[BUG] 1 or more SBML files have errors with the spatial package

[jonrkarr]

Example: biomodel_12119723__seven__12_00_model1.xml in 12119723

These errors were identified with libSBML experimental 5.19.0 (I used the experimental package because the main package doesn't have the spatial extension).

- MathML consistency (10210) at line 355, column 6: The arguments to the following MathML constructs must have a numeric type: <plus>, <minus>, <times>, <divide>, <power>, <root>, <abs>, <exp>, <ln>, <log>, <floor>, <ceiling>, <factorial>, <sin>, <cos>, <tan>, <sec>, <csc>, <cot>, <sinh>, <cosh>, <tanh>, <sech>, <csch>, <coth>, <arcsin>, <arccos>, <arctan>, <arcsec>, <arccsc>, <arccot>, <arcsinh>, <arccosh>, <arctanh>, <arcsech>, <arccsch>, <arccoth>. 
  Reference: L3V1 Section 3.4.9
   The formula '212682.897611908 * (2 + 2000 * lt(pow(-30 + x, 2) + pow(-4 + y, 2), 2.25))' in the math element of the <assignmentRule> uses an argument to a operator that expects a numeric value.

- MathML consistency (10210) at line 402, column 6: The arguments to the following MathML constructs must have a numeric type: <plus>, <minus>, <times>, <divide>, <power>, <root>, <abs>, <exp>, <ln>, <log>, <floor>, <ceiling>, <factorial>, <sin>, <cos>, <tan>, <sec>, <csc>, <cot>, <sinh>, <cosh>, <tanh>, <sech>, <csch>, <coth>, <arcsin>, <arccos>, <arctan>, <arcsec>, <arccsc>, <arccot>, <arcsinh>, <arccosh>, <arctanh>, <arcsech>, <arccsch>, <arccoth>. 
  Reference: L3V1 Section 3.4.9
   The formula '212682.897611908 * (2 + 2000 * lt(pow(-30 + x, 2) + pow(-4 + y, 2), 2.25))' in the math element of the <assignmentRule> uses an argument to a operator that expects a numeric value.

- MathML consistency (10210) at line 449, column 6: The arguments to the following MathML constructs must have a numeric type: <plus>, <minus>, <times>, <divide>, <power>, <root>, <abs>, <exp>, <ln>, <log>, <floor>, <ceiling>, <factorial>, <sin>, <cos>, <tan>, <sec>, <csc>, <cot>, <sinh>, <cosh>, <tanh>, <sech>, <csch>, <coth>, <arcsin>, <arccos>, <arctan>, <arcsec>, <arccsc>, <arccot>, <arcsinh>, <arccosh>, <arctanh>, <arcsech>, <arccsch>, <arccoth>. 
  Reference: L3V1 Section 3.4.9
   The formula '212682.897611908 * (2 + 2000 * lt(pow(-30 + x, 2) + pow(-4 + y, 2), 2.25))' in the math element of the <assignmentRule> uses an argument to a operator that expects a numeric value.

- MathML consistency (10210) at line 496, column 6: The arguments to the following MathML constructs must have a numeric type: <plus>, <minus>, <times>, <divide>, <power>, <root>, <abs>, <exp>, <ln>, <log>, <floor>, <ceiling>, <factorial>, <sin>, <cos>, <tan>, <sec>, <csc>, <cot>, <sinh>, <cosh>, <tanh>, <sech>, <csch>, <coth>, <arcsin>, <arccos>, <arctan>, <arcsec>, <arccsc>, <arccot>, <arcsinh>, <arccosh>, <arctanh>, <arcsech>, <arccsch>, <arccoth>. 
  Reference: L3V1 Section 3.4.9
   The formula '212682.897611908 * (2 + 2000 * lt(pow(-30 + x, 2) + pow(-4 + y, 2), 2.25))' in the math element of the <assignmentRule> uses an argument to a operator that expects a numeric value.

- MathML consistency (10210) at line 306, column 6: The arguments to the following MathML constructs must have a numeric type: <plus>, <minus>, <times>, <divide>, <power>, <root>, <abs>, <exp>, <ln>, <log>, <floor>, <ceiling>, <factorial>, <sin>, <cos>, <tan>, <sec>, <csc>, <cot>, <sinh>, <cosh>, <tanh>, <sech>, <csch>, <coth>, <arcsin>, <arccos>, <arctan>, <arcsec>, <arccsc>, <arccot>, <arcsinh>, <arccosh>, <arctanh>, <arcsech>, <arccsch>, <arccoth>. 
  Reference: L3V1 Section 3.4.9
   The formula '212682.897611908 * (2 + 2000 * lt(pow(-30 + x, 2) + pow(-4 + y, 2), 2.25))' in the math element of the <initialAssignment> uses an argument to a operator that expects a numeric value.

