (!GetSpotfireLinkForm())
{
return(false);
}
if (prompt)
{
uo2 = UserObjectSaveDialog.Show("Save Spotfire link Definition", UoIn);
if (uo2 == null)
{
return(false);
}
}
else
{
uo2 = UoIn.Clone();
}
uo2.Content = SpotfireViewProps.Serialize();
if (!UserObjectUtil.UserHasWriteAccess(uo2))
{ // is the user authorized to save this?
MessageBoxMx.ShowError("You are not authorized to save this Spotfire link");
return(false);
}
SessionManager.DisplayStatusMessage("Saving Spotfire link...");
//need the name of the folder to which the object will be saved
MetaTreeNode targetFolder = UserObjectTree.GetValidUserObjectTypeFolder(uo2);
if (targetFolder == null)
{
MessageBoxMx.ShowError("Failed to save your Spotfire link.");
return(false);
}
UserObjectDao.Write(uo2);
MainMenuControl.UpdateMruList(uo2.InternalName);
string title = "Edit Spotfire Link - " + uo2.Name;
Text = title;
UoIn = uo2.Clone(); // now becomes input object
SessionManager.DisplayStatusMessage("");
return(true);
}
/// <summary>
/// Create an annotation table given its metatable and user object
/// </summary>
/// <param name="mt"></param>
/// <param name="uo"></param>
public static void CreateAnnotationTable(
MetaTable mt,
UserObject uo)
{
uo.Type = UserObjectType.Annotation; // be sure type is set
uo.Content = mt.Serialize(); // serialize the metatable to the user object
UserObjectTree.GetValidUserObjectTypeFolder(uo);
UserObjectDao.Write(uo); // write the user object
MetaTableCollection.UpdateGlobally(mt); // update map with modified metatable
return;
}
/// <summary>
/// Save the specified list object
/// </summary>
/// <returns></returns>
public static UserObject SaveList(
CidList list,
string caption,
bool saveToTempList,
string tempListName)
{
UserObject uo = null;
String name, txt;
uo = new UserObject(UserObjectType.CnList);
if (saveToTempList)
{
if (Lex.IsNullOrEmpty(tempListName))
{
tempListName = InputBoxMx.Show("Enter the name of the temporary list to be saved to:", caption);
}
if (Lex.IsNullOrEmpty(tempListName))
{
return(null);
}
uo.Owner = SS.I.UserName;
uo.ParentFolder = UserObject.TempFolderName;
uo.Name = tempListName;
}
else
{
uo = UserObjectSaveDialog.Show(caption, uo); // save to permanent list
}
if (uo == null)
{
return(null);
}
if (!uo.IsTempObject) // assign valid folder unless current list
{
UserObjectTree.GetValidUserObjectTypeFolder(uo);
}
SessionManager.DisplayStatusMessage("Saving List " + uo.Name + "...");
list.UserObject = uo;
int rc = Write(list);
MainMenuControl.UpdateMruList(uo.InternalName);
SessionManager.DisplayStatusMessage("");
return(uo);
}
/// <summary>
/// Create an annotation table from a DataTable
/// </summary>
/// <param name="fullyQualifiedName">Fully qualified name to assign to table</param>
/// <param name="dataTable">DataTable containing table definition & data</param>
/// <param name="showProgress">Display dialog box showing progress of creation</param>
/// <returns>Internal name assigned to annotation table (ANNOTATION_12345)</returns>
public static MetaTable CreateAnnotationTable(
string fullyQualifiedName,
DataTable dataTable,
bool showProgress)
{
List <AnnotationVo> voList = new List <AnnotationVo>();
AnnotationVo avo;
if (dataTable == null)
{
DebugMx.ArgException("DataTable is null");
}
if (dataTable.Columns.Count == 0)
{
DebugMx.ArgException("No DataColumns are defined");
}
if (dataTable.Columns[0].DataType != typeof(CompoundId))
{
DebugMx.ArgException("The first column must be of type CompoundId");
}
if (showProgress)
{
Progress.Show("Creating annotation table...");
}
AnnotationDao aDao = new AnnotationDao();
UserObject auo = UserObjectUtil.ParseInternalUserObjectName(fullyQualifiedName);
auo.Type = UserObjectType.Annotation;
UserObjectTree.GetValidUserObjectTypeFolder(auo);
UserObject auo2 = UserObjectDao.Read(auo); // see if there already
