internal void ShowRunQueryUrl()
{
if (Query == null || Query.UserObject == null || Query.UserObject.Id <= 0)
{
MessageBoxMx.ShowError("The query must first be saved.");
return;
}
string folder = ServicesIniFile.Read("QueryLinksNetworkFolder"); // get unc form of folder
string fileName = "Run_Query_" + Query.UserObject.Id + ".bat"; // file name
string uncPath = folder + '\\' + fileName; // unc file to write now and read later
string tempFile = TempFile.GetTempFileName();
StreamWriter sw = new StreamWriter(tempFile);
string cmd = // batch command to start the Mobius client and run the specified query
Lex.AddDoubleQuotes(ClientDirs.ExecutablePath) + // path to executable in quotes
" Mobius:Command='Run Query " + Query.UserObject.Id + "'"; // the mobius command to run
sw.WriteLine(cmd);
sw.Close();
ServerFile.CopyToServer(tempFile, uncPath);
FileUtil.DeleteFile(tempFile);
string url = "file:///" + folder.Replace('\\', '/') + "/" + fileName; // put in "file:" schema & switch slashes to get URL from UNC name
InputBoxMx.Show(
"The following URL can be used from a web page " +
"to start Mobius and run the current query:",
"Run Query URL",
url);
//"Mobius:Command='Run Query " + Query.UserObject.Id + "'"); // this is better but isn't accepted by SharePoint
return;
}
/// <summary>
/// Write out the data and return the html/js to open the template .dxp file with the exported data file
/// </summary>
/// <param name="q"></param>
/// <param name="trvp"></param>
/// <returns></returns>
public static string CreateSpotfireAnalysisDocument(
Query q,
TargetSummaryOptions trvp)
{
ExportParms ep = new ExportParms();
ep.OutputDestination = OutputDest.TextFile;
ep.ExportFileFormat = ExportFileFormat.Csv;
ep.OutputFileName = TempFile.GetTempFileName(".csv"); // temp .csv file to export to
ep.IncludeDataTypes = true;
string result = UalUtil.IQueryExec.RunQuery(q, ep); // do the export
if (result == null)
{
return(null); // just return if cancelled
}
string templateLibFolder = // unc name of the lib folder (not currently used)
ServicesIniFile.Read("SpotfireLibraryFolder");
string templateLibUrl = // url of the library containing the Mobius templates
ServicesIniFile.Read("SpotfireLibraryUrl");
templateLibUrl = @"http://[server]/SpotfireWeb/Library.aspx?folder=DCRT%20(chemistry)%20users/Mobius/Templates";
string templateUrl = templateLibUrl + "/MultiDbView";
string html = templateUrl; // todo, build html/js to open the template with the specified file
return(html);
}
/// <summary>
/// Get security parms
/// </summary>
/// <returns></returns>
public static void ReadSecurityParms()
{
if (_readSecurityParms)
{
return;
}
if (ServicesIniFile.IniFile == null)
{
return;
}
_useActiveDirectory = ServicesIniFile.ReadBool("UseActiveDirectory", true);
_approvedMobiusUsersGroupName = ServicesIniFile.Read("ApprovedMobiusUsers", @"<domain>Approved_Mobius_Users");
_approvedMobiusChemViewGroupName = ServicesIniFile.Read("ApprovedMobiusChemView", @"<domain>Approved_Mobius_Chemview");
_approvedMobiusSequenceViewGroupName = ServicesIniFile.Read("ApprovedMobiusSequenceView", @"<domain>Lg_Mol_Search_Incl_Seq");
string txt = ServicesIniFile.Read("SpecialMobiusSystemAccounts", "MOBIUS");
_specialMobiusSystemAccounts = new HashSet <string>();
string[] sa = txt.Split(',');
foreach (string s in sa)
{
if (Lex.IsDefined(s))
{
_specialMobiusSystemAccounts.Add(s.Trim().ToUpper());
}
}
_readSecurityParms = true;
}
/// <summary>
/// Check to see if any Annotation table updates need to started
/// </summary>
public static string CheckForAllUsersImportFileUpdates()
{
if (!Security.IsMobius)
{
return("Only the account <mobiusAccount> can check for all annotation table updates");
}
UserData ud = new UserData();
if (!ServicesIniFile.ReadBool("RunBackgroundProcessesInForeground", false))
{
ParameterizedThreadStart ts = new ParameterizedThreadStart(ud.CheckForImportFileUpdatesThreadMethod);
Thread newThread = new Thread(ts);
newThread.IsBackground = true;
newThread.SetApartmentState(ApartmentState.STA);
newThread.Start(true);
}
else
{
ud.CheckForImportFileUpdatesThreadMethod(true);
}
return("CheckForAllUsersImportFileUpdates started");
}
/// <summary>
/// Main tool entry point
/// </summary>
/// <param name="args"></param>
/// <returns></returns>
public string Run(
string args)
{
QbUtil.SetMode(QueryMode.Build); // be sure in build mode
//List<StructureDbInfo> dbInfo = StructureDbInfo.GetList(); // get list of root structure tables
//MetaTable mt = MetaTableCollection.Get(dbInfo[0].StructureTable); // use first structure table
if (DatabasesToSearch.Text == "")
{ // default to first structure table
List <RootTable> dbInfo = RootTable.GetList(); // get list of root structure tables
if (dbInfo != null && dbInfo.Count > 0)
{
DatabasesToSearch.Text = dbInfo[0].Label;
}
}
if (ServicesIniFile.Read("MultStructSearchHelpUrl") != "")
{
Help.Enabled = true;
}
DialogResult dr = ShowDialog(SessionManager.ActiveForm);
return("");
}
/// <summary>
/// Return true if this column can be a secondary image column
/// </summary>
/// <param name="mc"></param>
/// <returns></returns>
public static bool CanBeSecondaryImageColumnObsolete(
MetaColumn mc)
{
if (!CanHaveRelatedImageColumn(mc))
{
return(false); // must be image column
}
bool allowSecondaryImageColumns = ServicesIniFile.ReadBool("AllowSecondaryImageColumns", false);
if (!allowSecondaryImageColumns)
{
return(false);
}
if (Lex.Contains(mc.Label, "Non Standard") || // nonstandards can be secondary
