libsbml.SBMLError Class Reference

Inheritance diagram for libsbml.SBMLError:

Detailed Description

Representation of errors, warnings and other diagnostics.

This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.

When a libSBML operation on SBML content results in an error, or when there is something wrong with the SBML content, the problems are reported as SBMLError objects. These are generally stored in an SBMLErrorLog object; this log object, in turn, is kept in the SBMLDocument object containing the SBML content. Applications can obtain the list of logged errors using SBMLDocument.getErrorLog() and then use the methods provided by SBMLErrorLog to access individual SBMLError objects. (Note that despite the word 'error' in the name, SBMLError objects are used to represent not only 'true' errors, but also warnings and some informational diagnostics. The name is a historical hold-over from early versions of libSBML, in which the object really was only used to report errors.)

Each SBMLError object instance has an identification number that identifies the nature of the problem. This 'error id' number will be up to five digits long,

Error codes are useful mainly for software. For human readers, SBMLError also includes text messages that describe the nature of a given problem. The messages can be accessed using SBMLError.getShortMessage() and SBMLError.getMessage(). The former provides a brief one-line description of the issue, while SBMLError.getMessage() provides a more detailed text, including (if appropriate) references to sections of the SBML specifications where relevant topics are discussed. These text strings are suitable for displaying to human users.

An SBMLError object also contains a category code; its value may be retrieved using the method SBMLError.getCategory(). Category values are

In addition, SBMLError also has a severity code. Its value may be retrieved using the method SBMLError.getSeverity(). The possible severity values are the same as those reported by

Finally, SBMLError records the line and column near where the problem occurred in the SBML content. The values may be retrieved using the methods SBMLError.getLine() and SBMLError.getColumn(). We say 'near', because a lot of factors affect how accurate the line/column information ultimately is. For example, different XML parsers have different conventions for which line and column number they report for a particular problem (which makes a difference when a problem involves an opening XML tag on one line and a closing tag on another line). In some situations, some parsers report invalid line and/or column numbers altogether. If this occurs, libSBML sets the line and/or column number in the SBMLError object to the the value of the maximum unsigned long integer representable on the platform where libSBML is running. (This is equal to the constant named ULONG_MAX in C and C++.) The probability that a true line or column number in an SBML model would equal this value is vanishingly small; thus, if an application encounters these values in an XMLError object, it can assume no valid line/column number could be provided by libSBML in that situation.

N = Not applicable

I = Informational

W = Warning

E = Error

F = Fatal

The text shown in the 'Meaning' is the text returned by the SBMLError.getShortMessage() method on a given SBMLError object. A longer and (hopefully) clearer explanation of the issue is returned by SBMLError.getMessage().

