update-repo-wrapper

[joeflack4]

resolves #435

Overview

Convenience command to automate some otherwise manual steps when running update_repo. Expected behavior is that it (i) temporarily updates the ODK_TAG used, and (ii) runs update_repo twice, until a fix for INCATools/ontology-development-kit#989 is in ODK.

Pre-merge checklist

• Docs
  • docs/ have been added/updated OR
  • No updates to the docs necessary after careful consideration.
• QC
  • sh run.sh make build-mondo-ingest has been run on this branch (after `docker pull obolibrary/odkfull:dev), and no errors occurred OR
  • No functional (code-related) changes to the pipeline are suggested, so no re-run is necessary.
• Account for any new packages
  • Open an ODK issue to request addition. Can also open a PR. Python package changes should occur in requirements.txt.full, and non-Python packages in Dockerfile.
• Reviewed
  • Has been sufficiently reviewed by at least one review from a different team member of the Mondo Technical team.

Changes

• Update: mondo-ingest.Makefile: Added goal 'update-repo-wrapper' to automate some steps required to run 'update_repo'.

[joeflack4]

UPDATE_REPO_ODK_TAG

Set to latest unless the user passes ODK_TAG, in which value is set to that.

ODK_TAG override usage:

• Works: sh run.sh make ODK_TAG=v1.4.3 update-repo-wrapper
• Fails: ODK_TAG=v1.4.3 sh run.sh make update-repo-wrapper. This doesn't cause the goal to fail, but the environmental variable doesn't get read.

[joeflack4]

update-repo-wrapper

1. Temporarily updates run.sh.conf ODK_TAG to value of UPDATE_REPO_ODK_TAG
2. Runs update_repo twice

• We can change this if ever update_repo: Run 2x to alleviate errors INCATools/ontology-development-kit#989 gets fixed.

I tested this out on a commit from before the merge of #432 today and confirmed that I got the expected behavior.

[joeflack4]

@matentzn But perhaps I should drop the 2nd run of update_repo. Have you found recently that you still need to do this? I haven't seen any difference after running it a 2nd time in the last year or more.

[joeflack4]

Docs

• Add docs if approved @joeflack4

I like this solution. If you guys like it, too, I'll update docs to reference running update-repo-wrapper instead of update_repo:

• add-new-source.md:
• Other instances
  I haven't looked at these files before but there are references to update_repo in these.
  • RepoManagement.md
  • components.md
  • README-editors.md

Considering all the places where there are docs for update_repo, this reinforces my liking of this solution. Otherwise if we went with the SOP solution instead of this, we'd have to add cumbersome references to that in multiple places.

I can also add a goal description for it it in:

• workflows.md
• mondo-ingest.Makefile's help

[twhetzel]

I have to defer this review and whether this is needed (at all and/or for the January release) to @matentzn.

Does this PR close all tasks in #435?

[joeflack4]

Definitely not needed for the January release. It's just quality of life.

It doesn't address the subtasks in #435, but it obsoletes it and is supposed to replace it with something better: a command instead of an SOP.

[matentzn]

There has been a recent development that makes this PR obsolete: The ODK runner: https://github.com/gouttegd/odkrunner

I am using it only now for interacting with ODK, and it will get rid of any issues, especially running the update multiple times etc.. Just install it and from then on:

odk make xyz instead of sh run.sh make xyz, and it will still recognise run.sh.conf!

[twhetzel]

Sounds like this PR is not needed now. Documenting the steps (now using the ODK runner) sounds like that is still needed so as this is done in #435 and the process tested we can check then if it's meeting all the needs that this PR aimed to address.

[joeflack4]

Oh, that looks very nice.