Lex.Contains(mc.Label, "_NS") ||
Lex.Contains(mc.Label, "(NS)"))
{
return(true);
}
foreach (string s in ImageResultTypes)
{
string resultCode = mc.Name.Substring(2); // get the assay metadata code
if (s == mc.MetaTable.Code + "." + resultCode)
{
return(true);
}
}
return(false);
}
/// <summary>
/// Build & return the full MetaTree
/// </summary>
///
public Dictionary <string, MetaTreeNode> GetMetaTree2()
{
if (ServiceFacade.UseRemoteServices)
{
NativeMethodTransportObject resultObject = ServiceFacade.CallServiceMethod(
ServiceCodes.MobiusMetaDataService,
MobiusMetaDataService.Build,
new object[] { false });
// Get the cache from the server if newer than the client cache
string cacheFile = ServicesIniFile.Read("CachedTreeFile", DefaultCachedTreeFile);
string serverCacheFile = @"<MetaDataDir>\MetaTrees\" + cacheFile;
string clientCacheFile = ClientDirs.CacheDir + @"\" + cacheFile;
//ServerFile.Get(serverCacheFile, clientCacheFile); // debug, always get
bool changed = ServerFile.GetIfChanged(serverCacheFile, clientCacheFile); // just get if changed
// Build the tree from the local copy of the cache
MetaFactoryNamespace.MetaTreeFactory.BuildFromCache(ClientDirs.CacheDir, false);
return(Mfn.MetaTreeFactory.Nodes);
}
else
{
Mfn.MetaTreeFactory.Build();
return(Mfn.MetaTreeFactory.Nodes);
}
}
void SetupGrid(List <UserObject> alerts)
{
string txt, tok;
DataTable dt = CreateDataTable();
foreach (UserObject uo in alerts) // fill the grid
{
UserObject uo2 = uo;
Alert alert = Alert.GetAlertFromUserObject(uo2, false);
UserObject quo = UserObjectDao.ReadHeader(alert.QueryObjId); // get query header for name
if (quo == null)
{
continue; // associated query missing?
}
alert.QueryName = quo.Name;
alert.LastQueryUpdate = quo.UpdateDateTime;
DataRow dr = dt.NewRow();
SetDataRow(dr, alert);
dt.Rows.Add(dr);
}
Grid.DataSource = dt;
Grid.Refresh();
if (ServicesIniFile.Read("AlertHelpUrl") != "")
{
Help.Enabled = true;
}
return;
}
public List <StructSearchMatch> MatchList; // merged list of matches
/// <summary>
/// InitializeForSession
/// </summary>
public static void InitializeForSession()
{
SearchCorpSimEnabled = ServicesIniFile.ReadBool("CdkSimSearchCorp", true);
SearchChemblSimEnabled = ServicesIniFile.ReadBool("CdkSimSearchChembl", true);
UseMultipleThreads = ServicesIniFile.ReadBool("CdkSimSearchUseMultipleThreads", true);
Debug = ServicesIniFile.ReadBool("CdkSimSearchDebug", false);
}
/// <summary>
/// Initialize the UAL
/// </summary>
public static void Initialize(string iniFileName)
{
ServicesDirs.ExecutablePath = Application.ExecutablePath;
ServicesDirs.ServerStartupDir = Application.StartupPath;
//DebugLog.Message("UalUtil.Initialize iniFileName: " + iniFileName);
ServicesIniFile.Initialize(iniFileName);
CommonConfigInfo.MiscConfigDir = ServicesIniFile.Read("MiscConfigDirectory");
ServicesDirs.MetaDataDir = ServicesIniFile.Read("MetaDataDirectory");
//DebugLog.Message("MetaDataDir: " + MetaDataDir);
ServicesDirs.TargetMapsDir = ServicesDirs.MetaDataDir + @"\TargetMaps"; // target maps relative to MetaDataDir
ServicesDirs.DocDir = ServicesIniFile.Read("DocumentDirectory");
ServicesDirs.LogDir = ServicesIniFile.Read("LogDirectory");
ServicesDirs.CacheDir = ServicesIniFile.Read("CacheDirectory");
ServicesDirs.TempDir = TempFile.TempDir = ServicesIniFile.Read("TempDirectory");
ServicesDirs.QueryResultsDataSetDir = ServicesIniFile.Read("QueryResultsDataSetDirectory");
ServicesDirs.BackgroundExportDir = ServicesIniFile.Read("BackgroundExportDirectory");
ServicesDirs.BinaryDataDir = ServicesIniFile.Read("BinaryDataDirectory");
ServicesDirs.ModelQueriesDir = ServicesIniFile.Read("ModelQueriesDirectory");
ServicesDirs.ModelQueriesDir = ServicesIniFile.Read("ModelQueriesDirectory");
ServicesDirs.ImageDir = ServicesIniFile.Read("ImageDirectory");
ServicesDirs.ImageDirUNC = ServicesIniFile.Read("ImageDirectoryUNC");
LogExecutionTimes = ServicesIniFile.ReadBool("LogUalExecutionTimes", false);
DbCommandMx.LogDatabaseCalls = ServicesIniFile.ReadBool("LogDatabaseCalls", DbCommandMx.LogDatabaseCalls);
return;
}
private void CreateUserGroupMenuItem_Click(object sender, EventArgs e)
{
if (!Security.IsAdministrator(SS.I.UserName) &&
!Security.HasPrivilege(SS.I.UserName, "CreateUserGroup") &&
!ServicesIniFile.ReadBool("CreateUserGroupByAnyUser", true))
{
MessageBoxMx.ShowError("Your account is not authorized to create and/or edit user groups");
return;
}
string groupName = InputBoxMx.Show("Enter the name of the new user group to be created.", "Create User Group");
if (Lex.IsNullOrEmpty(groupName))
{
return;
}
if (UserGroups.LookupExternalName(groupName) != null)
{
MessageBoxMx.ShowError("Group \"" + groupName + "\" already exists");
return;
}
DialogResult dr = PermissionsGroupEditor.Show(groupName, true);
if (dr == DialogResult.OK)
{
PermissionsList.ItemNameComboBox.Properties.Items.Clear(); // rebuild for new group
}
}
/// <summary>
/// New update the list of related compounds
/// </summary>
/// <param name="mt"></param>
/// <param name="cid"></param>
/// <param name="queryStruct"></param>
private void UpdateRelatedCidsDisplay(
MetaTable mt,
string cid,
MoleculeMx queryStruct,
int renderId)
{
bool useNew = ServicesIniFile.ReadBool("UseNewRelatedCompoundsPopup", true); // use new or old related compounds display
if (!useNew)
{
UpdateRelatedCidsDisplayOld(mt, cid, queryStruct);
return;
}
//if (!SS.I.AllowGroupingBySalts || // need this?