MetaTable oldMt = null;
if (auo2 == null) // get new identifier
{
auo.Id = UserObjectDao.GetNextId(); // id to store table under
}
else // reuse identifier
{
auo.Id = auo2.Id; // copy it over
aDao.DeleteTable(auo.Id); // delete any existing data
string oldMtName = "ANNOTATION_" + auo2.Id;
oldMt = MetaTableCollection.Get(oldMtName);
}
MetaTable mt = new MetaTable();
mt.MetaBrokerType = MetaBrokerType.Annotation;
mt.Name = "ANNOTATION_" + auo.Id; // name table by uo
mt.Label = auo.Name;
mt.Code = auo.Id.ToString(); // code for the metatable
int mtCode = auo.Id;
if (dataTable.ExtendedProperties.ContainsKey("ParentTableName"))
{
mt.Parent = MetaTableCollection.Get((string)dataTable.ExtendedProperties["ParentTableName"]);
}
foreach (DataColumn dc in dataTable.Columns)
{
MetaColumn mc = new MetaColumn();
mc.MetaTable = mt;
mc.Name = dc.ColumnName;
MetaColumn oldMc = null;
if (oldMt != null)
{
oldMc = oldMt.GetMetaColumnByName(mc.Name); // see if column name exists
}
if (oldMc != null && oldMc.ResultCode != "") // use any existing code
{
mc.ResultCode = oldMc.ResultCode;
}
else
{
mc.ResultCode = aDao.GetNextIdLong().ToString();
}
if (dc.Caption != null)
{
mc.Label = dc.Caption;
}
else
{
mc.Label = mc.Name;
}
if (dc.DataType == typeof(CompoundId))
{
mc.DataType = MetaColumnType.CompoundId;
if (dc.ExtendedProperties.ContainsKey("StorageType") && dc.ExtendedProperties["StorageType"] is MetaColumnType &&
((MetaColumnType)dc.ExtendedProperties["StorageType"]) == MetaColumnType.String)
{
mc.ColumnMap = "EXT_CMPND_ID_TXT"; // text column
}
else
{
mc.ColumnMap = "EXT_CMPND_ID_NBR"; // numeric column otherwise
}
}
else if (dc.DataType == typeof(int) || dc.DataType == typeof(Int16) || dc.DataType == typeof(Int32))
{
mc.DataType = MetaColumnType.Integer;
}
else if (dc.DataType == typeof(float) || dc.DataType == typeof(double))
{
mc.DataType = MetaColumnType.Number;
}
else if (dc.DataType == typeof(QualifiedNumber))
{
mc.DataType = MetaColumnType.QualifiedNo;
}
else if (dc.DataType == typeof(string))
{
mc.DataType = MetaColumnType.String;
}
else if (dc.DataType == typeof(DateTime))
{
mc.DataType = MetaColumnType.Date;
}
else if (dc.DataType == typeof(MoleculeMx))
{
mc.DataType = MetaColumnType.Structure;
}
else
{
throw new Exception("Invalid data type " + dc.DataType.ToString());
}
if (dc.ExtendedProperties.ContainsKey("DisplayLevel"))
{
mc.InitialSelection = (ColumnSelectionEnum)dc.ExtendedProperties["DisplayLevel"];
}
if (dc.ExtendedProperties.ContainsKey("DisplayWidth"))
{
mc.Width = (float)dc.ExtendedProperties["DisplayWidth"];
}
if (dc.ExtendedProperties.ContainsKey("DisplayFormat"))
{
mc.Format = (ColumnFormatEnum)dc.ExtendedProperties["DisplayFormat"];
}
if (dc.ExtendedProperties.ContainsKey("Decimals"))
{
mc.Decimals = (int)dc.ExtendedProperties["Decimals"];
}
mt.MetaColumns.Add(mc);
}
ToolHelper.CreateAnnotationTable(mt, auo);
aDao.BeginTransaction(); // insert all data in single transaction
if (showProgress)
{
Progress.Show("Writing data to annotation table...");
}
int t1 = TimeOfDay.Milliseconds();
int writeCount = 0;
foreach (DataRow dr in dataTable.Rows)
{
if (dr.IsNull(0))
{
continue; // shouldn't happen
}
string key = dr[0].ToString();
key = CompoundId.NormalizeForDatabase(key, mt.Root);
long rslt_grp_id = aDao.GetNextIdLong();
for (int ci = 1; ci < dataTable.Columns.Count; ci++) // do columns after key
{
if (dr.IsNull(ci))
{
continue;
}
DataColumn dc = dataTable.Columns[ci];
MetaColumn mc = mt.MetaColumns[ci];
int mcCode = Int32.Parse(mc.ResultCode);
avo = new AnnotationVo();
avo.rslt_grp_id = rslt_grp_id; // keep row together
if (dc.DataType == typeof(CompoundId)) // shouldn't happen since key processed already
{
avo.rslt_val_txt = dr[ci].ToString();
}
else if (dc.DataType == typeof(int) || dc.DataType == typeof(Int16) || dc.DataType == typeof(Int32) ||
