diff options
Diffstat (limited to 'etc')
| -rw-r--r-- | etc/default_settings.py | 35 |
1 files changed, 24 insertions, 11 deletions
diff --git a/etc/default_settings.py b/etc/default_settings.py index f3ca2e58..29b96861 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -2,27 +2,33 @@ # 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 # -# Note also that in the near future we will additionally fetch +# Note: 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() 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/" -# Flask configuration (see website) +# ---- Flask configuration (see website) TRAP_BAD_REQUEST_ERRORS = True SECURITY_CONFIRMABLE = True SECURITY_TRACKABLE = True @@ -34,14 +40,14 @@ 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' -# Behavioural settings (defaults) note that logger and log levels can -# be overridden at the module level and with enviroment settings +# ---- 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) LOG_LEVEL = 'WARNING' # Logger mode (DEBUG|INFO|WARNING|ERROR|CRITICAL) -LOG_LEVEL_DEBUG = '0' # Debug log level (0-5, 0 = show all) +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_BENCH = True # Log bench marks @@ -49,13 +55,20 @@ 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 -# Path overrides for Genenetwork +# Paths to JS libraries + +BIODALLIANCE_JS = os.environ['HOME']+"/genenetwork/biodalliance" + +# ---- 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" +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 +# Paths to invoked binaries 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()) - -BIODALLIANCE_PATH = os.environ['HOME']+"/dalliance" |