Remove all elasticsearch references in gn2

4 files changed, 1 insertions, 144 deletions

diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index 0cc963e5..32780ca6 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -5,14 +5,10 @@ import urllib.parse
 
 import numpy as np
 import pandas as pd
-from elasticsearch import Elasticsearch, TransportError
-from elasticsearch.helpers import bulk
 
 from flask import Flask, g, request
 
 from wqflask import app
-from utility.elasticsearch_tools import get_elasticsearch_connection
-from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT, SQL_URI
 
 
 def parse_db_uri():
@@ -106,20 +102,6 @@ if __name__ == '__main__':
     Conn = MySQLdb.Connect(**parse_db_uri())
     Cursor = Conn.cursor()
 
-    # es = Elasticsearch([{
-    #    "host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT
-    # }], timeout=60) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None
-
-    es = get_elasticsearch_connection(for_user=False)
-
-    #input_filename = "/home/zas1024/cfw_data/" + sys.argv[1] + ".txt"
-    #input_df = create_dataframe(input_filename)
-    #output_df = quantileNormalize(input_df)
-
-    #output_df.to_csv('quant_norm.csv', sep='\t')
-
-    #out_filename = sys.argv[1][:-4] + '_quantnorm.txt'
-
     success, _ = bulk(es, set_data(sys.argv[1]))
 
     response = es.search(
diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
deleted file mode 100644
index eae3ba03..00000000
--- a/wqflask/utility/elasticsearch_tools.py
+++ /dev/null
@@ -1,121 +0,0 @@
-# Elasticsearch support
-#
-# Some helpful commands to view the database:
-#
-# You can test the server being up with
-#
-#   curl -H 'Content-Type: application/json' http://localhost:9200
-#
-# List all indices
-#
-#   curl -H 'Content-Type: application/json' 'localhost:9200/_cat/indices?v'
-#
-# To see the users index 'table'
-#
-#   curl http://localhost:9200/users
-#
-# To list all user ids
-#
-# curl -H 'Content-Type: application/json' http://localhost:9200/users/local/_search?pretty=true -d '
-# {
-#     "query" : {
-#         "match_all" : {}
-#     },
-#     "stored_fields": []
-# }'
-#
-# To view a record
-#
-#   curl -H 'Content-Type: application/json' http://localhost:9200/users/local/_search?pretty=true -d '
-#   {
-#     "query" : {
-#       "match" : { "email_address": "pjotr2017@thebird.nl"}
-#     }
-#   }'
-#
-#
-# To delete the users index and data (dangerous!)
-#
-#   curl -XDELETE -H 'Content-Type: application/json' 'localhost:9200/users'
-
-
-from elasticsearch import Elasticsearch, TransportError
-import logging
-
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
-from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT
-
-
-def test_elasticsearch_connection():
-    es = Elasticsearch(['http://' + ELASTICSEARCH_HOST + \
-                        ":" + str(ELASTICSEARCH_PORT) + '/'], verify_certs=True)
-    if not es.ping():
-        logger.warning("Elasticsearch is DOWN")
-
-
-def get_elasticsearch_connection(for_user=True):
-    """Return a connection to ES. Returns None on failure"""
-    logger.info("get_elasticsearch_connection")
-    es = None
-    try:
-        assert(ELASTICSEARCH_HOST)
-        assert(ELASTICSEARCH_PORT)
-        logger.info("ES HOST", ELASTICSEARCH_HOST)
-
-        es = Elasticsearch([{
-            "host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT
-        }], timeout=30, retry_on_timeout=True) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None
-
-        if for_user:
-            setup_users_index(es)
-
-        es_logger = logging.getLogger("elasticsearch")
-        es_logger.setLevel(logging.INFO)
-        es_logger.addHandler(logging.NullHandler())
-    except Exception as e:
-        logger.error("Failed to get elasticsearch connection", e)
-        es = None
-
-    return es
-
-
-def setup_users_index(es_connection):
-    if es_connection:
-        index_settings = {
-            "properties": {
-                "email_address": {
-                    "type": "keyword"}}}
-
-        es_connection.indices.create(index='users', ignore=400)
-        es_connection.indices.put_mapping(
-            body=index_settings, index="users", doc_type="local")
-
-
-def get_user_by_unique_column(es, column_name, column_value, index="users", doc_type="local"):
-    return get_item_by_unique_column(es, column_name, column_value, index=index, doc_type=doc_type)
-
-
-def save_user(es, user, user_id):
-    es_save_data(es, "users", "local", user, user_id)
-
-
-def get_item_by_unique_column(es, column_name, column_value, index, doc_type):
-    item_details = None
-    try:
-        response = es.search(
-            index=index, doc_type=doc_type, body={
-                "query": {"match": {column_name: column_value}}
-            })
-        if len(response["hits"]["hits"]) > 0:
-            item_details = response["hits"]["hits"][0]["_source"]
-    except TransportError as te:
-        pass
-    return item_details
-
-
-def es_save_data(es, index, doc_type, data_item, data_id,):
-    from time import sleep
-    es.create(index, doc_type, body=data_item, id=data_id)
-    sleep(1)  # Delay 1 second to allow indexing
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 0efe8ca9..f28961ec 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -287,6 +287,7 @@ 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 = ""
 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
@@ -301,10 +302,6 @@ if ORCID_CLIENT_ID != 'UNKNOWN' and ORCID_CLIENT_SECRET:
         "&redirect_uri=" + GN2_BRANCH_URL + "n/login/orcid_oauth2"
     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()
 
 SMTP_CONNECT = get_setting('SMTP_CONNECT')
 SMTP_USERNAME = get_setting('SMTP_USERNAME')
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index 67e2e158..d3c4a62f 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -10,7 +10,6 @@ from flask import (Flask, g, render_template, url_for, request, make_response,
 from wqflask import app
 from utility import hmac
 
-#from utility.elasticsearch_tools import get_elasticsearch_connection
 from utility.redis_tools import get_redis_conn, get_user_id, get_user_by_unique_column, set_user_attribute, get_user_collections, save_collections
 Redis = get_redis_conn()