Implement benchmarking platform run periodically

[dkoslicki]

Say, on one of the Koslicki_Lab servers, use the Benchmarks repo to run the benchmarks and analyze the results (say, run once a week/month via cron job). Something like

fetch_results.sh

#!/bin/bash

subdirectories=("arax" "bte" "improving" "aragorn")
#bench=("OOPD" "RareDisease" "ameliorates" "three_hop" "treats" "drug_treats_rare_disease" "GTRx" "DrugCentral_creative" "CPIC")
bench=("ameliorates")
for bench in "${bench[@]}"; do
        for tool in "${subdirectories[@]}"; do
            nohup  benchmarks_fetch ${bench} ${tool} ${tool}/${bench} --n 4 --overwrite &
        done
        wait
done

analyze_results.sh

subdirectories=("arax" "bte" "improving" "aragorn")
#subdirectories=("bte")
bench=("OOPD" "RareDisease" "ameliorates" "three_hop" "treats" "drug_treats_rare_disease" "GTRx" "DrugCentral_creative" "CPIC")
for bench in "${bench[@]}"; do
        for tool in "${subdirectories[@]}"; do
            benchmarks_eval ${bench} ${tool}/${bench} --plots_dir ${tool}/${bench} --json ${tool}_${bench}.json
        done
done

Bonus points if the results (MRR, Hit@k, etc.) could be pushed somewhere publicly (eg. to a repo in the RTXteam org, maybe a new repo)