libSBML Python API
5.18.0
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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 byXMLError. 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.
SBMLError also tracks the Level 3 package extension, if any, was responsible for a given warning or error. Each diagnostic code logged by an libSBML extension for SBML Level 3 packages includes a record of the package that logged it. It can be retrieved using SBMLError.getPackage(). The information is a simple text string; the string will be the nickname of the package, such as 'comp'
for the Hierarchical Model Composition package, 'fbc'
for the Flux Balance Constraints package, and so on. If the value returned by SBMLError.getPackage() is an empty string or has the value 'core'
, then the error came from libSBML core.
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.
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:
= Not applicable | |
= Warning | |
= Error | |
= 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().
The error codes come from different lists depending on whether they're from libSBML core or from an SBML Level 3 package extension. However, in the language interfaces other than C++, all libSBML error codes are ultimately represented as integer constants rather than separate enumerations lists, and they are all stored in a single interface class. Codes from different libSBML extensions have names that begin with the package's nickname, such as Qual
for the Qualitative Models package, Layout
for the Layout package, and so on. If the name of a code does not begin with one of the package nicknames (Layout
, Fbc
, Comp
, Qual
, etc.), then it is a code from libSBML core.
Enumerator | Meaning | L1 V1 | L1 V2 | L2 V1 | L2 V2 | L2 V3 | L2 V4 | L3 V1 | L3 V2 |
---|---|---|---|---|---|---|---|---|---|
XMLUnknownError | Unknown error | ||||||||
XMLOutOfMemory | Out of memory | ||||||||
XMLFileUnreadable | File unreadable | ||||||||
XMLFileUnwritable | File unwritable | ||||||||
XMLFileOperationError | File operation error | ||||||||
XMLNetworkAccessError | Network access error | ||||||||
InternalXMLParserError | Internal XML parser error | ||||||||
UnrecognizedXMLParserCode | Unrecognized XML parser code | ||||||||
XMLTranscoderError | Transcoder error | ||||||||
MissingXMLDecl | Missing XML declaration | ||||||||
MissingXMLEncoding | Missing XML encoding attribute | ||||||||
BadXMLDecl | Bad XML declaration | ||||||||
BadXMLDOCTYPE | Bad XML DOCTYPE | ||||||||
InvalidCharInXML | Invalid character | ||||||||
BadlyFormedXML | Badly formed XML | ||||||||
UnclosedXMLToken | Unclosed token | ||||||||
InvalidXMLConstruct | Invalid XML construct | ||||||||
XMLTagMismatch | XML tag mismatch | ||||||||
DuplicateXMLAttribute | Duplicate attribute | ||||||||
UndefinedXMLEntity | Undefined XML entity | ||||||||
BadProcessingInstruction | Bad XML processing instruction | ||||||||
BadXMLPrefix | Bad XML prefix | ||||||||
BadXMLPrefixValue | Bad XML prefix value | ||||||||
MissingXMLRequiredAttribute | Missing required attribute | ||||||||
XMLAttributeTypeMismatch | Attribute type mismatch | ||||||||
XMLBadUTF8Content | Bad UTF8 content | ||||||||
MissingXMLAttributeValue | Missing attribute value | ||||||||
BadXMLAttributeValue | Bad attribute value | ||||||||
BadXMLAttribute | Bad XML attribute | ||||||||
UnrecognizedXMLElement | Unrecognized XML element | ||||||||
BadXMLComment | Bad XML comment | ||||||||
BadXMLDeclLocation | Bad XML declaration location | ||||||||
XMLUnexpectedEOF | Unexpected EOF | ||||||||
BadXMLIDValue | Bad XML ID value | ||||||||
BadXMLIDRef | Bad XML IDREF | ||||||||
UninterpretableXMLContent | Uninterpretable XML content | ||||||||
BadXMLDocumentStructure | Bad XML document structure | ||||||||
InvalidAfterXMLContent | Invalid content after XML content | ||||||||
XMLExpectedQuotedString | Expected quoted string | ||||||||
XMLEmptyValueNotPermitted | Empty value not permitted | ||||||||
XMLBadNumber | Bad number | ||||||||
XMLBadColon | Colon character not permitted | ||||||||
MissingXMLElements | Missing XML elements | ||||||||
XMLContentEmpty | Empty XML content | ||||||||
UnknownError | Encountered unknown internal libSBML error | ||||||||
NotUTF8 | File does not use UTF-8 encoding | ||||||||
UnrecognizedElement | Encountered unrecognized element | ||||||||
NotSchemaConformant | Document does not conform to the SBML XML schema | ||||||||
L3NotSchemaConformant | Document is not well-formed XML | ||||||||
InvalidMathElement | Invalid MathML | ||||||||
DisallowedMathMLSymbol | Disallowed MathML symbol found | ||||||||
DisallowedMathMLEncodingUse | Use of the MathML 'encoding' attribute is not allowed on this element | ||||||||
DisallowedDefinitionURLUse | Use of the MathML 'definitionURL' attribute is not allowed on this element | ||||||||
BadCsymbolDefinitionURLValue | Invalid <csymbol> 'definitionURL' attribute value | ||||||||
DisallowedMathTypeAttributeUse | Use of the MathML 'type' attribute is not allowed on this element | ||||||||
DisallowedMathTypeAttributeValue | Disallowed MathML 'type' attribute value | ||||||||
