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Bug in unit conversion/unit definition #336

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matthiaskoenig opened this issue Sep 23, 2021 · 0 comments
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Bug in unit conversion/unit definition #336

matthiaskoenig opened this issue Sep 23, 2021 · 0 comments
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@matthiaskoenig
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In simvastatin.whole_body some units are not correct. Possibly due to the conversion.

ARNING:sbmlutils.validation:E0: SBML unit consistency (core, L2467, code)
[Warning] The units of the function call's arguments are not consistent with its definition
The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. 
Reference: L3V1 Section 3.4
 The formula 'BW * COBW + (HR - HRrest) * COHRI / 60' in the math element of the <assignmentRule> can only act on variables with the same units.

WARNING:sbmlutils.validation:E1: SBML unit consistency (core, L4862, code)
[Warning] The units of the kinetic law are not 'substance'/'time'
The units of the 'math' formula in a <kineticLaw> definition are expected to be the equivalent of _substance per time_.
Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4
 In level 3 the expected units are extent_per_time. Expected units are mole (exponent = 1, multiplier = 0.001, scale = 0), second (exponent = -1, multiplier = 60, scale = 0) but the units returned by the <math> expression in the <kineticLaw> (from the <reaction> with id 'ldlc_utilization') are mole (exponent = 1, multiplier = 16.6667, scale = 0), second (exponent = -1, multiplier = 1, scale = 0).

WARNING:sbmlutils.validation:E2: SBML component consistency (comp, L1, code)
[Warning] Line numbers unreliable.
Due to the need to instantiate models, modelDefinitions, submodels etc. for the purposes of validation it is problematic to reliably report line numbers when performing validation on models using the Hierarchical Model Composition package.

WARNING:sbmlutils.validation:E3: SBML unit consistency (core, L2467, code)
[Warning] The units of the function call's arguments are not consistent with its definition
The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. 
Reference: L3V1 Section 3.4
 The formula 'BW * COBW + (HR - HRrest) * COHRI / 60' in the math element of the <assignmentRule> can only act on variables with the same units.

WARNING:sbmlutils.validation:E4: SBML unit consistency (core, L4862, code)
[Warning] The units of the kinetic law are not 'substance'/'time'
The units of the 'math' formula in a <kineticLaw> definition are expected to be the equivalent of _substance per time_.
Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4
 In level 3 the expected units are extent_per_time. Expected units are mole (exponent = 1, multiplier = 0.001, scale = 0), second (exponent = -1, multiplier = 60, scale = 0) but the units returned by the <math> expression in the <kineticLaw> (from the <reaction> with id 'ldlc_utilization') are mole (exponent = 1, multiplier = 16.6667, scale = 0), second (exponent = -1, multiplier = 1, scale = 0).

ERROR:sbmlutils.report.sbmlreport:`create_report` is currently not supported.
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