Merge branch 'master' into issue_1163

ontodev · Dec 4, 2023 · 04a0052 · 04a0052
2 parents f412fb7 + 182046b
commit 04a0052
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - '--annotate-with-source true' does not work with extract --method subset [#1160]
 - Fix how Template adds entities to the QuotedEntityChecker [#1104]
 - [`merge`] and 'annotate' operations '--annotate-defined-by' excludes reserved OWL 2 vocabularies [#1171]
+- Handle IRIs that are not entities in export [#1168]
 
 ## [1.9.5] - 2023-09-20
 
@@ -382,6 +383,7 @@ First official release of ROBOT!
 [`validate`]: http://robot.obolibrary.org/validate
 
 [#1171]: https://github.com/ontodev/robot/pull/1171
+[#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

diff --git a/robot-core/src/main/java/org/obolibrary/robot/ExportOperation.java b/robot-core/src/main/java/org/obolibrary/robot/ExportOperation.java
@@ -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 {

diff --git a/robot-core/src/test/java/org/obolibrary/robot/ExportOperationTest.java b/robot-core/src/test/java/org/obolibrary/robot/ExportOperationTest.java
@@ -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;
@@ -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.
    *
@@ -121,7 +141,7 @@ public void testLargeExcelExport() throws Exception {
    */
   @Test
   public void testExportNamedHeadingsSimple() throws Exception {
-    OWLOntology ontology = loadOntology("/simple.owl");
+    OWLOntology ontology = loadOntology("/simple_defined_by.owl");
     IOHelper ioHelper = new IOHelper();
     ioHelper.addPrefix(
         "simple", "https://github.com/ontodev/robot/robot-core/src/test/resources/simple.owl#");
@@ -135,6 +155,7 @@ public void testExportNamedHeadingsSimple() throws Exception {
             "CURIE",
             "Type",
             "SYNONYMS",
+            "rdfs:isDefinedBy",
             "SUBCLASSES",
             "SubClass Of",
             "SubProperty Of",
@@ -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
@@ -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");
   }
 
   /**