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-rw-r--r--wqflask/utility/authentication_tools.py2
-rw-r--r--wqflask/utility/elasticsearch_tools.py121
-rw-r--r--wqflask/utility/hmac.py3
-rw-r--r--wqflask/utility/redis_tools.py2
-rw-r--r--wqflask/utility/tools.py5
5 files changed, 1 insertions, 132 deletions
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index c4801c8c..afea69e1 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -1,7 +1,6 @@
import json
import requests
-from deprecated import deprecated
from flask import g
from base import webqtlConfig
@@ -127,7 +126,6 @@ def check_owner(dataset=None, trait_id=None, resource_id=None):
return False
-@deprecated
def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None):
if not resource_id:
if dataset.type == "Temp":
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/hmac.py b/wqflask/utility/hmac.py
index d6e515ed..29891677 100644
--- a/wqflask/utility/hmac.py
+++ b/wqflask/utility/hmac.py
@@ -1,14 +1,11 @@
import hmac
import hashlib
-from deprecated import deprecated
from flask import url_for
from wqflask import app
-@deprecated("This function leads to circular imports. "
- "If possible use wqflask.decorators.create_hmac instead.")
def hmac_creation(stringy):
"""Helper function to create the actual hmac"""
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index c2a3b057..a6c5875f 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -4,7 +4,6 @@ import datetime
import redis # used for collections
-from deprecated import deprecated
from utility.hmac import hmac_creation
from utility.logger import getLogger
logger = getLogger(__name__)
@@ -252,7 +251,6 @@ def get_resource_id(dataset, trait_id=None):
return resource_id
-@deprecated
def get_resource_info(resource_id):
resource_info = Redis.hget("resources", resource_id)
if resource_info:
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')