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Issue tracker for Open Targets Platform and Open Targets Genetics Portal
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Refactor step configuration #3132

Closed tskir closed 8 months ago

tskir commented 8 months ago

Under the current architecture there is a lot of reduncancy in the step configuration. We end up writing a lot of boilerplate code; and once we define the configuration variables, we then keep passing them around:


config/datasets/gcp.yaml, where the actual configuration is

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config/step/my_finngen.yaml, just passing through

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src/otg/config.py, just passing through

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Register config

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Add entry to the DAG definition

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The result is that every tiny action, such as adding or renaming a parameter, cascades into lots of changes all over the code. This is very distracting, creates friction, and slows down development. As the number of steps is expected to grow, especially the data ingestion steps, this has to be addressed.