ExecuteCommand
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Overview
ExecuteCommand allows script-based server management, for advanced users. Any of these commands can be run.
Syntax
Begin ExecuteCommand /Namespace=Server; Server "tcp://pathToServer:8065/RemoteServer" /UserID=UserName /Password=PasswordOfUser; Command CommandToRun; Options OptionsForServerCommand; OutputFile PathToOutputFileForResults; End;
Note: OutputFile must be an absolute/physical path on the machine where this OScript is being executed (i.e. if using oshell.exe --runscript on your local Windows machine, it will be a path on that machine but if sending the OScript to an OmicSoft Server via oshell.exe --queue or through the Run_Script_(Send_To_Queue), it will be a path on the OmicSoft Server host). Virtual paths not allowed even with the @@ prefix. To write output to standard output (so will appear at end of log), exclude OutputFile statement. All available commands to run can be found in WebServiceCommand.
The script can be run in Oshell and also ArrayStudio:
Examples
Retrieve expression data
Begin ExecuteCommand /Namespace=Server; Server "tcp://192.168.3.228:8065/RemoteServer" /UserID=gary /Password=abc123; Command IA_FetchVariableData; Options " ProjectID=blueprint expression markers Name=Blueprint.FPKM.Data IDs=DDX11L1,TP53"; OutputFile "/IData/OmicTest/ExpressionResults.txt"; End;
Search published projects
Begin ExecuteCommand /Namespace=Server; Server "tcp://192.168.1.36:8065/RemoteServer" /UserID=admin /Password=omicsoft; Command IA_SearchPublishedProjects; Options " ProjectPattern=Affymetrix.RAE230A->Platform "; OutputFile "/IData/OmicTest/_Oscript/20150828_WebServiceCall.oscript.ouput2.txt"; End;
More commands in ServiceCommand
Manage users
Begin ExecuteCommand /Namespace=Server; Server "tcp://localhost:8065/RemoteServer" /UserID=admin /Password=xxxxxx; Command ManageUsers.Update; Options " UserID=usera Password=helloworld UserGroups=standard users UserFolderReaders=standard users UserFolderEditors= "; OutputFile None; End;
Manage Land Access
Begin ExecuteCommand /Namespace=Server; Server "tcp://192.168.1.106:7065/RemoteServer" /UserID=admin /Password=xxxxxx; Command ManageLandUserControl; Options "LandName=TCGA2015 UserControl.Read=[usergroup]curators, [usergroup]standard users, [usergroup]administrators, gary UserControl.Write=[usergroup]administrators UserControl.Download=[usergroup]curators, [usergroup]standard users, [usergroup]administrators, gary UserControl.Refresh=[usergroup]administrators, gary UserControl.ManageSet=[usergroup]curators, [usergroup]standard users, gary UserControl.ManageMetaData=[usergroup]administrators, gary UserControl.ManageMeasurementData=[usergroup]administrators, gary UserControl.ViewBamFiles=[usergroup]curators, [usergroup]standard users, [usergroup]administrators, gary UserControl.AccessClinicalData=[usergroup]administrators, gary"; OutputFile None; End;
gary is a single user, and user group name requires [usergroup] prefix.