Closed joeflack4 closed 12 months ago
joeflack4
commented
1 year ago @matentzn The omim.sssom.tsv being released since I created this action was old, never being recreated. I just deactivated from including it in the release.
This is currently marked "Low" urgency. Can you increase and let me know if it should be a higher priority?
matentzn
commented
1 year ago Just always run everything in ODK - there is no need for custom install procedures! All dependencies you will need are in there.
joeflack4
commented
1 year ago @matentzn Alright, that makes sense. If you remember, we previously were not able to use ODK in GitHub actions, I think due to memory constraints. I'm going to reach out to @hrshdhgd for this though, as I believe he was somewhat recently able to get it to work.
joeflack4
commented
1 year ago @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'.
matentzn
commented
1 year ago ODK works in hundreds of GHAs! Its very very easy. https://github.com/obophenotype/bio-attribute-ontology/blob/master/.github/workflows/qc.yml#L22
joeflack4
commented
1 year ago 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.
matentzn
commented
1 year ago Yes, that's right. You cant build mondo ingest in GHA because of memory constraints
joeflack4
commented
1 year ago @matentzn I got the ODK GitHub action working, but I'm getting a new OBO GRAPH ERROR. The short of it is that I'd like you to pick one of possible solutions 'a', 'b', or 'c'. 'c' seems the easiest and I think you were also fine with this approach many months ago (not because of error; but because we didn't need it).
OBO GRAPH ERROR Could not convert ontology to OBO Graph (see https://github.com/geneontology/obographs)
For details see: http://robot.obolibrary.org/errors#obo-graph-errorThese parts of the log are the only thing indicative of the problem:
ERROR Input ontology contains 7310 triple(s) that could not be parsed:
_:genid-nodeid-node1h3dl19e1x7863 <https://w3id.org/biolink/vocab/has_evidence> Evidence: (3) The molecular basis for the disorder is known; a mutation has been found in the gene..
...
Hint: you have undeclared predicates - try adding 'rdf:type' declarations to the following:
- https://w3id.org/biolink/vocab/has_evidenceFull log: log.txt
I 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. biolink:category) that are not throwing this same warning.
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." .I'm not sure how.
http://robot.obolibrary.org/errors#obo-graph-error suggests this:
This may be due to problematic annotations, so you can create a subset using filter or remove containing only the necessary annotations and save that as JSON, for example (keeping only labels and definitions):
robot remove --input ont.owl \ --select annotation-properties \ --exclude-term rdfs:label \ --exclude-term IAO:0000115 \ --output ont.json
biolink:has_evidenceI think at some point in the past you suggested we don't need it. Notice also that we are already including an additional evidence comment.
[] a owl:Axiom ;
rdfs:comment "Evidence: (3) The molecular basis for the disorder is known; a mutation has been found in the gene." ;
...
biolink:has_evidence "Evidence: (3) The molecular basis for the disorder is known; a mutation has been found in the gene." .For every annotation property in your ontology, add a triple:
my:annotationProperty rdf:type owl:AnnotationPropertyand try again, e.g.:
biolink:has_evidence rdf:type owl:AnnotationPropertyThis 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.
joeflack4
commented
1 year ago Ah, ok. Thanks for these solutions! I like the first proposal of simply adding the declaration.
I see now that the reason that it was unhappy about biolink:has_evidence and not some of the other biolink preds is because it was used in an annotation property.
joeflack4
commented
1 year ago @matentzn Hmm... so I gave it a shot, but it's still giving an OBO GRAPH ERROR, except this time I can't find any useful information in the log or stacktrace.
I added biolink:has_evidence rdf:type owl:AnnotationProperty and re-ran, and I didn't get any errors/warnings about it anymore, so that's good. But I still got an OBO GRAPH ERROR, with no indication as to what's causing it.
robot removeThere's no indication in the error message that biolink:has_evidence has anything to do with it, but the only advice at http://robot.obolibrary.org/errors#obo-graph-error is in regards to problematic annotations, which it recommends removing, so I decided to try this anyway: robot remove --input omim.ttl --exclude-term biolink:has_evidence -o omim.json. Again, I can't locate any helpful information in the log / stacktrace.
.ofnI tried the OWL functional syntax idea you recommended: robot convert --input omim.ttl --output omim.ofn && robot convert -vvv -i omim.ofn -o omim.json. Again nothing helpful in the log.
biolink:has_evidence in initial .ttlJust trying random stuff. Tried a run removing biolink:has_evidence completely from the initial ingest, but still failing with the same error and no apparent useful information in log.
I tried opening omim.ttl in Protégé, and it initially loaded without error. But then I went to the "Classes" tab, and clicked to expand owl:Thing to explore it, but the app completely froze and crashed. Same for "Individuals by class". In the "Object properties" tab, and I can expand and see 4 RO predicates there.
robot or obographs repos about this?matentzn
commented
1 year ago After 1 hour of debugging I found the problem: https://github.com/geneontology/obographs/issues/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
matentzn
commented
1 year ago ( Solve issue by injecting this into the ontology:
<http://purl.obolibrary.org/obo/mondo/omim.owl> rdf:type owl:Ontology .)
joeflack4
commented
1 year ago 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.
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 #97OBO GRAPH ERRORSub-task details
1. Get
robotto runPossible solutions
a. ~Maybe I can simply download
robot/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.