Modernize to Python 3 / add Pipenv support / other improvements

.gitignore

@@ -1,2 +1,3 @@
 venv/
 yarn.lock
+Pipfile.lock

Pipfile

@@ -0,0 +1,17 @@
+[[source]]
+name = "pypi"
+url = "https://pypi.org/simple"
+verify_ssl = true
+
+[dev-packages]
+
+[packages]
+multinet = {path = "./multinet",editable = true}
+python-arango = "*"
+graphql-core = "*"
+
+[requires]
+python_version = "3.7"
+
+[pipenv]
+allow_prereleases = true

README.md

@@ -9,11 +9,11 @@ Follow the instructions at [multinet-server-poc](https://github.com/multinet-app
 ### Set Up Girder
 1. Clone this repository: `git clone
 https://github.com/multinet-app/multinet-girder; cd multinet-girder`
-2. Create and activate a Python virtual environment: `virtualenv venv; source
-./venv/bin/activate`
-3. Perform an editable install of the plugin package: `pip install -e multinet`
+2. Start the mongo and arango databases using docker-compose: `MULTINET_ROOT_PASSWORD=yourSecretPassword docker-compose up -d`
+2. Use pipenv to create a virtual environment and install the dependencies: `pipenv install`
+3. Start the pipenv shell to set up girder and run the websever: `pipenv shell`
 4. Build the Girder web client: `girder build`
-5. Serve the Girder client: `girder serve --database
+5. Serve the Girder client: `MULTINET_ROOT_PASSWORD=yourSecretPassword girder serve --database
    mongodb://localhost:27017/multinet --port 9090`
 6. Open the Girder client and register a user (which will become an admin user):
 http://localhost:9090

client/src/views/NodeDetail.vue

@@ -22,7 +22,7 @@
           <div v-if="nextIncoming" v-on:click="lastPage('incoming')">last</div>
         </div>
         <ul>
-          <li v-for="edge, index in incoming" :key="index">
+          <li v-for="(edge, index) in incoming" :key="index">
             <router-link :to="`/${workspace}/graph/${graph}/node/${edge.airport}`">{{edge.airport}}</router-link>
           </li>
         </ul>
@@ -38,7 +38,7 @@
           <div v-if="nextOutgoing" v-on:click="lastPage('outgoing')">last</div>
         </div>
         <ul>
-          <li v-for="edge, index in outgoing" :key="index">
+          <li v-for="(edge, index) in outgoing" :key="index">
             <router-link :to="`/${workspace}/graph/${graph}/node/${edge.airport}`">{{edge.airport}}</router-link>
           </li>
         </ul>

multinet/multinet/__init__.py

@@ -50,7 +50,7 @@ def graphql(self, params):
     )
     def bulk(self, params, workspace=None, table=None):
         logprint('Bulk Loading', level=logging.INFO)
-        rows = csv.DictReader(cherrypy.request.body)
+        rows = csv.DictReader(cherrypy.request.body.read().decode('utf8'))
         workspace = db.db(workspace)
         if workspace.has_collection(table):
             table = workspace.collection(table)

multinet/multinet/db.py

@@ -3,7 +3,7 @@
 from girder import logprint
 from arango import ArangoClient
 
-from types import *
+from .types import *
 
 def with_client(fun):
     def wrapper(*args, **kwargs):
@@ -46,10 +46,10 @@ def workspace_graphs(workspace, arango=None):
     return [graph['name'] for graph in space.graphs()]
 
 @with_client
-def table_fields(table, arango=None):
-    workspace = db(table.workspace, arango=arango)
-    if workspace.has_collection(table.table):
-        sample = workspace.collection(table.table).random()
+def table_fields(query, arango=None):
+    workspace = db(query.workspace, arango=arango)
+    if workspace.has_collection(query.table):
+        sample = workspace.collection(query.table).random()
         return sample.keys()
     else:
         return []
@@ -135,16 +135,16 @@ def create_graph(graph, node_types, edge_types, arango=None):
             graph.delete_edge_definition(table, purge=False)
 
     for table in graph.vertex_collections():
-        if table not in node_tables:
+        if table not in node_types:
             graph.delete_vertex_collection(table)
 