Enumerator	Meaning	L 1 V 1	L 1 V 2	L 2 V 1	L 2 V 2	L 2 V 3	L 2 V 4
`UnknownError`	Unknown internal libSBML error	F	F	F	F	F	F
`NotUTF8`	Not UTF8	E	E	E	E	E	E
`UnrecognizedElement`	Unrecognized element	E	E	E	E	E	E
`NotSchemaConformant`	Not conformant to SBML XML schema	E	E	E	E	E	E
`InvalidMathElement`	Invalid MathML	N	N	E	E	E	E
`DisallowedMathMLSymbol`	Disallowed MathML symbol	N	N	E	E	E	E
`DisallowedMathMLEncodingUse`	Disallowed use of MathML `encoding` attribute	N	N	E	E	E	E
`DisallowedDefinitionURLUse`	Disallowed use of MathML `definitionURL` attribute	N	N	E	E	E	E
`BadCsymbolDefinitionURLValue`	Invalid `<csymbol>` `definitionURL` attribute value	N	N	E	E	E	E
`DisallowedMathTypeAttributeUse`	Disallowed use of MathML `type` attribute	N	N	E	E	E	E
`DisallowedMathTypeAttributeValue`	Disallowed MathML `type` attribute value	N	N	E	E	E	E
`LambdaOnlyAllowedInFunctionDef`	Use of `<lambda>` not permitted outside of a `<functionDefinition>`	N	N	E	E	E	E
`BooleanOpsNeedBooleanArgs`	Non-boolean argument given to boolean operator	N	N	W	E	E	E
`NumericOpsNeedNumericArgs`	Non-numerical argument given to numerical operator	N	N	W	E	E	E
`ArgsToEqNeedSameType`	Arguments to `<eq>` or `<neq>` have inconsistent data types	N	N	W	E	E	E
`PiecewiseNeedsConsistentTypes`	`<piecewise>` terms have inconsistent data types	N	N	W	E	E	E
`PieceNeedsBoolean`	Second argument of `<piece>` must yield a boolean value	N	N	W	E	E	E
`ApplyCiMustBeUserFunction`	`<ci>` does not refer to a function definition	N	N	W	E	E	E
`ApplyCiMustBeModelComponent`	`<ci>`'s value is not a component in this model	N	N	W	E	E	E
`KineticLawParametersAreLocalOnly`	Cannot use `<kineticLaw>` parameter outside local scope	N	N	W	E	E	E
`MathResultMustBeNumeric`	Formula result is not a numerical value	N	N	W	E	E	E
`OpsNeedCorrectNumberOfArgs`	Incorrect number of arguments to operator	N	N	W	E	E	E
`InvalidNoArgsPassedToFunctionDef`	Incorrect number of arguments to function	N	N	N	N	N	E
`DuplicateComponentId`	Duplicate component identifier	E	E	E	E	E	E
`DuplicateUnitDefinitionId`	Duplicate unit definition identifier	E	E	E	E	E	E
`DuplicateLocalParameterId`	Duplicate local parameter identifier	E	E	E	E	E	E
`MultipleAssignmentOrRateRules`	Multiple rules for the same variable	E	E	E	E	E	E
`MultipleEventAssignmentsForId`	Multiple event assignments for the same variable	N	N	E	E	E	E
`EventAndAssignmentRuleForId`	`variable` value used in both event assignments and assignment rules	N	N	E	E	E	E
`DuplicateMetaId`	Duplicate `metaid` identifier	N	N	E	E	E	E
`InvalidSBOTermSyntax`	Invalid `sboTerm` value syntax	N	N	N	E	E	E
`InvalidMetaidSyntax`	Invalid `metaid` value syntax	N	N	E	E	E	E
`InvalidIdSyntax`	Invalid identifier syntax	E	E	E	E	E	E
`InvalidUnitIdSyntax`	Invalid unit identifier syntax	N	N	N	E	E	E
`MissingAnnotationNamespace`	Missing declaration of XML namespace for annotation	N	N	N	E	E	E
`DuplicateAnnotationNamespaces`	Multiple annotations using same XML namespace	N	N	N	E	E	E
`SBMLNamespaceInAnnotation`	Invalid use of SBML XML namespace in annotation	N	N	N	E	E	E
`InconsistentArgUnits`	Units of arguments to function call do not match function's definition	W	W	W	E	E	W
`AssignRuleCompartmentMismatch`	Mismatched units in assignment rule for compartment	E	E	E	E	E	W
`AssignRuleSpeciesMismatch`	Mismatched units in assignment rule for species	E	E	E	E	E	W
`AssignRuleParameterMismatch`	Mismatched units in assignment rule for parameter	E	E	E	E	E	W
`InitAssignCompartmenMismatch`	Mismatched units in initial assignment to compartment	N	N	N	E	E	W
`InitAssignSpeciesMismatch`	Mismatched units in initial assignment to species	N	N	N	E	E	W
`InitAssignParameterMismatch`	Mismatched units in initial assignment to parameter	N	N	N	E	E	W
`RateRuleCompartmentMismatch`	Mismatched units in rate rule for compartment	E	E	E	E	E	W
`RateRuleSpeciesMismatch`	Mismatched units in rate rule for species	E	E	E	E	E	W
`RateRuleParameterMismatch`	Mismatched units in rate rule for parameter	E	E	E	E	E	W
`KineticLawNotSubstancePerTime`	Kinetic law units are not `substance`/`time`	E	E	E	E	E	W
`DelayUnitsNotTime`	Units of delay are not units of time	N	N	E	E	E	W
`EventAssignCompartmentMismatch`	Mismatched units in event assignment for compartment	N	N	E	E	E	W
`EventAssignSpeciesMismatch`	Mismatched units in event assignment for species	N	N	E	E	E	W
`EventAssignParameterMismatch`	Mismatched units in event assignment for parameter	N	N	E	E	E	W
`OverdeterminedSystem`	Model is overdetermined	W	W	W	E	E	E
`InvalidModelSBOTerm`	Invalid `sboTerm` value for model	N	N	N	E	E	W
`InvalidFunctionDefSBOTerm`	Invalid `sboTerm` value for function definition	N	N	N	E	E	W
`InvalidParameterSBOTerm`	Invalid `sboTerm` value for parameter	N	N	N	E	E	W
`InvalidInitAssignSBOTerm`	Invalid `sboTerm` value for initial assignment	N	N	N	E	E	W
`InvalidRuleSBOTerm`	Invalid `sboTerm` value for rule	N	N	N	E	E	W
`InvalidConstraintSBOTerm`	Invalid `sboTerm` value for constraint	N	N	N	E	E	W
`InvalidReactionSBOTerm`	Invalid `sboTerm` value for reaction	N	N	N	E	E	W
`InvalidSpeciesReferenceSBOTerm`	Invalid `sboTerm` value for species reference	N	N	N	E	E	W
`InvalidKineticLawSBOTerm`	Invalid `sboTerm` value for kinetic law	N	N	N	E	E	W
`InvalidEventSBOTerm`	Invalid `sboTerm` value for event	N	N	N	E	E	W
`InvalidEventAssignmentSBOTerm`	Invalid `sboTerm` value for event assignment	N	N	N	E	E	W
`InvalidCompartmentSBOTerm`	Invalid `sboTerm` value for compartment	N	N	N	N	E	W
`InvalidSpeciesSBOTerm`	Invalid `sboTerm` value for species	N	N	N	N	E	W
`InvalidCompartmentTypeSBOTerm`	Invalid `sboTerm` value for compartment type	N	N	N	N	E	W
`InvalidSpeciesTypeSBOTerm`	Invalid `sboTerm` value for species type	N	N	N	N	E	W
`InvalidTriggerSBOTerm`	Invalid `sboTerm` value for event trigger	N	N	N	N	E	W
`InvalidDelaySBOTerm`	Invalid `sboTerm` value for event delay	N	N	N	N	E	W
