Make missing API key errors more friendly

[caufieldjh]

When missing API keys (and especially the Bioportal one), crashes can happen in the middle of operations.
If a template requires Bioportal in its annotators, for example, using that template in an extract command will raise an error, but only once the annotator is required.
This should instead either:

• Check to see if an API key will be required before running anything, or
• Raise an informative error noting which API key is missing