Merge pull request #53 from robertvi/test_xml3

added simple sbml test with example xml

Author: pgleeson

examples/sbml/example_sbml_minimal.xml

@@ -0,0 +1,12 @@
+<?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>
+  </model>
+</sbml>

examples/sbml/sbml32spec.py

@@ -0,0 +1,379 @@
+#!/usr/bin/env python3
+
+'''
+initial attempt at creating an SBML API using modelspec
+https://github.com/combine-org/compbiolibs/issues/28
+
+based on sbml.level-3.version-2.core.release-2.pdf
+'''
+
+import modelspec
+from modelspec import field, instance_of, optional
+from modelspec.base_types import Base
+from typing import List
+
+from sbml_validators import *
+
+@modelspec.define
+class Notes(Base):
+    '''
+    XHTML field of SBase
+
+    Args:
+        xmlns: str fixed "http://www.w3.org/1999/xhtml"
+        content: str valid XHTML
+    '''
+    xmlns: str = field(default="http://www.w3.org/1999/xhtml",validator=[instance_of(str),xmlns_notes])
+    content: str = field(default=None,validator=optional([instance_of(str),valid_xhtml]))
+
+@modelspec.define
+class Math(Base):
+    '''
+    Subset of MathML 2.0 used to define all formulae in SBML
+    '''
+    xmlns: str = field(default="http://www.w3.org/1998/Math/MathML",validator=[instance_of(str),xmlns_math])
+    content: str = field(default=None,validator=optional([instance_of(str),valid_mathml]))
+
+@modelspec.define
+class SBase(Base):
+    """
+    Abstract base class for all SBML objects
+
+    Args:
+        sid:     SId optional
+        name:    string optional
+        metaid:  XML ID optional
+        sboTerm: SBOTerm optional
+
+        notes:      XHTML 1.0 optional
+        annotation: XML content optional
+    """
+
+    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]))
+    sboTerm: str = field(default=None,validator=optional([instance_of(str),valid_sbo]))
+
+    notes:      Notes = field(default=None,validator=optional(instance_of(Notes)))
+    annotation: str = field(default=None,validator=optional([instance_of(str),valid_xml_content]))
+
+@modelspec.define
+class Trigger(SBase):
+    initialValue: bool = field(default=None,validator=instance_of(bool))
+    persistent: bool = field(default=None,validator=instance_of(bool))
+    math: str = field(default=None,validator=optional(instance_of(str)))
+
+@modelspec.define
+class Priority(SBase):
+    math: str = field(default=None,validator=optional(instance_of(str)))
+
+@modelspec.define
+class Delay(SBase):
+    math: str = field(default=None,validator=optional(instance_of(str)))
+
+@modelspec.define
+class EventAssignment(SBase):
+    '''
+    Args:
+        variable: SIdRef
+    '''
+    math: str = field(default=None,validator=optional(instance_of(str)))
+    variable:  str = field(default=None,validator=optional(instance_of(str)))
+
+@modelspec.define
+class Event(SBase):
+    useValuesFromTriggerTime: bool = field(default=None,validator=instance_of(bool))
+    trigger:  Trigger = field(default=None, validator=optional(instance_of(Trigger)))
+    priority: Priority = field(default=None, validator=optional(instance_of(Priority)))
+    delay:    Delay = field(default=None, validator=optional(instance_of(Delay)))
+    listOfEventAssignments: List[EventAssignment]   = field(factory=list)
+
+@modelspec.define
+class SimpleSpeciesReference(SBase):
+    """
+    Base class used by SpeciesReference and ModifierSpeciesReference
+
+    Args:
+        species: SIdRef
+    """
+
+    species: str = field(default=None,validator=instance_of(str))
+
+@modelspec.define
+class ModifierSpeciesReference(SimpleSpeciesReference):
+    ''
+
+@modelspec.define
+class SpeciesReference(SimpleSpeciesReference):
+    """
+    Args:
+        stoichiometry: double optional
+        constant: boolean
+    """
+
+    stoichiometry: float = field(default=None,validator=optional(instance_of(float)))
+    constant:      bool = field(default=None,validator=instance_of(bool))
+
+@modelspec.define
+class LocalParameter(SBase):
+    """
+    Args:
+        units: UnitSIdRef optional
+    """
+
+    value: float = field(default=None,validator=optional(instance_of(float)))
+    units: str = field(default=None,validator=optional(instance_of(str)))
+
+@modelspec.define
+class KineticLaw(SBase):
+    """
+    """
+
+    math: str = field(default=None,validator=optional(instance_of(str)))
+
+    listOfLocalParameters:           List[LocalParameter]   = field(factory=list)
+
+@modelspec.define
+class Reaction(SBase):
+    """
+    A model reaction
+
+    Args:
+        reversible: boolean
+        compartment: SIdRef optional
+    """
+
+    reversible:   bool = field(default=None,validator=instance_of(bool))
+    compartment:  str = field(default=None,validator=optional(instance_of(str)))
+
+    listOfReactants:           List[SpeciesReference]           = field(factory=list)
+    listOfProducts:            List[SpeciesReference]           = field(factory=list)
+    listOfModifiers:           List[ModifierSpeciesReference]   = field(factory=list)
+
+    kineticLaw:  KineticLaw = field(default=None, validator=optional(instance_of(KineticLaw)))
+
+@modelspec.define
+class Constraint(SBase):
+    """
+    A model constraint
+
+    Args:
+        math:    MathML optional
+        message: XHTML 1.0 optional
+    """
+
+    math:    str = field(default=None,validator=optional(instance_of(str)))
+    message: str = field(default=None,validator=optional(instance_of(str)))
+
+@modelspec.define
+class Rule(SBase):
+    """
+    A rule, either algebraic, assignment or rate
+
+    Args:
+        math: MathML optional
+    """
+
+    math: str = field(default=None,validator=optional(instance_of(str)))
+
+@modelspec.define
+class AlgebraicRule(Rule):
+    """
+    An algebraic rule
+    """
+
+@modelspec.define
+class AssignmentRule(Rule):
+    """
+    An assignment rule
+
+    Args:
+        variable: SIdRef required
+    """
+
+    variable: str = field(default=None,validator=instance_of(str))
+
+@modelspec.define
+class RateRule(Rule):
+    """
+    A rate rule
+
+    Args:
+        variable: SIdRef required
+    """
+
+    variable: str = field(default=None,validator=instance_of(str))
+
+@modelspec.define
+class InitialAssignment(SBase):
+    """
+    An initial assignment
+
+    Args:
+        symbol: SIdRef required
+        math: MathML optional
+    """
+
+    symbol: str = field(default=None,validator=instance_of(str))
+    math: str = field(default=None,validator=optional(instance_of(str)))
+
+@modelspec.define
+class Parameter(SBase):
+    """
+    A parameter
+
+    Args:
+        value: double optional
+        units: UnitSIdRef optional
+        constant: boolean
+    """
+
+    constant: bool = field(default=None,validator=instance_of(bool))
+
+    value: float = field(default=None,validator=optional(instance_of(float)))
+    units: str = field(default=None,validator=optional(instance_of(str)))
+
+@modelspec.define
+class Species(SBase):
+    """
+    A species: entities of the same kind participating in reactions within a specific compartment
+
+    Args:
+        compartment: SIdRef
+        initialAmount: double optional
+        initialConcentration: double optional
+        substanceUnits: UnitSIdRef optional
+        hasOnlySubstanceUnits: boolean
+        boundaryCondition: boolean
+        constant: boolean
+        conversionFactor: SIdRef optional
+    """
+
+    compartment: str = field(default=None,validator=instance_of(str))
+    hasOnlySubstanceUnits: bool = field(default=None,validator=instance_of(bool))
+    boundaryCondition: bool = field(default=None,validator=instance_of(bool))
+    constant: bool = field(default=None,validator=instance_of(bool))
+
+    initialAmount: float = field(default=None, validator=optional(instance_of(float)))
+    initialConcentration: float = field(default=None, validator=optional(instance_of(float)))
+    substanceUnits: str = field(default=None, validator=optional(instance_of(str)))
