libsbml.SBMLError Class Reference

Inheritance diagram for libsbml.SBMLError:

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List of all members.

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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, and it will come from one of two sets of static integer constants defined in the interface class libsbml: either the SBML error identifiers (described below) or the XML error identifiers (described in the documentation for the class XMLError). The former set of constants includes all the SBML validation rule numbers listed in the appendices of the SBML specification documents, as well as some additional libSBML-specific error codes.

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 drawn from a set of static integer constants defined in libsbml and having names beginning with the characters LIBSBML_CAT_. The list of possible codes is described in a separate section below. Categories are used to partition errors into distinct conceptual groups. This is principally used by the libSBML validation system to group classes of validation checks. For example, LIBSBML_CAT_IDENTIFIER_CONSISTENCY is the category for tests that check identifier consistency; LIBSBML_CAT_MATHML_CONSISTENCY is the category for MathML consistency checking; and so on.

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 XMLError. Severity levels currently range from informational (LIBSBML_SEV_INFO) to fatal errors (LIBSBML_SEV_FATAL). They can be used by an application to evaluate how serious a given problem is.

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.

Error codes associated with SBMLError objects

The error and warning codes returned by libSBML are listed in the table below. The method SBMLError.getErrorId() returns the error code of a given SBMLError object instance. In the libSBML Python language interface, these error identifiers are currently implemented as static integer constants defined in the interface class libsbml.

In this table, the right-hand columns titled 'L1V1', 'L1V2', etc. refer to Levels and Versions of the SBML specifications, and the entries in each column refer to whether the severity of the condition in that particular Level+Version of SBML. The codes stand for the following:

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	L 3 V 1
UnknownError	Encountered unknown internal libSBML error	F	F	F	F	F	F	F
NotUTF8	File does not use UTF-8 encoding	E	E	E	E	E	E	E
UnrecognizedElement	Encountered unrecognized element	E	E	E	E	E	E	E
NotSchemaConformant	Document does not conform to the SBML XML schema	E	E	E	E	E	E	E
L3NotSchemaConformant	Document is not well-formed XML	N	N	N	N	N	N	E
InvalidMathElement	Invalid MathML	N	N	E	E	E	E	E
DisallowedMathMLSymbol	Disallowed MathML symbol found	N	N	E	E	E	E	E
DisallowedMathMLEncodingUse	Use of the MathML 'encoding' attribute is not allowed on this element	N	N	E	E	E	E	E
DisallowedDefinitionURLUse	Use of the MathML 'definitionURL' attribute is not allowed on this element	N	N	E	E	E	E	E
BadCsymbolDefinitionURLValue	Invalid <csymbol> 'definitionURL' attribute value	N	N	E	E	E	E	E
DisallowedMathTypeAttributeUse	Use of the MathML 'type' attribute is not allowed on this element	N	N	E	E	E	E	E
DisallowedMathTypeAttributeValue	Disallowed MathML 'type' attribute value	N	N	E	E	E	E	E
LambdaOnlyAllowedInFunctionDef	Use of <lambda> not permitted outside of FunctionDefinition objects	N	N	E	E	E	E	E
BooleanOpsNeedBooleanArgs	Non-Boolean argument given to Boolean operator	N	N	W	E	E	E	E
NumericOpsNeedNumericArgs	Non-numerical argument given to numerical operator	N	N	W	E	E	E	E
ArgsToEqNeedSameType	Arguments to <eq> and <neq> must have the same data types	N	N	W	E	E	E	E
PiecewiseNeedsConsistentTypes	Terms in a <piecewise> expression must have consistent data types	N	N	W	E	E	E	E
PieceNeedsBoolean	The second argument of a <piece> expression must yield a Boolean value	N	N	W	E	E	E	E
ApplyCiMustBeUserFunction	A <ci> element in this context must refer to a function definition	N	N	W	E	E	E	E
ApplyCiMustBeModelComponent	A <ci> element in this context must refer to a model component	N	N	W	E	E	E	E
KineticLawParametersAreLocalOnly	Cannot use a KineticLaw local parameter outside of its local scope	N	N	W	E	E	E	E
MathResultMustBeNumeric	A formula's result in this context must be a numerical value	N	N	W	E	E	E	E
OpsNeedCorrectNumberOfArgs	Incorrect number of arguments given to MathML operator	N	N	W	E	E	E	E
InvalidNoArgsPassedToFunctionDef	Incorrect number of arguments given to function invocation	N	N	N	N	N	E	E
DisallowedMathUnitsUse	Attribute 'units' is only permitted on <cn> elements	N	N	N	N	N	N	E
InvalidUnitsValue	Invalid value given for the 'units' attribute	N	N	N	N	N	N	E
DuplicateComponentId	Duplicate 'id' attribute value	E	E	E	E	E	E	E
DuplicateUnitDefinitionId	Duplicate unit definition 'id' attribute value	E	E	E	E	E	E	E
DuplicateLocalParameterId	Duplicate local parameter 'id' attribute value	E	E	E	E	E	E	E
MultipleAssignmentOrRateRules	Multiple rules for the same variable are not allowed	E	E	E	E	E	E	E
MultipleEventAssignmentsForId	Multiple event assignments for the same variable are not allowed	N	N	E	E	E	E	E
EventAndAssignmentRuleForId	An event assignment and an assignment rule must not have the same value for 'variable'	N	N	E	E	E	E	E
DuplicateMetaId	Duplicate 'metaid' attribute value	N	N	E	E	E	E	E
InvalidSBOTermSyntax	Invalid syntax for an 'sboTerm' attribute value	N	N	N	E	E	E	E
InvalidMetaidSyntax	Invalid syntax for a 'metaid' attribute value	N	N	E	E	E	E	E
InvalidIdSyntax	Invalid syntax for an 'id' attribute value	E	E	E	E	E	E	E
InvalidUnitIdSyntax	Invalid syntax for the identifier of a unit	N	N	N	E	E	E	E
InvalidNameSyntax	Invalid syntax for a 'name' attribute value	N	N	N	N	N	N	E
MissingAnnotationNamespace	Missing declaration of the XML namespace for the annotation	N	N	N	E	E	E	E
DuplicateAnnotationNamespaces	Multiple annotations using the same XML namespace	N	N	N	E	E	E	E
SBMLNamespaceInAnnotation	The SBML XML namespace cannot be used in an Annotation object	N	N	N	E	E	E	N
MultipleAnnotations	Only one Annotation object is permitted under a given SBML object	N	N	N	N	N	N	E
InconsistentArgUnits	The units of the function call's arguments are not consistent with its definition	W	W	W	E	E	W	W
InconsistentKineticLawUnitsL3	The kinetic law's units are inconsistent with those of other kinetic laws in the model	N	N	N	N	N	N	W
AssignRuleCompartmentMismatch	Mismatched units in assignment rule for compartment	E	E	E	E	E	W	W
AssignRuleSpeciesMismatch	Mismatched units in assignment rule for species	E	E	E	E	E	W	W
AssignRuleParameterMismatch	Mismatched units in assignment rule for parameter	E	E	E	E	E	W	W
AssignRuleStoichiometryMismatch	Mismatched units in assignment rule for stoichiometry	N	N	N	N	N	N	W
InitAssignCompartmenMismatch	Mismatched units in initial assignment to compartment	N	N	N	E	E	W	W
InitAssignSpeciesMismatch	Mismatched units in initial assignment to species	N	N	N	E	E	W	W
InitAssignParameterMismatch	Mismatched units in initial assignment to parameter	N	N	N	E	E	W	W
InitAssignStoichiometryMismatch	Mismatched units in initial assignment to stoichiometry	N	N	N	N	N	N	W
RateRuleCompartmentMismatch	Mismatched units in rate rule for compartment	E	E	E	E	E	W	W
RateRuleSpeciesMismatch	Mismatched units in rate rule for species	E	E	E	E	E	W	W
RateRuleParameterMismatch	Mismatched units in rate rule for parameter	E	E	E	E	E	W	W
RateRuleStoichiometryMismatch	Mismatched units in rate rule for stoichiometry	N	N	N	N	N	N	W
KineticLawNotSubstancePerTime	The units of the kinetic law are not 'substance'/'time'	E	E	E	E	E	W	W
SpeciesInvalidExtentUnits	The species' units are not consistent with units of extent	N	N	N	N	N	N	W
DelayUnitsNotTime	The units of the delay expression are not units of time	N	N	E	E	E	W	W
EventAssignCompartmentMismatch	Mismatched units in event assignment for compartment	N	N	E	E	E	W	W
EventAssignSpeciesMismatch	Mismatched units in event assignment for species	N	N	E	E	E	W	W
EventAssignParameterMismatch	Mismatched units in event assignment for parameter	N	N	E	E	E	W	W
EventAssignStoichiometryMismatch	Mismatched units in event assignment for stoichiometry	N	N	N	N	N	N	W
PriorityUnitsNotDimensionless	The units of a priority expression must be 'dimensionless'	N	N	N	N	N	N	W
UpperUnitBound	Upper boundary of unit validation diagnostic codes	N	N	N	N	N	N	N
OverdeterminedSystem	The model is overdetermined	W	W	W	E	E	E	E
InvalidModelSBOTerm	Invalid 'sboTerm' attribute value for a Model object	N	N	N	E	E	W	W
InvalidFunctionDefSBOTerm	Invalid 'sboTerm' attribute value for a FunctionDefinition object	N	N	N	E	E	W	W
InvalidParameterSBOTerm	Invalid 'sboTerm' attribute value for a Parameter object	N	N	N	E	E	W	W
InvalidInitAssignSBOTerm	Invalid 'sboTerm' attribute value for an InitialAssignment object	N	N	N	E	E	W	W
InvalidRuleSBOTerm	Invalid 'sboTerm' attribute value for a Rule object	N	N	N	E	E	W	W
