Added script to quantile normalize a data set and enter its normalized sample data into ElasticSearch

Added option to replace trait page sample/strain values with normalized ones

Began editing Lei's scatterplot code

Changed elasticsearch_tools' get_elasticsearch_connection so that it can also be used for purposes other than user authentication (by adding a "for_user" parameter)

1 files changed, 3 insertions, 2 deletions

diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index cce210c3..293a9ae6 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -52,7 +52,7 @@ def test_elasticsearch_connection():
     if not es.ping():
         logger.warning("Elasticsearch is DOWN")
 
-def get_elasticsearch_connection():
+def get_elasticsearch_connection(for_user=True):
     """Return a connection to ES. Returns None on failure"""
     logger.info("get_elasticsearch_connection")
     es = None
@@ -65,7 +65,8 @@ def get_elasticsearch_connection():
             "host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT
         }]) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None
 
-        setup_users_index(es)
+        if for_user:
+            setup_users_index(es)
 
         es_logger = logging.getLogger("elasticsearch")
         es_logger.setLevel(logging.INFO)