// Lex.Ne(MetaTable.DefaultRootTable, mt.Name))
//{
// this.Height = RelatedStructuresPanel.Top;
// return;
//}
if (SS.I.FindRelatedCpdsInQuickSearch)
{
RSM.StartSearchAndRetrievalOfRelatedStructures(mt.Name, cid, queryStruct, RelatedStructureBrowser.StructureSearchTypes);
}
return;
}
/// <summary>
/// Initialize the UAL and load the MetaData
/// </summary>
//public void Initialize()
//{
// InitializeUAL();
// LoadMetaData();
// return;
//}
/// <summary>
/// Initialize the UAL so basic Oracle operations can be performed
/// </summary>
public void InitializeUAL()
{
lock (_lockObject)
{
// Set the ini file
if (ServicesIniFile.IniFile == null)
{
string iniFilePath = GetMobiusServicesIniFileLocation();
Mobius.UAL.UalUtil.Initialize(iniFilePath);
if (!System.IO.File.Exists(iniFilePath))
{
throw new Exception("IniFile doesn't exist: " + iniFilePath);
}
}
if (ServicesDirs.MetaDataDir == "")
{
ServicesDirs.MetaDataDir = ServicesIniFile.Read("MetaData");
}
string logFile = ServicesDirs.LogDir + @"\" + Mobius.ComOps.CommonConfigInfo.ServicesLogFileName; // log file name
Mobius.Services.Util.ServicesLog.Initialize(logFile); // initialize for logging
// Get list of valid privileges
Mobius.ComOps.PrivilegesMx.SetValidPrivilegeListFromInifile(ServicesIniFile.IniFile);
// Load data source meta info
if (Mobius.UAL.DataSourceMx.DataSources == null ||
Mobius.UAL.DataSourceMx.DataSources.Count == 0 ||
Mobius.UAL.DataSourceMx.Schemas == null ||
Mobius.UAL.DataSourceMx.Schemas.Count == 0)
{
Mobius.UAL.DataSourceMx.LoadMetadata();
}
// Foundation dependency injections
// Dependency injections for client components
//Mobius.Data.Query.IDataTableManager = new DataTableManager();
//Mobius.Data.ChemicalStructure.IChemicalStructureUtil = new Mobius.ClientComponents.ChemicalStructureUtil();
//Mobius.Data.RootTable.IServerFile = new ServerFile();
//Mobius.ServServiceFacade.ServiceFacade.IDebugLog = new DebugLogMediator();
Mobius.Data.ResultsViewProps.ResultsViewFactory = new Mobius.ClientComponents.ViewFactory();
Mobius.Data.Query.IDataTableManager = new Mobius.ClientComponents.DataTableManager();
Mobius.Data.CidList.ICidListDao = new Mobius.UAL.CidListDao();
Mobius.Data.MoleculeMx.IMoleculeMxUtil = new Mobius.QueryEngineLibrary.MoleculeUtil();
Mobius.Data.RootTable.IServerFile = new Mobius.UAL.ServerFile();
Mobius.Data.InterfaceRefs.IUserObjectDao = new Mobius.UAL.IUserObjectDaoMethods();
Mobius.Data.InterfaceRefs.IUserObjectIUD = new Mobius.ClientComponents.IUserObjectIUDMethods();
Mobius.Data.InterfaceRefs.IUserObjectTree = new Mobius.ClientComponents.IUserObjectTreeMethods();
Mobius.MolLib1.StructureConverter.ICdkUtil = new Mobius.CdkMx.CdkUtil();
}
}
/// <summary>
/// GetDefaultWebPlayerUrl
/// </summary>
/// <returns></returns>
static string GetDefaultWebPlayerUrl()
{
if (_defaultWebplayerUrl == null)
{
_defaultWebplayerUrl = ServicesIniFile.Read("SpotfireWebplayer", "https://[server]/spotfire/wp");
}
return(_defaultWebplayerUrl);
}
/// <summary>
/// Get server file name to export to
/// </summary>
/// <param name="rf"></param>
/// <param name="objId"></param>
/// <returns></returns>
static string GetServerFileName(ResultsFormat rf, int objId)
{
string clientFile = rf.OutputFileName; // file name on client
string ext = Path.GetExtension(clientFile);
string serverExpDir = ServicesIniFile.Read("BackgroundExportDirectory");
string serverFile = serverExpDir + @"\" + objId + ext; // use background export userobject id & client file extension
return(serverFile);
}
/// <summary>
/// Do initial read of the list of views and the users for each view.