InvalidConstraintSBOTerm	Invalid 'sboTerm' attribute value for a Constraint object	N	N	N	E	E	W	W
InvalidReactionSBOTerm	Invalid 'sboTerm' attribute value for a Reaction object	N	N	N	E	E	W	W
InvalidSpeciesReferenceSBOTerm	Invalid 'sboTerm' attribute value for a SpeciesReference object	N	N	N	E	E	W	W
InvalidKineticLawSBOTerm	Invalid 'sboTerm' attribute value for a KineticLaw object	N	N	N	E	E	W	W
InvalidEventSBOTerm	Invalid 'sboTerm' attribute value for an Event object	N	N	N	E	E	W	W
InvalidEventAssignmentSBOTerm	Invalid 'sboTerm' attribute value for an EventAssignment object	N	N	N	E	E	W	W
InvalidCompartmentSBOTerm	Invalid 'sboTerm' attribute value for a Compartment object	N	N	N	N	E	W	W
InvalidSpeciesSBOTerm	Invalid 'sboTerm' attribute value for a Species object	N	N	N	N	E	W	W
InvalidCompartmentTypeSBOTerm	Invalid 'sboTerm' attribute value for a CompartmentType object	N	N	N	N	E	W	N
InvalidSpeciesTypeSBOTerm	Invalid 'sboTerm' attribute value for a SpeciesType object	N	N	N	N	E	W	N
InvalidTriggerSBOTerm	Invalid 'sboTerm' attribute value for an Event Trigger object	N	N	N	N	E	W	W
InvalidDelaySBOTerm	Invalid 'sboTerm' attribute value for an Event Delay object	N	N	N	N	E	W	W
NotesNotInXHTMLNamespace	Notes must be placed in the XHTML XML namespace	E	E	E	E	E	E	E
NotesContainsXMLDecl	XML declarations are not permitted in Notes objects	N	N	N	E	E	E	E
NotesContainsDOCTYPE	XML DOCTYPE elements are not permitted in Notes objects	N	N	N	E	E	E	E
InvalidNotesContent	Invalid notes content found	N	N	N	E	E	E	N
OnlyOneNotesElementAllowed	Only one Notes subobject is permitted on a given SBML object	N	N	N	N	N	N	E
InvalidNamespaceOnSBML	Invalid XML namespace for the SBML container element	E	E	E	E	E	E	E
MissingOrInconsistentLevel	Missing or inconsistent value for the 'level' attribute	E	E	E	E	E	E	E
MissingOrInconsistentVersion	Missing or inconsistent value for the 'version' attribute	E	E	E	E	E	E	E
PackageNSMustMatch	Inconsistent or invalid SBML Level/Version for the package namespace declaration	N	N	N	N	N	N	E
LevelPositiveInteger	The 'level' attribute must have a positive integer value	N	N	N	N	N	N	E
VersionPositiveInteger	The 'version' attribute must have a positive integer value	N	N	N	N	N	N	E
AllowedAttributesOnSBML	Invalid attribute found on the SBML container element	N	N	N	N	N	N	E
MissingModel	No model definition found	E	E	E	E	E	E	E
IncorrectOrderInModel	Incorrect ordering of components within the Model object	E	E	E	E	E	E	N
EmptyListElement	Empty ListOf___ object found	E	E	E	E	E	E	E
NeedCompartmentIfHaveSpecies	The presence of a species requires a compartment	E	E	E	E	E	E	E
OneOfEachListOf	Only one of each kind of ListOf___ object is allowed inside a Model object	N	N	N	N	N	N	E
OnlyFuncDefsInListOfFuncDefs	Only FunctionDefinition, Notes and Annotation objects are allowed in ListOfFunctionDefinitions	N	N	N	N	N	N	E
OnlyUnitDefsInListOfUnitDefs	Only UnitDefinition, Notes and Annotation objects are allowed in ListOfUnitDefinitions objects	N	N	N	N	N	N	E
OnlyCompartmentsInListOfCompartments	Only Compartment, Notes and Annotation objects are allowed in ListOfCompartments objects	N	N	N	N	N	N	E
OnlySpeciesInListOfSpecies	Only Species, Notes and Annotation objects are allowed in ListOfSpecies objects	N	N	N	N	N	N	E
OnlyParametersInListOfParameters	Only Parameter, Notes and Annotation objects are allowed in ListOfParameters objects	N	N	N	N	N	N	E
OnlyInitAssignsInListOfInitAssigns	Only InitialAssignment, Notes and Annotation objects are allowed in ListOfInitialAssignments objects	N	N	N	N	N	N	E
OnlyRulesInListOfRules	Only Rule, Notes and Annotation objects are allowed in ListOfRules objects	N	N	N	N	N	N	E
OnlyConstraintsInListOfConstraints	Only Constraint, Notes and Annotation objects are allowed in ListOfConstraints objects	N	N	N	N	N	N	E
OnlyReactionsInListOfReactions	Only Reaction, Notes and Annotation objects are allowed in ListOfReactions objects	N	N	N	N	N	N	E
OnlyEventsInListOfEvents	Only Event, Notes and Annotation objects are allowed in ListOfEvents objects	N	N	N	N	N	N	E
L3ConversionFactorOnModel	A 'conversionFactor' attribute value must reference a Parameter object	N	N	N	N	N	N	E
L3TimeUnitsOnModel	Invalid 'timeUnits' attribute value	N	N	N	N	N	N	W
L3VolumeUnitsOnModel	Invalid 'volumeUnits' attribute value	N	N	N	N	N	N	W
L3AreaUnitsOnModel	Invalid 'areaUnits' attribute value	N	N	N	N	N	N	W
L3LengthUnitsOnModel	Invalid 'lengthUnits' attribute value	N	N	N	N	N	N	W
L3ExtentUnitsOnModel	Invalid 'extentUnits' attribute value	N	N	N	N	N	N	W
AllowedAttributesOnModel	Invalid attribute found on the Model object	N	N	N	N	N	N	E
AllowedAttributesOnListOfFuncs	Invalid attribute found on the ListOfFunctionDefinitions object	N	N	N	N	N	N	E
AllowedAttributesOnListOfUnitDefs	Invalid attribute found on the ListOfUnitDefinitions object	N	N	N	N	N	N	E
AllowedAttributesOnListOfComps	Invalid attribute found on the ListOfCompartments object	N	N	N	N	N	N	E
AllowedAttributesOnListOfSpecies	Invalid attribute found on the ListOfSpecies object	N	N	N	N	N	N	E
AllowedAttributesOnListOfParams	Invalid attribute found on the ListOfParameters object	N	N	N	N	N	N	E
AllowedAttributesOnListOfInitAssign	Invalid attribute found on the ListOfInitialAssignments object	N	N	N	N	N	N	E
AllowedAttributesOnListOfRules	Invalid attribute found on the ListOfRules object	N	N	N	N	N	N	E
AllowedAttributesOnListOfConstraints	Invalid attribute found on the ListOfConstraints object	N	N	N	N	N	N	E
AllowedAttributesOnListOfReactions	Invalid attribute found on the ListOfReactions object	N	N	N	N	N	N	E
AllowedAttributesOnListOfEvents	Invalid attribute found on the ListOfEvents object	N	N	N	N	N	N	E
FunctionDefMathNotLambda	Invalid expression found in the function definition	N	N	E	E	E	E	E
InvalidApplyCiInLambda	Invalid forward reference in the MathML <apply><ci>...</ci></apply> expression	N	N	E	E	E	N	N
RecursiveFunctionDefinition	Recursive function definitions are not permitted	N	N	E	E	E	E	E
InvalidCiInLambda	Invalid <ci> reference found inside the <lambda> mathematical formula	N	N	E	E	E	E	E
InvalidFunctionDefReturnType	A function's return type must be either a number or a Boolean	N	N	E	E	E	E	E
OneMathElementPerFunc	A FunctionDefinition object must contain one <math> element	N	N	N	N	N	N	E
AllowedAttributesOnFunc	Invalid attribute found on the FunctionDefinition object	N	N	N	N	N	N	E
InvalidUnitDefId	Invalid 'id' attribute value for a UnitDefinition object	E	E	E	E	E	E	E
InvalidSubstanceRedefinition	Invalid redefinition of built-in type 'substance'	E	E	E	E	E	E	N
InvalidLengthRedefinition	Invalid redefinition of built-in type 'length'	W	W	E	E	E	E	N
