Merge pull request #37 from Sage-Bionetworks/add-activities-post

Add activities post

synprov/graph/__init__.py

@@ -1,3 +1,4 @@
 from .models.activity import GraphActivity
 from .models.agent import GraphAgent
-from .models.reference import GraphReference
+from .models.reference import GraphReference
+from .builder import ActivityBuilder

synprov/graph/builder.py

@@ -105,4 +105,4 @@ def save(self):
                 rel.create()
                 self.gdb.create_relationship(rel)
 
-        return True
+        return self._find_activity()

synprov/graph/controllers/activities_controller.py

@@ -7,7 +7,7 @@
 from py2neo import Node, NodeMatcher
 
 from synprov.config import neo4j_connection as graph
-from synprov.graph import GraphActivity, GraphReference, GraphAgent
+from synprov.graph import ActivityBuilder
 from synprov.util import neo4j_to_d3
 
 
@@ -21,11 +21,16 @@ def create_activity(body=None):  # noqa: E501
 
     :rtype: Activity
     """
-    # act = Activity(**humps.decamelize(body))
-    # act.save()
-
-    # return act.node
-    return 'Not Implemented', 501
+    builder = ActivityBuilder(
+        **body.to_dict()
+    )
+    act_node = builder.save()
+    print(act_node)
+    return humps.camelize({
+        'id': str(act_node.identity),
+        'labels': list(act_node.labels),
+        'properties': dict(act_node)
+    })
 
 
 def get_activities_graph(sort_by=None, order=None, limit=None):  # noqa: E501
@@ -61,7 +66,7 @@ def get_activities_graph(sort_by=None, order=None, limit=None):  # noqa: E501
     results = graph.run(
         query_base,
     )
-    return neo4j_to_d3(results.data())
+    return humps.camelize(neo4j_to_d3(results.data()))
 
 
 def get_agent_subgraph(id, sort_by=None, order=None, limit=None):  # noqa: E501
@@ -100,7 +105,7 @@ def get_agent_subgraph(id, sort_by=None, order=None, limit=None):  # noqa: E501
         query_base,
         id=id
     )
-    return neo4j_to_d3(results.data())
+    return humps.camelize(neo4j_to_d3(results.data()))
 
 
 def get_reference_subgraph(id,
@@ -150,4 +155,4 @@ def get_reference_subgraph(id,
         query_base,
         id=id
     )
-    return neo4j_to_d3(results.data())
+    return humps.camelize(neo4j_to_d3(results.data()))

synprov/test/conftest.py

@@ -36,7 +36,7 @@ def mock_graph():
 def mock_graph_data(mock_graph):
     logger.info("setup: populating graph database")
     graph = mock_graph
-    random.seed(0)
+    random.seed(1)
     gc = GraphClient(graph)
     create_mock_graph(gc, 5)
     yield graph
@@ -46,37 +46,37 @@ def mock_graph_data(mock_graph):
 def mock_activity_form():
     used = [
         {
-            'name': 'Reference_5',
-            'target_id': 'TargetID_5',
+            'name': 'Reference_3',
+            'target_id': 'TargetID_3',
             'target_version_id': '1.0',
             '_class': 'Resource',
             'subclass': 'File'
+        },
+        {
+            'name': 'Reference_4',
+            'target_id': 'TargetID_4',
+            'target_version_id': '1.0',
+            '_class': 'Tool',
+            'subclass': 'Tool'
         }
-        # {
-        #     'name': 'Reference_5',
-        #     'target_id': 'TargetID_5',
-        #     'target_version_id': '1.0',
-        #     '_class': 'Tool',
-        #     'subclass': 'Tool'
-        # }
     ]
     generated = [
         {
-            'name': 'Reference_6',
-            'target_id': 'TargetID_6',
+            'name': 'Reference_5',
+            'target_id': 'TargetID_5',
             'target_version_id': '1.0',
             '_class': 'Resource',
             'subclass': 'State'
         }
     ]
     agents = [
         {
-            'name': 'User_2',
-            'user_id': 'UserID_2'
+            'name': 'User_1',
+            'user_id': 'UserID_1'
         }
     ]
     form = {
-        'name': 'Activity_3',
+        'name': 'Activity_2',
         '_class': 'Tool session',
         'agents': agents,
         'description': '',
@@ -86,3 +86,46 @@ def mock_activity_form():
     }
     yield form
 
