Make miscellaneous small-scale improvements (GraphQL refactor; upload endpoint namespacing; bugfixes)

client/src/views/WorkspaceDetail.vue

@@ -56,7 +56,7 @@ export default {
       fileList : null,
       fileTypes: {
         csv: {extension: ['csv'], queryCall: 'bulk'},
-        newick: {extension: ['phy'], queryCall: 'tree'}
+        newick: {extension: ['phy'], queryCall: 'newick'}
       },
       selectedType: null,
     }

multinet/multinet/__init__.py

@@ -15,14 +15,29 @@
 from .schema import schema
 from . import db
 
+
+def graphql_query(query):
+    result = graphql(schema, query)
+    if result:
+        errors= [error.message for error in result.errors] if result.errors else []
+        logprint("Errors in request: %s" % len(errors), level=logging.WARNING)
+        for error in errors[:10]:
+            logprint(error, level=logging.WARNING)
+    else:
+        errors = []
+    return dict(data=result.data, errors=errors)
+
+
 class MultiNet(Resource):
     def __init__(self, port):
         super(MultiNet, self).__init__()
         self.resourceName = 'multinet'
         self.arango_port = port
         self.route('POST', ('graphql',), self.graphql)
-        self.route('POST', ('bulk', ':workspace', ':table'), self.bulk)
-        self.route('POST', ('tree', ':workspace', ':table'), self.tree)
+        self.route('POST', ('csv', ':workspace', ':table'), self.bulk)
+
+        # Newick tree operations.
+        self.route('POST', ('newick', ':workspace', ':table'), self.tree)
 
     @access.public
     @autoDescribeRoute(
@@ -34,15 +49,7 @@ def graphql(self, params):
         query = getBodyJson()['query']
         logprint('request: %s' % query, level=logging.DEBUG)
 
-        result = graphql(schema, query)
-        if result:
-            errors= [error.message for error in result.errors] if result.errors else []
-            logprint("Errors in request: %s" % len(errors), level=logging.WARNING)
-            for error in errors[:10]:
-                logprint(error, level=logging.WARNING)
-        else:
-            errors = []
-        return dict(data=result.data, errors=errors)
+        return graphql_query(query)
 
     @access.public
     @autoDescribeRoute(

multinet/multinet/db.py

@@ -3,7 +3,7 @@
 from girder import logprint
 from arango import ArangoClient
 
-from multinet.types import Row, Entity
+from multinet.types import Row, Entity, Cursor
 
 def with_client(fun):
     def wrapper(*args, **kwargs):
@@ -60,7 +60,11 @@ def nodes(query, cursor, arango=None):
     graph = workspace.graph(query.graph)
     if query.entity_type:
         if query.id:
-            return [Entity(query.workspace, query.graph, query.entity_type, workspace.collection(query.entity_type).get(query.id))], 1
+            result = workspace.collection(query.entity_type).get(query.id)
+            if result is not None:
+                return [Entity(query.workspace, query.graph, query.entity_type, workspace.collection(query.entity_type).get(query.id))], 1
+            else:
+                return [], 0
         else:
             tables = [workspace.collection(query.entity_type)]
     else: