Thanks for pointing this out! It sounds like there are a couple issues here:
(1) My naive pandas dataframe concatenation didn't work as I intended because the DIAObjects have no way of being associated between two independent reruns. In other words, the DIAObject IDs differ, and database
shenanigans operations alone can't solve that. I could run source association on the two resulting databases if I cared about doing a proper analysis with take1 + take2 together. But that's outside the scope of this ticket.
(2) ap_pipe may not be able to handle the case where a user wants to point to an existing association database and have a new run continue associating sources to the stuff already in there. Chris Morrison says ap_association can do this via a config setting that points to the existing database, but Krzysztof Findeisen says ApPipeTask only reuses databases if it reuses an output repository. This needs to be addressed and may make a good CI test case. This functionality will be critical in the context of a survey where we regularly want to associate new DIASources to existing/known DIAObjects.
I'm going to make a note in my jupyter notebook that the pandas concatenation isn't doing what I intended and close this ticket. Point (2) here will undoubtedly spawn new tickets (to be discussed at a future ap_pipe meeting).