param to run ALL GO rules in ontobio-parse-assocs does not run all rules

[dustine32]

Related to #544

@dougli1sqrd Was having some trouble getting all rules to run using the new -l all param. I had a WB GPAD with two lines annotated to CC root but they used relation located_in, which violates GO rule 61. These didn't get repaired when running ontobio-parse-assocs.py with the -l all param.

Throwing on my debugger, I traced it to this line in assocparser.py:

ontobio/ontobio/io/assocparser.py

Line 268 in d4fff4a

elif rule_set == RuleSet.ALL:

Here, rule_set was coming in as list ["all"] but RuleSet.ALL is just the str "all":

ontobio/ontobio/io/assocparser.py

Line 193 in d4fff4a

ALL: ClassVar[str] = "all"

To fix, I just "listified" RuleSet.ALL in the conditional:

elif rule_set == [RuleSet.ALL]:

@dougli1sqrd I can PR this change and you can trash it if you don't like it. Thanks!

[dougli1sqrd]

Oh good catch. The reason, though, this is coming in as a list is because the command line option in ontobio-parse-assocs is being created as a list, so "all" is being inserted as an item.

My thought is that since this is an artifact of the argument parsing, we should parse that there in ontobio-parse-assocs. If the incoming args.rule_set contains RuleSet.ALL then we should just set the config to be RuleSet.ALL rather than a list, as expected by the logic in the config init.

[dustine32]

@dougli1sqrd Thanks! I just corrected it in the PR.