austinkline/windows (#6)

* Windows Compatibility

- Fix path generation to permit windows compatibility
- use `pip install -e .` when installing for unit and integration tests
- add install hooks for nbextensions using jupyter install syntax
- fix bug causing datetimes to not be serialized properly from Neptune

Co-authored-by: Austin Kline <[email protected]>

.github/workflows/integration.yml

@@ -43,7 +43,7 @@ jobs:
           if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
       - name: Install
         run: |
-          pip install .
+          pip install -e .
       - name: Create Stack
         id: create-stack
         run: |
@@ -79,7 +79,7 @@ jobs:
           if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
       - name: Install
         run: |
-          pip install .
+          pip install -e .
       - name: Give user /etc/hosts permission
         run: |
           sudo chmod 777 /etc/hosts

.github/workflows/unit.yml

@@ -25,7 +25,14 @@ jobs:
 
       - name: Install
         run: |
-          pip install .
+          pip install -e .
+      - name: Post-install commands
+        run: |
+          jupyter nbextension install --py --sys-prefix graph_notebook.widgets
+          jupyter nbextension enable  --py --sys-prefix graph_notebook.widgets
+          python -m graph_notebook.static_resources.install
+          python -m graph_notebook.nbextensions.install
+          python -m graph_notebook.notebooks.install
       - name: Test with pytest
         run: |
           pytest

MANIFEST.in

@@ -1,14 +1,10 @@
 include tsconfig.json
 include package.json
 include webpack.config.js
-include src/graph_notebook/widgets/labextension/*.tgz
 
 # Javascript files
-graft graph_notebook/widgets/nbextension
-graft graph_notebook/widgets/labextension
-graft graph_notebook/widgets/src
-graft graph_notebook/widgets/css
-graft **/node_modules
+recursive-include src/graph_notebook/widgets *
+prune **/node_modules
 prune coverage
 
 # Patterns to exclude from any directory

README.md

@@ -4,12 +4,14 @@ Python package integrating Jupyter notebooks with various graph-stores including
 [Apache TinkerPop](https://tinkerpop.apache.org/) and [RDF SPARQL](https://www.w3.org/TR/rdf-sparql-query/).
 
 ## Requirements
-- Python 3.6
+
+- Python 3.6.1 or higher, Python 3.7
 - Jupyter Notebook
 
 ## Introduction
 The graph-notebook provides a way to interact using a Jupyter notebook with any graph database that follows the Gremlin Server or RDF HTTP protocols. These databases could be running locally on your laptop, in a private data center or in the cloud. This project was initially created as a way to work with Amazon Neptune but is not limited to that database engine. For example you can connect to a Gremlin Server running on your laptop using this solution. The instructions below describe the process for connecting to Amazon Neptune. We encourage others to contribute configurations they find useful. There is an [`additional-databases`](additional-databases) folder where such information can be found. 
 
