remove dependency on flask_neomodel library

requirements.txt

@@ -7,4 +7,3 @@ py2neo >= 2.5.0
 healthcheck >= 1.3.3
 iso8601 >= 0.1.12
 pytz >= 2019.1
-git+https://github.com/pdonorio/flask-neomodel.git@master

synprov/__init__.py

@@ -2,12 +2,13 @@
 
 from healthcheck import HealthCheck
 
-from synprov import config
+from synprov.config import neo4j_connection
 
 def neo4j_available():
-    if config.neomod.test_connection():
+    try:
+        neo4j_connection.run('MATCH () RETURN 1 LIMIT 1')
         return True, "neo4j ok"
-    else:
+    except AttributeError:
         return False, "neo4j connection not found"
 
 

synprov/__main__.py

@@ -1,17 +1,13 @@
 #!/usr/bin/env python3
 
 import connexion
-from py2neo import Graph
 
 from synprov import create_app
-from synprov.config import neomod
+from synprov.config import neo4j_connection as graph
 from synprov.graph.client import GraphClient
 from synprov.mock.main import create_mock_graph
 
 
-graph = Graph(neomod.neo.db.url)
-
-
 def init_db(num_activities=30):
     graph.run(
         '''
@@ -26,7 +22,7 @@ def main():
     app = create_app()
 
     init_db()
-    app.run(host='localhost', port=8080, debug=True)
+    app.run(host='localhost', port=8080)
 
 
 if __name__ == '__main__':

synprov/config.py

@@ -3,20 +3,21 @@
 import os
 import connexion
 
-from flask_neomodel import NeoModel
+from py2neo import Graph
 
 
 connex_app = connexion.App(__name__, specification_dir='./openapi/')
 
 env_host = os.environ.get('NEO4J_HOST')
 neo4j_host = env_host if env_host is not None else 'localhost'
+print(neo4j_host)
 
 neo_user = os.environ['NEO4J_USERNAME']
 neo_pass = os.environ['NEO4J_PASSWORD']
 
-neomod = NeoModel(connex_app.app, variables={
-    'user': neo_user,
-    'password': neo_pass,
-    'host': neo4j_host,
-    'port': 7687
-})
+neo4j_connection = Graph(
+    scheme='bolt',
+    host=neo4j_host,
+    user=neo_user,
+    password=neo_pass
+)

synprov/graph/builder.py

@@ -2,7 +2,7 @@
 
 from py2neo import Graph
 
-from synprov.config import neomod
+from synprov.config import neo4j_connection as graph
 from synprov.models.activity_form import ActivityForm
 from synprov.graph.client import GraphClient
 from synprov.graph.models.activity import GraphActivity
@@ -12,7 +12,6 @@
 
 
 logger = logging.getLogger(__name__)
-graph = Graph(neomod.neo.db.url)
 
 
 class ActivityBuilder(ActivityForm):

synprov/graph/client.py

@@ -6,7 +6,7 @@
 """
 import logging
 
-from py2neo import Graph, Node
+from py2neo import Node
 
 from synprov.mock.dict import NodeRelationships
 

synprov/graph/controllers/activities_controller.py

@@ -4,16 +4,13 @@
 import humps
 import json
 
-from py2neo import Graph, Node, NodeMatcher
+from py2neo import Node, NodeMatcher
 
-from synprov.config import neomod
+from synprov.config import neo4j_connection as graph
 from synprov.graph import GraphActivity, GraphReference, GraphAgent
 from synprov.util import neo4j_to_d3
 
 
-graph = Graph(neomod.neo.db.url)
-
-
 def create_activity(body=None):  # noqa: E501
     """Create a new.
 

synprov/graph/controllers/agents_controller.py

@@ -3,15 +3,12 @@
 import uuid
 import humps
 
-from py2neo import Graph, Node, NodeMatcher
+from py2neo import Node, NodeMatcher
 
