Merge pull request #21 from Sage-Bionetworks/update-openapi

Update OpenAPI spec. Fixes #17. Will address other updates to Python to match spec in PR for #20.

synprov/controllers/activities_controller.py

@@ -2,11 +2,13 @@
 import six
 import uuid
 import humps
+import json
 
 from py2neo import Graph, Node, NodeMatcher
 
 from synprov.config import neomod
 from synprov.graphmodels import Activity, Reference, Agent
+from synprov.util import neo4j_to_d3
 
 
 graph = Graph(neomod.neo.db.url)
@@ -22,122 +24,31 @@ def create_activity(body):  # noqa: E501
 
     :rtype: Activity
     """
-    act = Activity(**humps.decamelize(body))
-    act.save()
+    # act = Activity(**humps.decamelize(body))
+    # act.save()
 
-    return act.node
-
-
-def delete_activity(id):  # noqa: E501
-    """Delete an.
-
-    Delete an Activity # noqa: E501
-
-    :param id: The id of activity to delete.
-    :type id: str
-
-    :rtype: file
-    """
+    # return act.node
     return 'Not Implemented', 501
 
 
-def get_activity(id):  # noqa: E501
-    """Get an existing.
-
-    Get an existing Activity # noqa: E501
-
-    :param id: The ID of the activity to fetch.
-    :type id: str
-
-    :rtype: Activity
-    """
-    matcher = NodeMatcher(graph)
-    activity = matcher.match('Activity',
-                             activity_id={id}).first()
-    return activity
-
-
-def get_activity_used(id):  # noqa: E501
-    """Get used by an existing.
-
-    Get entities used by an existing Activity # noqa: E501
-
-    :param id: The ID of the activity to fetch.
-    :type id: str
-
-    :rtype: List[Reference]
-    """
-    used = graph.run(
-        '''
-        MATCH (refs)<-[:USED]-(a:Activity {activity_id: {a_id}})
-        RETURN refs
-        ''',
-        a_id=id
-    )
-    return [r['refs'] for r in used.data()]
-
-
-def get_activity_generated(id):  # noqa: E501
-    """Get generated by an existing.
+def get_activities_graph(limit=20):  # noqa: E501
+    """Get provenance graph
 
-    Get entities generated by an existing Activity # noqa: E501
+    Retrieve all nodes and relationships in the graph that pass filters.  # noqa: E501
 
-    :param id: The ID of the activity to fetch.
-    :type id: str
+    :param limit: maximum number of nodes to return
+    :type limit: int
 
-    :rtype: List[Reference]
+    :rtype: D3Graph
     """
-    generated = graph.run(
+    # TODO: with the current query, the 'limit' parameter applies
+    # to relationships, not really to nodes
+    results = graph.run(
         '''
-        MATCH (refs)-[:WASGENERATEDBY]->(a:Activity {activity_id: {a_id}})
-        RETURN refs
+        MATCH (s)-[r]-(t)
+        RETURN s as source, r as relationship, t as target
+        LIMIT {limit}
         ''',
-        a_id=id
+        limit=limit
     )
-    return [r['refs'] for r in generated.data()]
-
-
-def get_activity_agents(id):  # noqa: E501
-    """Get agents for an existing.
-
-    Get agents associated with an existing Activity # noqa: E501
-
-    :param id: The ID of the activity to fetch.
-    :type id: str
-
-    :rtype: List[Agent]
-    """
-    agents = graph.run(
-        '''
-        MATCH (agts)<-[:WASASSOCIATEDWITH]->(a:Activity {activity_id: {a_id}})
-        RETURN agts
-        ''',
-        a_id=id
-    )
-    return [r['agts'] for r in agents.data()]
-
-
-def list_activities():  # noqa: E501
-    """.
-
-    List Activities # noqa: E501
-
-
-    :rtype: List[Activity]
-    """
-    return 'Not Implemented', 501
-
-
-def update_activity(id, body=None):  # noqa: E501
-    """Update an.
-
-    Update an Activity # noqa: E501
-
-    :param id: The id of the activity to update.
-    :type id: str
-    :param body: Update an Activity
-    :type body: dict | bytes
-
-    :rtype: Activity
-    """
-    return 'Not Implemented', 501
+    return neo4j_to_d3(results.data())

synprov/controllers/agents_controller.py

@@ -12,25 +12,14 @@
 graph = Graph(neomod.neo.db.url)
 
 
-def get_agent(id):  # noqa: E501
-    """Get an existing.
+def get_agent_subgraph(id):  # noqa: E501
+    """Get subgraph connected to an agent.
 
-    Get an existing Agent # noqa: E501
+    Retrieve all nodes and relationships in the graph that pass filters. # noqa: E501
 
     :param id: The ID of the agent to fetch.
     :type id: str
 
-    :rtype: Agent
+    :rtype: Graph
     """
-    return 'do some magic!'
-
-
-def list_agents():  # noqa: E501
-    """.
-
-    List Agents # noqa: E501
-
-
-    :rtype: List[Agent]
-    """
-    return 'do some magic!'
+    return 'Not Implemented', 501

synprov/controllers/references_controller.py

@@ -12,25 +12,14 @@
 graph = Graph(neomod.neo.db.url)
 
 
-def get_reference(id):  # noqa: E501
-    """Get an existing.
+def get_reference_subgraph(id):  # noqa: E501
+    """Get subgraph connected to an entity.
 
-    Get an existing Reference # noqa: E501
+    Retrieve the nodes and relationships in a neighborhood around a specified entity. # noqa: E501
 
     :param id: The ID of the entity to fetch.
     :type id: str
 
-    :rtype: Reference
+    :rtype: Graph
     """
-    return 'do some magic!'
-
-
-def list_references():  # noqa: E501
-    """.
-
-    List References # noqa: E501
-
-
-    :rtype: List[Reference]
-    """
-    return 'do some magic!'
+    return 'Not Implemented', 501