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sbmlteam · Sep 17, 2024 · 9370f2b · 9370f2b
1 parent c19d5b0
commit 9370f2b
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Showing 11 changed files with 1,112 additions and 998 deletions.
diff --git a/src/sbml/conversion/ExpressionAnalyser.cpp b/src/sbml/conversion/ExpressionAnalyser.cpp
diff --git a/src/sbml/conversion/ExpressionAnalyser.h b/src/sbml/conversion/ExpressionAnalyser.h
@@ -79,6 +79,7 @@ typedef enum
 |*/
 struct SubstitutionValues_t {
   std::string k_value;
+  double k_real_value;
   std::string x_value;
   std::string y_value;
   ASTNode * dxdt_expression;
@@ -223,7 +224,7 @@ class LIBSBML_EXTERN ExpressionAnalyser
    * @param node the node to check
    * @return true if the node is a constant number/parameter
    */
-  bool isNumericalConstantOrConstantParameter(ASTNode* node);
+  bool isNumericalConstantOrConstantParameter(ASTNode* node, bool& isNumber);
 
   /*
   * Have we already created a parameter for this expression

diff --git a/src/sbml/conversion/SBMLRateRuleConverter.cpp b/src/sbml/conversion/SBMLRateRuleConverter.cpp
@@ -581,7 +581,8 @@ SBMLRateRuleConverter::determineDerivativeSign(std::string variable, ASTNode* te
   }
   else
   {
-    ASTNode *deriv = term->derivative(variable);
+      ASTNode* deriv = term->derivative(variable);
+
     signDetermined = isPositive(deriv, posDeriv);
     if (!signDetermined)
     {
@@ -617,7 +618,7 @@ SBMLRateRuleConverter::isPositive(const ASTNode* node, bool& posDeriv)
     }
     else
     {
-      if (mDerivSign == NEGATIVE_DERIVATIVE) posDeriv = true;
+      if (mDerivSign == NEGATIVE_DERIVATIVE) posDeriv = false;
     }
     signDetermined = true;
   }

diff --git a/src/sbml/conversion/SBMLRateRuleConverter.h b/src/sbml/conversion/SBMLRateRuleConverter.h
@@ -62,6 +62,7 @@
 #include <sbml/conversion/SBMLConverter.h>
 #include <sbml/conversion/SBMLConverterRegister.h>
 #include <sbml/math/ASTNode.h>
+#include <iostream>
 
 typedef enum
 {
@@ -74,6 +75,7 @@ typedef enum
 
 
 LIBSBML_CPP_NAMESPACE_BEGIN
+
 typedef std::vector< std::pair< std::string, ASTNode*> > pairODEs;
 
 class LIBSBML_EXTERN SBMLRateRuleConverter : public SBMLConverter

diff --git a/src/sbml/conversion/test/TestSBMLRateRuleConverter.cpp b/src/sbml/conversion/test/TestSBMLRateRuleConverter.cpp
@@ -937,6 +937,98 @@ START_TEST(test_model_valid_52)
 }
 END_TEST
 
+START_TEST(test_model_valid_53)
+{
+	ConversionProperties props;
+	props.addOption("inferReactions", true);
+
+	SBMLConverter* converter = new SBMLRateRuleConverter();
+	converter->setProperties(&props);
+
+	std::string filename(TestDataDirectory);
+	filename += "valid_53_rr.xml";
+	std::string filename1(TestDataDirectory);
+	filename1 += "valid_53_bio.xml";
+
+	SBMLDocument* d = readSBMLFromFile(filename.c_str());
+
+	converter->setDocument(d);
+	fail_unless(converter->convert() == LIBSBML_OPERATION_SUCCESS);
+
+	SBMLDocument* d1 = readSBMLFromFile(filename1.c_str());
+	std::string out = writeSBMLToStdString(d);
+	std::string expected = writeSBMLToStdString(d1);
+
+	fail_unless(equals(expected.c_str(), out.c_str()));
+
+	delete converter;
+	delete d;
+	delete d1;
+}
+END_TEST
+
+START_TEST(test_model_valid_54)
+{
+	ConversionProperties props;
+	props.addOption("inferReactions", true);
+
+	SBMLConverter* converter = new SBMLRateRuleConverter();
+	converter->setProperties(&props);
+
+	std::string filename(TestDataDirectory);
+	filename += "valid_54_rr.xml";
+	std::string filename1(TestDataDirectory);
+	filename1 += "valid_54_bio.xml";
+
+	SBMLDocument* d = readSBMLFromFile(filename.c_str());
+
+	converter->setDocument(d);
+	fail_unless(converter->convert() == LIBSBML_OPERATION_SUCCESS);
+
+	SBMLDocument* d1 = readSBMLFromFile(filename1.c_str());
+	std::string out = writeSBMLToStdString(d);
+	std::string expected = writeSBMLToStdString(d1);
+
+	fail_unless(equals(expected.c_str(), out.c_str()));
+
+	delete converter;
+	delete d;
+	delete d1;
+}
+END_TEST
+
+
+START_TEST(test_model_valid_55)
+{
+	ConversionProperties props;
+	props.addOption("inferReactions", true);
+
+	SBMLConverter* converter = new SBMLRateRuleConverter();
+	converter->setProperties(&props);
+
+	std::string filename(TestDataDirectory);
+	filename += "valid_55_rr.xml";
+	std::string filename1(TestDataDirectory);
+	filename1 += "valid_55_bio.xml";
+
+	SBMLDocument* d = readSBMLFromFile(filename.c_str());
+
+	converter->setDocument(d);
+	fail_unless(converter->convert() == LIBSBML_OPERATION_SUCCESS);
+
+	SBMLDocument* d1 = readSBMLFromFile(filename1.c_str());
+	std::string out = writeSBMLToStdString(d);
+	std::string expected = writeSBMLToStdString(d1);
+
+	fail_unless(equals(expected.c_str(), out.c_str()));
+
+	delete converter;
+	delete d;
+	delete d1;
+}
+END_TEST
+
+
 Suite *
 create_suite_TestSBMLRateRuleConverter (void)
 { 
@@ -955,15 +1047,16 @@ create_suite_TestSBMLRateRuleConverter (void)
 //   tcase_add_test(tcase, test_model4);
 //   tcase_add_test(tcase, test_model5);
 //   tcase_add_test(tcase, test_model6);
-// tcase_add_test(tcase, test_model_valid_01); // this one works
+//   tcase_add_test(tcase, test_model_valid_01); // this one works
 //  tcase_add_test(tcase, test_model_valid_02);	// this one works
-//  tcase_add_test(tcase, test_model_valid_03);	// this one replaces the kinetic law'b' with the assignment rule for b
+// tcase_add_test(tcase, test_model_valid_03);	// this one replaces the kinetic law'b' with the assignment rule for b
 //  tcase_add_test(tcase, test_model_valid_04);	// this one works
-  tcase_add_test(tcase, test_model_valid_05);	// this one works
-  //tcase_add_test(tcase, test_model_valid_51);	// this one works although puts the kinetic law in a different order
+//   tcase_add_test(tcase, test_model_valid_05);	// this one works
+//   tcase_add_test(tcase, test_model_valid_51);	// this one works
 // tcase_add_test(tcase, test_model_valid_52);	// this one works although puts the kinetic law in a different order
-
-
+//  tcase_add_test(tcase, test_model_valid_53);	// this one has hidden species that I'm not picked up
+//tcase_add_test(tcase, test_model_valid_54);	//
+  tcase_add_test(tcase, test_model_valid_55);	// 
 
   suite_add_tcase(suite, tcase);