dc.DataType == typeof(float) || dc.DataType == typeof(double))
{
avo.rslt_val_nbr = (double)dr[ci];
}
else if (dc.DataType == typeof(QualifiedNumber))
{
QualifiedNumber qn = (QualifiedNumber)dr[ci];
avo.rslt_val_nbr = qn.NumberValue;
avo.rslt_val_prfx_txt = qn.Qualifier;
avo.rslt_val_txt = qn.TextValue;
avo.dc_lnk = qn.Hyperlink;
}
else if (dc.DataType == typeof(string))
{
avo.rslt_val_txt = dr[ci].ToString();
}
else if (dc.DataType == typeof(DateTime))
{
avo.rslt_val_dt = (DateTime)dr[ci];
}
else if (dc.DataType == typeof(MoleculeMx))
{
avo.rslt_val_txt = dr[ci].ToString();
}
AddAnnotationVoToList(avo, key, mtCode, mcCode, voList);
}
writeCount++;
if (Progress.CancelRequested) // check for cancel
{
aDao.Commit();
aDao.Insert(voList);
voList.Clear();
aDao.Commit();
aDao.Dispose();
if (showProgress)
{
Progress.Hide();
}
MessageBoxMx.ShowError("Writing of annotation table cancelled.");
return(null);
}
int t2 = TimeOfDay.Milliseconds();
if (showProgress && t2 - t1 >= 1000)
{
t1 = t2;
Progress.Show("Writing data to annotation table " + writeCount.ToString() +
" of " + dataTable.Rows.Count.ToString() + " ...");
aDao.Insert(voList);
voList.Clear();
aDao.Commit();
}
}
aDao.Insert(voList);
voList.Clear();
aDao.Commit();
aDao.Dispose();
if (showProgress)
{
Progress.Hide();
}
return(mt); // return metatable name
}
/// <summary>
/// Right-click commands on objects in a tree
/// </summary>
/// <param name="command">The command to process</param>
/// <param name="mtn">MetaTreeNode</param>
/// <param name="uo">Any associated user object</param>
/// <param name="ctc">ContentsTreeControl</param>
/// <returns></returns>
public static bool ProcessCommonRightClickObjectMenuCommands(
string command,
MetaTreeNode mtn,
UserObject[] uoArray,
ContentsTreeControl ctc)
{
UserObject uo2;
string txt;
UserObject uo = null;
if (uoArray != null && uoArray.Length == 1)
{
uo = uoArray[0];
}
//if (mtn == null)
//{
// MessageBoxMx.ShowError("Operation is not allowed for this Database Contents node.");
// return true;
//}
if (Lex.Eq(command, "Cut"))
{
CopyCutDelete(command, uoArray, ctc, true, true);
}
else if (Lex.Eq(command, "Copy"))
{
CopyCutDelete(command, uoArray, ctc, true, false);
}
else if (Lex.Eq(command, "Paste"))
{
try
{
txt = Clipboard.GetText();
//uo2 = UserObject.Deserialize(txt);
uoArray = Deserialize(txt);
if (uoArray == null)
{
throw new Exception("Not a UserObject");
}
//if (uo2 == null) throw new Exception("Not a UserObject");
}
catch (Exception ex)
{
MessageBoxMx.ShowError("The clipboard does not contain a recognized user objects");
return(true);
}
foreach (var userObject in uoArray)
{
Progress.Show("Pasting " + userObject.Name + "...", UmlautMobius.String, false);
Permissions.UpdateAclForNewOwner(userObject, userObject.Owner, SS.I.UserName); // fixup the ACL for the new owner
userObject.Owner = SS.I.UserName;
userObject.ParentFolder = mtn.Name;
mtn = UserObjectTree.GetValidUserObjectTypeFolder(userObject);
for (int ci = 0; ; ci++) // find a name that's not used
{
UserObject uo3 = UserObjectDao.ReadHeader(userObject);
if (uo3 == null)
{
break;
}
if (ci == 0)
{
userObject.Name = "Copy of " + userObject.Name;
}
else if (ci == 1)
{
userObject.Name = Lex.Replace(userObject.Name, "Copy of ", "Copy (2) of ");
}
else
{
userObject.Name = Lex.Replace(userObject.Name, "Copy (" + ci + ") of ", "Copy (" + (ci + 1) + ") of ");
}
}
UserObject userObjectFinal = null;
if (UserObjectDao.ReadHeader(userObject.Id) != null) // create a deep clone if orignal object exists
{
userObjectFinal = DeepClone(userObject);
}
if (userObjectFinal == null)
{
userObjectFinal = userObject;
}
UserObjectDao.Write(userObjectFinal, userObjectFinal.Id); // write using the current id
Progress.Hide();
}
//if (ctc != null) // need to update form directly?