/// </summary>
public static void ReadViews()
{
StreamReader sr;
ViewDict = new Dictionary <string, RestrictedDatabaseView>();
bool restrictionsActive = ServicesIniFile.ReadBool("UseRestrictedDatabaseViews", false);
if (!restrictionsActive)
{
return;
}
string dirName = ServicesDirs.MetaDataDir + @"\RestrictedDatabaseViews";
if (!Directory.Exists(dirName))
{
return; // throw new Exception("RestrictedDatabaseViews Directory does not exist: " + dirName);
}
string fileName = dirName + @"\ViewList.txt";
if (!File.Exists(fileName))
{
return;
}
try
{
sr = new StreamReader(fileName);
}
catch (Exception ex)
{ return; }
while (true)
{
string txt = sr.ReadLine();
if (txt == null)
{
break;
}
if (Lex.IsUndefined(txt) || txt.StartsWith(";"))
{
continue;
}
string viewName = txt.Trim().ToUpper();
RestrictedDatabaseView v = new RestrictedDatabaseView();
ViewDict[viewName] = v;
v.Name = viewName;
ReadViewUsers(v);
}
sr.Close();
}
/// <summary>
/// Send mail object
/// </summary>
/// <param name="mail"></param>
public static void SendEmail(
MailMessage mail)
{
SmtpClient mailClient = new SmtpClient();
string mailServerName = ServicesIniFile.Read("SmtpServer");
mailClient.Host = mailServerName;
mailClient.UseDefaultCredentials = true;
// mailClient.DeliveryMethod = SmtpDeliveryMethod.PickupDirectoryFromIis;
mailClient.Send(mail);
}
/// <summary>
/// Main tool entry point
/// </summary>
/// <param name="args"></param>
/// <returns></returns>
public string Run(
string args)
{
QbUtil.SetMode(QueryMode.Build); // be sure in build mode
if (ServicesIniFile.Read("RgroupDecompositionHelpUrl") != "")
{
Help.Enabled = true;
}
this.ShowDialog();
return("");
}
/// <summary>
/// Show NCBI Entre Gene web page for supplied geneId and/or symbol
/// </summary>
/// <param name="geneIdSymbol"></param>
public static string GetTargetDescriptionUrl(
string targetIdSymbol)
{
int targetId;
string targetSymbol;
if (String.IsNullOrEmpty(targetIdSymbol))
{
return(null);
}
else if (Lex.IsInteger(targetIdSymbol)) // numeric gene id
{
targetId = int.Parse(targetIdSymbol);
}
else if (targetIdSymbol.Contains("-")) // 1234-Symbol form
{
string[] sa = targetIdSymbol.Split('-');
targetSymbol = sa[1].ToUpper();
try { targetId = TargetSymbolToId(targetSymbol); }
catch { return(null); }
}
else // must be symbol
{
targetSymbol = targetIdSymbol.ToUpper();
try { targetId = TargetSymbolToId(targetSymbol); }
catch { return(null); }
}
if (targetId <= 0)
{
return(null);
}
string url = ServicesIniFile.Read("NcbiGeneIdUrlTemplate");
if (String.IsNullOrEmpty(url))
{
return(null);
}
url = url.Replace("<GENE_ID>", targetId.ToString());
return(url);
}
/// <summary>
/// Display any new news if requested
/// </summary>
public static bool ShowNewNews()
{
try
{
string lastNews = Preferences.Get("ShowNews");
if (lastNews == "false")
{
return(false); // user doesn't want to see news
}
if (ClientState.IsDeveloper)
{
return(false); // debug
}
string fileName = ServicesIniFile.Read("NewsFile");
if (fileName == "")
{
throw new Exception("NewsFile not defined");
}
DateTime dt = File.GetLastWriteTime(fileName);
string fileDate = String.Format("{0,4:0000}{1,2:00}{2,2:00}", dt.Year, dt.Month, dt.Day);
if (String.Compare(fileDate, lastNews) > 0 || lastNews == "")
{
ShowNews(); // show the news
UserObjectDao.SetUserParameter(SS.I.UserName, "ShowNews", fileDate);
return(true);
}
else
{
return(false);
}
}
catch (Exception ex)
{
//if (ClientState.IsDeveloper)
// MessageBoxMx.ShowError(ex.Message);
return(false);
}
}
/// <summary>
/// Check to see if any imports need to started
/// </summary>
public static string CheckForCurrentUserImportFileUpdates()
{
UserData ud = new UserData();
if (!ServicesIniFile.ReadBool("RunBackgroundProcessesInForeground", false)) // run as separate thread?
{
ParameterizedThreadStart ts = new ParameterizedThreadStart(ud.CheckForImportFileUpdatesThreadMethod);
Thread newThread = new Thread(ts);
newThread.IsBackground = true;
newThread.SetApartmentState(ApartmentState.STA);
newThread.Start(false);
}
else
{
ud.CheckForImportFileUpdatesThreadMethod(false);
}
return("CheckForImportFileUpdates started");
}
/// <summary>
/// Some methods in the AlertQueue class are static. Therefore the _alertQueueFileName will not be set in those cases.
/// This method will ensure we have a valid file name in all cases.
