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Treat raw IRI as an OWLClass in logical template cells #1211

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merged 3 commits into from
Oct 29, 2024
Merged

Treat raw IRI as an OWLClass in logical template cells #1211

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7e75ffd
Treat raw IRI as an OWLClass in template cells
jamesaoverton Jul 31, 2024
e51d9cb
Add check for HTTP IRI and test
jamesaoverton Oct 29, 2024
b82e88b
Merge branch 'master' into raw-iris-in-templates
jamesaoverton Oct 29, 2024
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8 changes: 8 additions & 0 deletions robot-core/src/main/java/org/obolibrary/robot/TemplateHelper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -991,6 +991,14 @@ protected static OWLClassExpression tryParse(
// If we have a checker, try to get the class by label
// This allows class labels with single quotes
expr = checker.getOWLClass(content, false);
if (expr == null) {
// If not found by label, is it just an IRI?
IRI iri = IRI.create(content);
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if (iri != null) {
// If so, create a new class for this IRI.
expr = checker.getOWLClass(content, true);
}
}
}
if (expr == null) {
// If not found by label, try to parse
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19 changes: 19 additions & 0 deletions robot-core/src/test/java/org/obolibrary/robot/TemplateHelperTest.java
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Expand Up @@ -128,6 +128,7 @@ public void testGetClassExpressions() throws Exception {
ManchesterOWLSyntaxClassExpressionParser parser =
new ManchesterOWLSyntaxClassExpressionParser(dataFactory, checker);

// Check CURIE
String template = "C part_of some %";
String value = "obo:UBERON_0000467";
Set<OWLClassExpression> expressions =
Expand All @@ -148,6 +149,24 @@ public void testGetClassExpressions() throws Exception {
for (OWLClassExpression expr : expressions) {
assertEquals(exprMatch.toString(), expr.toString());
}

// Check raw IRI
value = "http://purl.obolibrary.org/obo/UBERON_0000467";
expressions = TemplateHelper.getClassExpressions("", parser, template, value, 0, 0);
if (expressions.size() != 1) {
fail(String.format("Expected exactly 1 expression, got %d", expressions.size()));
}
for (OWLClassExpression expr : expressions) {
assertEquals(exprMatch.toString(), expr.toString());
}

// Check that gibberish fails
try {
value = "http.purl.obolibrary.org/obo/UBERON_0000467";
expressions = TemplateHelper.getClassExpressions("", parser, template, value, 0, 0);
fail("Gibberish value should not be parsed as Manchester expression");
} catch (Exception e) {
}
}

/**
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