Updates to core sbml model definition

Author: pgleeson

docs/sphinx/source/api/Contributors.md

@@ -3,7 +3,7 @@
 # Modelspec contributors
 
 This page list names and Github profiles of contributors to Modelspec, listed in no particular order.
-This page is generated periodically, most recently on 2023-09-13.
+This page is generated periodically, most recently on 2023-09-18.
 
 - Padraig Gleeson ([@pgleeson](https://github.com/pgleeson))
 - Manifest Chakalov  ([@mqnifestkelvin](https://github.com/mqnifestkelvin))

examples/sbml/example_sbml_minimal.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
   <model substanceUnits="mole" timeUnits="second" extentUnits="mole">
     <listOfUnitDefinitions>
       <unitDefinition id="per_second">

examples/sbml/sbml32spec.py

@@ -66,6 +66,7 @@ class SBase(Base):
 
     sid: str = field(default=None, validator=optional([instance_of(str), valid_sid]))
     name: str = field(default=None, validator=optional(instance_of(str)))
+
     metaid: str = field(
         default=None, validator=optional([instance_of(str), valid_xml_id])
     )
@@ -79,6 +80,12 @@ class SBase(Base):
     )
 
 
+@modelspec.define
+class SBaseWithId(SBase):
+
+    id: str = field(default=None, validator=optional([instance_of(str), valid_sid]))
+
+
 @modelspec.define
 class Trigger(SBase):
     initialValue: bool = field(default=None, validator=instance_of(bool))
@@ -345,7 +352,7 @@ class Unit(SBase):
 
 
 @modelspec.define
-class UnitDefinition(SBase):
+class unitDefinition(SBase):
     """
     A unit definition
 
@@ -412,7 +419,7 @@ class Model(SBase):
     )
 
     listOfFunctionDefinitions: List[FunctionDefinition] = field(factory=list)
-    listOfUnitDefinitions: List[UnitDefinition] = field(factory=list)
+    listOfUnitDefinitions: List[unitDefinition] = field(factory=list)
     listOfCompartments: List[Compartment] = field(factory=list)
     listOfSpecies: List[Species] = field(factory=list)
     listOfParameters: List[Parameter] = field(factory=list)
@@ -424,7 +431,7 @@ class Model(SBase):
 
 
 @modelspec.define
-class SBML(SBase):
+class sbml(SBaseWithId):
     """
     The top-level SBML container implementing SBML 3.2.
     See sbml.level-3.version-2.core.release-2.pdf section 4.
@@ -439,10 +446,11 @@ class SBML(SBase):
     """
 
     xmlns: str = field(
-        default="http://www.sbml.org/sbml/level3/version2/core",
+        default="http://www.sbml.org/sbml/level3/version%s/core" % SBML_VERSION,
         validator=[instance_of(str), xmlns_sbml],
     )
-    level: str = field(default="3", validator=[instance_of(str), fixed_level])
-    version: str = field(default="2", validator=[instance_of(str), fixed_version])
+    level: str = field(default=None, validator=[instance_of(str), fixed_level])
+    version: str = field(default=None, validator=[instance_of(str), fixed_version])
 
     model: Model = field(default=None, validator=optional(instance_of(Model)))
+    # models: List[Model] = field(factory=list)

examples/sbml/sbml_validators.py

@@ -6,13 +6,17 @@
 import re
 from lxml import etree
 from io import StringIO
+import sys
 
 # sbml.level-3.version-2.core.release-2.pdf Table 2
 sbml_si_units = """
 ampere coulomb gray joule litre mole radian steradian weber avogadro dimensionless henry katal lumen newton
 second tesla becquerel farad hertz kelvin lux ohm siemens volt candela gram item kilogram metre pascal sievert watt
 """.split()
 
+SBML_VERSION = "2"
+SBML_LEVEL = "3"
+
 
 def valid_kind(instance, attribute, value):
     if not value in sbml_si_units:
@@ -43,13 +47,13 @@ def xmlns_math(instance, attribute, value):
 
 
 def fixed_level(instance, attribute, value):
-    if value != "3":
-        raise ValueError("this implementation only supports level 3")
+    if value != SBML_LEVEL:
+        raise ValueError("this implementation only supports level %s" % SBML_LEVEL)
 
 
 def fixed_version(instance, attribute, value):
-    if value != "2":
-        raise ValueError("this implementation only supports level 2")
+    if value != SBML_VERSION:
+        raise ValueError("this implementation only supports version %s" % SBML_VERSION)
 
 
 def valid_sid(instance, attribute, value):
@@ -114,3 +118,60 @@ def valid_mathml(instance, attribute, value):
         raise ValueError(
             f"{value} doesn't look like MathML (this validator is only a stub)"
         )
+
+
+# from: https://github.com/combine-org/combine-notebooks
+
+
+def validate_sbml(doc, units_consistency: bool = False) -> None:
+    """Validate sbml."""
+    import libsbml
+
+    # 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)
+
+
+if __name__ == "__main__":
+
+    import libsbml
+
+    sbml_file = sys.argv[1]
+
+    print("Going to validate SBML file: %s" % sbml_file)
+    reader = libsbml.SBMLReader()
+    document = reader.readSBML(sbml_file)
+
+    validate_sbml(document, units_consistency=False)

test_all.sh

@@ -24,6 +24,11 @@ python neuroml2_spec.py
 pynml -validate hello_world_neuroml.net.nml
 pynml -validate TestNeuroML.xml
 
+## Test SBML example
+
+cd ../sbml
+./regenerateAndTest.sh
+
 cd ../..