Fixed upper and lower bounds not read correctly

EnzymeML · Apr 28, 2022 · 8486608 · 8486608
1 parent 6785b3f
commit 8486608
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Showing 4 changed files with 9 additions and 3 deletions.
diff --git a/pyenzyme/enzymeml/tools/enzymemlreader.py b/pyenzyme/enzymeml/tools/enzymemlreader.py
@@ -628,6 +628,8 @@ def _parse_parameter(self, parameter, enzmldoc):
         annotation = parameter.getAnnotationString()
         param_dict = self._parseSpeciesAnnotation(annotation)
 
+        print(param_dict)
+
         if unit_id:
             param_dict["unit"] = enzmldoc.getUnitString(unit_id)
 
@@ -645,8 +647,8 @@ def _parse_parameter(self, parameter, enzmldoc):
             unit=param_dict.get("unit"),
             ontology=self._sboterm_to_enum(parameter.getSBOTerm()),
             initial_value=param_dict.get("initial_value"),
-            upper=param_dict.get("upperbound"),
-            lower=param_dict.get("lowerbound"),
+            upper=param_dict.get("upper_bound"),
+            lower=param_dict.get("lower_bound"),
             stdev=param_dict.get("stdev"),
             constant=constant,
         )

diff --git a/tests/fixtures/enzmldoc_object.json b/tests/fixtures/enzmldoc_object.json
@@ -106,7 +106,9 @@
             "value": 10.0,
             "unit": "1 / s",
             "stdev": 0.1,
-            "initial_value": 10.0
+            "initial_value": 10.0,
+            "upper": 11.0,
+            "lower": 9.0
           }
         ]
       },

diff --git a/tests/fixtures/test_case.omex b/tests/fixtures/test_case.omex
diff --git a/tests/fixtures/write_xml_string.xml b/tests/fixtures/write_xml_string.xml
@@ -130,6 +130,8 @@
               <annotation>
                 <enzymeml:parameter xmlns:enzymeml="http://sbml.org/enzymeml/version2">
                   <enzymeml:initialValue>10.0</enzymeml:initialValue>
+                  <enzymeml:upperBound>11.0</enzymeml:upperBound>
+                  <enzymeml:lowerBound>9.0</enzymeml:lowerBound>
                   <enzymeml:stdev>0.1</enzymeml:stdev>
                 </enzymeml:parameter>
               </annotation>