`NotesNotInXHTMLNamespace`	Notes not placed in XHTML namespace	E	E	E	E	E	E
`NotesContainsXMLDecl`	XML declarations not permitted in notes	N	N	N	E	E	E
`NotesContainsDOCTYPE`	XML `DOCTYPE` not permitted in notes	N	N	N	E	E	E
`InvalidNotesContent`	Invalid notes content	N	N	N	E	E	E
`InvalidNamespaceOnSBML`	Invalid XML namespace for SBML container	E	E	E	E	E	E
`MissingOrInconsistentLevel`	Missing or inconsistent value for `level` attribute	E	E	E	E	E	E
`MissingOrInconsistentVersion`	Missing or inconsistent value for `version` attribute	E	E	E	E	E	E
`AnnotationNotesNotAllowedLevel1`	Annotation on `<sbml>` not permitted in SBML Level 1	E	E	N	N	N	N
`MissingModel`	Missing model	E	E	E	E	E	E
`IncorrectOrderInModel`	Incorrect ordering of components in model definition	E	E	E	E	E	E
`EmptyListElement`	A given `listOf___`, if present, cannot be empty	E	E	E	E	E	E
`NeedCompartmentIfHaveSpecies`	Missing compartment in species definition	E	E	E	E	E	E
`FunctionDefMathNotLambda`	Invalid expression in function definition	N	N	E	E	E	E
`InvalidApplyCiInLambda`	Invalid forward reference in `<apply><ci>`...`</ci></apply>` value	N	N	E	E	E	N
`RecursiveFunctionDefinition`	Recursive function definition	N	N	E	E	E	E
`InvalidCiInLambda`	Unknown `<ci>` reference in `<lambda>`	N	N	E	E	E	E
`InvalidFunctionDefReturnType`	Function return type must be either numerical or boolean	N	N	E	E	E	E
`InvalidUnitDefId`	Invalid `id` value for unit definition	E	E	E	E	E	E
`InvalidSubstanceRedefinition`	Invalid redefinition of `substance`	E	E	E	E	E	E
`InvalidLengthRedefinition`	Invalid redefinition of `length`	W	W	E	E	E	E
`InvalidAreaRedefinition`	Invalid redefinition of `area`	W	W	E	E	E	E
`InvalidTimeRedefinition`	Invalid redefinition of `time`	E	E	E	E	E	E
`InvalidVolumeRedefinition`	Invalid redefinition of `volume`	E	E	E	E	E	E
`VolumeLitreDefExponentNotOne`	Must use `exponent`=`1` when defining `volume` in terms of litres	E	E	E	E	E	N
`VolumeMetreDefExponentNot3`	Must use `exponent`=`3` when defining `volume` in terms of metres	N	N	E	E	E	N
`EmptyListOfUnits`	Empty list of units not permitted	E	E	E	E	E	E
`InvalidUnitKind`	Invalid value of `kind` in unit definition	E	E	E	E	E	E
`OffsetNoLongerValid`	`offset` not supported in this Level+Version of SBML	N	N	N	E	E	N
`CelsiusNoLongerValid`	`Celsius` not defined in this Level+Version of SBML	N	N	N	E	E	N
`ZeroDimensionalCompartmentSize`	Use of `size` is invalid for a zero-dimensional compartment	N	N	E	E	E	E
`ZeroDimensionalCompartmentUnits`	Use of `units` is invalid for a zero-dimensional compartment	N	N	E	E	E	E
`ZeroDimensionalCompartmentConst`	Zero-dimensional compartments cannot be non-constant	N	N	E	E	E	E
`UndefinedOutsideCompartment`	Undefined compartment used as `outside` value	E	E	E	E	E	E
`RecursiveCompartmentContainment`	Recursive nesting of compartments via `outside`	W	W	W	E	E	E
`ZeroDCompartmentContainment`	Invalid nesting of zero-dimensional compartments	N	N	W	E	E	E
`Invalid1DCompartmentUnits`	Invalid value of `units` for a one-dimensional compartment	N	N	E	E	E	E
`Invalid2DCompartmentUnits`	Invalid value of `units` for a two-dimensional compartment	N	N	E	E	E	E
`Invalid3DCompartmentUnits`	Invalid value of `units` for a three-dimensional compartment	E	E	E	E	E	E
`InvalidCompartmentTypeRef`	Invalid `compartmentType` reference	N	N	N	E	E	E
`InvalidSpeciesCompartmentRef`	Invalid `compartment` reference	E	E	E	E	E	E
`HasOnlySubsNoSpatialUnits`	No `spatialSizeUnits` permitted if `hasOnlySubstanceUnits`=`true`	N	N	E	E	N	N
`NoSpatialUnitsInZeroD`	No `spatialSizeUnits` permitted if compartment is zero-dimensional	N	N	E	E	N	N
`NoConcentrationInZeroD`	No `initialConcentration` permitted if compartment is zero-dimensional	N	N	E	E	E	E
`SpatialUnitsInOneD`	Invalid value of `spatialSizeUnits` for a one-dimensional compartment	N	N	E	E	N	N
`SpatialUnitsInTwoD`	Invalid value of `spatialSizeUnits` for a two-dimensional compartment	N	N	E	E	N	N
`SpatialUnitsInThreeD`	Invalid value of `spatialSizeUnits` for a three-dimensional compartment	N	N	E	E	N	N
`InvalidSpeciesSusbstanceUnits`	Invalid value of `units`	E	E	E	E	E	E
`BothAmountAndConcentrationSet`	Cannot set both `initialConcentration` and `initialAmount`	N	N	E	E	E	E
`NonBoundarySpeciesAssignedAndUsed`	Cannot use non-boundary species in both reactions and rules simultaneously	W	W	E	E	E	E
`NonConstantSpeciesUsed`	Cannot use non-boundary, constant species as reactant or product	N	N	E	E	E	E
`InvalidSpeciesTypeRef`	Invalid `speciesType` reference	N	N	N	E	E	E
`MultSpeciesSameTypeInCompartment`	Cannot have multiple species of the same type in the same compartment	N	N	N	E	E	E
`MissingSpeciesCompartment`	Missing `compartment` value for species	E	E	E	E	E	E
`SpatialSizeUnitsRemoved`	Attribute `spatialSizeUnits` not supported in this Level+Version of SBML	N	N	N	N	E	E
`InvalidParameterUnits`	Invalid value for `units` in parameter definition	E	E	E	E	E	E
`InvalidInitAssignSymbol`	Invalid `symbol` reference in initial assignment	N	N	N	E	E	E
`MultipleInitAssignments`	Multiple initial assignments for the same `symbol` value	N	N	N	E	E	E
`InitAssignmentAndRuleForSameId`	Cannot set a value with both initial assignments and assignment rules simultaneously	N	N	N	E	E	E
`InvalidAssignRuleVariable`	Invalid `variable` reference in assignment rule	E	E	E	E	E	E
`InvalidRateRuleVariable`	Invalid `variable` reference in rate rule	E	E	E	E	E	E
`AssignmentToConstantEntity`	Cannot reassign a constant in an assignment rule	N	N	E	E	E	E
`RateRuleForConstantEntity`	Cannot reassign a constant in a rate rule	N	N	E	E	E	E
`CircularRuleDependency`	Circular dependency involving rules and reactions	N	N	N	E	E	E
`ConstraintMathNotBoolean`	Non-boolean math expression in constraint definition	N	N	N	E	E	E
`IncorrectOrderInConstraint`	Incorrect order of elements in constraint definition	N	N	N	E	E	E