- MathML consistency (10217) at line 355, column 6: The MathML formulas in the following elements must yield numeric expressions: <math> in <kineticLaw>, <stoichiometryMath> in <speciesReference>, <math> in <initialAssignment>, <math> in <assignmentRule>, <math> in <rateRule>, <math> in <algebraicRule>, and <delay> in <event>, and <math> in <eventAssignment>. 
  Reference: L3V1 Sections 4.8, 4.9, 4.11 and 4.12
   The formula '212682.897611908 * (2 + 2000 * lt(pow(-30 + x, 2) + pow(-4 + y, 2), 2.25))' in the math element of the <assignmentRule> does not return a numeric result.

- MathML consistency (10217) at line 402, column 6: The MathML formulas in the following elements must yield numeric expressions: <math> in <kineticLaw>, <stoichiometryMath> in <speciesReference>, <math> in <initialAssignment>, <math> in <assignmentRule>, <math> in <rateRule>, <math> in <algebraicRule>, and <delay> in <event>, and <math> in <eventAssignment>. 
  Reference: L3V1 Sections 4.8, 4.9, 4.11 and 4.12
   The formula '212682.897611908 * (2 + 2000 * lt(pow(-30 + x, 2) + pow(-4 + y, 2), 2.25))' in the math element of the <assignmentRule> does not return a numeric result.

- MathML consistency (10217) at line 449, column 6: The MathML formulas in the following elements must yield numeric expressions: <math> in <kineticLaw>, <stoichiometryMath> in <speciesReference>, <math> in <initialAssignment>, <math> in <assignmentRule>, <math> in <rateRule>, <math> in <algebraicRule>, and <delay> in <event>, and <math> in <eventAssignment>. 
  Reference: L3V1 Sections 4.8, 4.9, 4.11 and 4.12
   The formula '212682.897611908 * (2 + 2000 * lt(pow(-30 + x, 2) + pow(-4 + y, 2), 2.25))' in the math element of the <assignmentRule> does not return a numeric result.

- MathML consistency (10217) at line 496, column 6: The MathML formulas in the following elements must yield numeric expressions: <math> in <kineticLaw>, <stoichiometryMath> in <speciesReference>, <math> in <initialAssignment>, <math> in <assignmentRule>, <math> in <rateRule>, <math> in <algebraicRule>, and <delay> in <event>, and <math> in <eventAssignment>. 
  Reference: L3V1 Sections 4.8, 4.9, 4.11 and 4.12
   The formula '212682.897611908 * (2 + 2000 * lt(pow(-30 + x, 2) + pow(-4 + y, 2), 2.25))' in the math element of the <assignmentRule> does not return a numeric result.

- MathML consistency (10217) at line 306, column 6: The MathML formulas in the following elements must yield numeric expressions: <math> in <kineticLaw>, <stoichiometryMath> in <speciesReference>, <math> in <initialAssignment>, <math> in <assignmentRule>, <math> in <rateRule>, <math> in <algebraicRule>, and <delay> in <event>, and <math> in <eventAssignment>. 
  Reference: L3V1 Sections 4.8, 4.9, 4.11 and 4.12
   The formula '212682.897611908 * (2 + 2000 * lt(pow(-30 + x, 2) + pow(-4 + y, 2), 2.25))' in the math element of the <initialAssignment> does not return a numeric result.

- SBML component consistency (1220751) at line 38, column 8: If the <geometry> of the <model> has exactly two <coordinateComponent> children, the attribute 'spatial:spatialDimensions' of a <domainType> may only have a value of '1' or '2'.
  Reference: L3V1 Spatial V1 Section
   A DomainType with id 'domainType_keratocyte' has a 'spatial:spatialDimensions' attribute of '3', but the ListOfCoordinateComponents has exactly two children.

- SBML component consistency (1220751) at line 39, column 8: If the <geometry> of the <model> has exactly two <coordinateComponent> children, the attribute 'spatial:spatialDimensions' of a <domainType> may only have a value of '1' or '2'.
  Reference: L3V1 Spatial V1 Section
   A DomainType with id 'domainType_subVolume0' has a 'spatial:spatialDimensions' attribute of '3', but the ListOfCoordinateComponents has exactly two children.

