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Merged
jamesaoverton merged 6 commits into from
Oct 30, 2025
Merged

Inherit OWLDocumentFormat when performing SPARQL update #1267

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e1ffff5
Inherit OWLDocument format when performing SPARQL update.
balhoff Oct 22, 2025
8fb51f3
Update CHANGELOG.
balhoff Oct 22, 2025
5c0d7e6
Add test prefix to update example.
balhoff Oct 29, 2025
238f998
Merge branch 'master' into issue-1266
jamesaoverton Oct 30, 2025
a9e5c7a
Move logic into QueryOperation, add unit test
jamesaoverton Oct 30, 2025
cbdf8f6
Remove STDERR message
jamesaoverton Oct 30, 2025
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -7,9 +7,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

## [Unreleased]

### Fixed
- Inherit OWLDocumentFormat when performing SPARQL update [#1267]
- Updated obographs to [version 0.3.2](https://github.com/geneontology/obographs/releases/tag/v0.3.2)


## [1.9.8] - 2025-05-15

### Added
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173 changes: 87 additions & 86 deletions docs/examples/nucleus.owl
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Expand Up @@ -3,6 +3,7 @@ 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#>
Prefix: foo: <http://example.org/foo/> # This prefix declaration should survive the SPARQL update roundtrip to OWL



Expand All @@ -11,178 +12,178 @@ Ontology: <http://robot.obolibrary.org/nucleus.owl>

AnnotationProperty: rdfs:label


Datatype: xsd:string


ObjectProperty: <http://purl.obolibrary.org/obo/BFO_0000050>

Characteristics:
Characteristics:
Transitive


Class: <http://purl.obolibrary.org/obo/GO_0005623>

Annotations:
Annotations:
rdfs:label "cell"
SubClassOf:

SubClassOf:
<http://purl.obolibrary.org/obo/GO_0005575>


Class: <http://purl.obolibrary.org/obo/GO_0043229>

Annotations:
Annotations:
rdfs:label "intracellular organelle"
SubClassOf:

SubClassOf:
<http://purl.obolibrary.org/obo/BFO_0000050> some <http://purl.obolibrary.org/obo/GO_0005622>,
<http://purl.obolibrary.org/obo/GO_0044424>,
<http://purl.obolibrary.org/obo/GO_0043226>


Class: <http://purl.obolibrary.org/obo/GO_0044464>

Annotations:
Annotations:
rdfs:label "cell part"
SubClassOf:

SubClassOf:
<http://purl.obolibrary.org/obo/BFO_0000050> some <http://purl.obolibrary.org/obo/GO_0005623>,
<http://purl.obolibrary.org/obo/GO_0005575>


Class: <http://purl.obolibrary.org/obo/GO_0043226>

Annotations:
Annotations:
rdfs:label "organelle"
SubClassOf:

SubClassOf:
<http://purl.obolibrary.org/obo/GO_0005575>


Class: <http://purl.obolibrary.org/obo/GO_0044428>

Annotations:
Annotations:
rdfs:label "nuclear part"
SubClassOf:

SubClassOf:
<http://purl.obolibrary.org/obo/BFO_0000050> some <http://purl.obolibrary.org/obo/GO_0005634>,
<http://purl.obolibrary.org/obo/GO_0044446>


Class: <http://purl.obolibrary.org/obo/GO_0043227>

Annotations:
Annotations:
rdfs:label "membrane-bounded organelle"
SubClassOf:

SubClassOf:
<http://purl.obolibrary.org/obo/GO_0043226>


Class: <http://purl.obolibrary.org/obo/GO_0005575>

Annotations:
Annotations:
rdfs:label "cellular_component"


Class: <http://purl.obolibrary.org/obo/GO_0044424>

Annotations:
Annotations:
rdfs:label "intracellular part"
SubClassOf:

SubClassOf:
<http://purl.obolibrary.org/obo/BFO_0000050> some <http://purl.obolibrary.org/obo/GO_0005622>,
<http://purl.obolibrary.org/obo/GO_0044464>


Class: <http://purl.obolibrary.org/obo/GO_0005622>

Annotations:
Annotations:
rdfs:label "intracellular"
SubClassOf:

SubClassOf:
<http://purl.obolibrary.org/obo/GO_0044464>


Class: <http://purl.obolibrary.org/obo/GO_0044422>

Annotations:
Annotations:
rdfs:label "organelle part"
SubClassOf:

SubClassOf:
<http://purl.obolibrary.org/obo/BFO_0000050> some <http://purl.obolibrary.org/obo/GO_0043226>,
<http://purl.obolibrary.org/obo/GO_0005575>


Class: <http://purl.obolibrary.org/obo/GO_0031974>

Annotations:
Annotations:
rdfs:label "membrane-enclosed lumen"
SubClassOf:

SubClassOf:
<http://purl.obolibrary.org/obo/GO_0005575>


Class: <http://purl.obolibrary.org/obo/GO_0005634>

Annotations:
Annotations:
rdfs:label "nucleus"
SubClassOf:

SubClassOf:
<http://purl.obolibrary.org/obo/GO_0043231>


Class: <http://purl.obolibrary.org/obo/GO_0044446>

Annotations:
Annotations:
rdfs:label "intracellular organelle part"
SubClassOf:

