From 85819dbeaf922456dc205e482e7e338952945d9b Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 29 Jan 2018 15:10:09 +0000
Subject: Gunicorn works
---
wqflask/run_gunicorn.py | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
create mode 100644 wqflask/run_gunicorn.py
(limited to 'wqflask/run_gunicorn.py')
diff --git a/wqflask/run_gunicorn.py b/wqflask/run_gunicorn.py
new file mode 100644
index 00000000..14a2d689
--- /dev/null
+++ b/wqflask/run_gunicorn.py
@@ -0,0 +1,19 @@
+# Run with gunicorn, see ./bin/genenetwork2 for an example
+#
+# Run standalone with
+#
+# ./bin/genenetwork2 ./etc/default_settings.py -c run_gunicorn.py
+
+# from flask import Flask
+# application = Flask(__name__)
+
+print "Starting up Gunicorn process"
+
+from wqflask import app
+
+@app.route("/gunicorn")
+def hello():
+ return "
Hello There!
"
+
+if __name__ == "__main__":
+ app.run(host='0.0.0.0')
--
cgit v1.2.3
From 3de1ecfa37b73b4cb011b634c8b4afc2362f858c Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 15 Feb 2018 10:30:52 +0000
Subject: Fixing authentication stuff so it uses parameters properly. Also no
PYTHONPATH needed as it is now in the Guix build.
---
bin/genenetwork2 | 12 +++++++-----
etc/default_settings.py | 18 ++++++++++++++++++
wqflask/run_gunicorn.py | 3 +++
wqflask/utility/elasticsearch_tools.py | 16 ++++++++++++----
wqflask/utility/tools.py | 29 +++++++++++------------------
wqflask/wqflask/user_manager.py | 7 +++++--
6 files changed, 56 insertions(+), 29 deletions(-)
(limited to 'wqflask/run_gunicorn.py')
diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 74ed7f9b..31fefbd3 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -95,11 +95,13 @@ export WQFLASK_OVERRIDES=$overrides # JSON
echo WQFLASK_SETTINGS=$settings
echo WQFLASK_OVERRIDES=$overrides
-if [ -z $ELASTICSEARCH_PROFILE ]; then
- echo -e "\033[1;33mWARNING: Elastic Search profile has not been set - use ELASTICSEARCH_PROFILE\033[0m";
-else
- PYTHONPATH="$PYTHONPATH${PYTHONPATH:+:}$ELASTICSEARCH_PROFILE/lib/python2.7/site-packages"
-fi
+# This is a temporary hack to inject ES - should have added python2-elasticsearch package to guix instead
+# if [ -z $ELASTICSEARCH_PROFILE ]; then
+# echo -e "WARNING: Elastic Search profile has not been set - use ELASTICSEARCH_PROFILE";
+# else
+# PYTHONPATH="$PYTHONPATH${PYTHONPATH:+:}$ELASTICSEARCH_PROFILE/lib/python2.7/site-packages"
+# fi
+
if [ -z $GN2_PROFILE ] ; then
echo "WARNING: GN2_PROFILE has not been set - you need the environment, so I hope you know what you are doing!"
export GN2_PROFILE=$(dirname $(dirname $(which genenetwork2)))
diff --git a/etc/default_settings.py b/etc/default_settings.py
index 699d21f1..a70d8aec 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -41,6 +41,24 @@ SECURITY_POST_LOGIN_VIEW = "/thank_you"
SERVER_PORT = 5003 # running on localhost
SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a\xbc\xfc\x80:*\xebc'
+GITHUB_CLIENT_ID = "UNKNOWN"
+GITHUB_CLIENT_SECRET = "UNKNOWN"
+GITHUB_AUTH_URL = "UNKNOWN"
+GITHUB_API_URL = "UNKNOWN"
+
+ORCID_CLIENT_ID = "UNKNOWN"
+ORCID_CLIENT_SECRET = "UNKNOWN"
+ORCID_AUTH_URL = "UNKNOWN"
+ORCID_TOKEN_URL = "UNKNOWN"
+
+ELASTICSEARCH_HOST = "localhost"
+ELASTICSEARCH_PORT = '9200'
+
+SMTP_CONNECT = "UNKNOWN"
+SMTP_USERNAME = "UNKNOWN"
+SMTP_PASSWORD = "UNKNOWN"
+
+
# ---- Behavioural settings (defaults) note that logger and log levels can
# be overridden at the module level and with enviroment settings
WEBSERVER_MODE = 'DEV' # Python webserver mode (DEBUG|DEV|PROD)
diff --git a/wqflask/run_gunicorn.py b/wqflask/run_gunicorn.py
index 14a2d689..ebe3add5 100644
--- a/wqflask/run_gunicorn.py
+++ b/wqflask/run_gunicorn.py
@@ -11,6 +11,9 @@ print "Starting up Gunicorn process"
from wqflask import app
+app.config['SESSION_TYPE'] = 'filesystem'
+app.config['SECRET_KEY'] = 'super secret key'
+
@app.route("/gunicorn")
def hello():
return "Hello There!