/// </summary>
/// <returns></returns>
private static string GetAlertQueueFileName()
{
if (_alertQueueFileName != null)
{
return(_alertQueueFileName);
}
if (_serverLogDir == null)
{
_serverLogDir = ServicesIniFile.Read("LogDirectory");
}
if (String.IsNullOrEmpty(_serverLogDir))
{
throw new Exception("Server LogDirectory not defined in config file");
}
if (_alertQueueFileName == null)
{
_alertQueueFileName = _serverLogDir + @"\AlertQueue.txt";
}
return(_alertQueueFileName);
}
public static void Initialize()
{
MetaTableXmlFolder = ServicesDirs.MetaDataDir + @"\MetaTables";
string rootFile = ServicesIniFile.Read("MetaTableRootFile", "Metatables.xml"); // root to start at
if (rootFile.IndexOf(@"\") < 0)
{
rootFile = MetaTableXmlFolder + @"\" + rootFile;
}
IncludeQualifiedNumberDetailColumnsInMetaTables = // get flag for including hidden Qualified Number detail cols in metatables
ServicesIniFile.ReadBool("IncludeQualifiedNumberDetailColumnsInMetaTables", true);
BuildFromXmlFile(rootFile); // get initial metatables
RegisterFactory("CalcField", new CalcFieldMetaFactory());
RegisterFactory("Annotation", new AnnotationMetaFactory());
RegisterFactory("MultiTable", new MultiTableMetaFactory());
RegisterFactory("Oracle", new OracleMetaFactory());
RegisterFactory("PubChem", new PubChemMetaFactory());
RegisterFactory("UnpivotedAssay", new UnpivotedAssayMetaFactory());
RegisterFactory("SpotfireLink", new SpotfireLinkMetafactory());
}
/// <summary>
/// Read and set the config settings
/// </summary>
public static void ReadConfigSettings()
{
if (ConfigSettingsHaveBeenRead)
{
return;
}
SearchFssEnabled = ServicesIniFile.ReadBool("RssSearchFss", true);
SearchCorpDbFssEnabled = ServicesIniFile.ReadBool("RssSearchCorpFss", true);
SearchChemblFssEnabled = ServicesIniFile.ReadBool("RssSearchChemblFss", true);
SearchMmpEnabled = ServicesIniFile.ReadBool("RssSearchMmp", true);
SearchCorpDbMmpEnabled = ServicesIniFile.ReadBool("RssSearchCorpMmp", true);
SearchChemblMmpEnabled = ServicesIniFile.ReadBool("RssSearchChemblMmp", false);
KeepHighestCidPairScoreOnlyEnabled = ServicesIniFile.ReadBool("RssKeepHighestCidPairScoreOnly", true);
SearchSmallWorldEnabled = ServicesIniFile.ReadBool("RssSearchSmallWorld", true);
SearchCorpDbSmallWorldEnabled = ServicesIniFile.ReadBool("RssSearchCorpSmallWorld", true);
SearchChemblSmallWorldEnabled = ServicesIniFile.ReadBool("RssSearchChemblSmallWorld", true);
//SearchSmallWorldEnabled = SearchCorpSmallWorldEnabled = SearchChemblSmallWorldEnabled = true; // for testing
SearchSimEnabled = ServicesIniFile.ReadBool("RssSearchSim", true);
SearchCorpSimEnabled = ServicesIniFile.ReadBool("RssSearchCorpSim", true);
SearchChemblSimEnabled = ServicesIniFile.ReadBool("RssSearchChemblSim", true);
SearchSssEnabled = ServicesIniFile.ReadBool("RssSearchSSS", true);
SearchCorpSssEnabled = ServicesIniFile.ReadBool("RssSearchCorpSSS", true);
SearchChemblSssEnabled = ServicesIniFile.ReadBool("RssSearchChemblSSS", true);
UseMultipleThreads = ServicesIniFile.ReadBool("RssUseMultipleThreads", true);
UseCachedResults = ServicesIniFile.ReadBool("RssUseCachedResults", true);
Debug = ServicesIniFile.ReadBool("RssDebug", false);
ConfigSettingsHaveBeenRead = true;
return;
}
/// <summary>
/// Display the news file
/// </summary>
public static void ShowNews()
{
try
{
string fileName = ServicesIniFile.Read("NewsFile");
if (fileName == "")
{
return;
}
if (Instance == null)
{
Instance = new NewsDialog();
}
Instance.ShowNewsCheckBox.Checked = Preferences.GetBool("ShowNews");
Instance.Show();
Application.DoEvents(); // allow form to draw before doing navigate
Instance.WebBrowser.Navigate(fileName);
}
catch (Exception ex) { return; }
}
/// <summary>
/// Create WinForms.ChromiumWebBrowser and navigate to the initial page
/// </summary>
public void LoadInitialPage()
{
if (Browser != null)
{
return;
}
string url = "";
if (RendererMode == KekuleJsControlMode.OffScreenBitmap)
{
url = ServicesIniFile.ReadWithException("KekuleJsRendererUrl");
}
else if (RendererMode == KekuleJsControlMode.BrowserViewOnly)
{
url = ServicesIniFile.ReadWithException("KekuleJsRendererUrl");
}
else if (RendererMode == KekuleJsControlMode.BrowserEditor)
{
url = ServicesIniFile.ReadWithException("KekuleJsEditorUrl");
}
if (Debug)
{
DebugLog.Message("Loading initial " + RendererMode + " mode page: " + url + IdText);
}
Browser = new WebBrowser(); // create the browser
Browser.Location = new Point(0, 0);
Browser.Size = new Size(256, 256);
Browser.Dock = DockStyle.None;
Browser.Anchor = (AnchorStyles.Top | AnchorStyles.Left | AnchorStyles.Bottom | AnchorStyles.Right);
Browser.Name = "WebBrowser";
Browser.ScrollBarsEnabled = false;