+
 ## Installation
 
 ```

requirements.txt

@@ -3,7 +3,7 @@ SPARQLWrapper==1.8.4
 networkx==2.4
 Jinja2==2.10.1
 jupyter
-notebook<=5.7.8
+notebook==5.7.10
 ipywidgets
 jupyter-contrib-nbextensions
 widgetsnbextension

setup.cfg

@@ -1,3 +1,8 @@
+[options]
+packages =
+    graph_notebook
+include_package_data = True
+
 [tool:pytest]
 minversion = 6.0
 addopts = -ra -q

setup.py

@@ -79,6 +79,8 @@ def get_version():
         'jupyter>=1.0.0'
     ],
     package_data={
+        'graph_notebook': ['graph_notebook/widgets/nbextensions/static/*.js',
+                           'graph_notebook/widgets/labextension/*.tgz'],
         '': ['*.ipynb', '*.html', '*.css', '*.js', '*.txt', '*.json', '*.ts', '*.css', '*.yaml', '*.md', '*.tgz']
     },
     cmdclass=cmd_class,

src/graph_notebook/__init__.py

@@ -3,4 +3,4 @@
 SPDX-License-Identifier: Apache-2.0
 """
 
-__version__ = '1.32.0'
+__version__ = '1.33.0'

src/graph_notebook/nbextensions/__init__.py

@@ -2,3 +2,28 @@
 Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
 SPDX-License-Identifier: Apache-2.0
 """
+
+
+def _jupyter_nbextension_paths():
+    return [
+        dict(
+            section="notebook",
+            src="gremlin_syntax/static",
+            dest="gremlin_syntax",
+            require="gremlin_syntax/main"),
+        dict(
+            section="notebook",
+            src="sparql_syntax/static",
+            dest="sparql_syntax",
+            require="sparql_syntax/main"),
+        dict(
+            section="notebook",
+            src="neptune_menu/static",
+            dest="neptune_menu",
+            require="neptune_menu/main"),
+        dict(
+            section="notebook",
+            src="playable_cells/static",
+            dest="playable_cells",
+            require="playable_cells/main"),
+    ]

src/graph_notebook/nbextensions/gremlin_syntax/__init__.py

@@ -2,3 +2,13 @@
 Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
 SPDX-License-Identifier: Apache-2.0
 """
+
+
+# template for this taken from
+# https://jupyter-notebook.readthedocs.io/en/stable/examples/Notebook/Distributing%20Jupyter%20Extensions%20as%20Python%20Packages.html#Defining-the-server-extension-and-nbextension
+def _jupyter_nbextension_paths():
+    return [dict(
+        section="notebook",
+        src="static",
+        dest="gremlin_syntax",
+        require="gremlin_syntax/main")]

src/graph_notebook/nbextensions/gremlin_syntax/static/__init__.py

@@ -0,0 +1,4 @@
+"""
+Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
+SPDX-License-Identifier: Apache-2.0
+"""

src/graph_notebook/nbextensions/install.py

@@ -1,3 +1,8 @@
+"""
+Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
+SPDX-License-Identifier: Apache-2.0
+"""
+
 import argparse
 import os
 
@@ -16,17 +21,9 @@ def main():
     parser.add_argument('--plugin-name', default='', type=str, help='install and enable this jupyter plugin')
 
     args = parser.parse_args()
-    if args.plugin_name == '':
-        for p in PLUGINS:
-            os.system(f'''echo "installing {p}";\
-                cd {dir_path}; \
-                jupyter nbextension install {p} --sys-prefix --overwrite;\
-                jupyter nbextension enable {p}/main --sys-prefix''')
-    else:
-        os.system(f'''echo "installing {args.plugin_name}";\
-            cd {dir_path}; \
-            jupyter nbextension install {args.plugin_name} --sys-prefix --overwrite;\
-            jupyter nbextension enable {args.plugin_name}/main --sys-prefix''')
+    plugin_name = 'graph_notebook.nbextensions' if args.plugin_name == '' else args.plugin_name
+    os.system(f'''jupyter nbextension install --py {plugin_name} --sys-prefix --overwrite''')
+    os.system(f'''jupyter nbextension enable --py {plugin_name} --sys-prefix''')
 
 
 if __name__ == '__main__':

src/graph_notebook/nbextensions/neptune_menu/__init__.py

@@ -2,3 +2,13 @@
 Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
 SPDX-License-Identifier: Apache-2.0
 """
+
+
+# template for this taken from
+# https://jupyter-notebook.readthedocs.io/en/stable/examples/Notebook/Distributing%20Jupyter%20Extensions%20as%20Python%20Packages.html#Defining-the-server-extension-and-nbextension
+def _jupyter_nbextension_paths():
+    return [dict(
+        section="notebook",
+        src="static",
+        dest="neptune_menu",
+        require="neptune_menu/main")]

src/graph_notebook/nbextensions/neptune_menu/static/__init__.py

@@ -0,0 +1,4 @@
+"""
+Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
+SPDX-License-Identifier: Apache-2.0
+"""

src/graph_notebook/nbextensions/playable_cells/__init__.py

