sbmlteam · skeating · Dec 24, 2025 · Dec 28, 2025 · Dec 28, 2025
diff --git a/src/sbml/conversion/SBMLRateRuleConverter.cpp b/src/sbml/conversion/SBMLRateRuleConverter.cpp
@@ -414,10 +414,15 @@ SBMLRateRuleConverter::isDocumentAppropriate(OperationReturnValues_t& returnValu
 
   if (mModel->getNumCompartments() > 1)
   {
-      mDocument->getErrorLog()->logError(ModelContainsMultipleCompartments, mDocument->getLevel(),
-          mDocument->getVersion(), "There are multiple compartments.");
-      returnValue = LIBSBML_OPERATION_FAILED;
-      return false;
+      if (speciesFromMultipleCompartmentsInSameRateRule())
+      {
+          mDocument->getErrorLog()->logError(ModelContainsMultipleCompartments, mDocument->getLevel(),
+              mDocument->getVersion(), "There are multiple compartments with species in the same rate rule.");
+          returnValue = LIBSBML_OPERATION_FAILED;
+          return false;
+      }
+      returnValue = LIBSBML_OPERATION_SUCCESS;
+      return true;
   }
 
   // 3. the document is invalid
@@ -434,6 +439,96 @@ SBMLRateRuleConverter::isDocumentAppropriate(OperationReturnValues_t& returnValu
 
 /** @cond doxygenIgnored */
 
+bool 
+SBMLRateRuleConverter::speciesFromMultipleCompartmentsInSameRateRule()
+{
+    listPairString compartmentSpeciesPairs = getCompartmentSpeciesPairs();
+    listPairString variablesRateRulePairs = getVariablesRateRulePairs();
+    for (listPairStringIt it_c = compartmentSpeciesPairs.begin(); 
+        it_c != compartmentSpeciesPairs.end(); ++it_c)
+    {
+        for (listPairStringIt it_r = variablesRateRulePairs.begin();
+            it_r != variablesRateRulePairs.end(); ++it_r)
+        {
+            if (it_c->second == it_r->second)
+            {
+                // species from compartment it_c->first is a participant in a rule it_r
+                std::string ruleVar = it_r->first;
+                std::string compartmentId = it_c->first;
+
+                // check that the variable for this rule is in a same compartment
+                for (listPairStringIt it_c1 = compartmentSpeciesPairs.begin();
+                    it_c1 != compartmentSpeciesPairs.end(); ++it_c1)
+                {
+                    if (it_c1 == it_c)
+                    {
+                        // skip the pair we have already considered
+                        continue;
+                    }
+                    if (it_c1->second == ruleVar)
+                    {
+                        if (it_c1->first != compartmentId)
+                        {
+                            // variable in different compartment
+                            return true;
+                        }
+                    }
+                }
+            }
+        }
+    }
+  return false;
+}
+
+listPairString 
+SBMLRateRuleConverter::getCompartmentSpeciesPairs()
+{
+  listPairString compartmentSpeciesPairs;
+  for (unsigned int n = 0; n < mDocument->getModel()->getNumCompartments(); n++)
+  {
+    Compartment* comp = mDocument->getModel()->getCompartment(n);
+    std::string compId = comp->getId();
+    for (unsigned int m = 0; m < mDocument->getModel()->getNumSpecies(); m++)
+    {
+      Species* spec = mDocument->getModel()->getSpecies(m);
+      if (spec->getCompartment() != compId)
+      {
+        continue;
+      }
+      pairString pair(comp->getId(), spec->getId());
+      compartmentSpeciesPairs.push_back(pair);
+    }
+  }
+
+  return compartmentSpeciesPairs;
+}
+
+listPairString 
+SBMLRateRuleConverter::getVariablesRateRulePairs()
+{
+  listPairString variablesRateRulePairs;
+  for (unsigned int n = 0; n < mDocument->getModel()->getNumRules(); n++)
+  {
+      Rule* rule = mDocument->getModel()->getRule(n);
+      if (rule->getType() != RULE_TYPE_RATE)
+      {
+          continue;
+      }
+      std::string varId = rule->getVariable();
+      const ASTNode* math = rule->getMath();
+      List* variables = math->getListOfNodes(ASTNode_isName);
+      for (ListIterator it = variables->begin(); it != variables->end(); ++it)
+      {
+          ASTNode* m = static_cast<ASTNode*>(*it);
+          std::string mId = m->getName();
+          pairString pair(varId, mId);
+          variablesRateRulePairs.push_back(pair);
+      }
+  }
+  return variablesRateRulePairs;
+}
+
+
 void 
 SBMLRateRuleConverter::addODEPair(std::string id, Model* model)
 {

diff --git a/src/sbml/conversion/SBMLRateRuleConverter.h b/src/sbml/conversion/SBMLRateRuleConverter.h
@@ -83,6 +83,8 @@ typedef std::vector<pairCoeff > setCoeff;
 typedef std::vector<std::pair<ASTNode*, std::vector<double> > >::iterator setCoeffIt;
 
 typedef std::pair<std::string, std::string > pairString;
+typedef std::vector< pairString > listPairString;
+typedef std::vector< pairString >::iterator listPairStringIt;
 typedef std::vector< std::vector<double> > setRnCoeffs;
 
