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Making prefix mapping less strict, fixes #702 #761

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Making prefix mapping less strict, fixes #702 #761

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ebcd75d
Making prefix mapping less strict, fixes #702
cmungall May 15, 2024
958b5a3
format
cmungall May 15, 2024
a20ecfe
add missing
cmungall May 15, 2024
d8c394a
add missing
cmungall May 15, 2024
5a5ec1f
fix GCI example
cmungall May 17, 2024
2b15538
fixed docs
cmungall Jun 5, 2024
246ca91
regenrate compliance test outputs
cmungall Jun 5, 2024
861dc0c
Ensure prefixmap is not mutated
cmungall Jun 5, 2024
4d1f4c3
relax test
cmungall Jun 5, 2024
53c965c
fmt
cmungall Jun 5, 2024
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2 changes: 1 addition & 1 deletion src/oaklib/interfaces/basic_ontology_interface.py
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Expand Up @@ -203,7 +203,7 @@ def converter(self) -> curies.Converter:
:return: A converter
"""
if self._converter is None:
self._converter = curies.Converter.from_prefix_map(self.prefix_map())
self._converter = curies.Converter.from_prefix_map(self.prefix_map(), strict=False)
return self._converter

def set_metamodel_mappings(self, mappings: Union[str, Path, List[Mapping]]) -> None:
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17 changes: 17 additions & 0 deletions tests/input/metadata-map-prefixes-test.obo
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format-version: 1.2
ontology: test.obo
idspace: dc http://purl.org/dc/elements/1.1/
idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl#
idspace: owl http://www.w3.org/2002/07/owl#
idspace: rdf http://www.w3.org/1999/02/22-rdf-syntax-ns#
idspace: rdfs http://www.w3.org/2000/01/rdf-schema#
idspace: terms http://purl.org/dc/terms/
idspace: xml http://www.w3.org/XML/1998/namespace
idspace: xsd http://www.w3.org/2001/XMLSchema#
idspace: HP http://purl.obolibrary.org/obo/HP_

[Term]
id: HP:0000001
name: All
def: "." [PMID:1]

61 changes: 61 additions & 0 deletions tests/input/obo-compliance.obo
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Expand Up @@ -565,6 +565,53 @@ idspace: Y http://example.org/Y/
id: X:1
created_by: Y:1

!! name: prefixes-conflict-oio
!! description: tests conflicting prefixes/contractions for oboInOwl namespace, where oio might be built-in
!! unstable: true
!! seeAlso: https://github.com/INCATools/ontology-access-kit/issues/760
idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl#

[Term]
id: X:1
name: X:1
def: "." []

!! name: prefixes-conflict-skos
!! description: tests conflicting prefixes for the SKOS namespace
!! unstable: true
!! seeAlso: https://github.com/INCATools/ontology-access-kit/issues/760
idspace: skos http://example.org/not-skos/

[Term]
id: X:1
property_value: skos:exactMatch Y:1

[Typedef]
id: skos:exactMatch
is_metadata_tag: true

!! name: prefixes-conflict-main-idspace
!! description: tests conflicting prefixes for the main ID space
!! invalid: true
!! seeAlso: https://github.com/INCATools/ontology-access-kit/issues/760
idspace: X http://example.org/X/
idspace: FAKEX http://example.org/X/

[Term]
id: X:1
name: X:1

!! name: expansion-conflict-main-idspace
!! description: tests conflicting expansions for the main ID space
!! invalid: true
!! seeAlso: https://github.com/INCATools/ontology-access-kit/issues/760
idspace: X http://example.org/X/
idspace: X http://example.org/FAKEX/

[Term]
id: X:1
name: X:1

!! # #########
!! # Headers
!! # #########
Expand Down Expand Up @@ -658,6 +705,20 @@ subset: S {source="PMID:123464"}
id: X:1
disjoint_from: X:2 {source="PMID:123465"}

!! name: gci-relation
!! description: General Class Inclusion relation

[Term]
id: X:1
relationship: R:1 X:2 {gci_predicate="R:2", gci_filler="X:3"}

!! name: gci-is-a
!! description: General Class Inclusion is_a

[Term]
id: X:1
is_a: X:2 {gci_predicate="R:2", gci_filler="X:3"}
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Shouldn’t that be gci_relation instead of gci_predicate? I don’t think I have ever seen that gci_predicate qualifier, and the OBO spec does not mention it at all.


!! name: created_by-annotated
!! description: Metadata for creator with annotation

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4 changes: 4 additions & 0 deletions .../obo-compliance/expansion-conflict-main-idspace/expansion-conflict-main-idspace.meta.yaml
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name: expansion-conflict-main-idspace
name: expansion-conflict-main-idspace
description: tests conflicting expansions for the main ID space
invalid: true
10 changes: 10 additions & 0 deletions .../input/obo-compliance/expansion-conflict-main-idspace/expansion-conflict-main-idspace.obo
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format-version: 1.4
ontology: expansion-conflict-main-idspace
idspace: X http://example.org/X/
idspace: X http://example.org/FAKEX/

[Term]
id: X:1
name: X:1


31 changes: 31 additions & 0 deletions tests/input/obo-compliance/gci-is-a/gci-is-a.expected.json
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{
"graphs" : [ {
"id" : "http://purl.obolibrary.org/obo/gci-is-a.owl",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion",
"val" : "1.4"
} ]
},
"nodes" : [ {
"id" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion",
"lbl" : "has_obo_format_version",
"type" : "PROPERTY"
}, {
"id" : "http://www.geneontology.org/formats/oboInOwl#id",
"lbl" : "id",
"type" : "PROPERTY"
} ],
"edges" : [ {
"sub" : "http://purl.obolibrary.org/obo/X_1",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/X_2",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#gci_predicate",
"val" : "R:2"
} ]
}
} ]
} ]
}
7 changes: 7 additions & 0 deletions tests/input/obo-compliance/gci-is-a/gci-is-a.expected.obo
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format-version: 1.2
ontology: gci-is-a