// UserObjectTree.RefreshSubtreeInTreeControl(uo2, ctc);
}
else if (Lex.Eq(command, "Delete"))
{
CopyCutDelete(command, uoArray, ctc, false, true);
}
else if (Lex.Eq(command, "Rename"))
{
if (!UserHasWriteAccess(uo))
{
MessageBoxMx.ShowError("You are not authorized to rename " + uo.Name);
return(true);
}
string newName = InputBoxMx.Show("Enter the new name for " + uo.Name,
"Rename", uo.Name);
if (newName == null || newName == "" || newName == uo.Name)
{
return(true);
}
if (!IsValidUserObjectName(newName))
{
MessageBoxMx.ShowError("The name " + newName + " is not valid.");
return(true);
}
uo2 = uo.Clone();
uo2.Name = newName;
uo2.Id = 0; // clear Id so not looked up by id
if (!Lex.Eq(newName, uo.Name) && UserObjectDao.ReadHeader(uo2) != null)
{
MessageBoxMx.ShowError(newName + " already exists.");
return(true);
}
uo2.Id = uo.Id;
UserObjectDao.UpdateHeader(uo2);
if (ctc != null)
{
UserObjectTree.UpdateObjectInTreeControl(uo, uo2, ctc);
}
}
else if (Lex.Eq(command, "MakePublic") ||
Lex.Eq(command, "MakePrivate"))
{
UserObjectAccess newAccess;
MetaTreeNode objFolder;
if (!UserHasWriteAccess(uo))
{
MessageBoxMx.ShowError("You are not authorized to make " + uo.Name +
((Lex.Eq(command, "MakePublic")) ? " public" : " private"));
return(true);
}
if (Lex.Eq(command, "MakePublic"))
{
if (uo.ParentFolder == "DEFAULT_FOLDER")
{
MessageBoxMx.ShowError("Items in the Default Folder cannot be made public");
return(true);
}
else
{
//check the folder id parentage to ensure that the current folder isn't a subfolder of the default folder
if (UserObjectTree.FolderNodes.ContainsKey(uo.ParentFolder))
{
objFolder = UserObjectTree.FolderNodes[uo.ParentFolder];
while (objFolder != null)
{
if (objFolder.Target == "DEFAULT_FOLDER")
{
MessageBoxMx.ShowError("Items in the Default Folder cannot be made public");
return(true);
}
objFolder = objFolder.Parent;
}
}
else
{
throw new Exception("Failed to recognize the folder that this object is in!");
}
}
newAccess = UserObjectAccess.Public;
}
else
{
//user folders cannot be made private if they contain public children
if (uo.Type == UserObjectType.Folder)
{
objFolder = UserObjectTree.BuildNode(uo);
if (UserObjectTree.FolderNodes.ContainsKey(objFolder.Target))
{
objFolder = UserObjectTree.FolderNodes[objFolder.Target];
for (int i = 0; i < objFolder.Nodes.Count; i++)
{
MetaTreeNode currentChild = (MetaTreeNode)objFolder.Nodes[i];
}
}
}
newAccess = UserObjectAccess.Private;
}
uo2 = UserObjectDao.Read(uo);
if (uo2 == null)
{
return(true);
}
if (uo2.AccessLevel == newAccess)
{
return(true); // no change
}
uo2.AccessLevel = newAccess;
UserObjectDao.UpdateHeader(uo2);
if (ctc != null) // need to update form directly?
{
UserObjectTree.RefreshSubtreeInTreeControl(uo2, ctc);
}
return(true);
}
else if (Lex.Eq(command, "ChangeOwner"))
{
string newOwner = InputBoxMx.Show("Enter the user name of the person to transfer ownership of " + Lex.AddDoubleQuotes(uo.Name) + " to:",
"Change Owner", "");
if (Lex.IsNullOrEmpty(newOwner))
{
return(true);
}
string result = UserObjectUtil.ChangeOwner(uo.Id, newOwner);
if (!Lex.IsNullOrEmpty(result))
{
MessageBoxMx.Show(result);
}
return(true);
}
else if (Lex.Eq(command, "Permissions")) // set object permissions
{
PermissionsDialog.Show(uo);
return(true);
}
else if (Lex.Eq(command, "ViewSource"))
{
uo = UserObjectDao.Read(uo);
if (uo == null)
{
return(true);
}
string ext = ".txt"; // default extension
if (uo.Type == UserObjectType.Query ||
uo.Type == UserObjectType.Annotation)
{
ext = ".xml";
}
string cFile = ClientDirs.TempDir + @"\Source" + ext;
StreamWriter sw = new StreamWriter(cFile);
sw.Write(uo.Content);
sw.Close();
SystemUtil.StartProcess(cFile); // show it
}
else
{
return(false); // command not recognized
}
return(true); // command recognized and processed
}
/// <summary>
/// Search button clicked, process input
/// </summary>
/// <returns></returns>
DialogResult ProcessInput()
{
CidList cidList = null;
StreamReader structureFileReader = null;
string qid; // query identifier, compoundId, file name or sdFile key value
QueryManager qm;
DataTableMx dt;
DataColumn dc;
DataRowMx dr;
//object[] dr; // if using Qe
DialogResult dlgRslt = DialogResult.OK;
Query q = null;
QueryTable qt = null;
QueryColumn simScoreQc, structQc; // query column containing latest query settings
MetaTable mt = null;
MetaColumn keyMc = null, structMc = null, dbSetMc = null, simScoreMc = null, mc;
MetaColumnType storageType;
string txt, tok;
if (DatabasesToSearch.Text == "")
{
MessageBoxMx.ShowError("Databases to search must be defined.");
DatabasesToSearch.Focus();
return(DialogResult.Cancel);
}
// Get list of databases
string[] dba = DatabasesToSearch.Text.Split(',');
List <MetaTable> tables = new List <MetaTable>();
