diff options
Diffstat (limited to 'etc')
| -rw-r--r-- | etc/VERSION | 1 | ||||
| -rw-r--r-- | etc/default_settings.py | 79 | ||||
| -rw-r--r-- | etc/nginx-genenetwork.conf | 54 |
3 files changed, 60 insertions, 74 deletions
diff --git a/etc/VERSION b/etc/VERSION new file mode 100644 index 00000000..a4320e6f --- /dev/null +++ b/etc/VERSION @@ -0,0 +1 @@ +2.11-rc2 diff --git a/etc/default_settings.py b/etc/default_settings.py index 6acea637..f368237b 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -2,27 +2,38 @@ # 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() +GN_SERVER_URL = "http://localhost:8880/" # REST API server + +# ---- MySQL + 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 +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 @@ -33,36 +44,64 @@ SECURITY_RECOVERABLE = True SECURITY_EMAIL_SENDER = "no-reply@genenetwork.org" SECURITY_POST_LOGIN_VIEW = "/thank_you" -SERVER_PORT = 5003 +# ---- SERVER_PORT needs an override before firing up the server +SERVER_PORT = os.environ['SERVER_PORT'] +if isinstance(SERVER_PORT, str): + SERVER_PORT = int(SERVER_PORT) # don't do this for other settings! +else: + 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_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()) diff --git a/etc/nginx-genenetwork.conf b/etc/nginx-genenetwork.conf deleted file mode 100644 index 06fd3c57..00000000 --- a/etc/nginx-genenetwork.conf +++ /dev/null @@ -1,54 +0,0 @@ -user nobody; -worker_processes 4; -pid /var/run/nginx.pid; - -error_log /var/log/nginx/error.log; - -events { - worker_connections 16; -} - -http { - include mime.types; - # default_type application/octet-stream; - - # sendfile on; - keepalive_timeout 480; - - server { - listen 80; - server_name localhost; - - location / { - root html; - index index.html index.htm; - } - - error_page 500 502 503 504 /50x.html; - location = /50x.html { - root html; - } - } - - server { - listen 80; - server_name test-gn2.genenetwork.org; - access_log logs/test-gn2.access.log; - - proxy_connect_timeout 3000; - proxy_send_timeout 3000; - proxy_read_timeout 3000; - send_timeout 3000; - - location / { - # proxy_set_header Host $host; - proxy_set_header Host $http_host; - # proxy_redirect off; - proxy_set_header Connection keep-alive; - proxy_set_header X-Real-IP $remote_addr; - proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; - proxy_set_header X-Forwarded-Host $server_name; - proxy_pass http://127.0.0.1:5003; - } - } -} |