@context missing the type definitions in version 0.4.0

[anitacaron]

The new release changed the @context when calling to_json, now only returning prefixes, instead of a complete definition of types in JSON-LD.

Expected @context returned in version 0.3.41

Click to view context version 0.3.41

{
"@context":{
"dcterms":"http://purl.org/dc/terms/",
"linkml":"https://w3id.org/linkml/",
"oboInOwl":"http://www.geneontology.org/formats/oboInOwl#",
"owl":"http://www.w3.org/2002/07/owl#",
"pav":"http://purl.org/pav/",
"prov":"http://www.w3.org/ns/prov#",
"rdf":"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdfs":"http://www.w3.org/2000/01/rdf-schema#",
"semapv":"https://w3id.org/semapv/vocab/",
"skos":"http://www.w3.org/2004/02/skos/core#",
"sssom":"https://w3id.org/sssom/",
"@vocab":"https://w3id.org/sssom/",
"author_id":{
"@type":"@id",
"@id":"pav:authoredBy"
},
"comment":{
"@id":"rdfs:comment"
},
"confidence":{
"@type":"xsd:double"
},
"creator_id":{
"@type":"@id",
"@id":"dcterms:creator"
},
"curation_rule":{
"@type":"@id"
},
"documentation":{
"@type":"@id"
},
"homepage":{
"@type":"@id"
},
"imports":{
"@type":"@id"
},
"issue_tracker":{
"@type":"@id"
},
"issue_tracker_item":{
"@type":"@id"
},
"last_updated":{
"@type":"xsd:date"
},
"license":{
"@type":"@id",
"@id":"dcterms:license"
},
"mapping_cardinality":{
"@context":{
"@vocab":"@null",
"text":"skos:notation",
"description":"skos:prefLabel",
"meaning":"@id"
}
},
"mapping_date":{
"@type":"xsd:date",
"@id":"pav:authoredOn"
},
"mapping_justification":{
"@type":"@id"
},
"mapping_provider":{
"@type":"@id"
},
"mapping_registry_id":{
"@type":"@id"
},
"mapping_set_description":{
"@id":"dcterms:description"
},
"mapping_set_id":{
"@type":"@id"
},
"mapping_set_references":{
"@type":"@id"
},
"mapping_set_source":{
"@type":"@id",
"@id":"prov:wasDerivedFrom"
},
"mapping_set_title":{
"@id":"dcterms:title"
},
"mapping_set_version":{
"@id":"owl:versionInfo"
},
"mapping_source":{
"@type":"@id"
},
"mappings":{
"@type":"@id"
},
"mirror_from":{
"@type":"@id"
},
"object_id":{
"@type":"@id",
"@id":"owl:annotatedTarget"
},
"object_match_field":{
"@type":"@id"
},
"object_preprocessing":{
"@type":"@id"
},
"object_source":{
"@type":"@id"
},
"object_type":{
"@context":{
"@vocab":"@null",
"text":"skos:notation",
"description":"skos:prefLabel",
"meaning":"@id"
}
},
"predicate_id":{
"@type":"@id",
"@id":"owl:annotatedProperty"
},
"predicate_modifier":{
"@context":{
"@vocab":"@null",
"text":"skos:notation",
"description":"skos:prefLabel",
"meaning":"@id"
}
},
"predicate_type":{
"@context":{
"@vocab":"@null",
"text":"skos:notation",
"description":"skos:prefLabel",
"meaning":"@id"
}
},
"publication_date":{
"@type":"xsd:date",
"@id":"dcterms:created"
},
"registry_confidence":{
"@type":"xsd:double"
},
"reviewer_id":{
"@type":"@id"
},
"see_also":{
"@id":"rdfs:seeAlso"
},
"semantic_similarity_score":{
"@type":"xsd:double"
},
"subject_id":{
"@type":"@id",
"@id":"owl:annotatedSource"
},
"subject_match_field":{
"@type":"@id"
},
"subject_preprocessing":{
"@type":"@id"
},
"subject_source":{
"@type":"@id"
},
"subject_type":{
"@context":{
"@vocab":"@null",
"text":"skos:notation",
"description":"skos:prefLabel",
"meaning":"@id"
}
},
"Mapping":{
"@id":"owl:Axiom"
},
"HP":"http://purl.obolibrary.org/obo/HP_",
"MP":"http://purl.obolibrary.org/obo/MP_",
"orcid":"https://orcid.org/",
"obo":"http://purl.obolibrary.org/obo/",
}
}

Click to view context in version 0.4.0

{
"@context":{
"owl":"http://www.w3.org/2002/07/owl#",
"rdf":"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdfs":"http://www.w3.org/2000/01/rdf-schema#",
"semapv":"https://w3id.org/semapv/vocab/",
"skos":"http://www.w3.org/2004/02/skos/core#",
"sssom":"https://w3id.org/sssom/",
"HP":"http://purl.obolibrary.org/obo/HP_",
"MP":"http://purl.obolibrary.org/obo/MP_",
"obo":"http://purl.obolibrary.org/obo/",
"orcid":"https://orcid.org/",
}
}

Is there another method to have the complete @context for JSON-LD file?

[matentzn]

@anitacaron thank you for the report; there is no test for the JSON serialisation other than checking that the mappings are present.

@cthoyt I missed this during a review of one of your PRs:

c31f44e

We need to undo this change urgently, as this breaks the JSON format; I started doing this here #479

The problem is that the jsonld base from which we originally created the context does not exist anymore. Which means I will have to revive quite a bit of code that was previously removed unfortunately..

How I missed this I cant understand, another reason for small PRs moving forward. Sorry about that @anitacaron.

@cthoyt If I don't hear from you I will roll back the jsonld context related changes.

@hrshdhgd can you find me a valid JSON version of any linkml converted file format? I just want to look how the json files look like..

[cthoyt]

looking into this...

more context about what code you're running would be helpful

[cthoyt]

so is the issue that the get_jsonld_context function loaded up some LinkML artifact that had extra stuff besides the prefix map that we need to retain?

[matentzn]

This is the consequence of running sssom convert --format json - any example would do.

so is the issue that the get_jsonld_context function loaded up some LinkML artifact that had extra stuff besides the prefix map that we need to retain?

Yes.

[cthoyt]

@anitacaron i updated Nico's PR in #479, it should solve the problem now with minimal changes, we just need to add a unit test to it.