Commits on Jul 16, 2021

1. Refactor filters into separate functions …

   Refactors filter logic into separate function with the same signature of
   `func(metadata, **kwargs)` that returns a `set` of strain names that
   pass the filter. Although this work does not reduce the complexity of
   the code by itself, it sets up a pattern that will allow us to move all
   filters into a single loop through all user-requested filters. This
   change should simplify the main logic and also allow us to short-cut
   evaluation when filters remove all possible strains (e.g.,
   `--exclude-all`), avoiding unnecessary checks.
   
   This refactoring also includes new functions for sequence-based filters.
   As part of these sequence-based functions, we update the sequence index
   data frame to be indexed by strain name to be consistent with the
   metadata data frame.
   
   One side-effect of this refactoring is the additional of a functional
   test for both `--include-where` and `--exclude-where` filters to make
   sure these are properly implemented and no regressions occur during
   refactoring. The lack of this test initially allowed the refactoring of
   `--exclude-where` logic to introduce a bug.
   
   Finally, we also define a new function to include strains by a query.
   Note that this implementation relies on the same query parser used by
   the `--exclude-where` argument which allows the negation operator and
   also the code that lowercases the strings before comparison. This change
   is backward compatible, however, and only adds functionality that is
   consistent with the `--exclude-where` functionality.

   

   huddlej committed Jul 16, 2021
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