foreach (string dbLabel0 in dba)
{
string dbLabel = dbLabel0.Trim();
RootTable dbInfo = RootTable.GetFromTableLabel(dbLabel);
if (dbInfo == null)
{
MessageBoxMx.ShowError("Can't find database " + DatabasesToSearch.Text);
DatabasesToSearch.Focus();
return(DialogResult.Cancel);
}
mt = MetaTableCollection.Get(dbInfo.MetaTableName);
if (mt == null)
{
MessageBoxMx.ShowError("Unable to locate parent structure table for database: " + DatabasesToSearch.Text);
DatabasesToSearch.Focus();
return(DialogResult.Cancel);
}
if (dbSetMc == null)
{
dbSetMc = mt.DatabaseListMetaColumn;
}
tables.Add(mt);
}
if (dbSetMc == null)
{
throw new Exception("\"Databases\" metacolumn not found for any of the databases to search");
}
// Validate other form values
RetrieveStructures = RetrieveMatchingStructures.Checked;
bool fromList = FromList.Checked;
int listCidsRead = 0;
int inputQueryCount = -1;
if (fromList) // using list, validate list name
{
if (SavedListUo == null)
{
MessageBoxMx.ShowError("Compound list must be defined.");
ListName.Focus();
return(DialogResult.Cancel);
}
cidList = CidListCommand.Read(SavedListUo);
if (cidList == null)
{
MessageBoxMx.ShowError("Error reading list.");
ListName.Focus();
return(DialogResult.Cancel);
}
inputQueryCount = cidList.Count;
}
else // Using SdFile, validate SdFile name
{
StructureFile = FileName.Text;
if (StructureFile == "")
{
MessageBoxMx.ShowError("File must be defined.");
FileName.Focus();
return(DialogResult.Cancel);
}
try { structureFileReader = new StreamReader(StructureFile); structureFileReader.Close(); }
catch (Exception ex)
{
MessageBoxMx.ShowError("Can't read file: " + Lex.Dq(StructureFile));
FileName.Focus();
return(DialogResult.Cancel);
}
keyField = KeyField.Text; // get key, blank to use name in 1st line
inputQueryCount = -1; // don't know how many queries unless we read the file (todo?)
}
tok = ResultsName.Text.Trim(); // name to store results under
if (tok == "")
{
MessageBoxMx.ShowError("A name for the results must be provided.");
ResultsName.Focus();
return(DialogResult.Cancel);
}
if (SubStruct.Checked)
{
Psc.SearchType = StructureSearchType.Substructure;
}
else if (Full.Checked)
{
Psc.SearchType = StructureSearchType.FullStructure;
}
else if (Similarity.Checked)
{
Psc.SearchType = StructureSearchType.MolSim;
}
else
{
throw new Exception("Unrecognized search type");
}
// Write initial log entries
SearchCount++;
string logFileName = ClientDirs.DefaultMobiusUserDocumentsFolder + @"\Multistructure Search " + SearchCount + ".txt";
if (!UIMisc.CanWriteFileToDefaultDir(logFileName))
{
return(DialogResult.Cancel);
}
LogStream = new StreamWriter(logFileName);
if (ResultsUo == null)
{
ResultsUo = new UserObject(UserObjectType.Annotation);
}
ResultsUo.Name = tok;
UserObjectTree.GetValidUserObjectTypeFolder(ResultsUo);
DateTime startTime = DateTime.Now;
WriteToLog("Multiple " + Psc.SearchType + " Search");
WriteToLog("Databases: " + DatabasesToSearch.Text);
WriteToLog("Date: " + startTime);
if (fromList)
{
WriteToLog("Input List: " + SavedListUo.Name);
}
else
{
WriteToLog("Input Structure File: " + StructureFile);
}
WriteToLog("Output List: " + ResultsUo.Name);
WriteToLog("Log File: " + logFileName);
WriteToLog("");
WriteToLog("Query, Match, Score");
int queryCount = 0;
int matchAtLeastOneCount = 0;
MoleculeMx queryStructure = null; // current structure being searched
CidList matchList = new CidList();
List <MatchData> matchData = new List <MatchData>();
if (FromFile.Checked) // open SdFile as required
{
structureFileReader = new StreamReader(StructureFile);
}
// Search of structures one at a time
while (true)
{
if (fromList) // get next structure from list
{
if (listCidsRead >= cidList.Count)
{
break;
}
qid = cidList[listCidsRead].Cid;
listCidsRead++;
if (qid.Trim() == "")
{
continue;
}
if (qid.ToLower().IndexOf(".mol") > 0 || qid.ToLower().IndexOf(".skc") > 0)
{ // file reference
if (!File.Exists(qid))
{
continue;
}
if (qid.ToLower().IndexOf(".mol") > 0)
{
queryStructure = MoleculeMx.ReadMolfile(qid);
}
else
{
queryStructure = MoleculeMx.ReadSketchFile(qid);
}
}
else
{
queryStructure = MoleculeUtil.SelectMoleculeForCid(qid);
}
if (queryStructure == null || queryStructure.AtomCount == 0)
{
continue; // oops
}
}
else // get next structure from input file
{
qid = null;
if (StructureFile.ToLower().EndsWith(".sdf"))
{
List <SdFileField> fList = SdFileDao.Read(structureFileReader);
if (fList == null) // end of sdFile
{
structureFileReader.Close();
break;
}
if (fList.Count == 0)
{
continue;
}
queryStructure = new MoleculeMx(MoleculeFormat.Molfile, fList[0].Data);
if (queryStructure == null || queryStructure.AtomCount == 0)
{
continue;
}
if (keyField != "") // key field specified?
