Release: Include omim.sssom.tsv to GH action
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@matentzn The This is currently marked "Low" urgency. Can you increase and let me know if it should be a higher priority? |
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Just always run everything in ODK - there is no need for custom install procedures! All dependencies you will need are in there. |
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@matentzn I though Harshad was able to get ODK to work in a GitHub action but he told me that is not the case. I don't know if you remember us speaking about how this was difficult / impossible fore. Do you want me to try? I would imagine this is a lower priority though than many of my other issues. In the interim, it would be much easier for me to implement solution 'a'. |
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ODK works in hundreds of GHAs! Its very very easy. https://github.com/obophenotype/bio-attribute-ontology/blob/master/.github/workflows/qc.yml#L22 |
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That is great to hear. I'll go ahead and try and use this. You probably remember we spoke about this a few different times in the past year? Maybe what you meant that everything couldn't be run due to memory issues, like NCIT, not that ODK / certain workflows couldn't be run. Because otherwise I'm sure we would use this in mondo-ingest as well. |
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Yes, that's right. You cant build mondo ingest in GHA because of memory constraints |
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@matentzn I got the ODK GitHub action working, but I'm getting a new Error messageThese parts of the log are the only thing indicative of the problem: Full log: log.txt InvestigationI don't understand why it says "undeclared predicates". I have its namespace declared in the header and turtle triple syntax seems correct. I do notice that the namespace https://w3id.org/biolink/vocab/ doesn't resolve to anything machine readable, so it makes sense that no declarations can be pulled from there if robot needs to do that, but I have other biolink predicates (e.g. Header declaration: @prefix biolink: <https://w3id.org/biolink/vocab/> .Example usage: [] a owl:Axiom ;
rdfs:comment "Evidence: (3) The molecular basis for the disorder is known; a mutation has been found in the gene." ;
owl:annotatedProperty rdfs:subClassOf ;
owl:annotatedSource OMIM:300644 ;
owl:annotatedTarget [ a owl:Restriction ;
owl:onProperty RO:0003302 ;
owl:someValuesFrom OMIM:301500 ] ;
biolink:has_evidence "Evidence: (3) The molecular basis for the disorder is known; a mutation has been found in the gene." .Possible solutionsa. Fix the declarationI'm not sure how. b. Filter stuff outhttp://robot.obolibrary.org/errors#obo-graph-error suggests this:
c. We can remove
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For every annotation property in your ontology, add a triple: and try again, e.g.: This is called a "declaration" Some serialisation need this. A hack I think that could work is this:
But better to inject declarations from the start into the TTL file. |
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Ah, ok. Thanks for these solutions! I like the first proposal of simply adding the declaration. |
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@matentzn Hmm... so I gave it a shot, but it's still giving an AttemptsAttempt 1: Adding the missing declarationI added LogAttempt 2:
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After 1 hour of debugging I found the problem: geneontology/obographs#100 I am sure you would have wasted many hours if not days on this, so good I checked it. Here is my technique on how to deal with failures where we don't have an intelligible error message:
This way I stumbled across the fix. Terrible technique but works :D |
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Those are some good steps. I'll file them in my personal notes. Definitely would have taken me forever if I was to continue cracking at it. A simple solution now that you found the problem! Will be a quick fix when I'm back from vacation. Thanks for opening up an issue about it as well. |
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Overview
Currently,
omim.sssom.tsvcan't be recreated because this command won't work:sssom parse omim.json -I obographs-json -m data/metadata.sssom.yml -o omim.sssom.tsv. This command fails because of missingrobotdependency. I need to figure out how to include arbitrary binaries in a GitHub action.Sub-tasks list
robotto run GH Action: Run in ODK #97OBO GRAPH ERRORSub-task details
1. Get
robotto runPossible solutions
a.
Maybe I can simply downloadrobot/robot.jarand place them in the root of the repo, either committing them, or downloading them at the start of the action.b.
But maybe there's a better practice.c.
Personally, I've always thought the best thing would be to create someonto-robo-pypackage that simply is a wrapper aroundrobot.jarand calls it via a subprocess.d. Run the action in ODK (#97) <--------
2. OBO GRAPH ERROR
When running
robot convert -i omim.ttl -o omim.jsonas a pre-step to doingsssom parse omim.json..., I get an error, but the cause is not known. I imagine that it has to do with the version ofrobotbeing different in ODK than what I was previously using to convert on my local machine. Nothing has changed significantly with the OMIM pipeline in a while.The text was updated successfully, but these errors were encountered: