update overview and instructions in README

README.md

@@ -4,43 +4,55 @@ Lightweight implementation of the Synapse Activity services, based on the PROV s
 
 ## Overview
 
-This is an OpenAPI-enabled (and documented) Flask server. This example uses the [Connexion](https://github.com/zalando/connexion) library on top of Flask. The [MongoEngine](https://github.com/MongoEngine/mongoengine) ODM library for Python is used to manage operations between RESTful API requests/responses and a MongoDB database. Additionally, the [Graphene-Mongo](https://github.com/graphql-python/graphene-mongo) library enables integration of MongoEngine with [Graphene](https://github.com/graphql-python/graphene) to provide a GraphQL endpoint.
+This is an OpenAPI-enabled (and documented) Flask server. This example uses the [Connexion](https://github.com/zalando/connexion) library on top of Flask. The [py2neo]() driver library for Python is used to manage operations between RESTful API requests/responses and a Neo4j database.
 
 ## Requirements
 
 Python 3.5.2+
 
-You should have a local installation of MongoDB (tested with 4.0.8) with a connection to a database named `provDB`. See [this tutorial](https://docs.mongodb.com/manual/tutorial/install-mongodb-on-os-x/) for getting set up with MongoDB on MacOS using `brew`.
+You should have access to a local installation of Neo4j, serving at `bolt://localhost/7687`.
+
+You'll also need to set two environment variables based on your Neo4j configuration (the Flask app uses these to connect to the database):
+
+```shell
+export NEO4J_USERNAME=<username>
+export NEO4J_PASSWORD=<password>
+```
 
 ## Usage
 
 To run the server, please execute the following from the root directory:
 
 ```
-pip install -r requirements.txt
-pip install .
+pip install -r requirements.txt .
 ```
 
-and open your browser to here:
-
+To start the app, you can use this command:
+```shell
+synprov
 ```
-http://localhost:8080/rest/ui/
+
+### Neo4j browser
+
+If you have the **Neo4j Desktop** application installed, you should be able to view and explore the graph database using Cypher queries. For example, to view all nodes and relationships:
+
+```cypher
+MATCH (n) RETURN n
 ```
 
-Your OpenAPI definition lives here:
+
+### Swagger UI
+
+You can also interact with the graph database through RESTful API queries. The service provides a Swagger UI endpoint to test requests through the browser:
 
 ```
-http://localhost:8080/rest/openapi.json
+http://localhost:8080/rest/ui/
 ```
 
-You can reach the GraphQL interface here:
+The OpenAPI definition lives here:
 
-http://localhost:8080/graphql/
-
-To launch the integration tests, use tox:
 ```
-sudo pip install tox
-tox
+http://localhost:8080/rest/openapi.json
 ```
 
 ## Running with Docker
@@ -57,18 +69,17 @@ After running this command, the URLs in the previous section should work.
 
 ## Development
 
-This server was originally generated by the [OpenAPI Generator](https://openapi-generator.tech) project. By using the [OpenAPI-Spec](https://openapis.org) from a remote server, you can easily generate a server stub.  
-
-Starting with the Synapse Activity API specification in a `swagger.yaml`, the contents of this repo were generated with the following command:
-
+To add changes locally, install the package in developer mode:
 ```
-npx openapi-generator generate -i swagger.yaml -g python-flask -DpackageName=synprov -o prov-service/
+pip install -r requirements.txt -e .
 ```
 
-After editing the OpenAPI YAML spec, controller and model code were iteratively regenerated with the following command:
+## OpenAPI Generator
+
+This server was originally generated by the [OpenAPI Generator](https://openapi-generator.tech) project. By using the [OpenAPI-Spec](https://openapis.org) from a remote server, you can easily generate a server stub.
+
+Starting with the Synapse Activity API specification in a `swagger.yaml`, the contents of this repo were generated with the following command:
 
 ```
-npx openapi-generator generate -i synprov/openapi/openapi.yaml -g python-flask -c .openapi-generator-config
+npx openapi-generator generate -i swagger.yaml -g python-flask -DpackageName=synprov -o prov-service/
 ```
-
-> **Note:** with the API spec now relatively stable, this process has been deprecated in favor of manually keeping the code and documentation in sync — `openapi-generator` will overwrite all controller code, in addition to updating models, which isn't as helpful with working methods in place.