Move default settings into gn2 module.

1 files changed, 0 insertions, 122 deletions

diff --git a/etc/default_settings.py b/etc/default_settings.py
deleted file mode 100644
index c49a3c25..00000000
--- a/etc/default_settings.py
+++ /dev/null
@@ -1,122 +0,0 @@
-# Default settings file defines a single Flask process for the Python
-# webserver running in developer mode with limited console
-# output. Copy this file and run it from ./bin/genenetwork2 configfile
-#
-# Note: these settings are fetched in ./wqflask/utilities/tools.py
-# which has support for overriding them through environment variables,
-# e.g.
-#
-#   env LOG_SQL=True USE_REDIS=False ./bin/genenetwork2
-#   env LOG_LEVEL=DEBUG ./bin/genenetwork2 ~/gn2_settings.py
-#
-# Typically you need to set GN2_PROFILE too.
-#
-# Note also that in the near future we will additionally fetch
-# settings from a JSON file
-#
-# Note: values for False and 0 have to be strings here - otherwise
-# Flask won't pick them up
-#
-# For GNU Guix deployment also check the paths in
-#
-#  ~/.guix-profile/lib/python3.8/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py
-
-import os
-import sys
-
-GN_VERSION = "2.11-rc2"
-
-SECRET_KEY = ""
-
-# Redis
-REDIS_URL = "redis://:@localhost:6379/0"
-
-# gn2-proxy
-GN2_PROXY = "http://localhost:8080"
-
-# GN PROXY
-GN_PROXY_URL="https://genenetwork.org/gn3-proxy/"
-
-# ---- MySQL
-
-SQL_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s"
-SQL_ALCHEMY_POOL_RECYCLE = 3600
-GN_SERVER_URL = "http://localhost:8880/api/" # REST API server
-AUTH_SERVER_URL="http://localhost:9094/"
-GN2_BASE_URL = "http://genenetwork.org/" # to pick up REST API
-GN2_BRANCH_URL = GN2_BASE_URL
-
-# ---- Flask configuration (see website)
-TRAP_BAD_REQUEST_ERRORS = True
-SECURITY_CONFIRMABLE = True
-SECURITY_TRACKABLE = True
-SECURITY_REGISTERABLE = True
-SECURITY_RECOVERABLE = True
-SECURITY_EMAIL_SENDER = "no-reply@genenetwork.org"
-SECURITY_POST_LOGIN_VIEW = "/thank_you"
-
-SERVER_PORT = 5003
-
-SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a\xbc\xfc\x80:*\xebc'
-
-GITHUB_CLIENT_ID = "UNKNOWN"
-GITHUB_CLIENT_SECRET = "UNKNOWN"
-GITHUB_AUTH_URL = "https://github.com/login/oauth/authorize"
-GITHUB_API_URL = "https://api.github.com/user"
-
-ORCID_CLIENT_ID = "UNKNOWN"
-ORCID_CLIENT_SECRET = "UNKNOWN"
-ORCID_AUTH_URL = "https://orcid.org/oauth/authorize"
-ORCID_TOKEN_URL = "https://orcid.org/oauth/token"
-
-ELASTICSEARCH_HOST = "localhost"
-ELASTICSEARCH_PORT = '9200'
-
-SMTP_CONNECT = "localhost"
-SMTP_USERNAME = "UNKNOWN"
-SMTP_PASSWORD = "UNKNOWN"
-
-
-# ---- Behavioural settings (defaults) note that logger and log levels can
-#      be overridden at the module level and with enviroment settings
-WEBSERVER_MODE = 'DEV'     # Python webserver mode (DEBUG|DEV|PROD)
-WEBSERVER_BRANDING = None   # Set the branding (nyi)
-WEBSERVER_DEPLOY = None     # Deployment specifics (nyi)
-WEBSERVER_URL = "http://localhost:" + str(SERVER_PORT) + "/" # external URL
-
-LOG_LEVEL = 'WARNING' # Logger mode (DEBUG|INFO|WARNING|ERROR|CRITICAL)
-LOG_LEVEL_DEBUG = '0'       # logger.debugf log level (0-5, 5 = show all)
-LOG_SQL = 'False'   # Log SQL/backend and GN_SERVER calls
-LOG_SQL_ALCHEMY = 'False'
-LOG_BENCH = True      # Log bench marks
-
-USE_REDIS = True      # REDIS caching (note that redis will be phased out)
-USE_GN_SERVER = 'False'   # Use GN_SERVER SQL calls
-HOME = os.environ['HOME']
-
-# ---- Default locations
-# base dir for all static data files
-GENENETWORK_FILES = HOME + "/genotype_files"
-
-# ---- Path overrides for Genenetwork - the defaults are normally
-#      picked up from Guix or in the HOME directory
-
-# TMPDIR is normally picked up from the environment
-# PRIVATE_FILES = HOME+"/gn2_private_data" # private static data files (unused)
-
-# ---- Local path to JS libraries - for development modules (only)
-JS_GN_PATH = os.environ['HOME'] + "/genenetwork/javascript"
-
-# ---- GN2 Executables (overwrite for testing only)
-# PLINK_COMMAND = str.strip(os.popen("which plink2").read())
-# GEMMA_COMMAND = str.strip(os.popen("which gemma").read())
-REAPER_COMMAND = os.environ['GN2_PROFILE'] + "/bin/qtlreaper"
-CORRELATION_COMMAND = os.environ["GN2_PROFILE"] + "/bin/correlation_rust"
-# GEMMA_WRAPPER_COMMAND = str.strip(os.popen("which gemma-wrapper").read())
-
-OAUTH2_CLIENT_ID="0bbfca82-d73f-4bd4-a140-5ae7abb4a64d"
-OAUTH2_CLIENT_SECRET="yadabadaboo"
-
-SESSION_TYPE = "redis"
-SESSION_PERMANENT = True
-SESSION_USE_SIGNER = True