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authorzsloan2018-03-29 10:36:12 -0500
committerGitHub2018-03-29 10:36:12 -0500
commitb215b5fe5c6d13f0ed445106230e1e38db71c918 (patch)
tree97f1f47b092bef38856ac34c1bd745e471c38311 /wqflask/utility/tools.py
parente67e3a76fca0bad4796853eb58140a412922bc9c (diff)
parente0c706c51c834caa836ecffd27a5d18fc23178ff (diff)
downloadgenenetwork2-b215b5fe5c6d13f0ed445106230e1e38db71c918.tar.gz
Merge pull request #297 from pjotrp/testing
Testing
Diffstat (limited to 'wqflask/utility/tools.py')
-rw-r--r--wqflask/utility/tools.py42
1 files changed, 27 insertions, 15 deletions
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index d3113302..59bb49d8 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -54,7 +54,7 @@ def get_setting(command_id,guess=None):
# print("Looking for "+command_id+"\n")
command = value(os.environ.get(command_id))
if command is None or command == "":
- command = OVERRIDES.get(command_id)
+ command = OVERRIDES.get(command_id) # currently not in use
if command is None:
# ---- Check whether setting exists in app
command = value(app.config.get(command_id))
@@ -220,7 +220,7 @@ def show_settings():
logger.info(OVERRIDES)
logger.info(BLUE+"Mr. Mojo Risin 2"+ENDC)
- print "runserver.py: ****** Webserver configuration ******"
+ print "runserver.py: ****** Webserver configuration - k,v pairs from app.config ******"
keylist = app.config.keys()
keylist.sort()
for k in keylist:
@@ -251,6 +251,31 @@ assert_dir(JS_GUIX_PATH)
JS_GN_PATH = get_setting('JS_GN_PATH')
# assert_dir(JS_GN_PATH)
+GITHUB_CLIENT_ID = get_setting('GITHUB_CLIENT_ID')
+GITHUB_CLIENT_SECRET = get_setting('GITHUB_CLIENT_SECRET')
+GITHUB_AUTH_URL = None
+if GITHUB_CLIENT_ID != 'UNKNOWN' 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('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 != 'UNKNOWN' 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('ORCID_TOKEN_URL')
+
+ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST')
+ELASTICSEARCH_PORT = get_setting('ELASTICSEARCH_PORT')
+import utility.elasticsearch_tools as es
+es.test_elasticsearch_connection()
+
+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)
@@ -265,18 +290,5 @@ assert_dir(JS_TWITTER_POST_FETCHER_PATH)
from six import string_types
-if os.environ.get('WQFLASK_OVERRIDES'):
- jsonfn = get_setting('WQFLASK_OVERRIDES')
- logger.info("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)
-
# assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData")
assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js")