Generates same example sbml; restructured handling of listOf... classes

Can certainly be made more succinct, but generating valid SBML

Author: pgleeson

examples/sbml/example_sbml_minimal.xml

@@ -1,5 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
+
+  <!-- An example of a simple SBML file known to be valid -->
+
   <model substanceUnits="mole" timeUnits="second" extentUnits="mole">
     <listOfUnitDefinitions>
       <unitDefinition id="per_second">

examples/sbml/sbml32spec.py

@@ -333,7 +333,7 @@ class Compartment(SBase):
 
 
 @modelspec.define
-class Unit(SBase):
+class unit(SBase):
     """
     A unit used to compose a unit definition.
     unit = (multiplier x 10^scale x kind)^exponent
@@ -352,17 +352,41 @@ class Unit(SBase):
 
 
 @modelspec.define
-class unitDefinition(SBase):
+class ListOfUnits(SBase):
+    """
+    A listOfUnits
+
+    Args:
+        listOfUnits: the actual list Of Units
+    """
+
+    listOfUnits: List[unit] = field(factory=list)
+
+
+@modelspec.define
+class unitDefinition(SBaseWithId):
     """
     A unit definition
 
     Args:
-        sid: UnitSid required (overrides SBase sid)
         listOfUnits: List of units used to compose the definition
     """
 
-    sid: str = field(default=None, validator=[instance_of(str), valid_unitsid])
-    listOfUnits: List[Unit] = field(factory=list)
+    listOfUnits: ListOfUnits = field(
+        default=None, validator=optional(instance_of(ListOfUnits))
+    )
+
+
+@modelspec.define
+class ListOfUnitDefinitions(SBase):
+    """
+    A listOfUnitDefinitions
+
+    Args:
+        listOfUnitDefinitions: the actual list Of Unit Definitions
+    """
+
+    listOfUnitDefinitions: List[unitDefinition] = field(factory=list)
 
 
 @modelspec.define
@@ -419,7 +443,11 @@ class Model(SBase):
     )
 
     listOfFunctionDefinitions: List[FunctionDefinition] = field(factory=list)
-    listOfUnitDefinitions: List[unitDefinition] = field(factory=list)
+
+    listOfUnitDefinitions: ListOfUnitDefinitions = field(
+        default=None, validator=optional(instance_of(ListOfUnitDefinitions))
+    )
+
     listOfCompartments: List[Compartment] = field(factory=list)
     listOfSpecies: List[Species] = field(factory=list)
     listOfParameters: List[Parameter] = field(factory=list)
@@ -435,7 +463,7 @@ class sbml(SBaseWithId):
     """
     The top-level SBML container implementing SBML 3.2.
     See sbml.level-3.version-2.core.release-2.pdf section 4.
-    http://www.sbml.org/sbml/level3/version2/core
+    http://www.sbml.org/sbml/level3/version2/
 
     Args:
         xmlns:   string, fixed to "http://www.sbml.org/sbml/level3/version2/core"

examples/sbml/sbml_validators.py

@@ -57,10 +57,11 @@ def fixed_version(instance, attribute, value):
 
 
 def valid_sid(instance, attribute, value):
-    if not re.fullmatch("[_A-Za-z][_A-Za-z0-9]*", value):
-        raise ValueError(
-            "an SId must match the regular expression: [_A-Za-z][_A-Za-z0-9]*"
-        )
+    if value is not None:
+        if not re.fullmatch("[_A-Za-z][_A-Za-z0-9]*", value):
+            raise ValueError(
+                "an SId must match the regular expression: [_A-Za-z][_A-Za-z0-9]*"
+            )
 
 
 def valid_unitsid(instance, attribute, value):
@@ -163,6 +164,8 @@ def validate_sbml(doc, units_consistency: bool = False) -> None:
             )
     print("-" * 80)
 
+    return len(warnings) + len(errors)
+
 
 if __name__ == "__main__":
 
@@ -174,4 +177,6 @@ def validate_sbml(doc, units_consistency: bool = False) -> None:
     reader = libsbml.SBMLReader()
     document = reader.readSBML(sbml_file)
 
-    validate_sbml(document, units_consistency=False)
+    issues = validate_sbml(document, units_consistency=False)
+
+    exit(issues)

examples/sbml/test_minimal_example.json

@@ -5,7 +5,21 @@
         "model": {
             "substanceUnits": "mole",
             "timeUnits": "second",
-            "extentUnits": "mole"
+            "extentUnits": "mole",
+            "listOfUnitDefinitions": {
+                "listOfUnitDefinitions": {
+                    "per_second": {
+                        "listOfUnits": {
+                            "listOfUnits": [
+                                {
+                                    "kind": "second",
+                                    "exponent": -1.0
+                                }
+                            ]
+                        }
+                    }
+                }
+            }
         }
     }
 }

examples/sbml/test_minimal_example.xml

@@ -1,4 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" id="test_minimal_example" level="3" version="2">
-    <model substanceUnits="mole" timeUnits="second" extentUnits="mole"/>
+    <model substanceUnits="mole" timeUnits="second" extentUnits="mole">
+        <listOfUnitDefinitions>
+            <unitDefinition id="per_second">
+                <listOfUnits>
+                    <unit kind="second" exponent="-1.0" scale="0" multiplier="1.0"/>
+                </listOfUnits>
+            </unitDefinition>
+        </listOfUnitDefinitions>
+    </model>
 </sbml>

examples/sbml/test_minimal_example.yaml

@@ -5,3 +5,10 @@ test_minimal_example:
         substanceUnits: mole
         timeUnits: second
         extentUnits: mole
+        listOfUnitDefinitions:
+            listOfUnitDefinitions:
+                per_second:
+                    listOfUnits:
+                        listOfUnits:
+                        -   kind: second
+                            exponent: -1.0

examples/sbml/test_sbml3.py

@@ -23,11 +23,15 @@ def test_example_sbml_minimal():
     model = Model(substanceUnits="mole", timeUnits="second", extentUnits="mole")
     sbml_doc.model = model
 
-    unit_def = unitDefinition(sid="per_second")
-    """
-    model.listOfUnitDefinitions.append(unit_def)
-    unit = Unit(kind="second", exponent=-1.0)
-    unit_def.listOfUnits.append(unit)"""
+    unit_def = unitDefinition(id="per_second")
+
+    model.listOfUnitDefinitions = ListOfUnitDefinitions()
+
+    model.listOfUnitDefinitions.listOfUnitDefinitions.append(unit_def)
+
+    unit_s = unit(kind="second", exponent=-1.0)
+    unit_def.listOfUnits = ListOfUnits()
+    unit_def.listOfUnits.listOfUnits.append(unit_s)
 
     print("------------------------------------------------")
     print(sbml_doc)