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authorzsloan2018-02-12 11:03:01 -0600
committerGitHub2018-02-12 11:03:01 -0600
commite8353466b9e1a90bc4ba6336532c743ae4b10fd2 (patch)
treece412a7f2efacbf676dc524a114334f1a2408702 /wqflask/utility
parent4ae2d548127eeeaa7cec0baf1b788005b5e8e51d (diff)
parent018c9d6c50e90d783bc7bd1b2a0d85b080ebf394 (diff)
downloadgenenetwork2-e8353466b9e1a90bc4ba6336532c743ae4b10fd2.tar.gz
Merge pull request #277 from pjotrp/gn-production
Gn production
Diffstat (limited to 'wqflask/utility')
-rw-r--r--wqflask/utility/tools.py13
1 files changed, 5 insertions, 8 deletions
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 57f97a81..d3113302 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -16,7 +16,7 @@ OVERRIDES = {}
def app_set(command_id, value):
"""Set application wide value"""
app.config.setdefault(command_id,value)
- value
+ return value
def get_setting(command_id,guess=None):
"""Resolve a setting from the environment or the global settings in
@@ -51,7 +51,7 @@ def get_setting(command_id,guess=None):
return None
# ---- Check whether environment exists
- logger.debug("Looking for "+command_id+"\n")
+ # print("Looking for "+command_id+"\n")
command = value(os.environ.get(command_id))
if command is None or command == "":
command = OVERRIDES.get(command_id)
@@ -63,7 +63,7 @@ def get_setting(command_id,guess=None):
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))
+ # print("Set "+command_id+"="+str(command))
return command
def get_setting_bool(id):
@@ -253,6 +253,7 @@ JS_GN_PATH = get_setting('JS_GN_PATH')
PYLMM_COMMAND = app_set("PYLMM_COMMAND",pylmm_command())
GEMMA_COMMAND = app_set("GEMMA_COMMAND",gemma_command())
+assert(GEMMA_COMMAND is not None)
PLINK_COMMAND = app_set("PLINK_COMMAND",plink_command())
GEMMA_WRAPPER_COMMAND = gemma_wrapper_command()
TEMPDIR = tempdir() # defaults to UNIX TMPDIR
@@ -266,7 +267,7 @@ from six import string_types
if os.environ.get('WQFLASK_OVERRIDES'):
jsonfn = get_setting('WQFLASK_OVERRIDES')
- logger.error("WQFLASK_OVERRIDES: %s" % jsonfn)
+ logger.info("WQFLASK_OVERRIDES: %s" % jsonfn)
with open(jsonfn) as data_file:
overrides = json.load(data_file)
for k in overrides:
@@ -278,8 +279,4 @@ if os.environ.get('WQFLASK_OVERRIDES'):
logger.debug(OVERRIDES)
# assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData")
-# assert_dir(get_setting("JS_BIODALLIANCE"))
-# assert_file(get_setting("JS_BIODALLIANCE")+"/build/dalliance-all.js")
-# assert_file(get_setting("JS_BIODALLIANCE")+"/build/worker-all.js")
-# assert_dir(get_setting("JS_TWITTER_POST_FETCHER"))
assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js")