config.py

import os

# Configure the app URL prefix
URL_PREFIX = os.environ.get('URL_PREFIX', '/ligysis')
STATIC_URL_PATH = f"{URL_PREFIX}/static"

# Base directory for session and data storage (including example data)
BASE_DIR = os.path.dirname(os.path.abspath(__file__))

# /path/to/LIGYSIS_PDB
EXAMPLES = os.path.join(BASE_DIR, "static", "data")
DATA_FOLDER = os.environ.get('APP_DATA_PATH', EXAMPLES)
if DATA_FOLDER == EXAMPLES:
    SPLIT_FOLDER = os.path.join(DATA_FOLDER, "biolip", "split")
else:
    SPLIT_FOLDER = DATA_FOLDER

ASSEMBLY_FOLDER = os.path.join(DATA_FOLDER, "data", "structures", "assembly") # IN EXAMPLE & CLUSTER
CIF_SIFTS_DIR = os.path.join(DATA_FOLDER, "data", "cif_sifts") # IN CLUSTER
CHAIN_MAPPING_DIR = os.path.join(DATA_FOLDER, "data", "chain_remapping") # IN CLUSTER

PROTS_FOLDER = os.path.join(DATA_FOLDER, "output_V2")

# Paths that can be resolved when with DATA_FOLDER or SPLIT_FOLDER
SITE_TABLES_FOLDER = os.path.join(SPLIT_FOLDER, "site_tables")
RES_TABLES_FOLDER = os.path.join(SPLIT_FOLDER, "res_tables")
REP_STRUCS_FOLDER = os.path.join(SPLIT_FOLDER,  "segment_coords")

#REP_STRUCS_FOLDER = os.path.join(DATA_FOLDER, "segment_rep_dicts") # IN CLUSTER

# USER_JOBS_FOLDER = os.path.join(BASE_DIR, "static", "data", "USER_JOBS") # THIS WILL NEED TO CHANGE WHEN MOVED TO CLUSTER
USER_JOBS_FOLDER = os.path.join(DATA_FOLDER, "USER_JOBS") # THIS WILL NEED TO CHANGE WHEN MOVED TO CLUSTER

USER_JOBS_IN_FOLDER = os.path.join(USER_JOBS_FOLDER, "IN") # THIS WILL NEED TO CHANGE WHEN MOVED TO CLUSTER

USER_JOBS_OUT_FOLDER = os.path.join(USER_JOBS_FOLDER, "OUT") # THIS WILL NEED TO CHANGE WHEN MOVED TO CLUSTER

# Config for users submission handling
SESSIONS_FOLDER = os.path.join(BASE_DIR, 'sessions')
SESSIONS_FOLDER = os.environ.get('APP_SESSIONS_PATH', SESSIONS_FOLDER)

# Add logging level and path configuration
LOG_LEVEL = os.environ.get('APP_LOG_LEVEL', 'INFO').upper()
LOG_PATH = os.path.join(BASE_DIR, 'logs')
LOG_PATH = os.environ.get('APP_LOG_PATH', LOG_PATH)

DATABASE_PATH = os.path.join(BASE_DIR, 'db', 'session.sqlite')
DATABASE_PATH = os.environ.get('APP_DATABASE_PATH', DATABASE_PATH)

SLIVKA_URL = os.environ.get('SLIVKA_URL', 'http://localhost:3203')
EXPIRATION_DAYS = float(os.environ.get('APP_EXPIRATION_DAYS', 7))

# Analytics configuration
ANALYTICS_DOMAIN = os.environ.get('ANALYTICS_DOMAIN')
ANALYTICS_SCRIPT_URL = os.environ.get('ANALYTICS_SCRIPT_URL')