Merge pull request #267 from robertvi/development

Testing sbml

pyneuroml/pynml.py

@@ -345,6 +345,11 @@ def parse_arguments():
         action="store_true",
         help=("(Via jNeuroML) Validate NeuroML file(s) against the\n" "v1.8.1 Schema"),
     )
+    mut_exc_opts.add_argument(
+        "-validate-sbml",
+        action="store_true",
+        help=("Validate SBML file(s)"),
+    )
 
     return parser.parse_args()
 
@@ -2111,6 +2116,14 @@ def evaluate_arguments(args):
     post_args = ""
     exit_on_fail = True
 
+    # Deal with the SBML validation option which doesn't call run_jneuroml
+    if args.validate_sbml:
+        from pyneuroml.sbml import validate_sbml_files
+
+        validate_sbml_files(" ".join(args.input_files))
+
+        return True
+
     # These do not use the shared option where files are supplied
     # They require the file name to be specified after
     # TODO: handle these better

pyneuroml/sbml/__init__.py

@@ -0,0 +1,64 @@
+"""
+use libsbml.SBMLDocument.checkConsistency to check validaity of an SBML document
+based on https://github.com/combine-org/combine-notebooks/blob/main/src/combine_notebooks/validation/validation_sbml.py
+"""
+
+import os
+import libsbml
+from libsbml import SBMLReader
+from typing import List
+
+
+def validate_sbml_files(input_files: str, units_consistency: bool = False):
+    """
+    validate each input file using libsbml.SBMLDocument.checkConsistency
+    input_files is a space separated list of one or more filepaths
+    """
+
+    for file_name in input_files.split():
+        if not os.path.isfile(file_name):
+            raise OSError(("Could not find SBML file %s" % file_name))
+
+        try:
+            reader = SBMLReader()
+            doc = reader.readSBML(file_name)
+        except Exception:
+            raise OSError(("SBMLReader failed to load the file %s" % file_name))
+
+        # set the unit checking, similar for the other settings
+        doc.setConsistencyChecks(
+            libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, units_consistency
+        )
+        doc.checkConsistency()
+        # get errors/warnings
+        n_errors: int = doc.getNumErrors()
+        errors: List[libsbml.SBMLError] = list()
+        warnings: List[libsbml.SBMLError] = list()
+        for k in range(n_errors):
+            error: libsbml.SBMLError = doc.getError(k)
+            severity = error.getSeverity()
+            if (severity == libsbml.LIBSBML_SEV_ERROR) or (
+                severity == libsbml.LIBSBML_SEV_FATAL
+            ):
+                errors.append(error)
+            else:
+                warnings.append(error)
+        # print results
+        print("-" * 80)
+        print(f"{'validation error(s)':<25}: {len(errors)}")
+        print(f"{'validation warning(s)':<25}: {len(warnings)}")
+        if len(errors) > 0:
+            print("--- errors ---")
+            for kerr in enumerate(errors):
+                print(f"E{kerr}: {error.getCategoryAsString()} L{error.getLine()}")
+                print(
+                    f"[{error.getSeverityAsString()}] {error.getShortMessage()} | {error.getMessage()}"
+                )
+        if len(warnings) > 0:
+            print("--- warnings ---")
+            for kwarn in enumerate(warnings):
+                print(f"E{kwarn}: {error.getCategoryAsString()} L{error.getLine()}")
+                print(
+                    f"[{error.getSeverityAsString()}] {error.getShortMessage()} | {error.getMessage()}"
+                )
+        print("-" * 80)

setup.cfg

@@ -101,6 +101,9 @@ plotly =
 nsg =
     pynsgr
 
+sbml =
+    python-libsbml
+
 all =
     pyNeuroML[neuron]
     pyNeuroML[brian]
@@ -113,6 +116,7 @@ all =
     pyNeuroML[vispy]
     pyNeuroML[plotly]
     pyNeuroML[nsg]
+    pyNeuroML[sbml]
 
 dev =
     pyNeuroML[all]

tests/sbml/test_data/test_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>

tests/sbml/test_sbml.py

@@ -0,0 +1,6 @@
+#!/usr/bin/env python3
+
+from pyneuroml import sbml
+
+fname = "tests/sbml/test_data/test_doc.sbml"
+doc = sbml.validate_sbml_files(fname)