ENH: Use ontology terms in for ebi command

The EBI command was not using the ontology terms contained in the
database, this has been changed to use it instead.
ENH: Update code to use new_investigation_type

new_investigation_type is a parameter used in to specify an
investigation type if "Other" is provided as the investigation_type.

Fixes #405
STY/ENH: Add changes as suggested by @adamrp
TST: Use new_investigation_type in test_ebi
STY: Fix requirements by flake8
BUG: Add missing argument
ENH: Use new_investigation_type from the GUI
First entry in CONTRIBUTING.md

Notes about making database changes
Add patches directory
skeleton of tests for qiita_pet
finish skeleton
add auth handlers tests
add analysis_handers tests
modifying the database to add a status on the raw data
Fixing tests due to changes in db
Adding add_filepaths_status property to RawData
Adding util functions to manage filepaths
Adding the clear_filepaths and remove_filepath function to the RawData object, and their tests
Removing unused variable
Addressing comment