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use fastobo::ast as obo;
use horned_owl::curie::PrefixMapping;
use horned_owl::model as owl;
use horned_owl::model::AnnotatedComponent;
use horned_owl::model::ForIRI;
use horned_owl::model::HigherKinded;
use horned_owl::model::OntologyID;
use horned_owl::ontology::set::SetOntology;
use super::Context;
use super::IntoOwlCtx;
use crate::constants::property;
use crate::constants::uri;
impl<A: ForIRI> IntoOwlCtx<A> for obo::HeaderClause {
type Owl = Vec<owl::AnnotatedComponent<A>>;
fn into_owl(self, ctx: &mut Context<A>) -> Self::Owl {
match self {
// `oboInOwl:hasOBOFormatVersion` annotation
obo::HeaderClause::FormatVersion(v) => vec![owl::AnnotatedComponent::from(
owl::OntologyAnnotation(owl::Annotation {
ap: ctx
.build
.annotation_property(property::obo_in_owl::HAS_OBO_FORMAT_VERSION),
av: v.into_owl(ctx).into(),
}),
)],
// no equivalent
// --> should be added as the Ontology IRI
obo::HeaderClause::DataVersion(_) => Vec::new(),
// `oboInOwl:hasDate` annotation
// --> QUESTION: should the datatype_iri be `dateTime` or `string` ?
obo::HeaderClause::Date(dt) => vec![owl::AnnotatedComponent::from(
owl::OntologyAnnotation(owl::Annotation {
ap: ctx
.build
.annotation_property(property::obo_in_owl::HAS_DATE),
av: dt.into_owl(ctx).into(),
}),
)],
// `oboInOwl:savedBy` annotation
obo::HeaderClause::SavedBy(n) => vec![owl::AnnotatedComponent::from(
owl::OntologyAnnotation(owl::Annotation {
ap: ctx
.build
.annotation_property(property::obo_in_owl::SAVED_BY),
av: n.into_owl(ctx).into(),
}),
)],
// `oboInOwl:autoGeneratedBy` annotation
// --> FIXME: not actually declared in `oboInOwl`!
obo::HeaderClause::AutoGeneratedBy(n) => vec![owl::AnnotatedComponent::from(
owl::OntologyAnnotation(owl::Annotation {
ap: ctx
.build
.annotation_property(property::obo_in_owl::AUTO_GENERATED_BY),
av: n.into_owl(ctx).into(),
}),
)],
// `owl::imports`:
// --> if in abbreviated form, use default http://purl.obolibrary.org/obo/ prefix
// --> if URL, simply use that
obo::HeaderClause::Import(import) => vec![owl::AnnotatedComponent::from(
owl::Component::from(horned_owl::model::Import(import.into_owl(ctx))),
)],
// `owl:AnnotationProperty`
// <owl:AnnotationProperty rdf:about=T(subset)>
// <rdfs:comment rdf:datatype="xsd:string">T(description)</rdfs:comment>
// <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
// </owl:AnnotationProperty>
obo::HeaderClause::Subsetdef(subset, desc) => vec![
owl::AnnotatedComponent::from(owl::DeclareAnnotationProperty(
owl::AnnotationProperty::from(subset.into_owl(ctx)),
)),
owl::AnnotatedComponent::from(owl::SubAnnotationPropertyOf {
sub: owl::AnnotationProperty::from(subset.into_owl(ctx)),
sup: owl::AnnotationProperty::from(
ctx.build.iri(property::obo_in_owl::SUBSET_PROPERTY),
),
}),
owl::AnnotatedComponent::from(owl::AnnotationAssertion {
subject: owl::AnnotationSubject::from(subset.into_owl(ctx)),
ann: owl::Annotation {
ap: ctx.build.annotation_property(property::rdfs::LABEL),
av: owl::AnnotationValue::Literal(owl::Literal::Simple {
literal: subset.to_string(),
}),
},
}),
owl::AnnotatedComponent::from(owl::AnnotationAssertion {
subject: owl::AnnotationSubject::from(subset.into_owl(ctx)),
ann: owl::Annotation {
ap: ctx.build.annotation_property(property::rdfs::COMMENT),
av: owl::AnnotationValue::Literal(desc.into_owl(ctx)),
},
}),
],
// `owl:AnnotationProperty`
// <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/go#systematic_synonym">
// <oboInOwl:hasScope rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
// <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Systematic synonym</rdfs:label>
// <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
// </owl:AnnotationProperty>
obo::HeaderClause::SynonymTypedef(ty, desc, optscope) => {
let mut axioms = vec![
owl::AnnotatedComponent::from(owl::DeclareAnnotationProperty(
owl::AnnotationProperty::from(ty.into_owl(ctx)),
)),
owl::AnnotatedComponent::from(owl::SubAnnotationPropertyOf {
sub: owl::AnnotationProperty::from(ty.into_owl(ctx)),
sup: owl::AnnotationProperty::from(
ctx.build.iri(property::obo_in_owl::SYNONYM_TYPE_PROPERTY),
),
}),
owl::AnnotatedComponent::from(owl::AnnotationAssertion {
subject: owl::AnnotationSubject::from(ty.into_owl(ctx)),
ann: owl::Annotation {
ap: ctx.build.annotation_property(property::rdfs::LABEL),
av: owl::AnnotationValue::Literal(desc.into_owl(ctx)),
},
}),
];
if let Some(scope) = optscope {
axioms.push(owl::AnnotatedComponent::from(owl::AnnotationAssertion {
subject: owl::AnnotationSubject::from(ty.into_owl(ctx)),
ann: owl::Annotation {
ap: ctx
.build
.annotation_property(property::obo_in_owl::HAS_SCOPE),
av: owl::AnnotationValue::IRI(scope.into_owl(ctx)),
},
}));
}
axioms
}
// `oboInOwl:hasDefaultNamespace` annotation
obo::HeaderClause::DefaultNamespace(ns) => vec![owl::AnnotatedComponent::from(
owl::OntologyAnnotation(owl::Annotation {
ap: ctx
.build
.annotation_property(property::obo_in_owl::HAS_DEFAULT_NAMESPACE),
av: owl::AnnotationValue::Literal(owl::Literal::Simple {
literal: ns.to_string(),
}),
}),
)],
// `oboInOwl:namespaceIdRule` annotation
obo::HeaderClause::NamespaceIdRule(r) => vec![owl::AnnotatedComponent::from(
owl::OntologyAnnotation(owl::Annotation {
ap: ctx
.build
.annotation_property(property::obo_in_owl::NAMESPACE_ID_RULE),
av: r.into_owl(ctx).into(),
}),
)],
// no actual OWL equivalent, but we expose the IDspace as an OWL
// prefix to retain the same CURIES in the OWL ontology.