-from synprov.config import neomod
+from synprov.config import neo4j_connection as graph
 from synprov.graph import GraphActivity, GraphReference, GraphAgent
 
 
-graph = Graph(neomod.neo.db.url)
-
-
 def get_agent_subgraph(id):  # noqa: E501
     """Get subgraph connected to an agent.
 

synprov/graph/controllers/references_controller.py

@@ -3,15 +3,12 @@
 import uuid
 import humps
 
-from py2neo import Graph, Node, NodeMatcher
+from py2neo import Node, NodeMatcher
 
-from synprov.config import neomod
+from synprov.config import neo4j_connection as graph
 from synprov.graph import GraphActivity, GraphReference, GraphAgent
 
 
-graph = Graph(neomod.neo.db.url)
-
-
 def get_reference_subgraph(id):  # noqa: E501
     """Get subgraph connected to an entity.
 

synprov/graph/models/activity.py

@@ -1,16 +1,9 @@
 import uuid
 
-from py2neo import Graph, Node, Relationship, NodeMatcher
-
-from synprov.config import neomod
 from synprov.models.activity import Activity
 from synprov.util import get_datetime
 
 
-graph = Graph(neomod.neo.db.url)
-matcher = NodeMatcher(graph)
-
-
 class GraphActivity(Activity):
 
     def __init__(self,

synprov/graph/models/agent.py

@@ -1,6 +1,5 @@
 import uuid
 
-from synprov.config import neomod
 from synprov.models.agent import Agent
 from synprov.util import get_datetime
 

synprov/graph/models/reference.py

@@ -1,15 +1,8 @@
 import uuid
 
-from py2neo import Graph, Node, Relationship, NodeMatcher
-
-from synprov.config import neomod
 from synprov.models.reference import Reference
-from synprov.models.agent import Agent
 from synprov.util import get_datetime
 
-graph = Graph(neomod.neo.db.url)
-matcher = NodeMatcher(graph)
-
 
 class GraphReference(Reference):
 

synprov/mock/main.py

@@ -3,9 +3,9 @@
 import argparse
 
 from random import randrange
-from py2neo import Graph, Node, NodeMatcher
+from py2neo import Node, NodeMatcher
 
-from synprov.config import neomod
+from synprov.config import neo4j_connection as graph
 from synprov.mock.models.activity import MockActivity
 from synprov.mock.mocker import ActivityMocker
 from synprov.graph.client import GraphClient
@@ -14,7 +14,6 @@
 logging.basicConfig(format='%(asctime)s | %(levelname)s : %(message)s',
                     level=logging.INFO,
                     stream=sys.stdout)
-graph = Graph(neomod.neo.db.url)
 matcher = NodeMatcher(graph)
 
 # ------------------------------

synprov/mock/mocker.py

@@ -3,7 +3,7 @@
 from random import randrange, sample
 from py2neo import Graph, NodeMatcher
 
-from synprov.config import neomod
+from synprov.config import neo4j_connection as graph
 from synprov.mock.models.activity import MockActivity
 from synprov.mock.models.agent import MockAgent
 from synprov.mock.models.reference import MockReference
@@ -12,7 +12,6 @@
 
 
 logger = logging.getLogger(__name__)
-graph = Graph(neomod.neo.db.url)
 matcher = NodeMatcher(graph)
 
 

synprov/test/conftest.py

@@ -6,7 +6,7 @@
 from py2neo import Graph
 
 from synprov import create_app
-from synprov.config import neomod
+from synprov.config import neo4j_connection as graph
 from synprov.graph.client import GraphClient
 from synprov.mock.main import create_mock_graph
 
@@ -26,7 +26,6 @@ def client():
 @pytest.fixture(scope='function')
 def mock_graph():
     logger.info("setup: initializing graph database")
-    graph = Graph(neomod.neo.db.url)
     yield graph
 
     logger.info("teardown: deleting graph database records")