From 6cebcefb15dab1d4f80bedff4e73ab98a9415885 Mon Sep 17 00:00:00 2001
From: dyrpsf <dyrpsf@gmail.com>
Date: Sat, 27 Jun 2026 15:49:53 +0530
Subject: [PATCH 1/3] Fix #354: Remove empty RDF Description nodes after
 unsetModifiedDates

---
 src/sbml/SBase.cpp | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/src/sbml/SBase.cpp b/src/sbml/SBase.cpp
index 081e5b9988..e1a643368c 100644
--- a/src/sbml/SBase.cpp
+++ b/src/sbml/SBase.cpp
@@ -6470,6 +6470,32 @@ SBase::reconstructRDFAnnotation()
    }
 }
 
+if (mAnnotation != NULL)
+  {
+    int rdfIndex = mAnnotation->getIndex("RDF");
+    if (rdfIndex >= 0)
+    {
+      XMLNode& rdfNode = mAnnotation->getChild((unsigned int)rdfIndex);
+      
+      // Iterate backwards since we are removing items from the list
+      for (int i = (int)rdfNode.getNumChildren() - 1; i >= 0; i--)
+      {
+        XMLNode& child = rdfNode.getChild((unsigned int)i);
+        
+        // If the Description node has no inner children, delete it
+        if (child.getName() == "Description" && child.getNumChildren() == 0)
+        {
+          delete rdfNode.removeChild((unsigned int)i);
+        }
+      }
+      
+      // If the RDF node itself is now completely empty, delete it as well
+      if (rdfNode.getNumChildren() == 0)
+      {
+        delete mAnnotation->removeChild((unsigned int)rdfIndex);
+      }
+    }
+  }
 
   if (history != NULL) delete history;
   if (cvTerms != NULL) delete cvTerms;

From bc0e4c41c7b445655d18f9933d0ec876082fb926 Mon Sep 17 00:00:00 2001
From: dyrpsf <dyrpsf@gmail.com>
Date: Sat, 27 Jun 2026 16:05:55 +0530
Subject: [PATCH 2/3] Add unit test for unsetModifiedDates (Issue #354)

---
 src/sbml/test/TestSBase.cpp | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/src/sbml/test/TestSBase.cpp b/src/sbml/test/TestSBase.cpp
index 2efd046fc1..0c015d5106 100644
--- a/src/sbml/test/TestSBase.cpp
+++ b/src/sbml/test/TestSBase.cpp
@@ -2654,6 +2654,35 @@ START_TEST(test_SBase_userData1)
 }
 END_TEST
 
+START_TEST (test_SBase_unsetModifiedDates_issue354)
+{
+  Model* m = new Model(3, 2);
+  m->setMetaId("foo");
+  
+  ModelHistory* h = new ModelHistory();
+  Date* d = new Date("2019-07-29T10:53:09Z");
+  h->addModifiedDate(d);
+  
+  m->setModelHistory(h);
+  
+  // Ensure the date was successfully added
+  fail_unless(m->getNumModifiedDates() == 1);
+  
+  // Unset the dates (This triggers the new cleanup logic we wrote in SBase.cpp)
+  m->unsetModifiedDates();
+  
+  // Force the annotation to sync and generate the XML string
+  std::string annotation = m->getAnnotationString();
+  
+  // Assert that the empty Description detritus was completely removed
+  size_t found = annotation.find("<rdf:Description rdf:about=\"#foo\"/>");
+  fail_unless(found == std::string::npos);
+  
+  delete d;
+  delete m;
+}
+END_TEST
+
 Suite *
 create_suite_SBase (void)
 {
@@ -2709,6 +2738,7 @@ create_suite_SBase (void)
   tcase_add_test(tcase, test_SBase_userData1);
 
   tcase_add_test(tcase, test_SBase_prefixMetaIdSBO);
+  tcase_add_test(tcase, test_SBase_unsetModifiedDates_issue354);
 
   suite_add_tcase(suite, tcase);
 

From 83599287b8aa13c081831e75b0ce6f9b5213f2e1 Mon Sep 17 00:00:00 2001
From: dyrpsf <dyrpsf@gmail.com>
Date: Tue, 30 Jun 2026 10:11:13 +0530
Subject: [PATCH 3/3] Apply fix for issue #354

---
 src/sbml/SBase.cpp          |  4 ----
 src/sbml/test/TestSBase.cpp | 13 ++++++-------
 2 files changed, 6 insertions(+), 11 deletions(-)

diff --git a/src/sbml/SBase.cpp b/src/sbml/SBase.cpp
index e1a643368c..4b8b1dafba 100644
--- a/src/sbml/SBase.cpp
+++ b/src/sbml/SBase.cpp
@@ -6477,19 +6477,15 @@ if (mAnnotation != NULL)
     {
       XMLNode& rdfNode = mAnnotation->getChild((unsigned int)rdfIndex);
       
-      // Iterate backwards since we are removing items from the list
       for (int i = (int)rdfNode.getNumChildren() - 1; i >= 0; i--)
       {
         XMLNode& child = rdfNode.getChild((unsigned int)i);
-        
-        // If the Description node has no inner children, delete it
         if (child.getName() == "Description" && child.getNumChildren() == 0)
         {
           delete rdfNode.removeChild((unsigned int)i);
         }
       }
       
-      // If the RDF node itself is now completely empty, delete it as well
       if (rdfNode.getNumChildren() == 0)
       {
         delete mAnnotation->removeChild((unsigned int)rdfIndex);
diff --git a/src/sbml/test/TestSBase.cpp b/src/sbml/test/TestSBase.cpp
index 0c015d5106..89786909e5 100644
--- a/src/sbml/test/TestSBase.cpp
+++ b/src/sbml/test/TestSBase.cpp
@@ -2665,20 +2665,19 @@ START_TEST (test_SBase_unsetModifiedDates_issue354)
   
   m->setModelHistory(h);
   
-  // Ensure the date was successfully added
-  fail_unless(m->getNumModifiedDates() == 1);
+  fail_unless(m->getModelHistory()->getNumModifiedDates() == 1);
   
-  // Unset the dates (This triggers the new cleanup logic we wrote in SBase.cpp)
-  m->unsetModifiedDates();
+  ModelHistory* h_ref = m->getModelHistory();
+  h_ref->unsetModifiedDates();
+  m->setModelHistory(h_ref); 
   
-  // Force the annotation to sync and generate the XML string
   std::string annotation = m->getAnnotationString();
   
-  // Assert that the empty Description detritus was completely removed
-  size_t found = annotation.find("<rdf:Description rdf:about=\"#foo\"/>");
+  size_t found = annotation.find("rdf:about=\"#foo\"");
   fail_unless(found == std::string::npos);
   
   delete d;
+  delete h;
   delete m;
 }
 END_TEST