You can use schedular to run transformer at a certian time, or to run a batch file calling a series of models.
Look up in the help files for your exact version of transformer command line options, but it will something like:
"C:\Program Files\Cognos\cer1\bin\trnsfrmr.exe" -n -s "FileName.pyi or .mdl" (I'm using Transformer 6.6. It is best that you leave the quotes there, so that Win parses the string correctly, but it can done without the quote marks if there are no embedded spaces in the path names.
If you have a whole bunch of cubes to run, it is better to stick them into a batch file, so you don't have to worry when one process finishes and the next one starts. If you use a batch file use the above command becomes
START /W "C:\program Files\Cognos...." in front of the command (without the quote marks). Use schedular to run the batch file with a command like "C:\BatchFile.bat"
I got this last hint off of Tek-Tips, but I cannot find who orginally posted it-sorry.
As for your 2nd question, do you mean the file time stamp? That is automaticlly updated at run time.
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