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fix handling of URIs in the default namespace #2365

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merged 7 commits into from
May 21, 2023
Merged

fix handling of URIs in the default namespace #2365

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a51e1f0
fix expand_curie to handle URIs in the default namespace; add Namespa…
jclerman Apr 18, 2023
21d4151
Merge remote-tracking branch 'upstream/main' into support-default-prefix
aucampia May 17, 2023
598f967
minor changes:
aucampia May 18, 2023
3c9fc83
add generate option to NamespaceManager.curie(), with default=True
jclerman May 21, 2023
2a97945
remove unused fixture
aucampia May 21, 2023
23b11fd
Remove unused import
aucampia May 21, 2023
f994de2
Slightly improve the docstring
aucampia May 21, 2023
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11 changes: 10 additions & 1 deletion rdflib/namespace/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -490,6 +490,15 @@ def qname(self, uri: str) -> str:
else:
return ":".join((prefix, name))

def curie(self, uri: str) -> str:
"""From a URI, generate a valid CURIE.

Result is guaranteed to contain a colon separating the prefix from the name,
even if the prefix is an empty string.
"""
prefix, namespace, name = self.compute_qname(uri)
return ":".join((prefix, name))

def qname_strict(self, uri: str) -> str:
prefix, namespace, name = self.compute_qname_strict(uri)
if prefix == "":
Expand Down Expand Up @@ -643,7 +652,7 @@ def expand_curie(self, curie: str) -> URIRef:
if not type(curie) is str:
raise TypeError(f"Argument must be a string, not {type(curie).__name__}.")
parts = curie.split(":", 1)
if len(parts) != 2 or len(parts[0]) < 1:
if len(parts) != 2:
raise ValueError(
"Malformed curie argument, format should be e.g. “foaf:name”."
)
Expand Down
7 changes: 7 additions & 0 deletions test/conftest.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
import os
import sys
from contextlib import ExitStack

Expand Down Expand Up @@ -44,6 +45,12 @@ def rdfs_graph() -> Graph:
return Graph().parse(TEST_DATA_DIR / "defined_namespaces/rdfs.ttl", format="turtle")


@pytest.fixture(scope="session")
def test_owl_graph() -> Graph:
onto_path: str = os.path.join(TEST_DATA_DIR, "owl", "test_ontology.owl")
return Graph().parse(source=onto_path)


_ServedBaseHTTPServerMocks = Tuple[ServedBaseHTTPServerMock, ServedBaseHTTPServerMock]


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315 changes: 315 additions & 0 deletions test/data/owl/test_ontology.owl
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Original file line number Diff line number Diff line change
@@ -0,0 +1,315 @@
<?xml version="1.0"?>
<rdf:RDF xmlns="http://www.example.org/ontologies/mini-ont#"
xml:base="http://www.example.org/ontologies/mini-ont"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:obo="http://purl.obolibrary.org/obo/"
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#"
xmlns:mini-ont="http://example.org/ontologies/mini-ont#">
<owl:Ontology rdf:about="http://www.example.org/ontologies/mini-ont">
<dc:creator>Orson B Osborn</dc:creator>
<dc:title>Test OBO ontology</dc:title>
<owl:versionInfo>0.1.0</owl:versionInfo>
</owl:Ontology>



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




<!-- http://purl.obolibrary.org/obo/IAO_0000111 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000111">
<obo:IAO_0000111 xml:lang="en">editor preferred term</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:&lt;http://purl.obolibrary.org/obo/obi&gt;</obo:IAO_0000119>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">editor preferred term</rdfs:label>
</owl:AnnotationProperty>



<!-- http://purl.obolibrary.org/obo/IAO_0000112 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000112">
<obo:IAO_0000111 xml:lang="en">example</obo:IAO_0000111>
<obo:IAO_0000111 xml:lang="en">example of usage</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not</obo:IAO_0000115>
<obo:IAO_0000115 xml:lang="en">A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:&lt;http://purl.obolibrary.org/obo/obi&gt;</obo:IAO_0000119>
<oboInOwl:hasDbXref>IAO:0000112</oboInOwl:hasDbXref>
<oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
<oboInOwl:id>example_of_usage</oboInOwl:id>
<oboInOwl:is_metadata_tag rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</oboInOwl:is_metadata_tag>
<oboInOwl:shorthand>example_of_usage</oboInOwl:shorthand>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">example of usage</rdfs:label>
</owl:AnnotationProperty>



<!-- http://purl.obolibrary.org/obo/IAO_0000114 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000114">
<rdfs:label xml:lang="en">has curation status</rdfs:label>
</owl:AnnotationProperty>