{
qid = SdFileDao.GetDataField(fList, keyField);
}
else // get name from 1st line of molfile
{
string molFile = fList[0].Data;
int i1 = molFile.IndexOf("\n");
if (i1 == 0)
{
qid = "";
}
else
{
qid = molFile.Substring(0, i1).Trim();
}
}
if (string.IsNullOrEmpty(qid))
{
qid = SdFileDao.GetDataField(fList, "compound_id");
}
}
else // assume smiles file
{
string smiles = structureFileReader.ReadLine();
if (smiles == null) // end of sdFile
{
structureFileReader.Close();
break;
}
smiles = smiles.Trim();
if (smiles.Length == 0)
{
continue;
}
int i1 = smiles.IndexOf(","); // get any preceeding queryId
if (i1 < 0)
{
i1 = smiles.IndexOf("\t");
}
if (i1 >= 0)
{
qid = smiles.Substring(0, i1).Trim();
smiles = smiles.Substring(i1 + 1).Trim();
}
queryStructure = new MoleculeMx(MoleculeFormat.Smiles, smiles);
if (queryStructure == null || queryStructure.AtomCount == 0)
{
continue;
}
}
if (qid == null || qid.Trim() == "")
{
qid = (queryCount + 1).ToString(); // be sure we have a query id
}
}
queryCount++; // count the query
if (queryStructure == null || queryStructure.AtomCount == 0)
{
WriteToLog("Error converting specific structure " + queryCount.ToString() + ", " + qid);
continue;
}
queryStructure.RemoveStructureCaption(); // remove any Mobius-added caption
Psc.Molecule = queryStructure;
string msg =
"Searching Structure: " + queryCount.ToString();
if (inputQueryCount > 0)
{
msg += " of " + inputQueryCount.ToString();
}
msg += "\n" +
"Structures with one or more matches: " + matchAtLeastOneCount.ToString() + "\n" +
"Total Matches: " + matchList.Count.ToString();
Progress.Show(msg);
// Do the search over the list of databases
for (int ti = 0; ti < tables.Count; ti++)
{
mt = tables[ti];
q = new Query(); // build basic query
//q.SingleStepExecution = true; // do in single step (doesn't currently return sim score)
q.ShowStereoComments = false;
qt = new QueryTable(mt);
q.AddQueryTable(qt);
qt.SelectKeyOnly(); // start selecting desired cols
keyMc = mt.KeyMetaColumn;
structMc = mt.FirstStructureMetaColumn;
structQc = qt.GetQueryColumnByName(structMc.Name);
structQc.Selected = RetrieveStructures;
dbSetMc = mt.DatabaseListMetaColumn;
if (dbSetMc == null)
{
throw new Exception("\"Databases\" metacolumn not found for table: " + mt.Label);
}
QueryColumn dbSetQc = qt.GetQueryColumnByName(dbSetMc.Name);
dbSetQc.Selected = true; // select the database name
RootTable root = RootTable.GetFromTableName(mt.Name);
txt = " in (" + root.Label + ")";
dbSetQc.Criteria = dbSetMc.Name + txt;
dbSetQc.CriteriaDisplay = txt;
simScoreMc = mt.SimilarityScoreMetaColumn;
simScoreQc = null;
if (simScoreMc != null) // get sim score if it exists
{
simScoreQc = qt.GetQueryColumnByName(simScoreMc.Name);
simScoreQc.Selected = true; // return sim score
}
Psc.QueryColumn = structQc;
ParsedStructureCriteria psc2 = AdjustSearchForSmallWorldAsNeeded(Psc);
psc2.ConvertToQueryColumnCriteria(structQc); // format the QC for the structure search
DateTime t0 = DateTime.Now;
//QueryEngine qe = new QueryEngine();
//qe.NextRowsMin = 1000; // minimum number of rows to prefetch
//qe.NextRowsMax = -1; // maximum number of rows to prefetch
//qe.NextRowsMaxTime = 10000; // max time in milliseconds for next fetch
//qe.ExecuteQuery(q);
qm = new QueryManager();
try { dlgRslt = qm.ExecuteQuery(ref q); }
catch (Exception ex)
{
WriteToLog("Error searching structure: " + ex.Message + ", " + queryCount.ToString() + ", " + qid);
continue;
}
if (dlgRslt != DialogResult.OK)
{
return(dlgRslt);
}
double executeTime = TimeOfDay.Delta(ref t0);
int offset = qm.DataTableManager.KeyValueVoPos + 1;
//int offset = 0; // for QE
int keyPos = offset++;
int strPos = RetrieveStructures ? offset++ : -1;
int dbPos = offset++;
int simPos = offset++;
int fetchCnt = 0;
while (true)
{
dr = qm.NextRow();
//dr = qe.NextRow(); // for Qe
if (dr == null)
{
break;
}
fetchCnt++;
if (fetchCnt == 1)
{
matchAtLeastOneCount++; // number of queries that have at least one match
}
MatchData md = new MatchData();
md.Qno = queryCount;
md.Qid = qid;
if (RetrieveStructures)
{
md.Qstr = "Chime=" + queryStructure.GetChimeString();
}
CompoundId cid = CompoundId.ConvertTo(dr[keyPos]);
md.Mid = cid.Value;
if (RetrieveStructures)
{
MoleculeMx ms = MoleculeMx.ConvertTo(dr[strPos]);
if (!NullValue.IsNull(ms))
{
md.Mstr = "Chime=" + ms.GetChimeString();
}
}
StringMx db = StringMx.ConvertTo(dr[dbPos]);
if (!NullValue.IsNull(db))
{
md.Db = db.Value;
}
if (Psc.SearchType == StructureSearchType.MolSim)
{
NumberMx nex = NumberMx.ConvertTo(dr[simPos]);
if (!NullValue.IsNull(nex))
{
md.Score = nex.Value;
}
}
if (matchList.Contains(cid.Value)) // already have compound id as match for other query?
