diff options
Diffstat (limited to 'etc/default_settings.py')
| -rw-r--r-- | etc/default_settings.py | 67 |
1 files changed, 47 insertions, 20 deletions
diff --git a/etc/default_settings.py b/etc/default_settings.py index 6acea637..75f84dc4 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -2,27 +2,32 @@ # webserver running in developer mode with limited console # output. Copy this file and run it from ./bin/genenetwork2 configfile # -# Note that these settings are fetched in ./wqflask/utilities/tools.py +# 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 that values for False and 0 have to be strings here - otherwise +# 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/python2.7/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py import os import sys -GN_VERSION = open("../VERSION","r").read() +GN_VERSION = open("../etc/VERSION","r").read() SQL_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s" -SQLALCHEMY_DATABASE_URI = 'mysql://gn2:mysql_password@localhost/db_webqtl_s' -SQLALCHEMY_POOL_RECYCLE = 3600 -GN_SERVER_URL = "http://localhost:8880/" +SQL_ALCHEMY_POOL_RECYCLE = 3600 +GN_SERVER_URL = "http://localhost:8880/" # REST API server # ---- Flask configuration (see website) TRAP_BAD_REQUEST_ERRORS = True @@ -33,36 +38,58 @@ SECURITY_RECOVERABLE = True SECURITY_EMAIL_SENDER = "no-reply@genenetwork.org" SECURITY_POST_LOGIN_VIEW = "/thank_you" -SERVER_PORT = 5003 +SERVER_PORT = 5003 # running on localhost 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 = "UNKNOWN" +GITHUB_API_URL = "UNKNOWN" + +ORCID_CLIENT_ID = "UNKNOWN" +ORCID_CLIENT_SECRET = "UNKNOWN" +ORCID_AUTH_URL = "UNKNOWN" +ORCID_TOKEN_URL = "UNKNOWN" + +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_SQLALCHEMY = 'False' +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'] -# Paths to JS libraries +# ---- Default locations +GENENETWORK_FILES = HOME+"/genotype_files" # base dir for all static data files -TWITTER_POST_FETCHER_JS_PATH = os.environ['HOME']+"/genenetwork/Twitter-Post-Fetcher" +# ---- Path overrides for Genenetwork - the defaults are normally +# picked up from Guix or in the HOME directory -# ---- Path overrides for Genenetwork # TMPDIR is normally picked up from the environment -HOME=os.environ['HOME'] -LOGFILE = HOME+"/genenetwork2.log" -GENENETWORK_FILES = HOME+"/gn2_data" # base dir for all static data files -LOCAL_PRIVATE_FILES = HOME+"/gn2_private_data" # private static data files - -# ---- GN2 Executables -PYLMM_COMMAND = str.strip(os.popen("which pylmm_redis").read()) -PLINK_COMMAND = str.strip(os.popen("which plink2").read()) -GEMMA_COMMAND = str.strip(os.popen("which gemma").read()) +# 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" +# GEMMA_WRAPPER_COMMAND = str.strip(os.popen("which gemma-wrapper").read()) |