InvalidAreaRedefinition	Invalid redefinition of built-in type name 'area'	W	W	E	E	E	E	N
InvalidTimeRedefinition	Invalid redefinition of built-in type name 'time'	E	E	E	E	E	E	N
InvalidVolumeRedefinition	Invalid redefinition of built-in type name 'volume'	E	E	E	E	E	E	N
VolumeLitreDefExponentNotOne	Must use 'exponent'=1 when defining 'volume' in terms of litres	E	E	E	E	E	N	N
VolumeMetreDefExponentNot3	Must use 'exponent'=3 when defining 'volume' in terms of metres	N	N	E	E	E	N	N
EmptyListOfUnits	An empty list of Unit objects is not permitted in a UnitDefinition object	E	E	E	E	E	E	N
InvalidUnitKind	Invalid value for the 'kind' attribute of a UnitDefinition object	E	E	E	E	E	E	E
OffsetNoLongerValid	Unit attribute 'offset' is not supported in this Level+Version of SBML	N	N	N	E	E	E	N
CelsiusNoLongerValid	Unit name 'Celsius' is not defined in this Level+Version of SBML	N	N	N	E	E	E	N
EmptyUnitListElement	A ListOfUnits object must not be empty	N	N	N	N	N	N	E
OneListOfUnitsPerUnitDef	At most one ListOfUnits object is allowed inside a UnitDefinition object	N	N	N	N	N	N	E
OnlyUnitsInListOfUnits	Only Unit, Notes and Annotation objects are allowed in ListOfUnits objects	N	N	N	N	N	N	E
AllowedAttributesOnUnitDefinition	Invalid attribute found on the UnitDefinition object	N	N	N	N	N	N	E
AllowedAttributesOnListOfUnits	Invalid attribute found on the ListOfUnits object	N	N	N	N	N	N	E
AllowedAttributesOnUnit	Invalid attribute found on the Unit object	N	N	N	N	N	N	E
ZeroDimensionalCompartmentSize	Invalid use of the 'size' attribute for a zero-dimensional compartment	N	N	E	E	E	E	N
ZeroDimensionalCompartmentUnits	Invalid use of the 'units' attribute for a zero-dimensional compartment	N	N	E	E	E	E	N
ZeroDimensionalCompartmentConst	Zero-dimensional compartments must be defined to be constant	N	N	E	E	E	E	N
UndefinedOutsideCompartment	Invalid value for the 'outside' attribute of a Compartment object	E	E	E	E	E	E	N
RecursiveCompartmentContainment	Recursive nesting of compartments via the 'outside' attribute is not permitted	W	W	W	E	E	E	N
ZeroDCompartmentContainment	Invalid nesting of zero-dimensional compartments	N	N	W	E	E	E	N
Invalid1DCompartmentUnits	Invalid value for the 'units' attribute of a one-dimensional compartment	N	N	E	E	E	E	W
Invalid2DCompartmentUnits	Invalid value for the 'units' attribute of a two-dimensional compartment	N	N	E	E	E	E	W
Invalid3DCompartmentUnits	Invalid value for the 'units' attribute of a three-dimensional compartment	E	E	E	E	E	E	W
InvalidCompartmentTypeRef	Invalid value for the 'compartmentType' attribute of a compartment	N	N	N	E	E	E	N
OneDimensionalCompartmentUnits	No units defined for 1-D compartment	N	N	N	N	N	N	W
TwoDimensionalCompartmentUnits	No units defined for 2-D compartment	N	N	N	N	N	N	W
ThreeDimensionalCompartmentUnits	No units defined for 3-D Compartment object	N	N	N	N	N	N	W
AllowedAttributesOnCompartment	Invalid attribute found on Compartment object	N	N	N	N	N	N	E
NoUnitsOnCompartment	No units defined for Compartment object	N	N	N	N	N	N	W
InvalidSpeciesCompartmentRef	Invalid value found for Species 'compartment' attribute	E	E	E	E	E	E	E
HasOnlySubsNoSpatialUnits	Attribute 'spatialSizeUnits' must not be set if 'hasOnlySubstanceUnits'='true'	N	N	E	E	N	N	N
NoSpatialUnitsInZeroD	Attribute 'spatialSizeUnits' must not be set if the compartment is zero-dimensional	N	N	E	E	N	N	N
NoConcentrationInZeroD	Attribute 'initialConcentration' must not be set if the compartment is zero-dimensional	N	N	E	E	E	E	N
SpatialUnitsInOneD	Invalid value for 'spatialSizeUnits' attribute of a one-dimensional compartment	N	N	E	E	N	N	N
SpatialUnitsInTwoD	Invalid value for the 'spatialSizeUnits' attribute of a two-dimensional compartment	N	N	E	E	N	N	N
SpatialUnitsInThreeD	Invalid value for the 'spatialSizeUnits' attribute of a three-dimensional compartment	N	N	E	E	N	N	N
InvalidSpeciesSusbstanceUnits	Invalid value for a Species 'units' attribute	E	E	E	E	E	E	W
BothAmountAndConcentrationSet	Cannot set both 'initialConcentration' and 'initialAmount' attributes simultaneously	N	N	E	E	E	E	E
NonBoundarySpeciesAssignedAndUsed	Cannot use a non-boundary species in both reactions and rules simultaneously	W	W	E	E	E	E	E
NonConstantSpeciesUsed	Cannot use a constant, non-boundary species as a reactant or product	N	N	E	E	E	E	E
InvalidSpeciesTypeRef	Invalid value for the 'speciesType' attribute of a species	N	N	N	E	E	E	N
MultSpeciesSameTypeInCompartment	Cannot have multiple species of the same species type in the same compartment	N	N	N	E	E	E	N
MissingSpeciesCompartment	Missing value for the 'compartment' attribute	E	E	E	E	E	E	E
SpatialSizeUnitsRemoved	Attribute 'spatialSizeUnits' is not supported in this Level+Version of SBML	N	N	N	N	E	E	N
SubstanceUnitsOnSpecies	No substance units defined for the species	N	N	N	N	N	N	W
ConversionFactorOnSpecies	Invalid value for the 'conversionFactor' attribute	N	N	N	N	N	N	E
AllowedAttributesOnSpecies	Invalid attribute found on Species object	N	N	N	N	N	N	E
InvalidParameterUnits	Invalid value for the 'units' attribute of a Parameter object	E	E	E	E	E	E	E
ParameterUnits	No units defined for the parameter	N	N	N	N	N	N	W
ConversionFactorMustConstant	A conversion factor must reference a Parameter object declared to be a constant	N	N	N	N	N	N	E
AllowedAttributesOnParameter	Invalid attribute found on Parameter object	N	N	N	N	N	N	E
InvalidInitAssignSymbol	Invalid value for the 'symbol' attribute of an InitialAssignment object	N	N	N	E	E	E	E
MultipleInitAssignments	Multiple initial assignments for the same 'symbol' value are not allowed	N	N	N	E	E	E	E
InitAssignmentAndRuleForSameId	Cannot set a value using both an initial assignment and an assignment rule simultaneously	N	N	N	E	E	E	E
OneMathElementPerInitialAssign	An InitialAssignment object must contain one <math> element	N	N	N	N	N	N	E
AllowedAttributesOnInitialAssign	Invalid attribute found on an InitialAssignment object	N	N	N	N	N	N	E
InvalidAssignRuleVariable	Invalid value for the 'variable' attribute of an AssignmentRule object	E	E	E	E	E	E	E
InvalidRateRuleVariable	Invalid value for the 'variable' attribute of a RateRule object	E	E	E	E	E	E	E
AssignmentToConstantEntity	An assignment rule cannot assign an entity declared to be constant	N	N	E	E	E	E	E
RateRuleForConstantEntity	A rate rule cannot assign an entity declared to be constant	N	N	E	E	E	E	E
CircularRuleDependency	Circular dependencies involving rules and reactions are not permitted	N	N	N	E	E	E	E
OneMathElementPerRule	A rule object must contain one <math> element	N	N	N	N	N	N	E
AllowedAttributesOnAssignRule	Invalid attribute found on an AssignmentRule object	N	N	N	N	N	N	E
