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Convert extension definitions to RDF in a deterministic order. #10

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Convert extension definitions to RDF in a deterministic order. #10

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6922617
Convert extension definitions to RDF in a deterministic order.
gouttegd Dec 15, 2024
de21a30
Also sort mappings when serialising to RDF.
gouttegd Dec 15, 2024
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3 changes: 3 additions & 0 deletions ext/src/main/java/org/incenp/obofoundry/sssom/rdf/RDFSerialiser.java
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Expand Up @@ -33,6 +33,7 @@
import org.eclipse.rdf4j.model.util.Values;
import org.eclipse.rdf4j.model.vocabulary.RDF;
import org.eclipse.rdf4j.model.vocabulary.XSD;
import org.incenp.obofoundry.sssom.DefaultMappingComparator;
import org.incenp.obofoundry.sssom.ExtraMetadataPolicy;
import org.incenp.obofoundry.sssom.PrefixManager;
import org.incenp.obofoundry.sssom.Slot;
Expand Down Expand Up @@ -149,6 +150,7 @@ public Model toRDF(MappingSet ms, PrefixManager prefixManager) {
SlotHelper.getMappingSetHelper().visitSlots(ms, setVisitor);

RDFSlotVisitor<Mapping> mappingVisitor = new RDFSlotVisitor<Mapping>(model, null, prefixManager, usedPrefixes);
ms.getMappings().sort(new DefaultMappingComparator());
for ( Mapping mapping : ms.getMappings() ) {
// Add individual mapping
BNode mappingNode = Values.bnode();
Expand Down Expand Up @@ -287,6 +289,7 @@ public Void visitExtensionDefinitions(T object, List<ExtensionDefinition> values
return null;
}

values.sort((a, b) -> a.getProperty().compareTo(b.getProperty()));
for ( ExtensionDefinition ed : values ) {
BNode edNode = Values.bnode();
// FIXME: The SSSOM spec does not say how extension definitions should be
Expand Down
22 changes: 19 additions & 3 deletions ext/src/test/java/org/incenp/obofoundry/sssom/rdf/RDFWriterTest.java
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Expand Up @@ -49,17 +49,33 @@ void testSimpleRDFWrite() {
}

@Test
void testWriteNonStandardMetadata() throws SSSOMFormatException, IOException {
void testWriteNoStandardMetadata() throws SSSOMFormatException, IOException {
TSVReader reader = new TSVReader("../core/src/test/resources/sets/exo2c-with-extensions.sssom.tsv");
reader.setExtraMetadataPolicy(ExtraMetadataPolicy.UNDEFINED);
MappingSet ms = reader.read();

assertWrittenAsExpected(ms, "test-ttl-output-extensions-none", null,
(w) -> w.setExtraMetadataPolicy(ExtraMetadataPolicy.NONE));
}

@Test
void testWriteDefinedNonStandardMetadata() throws SSSOMFormatException, IOException {
TSVReader reader = new TSVReader("../core/src/test/resources/sets/exo2c-with-extensions.sssom.tsv");
reader.setExtraMetadataPolicy(ExtraMetadataPolicy.UNDEFINED);
MappingSet ms = reader.read();

assertWrittenAsExpected(ms, "test-ttl-output-extensions-defined", null,
(w) -> w.setExtraMetadataPolicy(ExtraMetadataPolicy.DEFINED));
}

@Test
void testWriteUnDefinedNonStandardMetadata() throws SSSOMFormatException, IOException {
TSVReader reader = new TSVReader("../core/src/test/resources/sets/exo2c-with-extensions.sssom.tsv");
reader.setExtraMetadataPolicy(ExtraMetadataPolicy.UNDEFINED);
MappingSet ms = reader.read();

assertWrittenAsExpected(ms, "test-ttl-output-extensions-undefined", null,
(w) -> w.setExtraMetadataPolicy(ExtraMetadataPolicy.UNDEFINED));
assertWrittenAsExpected(ms, "test-ttl-output-extensions-none", null,
(w) -> w.setExtraMetadataPolicy(ExtraMetadataPolicy.NONE));
}

