From 21d14548c6c3799f36f0997a30a3853344dcc96b Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 18 Jun 2016 12:14:39 +0000
Subject: Logging settings

---
 etc/default_settings.py        |  2 +-
 wqflask/base/webqtlCaseData.py |  6 ++++--
 wqflask/runserver.py           |  6 ------
 wqflask/utility/logger.py      | 15 +++++++++------
 wqflask/utility/tools.py       | 25 ++++++++++++++++++++++++-
 5 files changed, 38 insertions(+), 16 deletions(-)

diff --git a/etc/default_settings.py b/etc/default_settings.py
index bdcb9c5d..0fafb474 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -34,7 +34,7 @@ SERVER_PORT = 5003
 SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a\xbc\xfc\x80:*\xebc'
 
 # Behavioural settings (defaults) note that logger and log levels can
-# be overridden at the module level
+# be overridden at the module level and with enviroment settings
 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)
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index 23f893fc..c80fcb65 100644
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -26,7 +26,10 @@
 
 from utility.logger import getLogger
 logger = getLogger(__name__)
-logger.info("Mr. Mojo Risin 2")
+
+import utility.tools
+
+utility.tools.show_settings()
 
 class webqtlCaseData(object):
     """one case data in one trait"""
@@ -72,4 +75,3 @@ class webqtlCaseData(object):
             return "%2.3f" % self.variance
         else:
             return "x"
-
diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index 0d91c57a..9339acf8 100644
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -16,12 +16,6 @@ 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))
 
diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py
index 0549a7fa..479f6c46 100644
--- a/wqflask/utility/logger.py
+++ b/wqflask/utility/logger.py
@@ -13,6 +13,11 @@
 #   import utility.logger
 #   logger = utility.logger.getLogger(__name__ )
 #
+# To override global behaviour set the LOG_LEVEL in default_settings.py
+# or use an environment variable, e.g.
+#
+#    env LOG_LEVEL=INFO ./bin/genenetwork2
+#
 # To override log level for a module replace that with, for example,
 #
 #   import logging
@@ -22,18 +27,16 @@
 # We'll add more overrides soon.
 
 import logging
-
 from utility.tools import LOG_LEVEL
 
-print("Set global log level to "+LOG_LEVEL)
-
-log_level = getattr(logging, LOG_LEVEL.upper())
-logging.basicConfig(level=log_level)
-
 # Get the module logger. You can override log levels at the
 # module level
 def getLogger(name, level = None):
     logger = logging.getLogger(name)
     if level:
         logger.setLevel(level)
+    else:
+        logger.setLevel(LOG_LEVEL)
+
+    logger.debug("Log "+name+" at level "+logging.getLevelName(logger.getEffectiveLevel()))
     return logger
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 1b31857e..bfb379f2 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -50,7 +50,7 @@ def get_setting(command_id,guess=None):
             command = value(guess)
             if command == None or command == "":
                 raise Exception(command_id+' setting unknown or faulty (update default_settings.py?).')
-    logger.info("Set "+command_id+"="+str(command))
+    logger.debug("Set "+command_id+"="+str(command))
     return command
 
 def get_setting_bool(id):
@@ -143,6 +143,29 @@ def locate_ignore_error(name, subdir=None):
 def tempdir():
     return valid_path(get_setting("TEMPDIR","/tmp"))
 
+BLUE  = '\033[94m'
+GREEN = '\033[92m'
+BOLD  = '\033[1m'
+ENDC  = '\033[0m'
+
+def show_settings():
+    from utility.tools import LOG_LEVEL
+
+    print("Set global log level to "+BLUE+LOG_LEVEL+ENDC)
+    log_level = getattr(logging, LOG_LEVEL.upper())
+    logging.basicConfig(level=log_level)
+
+    logger.info(BLUE+"Mr. Mojo Risin 2"+ENDC)
+    print "runserver.py: ****** The webserver has the following configuration ******"
+    keylist = app.config.keys()
+    keylist.sort()
+    for k in keylist:
+        try:
+            print("%s %s%s%s%s" % (k,BLUE,BOLD,get_setting(k),ENDC))
+        except:
+            print("%s %s%s%s%s" % (k,GREEN,BOLD,app.config[k],ENDC))
+
+
 # Cached values
 WEBSERVER_MODE     = get_setting('WEBSERVER_MODE')
 LOG_LEVEL          = get_setting('LOG_LEVEL')
-- 
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