`ConstraintNotInXHTMLNamespace`	Constraint message is not in XHTML XML namespace	N	N	N	E	E	E
`ConstraintContainsXMLDecl`	XML declarations not permitted in constraint messages	N	N	N	E	E	E
`ConstraintContainsDOCTYPE`	XML `DOCTYPE` not permitted in constraint messages	N	N	N	E	E	E
`InvalidConstraintContent`	Invalid content for constraint message	N	N	N	E	E	E
`NoReactantsOrProducts`	Cannot have a reaction with neither reactants nor products	E	E	E	E	E	E
`IncorrectOrderInReaction`	Incorrect ordering of components in reaction definition	E	E	E	E	E	E
`EmptyListInReaction`	Reaction components, if present, cannot be empty	E	E	E	E	E	E
`InvalidReactantsProductsList`	Invalid element in list of reactants or products	E	E	E	E	E	E
`InvalidModifiersList`	Invalid element in list of modifiers	N	N	E	E	E	E
`InvalidSpeciesReference`	Invalid `species` value in species reference	E	E	E	E	E	E
`BothStoichiometryAndMath`	Cannot use both `stoichiometry` and `<stoichiometryMath>` simultaneously	N	N	E	E	E	E
`UndeclaredSpeciesRef`	Undeclared species referenced in kinetic law formula	W	W	E	E	E	E
`IncorrectOrderInKineticLaw`	Incorrect ordering of components in kinetic law definition	N	N	E	E	E	E
`EmptyListInKineticLaw`	The list of parameters component, if present, cannot be empty	E	E	E	E	E	E
`NonConstantLocalParameter`	Parameters local to a kinetic law must have `constant`=`true`	N	N	W	E	E	E
`SubsUnitsNoLongerValid`	`substanceUnits` not supported in this Level+Version of SBML	N	N	N	E	E	N
`TimeUnitsNoLongerValid`	`timeUnits` not supported in this Level+Version of SBML	N	N	N	E	E	N
`UndeclaredSpeciesInStoichMath`	Undeclared species referenced in `<stoichiometryMath>` formula	N	N	W	E	E	E
`MissingTriggerInEvent`	Missing trigger in event definition	N	N	E	E	E	E
`TriggerMathNotBoolean`	Non-boolean math expression in trigger definition	N	N	E	E	E	E
`MissingEventAssignment`	Missing event assignment in event definition	N	N	E	E	E	E
`TimeUnitsEvent`	Units of `timeUnits` are not time units	N	N	E	E	N	N
`IncorrectOrderInEvent`	Incorrect ordering of components in event definition	N	N	E	E	E	E
`ValuesFromTriggerTimeNeedDelay`	`useValuesFromTriggerTime`=`false`, but no delay defined in event	N	N	N	N	N	E
`InvalidEventAssignmentVariable`	Invalid value for `variable` in event assignment	N	N	E	E	E	E
`EventAssignmentForConstantEntity`	Cannot assign to a constant component in an event assignment	N	N	W	E	E	E
`CompartmentShouldHaveSize`	It's best to define a size for every compartment in a model	N	N	W	W	W	W
`ParameterShouldHaveUnits`	It's best to declare units for every parameter in a model	W	W	W	W	W	W
`LocalParameterShadowsId`	Local parameters defined in a kinetic law shadow global parameters	W	W	W	W	W	W
`CannotConvertToL1V1`	Cannot convert to SBML Level 1 Version 1	N	E	E	E	E	E
`NoEventsInL1`	SBML Level 1 does not support events	N	N	E	E	E	E
`NoFunctionDefinitionsInL1`	SBML Level 1 does not support function definitions	N	N	E	E	E	E
`NoConstraintsInL1`	SBML Level 1 does not support constraints	N	N	N	W	W	W
`NoInitialAssignmentsInL1`	SBML Level 1 does not support initial assignments	N	N	N	E	E	E
`NoSpeciesTypesInL1`	SBML Level 1 does not support species types	N	N	N	W	W	W
`NoCompartmentTypeInL1`	SBML Level 1 does not support compartment types	N	N	N	W	W	W
`NoNon3DComparmentsInL1`	SBML Level 1 only supports three-dimensional compartments	N	N	E	E	E	E
`NoFancyStoichiometryMathInL1`	SBML Level 1 does not support non-integer nor non-rational stoichiometry formulas	N	N	E	E	E	E
`NoNonIntegerStoichiometryInL1`	SBML Level 1 does not support non-integer `stoichiometry` attribute values	N	N	E	E	E	E
`NoUnitMultipliersOrOffsetsInL1`	SBML Level 1 does not support multipliers or offsets in unit definitions	N	N	E	E	E	E
`SpeciesCompartmentRequiredInL1`	In SBML Level 1, a value for `compartment` is mandatory in species definitions	N	N	E	E	E	E
`NoSpeciesSpatialSizeUnitsInL1`	SBML Level 1 does not support species `spatialSizeUnits` settings	N	N	E	E	E	E
`NoSBOTermsInL1`	SBML Level 1 does not support the `sboTerm` attribute	N	N	N	W	W	W
`StrictUnitsRequiredInL1`	SBML Level 1 requires strict unit consistency	N	N	N	N	N	E
`NoConstraintsInL2v1`	SBML Level 2 Version 1 does not support constraints	N	N	N	W	W	W
`NoInitialAssignmentsInL2v1`	SBML Level 2 Version 1 does not support initial assignments	N	N	N	E	E	E
`NoSpeciesTypeInL2v1`	SBML Level 2 Version 1 does not support species types	N	N	N	W	W	W
`NoCompartmentTypeInL2v1`	SBML Level 2 Version 1 does not support compartment types	N	N	N	W	W	W
`NoSBOTermsInL2v1`	SBML Level 2 Version 1 does not support the `sboTerm` attribute	N	N	N	W	W	W
`NoIdOnSpeciesReferenceInL2v1`	SBML Level 2 Version 1 does not support the `id` attribute on species references	N	N	N	W	W	W
`NoDelayedEventAssignmentInL2v1`	Attribute `useValuesFromTriggerTime` not supported in this Level+Version of SBML	N	N	N	N	N	E
`StrictUnitsRequiredInL2v1`	SBML Level 2 Version 1 requires strict unit consistency	N	N	N	N	N	E
`SBOTermNotUniversalInL2v2`	The `sboTerm` attribute is invalid for this component in Level 2 Version 2	N	N	N	N	W	W
`NoUnitOffsetInL2v2`	The unit `offset` attribute is invalid in this Level+Version of SBML	N	N	E	N	N	N
`NoKineticLawTimeUnitsInL2v2`	The `timeUnits` attribute is invalid in this Level+Version of SBML	E	E	E	N	N	N
`NoKineticLawSubstanceUnitsInL2v2`	The `substanceUnits` attribute is invalid in this Level+Version of SBML	E	E	E	N	N	N
`NoDelayedEventAssignmentInL2v2`	Attribute `useValuesFromTriggerTime` not supported in this Level+Version of SBML	N	N	N	N	N	E
`ModelSBOBranchChangedBeyondL2v2`	The allowable `sboTerm` values for model differ for this SBML Level+Version	N	N	N	N	N	E
`StrictUnitsRequiredInL2v2`	SBML Level 2 Version 2 requires strict unit consistency	N	N	N	N	N	E
`StrictSBORequiredInL2v2`	SBML Level 2 Version 2 requires strict sbo consistency	N	N	N	N	N	E
