8000 Handle IRIs that are not entities in export by jamesaoverton · Pull Request #1168 · ontodev/robot · GitHub
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Handle IRIs that are not entities in export #1168

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Merged
merged 3 commits into from
Nov 30, 2023
Merged

Handle IRIs that are not entities in export #1168

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7dd5995
Handle IRIs that are not entities in export
jamesaoverton Nov 29, 2023
0a80902
Update CHANGELOG for export fix
jamesaoverton Nov 29, 2023
4acc9a6
Add writeXLSX utility method
jamesaoverton Nov 30, 2023
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Fixed
- '--annotate-with-source true' does not work with extract --method subset [#1160]
- Fix how Template adds entities to the QuotedEntityChecker [#1104]
- Handle IRIs that are not entities in export [#1168]

## [1.9.5] - 2023-09-20

Expand Down Expand Up @@ -380,6 +381,7 @@ First official release of ROBOT!
[`template`]: http://robot.obolibrary.org/template
[`validate`]: http://robot.obolibrary.org/validate

[#1168]: https://github.com/ontodev/robot/pull/1168
[#1160]: https://github.com/ontodev/robot/pull/1160
[#1148]: https://github.com/ontodev/robot/pull/1148
[#1135]: https://github.com/ontodev/robot/pull/1135
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8 changes: 6 additions & 2 deletions robot-core/src/main/java/org/obolibrary/robot/ExportOperation.java
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Expand Up @@ -496,8 +496,12 @@ private static List<String> getPropertyValues(
IRI iri = a.getValue().asIRI().orNull();
if (iri != null) {
Set<OWLEntity> entities = ontology.getEntitiesInSignature(iri);
for (OWLEntity e : entities) {
values.add(OntologyHelper.renderManchester(e, provider, rt));
if (entities.size() > 0) {
for (OWLEntity e : entities) {
values.add(OntologyHelper.renderManchester(e, provider, rt));
}
} else {
values.add(iri.toString());
}
}
} else {
Expand Down
31 changes: 28 additions & 3 deletions robot-core/src/test/java/org/obolibrary/robot/ExportOperationTest.java
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@@ -1,5 +1,8 @@
package org.obolibrary.robot;

import static org.junit.Assert.assertEquals;

import java.io.FileOutputStream;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
Expand Down Expand Up @@ -29,6 +32,23 @@
*/
public class ExportOperationTest extends CoreTest {

/**
* Utility method to write XLSX file for debugging.
*
* @param workbook Workfbook to write
* @param path Path (string) to save to, under `robot-core/`
*/
void writeXLSX(Workbook workbook, String path) {
try {
System.out.println("Writing result to robot-core/" + path);
FileOutputStream out = new FileOutputStream(path);
workbook.write(out);
out.close();
} catch (Exception ex) {
System.out.println("Error writing workbook: " + ex);
}
}

/**
* Test exporting simple.owl to XLSX.
*
Expand Down Expand Up @@ -121,7 +141,7 @@ public void testLargeExcelExport() throws Exception {
*/
@Test
public void testExportNamedHeadingsSimple() throws Exception {
OWLOntology class="x x-first x-last">simple.owl");
OWLOntology class="x x-first x-last">simple_defined_by.owl");
IOHelper ioHelper = new IOHelper();
ioHelper.addPrefix(
"simple", "https://github.com/ontodev/robot/robot-core/src/test/resources/simple.owl#");
Expand All @@ -135,6 +155,7 @@ public void testExportNamedHeadingsSimple() throws Exception {
"CURIE",
"Type",
"SYNONYMS",
"rdfs:isDefinedBy",
"SUBCLASSES",
"SubClass Of",
"SubProperty Of",
Expand All @@ -153,8 +174,7 @@ public void testExportNamedHeadingsSimple() throws Exception {
Workbook wb = t.asWorkbook("|");

Sheet s = wb.getSheetAt(0);
// There should be three rows (0, 1, 2)
assert (s.getLastRowNum() == 3);
assertEquals(s.getLastRowNum(), 4);

// Validate header
// should match size and label
Expand All @@ -176,6 +196,11 @@ public void testExportNamedHeadingsSimple() throws Exception {
String expectedHeader = columns.get(colIx);
assert (foundHeader.equals(expectedHeader));
}

// rdfs:isDefinedBy should work
assertEquals(
s.getRow(4).getCell(6).getStringCellValue(),
"https://github.com/ontodev/robot/robot-core/src/test/resources/simple.owl");
}

/**
Expand Down
0