Bugfix: Equivalence issues #3
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joeflack4
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| rm -rf tmp/ | ||
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| tmp/output/release/icd11foundation.owl: tmp/output/intermediate1-unicode-cleaned.owl | ||
| robot remove --axioms equivalent -i $< -o $@ |
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The essential change
This is the command that applies the fix.
- @joeflack4 Run
build-mondo-ingestusing the output from this to verify if it worked.
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I agree, I think that line (robot remove --axioms equivalent -i $< -o $@) is fine.
I'm not sure if https://robot.obolibrary.org/remove#preserving-the-structure is also needed. I think that was needed with something in the Mondo repo in Sep 2023, but I don't recall the details or am able to find it in the repo files yet. I am leaving this note here as a reminder in case things do not look as expected.
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I will look at your comment tomorrow, but I just wanted to report back here that the build passed!
edit: I looked now at what you wrote yesterday; I see that this is a note for the future if needed. FYI I looked at those docs and it does look like by default the structure is preserved by default (to not preserve, you'd do --preserve-structure false, so that's good. I wonder if in Mondo they had been explicitly not preserving the structure and then later found that to be a mistake.
| @@ -0,0 +1,85 @@ | |||
| #!/bin/sh | |||
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run.sh
This is a dependency / proxy for dependencies. Adding this file and using it is necessary to ensure the the ODK container is running, with all the correct versions of everything (e.g. robot in this case).
@twhetzel I don't like that adding this file is how I handle this dependency. The only other repo that currently does this is MedGen, and the way that I update it is to copy the run.sh manually from mondo-ingest. I did bring this up to Nico once prior, that I would prefer a solution such as a Python package that puts a wrapper around run.sh. Not a high priority I think, but would be nice eventually.
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Hmm, at the moment I'm not sure what the best solution/idea would be....
- 1. Add ticket (low priority) to track this possible future work
- 2. Is this step documented in the main README for mondo ingest?
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I may have already done (1) but it's on my todo list to check and do so shortly. Regarding (2), no and also on my todo list; may have a PR for that today!
edit:
(1) is done!
(2) done via:
Temporary fix for: ERROR org.obolibrary.robot.ReasonOperation - Only equivalent classes that have been asserted are allowed. Inferred equivalencies are forbidden. - Update: makefile: Goal for removing equivalents axioms.
joeflack4
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| @@ -8,8 +8,14 @@ SOURCE_URL=https://icd11files.blob.core.windows.net/tmp/whofic-2023-04-08.owl.gz | |||
| # MAIN COMMANDS / GOALS ------------------------------------------------------------------------------------------------ | |||
| all: tmp/output/release/icd11foundation.owl | |||
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| clean: | |||
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I just added that. I added it just as a command for convenience.
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It wasn't ever strictly needed. It's just there for convenience, and I don't think it's a harm to have such utilities.. I've seen this convention in a variety of other projects, such as in MedGen; I committed this, but this makefile goal (and much of the MedGen makefile) was copied over from a different location from work done by Chris Mungall.
Addresses:
Overview
This PR is a workaround for illogical class equivalence issues highlighted by the ontological reasoner. After applying this fix, it is expected that no such error will be thrown when running
build-mondo-ingest.Pre-merge checklist
docs/have been added/updated ORsh run.sh make build-mondo-ingesthas been run on this branch (after `docker pull obolibrary/odkfull:dev), and no errors occurred ORChanges
Bugfix: Equivalence issues
Temporary fix for:
ERROR org.obolibrary.robot.ReasonOperation - Only equivalent classes that have been asserted are allowed. Inferred equivalencies are forbidden.