`DuplicateAnnotationInvalidInL2v2`	Duplicate top level annotations invalid for this SBML Level+Version	W	W	W	N	N	N
`NoUnitOffsetInL2v3`	Attribute `offset` not supported in this Level+Version of SBML	N	N	E	N	N	N
`NoKineticLawTimeUnitsInL2v3`	Attribute `timeUnits` not supported in this Level+Version of SBML	E	E	E	N	N	N
`NoKineticLawSubstanceUnitsInL2v3`	Attribute `substanceUnits` not supported in this Level+Version of SBML	E	E	E	N	N	N
`NoSpeciesSpatialSizeUnitsInL2v3`	Attribute `spatialSizeUnits` not supported in this Level+Version of SBML	N	N	E	E	N	N
`NoEventTimeUnitsInL2v3`	Attribute `timeUnits` not supported in this Level+Version of SBML	N	N	E	E	N	N
`NoDelayedEventAssignmentInL2v3`	Attribute `useValuesFromTriggerTime` not supported in this Level+Version of SBML	N	N	N	N	N	E
`ModelSBOBranchChangedBeyondL2v3`	The allowable `sboTerm` values for model differ for this SBML Level+Version	N	N	N	N	N	E
`StrictUnitsRequiredInL2v3`	SBML Level 2 Version 3 requires strict unit consistency	N	N	N	N	N	E
`StrictSBORequiredInL2v3`	SBML Level 2 Version 3 requires strict sbo consistency	N	N	N	N	N	E
`DuplicateAnnotationInvalidInL2v3`	Duplicate top level annotations invalid for this SBML Level+Version	W	W	W	N	N	N
`NoUnitOffsetInL2v4`	The unit `offset` attribute is invalid in this Level+Version of SBML	N	N	E	N	N	N
`NoKineticLawTimeUnitsInL2v4`	The `timeUnits` attribute is invalid in this Level+Version of SBML	E	E	E	N	N	N
`NoKineticLawSubstanceUnitsInL2v4`	The `substanceUnits` attribute is invalid in this Level+Version of SBML	E	E	E	N	N	N
`NoSpeciesSpatialSizeUnitsInL2v4`	The `spatialSizeUnits` attribute is invalid in this Level+Version of SBML	N	N	E	E	N	N
`NoEventTimeUnitsInL2v4`	The `timeUnits` attribute is invalid in this Level+Version of SBML	N	N	E	E	N	N
`ModelSBOBranchChangedInL2v4`	The allowable `sboTerm` values for model differ for this SBML Level+Version	N	N	N	E	E	N
`DuplicateAnnotationInvalidInL2v4`	Duplicate top level annotations invalid for this SBML Level+Version	W	W	W	N	N	N
`InvalidSBMLLevelVersion`	Invalid SBML Level and Version	E	E	E	E	E	E
`InvalidRuleOrdering`	Invalid ordering of rules	E	E	E	N	N	N
`SubsUnitsAllowedInKL`	Disallowed value for attribute `substanceUnits`	E	E	E	N	N	N
`TimeUnitsAllowedInKL`	Disallowed value for attribute `timeUnits`	E	E	E	N	N	N
`FormulaInLevel1KL`	Only predefined functions are permitted in SBML Level 1 formulas	E	E	N	N	N	N
`TimeUnitsRemoved`	The `timeUnits` attribute is invalid in this Level+Version of SBML	N	N	N	N	E	E
`BadMathML`	Invalid MathML expression	N	N	E	E	E	E
`FailedMathMLReadOfDouble`	Failed to read floating-point number	N	N	E	E	E	E
`FailedMathMLReadOfInteger`	Failed to read an integer	N	N	E	E	E	E
`FailedMathMLReadOfExponential`	Failed to read an exponential expression	N	N	E	E	E	E
`FailedMathMLReadOfRational`	Failed to read a rational expression	N	N	E	E	E	E
`BadMathMLNodeType`	Invalid MathML element	N	N	E	E	E	E
`NoTimeSymbolInFunctionDef`	`<csymbol>` for `time` used within the `<math>` of a function definition	N	N	W	E	E	E
`UndeclaredUnits`	Undeclared units	W	W	W	W	W	W
`UnrecognisedSBOTerm`	Unrecognized `sboTerm` value	N	N	N	W	W	W
`ObseleteSBOTerm`	Obsolete `sboTerm` value	N	N	N	W	W	W
`IncorrectCompartmentSpatialDimensions`	in SBML Level 1, only three-dimensional compartments are permitted	E	E	N	N	N	N
`CompartmentTypeNotValidAttribute`	Compartment types not supported in this Level+Version of SBML	E	E	E	N	N	N
`ConstantNotValidAttribute`	Attribute `constant` not supported on this component in SBML Level 1	E	E	N	N	N	N
`MetaIdNotValidAttribute`	Attribute `metaid` not supported in SBML Level 1	E	E	N	N	N	N
`SBOTermNotValidAttributeBeforeL2V3`	`sboTerm` not available on this component before SBML Level 2 Version 3	E	E	E	E	N	N
`InvalidL1CompartmentUnits`	Invalid units for a compartment in SBML Level 1	E	E	N	N	N	N
`L1V1CompartmentVolumeReqd`	Compartment volume must be specified	E	N	N	N	N	N
`CompartmentTypeNotValidComponent`	Compartment types not supported in this Level+Version of SBML	E	E	E	N	N	N
`ConstraintNotValidComponent`	Constraints not supported in this Level+Version of SBML	E	E	E	N	N	N
`EventNotValidComponent`	Events not supported in this Level+Version of SBML	E	E	N	N	N	N
`SBOTermNotValidAttributeBeforeL2V2`	The `sboTerm` attribute is invalid for this component before Level 2 Version 2	E	E	E	N	N	N
`FuncDefNotValidComponent`	Function definitions are not supported in this Level+Version of SBML	E	E	N	N	N	N
`InitialAssignNotValidComponent`	Initial assignments are not supported in this Level+Version of SBML	E	E	E	N	N	N
`VariableNotValidAttribute`	Attribute `variable` not valid	E	E	E	E	E	E
`UnitsNotValidAttribute`	Attribute `units` not valid	E	E	E	E	E	E
`ConstantSpeciesNotValidAttribute`	Attribute `constant` on species not supported in SBML Level 1	E	E	N	N	N	N
`SpatialSizeUnitsNotValidAttribute`	Attribute `spatialSizeUnits` on species not supported in SBML Level 1	E	E	N	N	N	N
`SpeciesTypeNotValidAttribute`	Attribute `speciesType` on species not supported in SBML Level 1	E	E	E	N	N	N
`HasOnlySubsUnitsNotValidAttribute`	Attribute `hasOnlySubstanceUnits` on species not supported in SBML Level 1	E	E	N	N	N	N
`IdNotValidAttribute`	Attribute `id` on species references not supported in SBML Level 1	E	E	E	N	N	N
`NameNotValidAttribute`	Attribute `name` on species references not supported in SBML Level 1	E	E	E	N	N	N
`SpeciesTypeNotValidComponent`	Species types not supported in SBML Level 1	E	E	E	N	N	N
`StoichiometryMathNotValidComponent`	lt;stoichiometryMath> not supported in SBML Level 1	E	E	N	N	N	N
`MultiplierNotValidAttribute`	Attribute `multiplier` on units not supported in SBML Level 1	E	E	N	N	N	N
`OffsetNotValidAttribute`	Attribute `offset` on units only available in SBML Level 2 Version 1	E	E	N	N	N	N