LambdaOnlyAllowedInFunctionDef | Use of <lambda> not permitted outside of FunctionDefinition objects | ||||||||
BooleanOpsNeedBooleanArgs | Non-Boolean argument given to Boolean operator | ||||||||
NumericOpsNeedNumericArgs | Non-numerical argument given to numerical operator | ||||||||
ArgsToEqNeedSameType | Arguments to <eq> and <neq> must have the same data types | ||||||||
PiecewiseNeedsConsistentTypes | Terms in a <piecewise> expression must have consistent data types | ||||||||
PieceNeedsBoolean | The second argument of a <piece> expression must yield a Boolean value | ||||||||
ApplyCiMustBeUserFunction | A <ci> element in this context must refer to a function definition | ||||||||
ApplyCiMustBeModelComponent | A <ci> element in this context must refer to a model component | ||||||||
KineticLawParametersAreLocalOnly | Cannot use a KineticLaw local parameter outside of its local scope | ||||||||
MathResultMustBeNumeric | A formula's result in this context must be a numerical value | ||||||||
OpsNeedCorrectNumberOfArgs | Incorrect number of arguments given to MathML operator | ||||||||
InvalidNoArgsPassedToFunctionDef | Incorrect number of arguments given to function invocation | ||||||||
DisallowedMathUnitsUse | Attribute 'units' is only permitted on <cn> elements | ||||||||
InvalidUnitsValue | Invalid value given for the 'units' attribute | ||||||||
CiCannotReference0DCompartment | A <ci> element cannot reference a 0D compartment | ||||||||
RateOfTargetMustBeCi | A 'rateOf' <csymbol> must target only a single <ci> element | ||||||||
RateOfTargetCannotBeAssigned | The target of a 'rateOf' <csymbol> cannot be assigned | ||||||||
RateOfSpeciesTargetCompartmentNot | Compartments of non-substance <species> referenced by 'rateOf' must not vary | ||||||||
DuplicateComponentId | Duplicate 'id' attribute value | ||||||||
DuplicateUnitDefinitionId | Duplicate unit definition 'id' attribute value | ||||||||
DuplicateLocalParameterId | Duplicate local parameter 'id' attribute value | ||||||||
MultipleAssignmentOrRateRules | Multiple rules for the same variable are not allowed | ||||||||
MultipleEventAssignmentsForId | Multiple event assignments for the same variable are not allowed | ||||||||
EventAndAssignmentRuleForId | An event assignment and an assignment rule must not have the same value for 'variable' | ||||||||
DuplicateMetaId | Duplicate 'metaid' attribute value | ||||||||
InvalidSBOTermSyntax | Invalid syntax for an 'sboTerm' attribute value | ||||||||
InvalidMetaidSyntax | Invalid syntax for a 'metaid' attribute value | ||||||||
InvalidIdSyntax | Invalid syntax for an 'id' attribute value | ||||||||
InvalidUnitIdSyntax | Invalid syntax for the identifier of a unit | ||||||||
InvalidNameSyntax | Invalid syntax for a 'name' attribute value | ||||||||
DanglingUnitReference | Dangling reference to a unit. | ||||||||
MissingAnnotationNamespace | Missing declaration of the XML namespace for the annotation | ||||||||
DuplicateAnnotationNamespaces | Multiple annotations using the same XML namespace | ||||||||
SBMLNamespaceInAnnotation | The SBML XML namespace cannot be used in an Annotation object | ||||||||
MultipleAnnotations | Only one Annotation object is permitted under a given SBML object | ||||||||
InconsistentArgUnits | The units of the function call's arguments are not consistent with its definition | ||||||||
InconsistentKineticLawUnitsL3 | The kinetic law's units are inconsistent with those of other kinetic laws in the model | ||||||||
AssignRuleCompartmentMismatch | Mismatched units in assignment rule for compartment | ||||||||
AssignRuleSpeciesMismatch | Mismatched units in assignment rule for species | ||||||||
AssignRuleParameterMismatch | Mismatched units in assignment rule for parameter | ||||||||
AssignRuleStoichiometryMismatch | Mismatched units in assignment rule for stoichiometry | ||||||||
InitAssignCompartmenMismatch | Mismatched units in initial assignment to compartment | ||||||||
InitAssignSpeciesMismatch | Mismatched units in initial assignment to species | ||||||||
InitAssignParameterMismatch | Mismatched units in initial assignment to parameter | ||||||||
InitAssignStoichiometryMismatch | Mismatched units in initial assignment to stoichiometry | ||||||||
RateRuleCompartmentMismatch | Mismatched units in rate rule for compartment | ||||||||
RateRuleSpeciesMismatch | Mismatched units in rate rule for species | ||||||||
RateRuleParameterMismatch | Mismatched units in rate rule for parameter | ||||||||
RateRuleStoichiometryMismatch | Mismatched units in rate rule for stoichiometry | ||||||||
KineticLawNotSubstancePerTime | The units of the kinetic law are not 'substance'/'time' | ||||||||
SpeciesInvalidExtentUnits | The species' units are not consistent with units of extent | ||||||||
DelayUnitsNotTime | The units of the delay expression are not units of time | ||||||||
EventAssignCompartmentMismatch | Mismatched units in event assignment for compartment | ||||||||
EventAssignSpeciesMismatch | Mismatched units in event assignment for species | ||||||||
