Add reference files to database after download

Fixes #392
partial fix
Merge branch 'master' of github.com:qiime/QiiTa into no_id_templates
step 2
Step 3
Merge branch 'master' of github.com:qiime/QiiTa into no_id_templates
Adding utility function for getting the translate dictionaries
No more *_id columns on the templates
Partial fix for asking for the real categories instead for the *_id ones
Making the changes on the BaseSample object so it recognizes the user non *_id columns
Fixing remaining issues
Fixing comments
Merge branch 'master' of github.com:qiime/QiiTa into no_id_templates
Merge pull request #414 from josenavas/no_id_templates

No id columns required on the Sample/Prep templates
rename qiita_ware run.py
add new processing function and add to handler. Fix #420
Fix #421 and Fix #419
Merge branch 'master' of https://github.com/biocore/qiita into add_ref_to_db-issue-392

Conflicts:
	qiita_db/environment_manager.py
rename test file
Fix #424