Browser.ScriptErrorsSuppressed = JavaScriptManager.SuppressJavaScriptErrors;
Browser.ObjectForScripting = new JavaScriptManager(this); // create ScriptManager that can call back to this JavaScriptInterface instance from within web page JavaScript
// The following three events are also in WebBrowserWrapper (not needed here)
Browser.DocumentCompleted += new WebBrowserDocumentCompletedEventHandler(Browser_DocumentCompleted);
Browser.Navigated += new WebBrowserNavigatedEventHandler(this.WebBrowser_Navigated);
Browser.Navigating += new WebBrowserNavigatingEventHandler(this.WebBrowser_Navigating);
Browser.ProgressChanged += new WebBrowserProgressChangedEventHandler(Browser_ProgressChanged);
Browser.StatusTextChanged += new EventHandler(WebBrowserStatusTextChanged);
Browser.Resize += new EventHandler(WebBrowser_Resize);
Browser.SizeChanged += new EventHandler(Browser_SizeChanged);
if (ContainingControl != null)
{
Browser.Size = ContainingControl.Size;
ContainingControl.Controls.Clear();
ContainingControl.Controls.Add(Browser);
}
else
{
Browser.Size = new Size(1024, 768);
}
BrowserWrapper = new WebBrowserWrapper(Browser);
BrowserWrapper.NavigateAndWait(url); // navigate to the initial page
ResizeRendering();
if (Debug)
{
DebugLog.Message("Browser created, initial page loaded" + IdText);
}
return;
}
/// <summary>
/// Edit a new or existing calculated field
/// </summary>
/// <param name="cf"></param>
/// <param name="uoIn"></param>
/// <returns></returns>
public static UserObject Edit(
CalcField cf,
UserObject uoIn)
{
QueryTable qt;
MetaTable mt = null;
MetaColumn mc, field;
UserObject uo2;
CalcField cf2 = null;
string msg;
int i1;
CalcFieldEditor lastInstance = Instance;
CalcFieldEditor i = Instance = new CalcFieldEditor();
i.AdvancedPanel.BorderStyle = BorderStyle.None;
i.AdvancedPanel.Visible = false;
i.AdvancedPanel.Dock = DockStyle.Fill;
i.BasicPanel.BorderStyle = BorderStyle.None;
i.BasicPanel.Visible = true;
i.BasicPanel.Dock = DockStyle.Fill;
i.SetupStandardCalculatedFields();
if (ServicesIniFile.Read("CalcFieldHelpUrl") != "")
{
i.Help.Enabled = true;
}
if (lastInstance != null)
{
i.StartPosition = FormStartPosition.Manual;
i.Location = lastInstance.Location;
i.Size = lastInstance.Size;
lastInstance = null;
}
if (uoIn == null)
{
uoIn = new UserObject(UserObjectType.CalcField);
}
else if (uoIn.Id > 0) // get existing metatable for calc field for exclusion in BuildQuickSelectTableMenu
{
string tName = "CALCFIELD_" + uoIn.Id.ToString();
mt = MetaTableCollection.GetExisting(tName);
if (MainMenuControl != null)
{
MainMenuControl.UpdateMruList(tName);
}
}
Instance.UoIn = uoIn;
string title = "Edit Calculated Field";
if (!String.IsNullOrEmpty(uoIn.Name))
{
title += " - " + uoIn.Name;
}
Instance.Text = title;
Instance.CalcField = cf; // what we're editing
Instance.SetupForm(); // set up the form
DialogResult dr = Instance.ShowDialog(SessionManager.ActiveForm);
if (dr == DialogResult.Cancel)
{
return(null);
}
return(Instance.UoIn); // return saved object
}
public bool CanCreateTempTables = false; // true if the associated account can create temp tables
/// <summary>
/// Load metadata describing connections and associated schemas
/// </summary>
/// <param name="dsFileName"></param>
/// <returns></returns>
public static int LoadMetadata()
{
XmlAttributeCollection atts;
// Get some inifile parameters first
if (ServicesIniFile.IniFile == null)
{
throw new Exception("ServicesIniFile.IniFile is null");
}
SessionConnection.Pooling = ServicesIniFile.ReadBool("Pooling", true);
SessionConnection.MinPoolSize = ServicesIniFile.ReadInt("MinPoolSize", 1);
SessionConnection.IncrPoolSize = ServicesIniFile.ReadInt("IncrPoolSize", 5);
SessionConnection.MaxPoolSize = ServicesIniFile.ReadInt("MaxPoolSize", 100);
SessionConnection.DecrPoolSize = ServicesIniFile.ReadInt("DecrPoolSize", 1);
SessionConnection.ConnectionLifetime = ServicesIniFile.ReadInt("ConnectionLifetime", 0);
string tok = ServicesIniFile.Read("KeyListPredType", "Parameterized");
int enumInt = EnumUtil.Parse(typeof(KeyListPredTypeEnum), tok);
if (enumInt >= 0)
{
DbCommandMx.DefaultKeyListPredType = (KeyListPredTypeEnum)enumInt;
}
DbCommandMx.DbFetchRowCount = ServicesIniFile.ReadInt("DbFetchRowCount", DbCommandMx.DbFetchRowCount);
DbCommandMx.DbFetchSizeMax = ServicesIniFile.ReadInt("DbFetchSizeMax", DbCommandMx.DbFetchSizeMax);
DataSources = new Dictionary <string, DataSourceMx>(StringComparer.OrdinalIgnoreCase);
Schemas = new Dictionary <string, DbSchemaMx>(StringComparer.OrdinalIgnoreCase);
string dsFileName = ServicesDirs.MetaDataDir + @"\" + "DataSources.xml";
StreamReader sr = new StreamReader(dsFileName);
XmlDocument doc = new XmlDocument();
