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-rw-r--r--etc/default_settings.py2
-rw-r--r--wqflask/cfg/default_settings.py22
-rw-r--r--wqflask/runserver.py14
-rw-r--r--wqflask/utility/tools.py24
-rw-r--r--wqflask/wqflask/database.py1
-rw-r--r--wqflask/wqflask/user_manager.py5
6 files changed, 35 insertions, 33 deletions
diff --git a/etc/default_settings.py b/etc/default_settings.py
index 58e37e18..bdcb9c5d 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -38,8 +38,8 @@ SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a
WEBSERVER_MODE = 'DEV' # Python webserver mode (DEBUG|DEV|PROD)
LOG_LEVEL = 'WARNING' # Logger mode (DEBUG|INFO|WARNING|ERROR|CRITICAL)
DEBUG_LOG_LEVEL = 1 # Debug log level (0-5)
-LOG_SQL = False # Log SQL/backend calls
USE_REDIS = True # REDIS caching (note that redis will be phased out)
+LOG_SQL = 'False' # Log SQL/backend calls
# Path overrides for Genenetwork
GENENETWORK_FILES = HOME+"/gn2_data"
diff --git a/wqflask/cfg/default_settings.py b/wqflask/cfg/default_settings.py
index 88159321..5af61d5a 100644
--- a/wqflask/cfg/default_settings.py
+++ b/wqflask/cfg/default_settings.py
@@ -1,21 +1 @@
-LOGFILE = """/tmp/flask_gn_log"""
-
-#This is needed because Flask turns key errors into a
-#400 bad request response with no exception/log
-TRAP_BAD_REQUEST_ERRORS = True
-
-# http://pythonhosted.org/Flask-Security/configuration.html
-SECURITY_CONFIRMABLE = True
-SECURITY_TRACKABLE = True
-SECURITY_REGISTERABLE = True
-SECURITY_RECOVERABLE = True
-
-SECURITY_EMAIL_SENDER = "no-reply@genenetwork.org"
-
-SECURITY_POST_LOGIN_VIEW = "/thank_you"
-
-SQLALCHEMY_POOL_RECYCLE = 3600
-
-SECURITY_PASSWORD_HASH = "bcrypt"
-SESSION_TYPE = "filesystem"
-SECRET_KEY = "secretkey"
+# no longer in use
diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index 4556056d..344826ce 100644
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -24,7 +24,19 @@ import logging
import utility.logger
logger = utility.logger.getLogger(__name__ )
-logger.info(app.config)
+BLUE = '\033[94m'
+GREEN = '\033[92m'
+BOLD = '\033[1m'
+ENDC = '\033[0m'
+
+# We always output this information on startup
+print "runserver.py: ****** The webserver has the following configuration ******"
+keylist = app.config.keys()
+keylist.sort()
+for k in keylist:
+ print("%s %s%s%s%s" % (k,BLUE,BOLD,app.config[k],ENDC))
+
+logger.info("GN2 is running. Visit %shttp://localhost:5003/%s" % (BLUE,ENDC))
from utility.tools import WEBSERVER_MODE
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 824ce330..1b31857e 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -43,16 +43,26 @@ def get_setting(command_id,guess=None):
# ---- Check whether environment exists
logger.debug("Looking for "+command_id+"\n")
command = value(os.environ.get(command_id))
- if not command:
+ if command == None or command == "":
# ---- Check whether setting exists in app
command = value(app.config.get(command_id))
- if not command:
+ if command == None:
command = value(guess)
- if not command:
- raise Exception(command_id+' setting unknown or faulty (update settings.py?).')
+ if command == None or command == "":
+ raise Exception(command_id+' setting unknown or faulty (update default_settings.py?).')
logger.info("Set "+command_id+"="+str(command))
return command
+def get_setting_bool(id):
+ v = get_setting(id)
+ if v not in [0,False,'False','FALSE',None]:
+ return True
+ return False
+
+def get_setting_int(id):
+ v = get_setting(id)
+ return int(v)
+
def valid_bin(bin):
if os.path.islink(bin) or valid_file(bin):
return bin
@@ -136,9 +146,9 @@ def tempdir():
# Cached values
WEBSERVER_MODE = get_setting('WEBSERVER_MODE')
LOG_LEVEL = get_setting('LOG_LEVEL')
-DEBUG_LOG_LEVEL = get_setting('DEBUG_LOG_LEVEL')
-LOG_SQL = get_setting('LOG_SQL') in [True,'TRUE','True','true']
-USE_REDIS = get_setting('USE_REDIS') in [True,'TRUE','True','true']
+DEBUG_LOG_LEVEL = get_setting_int('DEBUG_LOG_LEVEL')
+LOG_SQL = get_setting_bool('LOG_SQL')
+USE_REDIS = get_setting_bool('USE_REDIS')
PYLMM_COMMAND = pylmm_command()
GEMMA_COMMAND = gemma_command()
diff --git a/wqflask/wqflask/database.py b/wqflask/wqflask/database.py
index f9c57d78..90612348 100644
--- a/wqflask/wqflask/database.py
+++ b/wqflask/wqflask/database.py
@@ -24,6 +24,5 @@ def init_db():
logger.debug("database.py: Creating all model metadata..")
Base.metadata.create_all(bind=engine)
logger.info("database.py: Done creating all model metadata...")
- logger.info("Point your browser at http://localhost:5003/")
init_db()
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 557708e9..6c67cc87 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -46,6 +46,7 @@ from wqflask.database import db_session
from wqflask import model
from utility import Bunch, Struct, after
+from utility.tools import LOG_SQL
import logging
from utility.logger import getLogger
@@ -144,8 +145,8 @@ class UserSession(object):
"""Actual sqlalchemy record"""
# Only look it up once if needed, then store it
try:
- logging.basicConfig()
- logging.getLogger('sqlalchemy.pool').setLevel(logging.DEBUG)
+ if LOG_SQL:
+ logging.getLogger('sqlalchemy.pool').setLevel(logging.DEBUG)
# Already did this before
return self.db_object