"
diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index a964b025..2d3d5add 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -1,10 +1,18 @@
from elasticsearch import Elasticsearch, TransportError
import logging
+from utility.logger import getLogger
+logger = getLogger(__name__)
+
+from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT
+
def get_elasticsearch_connection():
+ logger.info("get_elasticsearch_connection")
es = None
try:
- from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT
+ assert(ELASTICSEARCH_HOST)
+ assert(ELASTICSEARCH_PORT)
+ logger.info("ES HOST",ELASTICSEARCH_HOST)
es = Elasticsearch([{
"host": ELASTICSEARCH_HOST
@@ -31,12 +39,12 @@ def get_item_by_unique_column(es, column_name, column_value, index, doc_type):
response = es.search(
index = index
, doc_type = doc_type
- , body = {
- "query": { "match": { column_name: column_value } }
+ , body = {
+ "query": { "match": { column_name: column_value } }
})
if len(response["hits"]["hits"]) > 0:
item_details = response["hits"]["hits"][0]["_source"]
- except TransportError as te:
+ except TransportError as te:
pass
return item_details
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 005f9b0f..8c9fed96 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -251,32 +251,25 @@ 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())
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 6b667615..c8471cb1 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -55,9 +55,8 @@ logger = getLogger(__name__)
from base.data_set import create_datasets_list
import requests
-from utility.elasticsearch_tools import *
+from utility.elasticsearch_tools import get_elasticsearch_connection, get_user_by_unique_column, save_user
-es = get_elasticsearch_connection()
THREE_DAYS = 60 * 60 * 24 * 3
#THREE_DAYS = 45
@@ -479,6 +478,7 @@ def password_reset_step2():
password = request.form['password']
set_password(password, user)
+ es = get_elasticsearch_connection()
es.update(
index = "users"
, doc_type = "local"
@@ -620,6 +620,7 @@ class LoginUser(object):
"""Login through the normal form"""
params = request.form if request.form else request.args
logger.debug("in login params are:", params)
+ es = get_elasticsearch_connection()
if not params:
from utility.tools import GITHUB_AUTH_URL, ORCID_AUTH_URL
external_login = None
@@ -628,6 +629,7 @@ class LoginUser(object):
"github": GITHUB_AUTH_URL,
"orcid": ORCID_AUTH_URL
}
+ assert(es is not None)
return render_template(
"new_security/login_user.html"
, external_login=external_login
@@ -822,6 +824,7 @@ def register():
params = request.form if request.form else request.args
params = params.to_dict(flat=True)
+ es = get_elasticsearch_connection()
params["es_connection"] = es
if params:
--
cgit v1.2.3
From 7aae77762e47c9269591e138ab25320d3ed3a85f Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Tue, 20 Mar 2018 11:02:25 +0000
Subject: Refactor startup config for gunicorn and werkzeug
---
wqflask/run_gunicorn.py | 6 ++--
wqflask/runserver.py | 17 ++--------
wqflask/utility/elasticsearch_tools.py | 5 +++
wqflask/utility/startup_config.py | 39 ++++++++++++++++++++++
wqflask/utility/tools.py | 4 ++-
.../wqflask/templates/new_security/login_user.html | 8 ++++-
6 files changed, 59 insertions(+), 20 deletions(-)
create mode 100644 wqflask/utility/startup_config.py
(limited to 'wqflask/run_gunicorn.py')
diff --git a/wqflask/run_gunicorn.py b/wqflask/run_gunicorn.py
index ebe3add5..adffdca3 100644
--- a/wqflask/run_gunicorn.py
+++ b/wqflask/run_gunicorn.py
@@ -7,12 +7,12 @@
# from flask import Flask
# application = Flask(__name__)
-print "Starting up Gunicorn process"
+print "===> Starting up Gunicorn process"
from wqflask import app
+from utility.startup_config import app_config
-app.config['SESSION_TYPE'] = 'filesystem'
-app.config['SECRET_KEY'] = 'super secret key'
+app_config()
@app.route("/gunicorn")
def hello():
diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index a0c76e51..5f41d04d 100644
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -21,22 +21,9 @@ GREEN = '\033[92m'
BOLD = '\033[1m'
ENDC = '\033[0m'
-import os
-app.config['SECRET_KEY'] = os.urandom(24)
+from utility.startup_config import app_config
-from utility.tools import WEBSERVER_MODE,get_setting_int,get_setting,get_setting_bool
-
-port = get_setting_int("SERVER_PORT")
-
-print("GN2 API server URL is ["+BLUE+get_setting("GN_SERVER_URL")+ENDC+"]")
-
-if get_setting_bool("USE_GN_SERVER"):
- import requests
- page = requests.get(get_setting("GN_SERVER_URL"))
- if page.status_code != 200:
- raise Exception("API server not found!")
-
-print("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE,str(port),ENDC,get_setting("WEBSERVER_URL")))
+app_config()
werkzeug_logger = logging.getLogger('werkzeug')
diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index 2d3d5add..734379f7 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+":"+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..02e8e56c
--- /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
+ 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 4b4cd633..59bb49d8 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -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:
@@ -269,6 +269,8 @@ if ORCID_CLIENT_ID != 'UNKNOWN' and ORCID_CLIENT_SECRET:
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')
diff --git a/wqflask/wqflask/templates/new_security/login_user.html b/wqflask/wqflask/templates/new_security/login_user.html
index 6d597f6b..949760b6 100644
--- a/wqflask/wqflask/templates/new_security/login_user.html
+++ b/wqflask/wqflask/templates/new_security/login_user.html
@@ -15,7 +15,6 @@
Don't have an account?
-
{% if es_server: %}
Create a new account
{% else: %}
@@ -92,6 +91,13 @@
Please try again later.
{% endif %}
+ {% if not es_server and not external_login: %}
+
+
+ Note: it is safe to use GeneNetwork without a login. Login is only required for keeping track of
+ collections and getting access to some types of restricted data.
+
+ {% endif %}
--
cgit v1.2.3