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 is from the meeting Tuesday where we discussed the need to add these two columns to the table since this does not act using a ProcessedData object. I lumped them in here so I had all database changes done at once and didn't have to tweak access classes and populate_test_db twice.