[Term]
id: X:1
is_a: X:2 {gci_predicate="R:2"}

41 changes: 41 additions & 0 deletions tests/input/obo-compliance/gci-is-a/gci-is-a.expected.ofn
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Prefix(:=<http://purl.obolibrary.org/obo/gci-is-a.owl#>)
Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/gci-is-a.owl>
Annotation(<http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion> "1.4")

Declaration(Class(<http://purl.obolibrary.org/obo/X_1>))
Declaration(Class(<http://purl.obolibrary.org/obo/X_2>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#gci_predicate>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#id>))
############################
# Annotation Properties
############################

# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion> (has_obo_format_version)

AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion> "has_obo_format_version")

# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#id> (id)

AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#id> "id")



############################
# Classes
############################

# Class: <http://purl.obolibrary.org/obo/X_1> (<http://purl.obolibrary.org/obo/X_1>)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/X_1> "X:1")
SubClassOf(Annotation(<http://www.geneontology.org/formats/oboInOwl#gci_predicate> "R:2") <http://purl.obolibrary.org/obo/X_1> <http://purl.obolibrary.org/obo/X_2>)
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Is this expected? Should it be R:2 some X:2 subClassOf X:1?

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I think this is because the input file is using the wrong qualifier (see my other comment below).

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Good catch.

The main issue with this suite (as I mentioned here #751) is that it's self-bootstrapping there is a one-off TestByGuru run where both inputs and outputs need carefully checked against the spec.



)
83 changes: 83 additions & 0 deletions tests/input/obo-compliance/gci-is-a/gci-is-a.expected.owl
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<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/gci-is-a.owl#"
xml:base="http://purl.obolibrary.org/obo/gci-is-a.owl"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/gci-is-a.owl">
<oboInOwl:hasOBOFormatVersion>1.4</oboInOwl:hasOBOFormatVersion>
</owl:Ontology>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->




<!-- http://www.geneontology.org/formats/oboInOwl#gci_predicate -->

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#gci_predicate"/>



<!-- http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion -->

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion">
<rdfs:label>has_obo_format_version</rdfs:label>
</owl:AnnotationProperty>



<!-- http://www.geneontology.org/formats/oboInOwl#id -->

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id">
<rdfs:label>id</rdfs:label>
</owl:AnnotationProperty>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->




<!-- http://purl.obolibrary.org/obo/X_1 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/X_1">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/X_2"/>
<oboInOwl:id>X:1</oboInOwl:id>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/X_1"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/X_2"/>
<oboInOwl:gci_predicate>R:2</oboInOwl:gci_predicate>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/X_2 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/X_2"/>
</rdf:RDF>



<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->

3 changes: 3 additions & 0 deletions tests/input/obo-compliance/gci-is-a/gci-is-a.meta.yaml
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name: gci-is-a
name: gci-is-a
description: General Class Inclusion is_a
7 changes: 7 additions & 0 deletions tests/input/obo-compliance/gci-is-a/gci-is-a.obo
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format-version: 1.4
ontology: gci-is-a

[Term]
id: X:1
is_a: X:2 {gci_predicate="R:2", gci_filler="X:3"}

31 changes: 31 additions & 0 deletions tests/input/obo-compliance/gci-relation/gci-relation.expected.json
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{
"graphs" : [ {
"id" : "http://purl.obolibrary.org/obo/gci-relation.owl",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion",
"val" : "1.4"
} ]
},
"nodes" : [ {
"id" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion",
"lbl" : "has_obo_format_version",
"type" : "PROPERTY"
}, {
"id" : "http://www.geneontology.org/formats/oboInOwl#id",
"lbl" : "id",
"type" : "PROPERTY"
} ],
"edges" : [ {
"sub" : "http://purl.obolibrary.org/obo/X_1",
"pred" : "http://purl.obolibrary.org/obo/R_1",
"obj" : "http://purl.obolibrary.org/obo/X_2",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#gci_predicate",
"val" : "R:2"
} ]
}
} ]
} ]
}
7 changes: 7 additions & 0 deletions tests/input/obo-compliance/gci-relation/gci-relation.expected.obo
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format-version: 1.2
ontology: gci-relation

[Term]
id: X:1
relationship: R:1 X:2 {gci_predicate="R:2"}

43 changes: 43 additions & 0 deletions tests/input/obo-compliance/gci-relation/gci-relation.expected.ofn
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Prefix(:=<http://purl.obolibrary.org/obo/gci-relation.owl#>)
Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/gci-relation.owl>
Annotation(<http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion> "1.4")

Declaration(Class(<http://purl.obolibrary.org/obo/X_1>))
Declaration(Class(<http://purl.obolibrary.org/obo/X_2>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/R_1>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#gci_predicate>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#id>))
############################
# Annotation Properties
############################

# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion> (has_obo_format_version)

AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion> "has_obo_format_version")

# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#id> (id)

AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#id> "id")




############################
# Classes
############################

# Class: <http://purl.obolibrary.org/obo/X_1> (<http://purl.obolibrary.org/obo/X_1>)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/X_1> "X:1")
SubClassOf(Annotation(<http://www.geneontology.org/formats/oboInOwl#gci_predicate> "R:2") <http://purl.obolibrary.org/obo/X_1> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/R_1> <http://purl.obolibrary.org/obo/X_2>))


)
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