Making prefix mapping less strict, fixes #702

Adds test that currently codifies ambiguous behavior. See also #760 for broader issue. This PR also extends the obo test suite to include this, and adds some derived files previously missing.
INCATools · May 15, 2024 · ebcd75d · ebcd75d
1 parent aef24c8
commit ebcd75d
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diff --git a/src/oaklib/interfaces/basic_ontology_interface.py b/src/oaklib/interfaces/basic_ontology_interface.py
@@ -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:

diff --git a/tests/input/obo-compliance.obo b/tests/input/obo-compliance.obo
@@ -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
 !! # #########
@@ -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"}
+
 !! name: created_by-annotated
 !! description: Metadata for creator with annotation
 

diff --git a/.../obo-compliance/expansion-conflict-main-idspace/expansion-conflict-main-idspace.meta.yaml b/.../obo-compliance/expansion-conflict-main-idspace/expansion-conflict-main-idspace.meta.yaml
@@ -0,0 +1,4 @@
+name: expansion-conflict-main-idspace
+name: expansion-conflict-main-idspace
+description: tests conflicting expansions for the main ID space
+invalid: true
diff --git a/.../input/obo-compliance/expansion-conflict-main-idspace/expansion-conflict-main-idspace.obo b/.../input/obo-compliance/expansion-conflict-main-idspace/expansion-conflict-main-idspace.obo
@@ -0,0 +1,10 @@
+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
+
+
diff --git a/tests/input/obo-compliance/gci-is-a/gci-is-a.expected.json b/tests/input/obo-compliance/gci-is-a/gci-is-a.expected.json
@@ -0,0 +1,31 @@
+{
+  "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"
+        } ]
+      }
+    } ]
+  } ]
+}
diff --git a/tests/input/obo-compliance/gci-is-a/gci-is-a.expected.owl b/tests/input/obo-compliance/gci-is-a/gci-is-a.expected.owl
@@ -0,0 +1,83 @@
+<?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 -->
+
diff --git a/tests/input/obo-compliance/gci-is-a/gci-is-a.meta.yaml b/tests/input/obo-compliance/gci-is-a/gci-is-a.meta.yaml
@@ -0,0 +1,3 @@
+name: gci-is-a
+name: gci-is-a
+description: General Class Inclusion is_a
diff --git a/tests/input/obo-compliance/gci-is-a/gci-is-a.obo b/tests/input/obo-compliance/gci-is-a/gci-is-a.obo
@@ -0,0 +1,7 @@
+format-version: 1.4
+ontology: gci-is-a
+
+[Term]
+id: X:1
+is_a: X:2 {gci_predicate="R:2", gci_filler="X:3"}
+
diff --git a/tests/input/obo-compliance/gci-relation/gci-relation.expected.json b/tests/input/obo-compliance/gci-relation/gci-relation.expected.json
@@ -0,0 +1,31 @@
+{
+  "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"
+        } ]
+      }
+    } ]
+  } ]
+}
diff --git a/tests/input/obo-compliance/gci-relation/gci-relation.expected.owl b/tests/input/obo-compliance/gci-relation/gci-relation.expected.owl
@@ -0,0 +1,104 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/gci-relation.owl#"
+     xml:base="http://purl.obolibrary.org/obo/gci-relation.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-relation.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>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Object Properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/R_1 -->
+
+    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/R_1"/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/X_1 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/X_1">
+        <rdfs:subClassOf rdf:nodeID="genid1"/>
+        <oboInOwl:id>X:1</oboInOwl:id>
+    </owl:Class>
+    <owl:Restriction rdf:nodeID="genid1">
+        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/R_1"/>
+        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/X_2"/>
+    </owl:Restriction>
+    <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:nodeID="genid1"/>
+        <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 -->
+
diff --git a/tests/input/obo-compliance/gci-relation/gci-relation.meta.yaml b/tests/input/obo-compliance/gci-relation/gci-relation.meta.yaml
@@ -0,0 +1,3 @@
+name: gci-relation
+name: gci-relation
+description: General Class Inclusion relation
diff --git a/tests/input/obo-compliance/gci-relation/gci-relation.obo b/tests/input/obo-compliance/gci-relation/gci-relation.obo
@@ -0,0 +1,7 @@
+format-version: 1.4
+ontology: gci-relation
+
+[Term]
+id: X:1
+relationship: R:1 X:2 {gci_predicate="R:2", gci_filler="X:3"}
+
diff --git a/...ut/obo-compliance/prefixes-conflict-main-idspace/prefixes-conflict-main-idspace.meta.yaml b/...ut/obo-compliance/prefixes-conflict-main-idspace/prefixes-conflict-main-idspace.meta.yaml
@@ -0,0 +1,4 @@
+name: prefixes-conflict-main-idspace
+name: prefixes-conflict-main-idspace
+description: tests conflicting prefixes for the main ID space
+invalid: true
diff --git a/tests/input/obo-compliance/prefixes-conflict-main-idspace/prefixes-conflict-main-idspace.obo b/tests/input/obo-compliance/prefixes-conflict-main-idspace/prefixes-conflict-main-idspace.obo
@@ -0,0 +1,9 @@
+format-version: 1.4
+ontology: prefixes-conflict-main-idspace
+idspace: X http://example.org/X/
+idspace: FAKEX http://example.org/X/
+
+[Term]
+id: X:1
+name: X:1
+