Add a simple CLI for use in unified model interface

adityasharad commented 4 years ago

Related issues and PRs

Related to https://github.com/neherlab/covid19_scenarios/issues/663, though not yet a fully-featured CLI.

Description

This PR adds a simple CLI entry point that:

reads input JSON (of type ScenarioData) from a specified input path
runs the model by calling into run.ts
writes output JSON (of type AlgorithmResult) into the specified output path

This allows the model to be run in a unified model UI, such as the one we are maintaining at https://github.com/covid-modeling on the GitHub side. We are already using a version of this at https://github.com/covid-modeling/model-runner to run this model, but are currently tied to my fork that has the CLI entry point and an older version of your model. Having this code as part of the model repo enables the unified interface to keep up with model changes, and so better represent the latest state of your model.

@ivan-aksamentov @nnoll I would be grateful for a review, and hope this will minimally impact your existing work. Let me know if you have questions.

Impacted Areas in the application

No changes to existing code, introduces new entry point that calls run.

Testing

Usual schema preparation: yarn schema:clean && yarn schema:totypes.
Write a JSON object of type ScenarioData in a file, say input-file.json. One of the existing objects in scenarios.json will work.

yarn babel-node --extensions ".ts" src/algorithms/cli.ts path/to/input-file.json path/to/output-file.json

This will create output data at path/to/output-file.json, which is assumed to not already exist.

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ivan-aksamentov commented 4 years ago

Thanks! As you said, this is not exactly implementing a proper CLI and, honestly, not doing what I would expect, but I guess it does not hurt to have it around.

Would you be interested in continuing working in this direction? My main focus is still the application, but I can help here and there.

I will add a TODO list in the linked issue #663

Wouldn't it be more convenient for aggregators like "covid-modeling" to have a programmatic API instead of a CLI?

neherlab / covid19_scenarios