doc.Load(sr);
XmlNode node = doc.FirstChild;
while (node != null)
{
if (node.NodeType == XmlNodeType.Element)
{
break;
}
node = node.NextSibling;
if (node == null)
{
throw new Exception("No initial element found");
}
}
if (!Lex.Eq(node.Name, "DataSources"))
{
throw new Exception("Expected DataSources node: " + node.Name);
}
atts = node.Attributes; // datasources attributes
for (int i = 0; i < atts.Count; i++)
{
XmlNode att = atts.Item(i);
if (Lex.Eq(att.Name, "DblinkConnName"))
{
} // obsolete key word
else
{
throw new Exception
("Unexpected DataSources attribute: " + att.Name);
}
}
node = node.FirstChild;
while (node != null)
{
if (node.NodeType != XmlNodeType.Element)
{
; // ignore non-elements
}
else if (Lex.Eq(node.Name, "DataSource") || // connection element
Lex.Eq(node.Name, "Connection"))
{
DataSourceMx cd = new DataSourceMx();
atts = node.Attributes;
for (int i = 0; i < atts.Count; i++)
{
XmlNode att = atts.Item(i);
if (Lex.Eq(att.Name, "DatabaseType") || Lex.Eq(att.Name, "DbType"))
{
if (!Enum.TryParse <DatabaseType>(att.Value, true, out cd.DbType))
{
throw new Exception("Invalid Database type: " + att.Value);
}
}
else if (Lex.Eq(att.Name, "Name"))
{
cd.DataSourceName = att.Value.ToUpper().Trim();
}
else if (Lex.Eq(att.Name, "DatabaseName") || Lex.Eq(att.Name, "OracleName"))
{
cd.DatabaseLocator = att.Value.ToUpper().Trim();
}
else if (Lex.Eq(att.Name, "ConnectionString")) // keep case if connection string
{
cd.DatabaseLocator = att.Value.Trim();
}
else if (Lex.Eq(att.Name, "UserName"))
{
cd.UserName = att.Value.Trim(); // keep case as is (Oracle 11g)
}
else if (Lex.Eq(att.Name, "Password"))
{
cd.Password = att.Value.Trim(); // keep case as is (Oracle 11g)
}
else if (Lex.Eq(att.Name, "MdlInit")) // mdl initialization
{
cd.InitCommand = "select cdcaux.ctenvinit('" + att.Value.Trim() + "') from dual";
}
else if (Lex.Eq(att.Name, "InitCommand"))
{
cd.InitCommand = att.Value.Trim();
}
else if (Lex.Eq(att.Name, "KeyDataSource"))
{
bool.TryParse(att.Value.Trim(), out cd.IsKeyDataSource);
}
else if (Lex.Eq(att.Name, "CanCreateTempTables"))
{
bool.TryParse(att.Value.Trim(), out cd.CanCreateTempTables);
}
else if (Lex.Eq(att.Name, "AlwaysUseDbLink"))
{
} // obsolete
else
{
throw new Exception
("Unexpected Connection attribute: " + att.Name);
}
}
if (cd.DataSourceName == "")
{
DebugLog.Message("Connection is missing name: " + cd.DatabaseLocator);
}
else if (DataSourceMx.DataSources.ContainsKey(cd.DataSourceName))
{
DebugLog.Message("Data source defined twice: " + cd.DataSourceName);
}
else
{
DataSourceMx.DataSources.Add(cd.DataSourceName, cd);
}
}
else if (Lex.Eq(node.Name, "SchemaToDataSource") || // schema map element
Lex.Eq(node.Name, "SchemaToConnection"))
{
DbSchemaMx schema = new DbSchemaMx();
atts = node.Attributes;
for (int i = 0; i < atts.Count; i++)
{
XmlNode att = atts.Item(i);
if (Lex.Eq(att.Name, "Schema"))
{
schema.Name = att.Value.ToUpper().Trim();
}
else if (Lex.Eq(att.Name, "AliasFor"))
{
schema.AliasFor = att.Value.ToUpper().Trim();
}
else if (Lex.Eq(att.Name, "Connection"))
{
schema.DataSourceName = att.Value.ToUpper().Trim();
}
else if (Lex.Eq(att.Name, "Label") || Lex.Eq(att.Name, "L"))
{
schema.Label = att.Value.Trim();
}
else
{
throw new Exception
("Unexpected Connection attribute: " + att.Name);
}
}
if (schema.Name == "")
{
throw new Exception("Missing schema name");
}
if (schema.DataSourceName == "")
{
throw new Exception("Missing data source/connection name");
}
Schemas[schema.Name] = schema;
}
else
{
throw new Exception("Expected Connection or SchemaToDataSource element but saw " +
node.Name);
}
node = node.NextSibling;
}
sr.Close();
return(DataSources.Count);
}
/// <summary>
/// Method to run query in background and save the results for later retrieval
/// </summary>
/// <param name="q"></param>
/// <param name="emailSubject">Send email if defined</param>
/// <param name="templateName"></param>
/// <returns></returns>
public static string RunBackgroundQuery(
Query q,
string emailSubject,
string templateName)
{
ResultsFormat rf;
QueryManager qm;
DataTableManager dtm;
string msg = "", html = "", resultsFileName;
string viewCmd = "View Background Query Results";
bool notifyUserByEmail = !Lex.IsNullOrEmpty(emailSubject);
try // execute the query & read in all results
{
QbUtil.AddQueryAndRender(q, false); // add it to the query builder
q.BrowseSavedResultsUponOpen = false; // be sure query is run rather than using existing results
msg = QueryExec.RunQuery(q, OutputDest.WinForms);
qm = q.QueryManager as QueryManager;
dtm = qm.DataTableManager;
DialogResult dr = dtm.CompleteRetrieval();
}
catch (Exception ex) // some exceptions are normal, e.g. no criteria, others may be bugs
