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Combine e!g and e! REST

Marek Szuba requested to merge github/fork/nicklangridge/feature/joint-rest3 into master

Created by: nicklangridge

Requirements

  • Filling out the template is required. Any pull request that does not include enough information to be reviewed in a timely manner may be closed at the maintainers' discretion;
  • Review the contributing guidelines for this repository; remember in particular:
    • do not modify code without testing for regression
    • provide simple unit tests to test the changes
    • the PR must not fail unit testing
    • if you're adding/updating documentation of an endpoint, make sure you add/update the necessary parameters to the (template) configuration files in the ensembl-rest_private repo

Description

  • Merge in e!g info and lookup endpoints, documentation, and example params
  • Adapt lookup to use metadata db
  • Add registry and app preloading in Starman
  • Fix some documentation example params for existing endpoints

Use case

A single REST instance to serve all Ensembl divisions.

Benefits

We can retire Ensembl Genomes REST.

Possible Drawbacks

When all divisions are enabled we see

  • Increased memory footprint
  • Slow server start time due to registry preloading (startup takes a couple of minutes)

Testing

Tests for the new endpoints are in development and will follow in a separate PR (as agreed with Mag)

Changelog

Merge Ensembl Genomes REST functionality to allow a single REST instance to serve all Ensembl divisions.

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