Refactor CLI and add enumerated PMID option
Refactor CLI and add enumerated PMID option

This commit refactors common code needed to load and parse the
configuration as well as run the RAS Machine. Now, each CLI element
just has to implement the system that gets the pmids dictionary itself.
Could probably use more refactoring, but this works. Closes #294

johnbachman/belpy,johnbachman/belpy,sorgerlab/indra,johnbachman/indra,johnbachman/indra,bgyori/indra,johnbachman/belpy,pvtodorov/indra,sorgerlab/belpy,bgyori/indra,sorgerlab/belpy,sorgerlab/indra,pvtodorov/indra,johnbachman/indra,bgyori/indra,sorgerlab/belpy,pvtodorov/indra,pvtodorov/indra,sorgerlab/indra