EventAssignParameterMismatch | Mismatched units in event assignment for parameter | ||||||||
EventAssignStoichiometryMismatch | Mismatched units in event assignment for stoichiometry | ||||||||
PriorityUnitsNotDimensionless | The units of a priority expression must be 'dimensionless' | ||||||||
OverdeterminedSystem | The model is overdetermined | ||||||||
InvalidModelSBOTerm | Invalid 'sboTerm' attribute value for a Model object | ||||||||
InvalidFunctionDefSBOTerm | Invalid 'sboTerm' attribute value for a FunctionDefinition object | ||||||||
InvalidParameterSBOTerm | Invalid 'sboTerm' attribute value for a Parameter object | ||||||||
InvalidInitAssignSBOTerm | Invalid 'sboTerm' attribute value for an InitialAssignment object | ||||||||
InvalidRuleSBOTerm | Invalid 'sboTerm' attribute value for a Rule object | ||||||||
InvalidConstraintSBOTerm | Invalid 'sboTerm' attribute value for a Constraint object | ||||||||
InvalidReactionSBOTerm | Invalid 'sboTerm' attribute value for a Reaction object | ||||||||
InvalidSpeciesReferenceSBOTerm | Invalid 'sboTerm' attribute value for a SpeciesReference object | ||||||||
InvalidKineticLawSBOTerm | Invalid 'sboTerm' attribute value for a KineticLaw object | ||||||||
InvalidEventSBOTerm | Invalid 'sboTerm' attribute value for an Event object | ||||||||
InvalidEventAssignmentSBOTerm | Invalid 'sboTerm' attribute value for an EventAssignment object | ||||||||
InvalidCompartmentSBOTerm | Invalid 'sboTerm' attribute value for a Compartment object | ||||||||
InvalidSpeciesSBOTerm | Invalid 'sboTerm' attribute value for a Species object | ||||||||
InvalidCompartmentTypeSBOTerm | Invalid 'sboTerm' attribute value for a CompartmentType object | ||||||||
InvalidSpeciesTypeSBOTerm | Invalid 'sboTerm' attribute value for a SpeciesType object | ||||||||
InvalidTriggerSBOTerm | Invalid 'sboTerm' attribute value for an Event Trigger object | ||||||||
InvalidDelaySBOTerm | Invalid 'sboTerm' attribute value for an Event Delay object | ||||||||
InvalidLocalParameterSBOTerm | Invalid 'sboTerm' attribute value for a LocalParameter object | ||||||||
InvalidSBMLElementSBOTerm | Invalid 'sboTerm' attribute value for the <sbml> element | ||||||||
NotesNotInXHTMLNamespace | Notes must be placed in the XHTML XML namespace | ||||||||
NotesContainsXMLDecl | XML declarations are not permitted in Notes objects | ||||||||
NotesContainsDOCTYPE | XML DOCTYPE elements are not permitted in Notes objects | ||||||||
InvalidNotesContent | Invalid notes content found | ||||||||
OnlyOneNotesElementAllowed | Only one Notes subobject is permitted on a given SBML object | ||||||||
InvalidNamespaceOnSBML | Invalid XML namespace for the SBML container element | ||||||||
MissingOrInconsistentLevel | Missing or inconsistent value for the 'level' attribute | ||||||||
MissingOrInconsistentVersion | Missing or inconsistent value for the 'version' attribute | ||||||||
PackageNSMustMatch | Inconsistent or invalid SBML Level/Version for the package namespace declaration | ||||||||
LevelPositiveInteger | The 'level' attribute must have a positive integer value | ||||||||
VersionPositiveInteger | The 'version' attribute must have a positive integer value | ||||||||
AllowedAttributesOnSBML | Invalid attribute found on the SBML container element | ||||||||
L3PackageOnLowerSBML | An L3 package ns found on the SBML container element | ||||||||
MissingModel | No model definition found | ||||||||
IncorrectOrderInModel | Incorrect ordering of components within the Model object | ||||||||
EmptyListElement | Empty ListOf___ object found | ||||||||
NeedCompartmentIfHaveSpecies | The presence of a species requires a compartment | ||||||||
OneOfEachListOf | Only one of each kind of ListOf___ object is allowed inside a Model object | ||||||||
OnlyFuncDefsInListOfFuncDefs | Only FunctionDefinition, Notes and Annotation objects are allowed in ListOfFunctionDefinitions | ||||||||
OnlyUnitDefsInListOfUnitDefs | Only UnitDefinition, Notes and Annotation objects are allowed in ListOfUnitDefinitions objects | ||||||||
OnlyCompartmentsInListOfCompartments | Only Compartment, Notes and Annotation objects are allowed in ListOfCompartments objects | ||||||||
OnlySpeciesInListOfSpecies | Only Species, Notes and Annotation objects are allowed in ListOfSpecies objects | ||||||||
OnlyParametersInListOfParameters | Only Parameter, Notes and Annotation objects are allowed in ListOfParameters objects | ||||||||
OnlyInitAssignsInListOfInitAssigns | Only InitialAssignment, Notes and Annotation objects are allowed in ListOfInitialAssignments objects | ||||||||
OnlyRulesInListOfRules | Only Rule, Notes and Annotation objects are allowed in ListOfRules objects | ||||||||
OnlyConstraintsInListOfConstraints | Only Constraint, Notes and Annotation objects are allowed in ListOfConstraints objects | ||||||||
OnlyReactionsInListOfReactions | Only Reaction, Notes and Annotation objects are allowed in ListOfReactions objects | ||||||||
OnlyEventsInListOfEvents | Only Event, Notes and Annotation objects are allowed in ListOfEvents objects | ||||||||
