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"""Configuration settings for this project"""
import tempfile
import os
import pathlib
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/"
# R script
R_SCRIPTS = pathlib.Path("./scripts/").absolute()
WGCNA_RSCRIPT = "wgcna_analysis.R"
# qtlreaper command
REAPER_COMMAND = f"{os.environ.get('GUIX_ENVIRONMENT')}/bin/qtlreaper"
# 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
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