Merge from the diet branch.

  * refactored ./bin/genenetwork2 and /etc/default_settings
    - better detection of Guix
    - removed unused parameters, such as GEMMA_RESULT_PATH and TEMP_TRAITS
    - removing some default settings, such as PYLMM_COMMAND
    - rename some settings, such as SQL_URI and LOG_SQL_ALCHEMY
    - added GUIX_JS_PATH for JS modules
  * Added documentation on installing binary GN2
  * Updated Twitter board to latest version in Guix - it had broken
  * Updated many tools in the latest Guix profile

1 files changed, 17 insertions, 16 deletions

diff --git a/etc/default_settings.py b/etc/default_settings.py
index 6acea637..4f3a6f5c 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -9,6 +9,8 @@
 #   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
 #
@@ -18,10 +20,9 @@
 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
+SQL_ALCHEMY_POOL_RECYCLE = 3600
 GN_SERVER_URL = "http://localhost:8880/"
 
 # ---- Flask configuration (see website)
@@ -45,24 +46,24 @@ WEBSERVER_DEPLOY = None     # Deployment specifics (nyi)
 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
-
-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
+# GENENETWORK_FILES   = HOME+"/gn2_data"  # base dir for all static data files
+# PRIVATE_FILES = HOME+"/gn2_private_data" # private static data files (unused)
+
+# ---- Local path to JS libraries - for development modules (only)
+# GN2_JS_PATH = os.environ['HOME']+"/genenetwork/javascript" (unused)
 
-# ---- 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())
+# ---- GN2 Executables (overwrite for testing only)
+# 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())