Merge branch 'master' of github.com:genenetwork/genenetwork2 into mechanize

3 files changed, 43 insertions, 15 deletions

diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index 149ee553..377f6b26 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -5,19 +5,21 @@ from base import data_set
 from base.species import TheSpecies
 
 from wqflask import user_manager
+import logging
+logger = logging.getLogger(__name__ )
 
 
 def get_species_dataset_trait(self, start_vars):
     #assert type(read_genotype) == type(bool()), "Expecting boolean value for read_genotype"
     self.dataset = data_set.create_dataset(start_vars['dataset'])
-    print("After creating dataset")
+    logger.debug("After creating dataset")
     self.species = TheSpecies(dataset=self.dataset)
-    print("After creating species")
+    logger.debug("After creating species")
     self.this_trait = GeneralTrait(dataset=self.dataset,
                                    name=start_vars['trait_id'],
                                    cellid=None,
                                    get_qtl_info=True)
-    print("After creating trait")
+    logger.debug("After creating trait")
 
     #if read_genotype:
     #self.dataset.group.read_genotype_file()
@@ -27,7 +29,7 @@ def get_species_dataset_trait(self, start_vars):
 def get_trait_db_obs(self, trait_db_list):
     if isinstance(trait_db_list, basestring):
         trait_db_list = trait_db_list.split(",")
-        
+
     self.trait_list = []
     for trait in trait_db_list:
         data, _separator, hmac = trait.rpartition(':')
@@ -38,4 +40,4 @@ def get_trait_db_obs(self, trait_db_list):
         trait_ob = GeneralTrait(dataset=dataset_ob,
                                name=trait_name,
                                cellid=None)
-        self.trait_list.append((trait_ob, dataset_ob))
\ No newline at end of file
+        self.trait_list.append((trait_ob, dataset_ob))
diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py
index ddc0ea82..b873e16f 100644
--- a/wqflask/utility/logger.py
+++ b/wqflask/utility/logger.py
@@ -31,6 +31,7 @@ import string
 from inspect import isfunction
 from pprint import pformat as pf
 from inspect import stack
+import datetime
 
 from utility.tools import LOG_LEVEL, LOG_LEVEL_DEBUG, LOG_SQL, LOG_FORMAT
 
@@ -66,7 +67,10 @@ LOG_LEVEL_DEBUG (NYI).
 
     def error(self,*args):
         """Call logging.error for multiple args"""
-        self.collect(self.logger.error,*args)
+        now = datetime.datetime.utcnow()
+        time_str = now.strftime('%H:%M:%S UTC %Y%m%d')
+        l = [time_str]+list(args)
+        self.collect(self.logger.error,*l)
 
     def infof(self,*args):
         """Call logging.info for multiple args lazily"""
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 22779739..23d6fb62 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -3,6 +3,7 @@
 
 import os
 import sys
+import json
 
 from wqflask import app
 
@@ -10,6 +11,8 @@ from wqflask import app
 import logging
 logger = logging.getLogger(__name__ )
 
+OVERRIDES = {}
+
 def get_setting(command_id,guess=None):
     """Resolve a setting from the environment or the global settings in
     app.config, with valid_path is a function checking whether the
@@ -45,13 +48,15 @@ def get_setting(command_id,guess=None):
     logger.debug("Looking for "+command_id+"\n")
     command = value(os.environ.get(command_id))
     if command is None or command == "":
-        # ---- Check whether setting exists in app
-        command = value(app.config.get(command_id))
+        command = OVERRIDES.get(command_id)
         if command is None:
-            command = value(guess)
-            if command is None or command == "":
-                print command
-                raise Exception(command_id+' setting unknown or faulty (update default_settings.py?).')
+            # ---- Check whether setting exists in app
+            command = value(app.config.get(command_id))
+            if command is None:
+                command = value(guess)
+                if command is None or command == "":
+                    # print command
+                    raise Exception(command_id+' setting unknown or faulty (update default_settings.py?).')
     logger.debug("Set "+command_id+"="+str(command))
     return command
 
@@ -169,18 +174,20 @@ def show_settings():
     log_level = getattr(logging, LOG_LEVEL.upper())
     logging.basicConfig(level=log_level)
 
+    logger.info(OVERRIDES)
     logger.info(BLUE+"Mr. Mojo Risin 2"+ENDC)
-    print "runserver.py: ****** The webserver has the following configuration ******"
+    print "runserver.py: ****** Webserver 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))
+            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))
+            print("%s: %s%s%s%s" % (k,GREEN,BOLD,app.config[k],ENDC))
 
 
 # Cached values
+HOME               = get_setting('HOME')
 WEBSERVER_MODE     = get_setting('WEBSERVER_MODE')
 GN_SERVER_URL      = get_setting('GN_SERVER_URL')
 SQL_URI            = get_setting('SQL_URI')
@@ -199,3 +206,18 @@ PYLMM_COMMAND      = pylmm_command()
 GEMMA_COMMAND      = gemma_command()
 PLINK_COMMAND      = plink_command()
 TEMPDIR            = tempdir()
+
+from six import string_types
+
+if os.environ.get('WQFLASK_OVERRIDES'):
+    jsonfn = get_setting('WQFLASK_OVERRIDES')
+    logger.error("WQFLASK_OVERRIDES: %s" % jsonfn)
+    with open(jsonfn) as data_file:
+        overrides = json.load(data_file)
+        for k in overrides:
+            cmd = overrides[k]
+            if isinstance(cmd, string_types):
+                OVERRIDES[k] = eval(cmd)
+            else:
+                OVERRIDES[k] = cmd
+            logger.debug(OVERRIDES)