AllowedAttributesOnRateRule	Invalid attribute found on a RateRule object	N	N	N	N	N	N	E
AllowedAttributesOnAlgRule	Invalid attribute found on an AlgebraicRule object	N	N	N	N	N	N	E
ConstraintMathNotBoolean	A Constraint object's <math> must evaluate to a Boolean value	N	N	N	E	E	E	E
IncorrectOrderInConstraint	Subobjects inside the Constraint object are not in the prescribed order	N	N	N	E	E	E	N
ConstraintNotInXHTMLNamespace	A Constraint's Message subobject must be in the XHTML XML namespace	N	N	N	E	E	E	N
ConstraintContainsXMLDecl	XML declarations are not permitted within Constraint's Message objects	N	N	N	E	E	E	E
ConstraintContainsDOCTYPE	XML DOCTYPE elements are not permitted within Constraint's Message objects	N	N	N	E	E	E	E
InvalidConstraintContent	Invalid content for a Constraint object's Message object	N	N	N	E	E	E	N
OneMathElementPerConstraint	A Constraint object must contain one <math> element	N	N	N	N	N	N	E
OneMessageElementPerConstraint	A Constraint object must contain one Message subobject	N	N	N	N	N	N	E
AllowedAttributesOnConstraint	Invalid attribute found on Constraint object	N	N	N	N	N	N	E
NoReactantsOrProducts	Cannot have a reaction with neither reactants nor products	E	E	E	E	E	E	E
IncorrectOrderInReaction	Subobjects inside the Reaction object are not in the prescribed order	E	E	E	E	E	E	N
EmptyListInReaction	Reaction components, if present, cannot be empty	E	E	E	E	E	E	E
InvalidReactantsProductsList	Invalid object found in the list of reactants or products	E	E	E	E	E	E	E
InvalidModifiersList	Invalid object found in the list of modifiers	N	N	E	E	E	E	E
OneSubElementPerReaction	A Reaction object can only contain one of each allowed type of object	N	N	N	N	N	N	E
CompartmentOnReaction	Invalid value for the Reaction 'compartment' attribute	N	N	N	N	N	N	E
AllowedAttributesOnReaction	Invalid attribute for a Reaction object	N	N	N	N	N	N	E
InvalidSpeciesReference	Invalid 'species' attribute value in SpeciesReference object	E	E	E	E	E	E	E
BothStoichiometryAndMath	The 'stoichiometry' attribute and StoichiometryMath subobject are mutually exclusive	N	N	E	E	E	E	N
AllowedAttributesOnSpeciesReference	Invalid attribute found on the SpeciesReference object	N	N	N	N	N	N	E
AllowedAttributesOnModifier	Invalid attribute found on the ModifierSpeciesReference object	N	N	N	N	N	N	E
UndeclaredSpeciesRef	Unknown species referenced in the kinetic law <math> formula	W	W	E	E	E	E	E
IncorrectOrderInKineticLaw	Incorrect ordering of components in the KineticLaw object	N	N	E	E	E	E	N
EmptyListInKineticLaw	The list of parameters, if present, cannot be empty	E	E	E	E	E	E	E
NonConstantLocalParameter	Parameters local to a KineticLaw object must have a 'constant' attribute value of 'true'	N	N	W	E	E	E	N
SubsUnitsNoLongerValid	Attribute 'substanceUnits' is not supported in this Level+Version of SBML	N	N	N	E	E	E	N
TimeUnitsNoLongerValid	Attribute 'timeUnits' is not supported in this Level+Version of SBML	N	N	N	E	E	E	N
OneListOfPerKineticLaw	Only one ListOfLocalParameters object is permitted within a KineticLaw object	N	N	N	N	N	N	E
OnlyLocalParamsInListOfLocalParams	Only LocalParameter, Notes and Annotation objects are allowed in ListOfLocalParameter objects	N	N	N	N	N	N	E
AllowedAttributesOnListOfLocalParam	Invalid attribute found on the ListOfLocalParameters object	N	N	N	N	N	N	E
OneMathPerKineticLaw	Only one <math> element is allowed in a KineticLaw object	N	N	E	E	E	E	E
UndeclaredSpeciesInStoichMath	Unknown species referenced in the StoichiometryMath object's <math> formula	N	N	W	E	E	E	N
AllowedAttributesOnKineticLaw	Invalid attribute found on the KineticLaw object	N	N	N	N	N	N	E
AllowedAttributesOnListOfSpeciesRef	Invalid attribute found on the ListOfSpeciesReferences object	N	N	N	N	N	N	E
AllowedAttributesOnListOfMods	Invalid attribute found on the ListOfModifiers object	N	N	N	N	N	N	E
AllowedAttributesOnLocalParameter	Invalid attribute found on the LocalParameter object	N	N	N	N	N	N	E
MissingTriggerInEvent	The Event object is missing a Trigger subobject	N	N	E	E	E	E	E
TriggerMathNotBoolean	A Trigger object's <math> expression must evaluate to a Boolean value	N	N	E	E	E	E	E
MissingEventAssignment	The Event object is missing an EventAssignment subobject	N	N	E	E	E	E	E
TimeUnitsEvent	Units referenced by 'timeUnits' attribute are not compatible with units of time	N	N	E	E	N	N	N
IncorrectOrderInEvent	Incorrect ordering of components in Event object	N	N	E	E	E	E	N
ValuesFromTriggerTimeNeedDelay	Attribute 'useValuesFromTriggerTime'='false', but the Event object does not define a delay	N	N	N	N	N	E	N
DelayNeedsValuesFromTriggerTime	The use of a Delay object requires the Event attribute 'useValuesFromTriggerTime'	N	N	N	N	N	N	N
OneMathPerTrigger	A Trigger object must have one <math> element	N	N	N	N	N	N	E
OneMathPerDelay	A Delay object must have one <math> element	N	N	N	N	N	N	E
InvalidEventAssignmentVariable	Invalid 'variable' attribute value in Event object	N	N	E	E	E	E	E
EventAssignmentForConstantEntity	An EventAssignment object cannot assign to a component having attribute 'constant'='true'	N	N	W	E	E	E	E
OneMathPerEventAssignment	An EventAssignment object must have one <math> element	N	N	N	N	N	N	E
AllowedAttributesOnEventAssignment	Invalid attribute found on the EventAssignment object	N	N	N	N	N	N	E
OnlyOneDelayPerEvent	An Event object can only have one Delay subobject	N	N	N	N	N	N	E
OneListOfEventAssignmentsPerEvent	An Event object can only have one ListOfEventAssignments subobject	N	N	N	N	N	N	E
OnlyEventAssignInListOfEventAssign	Only EventAssignment, Notes and Annotation objects are allowed in ListOfEventAssignments	N	N	N	N	N	N	E
AllowedAttributesOnListOfEventAssign	Invalid attribute found on the ListOfEventAssignments object	N	N	N	N	N	N	E
AllowedAttributesOnEvent	Invalid attribute found on the Event object	N	N	N	N	N	N	E
AllowedAttributesOnTrigger	Invalid attribute found on the Trigger object	N	N	N	N	N	N	E
AllowedAttributesOnDelay	Invalid attribute found on the Delay object	N	N	N	N	N	N	E
PersistentNotBoolean	The Trigger attribute 'persistent' must evaluate to a Boolean value	N	N	N	N	N	N	E
InitialValueNotBoolean	The Trigger attribute 'initialValue' must evaluate to a Boolean value	N	N	N	N	N	N	E
OnlyOnePriorityPerEvent	An Event object can only have one Priority subobject	N	N	N	N	N	N	E
OneMathPerPriority	A Priority object must have one <math> element	N	N	N	N	N	N	E
AllowedAttributesOnPriority	Invalid attribute found on the Priority object	N	N	N	N	N	N	E
GeneralWarningNotSpecified	Unknown error	N	N	N	N	N	N	N
CompartmentShouldHaveSize	It's best to define a size for every compartment in a model	N	N	W	W	W	W	W
