use ARMFIDER_DB env var to locate armfinder databases

[EricDeveaud]

Hello

armfinder can use n environnement variable to locate the armfinder database.

I think it would be a good idea if bakta/utils.py can use this one to in order to locate the database this will avoid the need of duplication of amrfinder databases if it's already installed and configured.

best regards

Eric

[oschwengers]

Hi @EricDeveaud , thanks for pointing out. Yes, it shouldn't be much of an issue. Do you ask because of the duplicated db or because of an existing installation that is regularly updated? I'm asking because the AMRFinder db is a mere 200 Mb of a total of 59 Gb of the Bakta db. So disk storage should be no problem.

Best regards, Oliver

[EricDeveaud]

Hello,

my first concern is. to have bakta and amrfinder installation as independant as possible. amrfinder db update is handled automaticaly in our setup. I don't want to have divergence in the db content that may implies divergence in the results.

currently I may have the following setup bakta -> amrfinderdb (version N) amrfinder -> amrfinder (version N+1)

as for coding avoid duplication as much s possible NB using symbolic links will be a no way for me ;-)

I think using native information//capabilities from the external tool your code calls wil be a good idea.

NB bakta/expert/amrfinder.py will also gain from using AMRFINDER_DBenvironnement variable

regards

Eric