+@pytest.fixture(scope='function')
+def mock_activity_request():
+    used = [
+        {
+            'name': 'Reference_3',
+            'targetId': 'TargetID_3',
+            'targetVersionId': '1.0',
+            'class': 'Resource',
+            'subclass': 'File'
+        },
+        {
+            'name': 'Reference_4',
+            'target_id': 'TargetID_4',
+            'target_version_id': '1.0',
+            '_class': 'Tool',
+            'subclass': 'Tool'
+        }
+    ]
+    generated = [
+        {
+            'name': 'Reference_5',
+            'targetId': 'TargetID_5',
+            'targetVersionId': '1.0',
+            'class': 'Resource',
+            'subclass': 'State'
+        }
+    ]
+    agents = [
+        {
+            'name': 'User_1',
+            'userId': 'UserID_1'
+        }
+    ]
+    form = {
+        'name': 'Activity_3',
+        'class': 'Tool session',
+        'agents': agents,
+        'description': '',
+        'used': used,
+        'generated': generated
+
+    }
+    yield form

synprov/test/test_controllers.py

@@ -0,0 +1,47 @@
+import logging
+import pytest
+
+from synprov.models import ActivityForm
+from synprov.graph.controllers import activities_controller
+
+
+logging.basicConfig(level=logging.DEBUG)
+logger = logging.getLogger(__name__)
+
+
+class TestActivitiesController:
+
+    def test_create_activity_exists(self,
+                                    mock_graph_data,
+                                    mock_activity_request):
+        node_count = len(mock_graph_data.nodes)
+        rel_count = len(mock_graph_data.relationships)
+        body = ActivityForm.from_dict(mock_activity_request)
+        act_node = activities_controller.create_activity(body)
+        assert len(mock_graph_data.nodes) == node_count
+        assert len(mock_graph_data.relationships) == rel_count
+        assert all([key in act_node for key in ['id', 'labels', 'properties']])
+
+    def test_create_activity_new(self,
+                                 mock_graph,
+                                 mock_activity_request):
+        node_count = len(mock_graph.nodes)
+        rel_count = len(mock_graph.relationships)
+        body = ActivityForm.from_dict(mock_activity_request)
+        act_node = activities_controller.create_activity(body)
+
+        new_nodes = sum([
+            len(mock_activity_request['used']),
+            len(mock_activity_request['generated']),
+            len(mock_activity_request['agents']),
+            1
+        ])
+        new_rels = sum([
+            len(mock_activity_request['used']),
+            len(mock_activity_request['generated']),
+            len(mock_activity_request['agents']) * 2,
+        ])
+
+        assert len(mock_graph.nodes) == (node_count + new_nodes)
+        assert len(mock_graph.relationships) == (rel_count + new_rels)
+        assert all([key in act_node for key in ['id', 'labels', 'properties']])

synprov/util.py

@@ -8,9 +8,6 @@
 import typing
 import socket
 
-
-from datetime import datetime
-
 from functools import wraps
 from hashlib import sha256
 
@@ -174,19 +171,9 @@ def _convert_keys(obj):
         return obj
 
 
-def neo4j_to_d3(results):
-    nodes = []
-    rels = []
-    for record in results:
-        nodes.append(_convert_node(record['source']))
-        nodes.append(_convert_node(record['target']))
-        rels.append(_convert_relationship(record['relationship']))
-    return {"nodes": nodes, "links": rels}
-
-
 def get_datetime(now=None):
     if now is None:
-        now = datetime.now()
+        now = datetime.datetime.now()
     _date_obj = iso8601.parse_date(now.isoformat())
     _date_utc = _date_obj.astimezone(pytz.utc)
     return _date_utc.strftime('%Y-%m-%dT%H:%M:%SZ')