I'm still not fully understanding your usage scenario.

> A simple example is the creation of a full history based log file.

I imagine that this would be an ideal use of the history API. Rather than 
having tools log history, write a script that uses the API to generate a 
history log.

> My more detailed need is to parallel an existing analysis pipeline in galaxy, 
> using the same underlying code.  Reusing the same code from within galaxy has 
> the great advantage of ensuring exactly the same process is run, allowing the 
> "official" analysis to be repeated by outsiders.  This pipeline works on a 
> number of inputs (paired end reads, multiple replicates, etc.) and goes 
> through a number of intervening steps where massive temporary files may be 
> reused in several steps, then ultimately deleted after obtaining final 
> results.  The existing pipeline, outside of galaxy, creates these shared 
> files in a temporary directory, exclusive to the "experiment" being run.  In 
> Galaxy however, ensuring that an "experiment" named by one user will not 
> collide with one named by another user, accidentally overwriting existing 
> files becomes a great deal easier if the temporary experiment directories 
> have history_id based names.  

Why not use mktemp() to ensure a unique directory that can house an 
experiment's data?

> Since the histories could be shared among multiple users, the user_id will 
> not be effective.  

How are Galaxy histories shared amongst users?

J.

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