Fixing authentication stuff so it uses parameters properly. Also no PYTHONPATH needed as

it is now in the Guix build.

6 files changed, 56 insertions, 29 deletions

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 "<h1 style='color:blue'>Hello There!</h1>"
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: