[SBML] Add patch to add missing function to C API (#5147)

S/SBML/build_tarballs.jl

@@ -13,9 +13,14 @@ sources = [
 script = raw"""
 cd ${WORKSPACE}/srcdir/libsbml-*
 
+# https://github.com/sbmlteam/libsbml/pull/225
 atomic_patch -p1 ../patches/0001-User-lowercase-name-for-Windows-library.patch
+# https://github.com/sbmlteam/libsbml/pull/235
 atomic_patch -p1 ../patches/0002-Add-SBMLNamespaces_addPackageNamespace-s-functions-t.patch
+# https://github.com/sbmlteam/libsbml/pull/237
 atomic_patch -p1 ../patches/0003-Fix-signature-of-SBase_getNumPlugins-in-prototype.patch
+# https://github.com/sbmlteam/libsbml/pull/247
+atomic_patch -p1 ../patches/0004-add-FbcReactionPlugin_createGeneProductAssociation-to-C-API.patch
 
 mkdir build
 cd build

S/SBML/bundled/patches/0004-add-FbcReactionPlugin_createGeneProductAssociation-to-C-API.patch

@@ -0,0 +1,53 @@
+From 3463655e23a15c6f55e028dce631b7791763abb9 Mon Sep 17 00:00:00 2001
+From: Mirek Kratochvil <miroslav.kratochvil@uni.lu>
+Date: Thu, 14 Jul 2022 11:34:34 +0200
+Subject: [PATCH] add FbcReactionPlugin_createGeneProductAssociation to C API
+
+---
+ .../packages/fbc/extension/FbcReactionPlugin.cpp   |  7 +++++++
+ .../packages/fbc/extension/FbcReactionPlugin.h     | 14 ++++++++++++++
+ 2 files changed, 21 insertions(+)
+
+diff --git a/src/sbml/packages/fbc/extension/FbcReactionPlugin.cpp b/src/sbml/packages/fbc/extension/FbcReactionPlugin.cpp
+index 19924171d..32f188982 100644
+--- a/src/sbml/packages/fbc/extension/FbcReactionPlugin.cpp
++++ b/src/sbml/packages/fbc/extension/FbcReactionPlugin.cpp
+@@ -994,6 +994,13 @@ FbcReactionPlugin::accept(SBMLVisitor& v) const
+ #endif /* __cplusplus */
+
+
++LIBSBML_EXTERN
++GeneProductAssociation_t *
++FbcReactionPlugin_createGeneProductAssociation(FbcSBasePlugin_t * fbc)
++{
++  return  (fbc != NULL) ? static_cast<FbcReactionPlugin*>(fbc)->createGeneProductAssociation() : NULL;
++}
++
+ LIBSBML_EXTERN
+ char *
+ FbcReactionPlugin_getUpperFluxBound(FbcSBasePlugin_t * fbc)
+diff --git a/src/sbml/packages/fbc/extension/FbcReactionPlugin.h b/src/sbml/packages/fbc/extension/FbcReactionPlugin.h
+index 4a15cc82b..bdc45c72f 100644
+--- a/src/sbml/packages/fbc/extension/FbcReactionPlugin.h
++++ b/src/sbml/packages/fbc/extension/FbcReactionPlugin.h
+@@ -722,6 +722,20 @@ BEGIN_C_DECLS
+
+
+
++/**
++ * Creates a new GeneProductAssociation_t object and adds it to the FbcReactionPlugin_t object.
++ *
++ * @param fbc the FbcReactionPlugin_t that should have the GeneProductAssociation_t added
++ *
++ * @copydetails doc_note_geneproduct_v2_only
++ *
++ * @return pointer to the newly created GeneProductAssociation_t object.
++ */
++LIBSBML_EXTERN
++GeneProductAssociation_t*
++FbcReactionPlugin_createGeneProductAssociation(FbcSBasePlugin_t * fbc);
++
++
+ /**
+  * Takes a FbcReactionPlugin_t structure and returns its "upperFluxBound" attribute.
+  *