Making prefix mapping less strict, fixes #702 (#761)

* 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.

* format

* add missing

* add missing

* fix GCI example

* fixed docs

* regenrate compliance test outputs

* Ensure prefixmap is not mutated

* relax test

* fmt

src/oaklib/interfaces/basic_ontology_interface.py

@@ -2,6 +2,7 @@
 import logging
 from abc import ABC
 from collections import defaultdict
+from copy import copy
 from dataclasses import dataclass, field
 from functools import lru_cache
 from pathlib import Path
@@ -164,6 +165,8 @@ class BasicOntologyInterface(OntologyInterface, ABC):
     _edge_index: Optional[EdgeIndex] = None
     _entailed_edge_index: Optional[EdgeIndex] = None
 
+    _prefix_map: Optional[PREFIX_MAP] = None
+
     def prefix_map(self) -> PREFIX_MAP:
         """
         Return a dictionary mapping all prefixes known to the resource to their URI expansion.
@@ -183,7 +186,9 @@ def prefix_map(self) -> PREFIX_MAP:
 
         :return: prefix map
         """
-        return get_default_prefix_map()
+        if not self._prefix_map:
+            self._prefix_map = copy(get_default_prefix_map())
+        return self._prefix_map
 
     @deprecated("Replaced by prefix_map")
     def get_prefix_map(self) -> PREFIX_MAP:
@@ -203,7 +208,7 @@ 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:

tests/input/metadata-map-prefixes-test.obo

@@ -0,0 +1,17 @@
+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]
+

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_relation="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_relation="R:2", gci_filler="X:3"}
+
 !! name: created_by-annotated
 !! description: Metadata for creator with annotation
 

tests/input/obo-compliance/expansion-conflict-main-idspace/expansion-conflict-main-idspace.meta.yaml

@@ -0,0 +1,5 @@
+name: expansion-conflict-main-idspace
+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

tests/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
+
+

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"
+        } ]
+      }
+    } ]
+  } ]
+}

tests/input/obo-compliance/gci-is-a/gci-is-a.expected.obo

@@ -0,0 +1,7 @@
+format-version: 1.2
+ontology: gci-is-a
+
+[Term]
+id: X:1
+is_a: X:2 {gci_predicate="R:2"}
+

tests/input/obo-compliance/gci-is-a/gci-is-a.expected.ofn

@@ -0,0 +1,41 @@
+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>)
+
+
+)

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 -->
+

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

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_relation="R:2", gci_filler="X:3"}
+

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"
+        } ]
+      }
+    } ]
+  } ]
+}

tests/input/obo-compliance/gci-relation/gci-relation.expected.obo

@@ -0,0 +1,7 @@
+format-version: 1.2
+ontology: gci-relation
+
+[Term]
+id: X:1
+relationship: R:1 X:2 {gci_predicate="R:2"}
+