L3ConversionFactorOnModel | A 'conversionFactor' attribute value must reference a Parameter object | ||||||||
L3TimeUnitsOnModel | Invalid 'timeUnits' attribute value | ||||||||
L3VolumeUnitsOnModel | Invalid 'volumeUnits' attribute value | ||||||||
L3AreaUnitsOnModel | Invalid 'areaUnits' attribute value | ||||||||
L3LengthUnitsOnModel | Invalid 'lengthUnits' attribute value | ||||||||
L3ExtentUnitsOnModel | Invalid 'extentUnits' attribute value | ||||||||
AllowedAttributesOnModel | Invalid attribute found on the Model object | ||||||||
AllowedAttributesOnListOfFuncs | Invalid attribute found on the ListOfFunctionDefinitions object | ||||||||
AllowedAttributesOnListOfUnitDefs | Invalid attribute found on the ListOfUnitDefinitions object | ||||||||
AllowedAttributesOnListOfComps | Invalid attribute found on the ListOfCompartments object | ||||||||
AllowedAttributesOnListOfSpecies | Invalid attribute found on the ListOfSpecies object | ||||||||
AllowedAttributesOnListOfParams | Invalid attribute found on the ListOfParameters object | ||||||||
AllowedAttributesOnListOfInitAssign | Invalid attribute found on the ListOfInitialAssignments object | ||||||||
AllowedAttributesOnListOfRules | Invalid attribute found on the ListOfRules object | ||||||||
AllowedAttributesOnListOfConstraints | Invalid attribute found on the ListOfConstraints object | ||||||||
AllowedAttributesOnListOfReactions | Invalid attribute found on the ListOfReactions object | ||||||||
AllowedAttributesOnListOfEvents | Invalid attribute found on the ListOfEvents object | ||||||||
L3V2SubstanceUnitsOnModel | Invalid 'substanceUnits' attribute value | ||||||||
FunctionDefMathNotLambda | Invalid expression found in the function definition | ||||||||
InvalidApplyCiInLambda | Invalid forward reference in the MathML <apply> <ci> ...</ci> </apply> expression | ||||||||
RecursiveFunctionDefinition | Recursive function definitions are not permitted | ||||||||
InvalidCiInLambda | Invalid <ci> reference found inside the <lambda> mathematical formula | ||||||||
InvalidFunctionDefReturnType | A function's return type must be either a number or a Boolean | ||||||||
OneMathElementPerFunc | A FunctionDefinition object may contain one <math> element | ||||||||
AllowedAttributesOnFunc | Invalid attribute found on the FunctionDefinition object | ||||||||
InvalidUnitDefId | Invalid 'id' attribute value for a UnitDefinition object | ||||||||
InvalidSubstanceRedefinition | Invalid redefinition of built-in type 'substance' | ||||||||
InvalidLengthRedefinition | Invalid redefinition of built-in type 'length' | ||||||||
InvalidAreaRedefinition | Invalid redefinition of built-in type name 'area' | ||||||||
InvalidTimeRedefinition | Invalid redefinition of built-in type name 'time' | ||||||||
InvalidVolumeRedefinition | Invalid redefinition of built-in type name 'volume' | ||||||||
VolumeLitreDefExponentNotOne | Must use 'exponent'=1 when defining 'volume' in terms of litres | ||||||||
VolumeMetreDefExponentNot3 | Must use 'exponent'=3 when defining 'volume' in terms of metres | ||||||||
EmptyListOfUnits | An empty list of Unit objects is not permitted in a UnitDefinition object | ||||||||
InvalidUnitKind | Invalid value for the 'kind' attribute of a UnitDefinition object | ||||||||
OffsetNoLongerValid | Unit attribute 'offset' is not supported in this Level+Version of SBML | ||||||||
CelsiusNoLongerValid | Unit name 'Celsius' is not defined in this Level+Version of SBML | ||||||||
EmptyUnitListElement | A ListOfUnits object must not be empty | ||||||||
OneListOfUnitsPerUnitDef | At most one ListOfUnits object is allowed inside a UnitDefinition object | ||||||||
OnlyUnitsInListOfUnits | Only Unit, Notes and Annotation objects are allowed in ListOfUnits objects | ||||||||
AllowedAttributesOnUnitDefinition | Invalid attribute found on the UnitDefinition object | ||||||||
AllowedAttributesOnListOfUnits | Invalid attribute found on the ListOfUnits object | ||||||||
AllowedAttributesOnUnit | Invalid attribute found on the Unit object | ||||||||
ZeroDimensionalCompartmentSize | Invalid use of the 'size' attribute for a zero-dimensional compartment | ||||||||
ZeroDimensionalCompartmentUnits | Invalid use of the 'units' attribute for a zero-dimensional compartment | ||||||||
ZeroDimensionalCompartmentConst | Zero-dimensional compartments must be defined to be constant | ||||||||
UndefinedOutsideCompartment | Invalid value for the 'outside' attribute of a Compartment object | ||||||||
RecursiveCompartmentContainment | Recursive nesting of compartments via the 'outside' attribute is not permitted | ||||||||
ZeroDCompartmentContainment | Invalid nesting of zero-dimensional compartments | ||||||||
Invalid1DCompartmentUnits | Invalid value for the 'units' attribute of a one-dimensional compartment | ||||||||
Invalid2DCompartmentUnits | Invalid value for the 'units' attribute of a two-dimensional compartment | ||||||||
Invalid3DCompartmentUnits | Invalid value for the 'units' attribute of a three-dimensional compartment | ||||||||
InvalidCompartmentTypeRef | Invalid value for the 'compartmentType' attribute of a compartment | ||||||||
