Script for updating local genome-scale model database

bigg-models-updater.sh

#!/bin/bash

check_installed() {
    command -v "$1" >/dev/null 2>&1 || { 
        echo >&2 "$1 required but it's not installed. Aborting."
        exit 1 
    }
}

# Check required commands
check_installed 'curl'
check_installed 'jq'

# Get a list of models
MODELS=$(curl -s 'http://bigg.ucsd.edu/api/v2/models')

# Save models info to file
echo "$MODELS" | jq '.' > 'models.json'

# Get a number of models in list
MODEL_COUNT=$(echo "$MODELS" | jq '.results_count')

# Set a counter
MODEL_INDEX=0

echo "$MODELS" | jq -c '.results[]' | while read -r LINE; do
    MODEL_INDEX=$(( MODEL_INDEX + 1 ))
    ID=$(echo "$LINE" | jq -r '.bigg_id')
    INFO=$(echo "$LINE" | jq -r '"\"\(.organism)\" (\(.bigg_id), \(.gene_count)/\(.reaction_count)/\(.metabolite_count))"')
    echo -e "($MODEL_INDEX/$MODEL_COUNT) Downloading $INFO: \c"
    mkdir -p "$ID"
    XML_URL="http://bigg.ucsd.edu/static/models/$ID.xml.gz"
    XML_FILE="./$ID/$ID.xml.gz"
    ETAG_FILE="./$ID/$ID.etag"
    ETAG=$([[ -f "$ETAG_FILE" ]] && cat "$ETAG_FILE" || echo "None")
    RESPONSE_CODE=$(curl -I -H "If-None-Match: \"$ETAG\"" -s -o /dev/null -w "%{http_code}" "$XML_URL")
    if [ "$RESPONSE_CODE" == "304" ]; then
        echo "Not changed"
    else
        curl -s "http://bigg.ucsd.edu/api/v2/models/$ID" | jq '.' > "./$ID/model.json"
        curl -s -D - "$XML_URL" -o "$XML_FILE" | grep -ioP 'Etag:\s*"?\K[^"]+' > "$ETAG_FILE" && echo "Saved" || echo "Error"
    fi
done