Merge GREMLIN35-v2 into GREMLIN35 (#208)

* Pin ipython and ipykernel dependency versions (#207)

* Pin ipython and ipykernel dependency versions

* Update Changelog

Co-authored-by: Michael Chin <chnmch@amazon.com>

* Apply nest_asyncio for Gremlin client requests, Update dependencies and install docs

* Switch to python script for starting jupyter

* Allow specifying notebooks directory on startup

* Pinning nbconvert version to resolve ipython-contrib/jupyter_contrib_nbextensions#1529

* Fix OC query smart indent bug

* Fix failure to overwrite notebook.json

Co-authored-by: Michael Chin <chnmch@amazon.com>

ChangeLog.md

@@ -7,6 +7,7 @@ Starting with v1.31.6, this file will contain a record of major features and upd
 - Allow `%%neptune_ml` to accept JSON blob as parameter input for most phases ([Link to PR](https://github.com/aws/graph-notebook/pull/202))
 - Added `--silent` option for suppressing query output ([PR #1](https://github.com/aws/graph-notebook/pull/201)) ([PR #2](https://github.com/aws/graph-notebook/pull/203))
 - Added all `parserConfiguration` options to `%load` ([Link to PR](https://github.com/aws/graph-notebook/pull/205))
+- Pinned `ipython` and `ipykernel` dependency versions ([Link to PR](https://github.com/aws/graph-notebook/pull/207))
 
 ## Release 3.0.6 (September 20, 2021)
 - Added a new `%stream_viewer` magic that allows interactive exploration of the Neptune CDC stream (if enabled). ([Link to PR](https://github.com/aws/graph-notebook/pull/191))

README.md

@@ -89,9 +89,7 @@ It is recommended to check the [ChangeLog.md](ChangeLog.md) file periodically to
 
 You will need:
 
-* [Python](https://www.python.org/downloads/) 3.6.1-3.6.12
-* [Jupyter Notebook](https://jupyter.org/install) 5.7.13
-* [Tornado](https://pypi.org/project/tornado/) 4.5.3
+* [Python](https://www.python.org/downloads/) 3.6.13-3.9.7
 * [RDFLib](https://pypi.org/project/rdflib/) 5.0.0
 * A graph database that provides one or more of:
   *  A SPARQL 1.1 endpoint 
@@ -101,9 +99,7 @@ You will need:
 ## Installation
 
 ```
-# pin specific versions of Jupyter, Tornado, and RDFLib dependencies
-pip install notebook==5.7.13
-pip install tornado==4.5.3
+# pin specific versions of required dependencies
 pip install rdflib==5.0.0
 
 # install the package
@@ -121,7 +117,7 @@ python -m graph_notebook.nbextensions.install
 python -m graph_notebook.notebooks.install --destination ~/notebook/destination/dir  
 
 # start jupyter
-jupyter notebook ~/notebook/destination/dir
+python -m graph_notebook.start_notebook --notebooks-dir ~/notebook/destination/dir
 ```
 
 ## Connecting to a graph database

requirements.txt

@@ -1,19 +1,20 @@
-tornado==4.5.3
 SPARQLWrapper==1.8.4
 networkx==2.4
 Jinja2==2.11.3
 jupyter
-notebook==5.7.13
+notebook>=6.1.5
 ipywidgets==7.5.1
 jupyter-contrib-nbextensions
 widgetsnbextension
-gremlinpython<=3.4.*
+gremlinpython>=3.5.1
 requests==2.24.0
-ipython==7.16.1
+ipython>=7.16.1
+ipykernel==5.3.4
 neo4j==4.2.1
 rdflib~=5.0.0
 traitlets~=4.3.3
 setuptools~=40.6.2
+nbconvert<6
 
 # requirements for testing
 botocore~=1.18.18

setup.py

@@ -66,14 +66,13 @@ def get_version():
     package_dir={'': 'src'},
     include_package_data=True,
     install_requires=[
-        'gremlinpython<3.5.*',
+        'gremlinpython>=3.5.1',
         'SPARQLWrapper==1.8.4',
-        'tornado==4.5.3',
         'requests',
         'ipywidgets',
         'networkx==2.4',
         'Jinja2==2.11.3',
-        'notebook',
+        'notebook>=6.1.5',
         'jupyter-contrib-nbextensions',
         'widgetsnbextension',
         'jupyter>=1.0.0',
@@ -82,7 +81,9 @@ def get_version():
         'boto3>=1.17.58',
         'ipython>=7.16.1',
         'neo4j==4.3.2',
-        'rdflib==5.0.0'
+        'rdflib==5.0.0',
+        'ipykernel==5.3.4',
+        'nbconvert==5.6.1'
     ],
     package_data={
         'graph_notebook': ['graph_notebook/widgets/nbextensions/static/*.js',

src/graph_notebook/neptune/client.py

@@ -14,7 +14,7 @@
 from botocore.awsrequest import AWSRequest
 from gremlin_python.driver import client
 from neo4j import GraphDatabase
-from tornado import httpclient
+import nest_asyncio
 
 # This patch is no longer needed when graph_notebook is using the a Gremlin Python
 # client >= 3.5.0 as the HashableDict is now part of that client driver.
@@ -160,6 +160,8 @@ def sparql_cancel(self, query_id: str, silent: bool = False):
         return self._query_status('sparql', query_id=query_id, silent=silent, cancelQuery=True)
 
     def get_gremlin_connection(self) -> client.Client:
+        nest_asyncio.apply()
+
         uri = f'{self._http_protocol}://{self.host}:{self.port}/gremlin'
         request = self._prepare_request('GET', uri)
 

src/graph_notebook/start_notebook.py

@@ -0,0 +1,48 @@
+"""
+Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
+SPDX-License-Identifier: Apache-2.0
+"""
+
+import os
+import argparse
+import json
+
+HOME_PATH = os.path.expanduser("~")
+NOTEBOOK_CFG_PATH = HOME_PATH + '/.jupyter/nbconfig/notebook.json'
+
+
+def patch_cm_cypher_config():
+    cypher_cfg = {
+        "cm_config": {
+            "smartIndent": False,
+            "mode": "cypher"
+        }
+    }
+
+    try:
+        with open(NOTEBOOK_CFG_PATH, 'r') as file:
+            notebook_cfg = json.load(file)
+    except (json.decoder.JSONDecodeError, FileNotFoundError) as e:
+        notebook_cfg = {}
+
+    notebook_cfg["CodeCell"] = cypher_cfg
+
+    with open(NOTEBOOK_CFG_PATH, 'w') as file:
+        json.dump(notebook_cfg, file)
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--notebooks-dir', default='', type=str, help='The directory to start Jupyter from.')
+
+    args = parser.parse_args()
+
+    patch_cm_cypher_config()
+
+    kernel_manager_option = "--NotebookApp.kernel_manager_class=notebook.services.kernels.kernelmanager.AsyncMappingKernelManager"
+    notebooks_dir = '~/notebook/destination/dir' if args.notebooks_dir == '' else args.notebooks_dir
+    os.system(f'''jupyter notebook {kernel_manager_option} {notebooks_dir}''')
+
+
+if __name__ == '__main__':
+    main()