OneDimensionalCompartmentUnits | No units defined for 1-D compartment | ||||||||
TwoDimensionalCompartmentUnits | No units defined for 2-D compartment | ||||||||
ThreeDimensionalCompartmentUnits | No units defined for 3-D Compartment object | ||||||||
AllowedAttributesOnCompartment | Invalid attribute found on Compartment object | ||||||||
NoUnitsOnCompartment | No units defined for Compartment object | ||||||||
InvalidSpeciesCompartmentRef | Invalid value found for Species 'compartment' attribute | ||||||||
HasOnlySubsNoSpatialUnits | Attribute 'spatialSizeUnits' must not be set if 'hasOnlySubstanceUnits'='true' | ||||||||
NoSpatialUnitsInZeroD | Attribute 'spatialSizeUnits' must not be set if the compartment is zero-dimensional | ||||||||
NoConcentrationInZeroD | Attribute 'initialConcentration' must not be set if the compartment is zero-dimensional | ||||||||
SpatialUnitsInOneD | Invalid value for 'spatialSizeUnits' attribute of a one-dimensional compartment | ||||||||
SpatialUnitsInTwoD | Invalid value for the 'spatialSizeUnits' attribute of a two-dimensional compartment | ||||||||
SpatialUnitsInThreeD | Invalid value for the 'spatialSizeUnits' attribute of a three-dimensional compartment | ||||||||
InvalidSpeciesSusbstanceUnits | Invalid value for a Species 'units' attribute | ||||||||
BothAmountAndConcentrationSet | Cannot set both 'initialConcentration' and 'initialAmount' attributes simultaneously | ||||||||
NonBoundarySpeciesAssignedAndUsed | Cannot use a non-boundary species in both reactions and rules simultaneously | ||||||||
NonConstantSpeciesUsed | Cannot use a constant, non-boundary species as a reactant or product | ||||||||
InvalidSpeciesTypeRef | Invalid value for the 'speciesType' attribute of a species | ||||||||
MultSpeciesSameTypeInCompartment | Cannot have multiple species of the same species type in the same compartment | ||||||||
MissingSpeciesCompartment | Missing value for the 'compartment' attribute | ||||||||
SpatialSizeUnitsRemoved | Attribute 'spatialSizeUnits' is not supported in this Level+Version of SBML | ||||||||
SubstanceUnitsOnSpecies | No substance units defined for the species | ||||||||
ConversionFactorOnSpecies | Invalid value for the 'conversionFactor' attribute | ||||||||
AllowedAttributesOnSpecies | Invalid attribute found on Species object | ||||||||
InvalidParameterUnits | Invalid value for the 'units' attribute of a Parameter object | ||||||||
ParameterUnits | No units defined for the parameter | ||||||||
ConversionFactorMustConstant | A conversion factor must reference a Parameter object declared to be a constant | ||||||||
AllowedAttributesOnParameter | Invalid attribute found on Parameter object | ||||||||
InvalidInitAssignSymbol | Invalid value for the 'symbol' attribute of an InitialAssignment object | ||||||||
MultipleInitAssignments | Multiple initial assignments for the same 'symbol' value are not allowed | ||||||||
InitAssignmentAndRuleForSameId | Cannot set a value using both an initial assignment and an assignment rule simultaneously | ||||||||
OneMathElementPerInitialAssign | An InitialAssignment object may contain one <math> element | ||||||||
AllowedAttributesOnInitialAssign | Invalid attribute found on an InitialAssignment object | ||||||||
InitAssignmentCannotRef0DComp | InitialAssignment cannot reference 0D compartment | ||||||||
InvalidAssignRuleVariable | Invalid value for the 'variable' attribute of an AssignmentRule object | ||||||||
InvalidRateRuleVariable | Invalid value for the 'variable' attribute of a RateRule object | ||||||||
AssignmentToConstantEntity | An assignment rule cannot assign an entity declared to be constant | ||||||||
RateRuleForConstantEntity | A rate rule cannot assign an entity declared to be constant | ||||||||
CircularRuleDependency | Circular dependencies involving rules and reactions are not permitted | ||||||||
OneMathElementPerRule | A rule object may contain one <math> element | ||||||||
AllowedAttributesOnAssignRule | Invalid attribute found on an AssignmentRule object | ||||||||
AllowedAttributesOnRateRule | Invalid attribute found on a RateRule object | ||||||||
AllowedAttributesOnAlgRule | Invalid attribute found on an AlgebraicRule object | ||||||||
RuleCannotRef0DComp | Rule cannot reference 0D compartment | ||||||||
CircularDependencyRateOf | Circular dependencies are not permitted in RateRule and KineticLaw objects | ||||||||
ConstraintMathNotBoolean | A Constraint object's <math> must evaluate to a Boolean value | ||||||||
IncorrectOrderInConstraint | Subobjects inside the Constraint object are not in the prescribed order | ||||||||
ConstraintNotInXHTMLNamespace | A Constraint's Message subobject must be in the XHTML XML namespace | ||||||||
ConstraintContainsXMLDecl | XML declarations are not permitted within Constraint's Message objects | ||||||||
ConstraintContainsDOCTYPE | XML DOCTYPE elements are not permitted within Constraint's Message objects | ||||||||
InvalidConstraintContent | Invalid content for a Constraint object's Message object | ||||||||
