run.sh

#!/bin/bash
dset_dir="$1"
spectra_dir="$dset_dir/mgf"
output_root_dir="./outputs"
overlay_size=1024

# TODO maybe now we need separate output dir for each dataset
dset_name=$(basename "$dset_dir")
output_dir="$output_root_dir/$dset_name"

recalculate=false

while getopts ":r" opt; do
  case $opt in
    r) recalculate=true
    ;;
    \?) echo "Invalid option -$OPTARG" >&2
    ;;
  esac
done
echo "Recalculate all algorithm outputs: $recalculate"

if "$recalculate"; then
    # Clean output dir 
    rm -rf "$output_dir"
fi

# Create the output directory if it doesn't exist
mkdir -p "$output_dir"

# List input files
echo "Processing dataset: $dset_name ($dset_dir)"
ls "$spectra_dir"/*.mgf

# Loop through each algorithm in the algorithms directory
for algorithm_dir in algorithms/*; do
    # if [ -d "$algorithm_dir" ]; then
    if [ -d "$algorithm_dir" ] && [ $(basename "$algorithm_dir") != "base" ]; then
        algorithm_name=$(basename "$algorithm_dir")
        output_file="$output_dir/${algorithm_name}_output.csv"
        echo "$output_file"
        
        # Check if the output file does not exist
        if [ ! -e "$output_file" ]; then
            echo "Processing algorithm: $algorithm_name"

            # Remove an existing container overlay, if any
            rm -rf "algorithms/${algorithm_name}/overlay.img"
            # Create writable overlay for the container
            apptainer overlay create --fakeroot --size $overlay_size --sparse "algorithms/${algorithm_name}/overlay.img"

            # Calculate predicitons
            echo "RUN ALGORITHM"
            apptainer exec --fakeroot --nv \
                --overlay "algorithms/${algorithm_name}/overlay.img" \
                -B "${spectra_dir}":"/algo/${dset_name}" \
                "algorithms/${algorithm_name}/container.sif" \
                bash -c "cd /algo && ./make_predictions.sh ${dset_name}"
            
            # Collect predictions in output_dir
            echo "EXPORT PREDICTIONS"
            apptainer exec --fakeroot \
                --overlay "algorithms/${algorithm_name}/overlay.img" \
                -B "${output_dir}":/algo/outputs \
                "algorithms/${algorithm_name}/container.sif" \
                bash -c "cp /algo/outputs.csv /algo/outputs/${algorithm_name}_output.csv"

        else
            echo "Skipping algorithm: $algorithm_name. Output file already exists."
        fi
    fi
done

# Evaluate predictions
# TODO: add results_dir explicit definition
echo "EVALUATE PREDICTIONS"
apptainer exec --fakeroot "evaluation.sif" \
    bash -c "python evaluate.py ${output_dir}/ ${dset_dir}"
# TODO change to dset_dir/labels?