SubClassOf:
<http://purl.obolibrary.org/obo/BFO_0000050> some <http://purl.obolibrary.org/obo/GO_0005622>,
<http://purl.obolibrary.org/obo/BFO_0000050> some <http://purl.obolibrary.org/obo/GO_0043229>,
<http://purl.obolibrary.org/obo/GO_0044422>,
<http://purl.obolibrary.org/obo/GO_0044424>,
<http://purl.obolibrary.org/obo/BFO_0000050> some <http://purl.obolibrary.org/obo/GO_0043226>


Class: <http://purl.obolibrary.org/obo/GO_0070013>

Annotations:
Annotations:
rdfs:label "intracellular organelle lumen"
SubClassOf:

SubClassOf:
<http://purl.obolibrary.org/obo/GO_0043233>,
<http://purl.obolibrary.org/obo/BFO_0000050> some <http://purl.obolibrary.org/obo/GO_0043229>,
<http://purl.obolibrary.org/obo/GO_0044446>


Class: <http://purl.obolibrary.org/obo/GO_0043231>

Annotations:
Annotations:
rdfs:label "intracellular membrane-bounded organelle"
SubClassOf:

SubClassOf:
<http://purl.obolibrary.org/obo/GO_0043227>,
<http://purl.obolibrary.org/obo/GO_0043229>


Class: <http://purl.obolibrary.org/obo/GO_0031981>

Annotations:
Annotations:
rdfs:label "nuclear lumen"
SubClassOf:

SubClassOf:
<http://purl.obolibrary.org/obo/BFO_0000050> some <http://purl.obolibrary.org/obo/GO_0005634>,
<http://purl.obolibrary.org/obo/GO_0070013>,
<http://purl.obolibrary.org/obo/GO_0044428>


Class: <http://purl.obolibrary.org/obo/GO_0043233>

Annotations:
Annotations:
rdfs:label "organelle lumen"
SubClassOf:

SubClassOf:
<http://purl.obolibrary.org/obo/GO_0031974>,
<http://purl.obolibrary.org/obo/BFO_0000050> some <http://purl.obolibrary.org/obo/GO_0043226>,
<http://purl.obolibrary.org/obo/GO_0044422>
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6 changes: 5 additions & 1 deletion robot-command/src/main/java/org/obolibrary/robot/QueryCommand.java
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Expand Up @@ -15,6 +15,7 @@
import org.apache.jena.query.Dataset;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.tdb.TDBFactory;
import org.semanticweb.owlapi.model.OWLDocumentFormat;
import org.semanticweb.owlapi.model.OWLOntology;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
Expand Down Expand Up @@ -338,7 +339,10 @@ private static OWLOntology executeUpdate(
catalogPath = null;
}
}
return QueryOperation.convertModel(model, ioHelper, catalogPath, useTemporaryFile);

OWLDocumentFormat format =
inputOntology.getOWLOntologyManager().getOntologyFormat(inputOntology);
return QueryOperation.convertModel(model, ioHelper, catalogPath, useTemporaryFile, format);
}

/**
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36 changes: 33 additions & 3 deletions robot-core/src/main/java/org/obolibrary/robot/QueryOperation.java
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Expand Up @@ -267,20 +267,50 @@ public static OWLOntology convertModel(Model model, IOHelper ioHelper, String ca
public static OWLOntology convertModel(
Model model, IOHelper ioHelper, String catalogPath, boolean useTemporaryFile)
throws IOException {
return convertModel(model, ioHelper, catalogPath, false, null);
}

/**
* Given a Model, an IOHelper, and a path to an XML catalog, convert the model to an OWLOntology
* object.
*
* @param model Model to convert to OWLOntology
* @param ioHelper IOHelper to load ontology
* @param catalogPath String path to XML catalog
* @param useTemporaryFile whether to use a temporary file to store intermediate results or to
* keep them in memory.
* @param format The OWLDocumentFormat to use in the conversion.
* @return OWLOntology object version of model
* @throws IOException on issue loading ontology
*/
public static OWLOntology convertModel(
Model model,
IOHelper ioHelper,
String catalogPath,
boolean useTemporaryFile,
OWLDocumentFormat format)
throws IOException {
OWLOntology updatedOntology;
if (useTemporaryFile) {
final File tempFile = File.createTempFile("robot", ".owl");
tempFile.deleteOnExit();
try (final BufferedOutputStream os =
new BufferedOutputStream(new FileOutputStream(tempFile))) {
RDFDataMgr.write(os, model, Lang.TTL);
}
return ioHelper.loadOntology(
new BufferedInputStream(new FileInputStream(tempFile)), catalogPath);
updatedOntology =
ioHelper.loadOntology(
new BufferedInputStream(new FileInputStream(tempFile)), catalogPath);
} else {
ByteArrayOutputStream os = new ByteArrayOutputStream();
RDFDataMgr.write(os, model, Lang.TTL);
return ioHelper.loadOntology(new ByteArrayInputStream(os.toByteArray()), catalogPath);
updatedOntology =
ioHelper.loadOntology(new ByteArrayInputStream(os.toByteArray()), catalogPath);
}
if (format != null) {
updatedOntology.getOWLOntologyManager().setOntologyFormat(updatedOntology, format);
}
return updatedOntology;
}

/**
Expand Down
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