OneMathElementPerConstraint | A Constraint object may contain one <math> element | ||||||||
OneMessageElementPerConstraint | A Constraint object can only have one Message subobject | ||||||||
AllowedAttributesOnConstraint | Invalid attribute found on Constraint object | ||||||||
NoReactantsOrProducts | Cannot have a reaction with neither reactants nor products | ||||||||
IncorrectOrderInReaction | Subobjects inside the Reaction object are not in the prescribed order | ||||||||
EmptyListInReaction | Reaction components, if present, cannot be empty | ||||||||
InvalidReactantsProductsList | Invalid object found in the list of reactants or products | ||||||||
InvalidModifiersList | Invalid object found in the list of modifiers | ||||||||
OneSubElementPerReaction | A Reaction object can only contain one of each allowed type of object | ||||||||
CompartmentOnReaction | Invalid value for the Reaction 'compartment' attribute | ||||||||
AllowedAttributesOnReaction | Invalid attribute for a Reaction object | ||||||||
InvalidSpeciesReference | Invalid 'species' attribute value in SpeciesReference object | ||||||||
BothStoichiometryAndMath | The 'stoichiometry' attribute and StoichiometryMath subobject are mutually exclusive | ||||||||
AllowedAttributesOnSpeciesReference | Invalid attribute found on the SpeciesReference object | ||||||||
AllowedAttributesOnModifier | Invalid attribute found on the ModifierSpeciesReference object | ||||||||
UndeclaredSpeciesRef | Unknown species referenced in the kinetic law <math> formula | ||||||||
IncorrectOrderInKineticLaw | Incorrect ordering of components in the KineticLaw object | ||||||||
EmptyListInKineticLaw | The list of parameters, if present, cannot be empty | ||||||||
NonConstantLocalParameter | Parameters local to a KineticLaw object must have a 'constant' attribute value of 'true' | ||||||||
SubsUnitsNoLongerValid | Attribute 'substanceUnits' is not supported in this Level+Version of SBML | ||||||||
TimeUnitsNoLongerValid | Attribute 'timeUnits' is not supported in this Level+Version of SBML | ||||||||
OneListOfPerKineticLaw | Only one ListOfLocalParameters object is permitted within a KineticLaw object | ||||||||
OnlyLocalParamsInListOfLocalParams | Only LocalParameter, Notes and Annotation objects are allowed in ListOfLocalParameter objects | ||||||||
AllowedAttributesOnListOfLocalParam | Invalid attribute found on the ListOfLocalParameters object | ||||||||
OneMathPerKineticLaw | Only one <math> element is allowed in a KineticLaw object | ||||||||
UndeclaredSpeciesInStoichMath | Unknown species referenced in the StoichiometryMath object's <math> formula | ||||||||
AllowedAttributesOnKineticLaw | Invalid attribute found on the KineticLaw object | ||||||||
AllowedAttributesOnListOfSpeciesRef | Invalid attribute found on the ListOfSpeciesReferences object | ||||||||
AllowedAttributesOnListOfMods | Invalid attribute found on the ListOfModifiers object | ||||||||
L3V2FastDeprecated | Fast attribute deprecated | ||||||||
AllowedAttributesOnLocalParameter | Invalid attribute found on the LocalParameter object | ||||||||
LocalParameterShadowsSpecies | Invalid attribute found on the LocalParameter object | ||||||||
MissingTriggerInEvent | The Event object is missing a Trigger subobject | ||||||||
TriggerMathNotBoolean | A Trigger object's <math> expression must evaluate to a Boolean value | ||||||||
MissingEventAssignment | The Event object is missing an EventAssignment subobject | ||||||||
TimeUnitsEvent | Units referenced by 'timeUnits' attribute are not compatible with units of time | ||||||||
IncorrectOrderInEvent | Incorrect ordering of components in Event object | ||||||||
ValuesFromTriggerTimeNeedDelay | Attribute 'useValuesFromTriggerTime'='false', but the Event object does not define a delay | ||||||||
DelayNeedsValuesFromTriggerTime | The use of a Delay object requires the Event attribute 'useValuesFromTriggerTime' | ||||||||
OneMathPerTrigger | A Trigger object may have one <math> element | ||||||||
OneMathPerDelay | A Delay object may have one <math> element | ||||||||
InvalidEventAssignmentVariable | Invalid 'variable' attribute value in Event object | ||||||||
EventAssignmentForConstantEntity | An EventAssignment object cannot assign to a component having attribute 'constant'='true' | ||||||||
OneMathPerEventAssignment | An EventAssignment object may have one <math> element | ||||||||
AllowedAttributesOnEventAssignment | Invalid attribute found on the EventAssignment object | ||||||||
OnlyOneDelayPerEvent | An Event object can only have one Delay subobject | ||||||||
OneListOfEventAssignmentsPerEvent | An Event object can only have one ListOfEventAssignments subobject | ||||||||
OnlyEventAssignInListOfEventAssign | Only EventAssignment, Notes and Annotation objects are allowed in ListOfEventAssignments | ||||||||
AllowedAttributesOnListOfEventAssign | Invalid attribute found on the ListOfEventAssignments object | ||||||||
AllowedAttributesOnEvent | Invalid attribute found on the Event object | ||||||||
AllowedAttributesOnTrigger | Invalid attribute found on the Trigger object | ||||||||