{
if (Psc.SearchType != StructureSearchType.MolSim)
{
continue; // if similarity search see if more similar
}
CidListElement le = matchList.Get(cid.Value); // reference current score
if (le.Tag > md.Score)
{
continue; // only replace if more similar
}
matchList.Remove(le.Cid); // remove from list
for (int mi = 0; mi < matchData.Count; mi++) // remove from data
{
if (matchData[mi].Mid == md.Mid)
{
matchData.RemoveAt(mi);
break;
}
}
}
matchList.Add(md.Mid);
matchList.Get(md.Mid).Tag = md.Score; // keep score in list
matchData.Add(md); // add to results
txt = md.Qid + ", " + md.Mid + ", " + md.Score.ToString();
WriteToLog(txt);
} // Fetch result loop
double fetchTime = TimeOfDay.Delta(ref t0);
} // DB loop
if (Progress.CancelRequested)
{
Progress.Hide();
MessageBoxMx.ShowError("Search cancelled.");
try { LogStream.Close(); } catch { }
return(DialogResult.Cancel);
}
} // key loop
CidListCommand.WriteCurrentList(matchList); // write the list of numbers
UsageDao.LogEvent("MultipleStructSearch");
txt =
"=== Multiple structure search complete ===\r\n\r\n" +
"Structures Searched: " + queryCount.ToString() + "\r\n";
txt +=
"Structures with one or more matches: " + matchAtLeastOneCount.ToString() + "\r\n" +
"Total Matches: " + matchList.Count.ToString() + "\r\n";
TimeSpan ts = DateTime.Now.Subtract(startTime);
ts = new TimeSpan(ts.Hours, ts.Minutes, ts.Seconds);
txt += "Total Time: " + ts + "\r\n\r\n";
WriteToLog("\r\n" + txt);
try { LogStream.Close(); } catch { }
if (matchList.Count == 0)
{
Progress.Hide();
MessageBoxMx.ShowError("No matches have been found.");
return(DialogResult.Cancel);
}
tok = "Matching compound ids";
if (Psc.SearchType == StructureSearchType.MolSim)
{
tok = "Similar compound ids";
}
txt += tok + " have been written to the current list: " + ResultsUo.Name + "\n" +
"Log file written to: " + logFileName + "\n\n" +
"Do you want to view the match results?";
DialogResult dRslt = MessageBoxMx.Show(txt, "Multiple Structure Search", MessageBoxButtons.YesNoCancel, MessageBoxIcon.Question);
if (dRslt == DialogResult.Cancel)
{
return(DialogResult.Cancel);
}
else if (dRslt == DialogResult.No) // show log
{
SystemUtil.StartProcess(logFileName);
return(DialogResult.Cancel);
}
// Display results
Progress.Show("Formatting results...");
mt = new MetaTable();
mt.Name = "MULTSTRUCTSEARCH_" + SearchCount;
mt.Label = "Multiple Structure Search " + SearchCount;
mt.TableMap = "Mobius.Tools.MultStructSearch"; // plugin id
mt.MetaBrokerType = MetaBrokerType.NoSql;
ColumnSelectionEnum structureColumnSelection = RetrieveStructures ? ColumnSelectionEnum.Selected : ColumnSelectionEnum.Unselected;
keyMc = keyMc.Clone();
keyMc.Name = "MatchingCid";
keyMc.Label = "Matching Compound Id";
mt.AddMetaColumn(keyMc);
structMc = structMc.Clone();
structMc.Name = "MatchingStructure";
structMc.Label = "Matching Structure";
structMc.InitialSelection = structureColumnSelection;
mt.AddMetaColumn(structMc);
dbSetMc = dbSetMc.Clone();
dbSetMc.Name = "Database";
mt.AddMetaColumn(dbSetMc);
//if (DatabasesToSearch.Text.Contains(","))
dbSetMc.InitialSelection = ColumnSelectionEnum.Selected;
mc = mt.AddMetaColumn("Molsimilarity", "Similarity Search Score", MetaColumnType.Number, ColumnSelectionEnum.Unselected, 10);
if (Psc.SearchType == StructureSearchType.MolSim)
{
mc.InitialSelection = ColumnSelectionEnum.Selected;
}
mc = mt.AddMetaColumn("QueryNo", "Query Number", MetaColumnType.Integer);
//mc = mt.AddMetaColumn("QueryMatchNo", "Query Match Number", MetaColumnType.Integer);
mc = mt.AddMetaColumn("QueryId", "Query Id", MetaColumnType.String);
mc = mt.AddMetaColumn("QueryStructure", "Query Structure", MetaColumnType.Structure);
