"""Configuration settings for this project""" import tempfile import os BCRYPT_SALT = "$2b$12$mxLvu9XRLlIaaSeDxt8Sle" # Change this! DATA_DIR = "" GEMMA_WRAPPER_CMD = os.environ.get("GEMMA_WRAPPER", "gemma-wrapper") RQTL_WRAPPER_CMD = os.environ.get("RQTL_WRAPPER") CACHEDIR = "" REDIS_URI = "redis://localhost:6379/0" REDIS_JOB_QUEUE = "GN3::job-queue" TMPDIR = os.environ.get("TMPDIR", tempfile.gettempdir()) RQTL_WRAPPER = "rqtl_wrapper.R" # SPARQL endpoint SPARQL_ENDPOINT = "http://localhost:8891/sparql" # SQL confs SQL_URI = os.environ.get( "SQL_URI", "mysql://webqtlout:webqtlout@localhost/db_webqtl") SECRET_KEY = "password" # gn2 results only used in fetching dataset info GN2_BASE_URL = "http://www.genenetwork.org/" # wgcna script WGCNA_RSCRIPT = "wgcna_analysis.R" # qtlreaper command REAPER_COMMAND = f"{os.environ.get('GUIX_ENVIRONMENT')}/bin/qtlreaper" # correlation command CORRELATION_COMMAND = f"{os.environ.get('GUIX_ENVIRONMENT')}/bin/correlation_rust" # genotype files GENOTYPE_FILES = os.environ.get( "GENOTYPE_FILES", f"{os.environ.get('HOME')}/genotype_files/genotype") # CROSS-ORIGIN SETUP def parse_env_cors(default): """Parse comma-separated configuration into list of strings.""" origins_str = os.environ.get("CORS_ORIGINS", None) if origins_str: return [ origin.strip() for origin in origins_str.split(",") if origin != ""] return default CORS_ORIGINS = parse_env_cors([ "http://localhost:*", "http://127.0.0.1:*" ]) CORS_HEADERS = [ "Content-Type", "Authorization", "Access-Control-Allow-Credentials" ] GNSHARE = os.environ.get("GNSHARE", "/gnshare/gn/") TEXTDIR = f"{GNSHARE}/web/ProbeSetFreeze_DataMatrix" ROUND_TO = 10 MULTIPROCESSOR_PROCS = 6 # Number of processes to spawn