SpeciesShouldHaveValue	It's best to define an initial amount or initial concentration for every species in a model	N	N	W	W	W	W	W
ParameterShouldHaveUnits	It's best to declare units for every parameter in a model	W	W	W	W	W	W	W
LocalParameterShadowsId	Local parameters defined within a kinetic law shadow global object symbols	W	W	W	W	W	W	W
CannotConvertToL1V1	Cannot convert to SBML Level 1 Version 1	N	E	E	E	E	E	E
NoEventsInL1	SBML Level 1 does not support events	N	N	E	E	E	E	E
NoFunctionDefinitionsInL1	SBML Level 1 does not support function definitions	N	N	E	E	E	E	E
NoConstraintsInL1	SBML Level 1 does not support constraints	N	N	N	W	W	W	W
NoInitialAssignmentsInL1	SBML Level 1 does not support initial assignments	N	N	N	E	E	E	E
NoSpeciesTypesInL1	SBML Level 1 does not support species types	N	N	N	W	W	W	N
NoCompartmentTypeInL1	SBML Level 1 does not support compartment types	N	N	N	W	W	W	N
NoNon3DCompartmentsInL1	SBML Level 1 only supports three-dimensional compartments	N	N	E	E	E	E	E
NoFancyStoichiometryMathInL1	SBML Level 1 does not support non-integer nor non-rational stoichiometry formulas	N	N	E	E	E	E	E
NoNonIntegerStoichiometryInL1	SBML Level 1 does not support non-integer 'stoichiometry' attribute values	N	N	E	E	E	E	E
NoUnitMultipliersOrOffsetsInL1	SBML Level 1 does not support multipliers or offsets in unit definitions	N	N	E	E	E	E	E
SpeciesCompartmentRequiredInL1	In SBML Level 1, a value for 'compartment' is mandatory in species definitions	N	N	E	E	E	E	E
NoSpeciesSpatialSizeUnitsInL1	SBML Level 1 does not support species 'spatialSizeUnits' settings	N	N	E	E	E	E	N
NoSBOTermsInL1	SBML Level 1 does not support the 'sboTerm' attribute	N	N	N	W	W	W	W
StrictUnitsRequiredInL1	SBML Level 1 requires strict unit consistency	N	N	N	N	N	W	W
ConversionFactorNotInL1	SBML Level 1 does not support the 'conversionFactor' attribute	N	N	N	N	N	N	E
CompartmentNotOnL1Reaction	SBML Level 1 does not support the 'compartment' attribute on Reaction objects	N	N	N	N	N	N	W
ExtentUnitsNotSubstance	Units of extent must be compatible with units of substance	N	N	N	N	N	N	E
NoConstraintsInL2v1	SBML Level 2 Version 1 does not support Constraint objects	N	N	N	W	W	W	W
NoInitialAssignmentsInL2v1	SBML Level 2 Version 1 does not support InitialAssignment objects	N	N	N	E	E	E	E
NoSpeciesTypeInL2v1	SBML Level 2 Version 1 does not support SpeciesType objects	N	N	N	W	W	W	N
NoCompartmentTypeInL2v1	SBML Level 2 Version 1 does not support CompartmentType objects	N	N	N	W	W	W	N
NoSBOTermsInL2v1	SBML Level 2 Version 1 does not support the 'sboTerm' attribute	N	N	N	W	W	W	W
NoIdOnSpeciesReferenceInL2v1	SBML Level 2 Version 1 does not support the 'id' attribute on SpeciesReference objects	N	N	N	W	W	W	W
NoDelayedEventAssignmentInL2v1	SBML Level 2 Version 1 does not support the 'useValuesFromTriggerTime' attribute	N	N	N	N	N	E	E
StrictUnitsRequiredInL2v1	SBML Level 2 Version 1 requires strict unit consistency	N	N	N	N	N	W	W
IntegerSpatialDimensions	SBML Level 2 Version 1 requires that compartments have spatial dimensions of 0-3	N	N	N	N	N	N	E
StoichiometryMathNotYetSupported	Conversion to StoichiometryMath objects not yet supported	N	N	N	N	N	N	N
PriorityLostFromL3	SBML Level 2 Version 1 does not support priorities on Event objects	N	N	N	N	N	N	W
NonPersistentNotSupported	SBML Level 2 Version 1 does not support the 'persistent' attribute on Trigger objects	N	N	N	N	N	N	E
InitialValueFalseEventNotSupported	SBML Level 2 Version 1 does not support the 'initialValue' attribute on Trigger objects	N	N	N	N	N	N	E
SBOTermNotUniversalInL2v2	The 'sboTerm' attribute is invalid for this component in SBML Level 2 Version 2	N	N	N	N	W	W	W
NoUnitOffsetInL2v2	This Level+Version of SBML does not support the 'offset' attribute on Unit objects	N	N	E	N	N	N	N
NoKineticLawTimeUnitsInL2v2	This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects	E	E	E	N	N	N	N
NoKineticLawSubstanceUnitsInL2v2	This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects	E	E	E	N	N	N	N
NoDelayedEventAssignmentInL2v2	This Level+Version of SBML does not support the 'useValuesFromTriggerTime' attribute	N	N	N	N	N	E	E
ModelSBOBranchChangedBeyondL2v2	The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version	N	N	N	N	N	E	E
StrictUnitsRequiredInL2v2	SBML Level 2 Version 2 requires strict unit consistency	N	N	N	N	N	W	W
StrictSBORequiredInL2v2	SBML Level 2 Version 2 requires strict SBO term consistency	N	N	N	N	N	W	W
DuplicateAnnotationInvalidInL2v2	Duplicate top-level annotations are invalid in SBML Level 2 Version 2	W	W	W	N	N	N	N
NoUnitOffsetInL2v3	This Level+Version of SBML does not support the 'offset' attribute on Unit objects	N	N	E	N	N	N	N
NoKineticLawTimeUnitsInL2v3	This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects	E	E	E	N	N	N	N
NoKineticLawSubstanceUnitsInL2v3	This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects	E	E	E	N	N	N	N
NoSpeciesSpatialSizeUnitsInL2v3	This Level+Version of SBML does not support the 'spatialSizeUnit' attribute on Species objects	N	N	E	E	N	N	N
NoEventTimeUnitsInL2v3	This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects	N	N	E	E	N	N	N
NoDelayedEventAssignmentInL2v3	This Level+Version of SBML does not support the 'useValuesFromTriggerTime' attribute	N	N	N	N	N	E	E
ModelSBOBranchChangedBeyondL2v3	The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version	N	N	N	N	N	E	E
StrictUnitsRequiredInL2v3	SBML Level 2 Version 3 requires strict unit consistency	N	N	N	N	N	W	W
StrictSBORequiredInL2v3	SBML Level 2 Version 3 requires strict SBO term consistency	N	N	N	N	N	W	W
DuplicateAnnotationInvalidInL2v3	Duplicate top-level annotations are invalid in SBML Level 2 Version 3	W	W	W	N	N	N	N
NoUnitOffsetInL2v4	This Level+Version of SBML does not support the 'offset' attribute on Unit objects	N	N	E	N	N	N	N
NoKineticLawTimeUnitsInL2v4	This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects	E	E	E	N	N	N	N
NoKineticLawSubstanceUnitsInL2v4	This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects	E	E	E	N	N	N	N
NoSpeciesSpatialSizeUnitsInL2v4	This Level+Version of SBML does not support the 'spatialSizeUnit' attribute on Species objects	N	N	E	E	N	N	N
NoEventTimeUnitsInL2v4	This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects	N	N	E	E	N	N	N
ModelSBOBranchChangedInL2v4	The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version	N	N	N	E	E	N	N
DuplicateAnnotationInvalidInL2v4	Duplicate top-level annotations are invalid in SBML Level 2 Version 4	W	W	W	N	N	N	N
NoSpeciesTypeInL3v1	SBML Level 3 Version 1 does not support SpeciesType objects	N	N	N	W	W	W	N
NoCompartmentTypeInL3v1	SBML Level 3 Version 1 does not support CompartmentType objects	N	N	N	W	W	W	N
