Provenance Service

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Lightweight implementation of the Synapse Activity services, based on the PROV spec.

Overview

This is an OpenAPI-enabled (and documented) Flask server. This example uses the 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.

This server was originally generated by the OpenAPI Generator project. Starting with the Synapse Activity API specification in a swagger.yaml file, the contents of this repo were originally generated with the following command:

npx openapi-generator generate -i swagger.yaml -g python-flask -DpackageName=synprov -o prov-service/

Requirements

Python 3.6

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):

export NEO4J_USERNAME=<username> # must be 'neo4j'
export NEO4J_PASSWORD=<password>

*In some cases, the Neo4j Desktop app decides to serve the database on port 11001 instead of 7687. If this happens, you can set an additional environment variable:

export NEO4J_PORT=11001

Usage

To run the server, please execute the following from the root directory:

pip install -r requirements.txt .

To start the app, you can use this command:

synprov

To initialize the graph database with mock activity records, you can run the app with additional parameters:

synprov --mock_db --db_size 30

To view the full set of parameters:

synprov --help

Usage: synprov [OPTIONS]

Options:
  --mock_db          Initialize Neo4j database with mock graph records
                     [default: False]
  --db_size INTEGER  Number of mock activity records to create in the graph
                     database (ignored if 'init_db' is False).  [default: 50]
  --help             Show this message and exit.

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:

MATCH (n) RETURN n

Assuming that you populated the graph database with mock/example records as described above, you should see something that looks like this (minus the custom colors):

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/ui/

If the above URL doesn't work, try this instead:

http://0.0.0.0:8080/rest/ui/

The OpenAPI definition lives here:

http://localhost:8080/rest/openapi.json

Running with Docker

To run the server on a Docker container, execute the following from the root directory:

docker-compose up --build

Note: In order to use the server container, which requires a Neo4j database connection, you should have Docker Compose installed.

After running this command, the URLs in the previous section should work.

Development

To add changes locally, install the package in developer mode:

pip install -r requirements.txt -e .

OpenAPI Generator

The core models and controllers for the server are generated automatically from the OpenAPI specification. Classses and methods used for operations within the app all inherit from auto-generated definitions.

Anytime the OpenAPI spec is modified, controller and model code should be regenerated with the following command:

npx openapi-generator generate \
    -c .openapi-generator-config \
    -t .codegen/server \
    -Dmodels \
    -DmodelTests=false \
    -Dapis \
    -DapiTests=false \
    -i synprov/openapi/openapi.yaml \
    -g python-flask \
    -o .

Note: this will happen during the continuous integration process regardless, so regenerating and testing locally is just advised to save time troubleshooting.

Sage-Bionetworks/prov-service