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-rw-r--r--wqflask/utility/tools.py42
1 files changed, 16 insertions, 26 deletions
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index ec673cf5..8c9fed96 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):
@@ -251,35 +251,29 @@ assert_dir(JS_GUIX_PATH)
JS_GN_PATH = get_setting('JS_GN_PATH')
# assert_dir(JS_GN_PATH)
-def get_setting_safe(setting):
- try:
- return get_setting(setting)
- except:
- print("Could not find the setting '", setting, "'. Continuing with value unset")
- return None
-
-GITHUB_CLIENT_ID = get_setting_safe('GITHUB_CLIENT_ID')
-GITHUB_CLIENT_SECRET = get_setting_safe('GITHUB_CLIENT_SECRET')
+GITHUB_CLIENT_ID = get_setting('GITHUB_CLIENT_ID')
+GITHUB_CLIENT_SECRET = get_setting('GITHUB_CLIENT_SECRET')
GITHUB_AUTH_URL = None
if GITHUB_CLIENT_ID and GITHUB_CLIENT_SECRET:
GITHUB_AUTH_URL = "https://github.com/login/oauth/authorize?client_id="+GITHUB_CLIENT_ID+"&client_secret="+GITHUB_CLIENT_SECRET
-GITHUB_API_URL = get_setting_safe('GITHUB_API_URL')
-ORCID_CLIENT_ID = get_setting_safe('ORCID_CLIENT_ID')
-ORCID_CLIENT_SECRET = get_setting_safe('ORCID_CLIENT_SECRET')
+GITHUB_API_URL = get_setting('GITHUB_API_URL')
+ORCID_CLIENT_ID = get_setting('ORCID_CLIENT_ID')
+ORCID_CLIENT_SECRET = get_setting('ORCID_CLIENT_SECRET')
ORCID_AUTH_URL = None
if ORCID_CLIENT_ID and ORCID_CLIENT_SECRET:
ORCID_AUTH_URL = "https://sandbox.orcid.org/oauth/authorize?response_type=code&scope=/authenticate&show_login=true&client_id="+ORCID_CLIENT_ID+"&client_secret="+ORCID_CLIENT_SECRET
-ORCID_TOKEN_URL = get_setting_safe('ORCID_TOKEN_URL')
+ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL')
-ELASTICSEARCH_HOST = get_setting_safe('ELASTICSEARCH_HOST')
-ELASTICSEARCH_PORT = get_setting_safe('ELASTICSEARCH_PORT')
+ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST')
+ELASTICSEARCH_PORT = get_setting('ELASTICSEARCH_PORT')
-SMTP_CONNECT = get_setting_safe('SMTP_CONNECT')
-SMTP_USERNAME = get_setting_safe('SMTP_USERNAME')
-SMTP_PASSWORD = get_setting_safe('SMTP_PASSWORD')
+SMTP_CONNECT = get_setting('SMTP_CONNECT')
+SMTP_USERNAME = get_setting('SMTP_USERNAME')
+SMTP_PASSWORD = get_setting('SMTP_PASSWORD')
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
@@ -293,7 +287,7 @@ 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:
@@ -305,8 +299,4 @@ 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")