""" Default configuration settings for this project. DO NOT import from this file, use `flask.current_app.config` instead to get the application settings. """ import os import uuid import tempfile 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 = os.environ.get( "SPARQL_ENDPOINT", "http://localhost:9082/sparql") # LMDB path LMDB_PATH = os.environ.get( "LMDB_PATH", f"{os.environ.get('HOME')}/tmp/dataset") # 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 # FAHAMU API TOKEN FAHAMU_AUTH_TOKEN = "" 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('GN2_PROFILE')}/bin/correlation_rust" # genotype files GENOTYPE_FILES = os.environ.get( "GENOTYPE_FILES", f"{os.environ.get('HOME')}/genotype_files/genotype") # Xapian index XAPIAN_DB_PATH = "xapian" # 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("*") 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 AUTH_SERVER_URL = "" AUTH_MIGRATIONS = "migrations/auth" AUTH_DB = os.environ.get( "AUTH_DB", f"{os.environ.get('HOME')}/genenetwork/gn3_files/db/auth.db") OAUTH2_SCOPE = ( "profile", "group", "role", "resource", "user", "masquerade", "introspect") GNQA_DB = os.environ.get( "GNQA_DB", f"{os.environ.get('HOME')}/genenetwork/gn3_files/db/gnqa.db") try: # *** SECURITY CONCERN *** # Clients with access to this privileges create a security concern. # Be careful when adding to this configuration OAUTH2_CLIENTS_WITH_INTROSPECTION_PRIVILEGE = tuple( uuid.UUID(client_id) for client_id in os.environ.get( "OAUTH2_CLIENTS_WITH_INTROSPECTION_PRIVILEGE", "").split(",")) except ValueError as _valerr: OAUTH2_CLIENTS_WITH_INTROSPECTION_PRIVILEGE = tuple() try: # *** SECURITY CONCERN *** # Clients with access to this privileges create a security concern. # Be careful when adding to this configuration OAUTH2_CLIENTS_WITH_DATA_MIGRATION_PRIVILEGE = tuple( uuid.UUID(client_id) for client_id in os.environ.get( "OAUTH2_CLIENTS_WITH_DATA_MIGRATION_PRIVILEGE", "").split(",")) except ValueError as _valerr: OAUTH2_CLIENTS_WITH_DATA_MIGRATION_PRIVILEGE = tuple()