added simple examples to test-ghactions.sh

NeuroML · Nov 13, 2023 · c358b2f · c358b2f
1 parent d30e57d
commit c358b2f
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Showing 4 changed files with 52 additions and 2 deletions.
diff --git a/examples/test_data/valid_doc.sbml b/examples/test_data/valid_doc.sbml
@@ -0,0 +1,42 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+  <model substanceUnits="mole" timeUnits="second" extentUnits="mole">
+    <listOfUnitDefinitions>
+      <unitDefinition id="per_second">
+        <listOfUnits>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="c1" spatialDimensions="3" size="1" units="litre" constant="true"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="S1" compartment="c1" initialAmount="5" substanceUnits="mole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="S2" compartment="c1" initialAmount="0" substanceUnits="mole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="k" value="1" units="per_second" constant="true"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction id="r1" reversible="false" fast="false">
+        <listOfReactants>
+          <speciesReference species="S1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="S2" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> k </ci>
+              <ci> S1 </ci>
+              <ci> c1 </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>
diff --git a/pyneuroml/pynml.py b/pyneuroml/pynml.py
@@ -2143,7 +2143,7 @@ def evaluate_arguments(args):
         try:
             result = validate_sbml_files(args.input_files, strict_units)
         except Exception as e:
-            logger.critical(f"validate_sbml_files failed with {e.message}")
+            logger.critical(f"validate_sbml_files failed with {str(e)}")
             sys.exit(UNKNOWN_ERR)
 
         if result:

diff --git a/pyneuroml/sbml/__init__.py b/pyneuroml/sbml/__init__.py
@@ -4,6 +4,7 @@
 """
 
 import os
+import errno
 import libsbml
 from libsbml import SBMLReader
 from typing import List
@@ -25,7 +26,7 @@ def validate_sbml_files(input_files: List[str], strict_units: bool = False) -> b
         # These checks are already implemented by SBMLReader
         # But could just be logged along with the other error types rather than causing exceptions
         if not os.path.isfile(file_name):
-            raise FileNotFoundError(f"Could not find SBML file {file_name}")
+            raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), file_name)
 
         if not os.access(file_name, os.R_OK):
             raise IOError(f"Could not read SBML file {file_name}")

diff --git a/test-ghactions.sh b/test-ghactions.sh
@@ -70,6 +70,13 @@ pynml LEMS_NML2_Ex9_FN.xml -spineml
 pynml LEMS_NML2_Ex9_FN.xml -sbml
 
 
+echo
+echo "################################################"
+echo "##   Simple SBML validation example"
+
+pynml -validate-sbml test_data/valid_doc.sbml
+pynml -validate-sbml-units test_data/valid_doc.sbml
+
 
 echo
 echo "################################################"