NoUnitOffsetInL3v1	This Level+Version of SBML does not support the 'offset' attribute on Unit objects	N	N	E	N	N	N	N
NoKineticLawTimeUnitsInL3v1	This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects	E	E	E	N	N	N	N
NoKineticLawSubstanceUnitsInL3v1	This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects	E	E	E	N	N	N	N
NoSpeciesSpatialSizeUnitsInL3v1	This Level+Version of SBML does not support the 'spatialSizeUnit' attribute on Species objects	N	N	E	E	N	N	N
NoEventTimeUnitsInL3v1	This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects	N	N	E	E	N	N	N
ModelSBOBranchChangedInL3v1	The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version	N	N	N	E	E	N	N
DuplicateAnnotationInvalidInL3v1	Duplicate top-level annotations are invalid in SBML Level 3 Version 1	W	W	W	N	N	N	N
NoCompartmentOutsideInL3v1	This Level+Version of SBML does not support the 'outside' attribute on Compartment objects	W	W	W	W	W	W	N
NoStoichiometryMathInL3v1	This Level+Version of SBML does not support the StoichiometryMath object	N	N	E	E	E	E	N
InvalidSBMLLevelVersion	Unknown Level+Version combination of SBML	E	E	E	E	E	E	E
AnnotationNotesNotAllowedLevel1	Annotation objects on the SBML container element are not permitted in SBML Level 1	E	E	N	N	N	N	N
InvalidRuleOrdering	Invalid ordering of rules	E	E	E	N	N	N	N
RequiredPackagePresent	The SBML document requires an SBML Level 3 package unavailable in this software	N	N	N	N	N	N	E
UnrequiredPackagePresent	The SBML document uses an SBML Level 3 package unavailable in this software	N	N	N	N	N	N	W
SubsUnitsAllowedInKL	Disallowed value for attribute 'substanceUnits' on KineticLaw object	E	E	E	N	N	N	N
TimeUnitsAllowedInKL	Disallowed value for attribute 'timeUnits' on KineticLaw object	E	E	E	N	N	N	N
FormulaInLevel1KL	Only predefined functions are allowed in SBML Level 1 formulas	E	E	N	N	N	N	N
TimeUnitsRemoved	This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects	N	N	N	N	E	E	E
BadMathML	Invalid MathML expression	N	N	E	E	E	E	E
FailedMathMLReadOfDouble	Missing or invalid floating-point number in MathML expression	N	N	E	E	E	E	E
FailedMathMLReadOfInteger	Missing or invalid integer in MathML expression	N	N	E	E	E	E	E
FailedMathMLReadOfExponential	Missing or invalid exponential expression in MathML	N	N	E	E	E	E	E
FailedMathMLReadOfRational	Missing or invalid rational expression in MathML	N	N	E	E	E	E	E
BadMathMLNodeType	Invalid MathML element	N	N	E	E	E	E	E
NoTimeSymbolInFunctionDef	Use of <csymbol> for 'time' not allowed within FunctionDefinition objects	N	N	W	E	E	E	E
NoBodyInFunctionDef	There must be a <lambda> body within the <math> element of a FunctionDefinition object	N	N	E	E	E	E	E
UndeclaredUnits	Missing unit declarations on parameters or literal numbers in expression	W	W	W	W	W	W	W
UndeclaredTimeUnitsL3	Unable to verify consistency of units: the unit of time has not been declared	N	N	N	N	N	N	W
UndeclaredExtentUnitsL3	Unable to verify consistency of units: the units of reaction extent have not been declared	N	N	N	N	N	N	W
UndeclaredObjectUnitsL3	Unable to verify consistency of units: encountered a model entity with no declared units	N	N	N	N	N	N	W
UnrecognisedSBOTerm	Unrecognized 'sboTerm' attribute value	N	N	N	W	W	W	W
ObseleteSBOTerm	Obsolete 'sboTerm' attribute value	N	N	N	W	W	W	W
IncorrectCompartmentSpatialDimensions	In SBML Level 1, only three-dimensional compartments are allowed	E	E	N	N	N	N	N
CompartmentTypeNotValidAttribute	CompartmentType objects are not available in this Level+Version of SBML	E	E	E	N	N	N	E
ConstantNotValidAttribute	This Level+Version of SBML does not support the 'constant' attribute on this component	E	E	N	N	N	N	N
MetaIdNotValidAttribute	Attribute 'metaid' is not available in SBML Level 1	E	E	N	N	N	N	N
SBOTermNotValidAttributeBeforeL2V3	The 'sboTerm' attribute is not available on this component before SBML Level 2 Version 3	E	E	E	E	N	N	N
InvalidL1CompartmentUnits	Invalid units for a compartment in SBML Level 1	E	E	N	N	N	N	N
L1V1CompartmentVolumeReqd	In SBML Level 1, a compartment's volume must be specified	E	N	N	N	N	N	N
CompartmentTypeNotValidComponent	CompartmentType objects are not available in this Level+Version of SBML	E	E	E	N	N	N	E
ConstraintNotValidComponent	Constraint objects are not available in this Level+Version of SBML	E	E	E	N	N	N	N
EventNotValidComponent	Event objects are not available in this Level+Version of SBML	E	E	N	N	N	N	N
SBOTermNotValidAttributeBeforeL2V2	The 'sboTerm' attribute is invalid for this component before Level 2 Version 2	E	E	E	N	N	N	N
FuncDefNotValidComponent	FunctionDefinition objects are not available in this Level+Version of SBML	E	E	N	N	N	N	N
InitialAssignNotValidComponent	InitialAssignment objects are not available in this Level+Version of SBML	E	E	E	N	N	N	N
VariableNotValidAttribute	Attribute 'variable' is not available on this component in this Level+Version of SBML	E	E	E	E	E	E	E
UnitsNotValidAttribute	Attribute 'units' is not available on this component in this Level+Version of SBML	E	E	E	E	E	E	E
ConstantSpeciesNotValidAttribute	Attribute 'constant' is not available on Species objects in SBML Level 1	E	E	N	N	N	N	N
SpatialSizeUnitsNotValidAttribute	Attribute 'spatialSizeUnits' is not available on Species objects in SBML Level 1	E	E	N	N	N	N	N
SpeciesTypeNotValidAttribute	Attribute 'speciesType' is not available on Species objects in SBML Level 1	E	E	E	N	N	N	E
HasOnlySubsUnitsNotValidAttribute	Attribute 'hasOnlySubstanceUnits' is not available on Species objects in SBML Level 1	E	E	N	N	N	N	N
IdNotValidAttribute	Attribute 'id' is not available on SpeciesReference objects in SBML Level 1	E	E	E	N	N	N	N
NameNotValidAttribute	Attribute 'name' is not available on SpeciesReference objects in SBML Level 1	E	E	E	N	N	N	N
SpeciesTypeNotValidComponent	The SpeciesType object is not supported in SBML Level 1	E	E	E	N	N	N	E
StoichiometryMathNotValidComponent	The StoichiometryMath object is not supported in SBML Level 1	E	E	N	N	N	N	E
MultiplierNotValidAttribute	Attribute 'multiplier' on Unit objects is not supported in SBML Level 1	E	E	N	N	N	N	N
OffsetNotValidAttribute	Attribute 'offset' on Unit objects is only available in SBML Level 2 Version 1	E	E	N	N	N	N	N
L3SpatialDimensionsUnset	No value given for 'spatialDimensions' attribute; assuming a value of 3	N	N	N	N	N	N	W
PackageConversionNotSupported	Conversion of SBML Level 3 package constructs is not yet supported	E	E	E	E	E	E	E
InvalidTargetLevelVersion	The requested SBML Level/Version combination is not known to exist	E	E	E	E	E	E	E
L3NotSupported	SBML Level 3 is not yet supported	E	E	E	E	E	E	E