@@ -2,3 +2,13 @@
 Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
 SPDX-License-Identifier: Apache-2.0
 """
+
+
+# template for this taken from
+# https://jupyter-notebook.readthedocs.io/en/stable/examples/Notebook/Distributing%20Jupyter%20Extensions%20as%20Python%20Packages.html#Defining-the-server-extension-and-nbextension
+def _jupyter_nbextension_paths():
+    return [dict(
+        section="notebook",
+        src="static",
+        dest="playable_cells",
+        require="playable_cells/main")]

src/graph_notebook/nbextensions/playable_cells/static/__init__.py

@@ -0,0 +1,4 @@
+"""
+Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
+SPDX-License-Identifier: Apache-2.0
+"""

src/graph_notebook/nbextensions/sparql_syntax/__init__.py

@@ -2,3 +2,13 @@
 Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
 SPDX-License-Identifier: Apache-2.0
 """
+
+
+# template for this taken from
+# https://jupyter-notebook.readthedocs.io/en/stable/examples/Notebook/Distributing%20Jupyter%20Extensions%20as%20Python%20Packages.html#Defining-the-server-extension-and-nbextension
+def _jupyter_nbextension_paths():
+    return [dict(
+        section="notebook",
+        src="static",
+        dest="sparql_syntax",
+        require="sparql_syntax/main")]

src/graph_notebook/nbextensions/sparql_syntax/static/__init__.py

@@ -0,0 +1,4 @@
+"""
+Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
+SPDX-License-Identifier: Apache-2.0
+"""

src/graph_notebook/network/gremlin/GremlinNetwork.py

@@ -50,7 +50,7 @@ def parse_pattern_list_str(pattern_str: str) -> list:
 
 
 def generate_id_from_dict(data: dict) -> str:
-    data_str = json.dumps(data)
+    data_str = json.dumps(data, default=str)
     hashed = hashlib.md5(data_str.encode())
     generate_id = hashed.hexdigest()
     return f'graph_notebook-{generate_id}'

src/graph_notebook/seed/load_query.py

@@ -4,18 +4,19 @@
 """
 
 import os
+from os.path import join as pjoin
 
 
 # returns a list of queries which correspond to a given query language and name
 def get_queries(query_language, name):
     d = os.path.dirname(os.path.realpath(__file__))
-    path_to_data_sets = f'{d}/queries/{query_language}/{name}'
+    path_to_data_sets = pjoin(d, 'queries', query_language, name)
     queries = []
 
     for file in os.listdir(path_to_data_sets):
         if file == '__init__.py' or file == '__pycache__':
             continue
-        full_path = f'{path_to_data_sets}/{file}'
+        full_path = pjoin(path_to_data_sets, file)
         with open(full_path, mode='r', encoding="utf-8") as f:
             query = {
                 'name': file,
@@ -29,9 +30,9 @@ def get_queries(query_language, name):
 def get_data_sets(query_language):
     query_language = query_language.lower()
     d = os.path.dirname(os.path.realpath(__file__))
-    path_to_data_sets = f'{d}/queries/{query_language}'
+    path_to_data_sets = pjoin(d, 'queries', query_language)
     data_sets = []
     for data_set in os.listdir(path_to_data_sets):
-        if data_set != '__pycache__' and os.path.isdir(f'{path_to_data_sets}/{data_set}'):
+        if data_set != '__pycache__' and os.path.isdir(pjoin(path_to_data_sets, data_set)):
             data_sets.append(data_set)
     return data_sets

src/graph_notebook/static_resources/install.py

@@ -6,6 +6,7 @@
 import os
 import site
 from shutil import copy2
+from os.path import join as pjoin
 
 files = [
     'datatables.css',
@@ -14,12 +15,13 @@
 
 
 def main():
-    sitepackages = site.getsitepackages()[0]
-    destination = f'{sitepackages}/notebook/static'
+    sitepackages = site.getsitepackages()
+    static_base_directory = sitepackages[0] if os.name != 'nt' else sitepackages[1]
+    destination = pjoin(static_base_directory, 'notebook', 'static')
 
     dir_path = os.path.dirname(os.path.realpath(__file__))
     for file in files:
-        full_path = f'{dir_path}/{file}'
+        full_path = pjoin(dir_path, file)
         print(f'copying file {file} to {destination}')
         copy2(full_path, destination)
 

src/graph_notebook/widgets/__init__.py

@@ -3,9 +3,19 @@
 SPDX-License-Identifier: Apache-2.0
 """
 
+import json
+import os
+
 from .force import Force  # noqa F401
 
 
+def get_package_json():
+    dir_path = os.path.dirname(os.path.realpath(__file__))
+    with open(os.path.join(dir_path, 'package.json'), 'r') as file:
+        package_json = json.load(file)
+    return package_json
+
+
 def _jupyter_nbextension_paths():
     """Called by Jupyter Notebook Server to detect if it is a valid nbextension and
     to install the widget