Monarch-Py

Monarch-Py is a Python library for interfacing with the Monarch Initiative Knowledge graph. The monarch-py package can be used from CLI, as a module, or as a FastAPI app.

Requirements

If you are running the whole monarch-app suite locally you will want to review the README.md or CONTRIBUTING.md files in the repository root for information on the requirements for monarch-app at large. If you intend to run just the backend for end-user usage or testing you will only need the following prerequisites.

• Python version 3.9+, version 3.10.12 recommended for development.
• Poetry - For managing dependencies in monarch-py.
• Docker - For running the Solr instance locally.
• Rust - For running the semsimian server locally.

For development of monarch-py, please refer to the backend/CONTRUBUTING.md for additional details.

Usage

Basic installation can be performed using pip/pipx or your favorite package manager.

pip install monarch-py

The monarch-py module and CLI use the Monarch-KG using a Solr instance running locally.
This requires Docker to be installed and running on your computer.

monarch solr download
monarch solr start

This will download and then run the monarch Solr image locally on port 8983.
Note You may need to change permissions on the file in order to install and run the Solr container.

sudo chgrp -R 8983 ~/.data/monarch
sudo chmod -R g+w ~/.data/monarch

To check if Solr is running correctly on your computer you can check you can check using Docker or the monarch CLI.

Using Docker:

docker ps

For docker you should see output resembling this:

66da4aeed48e   solr:8            "docker-entrypoint.s…"   3 weeks ago    Up 5 days    0.0.0.0:8983->8983/tcp, :::8983->8983/tcp   monarch_solr

Using the monarch CLI:

monarch solr status

For the monarch CLI you should see output similar to this:

Checking for Solr container...

Found monarch_solr container: 66da4aeed48e7f71241f85f31f1e3366f9255cb53b78f16b13fb79bcfb2b36f2
Container status: running

monarch-ingest creates it's own Solr docker instance which mounts its own data output from closurizer and makes it's own Solr artifact.

Developers

For instructions on how to test monarch-py locally or how to start with developing please see the CONTRIBUTING.md file in the root of the Monarch-App repository.
For instructions specific to monarch-py (the Monarch-App backend), see the backend/CONTRIBUTING.md file.

For Developers

Running the API:

Local development:

• Connect to and expose the SOLR database: gcloud compute ssh monarch-solr-dev -- -L 8983:localhost:8983

• Start the uvicorn server: cd <path-to>/monarch-api && uvicorn main:app --reload

GCP deployment:

• First, connect to the GCP SOLR machine: gcloud compute ssh monarch-api-dev -- -L 8000:localhost:8000

• Then, start the uvicorn server: nohup uvicorn main:app --reload --host 0.0.0.0 &

Building and using the Docker image:

• Build the docker image: docker build --rm --tag us-central1-docker.pkg.dev/monarch-initiative/monarch-api/monarch-api:{VERSION} .

• Push the docker image: docker push us-central1-docker.pkg.dev/monarch-initiative/monarch-api/monarch-api:{VERSION}