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, 0 insertions, 53 deletions

diff --git a/wqflask/base/trait_collection.py b/wqflask/base/trait_collection.py
deleted file mode 100644
index d388a3af..00000000
--- a/wqflask/base/trait_collection.py
+++ /dev/null
@@ -1,53 +0,0 @@
-class TraitCollection(object):

-    

-    def __init__(self, is_anon=False):

-        self.is_anon = is_anon

-        

-        

-    @app.route("/collections/remove", methods=('POST',))

-    def remove_traits():

-        if is_anon:

-            AnonCollection.remove_traits()

-        else:

-            UserCollection.remove_traits()

-            

-        params = request.form

-        print("params are:", params)

-        uc_id = params['uc_id']

-        uc = model.UserCollection.query.get(uc_id)

-        traits_to_remove = params.getlist('traits[]')

-        print("traits_to_remove are:", traits_to_remove)

-        traits_to_remove = process_traits(traits_to_remove)

-        print("\n\n  after processing, traits_to_remove:", traits_to_remove)

-        all_traits = uc.members_as_set()

-        print("  all_traits:", all_traits)

-        members_now = all_traits - traits_to_remove

-        print("  members_now:", members_now)

-        print("Went from {} to {} members in set.".format(len(all_traits), len(members_now)))

-        uc.members = json.dumps(list(members_now))

-        uc.changed_timestamp = datetime.datetime.utcnow()

-        db_session.commit()

-    

-        # We need to return something so we'll return this...maybe in the future

-        # we can use it to check the results

-        return str(len(members_now))

-

-    def __init__(self, anon_id)

-        self.anon_key = anon_key

-        self.collection_members = Redis.smembers(self.anon_id)

-        print("self.collection_members is:", self.collection_members)

-        self.num_members = len(self.collection_members)

-        

-

-    @app.route("/collections/remove", methods=('POST',))

-    def remove_traits(traits_to_remove):

-        print("traits_to_remove:", traits_to_remove)

-        for trait in traits_to_remove:

-            Redis.srem(self.anon_id, trait)

-        members_now = self.collection_members - traits_to_remove

-        print("members_now:", members_now)

-        print("Went from {} to {} members in set.".format(len(self.collection_members), len(members_now)))

-

-        # We need to return something so we'll return this...maybe in the future

-        # we can use it to check the results

-        return str(len(members_now))