+    conversionFactor: str = field(default=None, validator=optional(instance_of(str)))
+
+@modelspec.define
+class Compartment(SBase):
+    """
+    A compartment
+
+    Args:
+        spatialDimensions: eg 3 for three dimensional space etc
+        size: initial size of compartment
+        units: units being used to define the compartment's size
+        constant: whether size is fixed
+    """
+
+    constant: bool = field(default=None,validator=instance_of(bool))
+
+    spatialDimensions: float = field(default=None,validator=optional(instance_of(float)))
+    size: float = field(default=None,validator=optional(instance_of(float)))
+    units: str = field(default=None,validator=optional(instance_of(str)))
+
+@modelspec.define
+class Unit(SBase):
+    """
+    A unit used to compose a unit definition.
+    unit = (multiplier x 10^scale x kind)^exponent
+
+    Args:
+        kind: base unit (base or derived SI units only, see Table 2 of the SBML spec)
+        exponent: double
+        scale: integer
+        multiplier: double
+    """
+
+    kind:       str = field(default=None,validator=[instance_of(str),valid_kind])
+    exponent:   str = field(default=1.0, validator=instance_of(float))
+    scale:      str = field(default=0,   validator=instance_of(int))
+    multiplier: str = field(default=1.0, validator=instance_of(float))
+
+@modelspec.define
+class UnitDefinition(SBase):
+    """
+    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)
+
+@modelspec.define
+class FunctionDefinition(SBase):
+    """
+    A function definition using MathML
+
+    Args:
+        sid:  SId required
+
+        math: MathML function definition optional
+    """
+
+    sid:     str = field(default=None,validator=[instance_of(str),valid_sid])
+
+    math: Math = field(default=None, validator=optional(instance_of(Math)))
+
+@modelspec.define
+class Model(SBase):
+    """
+    The model
+
+    Args:
+        substanceUnits:   UnitSIdRef optional
+        timeUnits:        UnitSIdRef optional
+        volumeUnits:      UnitSIdRef optional
+        areaUnits:        UnitSIdRef optional
+        lengthUnits:      UnitSIdRef optional
+        extentUnits:      UnitSIdRef optional
+        conversionFactor: SIdRef optional
+    """
+
+    substanceUnits:   str = field(default=None, validator=optional([instance_of(str),valid_unitsid]))
+    timeUnits:        str = field(default=None, validator=optional([instance_of(str),valid_unitsid]))
+    volumeUnits:      str = field(default=None, validator=optional([instance_of(str),valid_unitsid]))
+    areaUnits:        str = field(default=None, validator=optional([instance_of(str),valid_unitsid]))
+    lengthUnits:      str = field(default=None, validator=optional([instance_of(str),valid_unitsid]))
+    extentUnits:      str = field(default=None, validator=optional([instance_of(str),valid_unitsid]))
+    conversionFactor: str = field(default=None, validator=optional([instance_of(str),valid_unitsid]))
+
+    listOfFunctionDefinitions: List[FunctionDefinition] = 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)
+    listOfInitialAssignments:  List[InitialAssignment]  = field(factory=list)
+    listOfRules:               List[Rule]               = field(factory=list)
+    listOfConstraints:         List[Constraint]         = field(factory=list)
+    listOfReactions:           List[Reaction]           = field(factory=list)
+    listOfEvents:              List[Event]              = field(factory=list)
+
+@modelspec.define
+class SBML(SBase):
+    """
+    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
+
+    Args:
+        xmlns:   string, fixed to "http://www.sbml.org/sbml/level3/version2/core"
+        level:   SBML level, fixed to 3
+        version: SBML version, fixed to 2
+
+        model:   Optional model
+    """
+
+    xmlns:   str = field(default="http://www.sbml.org/sbml/level3/version2/core",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])
+
+    model: Model = field(default=None, validator=optional(instance_of(Model)))