Handle composite IDs, refactor tests

[bruhad-dave]

• Added support to handle cases where key/ID column values in input tabular files are not unique, but can be made unique when joined with values from another column (eg. cases where sample_id may not have all unique values, but sample_id when combined with, for example, something like replicate_number, forms a unique ID)
• Refactored tests to reduce use of file comparisons of test outputs against fixed expected files
• Added explicit handling of "" as None rather than string, updated corresponding test