 @with_client
-def table(table, arango=None):
-    workspace = db(table.workspace, arango=arango)
-    if workspace.has_collection(table.table):
-        return workspace.collection(table.table)
+def table(query, arango=None):
+    workspace = db(query.workspace, arango=arango)
+    if workspace.has_collection(query.table):
+        return workspace.collection(query.table)
     elif create:
-        return workspace.create_collection(table.table)
+        return workspace.create_collection(query.table)
     else:
         return None
 
@@ -159,7 +159,7 @@ def graph(graph, create=False, arango=None):
         return None
 
 def countRows(query):
-    collection = table(query.table)
+    collection = table(query)
     if query.id:
         return 1
     elif query.search:
@@ -168,7 +168,7 @@ def countRows(query):
         return collection.count()
 
 def fetchRows(query, cursor):
-    collection = table(query.table)
+    collection = table(query)
     if query.id:
         return [collection.get(query.id)]
     elif query.search:

multinet/multinet/multinet.gql

@@ -0,0 +1,102 @@
+type Attribute {
+  # the key is the table name followed by the column name delimited by a slash, eg table/col
+  key: String!
+  # json representation of the value
+  value: String!
+}
+
+# type Property {
+#     label: String!
+#     key: String!
+# }
+
+# type EntityType {
+#     name: String!
+#     properties: [Property!]!
+# }
+
+interface Entity {
+  # this is the id of the entity in all tables it's associated with
+  key: String!
+  type: String!
+  properties (keys: [String!]): [Attribute!]
+}
+
+type Node implements Entity {
+  key: String!
+  type: String!
+  outgoing (limit: Int, offset: Int): EdgeList!
+  incoming (limit: Int, offset: Int): EdgeList!
+  properties (keys: [String!]): [Attribute!]
+}
+
+type Edge implements Entity {
+  key: String!
+  type: String!
+  source: Node!
+  target: Node!
+  properties (keys: [String!]): [Attribute!]
+}
+
+type Row {
+  key: String!
+  columns (keys: [String!]): [Attribute!]!
+}
+
+type NodeList {
+  total: Int!
+  nodes (offset: Int, limit: Int): [Node!]!
+}
+
+type EdgeList {
+  total: Int!
+  edges (offset: Int, limit: Int): [Edge!]!
+}
+
+type RowList {
+  total: Int!
+  rows (offset: Int, limit: Int): [Row!]!
+}
+
+type Table {
+  name: String!
+  primaryKey: String!
+  # a list of key strings as they would appear in Attribute
+  fields: [String!]!
+  rows: RowList!
+}
+
+type Graph {
+  name: String!
+  nodeTypes: [String!]!
+  edgeTypes: [String!]!
+  nodes: NodeList!
+  edges: EdgeList!
+}
+
+type Workspace {
+  name: String!
+  tables: [Table!]!
+  graphs: [Graph!]!
+}
+
+type Query {
+  nodes (workspace: String!, graph: String!, nodeType: String, key: String, search: String): NodeList!
+  edges (workspace: String!, graph: String!, edgeType: String, key: String, search: String): EdgeList!
+  rows (workspace: String!, table: String!, key: String, search: String): RowList!
+
+  workspaces (name: String): [Workspace!]!
+  graphs (workspace: String!, name: String): [Graph!]!
+  tables (workspace: String!, name: String): [Table!]!
+}
+
+type Mutation {
+  workspace (name: String!): String!
+  graph (workspace: String!, name: String!, nodeTypes: [String!]!, edgeTypes: [String!]!): Graph!
+  table (workspace: String!, name: String!, fields: [String!]!, primaryKey: String): Table!
+}
+
+schema {
+  query: Query
+  mutation: Mutation
+}

multinet/multinet/resolvers.py

@@ -1,7 +1,7 @@
 import os
 import logging
 from girder import plugin, logprint
-from types import *
+from .types import *
 