AllowedAttributesOnDelay | Invalid attribute found on the Delay object | ||||||||
PersistentNotBoolean | The Trigger attribute 'persistent' must evaluate to a Boolean value | ||||||||
InitialValueNotBoolean | The Trigger attribute 'initialValue' must evaluate to a Boolean value | ||||||||
OnlyOnePriorityPerEvent | An Event object can only have one Priority subobject | ||||||||
OneMathPerPriority | A Priority object may have one <math> element | ||||||||
AllowedAttributesOnPriority | Invalid attribute found on the Priority object | ||||||||
CompartmentShouldHaveSize | It's best to define a size for every compartment in a model | ||||||||
SpeciesShouldHaveValue | It's best to define an initial amount or initial concentration for every species in a model | ||||||||
ParameterShouldHaveUnits | It's best to declare units for every parameter in a model | ||||||||
ParameterShouldHaveValue | It's best to declare values for every parameter in a model | ||||||||
LocalParameterShadowsId | Local parameters defined within a kinetic law shadow global object symbols | ||||||||
CannotConvertToL1V1 | Cannot convert to SBML Level 1 Version 1 | ||||||||
NoEventsInL1 | SBML Level 1 does not support events | ||||||||
NoFunctionDefinitionsInL1 | SBML Level 1 does not support function definitions | ||||||||
NoConstraintsInL1 | SBML Level 1 does not support constraints | ||||||||
NoInitialAssignmentsInL1 | SBML Level 1 does not support initial assignments | ||||||||
NoSpeciesTypesInL1 | SBML Level 1 does not support species types | ||||||||
NoCompartmentTypeInL1 | SBML Level 1 does not support compartment types | ||||||||
NoNon3DCompartmentsInL1 | SBML Level 1 only supports three-dimensional compartments | ||||||||
NoFancyStoichiometryMathInL1 | SBML Level 1 does not support non-integer nor non-rational stoichiometry formulas | ||||||||
NoNonIntegerStoichiometryInL1 | SBML Level 1 does not support non-integer 'stoichiometry' attribute values | ||||||||
NoUnitMultipliersOrOffsetsInL1 | SBML Level 1 does not support multipliers or offsets in unit definitions | ||||||||
SpeciesCompartmentRequiredInL1 | In SBML Level 1, a value for 'compartment' is mandatory in species definitions | ||||||||
NoSpeciesSpatialSizeUnitsInL1 | SBML Level 1 does not support species 'spatialSizeUnits' settings | ||||||||
NoSBOTermsInL1 | SBML Level 1 does not support the 'sboTerm' attribute | ||||||||
StrictUnitsRequiredInL1 | SBML Level 1 requires strict unit consistency | ||||||||
ConversionFactorNotInL1 | SBML Level 1 does not support the 'conversionFactor' attribute | ||||||||
CompartmentNotOnL1Reaction | SBML Level 1 does not support the 'compartment' attribute on Reaction objects | ||||||||
ExtentUnitsNotSubstance | Units of extent must be compatible with units of substance | ||||||||
GlobalUnitsNotDeclared | Global units must be refer to unit kind or unitDefinition | ||||||||
HasOnlySubstanceUnitsNotinL1 | The concept of hasOnlySubstanceUnits was not available in SBML Level 1 | ||||||||
AvogadroNotSupported | Avogadro not supported in Levels 2 and 1 | ||||||||
NoConstraintsInL2v1 | SBML Level 2 Version 1 does not support Constraint objects | ||||||||
NoInitialAssignmentsInL2v1 | SBML Level 2 Version 1 does not support InitialAssignment objects | ||||||||
NoSpeciesTypeInL2v1 | SBML Level 2 Version 1 does not support SpeciesType objects | ||||||||
NoCompartmentTypeInL2v1 | SBML Level 2 Version 1 does not support CompartmentType objects | ||||||||
NoSBOTermsInL2v1 | SBML Level 2 Version 1 does not support the 'sboTerm' attribute | ||||||||
NoIdOnSpeciesReferenceInL2v1 | SBML Level 2 Version 1 does not support the 'id' attribute on SpeciesReference objects | ||||||||
NoDelayedEventAssignmentInL2v1 | SBML Level 2 Version 1 does not support the 'useValuesFromTriggerTime' attribute | ||||||||
StrictUnitsRequiredInL2v1 | SBML Level 2 Version 1 requires strict unit consistency | ||||||||
IntegerSpatialDimensions | SBML Level 2 Version 1 requires that compartments have spatial dimensions of 0-3 | ||||||||
StoichiometryMathNotYetSupported | Conversion to StoichiometryMath objects not yet supported | ||||||||
PriorityLostFromL3 | SBML Level 2 Version 1 does not support priorities on Event objects | ||||||||
NonPersistentNotSupported | SBML Level 2 Version 1 does not support the 'persistent' attribute on Trigger objects | ||||||||
InitialValueFalseEventNotSupported | SBML Level 2 Version 1 does not support the 'initialValue' attribute on Trigger objects | ||||||||
SBOTermNotUniversalInL2v2 | The 'sboTerm' attribute is invalid for this component in SBML Level 2 Version 2 | ||||||||
NoUnitOffsetInL2v2 | This Level+Version of SBML does not support the 'offset' attribute on Unit objects | ||||||||
NoKineticLawTimeUnitsInL2v2 | This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects | ||||||||
NoKineticLawSubstanceUnitsInL2v2 | This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects | ||||||||
NoDelayedEventAssignmentInL2v2 | This Level+Version of SBML does not support the 'useValuesFromTriggerTime' attribute | ||||||||
ModelSBOBranchChangedBeyondL2v2 | The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version | ||||||||