<!-- http://purl.obolibrary.org/obo/IAO_0000115 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
<rdfs:label xml:lang="en">definition</rdfs:label>
</owl:AnnotationProperty>



<!-- http://purl.obolibrary.org/obo/IAO_0000117 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000117">
<rdfs:label xml:lang="en">term editor</rdfs:label>
</owl:AnnotationProperty>



<!-- http://purl.obolibrary.org/obo/IAO_0000118 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000118">
<rdfs:label xml:lang="en">alternative term</rdfs:label>
</owl:AnnotationProperty>



<!-- http://purl.obolibrary.org/obo/IAO_0000119 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000119">
<rdfs:label xml:lang="en">definition source</rdfs:label>
</owl:AnnotationProperty>



<!-- http://purl.obolibrary.org/obo/RO_0002575 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002575">
<rdfs:label>is direct form of</rdfs:label>
</owl:AnnotationProperty>



<!-- http://purl.org/dc/elements/1.1/creator -->

<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/creator"/>



<!-- http://purl.org/dc/elements/1.1/title -->

<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/title"/>



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

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



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

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



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

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



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

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



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

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



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

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



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

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



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

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



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Object Properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->




<!-- http://purl.obolibrary.org/obo/BFO_0000063 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000063">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002222"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<obo:IAO_0000111 xml:lang="en">precedes</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) &lt;= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.</obo:IAO_0000115>
<oboInOwl:hasDbXref>BFO:0000063</oboInOwl:hasDbXref>
<oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
<oboInOwl:id>precedes</oboInOwl:id>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<oboInOwl:shorthand>precedes</oboInOwl:shorthand>
<rdfs:label xml:lang="en">precedes</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_0002090 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002090">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000063"/>
<obo:IAO_0000117>David Osumi-Sutherland</obo:IAO_0000117>
<obo:IAO_0000118>ends_at_start_of</obo:IAO_0000118>
<obo:IAO_0000118>meets</obo:IAO_0000118>
<obo:RO_0002575 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000063"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:comment xml:lang="en">X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)</rdfs:comment>
<rdfs:label xml:lang="en">immediately precedes</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_0002222 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002222">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<rdfs:comment>A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.</rdfs:comment>
<rdfs:label>temporally related to</rdfs:label>
</owl:ObjectProperty>



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




<!-- http://purl.obolibrary.org/obo/BFO_0000001 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000001">
<rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
<rdfs:label xml:lang="en">entity</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/BFO_0000002 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000002">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
<rdfs:label xml:lang="en">occurrent</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/BFO_0000003 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000003">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
<rdfs:label xml:lang="en">continuant</rdfs:label>
</owl:Class>



<!-- http://www.example.org/ontologies/mini-ont#chair -->

<owl:Class rdf:about="http://www.example.org/ontologies/mini-ont#chair">
<rdfs:subClassOf rdf:resource="http://www.example.org/ontologies/mini-ont#furniture_item"/>
<oboInOwl:created_by>Jeff Lerman</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2023-03-29T00:33:04Z</oboInOwl:creation_date>
<rdfs:comment>This is a comment which will be a fallback definition.</rdfs:comment>
<rdfs:label>chair</rdfs:label>
</owl:Class>



<!-- http://www.example.org/ontologies/mini-ont#furniture_item -->

<owl:Class rdf:about="http://www.example.org/ontologies/mini-ont#furniture_item">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<oboInOwl:created_by>Jeff Lerman</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2023-03-29T00:32:55Z</oboInOwl:creation_date>
<rdfs:label>furniture item</rdfs:label>
</owl:Class>



<!-- http://www.example.org/ontologies/mini-ont#office_chair -->

<owl:Class rdf:about="http://www.example.org/ontologies/mini-ont#office_chair">
<rdfs:subClassOf rdf:resource="http://www.example.org/ontologies/mini-ont#chair"/>
<oboInOwl:created_by>Jeff Lerman</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2023-03-29T00:33:24Z</oboInOwl:creation_date>
<rdfs:label>office chair</rdfs:label>
</owl:Class>



<!-- http://www.example.org/ontologies/mini-ont#table -->

<owl:Class rdf:about="http://www.example.org/ontologies/mini-ont#table">
<rdfs:subClassOf rdf:resource="http://www.example.org/ontologies/mini-ont#furniture_item"/>
<oboInOwl:created_by>Jeff Lerman</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2023-03-29T00:32:46Z</oboInOwl:creation_date>
<rdfs:label>table</rdfs:label>
</owl:Class>
</rdf:RDF>



<!-- Generated by the OWL API (version 4.5.25.2023-02-15T19:15:49Z) https://github.com/owlcs/owlapi -->

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