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-rw-r--r--wqflask/utility/elasticsearch_tools.py5
-rw-r--r--wqflask/utility/startup_config.py39
-rw-r--r--wqflask/utility/tools.py34
-rw-r--r--wqflask/utility/type_checking.py42
4 files changed, 99 insertions, 21 deletions
diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index 2d3d5add..075a8f65 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -6,6 +6,11 @@ logger = getLogger(__name__)
from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT
+def test_elasticsearch_connection():
+ es = Elasticsearch(['http://'+ELASTICSEARCH_HOST+":"+str(ELASTICSEARCH_PORT)+'/'], verify_certs=True)
+ if not es.ping():
+ logger.warning("Elasticsearch is DOWN")
+
def get_elasticsearch_connection():
logger.info("get_elasticsearch_connection")
es = None
diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py
new file mode 100644
index 00000000..5a62cc50
--- /dev/null
+++ b/wqflask/utility/startup_config.py
@@ -0,0 +1,39 @@
+
+from wqflask import app
+from utility.tools import WEBSERVER_MODE, show_settings, get_setting_int, get_setting, get_setting_bool
+
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
+
+BLUE = '\033[94m'
+GREEN = '\033[92m'
+BOLD = '\033[1m'
+ENDC = '\033[0m'
+
+def app_config():
+ app.config['SESSION_TYPE'] = 'filesystem'
+ if not app.config.get('SECRET_KEY'):
+ import os
+ app.config['SECRET_KEY'] = str(os.urandom(24))
+
+ mode = WEBSERVER_MODE
+ if mode == "DEV" or mode == "DEBUG":
+ app.config['TEMPLATES_AUTO_RELOAD'] = True
+ # if mode == "DEBUG":
+ # app.config['EXPLAIN_TEMPLATE_LOADING'] = True <--- use overriding app param instead
+ print("==========================================")
+ show_settings()
+
+ port = get_setting_int("SERVER_PORT")
+
+ if get_setting_bool("USE_GN_SERVER"):
+ print("GN2 API server URL is ["+BLUE+get_setting("GN_SERVER_URL")+ENDC+"]")
+ import requests
+ page = requests.get(get_setting("GN_SERVER_URL"))
+ if page.status_code != 200:
+ raise Exception("API server not found!")
+
+ import utility.elasticsearch_tools as es
+ es.test_elasticsearch_connection()
+
+ print("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE,str(port),ENDC,get_setting("WEBSERVER_URL")))
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 8c9fed96..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:
@@ -254,18 +254,23 @@ JS_GN_PATH = get_setting('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 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')
+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 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')
+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')
@@ -285,18 +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")
diff --git a/wqflask/utility/type_checking.py b/wqflask/utility/type_checking.py
new file mode 100644
index 00000000..220e5f62
--- /dev/null
+++ b/wqflask/utility/type_checking.py
@@ -0,0 +1,42 @@
+# Type checking functions
+
+def is_float(value):
+ try:
+ float(value)
+ return True
+ except:
+ return False
+
+def is_int(value):
+ try:
+ int(value)
+ return True
+ except:
+ return False
+
+def is_str(value):
+ if value is None:
+ return False
+ try:
+ str(value)
+ return True
+ except:
+ return False
+
+def get_float(vars,name,default=None):
+ if name in vars:
+ if is_float(vars[name]):
+ return float(vars[name])
+ return None
+
+def get_int(vars,name,default=None):
+ if name in vars:
+ if is_int(vars[name]):
+ return float(vars[name])
+ return default
+
+def get_string(vars,name,default=None):
+ if name in vars:
+ if not vars[name] is None:
+ return str(vars[name])
+ return default
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-24 11:48:46 +0000