use addXHTMLMarkup option on setNotes() to reduce dependence on str_t…

…o_xmlstr
KarrLab · Nov 10, 2017 · 5f4fa1d · 5f4fa1d
1 parent a4c5c48
commit 5f4fa1d
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/wc_lang/core.py b/wc_lang/core.py
@@ -964,7 +964,7 @@ def add_to_sbml_doc(self, sbml_document):
         wrap_libsbml(sbml_compartment.setSize, self.initial_volume)
         wrap_libsbml(sbml_compartment.setConstant, False)
         if self.comments:
-            wrap_libsbml(sbml_compartment.appendNotes, str_to_xmlstr(self.comments))
+            wrap_libsbml(sbml_compartment.setNotes, self.comments, True)
         return sbml_compartment
 
 
@@ -1175,7 +1175,7 @@ def add_to_sbml_doc(self, sbml_document):
         # add some SpeciesType data
         wrap_libsbml(sbml_species.setName, self.species_type.name)
         if self.species_type.comments:
-            wrap_libsbml(sbml_species.appendNotes, str_to_xmlstr(self.species_type.comments))
+            wrap_libsbml(sbml_species.setNotes, self.species_type.comments, True)
 
         # set Compartment, which must already be in the SBML document
         wrap_libsbml(sbml_species.setCompartment, self.compartment.id)
@@ -1290,7 +1290,7 @@ def add_to_sbml_doc(self, sbml_document):
         wrap_libsbml(sbml_reaction.setFast, False)
         wrap_libsbml(sbml_reaction.setCompartment, self.submodel.compartment.id)
         if self.comments:
-            wrap_libsbml(sbml_reaction.appendNotes, str_to_xmlstr(self.comments))
+            wrap_libsbml(sbml_reaction.setNotes, self.comments, True)
 
         # write reaction participants to SBML document
         for participant in self.participants:
@@ -1680,7 +1680,7 @@ def add_to_sbml_doc(self, sbml_document):
         wrap_libsbml(sbml_reaction.setReversible, False)
         wrap_libsbml(sbml_reaction.setFast, False)
         if self.comments:
-            wrap_libsbml(sbml_reaction.appendNotes, str_to_xmlstr(self.comments))
+            wrap_libsbml(sbml_reaction.setNotes, self.comments, True)
 
         # write biomass reaction participants to SBML document
         for biomass_component in self.biomass_components:

diff --git a/wc_lang/sbml/util.py b/wc_lang/sbml/util.py
@@ -206,9 +206,11 @@ def wrap_libsbml(method, *args, **kwargs):
     returns_int = False
     if 'returns_int' in kwargs:
         returns_int = kwargs['returns_int']
+        del kwargs['returns_int']
     debug = False
     if 'debug' in kwargs:
         debug = kwargs['debug']
+        del kwargs['debug']
 
     # warn about unused kwargs
     for k in kwargs.keys():