- SBML component consistency (1220951) at line 27, column 12: If the <geometry> of the <model> has exactly two <coordinateComponent> children, an <interiorPoint> object must define the attributes 'coord1' and 'coord2', and must not define the attribute 'coord3'.
  Reference: L3V1 Spatial V1 Section
   An <interiorPoint> defines a coord3 with a value of '5', but the <listOfCoordinateComponents> has exactly two children.

- SBML component consistency (1220951) at line 32, column 12: If the <geometry> of the <model> has exactly two <coordinateComponent> children, an <interiorPoint> object must define the attributes 'coord1' and 'coord2', and must not define the attribute 'coord3'.
  Reference: L3V1 Spatial V1 Section
   An <interiorPoint> defines a coord3 with a value of '5', but the <listOfCoordinateComponents> has exactly two children.

- SBML component consistency (1223606) at line 238, column 8: The value of the attribute 'spatial:coordinateBoundary' of a <boundaryCondition> object must be the identifier of an existing <boundary> object defined in the enclosing <model> object.
  Reference: L3V1 Spatial V1 Section
   A <boundaryCondition> has a value of 'Xmin' for its 'coordinateBoundary', but the <geometry> does not contain a <boundaryMax> or <boundaryMin> with that id.

- SBML component consistency (1223606) at line 244, column 8: The value of the attribute 'spatial:coordinateBoundary' of a <boundaryCondition> object must be the identifier of an existing <boundary> object defined in the enclosing <model> object.
  Reference: L3V1 Spatial V1 Section
   A <boundaryCondition> has a value of 'Ymin' for its 'coordinateBoundary', but the <geometry> does not contain a <boundaryMax> or <boundaryMin> with that id.

- SBML component consistency (1223606) at line 253, column 8: The value of the attribute 'spatial:coordinateBoundary' of a <boundaryCondition> object must be the identifier of an existing <boundary> object defined in the enclosing <model> object.
  Reference: L3V1 Spatial V1 Section
   A <boundaryCondition> has a value of 'Xmin' for its 'coordinateBoundary', but the <geometry> does not contain a <boundaryMax> or <boundaryMin> with that id.

- SBML component consistency (1223606) at line 259, column 8: The value of the attribute 'spatial:coordinateBoundary' of a <boundaryCondition> object must be the identifier of an existing <boundary> object defined in the enclosing <model> object.
  Reference: L3V1 Spatial V1 Section
   A <boundaryCondition> has a value of 'Ymin' for its 'coordinateBoundary', but the <geometry> does not contain a <boundaryMax> or <boundaryMin> with that id.

- SBML component consistency (1223606) at line 265, column 8: The value of the attribute 'spatial:coordinateBoundary' of a <boundaryCondition> object must be the identifier of an existing <boundary> object defined in the enclosing <model> object.
  Reference: L3V1 Spatial V1 Section
   A <boundaryCondition> has a value of 'Xmin' for its 'coordinateBoundary', but the <geometry> does not contain a <boundaryMax> or <boundaryMin> with that id.

- SBML component consistency (1223606) at line 271, column 8: The value of the attribute 'spatial:coordinateBoundary' of a <boundaryCondition> object must be the identifier of an existing <boundary> object defined in the enclosing <model> object.
  Reference: L3V1 Spatial V1 Section
   A <boundaryCondition> has a value of 'Ymin' for its 'coordinateBoundary', but the <geometry> does not contain a <boundaryMax> or <boundaryMin> with that id.

- SBML component consistency (1223606) at line 280, column 8: The value of the attribute 'spatial:coordinateBoundary' of a <boundaryCondition> object must be the identifier of an existing <boundary> object defined in the enclosing <model> object.
  Reference: L3V1 Spatial V1 Section
   A <boundaryCondition> has a value of 'Xmin' for its 'coordinateBoundary', but the <geometry> does not contain a <boundaryMax> or <boundaryMin> with that id.

- SBML component consistency (1223606) at line 286, column 8: The value of the attribute 'spatial:coordinateBoundary' of a <boundaryCondition> object must be the identifier of an existing <boundary> object defined in the enclosing <model> object.
  Reference: L3V1 Spatial V1 Section
   A <boundaryCondition> has a value of 'Ymin' for its 'coordinateBoundary', but the <geometry> does not contain a <boundaryMax> or <boundaryMin> with that id.