1 files changed, 122 insertions, 0 deletions
diff --git a/gn2/default_settings.py b/gn2/default_settings.py
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+++ b/gn2/default_settings.py
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+# 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/gn2/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