Enumerator	Meaning
`LIBSBML_CAT_SBML`	General error not falling into another category below.
`LIBSBML_CAT_SBML_L1_COMPAT`	Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model from SBML Level 2 to SBML Level 1.
`LIBSBML_CAT_SBML_L2V1_COMPAT`	Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 2 Version 1.
`LIBSBML_CAT_SBML_L2V2_COMPAT`	Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 2 Version 2.
`LIBSBML_CAT_GENERAL_CONSISTENCY`	Category of errors that can occur while validating general SBML constructs. With respect to the SBML specification, these concern failures in applying the validation rules numbered 2xxxx in the Level 2 Versions 2 and 3 specifications.
`LIBSBML_CAT_IDENTIFIER_CONSISTENCY`	Category of errors that can occur while validating symbol identifiers in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 103xx in the Level 2 Versions 2 and 3 specifications.
`LIBSBML_CAT_UNITS_CONSISTENCY`	Category of errors that can occur while validating the units of measurement on quantities in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 105xx in the Level 2 Versions 2 and 3 specifications.
`LIBSBML_CAT_MATHML_CONSISTENCY`	Category of errors that can occur while validating MathML formulas in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 102xx in the Level 2 Versions 2 and 3 specifications.
`LIBSBML_CAT_SBO_CONSISTENCY`	Category of errors that can occur while validating SBO identifiers in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 107xx in the Level 2 Versions 2 and 3 specifications.
`LIBSBML_CAT_OVERDETERMINED_MODEL`	Error in the system of equations in the model: the system is overdetermined, therefore violating a tenet of proper SBML. With respect to the SBML specification, this is validation rule #10601 in the SBML Level 2 Versions 2 and 3 specifications.
`LIBSBML_CAT_SBML_L2V3_COMPAT`	Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 2 Version 3.
`LIBSBML_CAT_MODELING_PRACTICE`	Category of warnings about recommended good practices involving SBML and computational modeling. (These are tests performed by libSBML and do not have equivalent SBML validation rules.)
`LIBSBML_CAT_INTERNAL_CONSISTENCY`	Category of errors that can occur while validating libSBML's internal representation of SBML constructs. (These are tests performed by libSBML and do not have equivalent SBML validation rules.)
`LIBSBML_CAT_SBML_L2V4_COMPAT`	Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 2 Version 4.