 from . import db
 
@@ -50,7 +50,7 @@ def rows(query, info, offset=0, limit=10):
     return db.fetchRows(query, Cursor(offset, limit))
 
 def table_rows(table, info):
-    return RowQuery(table, None, None)
+    return RowQuery(table.workspace, table.table, None, None)
 
 def workspace_name(workspace, info):
     return workspace
@@ -95,7 +95,7 @@ def nodeIncoming(node, info):
     return RealizedQuery(db.incoming(node))
 
 def attributes(entity, info, keys=None):
-    return [(key, value) for key, value in entity.data.iteritems() if (keys is None) or (key in keys)]
+    return [(key, value) for key, value in entity.data.items() if (keys is None) or (key in keys)]
 
 # MUTATIONS
 def create_workspace(root, info, name):

multinet/multinet/schema.py

@@ -1,112 +1,15 @@
+import os.path
+
 from graphql import build_ast_schema
 from graphql.language.parser import parse
 
 from . import resolvers
 
-schema = build_ast_schema(parse("""
-    type Attribute {
-        # the key is the table name followed by the column name delimited by a slash, eg table/col
-        key: String!
-        # json representation of the value
-        value: String!
-    }
-
-    # type Property {
-    #     label: String!
-    #     key: String!
-    # }
-
-    # type EntityType {
-    #     name: String!
-    #     properties: [Property!]!
-    # }
-
-    interface Entity {
-        # this is the id of the entity in all tables it's associated with
-        key: String!
-        type: String!
-        properties (keys: [String!]): [Attribute!]
-    }
-
-    type Node implements Entity {
-        key: String!
-        type: String!
-        outgoing (limit: Int, offset: Int): EdgeList!
-        incoming (limit: Int, offset: Int): EdgeList!
-        properties (keys: [String!]): [Attribute!]
-    }
-
-    type Edge implements Entity {
-        key: String!
-        type: String!
-        source: Node!
-        target: Node!
-        properties (keys: [String!]): [Attribute!]
-    }
-
-    type Row {
-        key: String!
-        columns (keys: [String!]): [Attribute!]!
-    }
-
-    type NodeList {
-        total: Int!
-        nodes (offset: Int, limit: Int): [Node!]!
-    }
-
-    type EdgeList {
-        total: Int!
-        edges (offset: Int, limit: Int): [Edge!]!
-    }
-
-    type RowList {
-        total: Int!
-        rows (offset: Int, limit: Int): [Row!]!
-    }
-
-    type Table {
-        name: String!
-        primaryKey: String!
-        # a list of key strings as they would appear in Attribute
-        fields: [String!]!
-        rows: RowList!
-    }
-
-    type Graph {
-        name: String!
-        nodeTypes: [String!]!
-        edgeTypes: [String!]!
-        nodes: NodeList!
-        edges: EdgeList!
-    }
-
-    type Workspace {
-        name: String!
-        tables: [Table!]!
-        graphs: [Graph!]!
-    }
-
-    type Query {
-        nodes (workspace: String!, graph: String!, nodeType: String, key: String, search: String): NodeList!
-        edges (workspace: String!, graph: String!, edgeType: String, key: String, search: String): EdgeList!
-        rows (workspace: String!, table: String!, key: String, search: String): RowList!
-
-        workspaces (name: String): [Workspace!]!
-        graphs (workspace: String!, name: String): [Graph!]!
-        tables (workspace: String!, name: String): [Table!]!
-    }
-
-    type Mutation {
-        workspace (name: String!): String!
-        graph (workspace: String!, name: String!, nodeTypes: [String!]!, edgeTypes: [String!]!): Graph!
-        table (workspace: String!, name: String!, fields: [String!]!, primaryKey: String): Table!
-    }
-
-    schema {
-      query: Query
-      mutation: Mutation
-    }
-"""))
+schema_text = None
+with open(os.path.join(os.path.dirname(__file__), 'multinet.gql')) as f:
+    schema_text = f.read()
+
+schema = build_ast_schema(parse(schema_text))
 
 fields = schema.get_type('Query').fields
 fields['nodes'].resolver = resolvers.query_nodes