From 22dd02c6a87470bce651b59a377a6a22ffffcc7a Mon Sep 17 00:00:00 2001
From: dyrpsf <dyrpsf@gmail.com>
Date: Mon, 2 Feb 2026 13:59:16 +0530
Subject: [PATCH] Make offline validation the documented default and add test
 (#246)

---
 core/src/org/sbml/jsbml/SBMLDocument.java     | 14 ++--
 .../test/SBMLDocumentValidationModeTest.java  | 69 +++++++++++++++++++
 2 files changed, 77 insertions(+), 6 deletions(-)
 create mode 100644 core/test/org/sbml/jsbml/test/SBMLDocumentValidationModeTest.java

diff --git a/core/src/org/sbml/jsbml/SBMLDocument.java b/core/src/org/sbml/jsbml/SBMLDocument.java
index e06c33ba4..ba999db87 100644
--- a/core/src/org/sbml/jsbml/SBMLDocument.java
+++ b/core/src/org/sbml/jsbml/SBMLDocument.java
@@ -336,9 +336,9 @@ private void removePackageDeclaration(String packageName) {
    * flag in the individual SBMLError objects returned by
    * {@link SBMLDocument#getError(int)} to determine the nature of the failures.
    * 
-   * <p>The offline validator is not yet as complete as the online one so it is not
-   * currently used by default when calling {@link #checkConsistency()} but it might be
-   * in future versions. To get an up to date status, please check the page 
+   * <p>The offline validator was initially less complete than the online one but
+   * has evolved and is now used by default when calling {@link #checkConsistency()}.
+   * The online validator remains available via {@link #checkConsistencyOnline()}. 
    * <a href="https://github.com/sbmlteam/jsbml/wiki/Offline-validator-status">Offline-validator-status</a>.</p>
    * 
    * @return the number of errors found
@@ -580,9 +580,11 @@ public int checkConsistencyOnline() {
 
   /**
    * Validates the {@link SBMLDocument}.
-   * 
-   * <p> The validation is currently performed using the
-   * SBML.org online validator (http://sbml.org/validator/).</p>
+   *
+   * <p>The validation is currently performed using the JSBML internal
+   * offline validator, see {@link #checkConsistencyOffline()}. The SBML.org
+   * online validator (http://sbml.org/validator/) is still available via
+   * {@link #checkConsistencyOnline()}.</p>
    * 
    * <p>
    * You can control the consistency checks that are performed when
diff --git a/core/test/org/sbml/jsbml/test/SBMLDocumentValidationModeTest.java b/core/test/org/sbml/jsbml/test/SBMLDocumentValidationModeTest.java
new file mode 100644
index 000000000..16fc9fcd8
--- /dev/null
+++ b/core/test/org/sbml/jsbml/test/SBMLDocumentValidationModeTest.java
@@ -0,0 +1,69 @@
+/*
+ * ----------------------------------------------------------------------------
+ * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
+ * for the latest version of JSBML and more information about SBML.
+ *
+ * Copyright (C) 2009-2022 jointly by the following organizations:
+ * 1. The University of Tuebingen, Germany
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ * 3. The California Institute of Technology, Pasadena, CA, USA
+ * 4. The University of California, San Diego, La Jolla, CA, USA
+ * 5. The Babraham Institute, Cambridge, UK
+ * 
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as <http://sbml.org/Software/JSBML/License>.
+ * ----------------------------------------------------------------------------
+ */
+
+package org.sbml.jsbml.test;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import org.junit.Test;
+import org.sbml.jsbml.SBMLDocument;
+
+/**
+ * Tests that {@link SBMLDocument#checkConsistency()} uses the offline
+ * validator by default.
+ */
+public class SBMLDocumentValidationModeTest {
+
+  /**
+   * Small test subclass of {@link SBMLDocument} that records whether the
+   * offline or online validation methods are called.
+   */
+  private static class TestDocument extends SBMLDocument {
+
+    boolean offlineCalled = false;
+    boolean onlineCalled = false;
+
+    @Override
+    public int checkConsistencyOffline() {
+      offlineCalled = true;
+      // return a distinctive value so we can verify it is propagated
+      return 7;
+    }
+
+    @Override
+    public int checkConsistencyOnline() {
+      onlineCalled = true;
+      return 13;
+    }
+  }
+
+  @Test
+  public void checkConsistencyUsesOfflineValidatorByDefault() {
+    TestDocument doc = new TestDocument();
+
+    int result = doc.checkConsistency();
+
+    assertTrue("Offline validator should be used by default.", doc.offlineCalled);
+    assertFalse("Online validator should not be used when calling checkConsistency().", doc.onlineCalled);
+    assertEquals("checkConsistency() should return the offline validator result.", 7, result);
+  }
+}
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