add more logging, use logger consistently

synprov/__init__.py

@@ -1,19 +1,28 @@
+import logging
 import connexion
 
 from healthcheck import HealthCheck
 
+from synprov.config import connex_app
 from synprov.config import neo4j_connection
 
+
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+
 def neo4j_available():
     try:
+        logger.info("Checking connection at {}"
+                     .format(neo4j_connection.database.uri))
         neo4j_connection.run('MATCH () RETURN 1 LIMIT 1')
         return True, "neo4j ok"
     except AttributeError:
         return False, "neo4j connection not found"
 
 
 def create_app():
-    app = config.connex_app
+    app = connex_app
     app.add_api('openapi.yaml', arguments={'title': 'Provenance Service'})
     # wrap the flask app and give a heathcheck url
     health = HealthCheck(app, "/healthcheck")

synprov/__main__.py

@@ -1,20 +1,21 @@
 #!/usr/bin/env python3
 
 import connexion
+import logging
 
 from synprov import create_app
 from synprov.config import neo4j_connection as graph
 from synprov.graph.client import GraphClient
 from synprov.mock.main import create_mock_graph
 
 
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+
 def init_db(num_activities=30):
-    graph.run(
-        '''
-        MATCH (n)
-        DETACH DELETE n
-        '''
-    )
+    graph.delete_all()
+    logger.info("Populating mock graph")
     create_mock_graph(GraphClient(graph), num_activities)
 
 

synprov/config.py

@@ -1,20 +1,24 @@
 #!/usr/bin/env python3
-
+import logging
 import os
 import connexion
 
 from py2neo import Graph
 
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
 
 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'
+neo4j_host = env_host if env_host is not None else '0.0.0.0'
 print(neo4j_host)
 
 neo_user = os.environ['NEO4J_USERNAME']
 neo_pass = os.environ['NEO4J_PASSWORD']
 
+logger.info("Connecting to neo4j database")
 neo4j_connection = Graph(
     scheme='bolt',
     host=neo4j_host,

synprov/mock/main.py

@@ -11,9 +11,10 @@
 from synprov.graph.client import GraphClient
 
 
-logging.basicConfig(format='%(asctime)s | %(levelname)s : %(message)s',
-                    level=logging.INFO,
-                    stream=sys.stdout)
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+
 matcher = NodeMatcher(graph)
 
 # ------------------------------
@@ -38,21 +39,21 @@ def add_activities(kt):
     return x
 
 
-def create_mock_graph(graph_db, NUMACTIVITIES):
+def create_mock_graph(graph_client, NUMACTIVITIES):
     # SCRIPT
 
     # step 1 - Create activities:
-    logging.info("Generating table of Activities...")
+    logger.info("Generating table of Activities...")
     activity_array = add_activities(NUMACTIVITIES)
 
     # step 2 - Create corresponding nodes and relationships
     # for each activity:
     ref_num = 0
     agt_num = 0
     for i in activity_array:
-        logging.info("Building Activity '{}' of class '{}'"
+        logger.info("Building Activity '{}' of class '{}'"
                      .format(i.name, i._class))
-        act = ActivityMocker(graph_db, i, ref_num, agt_num)
+        act = ActivityMocker(graph_client, i, ref_num, agt_num)
         (rn, an) = act.save()
         ref_num += rn
         agt_num += an