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Fixes #1

@jamesaoverton
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jamesaoverton commented Feb 24, 2020

Very good! I'd like some changes mostly to make this more generic and not OBI-specific:

  1. I think I want a configuration YAML file. It should not contain secrets. Ideally we could reuse ODK YAML config files like these by reusing their keys: id, github_org, repo. I guess we will needs an optional --config FILE argument, but the default should be to look in the same directory as this script for gizmos.yml. GITHUB_REPO and GITHUB_OWNER must be in there or there's an error. GITHUB_BRANCH, PUBLISHED_FILE, and RESERVED_FILE might be in there, but with the current values as defaults.
  2. The term ID pattern must be configurable, minimally with the IDSPACE (e.g. OBI) and the number of digits (e.g. 7), but there might be a more clever way to do it. The IDSPACE must be in the config file. The digits can be specified in the config or default to 7.
  3. Please change --commit_message to --message
  4. Please change --terms to --labels
  5. Please add short options for everything: -m -l -i -c
  6. Can we optionally read from STDIN?

…ames, idspace and id digits to config file
@lmcmicu
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lmcmicu commented Feb 26, 2020

@jamesaoverton Please review

@jamesaoverton jamesaoverton marked this pull request as draft May 11, 2021 16:22
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Script to reserve ontology term IDs

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