// earlier when creating the conversion context.
obo::HeaderClause::Idspace(_, _, _) => Vec::new(),
// no equivalent, macros should be resolved before conversion.
obo::HeaderClause::TreatXrefsAsEquivalent(_) => Vec::new(),
obo::HeaderClause::TreatXrefsAsGenusDifferentia(_, _, _) => Vec::new(),
obo::HeaderClause::TreatXrefsAsReverseGenusDifferentia(_, _, _) => Vec::new(),
obo::HeaderClause::TreatXrefsAsRelationship(_, _) => Vec::new(),
obo::HeaderClause::TreatXrefsAsIsA(_) => Vec::new(),
obo::HeaderClause::TreatXrefsAsHasSubclass(_) => Vec::new(),
// `rdfs:comment` annotation
obo::HeaderClause::Remark(v) => vec![owl::AnnotatedComponent::from(
owl::OntologyAnnotation(owl::Annotation {
ap: ctx.build.annotation_property(property::rdfs::COMMENT),
av: v.into_owl(ctx).into(),
}),
)],
// translate as an annotation
obo::HeaderClause::PropertyValue(pv) => vec![owl::AnnotatedComponent::from(
owl::OntologyAnnotation(pv.into_owl(ctx)),
)],
// no actual OWL equivalent, but exposed as the Ontology IRI
// when creating the conversion context.
obo::HeaderClause::Ontology(_) => Vec::new(),
// handled in the header frame translation.
obo::HeaderClause::OwlAxioms(_) => Vec::new(),
// no equivalent for undefined header tag/values
obo::HeaderClause::Unreserved(_, _) => Vec::new(),
}
}
}
impl<A: ForIRI> IntoOwlCtx<A> for obo::HeaderFrame {
type Owl = Vec<owl::AnnotatedComponent<A>>;
fn into_owl(self, ctx: &mut Context<A>) -> Self::Owl {
let mut owl_axioms: Vec<String> = Vec::new();
let mut axioms: Vec<owl::AnnotatedComponent<A>> = Vec::with_capacity(self.len());
// declare the IRI and Version IRI for the ontology.
if let Ok(name) = self.ontology() {
let oid = OntologyID {
iri: Some(ctx.build.iri(format!("{}{}.owl", uri::OBO, name))),
viri: self
.data_version()
.map(|dv| {
ctx.build
.iri(format!("{}{}/{}/{}.owl", uri::OBO, name, dv, name))
})
.ok(),
};
axioms.push(AnnotatedComponent::from(oid));
} else {
axioms.push(AnnotatedComponent::from(OntologyID::default()));
}
// Process the header frame clauses
for clause in self.into_iter() {
if let obo::HeaderClause::OwlAxioms(s) = clause {
owl_axioms.push(s.into_string());
} else {
axioms.append(&mut clause.into_owl(ctx))
}
}
// FIXME: https://github.com/owlcollab/oboformat/issues/116
// Parse the remaining axioms in `owl-axioms` clauses.
if !owl_axioms.is_empty() {
let text = owl_axioms.join("\n");
let reader = std::io::BufReader::new(std::io::Cursor::new(&text));
let (ont, _): (SetOntology<A>, PrefixMapping) =
horned_owl::io::ofn::reader::read_with_build(reader, &ctx.build)
.expect("invalid functional ontology");
axioms.extend(ont.into_iter().filter(|c| !c.is_meta()));
}
axioms
}
}
impl<A: ForIRI> IntoOwlCtx<A> for obo::Import {
type Owl = owl::IRI<A>;
fn into_owl(self, ctx: &mut Context<A>) -> Self::Owl {
// `owl::imports`:
// --> if in abbreviated form, use default http://purl.obolibrary.org/obo/ prefix
// --> if URL, simply use that
match self {
obo::Import::Url(url) => ctx.build.iri(url.as_str()),
obo::Import::Abbreviated(id) => ctx
.build
.iri(format!("http://purl.obolibrary.org/obo/{}.owl", id)),
}
}
}