Merge master and testing master

1 files changed, 15 insertions, 10 deletions

diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index f12b0d76..2914d354 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -107,8 +107,8 @@ def js_path(module=None):
         return try_guix
     raise "No JS path found for "+module+" (if not in Guix check JS_GN_PATH)"
 
-def pylmm_command(guess=None):
-    return assert_bin(get_setting("PYLMM_COMMAND",guess))
+def reaper_command(guess=None):
+    return get_setting("REAPER_COMMAND",guess)
 
 def gemma_command(guess=None):
     return assert_bin(get_setting("GEMMA_COMMAND",guess))
@@ -235,7 +235,10 @@ GN_VERSION         = get_setting('GN_VERSION')
 HOME               = get_setting('HOME')
 SERVER_PORT        = get_setting('SERVER_PORT')
 WEBSERVER_MODE     = get_setting('WEBSERVER_MODE')
+GN2_BASE_URL       = get_setting('GN2_BASE_URL')
+GN2_BRANCH_URL     = get_setting('GN2_BRANCH_URL')
 GN_SERVER_URL      = get_setting('GN_SERVER_URL')
+SERVER_PORT        = get_setting_int('SERVER_PORT')
 SQL_URI            = get_setting('SQL_URI')
 LOG_LEVEL          = get_setting('LOG_LEVEL')
 LOG_LEVEL_DEBUG    = get_setting_int('LOG_LEVEL_DEBUG')
@@ -254,7 +257,6 @@ 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 != 'UNKNOWN' and GITHUB_CLIENT_SECRET:
     GITHUB_AUTH_URL = "https://github.com/login/oauth/authorize?client_id=" + \
                       GITHUB_CLIENT_ID+"&client_secret="+GITHUB_CLIENT_SECRET
@@ -264,20 +266,20 @@ 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_AUTH_URL = "https://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()
+# 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())
+REAPER_COMMAND     = app_set("REAPER_COMMAND",reaper_command())
 GEMMA_COMMAND      = app_set("GEMMA_COMMAND",gemma_command())
 assert(GEMMA_COMMAND is not None)
 PLINK_COMMAND      = app_set("PLINK_COMMAND",plink_command())
@@ -289,11 +291,14 @@ assert_dir(TEMPDIR)
 JS_GUIX_PATH = get_setting("JS_GUIX_PATH")
 assert_dir(JS_GUIX_PATH)
 assert_dir(JS_GUIX_PATH+'/cytoscape-panzoom')
+
 CSS_PATH = "UNKNOWN"
 # assert_dir(JS_PATH)
-JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("Twitter-Post-Fetcher"))
+
+JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("javascript-twitter-post-fetcher"))
 assert_dir(JS_TWITTER_POST_FETCHER_PATH)
 assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js")
+
 JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH",js_path("cytoscape"))
 assert_dir(JS_CYTOSCAPE_PATH)
 assert_file(JS_CYTOSCAPE_PATH+'/cytoscape.min.js')