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How are you getting your .zip file to server? is it on a shared drive? Are you using a blob input tool? Hypothetically you could do something like a blob input tool that takes in a ..zip file and places it in a static location on your server (say a directory related to staging & services or wherever) then your second app (or second component of that app) uses R or Python to unzip and get a roster of files. Your next component would read in the unzip files.
This is not ideal and could take an extended amount of time and require decent-know how of building workflows for Server and Server file locations and I obviously can't speak to any security concerns you may have.