 
@@ -227,6 +229,12 @@ class LIBSBML_EXTERN SBMLRateRuleConverter : public SBMLConverter
 
   bool useStoichiometryFromMath();
 
+  // functions to deal with multiple compartments
+  bool speciesFromMultipleCompartmentsInSameRateRule();
+
+  listPairString getCompartmentSpeciesPairs();
+
+  listPairString getVariablesRateRulePairs();
 
   // functions for populateODEinfo()
 

diff --git a/src/sbml/conversion/test/TestSBMLRateRuleConverter.cpp b/src/sbml/conversion/test/TestSBMLRateRuleConverter.cpp
@@ -1113,7 +1113,7 @@ START_TEST(test_converter_errors_3)
 	delete d;
 }
 END_TEST
-START_TEST(test_converter_errors_4)
+ START_TEST(test_converter_errors_4)
 {
 	std::string raterule_file(TestDataDirectory);
 	raterule_file += "rn_rr_fail_90104.xml";
@@ -1134,6 +1134,62 @@ START_TEST(test_converter_errors_4)
 	delete d;
 }
 END_TEST
+START_TEST(test_converter_errors_5)
+{
+	std::string raterule_file(TestDataDirectory);
+	raterule_file += "rn_rr_pass_90104.xml";
+
+	SBMLDocument* d = readSBMLFromFile(raterule_file.c_str());
+
+	rule_rn_props.addOption("useStoichiometryFromMath", true);
+	rule_rn_converter->setProperties(&rule_rn_props);
+
+
+	rule_rn_converter->setDocument(d);
+	int ret = rule_rn_converter->convert();
+	fail_unless(ret == LIBSBML_OPERATION_SUCCESS);
+	fail_unless(d->getNumErrors() == 0);
+
+	delete d;
+}
+END_TEST
+
+START_TEST(test_converter_errors_6)
+{
+	std::string raterule_file(TestDataDirectory);
+	raterule_file += "rn_rr_fail_90104_1.xml";
+
+	SBMLDocument* d = readSBMLFromFile(raterule_file.c_str());
+
+	rule_rn_props.addOption("useStoichiometryFromMath", true);
+	rule_rn_converter->setProperties(&rule_rn_props);
+
+
+	rule_rn_converter->setDocument(d);
+	int ret = rule_rn_converter->convert();
+	fail_unless(ret == LIBSBML_OPERATION_FAILED);
+	fail_unless(d->getNumErrors() == 1);
+	fail_unless(d->getError(0)->getErrorId() == 90104);
+	fail_unless(d->getError(0)->getCategory() == LIBSBML_CAT_RATE_RULE_CONVERSION);
+
+	delete d;
+}
+END_TEST
+
+
+START_TEST(test_rule_reaction_multi_compartment)
+{
+	std::string raterule_file(TestDataDirectory);
+	raterule_file += "rr_rn_multi_compartments.xml";
+
+	std::string reaction_file(TestDataDirectory);
+	reaction_file += "rr_rn_multi_compartments_reactions.xml";
+
+	bool result = test_rule_to_reaction(raterule_file, reaction_file);
+
+	fail_unless(result == true);
+}
+END_TEST
 
 Suite *
 create_suite_TestSBMLRateRuleConverter (void)
@@ -1143,10 +1199,10 @@ Suite *suite = suite_create("SBMLRateRuleConverter");
   TCase *tcase = tcase_create("SBMLRateRuleConverter");
   tcase_add_checked_fixture(tcase, RateRuleConverter_setup,
 	  RateRuleConverter_teardown);
-
+  
   if (testing)
   {
-	  tcase_add_test(tcase, test_rule_reaction_07);
+	  tcase_add_test(tcase, test_converter_errors_6);
   }
   else
   {
@@ -1184,6 +1240,9 @@ Suite *suite = suite_create("SBMLRateRuleConverter");
 	  tcase_add_test(tcase, test_converter_errors_2);
 	  tcase_add_test(tcase, test_converter_errors_3);
 	  tcase_add_test(tcase, test_converter_errors_4);
+	  tcase_add_test(tcase, test_converter_errors_5);
+	  tcase_add_test(tcase, test_converter_errors_6);
+	  tcase_add_test(tcase, test_rule_reaction_multi_compartment);
 
