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PloverDB

Plover is an in-memory Python-based platform for hosting/serving Biolink-compliant knowledge graphs as TRAPI APIs.

In answering queries, Plover abides by all Translator Knowledge Provider reasoning requirements; it also can normalize the underlying graph and convert query node IDs to the proper equivalent identifiers for the given knowledge graph.

More specifically, Plover can answer these kinds of queries:

  1. Single-hop: (>=1 curies)--[>=0 predicates]--(>=0 categories, >=0 curies)
  2. Edge-less: Consist only of QNodes (all of which must have curies specified)

The knowledge graph to be hosted needs to be in a Biolink-compliant format with separate nodes and edges files; both TSV and JSON Lines formats are supported.

You must provide URLs from which the nodes/edges files can be downloaded in a config JSON file in PloverDB/app/ (e.g., config_kg2c.json). The config file includes a number of settings that can be customized and also defines the way in which node/edge properties should be loaded into TRAPI attributes.

Nodes and edges files

TODO

Config file

TODO

Multiple KPs

TODO

How to run

Install Docker. * For Ubuntu 20.04, try sudo apt-get install -y docker.io * For Mac, brew install --cask docker worked for me with macOS Big Sur

How to run a dev Plover

TODO

  1. Clone this repo and cd into PloverDB/
  2. Edit PloverDB/config.json for your particular graph
  3. Run the following command:
    • bash -x run.sh -s true

This will build a Plover Docker image and run a container off of it, publishing it at port 9990. The -s true parameter tells Plover to skip configuring SSL certificates.

Note that by default, this script will use the sudo docker command; use the optional -d parameter to specify a different docker command (e.g., bash -x run.sh -s true -d docker).

How to deploy Plover on a new instance

TODO

Use Ubuntu..

  1. Make sure port 9990 on your host machine is open
  2. Fork the Plover repo
  3. Edit the config file at PloverDB/app/config_kg2c.json to work for your KP
    1. Most notably, you need to point to nodes/edges files for your graph in TSV or JSON Lines Biolink-style format
    2. We suggest also changing the name of this file to something like config_mykp.json; the default template is for RTX-KG2c
    3. More info on the config file contents is here (TODO)
  4. Run bash -x PloverDB/run.sh

How to deploy a new KP to an existing Plover

TODO

For ITRB

Instructions tailored for ITRB deployments:

Assuming an Ubuntu instance with Docker installed and SSL certificates already handled, simply run (from the desired branch):

sudo docker build -t ploverimage .
sudo docker run -d --name plovercontainer -p 9990:443 ploverimage

Provided endpoints

TODO

How to test

You should now be able to send your Plover TRAPI query POST requests at port 9990; the URL for this would look something like: https://yourinstance.rtx.ai:9990/query. Or, if you are just using Plover locally: http://localhost:9990/query.

To verify that your new service is working, you can check a few endpoints (plug in your domain name in place of 'kg2cplover.rtx.ai'):

  1. Navigate to https://kg2cplover.rtx.ai:9990/code_version in your browser; it should display information about the build
  2. Naviagte to https://kg2cplover.rtx.ai:9990/get_logs in your browser; it should display log messages
  3. Navigate to https://kg2cplover.rtx.ai:9990/meta_knowledge_graph in your browser; it should display the meta knowledge graph
  4. Navigate to https://kg2cplover.rtx.ai:9990/sri_test_triples in your browser; it should display the SRI test triples
  5. Try sending a TRAPI query to https://kg2cplover.rtx.ai:9990/query

Debugging

To view logs in your browser, go to https://kg2cplover.rtx.ai:9990/get_logs. This will show information from the Plover and Gunicorn logs. By default, the last 100 lines in each log are displayed; you can change this using the num_lines parameter - e.g., https://kg2cplover.rtx.ai:9990/get_logs?num_lines=500.

To see the logs via the terminal (includes all components - Gunicorn, etc.), run:

docker logs plovercontainer

If you want to save the contents of the log to a file locally, run:

docker logs plovercontainer >& logs/mylog.log

If you want to use cURL to debug PloverDB, make sure to specify the -L (i.e., --location) option for the curl command, since PloverDB seems to use redirection. Like this:

curl -L -X POST -d @test20.json -H 'Content-Type: application/json' -H 'accept: application/json' https://kg2cplover.rtx.ai:9990/query

If you want to see the code version for the RTXteam/PloverDB project that was used for the running service, as well as the versions of the knowledge graphs it ingested, you can use the code_version API endpoint (https://kg2cplover.rtx.ai:9990/code_version):

curl -L -X GET -H 'accept: application/json' https://kg2cplover.rtx.ai:9990/code_version

Credits

  • Author: Amy Glen
  • Inspiration/advice: Stephen Ramsey, Eric Deutsch, David Koslicki