From afeb81a3f94d9779277bc1815fb45e2fdb81c1fb Mon Sep 17 00:00:00 2001
From: Silvio Waschina <s.waschina@nutrinf.uni-kiel.de>
Date: Fri, 6 Dec 2024 16:10:31 +0100
Subject: [PATCH] Enable reading SBML level 2 models and models with FBC v1

Fixes #11
---
 src/SBML.cpp | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/src/SBML.cpp b/src/SBML.cpp
index 34eaf26..dcb33b2 100644
--- a/src/SBML.cpp
+++ b/src/SBML.cpp
@@ -7,6 +7,7 @@
 #include <sbml/packages/groups/common/GroupsExtensionTypes.h>
 #include <sbml/xml/XMLNode.h>
 #include <sbml/annotation/CVTerm.h>
+#include <sbml/conversion/ConversionProperties.h>
 // [[Rcpp::depends(RcppArmadillo)]]
 
 using namespace Rcpp;
@@ -34,6 +35,35 @@ SEXP readSBMLfile(std::string file_path) {
     Rcpp::stop("Error reading SBML document.");
   }
 
+  // Convert SBML Level 2 to SBML Level 3 with FBC extension
+  if(document->getLevel() == 2) {
+    std::cout << "Converting COBRA-style SBML Level 2 model to SBML Level 3 using the Flux Balance Constraints (FBC)." << std::endl;
+
+    ConversionProperties props;
+    props.addOption("convert cobra", true, "Convert Cobra model to FBC");
+    int result = document->convert(props);
+
+    if (result != LIBSBML_OPERATION_SUCCESS) {
+      std::cout<< "SBML level conversion failed ... " << std::endl;
+      exit(0);
+    }
+  }
+
+  // Convert FBC v1 to FBC v2
+  FbcSBMLDocumentPlugin* dplugin = static_cast<FbcSBMLDocumentPlugin*>(document->getPlugin("fbc"));
+  if(dplugin->getPackageVersion() == 1) {
+    std::cout << "Converting FBC V1 to FBC V2." << std::endl;
+
+    ConversionProperties propsFBC;
+    propsFBC.addOption("convert fbc v1 to fbc v2");
+    int result = document->convert(propsFBC);
+
+    if (result != LIBSBML_OPERATION_SUCCESS) {
+      std::cout<< "FBC conversion failed ... " << std::endl;
+      exit(0);
+    }
+  }
+
   return Rcpp::XPtr<SBMLDocument>(document, false);
 }