{
msg = "RunQueryInBackground could not complete due to an unexpected exception: " + DebugLog.FormatExceptionMessage(ex);
ServicesLog.Message(msg);
if (notifyUserByEmail)
{
Email.Send(null, SS.I.UserInfo.EmailAddress, emailSubject, msg);
}
return(msg);
}
if (dtm.KeyCount == 0)
{
msg = "Query " + Lex.Dq(q.UserObject.Name) + " returned no results.";
if (notifyUserByEmail)
{
Email.Send(null, SS.I.UserInfo.EmailAddress, emailSubject, msg);
}
return(msg);
}
try
{
resultsFileName = q.ResultsDataTableFileName; // see if name supplied in query
if (Lex.IsNullOrEmpty(resultsFileName))
{
resultsFileName = "Query_" + q.UserObject.Id + "_Results.bin";
}
resultsFileName = ServicesIniFile.Read("BackgroundExportDirectory") + @"\" + resultsFileName;
dtm.WriteBinaryResultsFile(resultsFileName); // write the file
UserObject cidListUo = SaveBackgroundQueryResultsReferenceObject(qm, "BkgrndQry", resultsFileName);
if (!Lex.IsNullOrEmpty(templateName))
{
html = ReadTemplateFile(templateName);
}
if (notifyUserByEmail)
{
AlertUtil.MailResultsAvailableMessage( // send the mail
q,
dtm.KeyCount,
SS.I.UserInfo.EmailAddress,
emailSubject,
viewCmd,
cidListUo.Id,
null,
html);
}
else
{
html = SubstituteBackgroundExportParameters(html, "", "", dtm.RowCount, dtm.KeyCount, false, "");
return(html); // return the html
}
}
catch (Exception ex)
{
msg = "Error sending background query results: " + DebugLog.FormatExceptionMessage(ex);
ServicesLog.Message(msg);
}
return(msg);
}
/// <summary>
/// Get image & coordinates file from KEGG FTP
/// </summary>
/// <param name="pathwayId"></param>
/// <returns></returns>
public static TargetMap GetKeggPathway(
string pathwayId)
{
String ftpPath, rec;
if (TargetMapDict == null)
{
ReadTargetMapDict();
}
TargetMap tm = new TargetMap();
tm.Name = pathwayId;
tm.Label = pathwayId; // default label
tm.Source = "KEGG";
tm.Type = "Pathway";
// Build basic paths
string ftpFolder = ServicesIniFile.Read("KeggPathWayFtpDirectory"); // get from here
if (String.IsNullOrEmpty(ftpFolder))
{
throw new Exception("KeggPathWayFtpDirectory not defined");
}
if (!ftpFolder.EndsWith(@"/"))
{
ftpFolder += @"/";
}
// Get map_title file and read title for pathway
string filePath = TargetMapDir + @"\map_title.tab";
string pathwayPrefix = pathwayId.Substring(0, 3);
string pathwayNbr = pathwayId.Substring(3); //
bool download = false;
if (!File.Exists(filePath))
{
download = true;
}
while (true)
{
if (download)
{
ftpPath = ftpFolder + "map_title.tab";
Download(ftpPath, filePath);
}
StreamReader sr = new StreamReader(filePath);
while (true)
{
rec = sr.ReadLine();
if (rec == null)
{
break;
}
if (!rec.StartsWith(pathwayNbr))
{
continue;
}
string[] sa = rec.Split('\t');
tm.Label = sa[1].Trim() + " (KEGG: " + pathwayId + ")";
break;
}
sr.Close();
if (!String.IsNullOrEmpty(tm.Label))
{
break; // have it
}
else if (download) // already downloaded but not found
{
tm.Label = pathwayId;
break;
}
else
{ // download again if not done yet
download = true;
continue;
}
}
// Get gif file
if (Lex.Ne(pathwayPrefix, "map")) // if not a base level map then in organisms
{
ftpFolder += @"organisms/";
}
ftpFolder += pathwayPrefix + @"/";
ftpPath = ftpFolder + pathwayId + ".gif";
filePath = TargetMapDir + @"\" + pathwayId + ".gif";
Download(ftpPath, filePath);
Image img = Image.FromFile(filePath);
tm.Bounds = new Rectangle(0, 0, img.Width, img.Height);
tm.MarkBounds = true;
filePath = TargetMapDir + @"\" + pathwayId + ".png"; // save as .png file that Spotfire can read
img.Save(filePath, System.Drawing.Imaging.ImageFormat.Png);
tm.ImageType = "png";
tm.ImageFile = Path.GetFileName(filePath); // store just file name
// Get coordinates file
if (Lex.Eq(pathwayPrefix, "map"))
{
ftpPath = ftpFolder + pathwayId + "_ec.coord";
filePath = TargetMapDir + @"\" + pathwayId + "_ec.coord";
}
else
{
ftpPath = ftpFolder + pathwayId + "_gene.coord";
filePath = TargetMapDir + @"\" + pathwayId + "_gene.coord";
}
Download(ftpPath, filePath);
tm.CoordsFile = Path.GetFileName(filePath);
TargetMapDict[tm.Name.ToUpper()] = tm; // add to list of maps
TargetMapDictByLabel[tm.Label.ToUpper()] = tm;
GetMapWithCoords(pathwayId); // read in coords to validate file format
// Write out the map file containing basic map data
filePath = TargetMapDir + @"\" + pathwayId + ".map";
StreamWriter sw = new StreamWriter(filePath);
rec =
tm.Name + "\t" +
tm.Label + "\t" +
tm.Source + "\t" +
tm.Type + "\t" +
tm.ImageType + "\t" +
tm.ImageFile + "\t" +
tm.Bounds.Left + "\t" +
tm.Bounds.Top + "\t" +
tm.Bounds.Right + "\t" +
tm.Bounds.Bottom + "\t" +
tm.MarkBounds + "\t" +
tm.CoordsFile;
sw.WriteLine(rec);
sw.Close();
return(tm);
}
