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authoracenteno2020-04-21 17:35:34 -0500
committerGitHub2020-04-21 17:35:34 -0500
commit660589b9c2a507529e8e51ca6ce66ca97ad982c5 (patch)
tree27f63957278581bc2fce2b88744bfe20c8a81558 /etc/default_settings.py
parentd97fdc18359233f07c1a1c7b83fe7e88eb225043 (diff)
parentf2a3ae13231a7d270a5bb6911c248aa713f1ef91 (diff)
downloadgenenetwork2-660589b9c2a507529e8e51ca6ce66ca97ad982c5.tar.gz
Merge pull request #1 from genenetwork/testing
Updating my testing branch
Diffstat (limited to 'etc/default_settings.py')
-rw-r--r--etc/default_settings.py67
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())