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PIS — Open Targets Pipeline Input Stage

Fetch, validate and arrange the data required by the Open Targets data pipeline.

Summary

This application uses the Otter library to define the steps of the pipeline that pull all the required input data for a run of the Open Targets pipeline.

Check out the config.yaml file to see the steps and the tasks that make them up.

Installation and running

PIS uses UV as its package manager. It is compatible with PIP, so you can also fall back to it if you feel more comfortable.

uv run pis -h

Tip

You can also use PIS with Make. Running make without any target shows help.

Running with Docker

You can also launch PIS with Docker:

docker run ghcr.io/opentargets/pis:latest -h

PIS can upload the files it fetches into different cloud storage services. Open Targets uses Google Cloud. To enable it in a docker container, you must have a credentials file. Assuming you do, you can run the following command:

docker run \
  -v /path/to/credentials.json:/app/credentials.json \
  -e GOOGLE_APPLICATION_CREDENTIALS=/app/credentials.json \
  ghcr.io/opentargets/pis:latest -h

To build your own Docker image, run the following command from the root of the repository:

docker build -t pis .

Development

Important

Remember to run make dev before starting development. This will set up a very simple git hook that does a few checks before committing.

Development of PIS can be done straight away in the local environment. You can run the application just like before (uv run pis) to check the changes you make.

Tip

Take a look at the Otter docs, it is a very helpful guide when developing new tasks.

You can test the changes by running a small step, like so:

uv run pis --step so

Copyright

Copyright 2014-2024 EMBL - European Bioinformatics Institute, Genentech, GSK, MSD, Pfizer, Sanofi and Wellcome Sanger Institute

This software was developed as part of the Open Targets project. For more information please see: http://www.opentargets.org

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.