 
 

diff --git a/src/sbml/conversion/test/test-data/rn_rr_fail_90104.xml b/src/sbml/conversion/test/test-data/rn_rr_fail_90104.xml
@@ -6,29 +6,21 @@
       <compartment id="compartmentTwo" spatialDimensions="3" size="1" constant="true"/>
     </listOfCompartments>
     <listOfSpecies>
-      <species id="y_1" name="y_1" compartment="compartmentOne" initialConcentration="2" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="y_1" name="y_1" compartment="compartmentOne" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="y_2" name="y_2" compartment="compartmentTwo" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="y_3" compartment="compartmentTwo" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
     </listOfSpecies>
-    <listOfParameters>
-      <parameter id="a" name="a" value="0.5" constant="true"/>
-      <parameter id="b" name="b" constant="false"/>
-      <parameter id="t" name="t" value="0" constant="false"/>
-    </listOfParameters>
     <listOfRules>
-      <rateRule variable="b">
+      <rateRule variable="y_1">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <times/>
-            <cn> 2 </cn>
-            <ci> t </ci>
-          </apply>
+          <ci> y_3 </ci>
         </math>
       </rateRule>
-      <assignmentRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
+      <rateRule variable="y_2">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">    
+          <cn> 22 </cn>
         </math>
-      </assignmentRule>
-    </listOfRules>
-
+      </rateRule>
+    </listOfRules>  
   </model>
 </sbml>
diff --git a/src/sbml/conversion/test/test-data/rn_rr_fail_90104_1.xml b/src/sbml/conversion/test/test-data/rn_rr_fail_90104_1.xml
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+  <model>
+    <listOfCompartments>
+      <compartment id="compartmentOne" spatialDimensions="3" size="1" constant="true"/>
+      <compartment id="compartmentTwo" spatialDimensions="3" size="1" constant="true"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="y_1" name="y_1" compartment="compartmentOne" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="y_2" name="y_2" compartment="compartmentOne" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="y_3" compartment="compartmentTwo" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+    </listOfSpecies>
+    <listOfRules>
+      <rateRule variable="y_1">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <apply>
+            <plus/>
+            <ci> y_2 </ci>
+            <ci> y_3 </ci>
+          </apply>
+        </math>
+      </rateRule>
+    </listOfRules>  
+  </model>
+</sbml>
diff --git a/src/sbml/conversion/test/test-data/rn_rr_pass_90104.xml b/src/sbml/conversion/test/test-data/rn_rr_pass_90104.xml
@@ -0,0 +1,34 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+  <model>
+    <listOfCompartments>
+      <compartment id="compartmentOne" spatialDimensions="3" size="1" constant="true"/>
+      <compartment id="compartmentTwo" spatialDimensions="3" size="1" constant="true"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="y_1" name="y_1" compartment="compartmentOne" initialConcentration="2" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="a" name="a" value="0.5" constant="true"/>
+      <parameter id="b" name="b" constant="false"/>
+      <parameter id="t" name="t" value="0" constant="false"/>
+    </listOfParameters>
+    <listOfRules>
+      <rateRule variable="b">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <apply>
+            <times/>
+            <cn> 2 </cn>
+            <ci> t </ci>
+          </apply>
+        </math>
+      </rateRule>
+      <assignmentRule variable="t">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
+        </math>
+      </assignmentRule>
+    </listOfRules>
+
+  </model>
+</sbml>
diff --git a/src/sbml/conversion/test/test-data/rr_rn_multi_compartments.xml b/src/sbml/conversion/test/test-data/rr_rn_multi_compartments.xml
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+  <model>
+    <listOfCompartments>
+      <compartment id="compartmentOne" spatialDimensions="3" size="1" constant="true"/>
+      <compartment id="compartmentTwo" spatialDimensions="3" size="1" constant="true"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="y_1" name="y_1" compartment="compartmentOne" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="y_2" name="y_2" compartment="compartmentTwo" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+    </listOfSpecies>
+    <listOfRules>
+      <rateRule variable="y_1">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <cn> 11 </cn>
+        </math>
+      </rateRule>
+      <rateRule variable="y_2">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">    
+          <cn> 22 </cn>
+        </math>
+      </rateRule>
+    </listOfRules>  
+  </model>
+</sbml>
diff --git a/src/sbml/conversion/test/test-data/rr_rn_multi_compartments_reactions.xml b/src/sbml/conversion/test/test-data/rr_rn_multi_compartments_reactions.xml
@@ -0,0 +1,35 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+  <model>
+    <listOfCompartments>
+      <compartment id="compartmentOne" spatialDimensions="3" size="1" constant="true"/>
+      <compartment id="compartmentTwo" spatialDimensions="3" size="1" constant="true"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="y_1" name="y_1" compartment="compartmentOne" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="y_2" name="y_2" compartment="compartmentTwo" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+    </listOfSpecies>
+    <listOfReactions>
+      <reaction id="J1" reversible="false" fast="false">
+        <listOfProducts>
+          <speciesReference species="y_1" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <cn> 11 </cn>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction id="J2" reversible="false" fast="false">
+        <listOfProducts>
+          <speciesReference species="y_2" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <cn> 22 </cn>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>