app.py

from flask import Flask, jsonify,request
import subprocess
import os,glob

app = Flask(__name__)

def run_ldsc_command(pop, genome_build, filename,ldwindow,windUnit):
    fileDir = f"/data/tmp/uploads"
    print(filename)
    ldwindow_value = 1  # Example value, replace with actual value

    # Check if ldwindow is an integer greater than 0, if not set it to 1
    try:
        ldwindow_value = int(ldwindow)
        if ldwindow_value <= 0:
            ldwindow_value = 1
    except ValueError:
        ldwindow_value = 1

    windFlag = '--ld-wind-cm'
    if windUnit == 'cm':
        windFlag = "--ld-wind-cm"
    elif windUnit == 'kb':
        windFlag = "--ld-wind-kb"

    if filename:
        file_parts = filename.split('.')
        file_chromo = None
        for part in file_parts:
            if part.isdigit() and 1 <= int(part) <= 22:
                file_chromo = part
                break
    
    if file_chromo:
        # Find the file in the directory
        pattern = os.path.join(fileDir, f"{filename}.*")
        for file_path in glob.glob(pattern):
            extension = file_path.split('.')[-1]
            new_filename = f"{file_chromo}.{extension}"
            new_file_path = os.path.join(fileDir, new_filename)
            os.rename(file_path, new_file_path)
        
    try:
        # Run the command
        # 'cd 1kg_eur && python ../ldsc.py --bfile 22 --l2 --ld-wind-cm 1 --out 22'
        command = f"cd {fileDir} && python /app/ldsc.py --bfile {file_chromo} --l2 {windFlag} {ldwindow_value} --out {file_chromo}"
        result = subprocess.run(
            ['bash', '-c', command],
            check=True,
            capture_output=True,
            text=True
        )
        return result.stdout
    except subprocess.CalledProcessError as e:
        return f"An error occurred: {e.stderr}"

@app.route('/ldscore')
def ldscore():
    pop = request.args.get('pop')
    genome_build = request.args.get('genome_build')
    filename = request.args.get('filename')
    print(f"pop: {pop}, genome_build: {genome_build}, filename: {filename}")
    output = run_ldsc_command(pop, genome_build, filename)
    return jsonify({"output": output})

if __name__ == '__main__':
    app.run(host='0.0.0.0', port=5000)