Merge pull request #1 from genenetwork/testing

Updating my testing branch

3 files changed, 48 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..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())
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;
-        }
-    }
-}