mc.InitialSelection = structureColumnSelection;
q = ToolHelper.InitEmbeddedDataToolQuery(mt);
dt = q.ResultsDataTable as DataTableMx;
for (int mi = 0; mi < matchData.Count; mi++)
{
MatchData md = matchData[mi];
dr = dt.NewRow();
dr[qt.Alias + ".MatchingCid"] = new CompoundId(md.Mid);
if (RetrieveStructures)
{
dr[qt.Alias + ".MatchingStructure"] = new MoleculeMx(MoleculeFormat.Chime, md.Mstr);
}
dr[qt.Alias + ".Database"] = new StringMx(md.Db);
if (Psc.SearchType == StructureSearchType.MolSim)
{
dr[qt.Alias + ".Molsimilarity"] = new NumberMx(md.Score);
}
dr[qt.Alias + ".QueryNo"] = new NumberMx(md.Qno);
dr[qt.Alias + ".QueryId"] = new StringMx(md.Qid);
if (RetrieveStructures)
{
dr[qt.Alias + ".QueryStructure"] = new MoleculeMx(MoleculeFormat.Chime, md.Qstr);
}
dt.Rows.Add(dr);
}
ToolHelper.DisplayData(q, dt, true);
Progress.Hide();
return(DialogResult.OK);
}
/// <summary>
/// Save/SaveAs the list
/// </summary>
/// <param name="saveAs">SaveAs under another list name</param>
/// <param name="saveAsTempList">Save as a temp list</param>
/// <param name="tempListName">Temp list name to save under, prompt if null</param>
/// <returns></returns>
bool Save(
bool saveAs,
bool saveAsTempList,
string tempListName)
{
if (!ValidateList())
{
return(false); // Validate the list if requested
}
// Get list name if needed & check that user can modify it
if (saveAs || CidList.UserObject.Id == 0)
{
CidList.UserObject.Id = 0; // assign new id
if (saveAsTempList)
{
if (tempListName == null) // prompt for name
{
tempListName = CidListCommand.PromptForNewTempListName();
if (tempListName == null)
{
return(false);
}
}
CidList.UserObject = new UserObject(UserObjectType.CnList);
CidList.UserObject.ParentFolder = UserObject.TempFolderName;
CidList.UserObject.Name = tempListName;
CidList.UserObject.Owner = SS.I.UserName;
}
else // save as permanent list
{
UserObject existingUo = CidList.UserObject;
if (CidList.UserObject.Id == 0)
{
existingUo = new UserObject(UserObjectType.CnList);
}
UserObject listUo = UserObjectSaveDialog.Show("Save As", existingUo);
if (listUo == null)
{
return(false);
}
CidList.UserObject = listUo;
}
}
if (!UserObjectUtil.UserHasWriteAccess(CidList.UserObject))
{ // is the user authorized to save this list?
MessageBoxMx.ShowError("You are not authorized to save this list");
return(false);
}
// Write out the list
DisplayStatusMsg("Saving list...");
if (CidList.UserObject.HasDefinedParentFolder)
{
MetaTreeNode targetFolder = UserObjectTree.GetValidUserObjectTypeFolder(CidList.UserObject);
if (targetFolder == null)
{ // shouldn't happen
MessageBoxMx.ShowError("The list could not be saved because the folder it was in no longer exists. Please try SaveAs instead.");
return(false);
}
}
GetNormalizedListFromControl(CidList);
if (!CidList.UserObject.IsCurrentObject) // normal list?
{
CidListCommand.Write(CidList);
}
else // special processing for current list
{
SessionManager.LockResultsKeys = true; // avoid possible overwrite of ResultsKeys if in single step query
int rc = CidListCommand.Write(CidList);
List <string> curListString = CidListCommand.ReadCurrentListLocal().ToStringList();
SessionManager.CurrentResultKeys = curListString;
SessionManager.DisplayCurrentCount();
SessionManager.LockResultsKeys = false;
}
//string cFile = SS.I.ClientDefaultDir + @"\Previous.lst"
//if (UIMisc.CanWriteFileToDefaultDir(cFile))
//{
// StreamWriter sw = new StreamWriter(cFile); // save copy to disk
// sw.Write(CidList.UserObject.Content);
// sw.Close();
//}
int cncnt = CidList.Count;
DisplayStatusMsg("List saved");
Before = CidListCtl.Text;
string tok = UserObjectUtil.GetName(ListName);
Text = "Edit List - [" + CidList.UserObject.Name + "]";
return(true);
}