curate apply-geolocation-rules: Allow rule overrides

[joverlee521]

Context

augur curate apply-geolocation-rules currently only takes one set of geolocation rules without any concept of priority. If there any of the rules overwrite each other, then the command eventually raises a CyclicGeolocationRulesError.

As @jameshadfield commented:

If we're going to continue with the pattern of a master-list plus some repo-specific additions it'd be nice if those additions could function as overrides. I.e. if the master list replaces X with Y, we could add an override of Y to X (or Y to Z etc) in a repo-specific manner.

This aligns with the plan to create a curated standard list of geolocation rules that users can override with their own rules.

Possible solution

We can add an optional arg to the command that expects a separate file of "prioritized" rules. If provided, the prioritized rules will be applied to the records first. If none of the prioritized rule are applied, then the general rules are applied.

Cyclic rules within each rule set should still be considered a user error and raise an error. However, cyclic rules do not have to be checked between the two sets of rules to allow the prioritized rules to override any of the general rules.

[joverlee521]

@kimandrews ran into the CyclicGeolocationRulesError again when trying to change the French Guiana location from Europe/France to South America/French Guiana for rabies.

Working around this by changing to South America/French Guiana (France) so that the rules are no longer cyclical.