From 903f1812c5415615726465ce8eff87926c193f06 Mon Sep 17 00:00:00 2001
From: Melissa Linkert <melissa@glencoesoftware.com>
Date: Tue, 9 Dec 2025 10:34:25 -0600
Subject: [PATCH] Add some tests for reference handling and MetadataConverter

---
 .../java/ome/xml/utests/ReferenceTest.java    | 119 ++++++++++++++++++
 1 file changed, 119 insertions(+)
 create mode 100644 ome-xml/src/test/java/ome/xml/utests/ReferenceTest.java

diff --git a/ome-xml/src/test/java/ome/xml/utests/ReferenceTest.java b/ome-xml/src/test/java/ome/xml/utests/ReferenceTest.java
new file mode 100644
index 000000000..599df5140
--- /dev/null
+++ b/ome-xml/src/test/java/ome/xml/utests/ReferenceTest.java
@@ -0,0 +1,119 @@
+/*
+ * #%L
+ * OME XML library
+ * %%
+ * Copyright (C) 2006 - 2025 Open Microscopy Environment:
+ *   - Massachusetts Institute of Technology
+ *   - National Institutes of Health
+ *   - University of Dundee
+ *   - Board of Regents of the University of Wisconsin-Madison
+ *   - Glencoe Software, Inc.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package ome.xml.utests;
+
+import static org.testng.AssertJUnit.*;
+
+import ome.xml.meta.MetadataConverter;
+import ome.xml.meta.OMEXMLMetadataImpl;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+/**
+ */
+public class ReferenceTest {
+
+  public static final String IMAGE_ID = "Image:0";
+
+  public static final String[] ROI_IDS = {"ROI:0", "ROI:1", "ROI:2"};
+
+  private OMEXMLMetadataImpl metadata;
+
+  @BeforeMethod
+  public void setUp() {
+    metadata = new OMEXMLMetadataImpl();
+    metadata.setImageID(IMAGE_ID, 0);
+
+    for (int i=0; i<ROI_IDS.length; i++) {
+      metadata.setROIID(ROI_IDS[i], i);
+    }
+  }
+
+  @Test
+  public void checkResolvedReferences() {
+    for (int i=0; i<ROI_IDS.length; i++) {
+      metadata.setImageROIRef(ROI_IDS[i], 0, i);
+    }
+    metadata.resolveReferences();
+    OMEXMLMetadataImpl converted = new OMEXMLMetadataImpl();
+    MetadataConverter.convertMetadata(metadata, converted);
+    converted.resolveReferences();
+
+    assertEquals(converted.getImageROIRefCount(0), ROI_IDS.length);
+    for (int i=0; i<ROI_IDS.length; i++) {
+      assertEquals(converted.getImageROIRef(0, i), ROI_IDS[i]);
+    }
+  }
+
+  @Test
+  public void checkAutoReferenceResolution() {
+    for (int i=0; i<ROI_IDS.length; i++) {
+      metadata.setImageROIRef(ROI_IDS[i], 0, i);
+    }
+    OMEXMLMetadataImpl converted = new OMEXMLMetadataImpl();
+    MetadataConverter.convertMetadata(metadata, converted);
+
+    assertEquals(converted.getImageROIRefCount(0), ROI_IDS.length);
+    for (int i=0; i<ROI_IDS.length; i++) {
+      assertEquals(converted.getImageROIRef(0, i), ROI_IDS[i]);
+    }
+  }
+
+  @Test
+  public void checkUpdatedReference() {
+    metadata.setImageROIRef(ROI_IDS[1], 0, 0);
+    metadata.setImageROIRef(ROI_IDS[0], 0, 0);
+
+    OMEXMLMetadataImpl converted = new OMEXMLMetadataImpl();
+    MetadataConverter.convertMetadata(metadata, converted);
+    assertEquals(converted.getImageROIRefCount(0), 1);
+    assertEquals(converted.getImageROIRef(0, 0), ROI_IDS[0]);
+  }
+
+  @Test
+  public void checkReferencesOutOfOrder() {
+    for (int i=0; i<ROI_IDS.length; i++) {
+      metadata.setImageROIRef(ROI_IDS[i], 0, ROI_IDS.length - i - 1);
+    }
+    OMEXMLMetadataImpl converted = new OMEXMLMetadataImpl();
+    MetadataConverter.convertMetadata(metadata, converted);
+    assertEquals(converted.getImageROIRefCount(0), ROI_IDS.length);
+    for (int i=0; i<ROI_IDS.length; i++) {
+      assertEquals(converted.getImageROIRef(0, ROI_IDS.length - i - 1), ROI_IDS[i]);
+    }
+  }
+
+}