Definition at line 30815 of file libsbml.py.


Public Member Functions
def	__eq__
def	__init__
def	__ne__
def	getCategory
def	getCategoryAsString
def	getColumn
def	getErrorId
def	getLine
def	getMessage
def	getSeverity
def	getSeverityAsString
def	getShortMessage
def	getStandardMessage
def	isError
def	isFatal
def	isInfo
def	isInternal
def	isSystem
def	isWarning
def	isXML
def	setColumn
def	setLine
Public Attributes
	this

Member Function Documentation

def libsbml.XMLError.__eq__	(	self,
		rhs
	)		`[inherited]`

Definition at line 30289 of file libsbml.py.

def libsbml.SBMLError.__init__	(	self,
		args
	)

Python method signature(s):

__init__(self, unsigned int errorId = 0, unsigned int level = 2, unsigned int version = 4, 
    string details = "", 
    unsigned int line = 0, unsigned int column = 0, 
    unsigned int severity = LIBSBML_SEV_ERROR, 
    unsigned int category = LIBSBML_CAT_SBML)    SBMLError
__init__(self, unsigned int errorId = 0, unsigned int level = 2, unsigned int version = 4, 
    string details = "", 
    unsigned int line = 0, unsigned int column = 0, 
    unsigned int severity = LIBSBML_SEV_ERROR)    SBMLError
__init__(self, unsigned int errorId = 0, unsigned int level = 2, unsigned int version = 4, 
    string details = "", 
    unsigned int line = 0, unsigned int column = 0)    SBMLError
__init__(self, unsigned int errorId = 0, unsigned int level = 2, unsigned int version = 4, 
    string details = "", 
    unsigned int line = 0)    SBMLError
__init__(self, unsigned int errorId = 0, unsigned int level = 2, unsigned int version = 4, 
    string details = "")    SBMLError
__init__(self, unsigned int errorId = 0, unsigned int level = 2, unsigned int version = 4)    SBMLError
__init__(self, unsigned int errorId = 0, unsigned int level = 2)    SBMLError
__init__(self, unsigned int errorId = 0)    SBMLError
__init__(self)    SBMLError
__init__(self, SBMLError orig)    SBMLError

Copy constructor; creates a copy of this SBMLError.

Reimplemented from libsbml.XMLError.

Definition at line 31377 of file libsbml.py.

def libsbml.XMLError.__ne__	(	self,
		rhs
	)		`[inherited]`

Definition at line 30296 of file libsbml.py.

def libsbml.XMLError.getCategory ( self ) [inherited]

Python method signature(s):

getCategory(self)    unsigned int

Returns the category of this error.

XMLError defines an enumeration of category codes for the XML layer. Applications that build on XMLError by subclassing it may add their own categories with numbers higher than those in the predefined set of category codes.

Categories can be used to partition errors into distinct groups. Among other things, this can be used to prevent id conflicts by uniquely identifying an XMLError by both id and category.

Returns:: the category of this XMLError.

See also:: getSeverity()
getCategoryAsString()

Definition at line 29979 of file libsbml.py.

def libsbml.XMLError.getCategoryAsString ( self ) [inherited]

Python method signature(s):

getCategoryAsString(self)    string

Returns a string describing the category of this error.

XMLError defines an enumeration of category codes for the XML layer. Applications that build on XMLError by subclassing it may add their own categories with numbers higher than those in the predefined set of category codes.

Categories can be used to partition errors into distinct groups. Among other things, this can be used to prevent id conflicts by uniquely identifying an XMLError by both id and category.

Returns:: string representing the category of this XMLError.

See also:: getCategory()
getSeverityAsString()

Definition at line 30006 of file libsbml.py.

def libsbml.XMLError.getColumn ( self ) [inherited]

Python method signature(s):

getColumn(self)    unsigned int

Returns the column number in the XML input near where the error, warning or other diagnostic occurred.

We say 'near where the problem occurred', because many factors affect how accurate the line/column information ultimately is. For example, different XML parsers have different conventions for which line and column number they report for a particular problem (which in turn makes a difference when a problem involves an opening XML tag on one line and a closing tag on another line). In some situations, some parsers report invalid line and/or column numbers altogether. If this occurs, the line and/or column number in the XMLError object will be set to the the value of the maximum unsigned long integer representable on the platform where libSBML is running. (This is equal to the constant named ULONG_MAX in C and C++.) The probability that a true line or column number in an SBML model would equal this value is vanishingly small; thus, if an application encounters these values in an XMLError object, it can assume no valid line/column number could be provided by libSBML in that situation.

Returns:: the column number

See also:: getLine()

Definition at line 29899 of file libsbml.py.

def libsbml.XMLError.getErrorId ( self ) [inherited]

Python method signature(s):

getErrorId(self)    unsigned int

Returns the identifier of this error.

Returns:: the id of this XMLError.

See also:

Definition at line 29789 of file libsbml.py.

def libsbml.XMLError.getLine ( self ) [inherited]

Python method signature(s):

getLine(self)    unsigned int

Returns the line number in the XML input near where the error, warning or other diagnostic occurred.

We say 'near where the problem occurred', because many factors affect how accurate the line/column information ultimately is. For example, different XML parsers have different conventions for which line and column number they report for a particular problem (which in turn makes a difference when a problem involves an opening XML tag on one line and a closing tag on another line). In some situations, some parsers report invalid line and/or column numbers altogether. If this occurs, the line and/or column number in the XMLError object will be set to the the value of the maximum unsigned long integer representable on the platform where libSBML is running. (This is equal to the constant named ULONG_MAX in C and C++.) The probability that a true line or column number in an SBML model would equal this value is vanishingly small; thus, if an application encounters these values in an XMLError object, it can assume no valid line/column number could be provided by libSBML in that situation.

Returns:: the line number

See also:: getColumn()

Definition at line 29865 of file libsbml.py.

def libsbml.XMLError.getMessage ( self ) [inherited]

Python method signature(s):

getMessage(self)    string

Returns the message text of this error.

The message associated with an error object describes the nature of the problem. The message returned by this method is generally longer and clearer than the message returned by XMLError.getShortMessage(), but not in all cases.

Callers may use XMLError.getCategory() and XMLError.getSeverity() to obtain additional information about the nature and severity of the problem.