Category codes associated with SBMLError objects

As discussed above, each SBMLError object contains a value for a category identifier, describing the type of issue that the SBMLError object represents. The category can be retrieved from an SBMLError object using the method SBMLError.getCategory(). The following table lists each possible value and a brief description of its meaning.

As is the case with the error codes, in the libSBML Python language interface, the category identifiers are currently implemented as static integer constants defined in the interface class libsbml.

The following table lists each possible value and a brief description of its meaning.

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 2–4 and Level 3 Version 1 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 2–4 and Level 3 Version 1 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 2–4 and Level 3 Version 1 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 2–4 and Level 3 Version 1 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 2–4 and Level 3 Version 1 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 2–4 and Level 3 Version 1 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.
LIBSBML_CAT_SBML_L3V1_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 3 Version 1.

Severity codes associated with SBMLError objects

In libSBML version 5.3.0 there are no additional severity codes beyond those defined by XMLError. They are implemented as static integer constants defined in the interface class libsbml, and have names beginning with LIBSBML_SEV_.

Public Member Functions
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	isValid
def	isWarning
def	isXML
def	setColumn
def	setLine

---

Member Function Documentation

def libsbml.XMLError.getCategory

(

self

)

[inherited]

Python method signature(s):

getCategory()    long

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()

def libsbml.XMLError.getCategoryAsString

(

self

)

[inherited]

Python method signature(s):

getCategoryAsString()    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()

def libsbml.XMLError.getColumn

(

self

)

[inherited]

Python method signature(s):

getColumn()    long

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 longeger declared for SBML. (We use this rather than a machine specific constant as it guarantees uniformity.) 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()

def libsbml.XMLError.getErrorId

(

self

)

[inherited]

Python method signature(s):

getErrorId()    long

Returns the identifier of this error.

Returns:

the error code for this error.

See also:

getMessage()

getShortMessage()

getCategory()

getSeverity()

def libsbml.XMLError.getLine

(

self

)

[inherited]

Python method signature(s):

getLine()    long

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 longeger declared for SBML. (We use this rather than a machine specific constant as it guarantees uniformity.) 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()

def libsbml.XMLError.getMessage

(

self

)

[inherited]

Python method signature(s):

getMessage()    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:

getErrorId()

getShortMessage()

getCategory()

getSeverity()

def libsbml.XMLError.getSeverity

(

self

)

[inherited]

Python method signature(s):

getSeverity()    long

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()

def libsbml.XMLError.getSeverityAsString

(

self

)

[inherited]

Python method signature(s):

getSeverityAsString()    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()

def libsbml.XMLError.getShortMessage

(

self

)

[inherited]

Python method signature(s):

getShortMessage()    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:

getErrorId()

getMessage()

getCategory()

getSeverity()

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 the set of predefined error identifiers.

def libsbml.XMLError.isError

(

self

)

[inherited]

Python method signature(s):

isError()    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 set of predefined severity codes.

Returns:

true if this error is an error, false otherwise.

See also:

isInfo()

isWarning()

isFatal()

def libsbml.XMLError.isFatal

(

self

)

[inherited]

Python method signature(s):

isFatal()    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 set of predefined severity codes.

Returns:

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

See also:

isInfo()

isWarning()

isError()

def libsbml.XMLError.isInfo

(

self

)

[inherited]

Python method signature(s):

isInfo()    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 set of predefined severity codes.

Returns:

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

See also:

isWarning()

isError()

isFatal()

def libsbml.XMLError.isInternal

(

self

)

[inherited]

Python method signature(s):

isInternal()    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 set of predefined category codes.

Returns:

true or false

See also:

isSystem()

isXML()

def libsbml.XMLError.isSystem

(

self

)

[inherited]

Python method signature(s):

isSystem()    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 set of predefined category codes.

Returns:

true or false

See also:

isInternal()

isXML()

def libsbml.XMLError.isValid

(

self

)

[inherited]

Python method signature(s):

isValid()    bool

Predicate returning true or false depending on whether this error resulted from a problem or whether it was logged as an unknown error.

This is equivalent to obtaining the error identifier from an XMLError object (via XMLError.getErrorId()) and then comparing it to the value XMLUnknownError or UnknownError from the set of predefined error codes.

Returns:

true or false

def libsbml.XMLError.isWarning

(

self

)

[inherited]

Python method signature(s):

isWarning()    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 set of predefined severity codes.

Returns:

true if this error is a warning, false otherwise.

See also:

isInfo()

isError()

isFatal()

def libsbml.XMLError.isXML

(

self

)

[inherited]

Python method signature(s):

isXML()    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 set of predefined category codes.

Returns:

true or false

See also:

isInternal()

isSystem()

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

Python method signature(s):

setColumn(long column)    int

Sets the column number where this error occurred.

Parameters:

column

a long integer, 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()

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

Python method signature(s):

setLine(long line)    int

Sets the line number where this error occurred.

Parameters:

line

a long integer, 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()