opentargets-otter 25.0.12

Open Targets Task ExcutoR

Otter — Open Targets' Task ExecutoR

Otter is a the task execution framework used in the Open Targets data Pipeline.

It provides an easy to use API to implement generic tasks that are then used by describing the flow in a YAML configuration file.

Take a look at a Simple example.

Features

This is a list of what you get for free by using Otter:

• Parallel execution: Tasks are run in parallel, and Otter will take care of the dependency planning.
• Declarative configuration: Steps are described in a YAML file, as list of tasks with different specifications. The task themselves are implemented in Python enabling a lot of flexibility.
• Logging: Otter uses the loguru library for logging. It handles all the logging related the task flow, and also logs into the manifest (see next item).
• Manifest: Otter manages a manifest file that describes a pipeline run. It is used to both for debugging and for tracking the provenance of the data. A series of simple JQ queries can be used to extract information from it (see Useful JQ queries).
• Error management: Otter will stop the execution of the pipeline if a task fails, and will log the error in the manifest.
• Scratchpad: A place to store variables that can be overwritten into the configuration file (something like a very simple templating engine), enabling easy parametrization of runs, and passing of data between tasks.
• Utilities: Otter provides interfaces to use Google Cloud Storage and other remote storage services, and a bunch of utilities to help you write tasks.

Documentation

See it in here.

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.