1 files changed, 0 insertions, 115 deletions
diff --git a/gn3/settings.py b/gn3/settings.py
deleted file mode 100644
index 04aa129..0000000
--- a/gn3/settings.py
+++ /dev/null
@@ -1,115 +0,0 @@
-"""
-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")
-CACHEDIR = ""
-REDIS_URI = "redis://localhost:6379/0"
-REDIS_JOB_QUEUE = "GN3::job-queue"
-TMPDIR = os.environ.get("TMPDIR", tempfile.gettempdir())
-
-# 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"
-
-# sqlite path
-
-LLM_DB_PATH = ""
-# 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 = "https://auth.genenetwork.org"
-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")
-
-
-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()