private void assertWrittenAsExpected(MappingSet ms, String expectedBasename, String actualBasename,
Expand Down
8 changes: 4 additions & 4 deletions ext/src/test/resources/output/test-ttl-output-extensions-defined.ttl
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Expand Up @@ -19,10 +19,6 @@
<http://sssom.invalid/ext_undeclared_foo> "Foo B";
EXPROP:fooProperty "Foo A";
sssom:extension_definitions [
sssom:property EXPROP:fooProperty;
sssom:slot_name "ext_foo";
sssom:type_hint xsd:string
], [
sssom:property <http://sssom.invalid/ext_undeclared_baz>;
sssom:slot_name "ext_undeclared_baz";
sssom:type_hint xsd:string
Expand All @@ -38,6 +34,10 @@
sssom:property EXPROP:bazProperty;
sssom:slot_name "ext_baz";
sssom:type_hint linkml:Uriorcurie
], [
sssom:property EXPROP:fooProperty;
sssom:slot_name "ext_foo";
sssom:type_hint xsd:string
];
sssom:mapping_set_id "https://example.org/sets/exo2c-with-extensions"^^xsd:anyURI;
sssom:mappings [ a owl:Axiom;
Expand Down
76 changes: 38 additions & 38 deletions ext/src/test/resources/output/test-ttl-output-extensions-undefined.ttl
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Expand Up @@ -19,44 +19,6 @@
EXPROP:fooProperty "Foo A";
sssom:mapping_set_id "https://example.org/sets/exo2c-with-extensions"^^xsd:anyURI;
sssom:mappings [ a owl:Axiom;
<http://sssom.invalid/ext_undeclared_baz> "BAZ A";
owl:annotatedProperty skos:closeMatch;
owl:annotatedSource ORGENT:0001;
owl:annotatedTarget COMENT:0011;
EXPROP:barProperty "111"^^xsd:int;
EXPROP:bazProperty ORGENT:BAZ_0001;
sssom:mapping_justification semapv:ManualMappingCuration;
sssom:object_label "alpha";
sssom:subject_label "alice"
], [ a owl:Axiom;
owl:annotatedProperty skos:closeMatch;
owl:annotatedSource ORGENT:0002;
owl:annotatedTarget COMENT:0012;
EXPROP:barProperty "112"^^xsd:int;
EXPROP:bazProperty ORGENT:BAZ_0002;
sssom:mapping_justification semapv:ManualMappingCuration;
sssom:object_label "beta";
sssom:subject_label "bob"
], [ a owl:Axiom;
<http://sssom.invalid/ext_undeclared_baz> "Baz C";
owl:annotatedProperty skos:closeMatch;
owl:annotatedSource ORGENT:0004;
owl:annotatedTarget COMENT:0014;
EXPROP:barProperty "114"^^xsd:int;
sssom:mapping_justification semapv:ManualMappingCuration;
sssom:object_label "delta";
sssom:subject_label "daphne"
], [ a owl:Axiom;
<http://sssom.invalid/ext_undeclared_baz> "Baz E";
owl:annotatedProperty skos:closeMatch;
owl:annotatedSource ORGENT:0005;
owl:annotatedTarget COMENT:0015;
EXPROP:barProperty "115"^^xsd:int;
EXPROP:bazProperty ORGENT:BAZ_0005;
sssom:mapping_justification semapv:ManualMappingCuration;
sssom:object_label "epsilon";
sssom:subject_label "eve"
], [ a owl:Axiom;
<http://sssom.invalid/ext_undeclared_baz> "Baz F";
owl:annotatedProperty skos:closeMatch;
owl:annotatedSource ORGENT:0006;
Expand Down Expand Up @@ -96,4 +58,42 @@
sssom:mapping_justification semapv:ManualMappingCuration;
sssom:object_label "iota";
sssom:subject_label "ivan"
], [ a owl:Axiom;
<http://sssom.invalid/ext_undeclared_baz> "BAZ A";
owl:annotatedProperty skos:closeMatch;
owl:annotatedSource ORGENT:0001;
owl:annotatedTarget COMENT:0011;
EXPROP:barProperty "111"^^xsd:int;
EXPROP:bazProperty ORGENT:BAZ_0001;
sssom:mapping_justification semapv:ManualMappingCuration;
sssom:object_label "alpha";
sssom:subject_label "alice"
], [ a owl:Axiom;
owl:annotatedProperty skos:closeMatch;
owl:annotatedSource ORGENT:0002;
owl:annotatedTarget COMENT:0012;
EXPROP:barProperty "112"^^xsd:int;
EXPROP:bazProperty ORGENT:BAZ_0002;
sssom:mapping_justification semapv:ManualMappingCuration;
sssom:object_label "beta";
sssom:subject_label "bob"
], [ a owl:Axiom;
<http://sssom.invalid/ext_undeclared_baz> "Baz C";
owl:annotatedProperty skos:closeMatch;
owl:annotatedSource ORGENT:0004;
owl:annotatedTarget COMENT:0014;
EXPROP:barProperty "114"^^xsd:int;
sssom:mapping_justification semapv:ManualMappingCuration;
sssom:object_label "delta";
sssom:subject_label "daphne"
], [ a owl:Axiom;
<http://sssom.invalid/ext_undeclared_baz> "Baz E";
owl:annotatedProperty skos:closeMatch;
owl:annotatedSource ORGENT:0005;
owl:annotatedTarget COMENT:0015;
EXPROP:barProperty "115"^^xsd:int;
EXPROP:bazProperty ORGENT:BAZ_0005;
sssom:mapping_justification semapv:ManualMappingCuration;
sssom:object_label "epsilon";
sssom:subject_label "eve"
] .
10 changes: 5 additions & 5 deletions ext/src/test/resources/output/test-ttl-output.ttl
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Expand Up @@ -16,6 +16,11 @@
dcterms:license "https://creativecommons.org/licenses/by/4.0/"^^xsd:anyURI;
sssom:mapping_set_id "https://example.org/sets/exo2c"^^xsd:anyURI;
sssom:mappings [ a owl:Axiom;
owl:annotatedProperty skos:closeMatch;
owl:annotatedSource FBbt:12345678;
owl:annotatedTarget UBERON:1234567;
sssom:mapping_justification semapv:ManualMappingCuration
], [ a owl:Axiom;
owl:annotatedProperty skos:closeMatch;
owl:annotatedSource ORGENT:0001;
owl:annotatedTarget COMENT:0011;
Expand All @@ -32,9 +37,4 @@
sssom:object_label "beta";
sssom:subject_label "bob";
sssom:subject_type owl:Class
], [ a owl:Axiom;
owl:annotatedProperty skos:closeMatch;
owl:annotatedSource FBbt:12345678;
owl:annotatedTarget UBERON:1234567;
sssom:mapping_justification semapv:ManualMappingCuration
] .
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