Returns:: the message text

See also:

Definition at line 29809 of file libsbml.py.

def libsbml.XMLError.getSeverity ( self ) [inherited]

Python method signature(s):

getSeverity(self)    unsigned int

Returns the severity of this error.

XMLError defines an enumeration of severity codes for the XML layer. Applications that build on XMLError by subclassing it may add their own severity codes with numbers higher than those in the predefined set of severity codes.

Returns:: the severity of this XMLError.

See also:: getSeverityAsString()
getCategory()

Definition at line 29933 of file libsbml.py.

def libsbml.XMLError.getSeverityAsString ( self ) [inherited]

Python method signature(s):

getSeverityAsString(self)    string

Returns a string describing the severity level of this error.

XMLError defines an enumeration of severity codes for the XML layer. Applications that build on XMLError by subclassing it may add their own severity codes with numbers higher than those in the predefined set of severity codes.

Returns:: string representing the severity of this XMLError.

See also:: getSeverity()
getCategoryAsString()

Definition at line 29956 of file libsbml.py.

def libsbml.XMLError.getShortMessage ( self ) [inherited]

Python method signature(s):

getShortMessage(self)    string

Returns a brief message for this error.

This is an alternative error message that, in general, is as short as the authors could make it. However, brevity is often inversely proportional to clarity, so this short message may not be sufficiently informative to understand the nature of the error. Calling applications may wish to check XMLError.getMessage() in addition or instead.

Returns:: the short error message text

See also:

Definition at line 29838 of file libsbml.py.

def libsbml.XMLError.getStandardMessage ( args ) [inherited]

Python method signature(s):

getStandardMessage(int code)    string

Returns a copy of the message string associated with the given predefined XMLError code.

Parameters:

code

the error code whose message is sought; it must be a predefined value from

Definition at line 30267 of file libsbml.py.

def libsbml.XMLError.isError ( self ) [inherited]

Python method signature(s):

isError(self)    bool

Predicate returning true or false depending on whether this error is a significant error.

This is equivalent to obtaining the severity code from an XMLError object (via XMLError.getSeverity()) and then comparing it to the value LIBSBML_SEV_ERROR from the

Returns:: true if this error is an error, false otherwise.

See also:

isInfo()

isWarning()

isFatal()

Definition at line 30088 of file libsbml.py.

def libsbml.XMLError.isFatal ( self ) [inherited]

Python method signature(s):

isFatal(self)    bool

Predicate returning true or false depending on whether this error is a fatal run-time error.

This is equivalent to obtaining the severity code from an XMLError object (via XMLError.getSeverity()) and then comparing it to the value LIBSBML_SEV_FATAL from the

Returns:: true if this error is a fatal error, false otherwise.

See also:

isInfo()

isWarning()

isError()

Definition at line 30115 of file libsbml.py.

def libsbml.XMLError.isInfo ( self ) [inherited]

Python method signature(s):

isInfo(self)    bool

Predicate returning true or false depending on whether this error object is for information purposes only.

This is equivalent to obtaining the severity code from an XMLError object (via XMLError.getSeverity()) and then comparing it to the value LIBSBML_SEV_INFO from the

Returns:: true if this XMLError is for informational purposes only, false otherwise.

See also:

isWarning()

isError()

isFatal()

Definition at line 30033 of file libsbml.py.

def libsbml.XMLError.isInternal ( self ) [inherited]

Python method signature(s):

isInternal(self)    bool

Predicate returning true or false depending on whether this error resulted from an internal program error.

This is equivalent to obtaining the category identifier from an XMLError object (via XMLError.getCategory()) and then comparing it to the value LIBSBML_CAT_INTERNAL from the

Returns:: true or false

See also:: isSystem()
isXML()

Definition at line 30142 of file libsbml.py.

def libsbml.XMLError.isSystem ( self ) [inherited]

Python method signature(s):

isSystem(self)    bool

Predicate returning true or false depending on whether this error was generated by the operating system.

This is equivalent to obtaining the category identifier from an XMLError object (via XMLError.getCategory()) and then comparing it to the value LIBSBML_CAT_SYSTEM from the

Returns:: true or false

See also:: isInternal()
isXML()

Definition at line 30168 of file libsbml.py.

def libsbml.XMLError.isWarning ( self ) [inherited]

Python method signature(s):

isWarning(self)    bool

Predicate returning true or false depending on whether this error object is a warning.

This is equivalent to obtaining the severity code from an XMLError object (via XMLError.getSeverity()) and then comparing it to the value LIBSBML_SEV_WARNING from the

Returns:: true if this error is a warning, false otherwise.

See also:

isInfo()

isError()

isFatal()

Definition at line 30061 of file libsbml.py.

def libsbml.XMLError.isXML ( self ) [inherited]

Python method signature(s):

isXML(self)    bool

Predicate returning true or false depending on whether this error resulted from a problem in the XML input (e.g., an XML syntax error).

This is equivalent to obtaining the category identifier from an XMLError object (via XMLError.getCategory()) and then comparing it to the value LIBSBML_CAT_XML from the

Returns:: true or false

See also:: isInternal()
isSystem()

Definition at line 30194 of file libsbml.py.

def libsbml.XMLError.setColumn	(	self,
		args
	)		`[inherited]`

Python method signature(s):

setColumn(self, unsigned int column)    int

Sets the column number where this error occurred.

Parameters:

column

an unsigned int, the column number to set.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

See also:: setLine(unsigned int line)

Definition at line 30244 of file libsbml.py.

def libsbml.XMLError.setLine	(	self,
		args
	)		`[inherited]`

Python method signature(s):

setLine(self, unsigned int line)    int

Sets the line number where this error occurred.

Parameters:

line

an unsigned int, the line number to set.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

See also:: setColumn(unsigned int column)

Definition at line 30221 of file libsbml.py.

Member Data Documentation

libsbml.SBMLError.this

Reimplemented from libsbml.XMLError.

Definition at line 31411 of file libsbml.py.

libsbml.SBMLError Class Reference

Detailed Description

Public Member Functions

Public Attributes

Member Function Documentation

Member Data Documentation