Better handle different errors for all commands

[Karan-Palan]

Found this one with format:

The extension does not load when the file is not a json/yaml:

It should show "Not a valid file" or something like that

[jviotti]

On what schema?

[Karan-Palan]

@jviotti - https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/module/ontology/ethnicity_ontology.json