DB changes for issue 215

This adds the `study_id` column to the `analysis_samples` table as discussed in issue #215. This also adds the two columns to the analysis_filepath table that were discussed in the Tuesday meeting. All objects and test data are also updated to reflect these added columns.
This requires some tweaking of the ProcessedData object to allow creation without files and to check that it is in a nulled state or not, as opposed to just letting this column be nullable. Before I make this change, can we confirm this is what we want?.