StrictUnitsRequiredInL2v2 | SBML Level 2 Version 2 requires strict unit consistency | ||||||||
StrictSBORequiredInL2v2 | SBML Level 2 Version 2 requires strict SBO term consistency | ||||||||
DuplicateAnnotationInvalidInL2v2 | Duplicate top-level annotations are invalid in SBML Level 2 Version 2 | ||||||||
NoUnitOffsetInL2v3 | This Level+Version of SBML does not support the 'offset' attribute on Unit objects | ||||||||
NoKineticLawTimeUnitsInL2v3 | This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects | ||||||||
NoKineticLawSubstanceUnitsInL2v3 | This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects | ||||||||
NoSpeciesSpatialSizeUnitsInL2v3 | This Level+Version of SBML does not support the 'spatialSizeUnit' attribute on Species objects | ||||||||
NoEventTimeUnitsInL2v3 | This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects | ||||||||
NoDelayedEventAssignmentInL2v3 | This Level+Version of SBML does not support the 'useValuesFromTriggerTime' attribute | ||||||||
ModelSBOBranchChangedBeyondL2v3 | The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version | ||||||||
StrictUnitsRequiredInL2v3 | SBML Level 2 Version 3 requires strict unit consistency | ||||||||
StrictSBORequiredInL2v3 | SBML Level 2 Version 3 requires strict SBO term consistency | ||||||||
DuplicateAnnotationInvalidInL2v3 | Duplicate top-level annotations are invalid in SBML Level 2 Version 3 | ||||||||
NoUnitOffsetInL2v4 | This Level+Version of SBML does not support the 'offset' attribute on Unit objects | ||||||||
NoKineticLawTimeUnitsInL2v4 | This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects | ||||||||
NoKineticLawSubstanceUnitsInL2v4 | This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects | ||||||||
NoSpeciesSpatialSizeUnitsInL2v4 | This Level+Version of SBML does not support the 'spatialSizeUnit' attribute on Species objects | ||||||||
NoEventTimeUnitsInL2v4 | This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects | ||||||||
ModelSBOBranchChangedInL2v4 | The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version | ||||||||
DuplicateAnnotationInvalidInL2v4 | Duplicate top-level annotations are invalid in SBML Level 2 Version 4 | ||||||||
NoSpeciesTypeInL3v1 | SBML Level 3 Version 1 does not support SpeciesType objects | ||||||||
NoCompartmentTypeInL3v1 | SBML Level 3 Version 1 does not support CompartmentType objects | ||||||||
NoUnitOffsetInL3v1 | This Level+Version of SBML does not support the 'offset' attribute on Unit objects | ||||||||
NoKineticLawTimeUnitsInL3v1 | This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects | ||||||||
NoKineticLawSubstanceUnitsInL3v1 | This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects | ||||||||
NoSpeciesSpatialSizeUnitsInL3v1 | This Level+Version of SBML does not support the 'spatialSizeUnit' attribute on Species objects | ||||||||
NoEventTimeUnitsInL3v1 | This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects | ||||||||
ModelSBOBranchChangedInL3v1 | The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version | ||||||||
DuplicateAnnotationInvalidInL3v1 | Duplicate top-level annotations are invalid in SBML Level 3 Version 1 | ||||||||
NoCompartmentOutsideInL3v1 | This Level+Version of SBML does not support the 'outside' attribute on Compartment objects | ||||||||
NoStoichiometryMathInL3v1 | This Level+Version of SBML does not support the StoichiometryMath object | ||||||||
DoubleExponentNotSupported | Exponent of type float not supported in Levels 2 and 1. | ||||||||
MathMLElementNotSupported | This MathML element is only permitted in L3V2 | ||||||||
EmptyListOfElementNotSupported | Empty 'ListOf' element is only permitted in L3V2 | ||||||||
MissingMathElementNotSupported | Missing <math> element is only permitted in L3V2 | ||||||||
MissingTriggerElementNotSupported | missing <trigger> element is only permitted in L3V2 | ||||||||
BooleanNumericDiscrepancy | Interchange of Boolean and numeric values only permitted in L3V2 | ||||||||
IdNameSBaseInL3V2 | Conversion will lose attributes only available in L3V2 and higher | ||||||||
MissingParticipantsNotSupported | Omission of both <listOfReactants> and <listOfProducts> is only valid in L3V2 | ||||||||
ConvertibleMathInitialAssignment | Some L3V2-specific MathML elements are not permitted in InitialAssignment objects | ||||||||
FastReactionsNotSupported | Conversion of reactions employing the 'fast' attribute is not supported | ||||||||
InvalidSBMLLevelVersion | Unknown Level+Version combination of SBML | ||||||||
AnnotationNotesNotAllowedLevel1 | Annotation objects on the SBML container element are not permitted in SBML Level 1 | ||||||||
InvalidRuleOrdering | Invalid ordering of rules | ||||||||
RequiredPackagePresent | The SBML document requires an SBML Level 3 package unavailable in this software | ||||||||
UnrequiredPackagePresent | The SBML document uses an SBML Level 3 package unavailable in this software | ||||||||
PackageRequiredShouldBeFalse | This package expects required to be false | ||||||||
SubsUnitsAllowedInKL | Disallowed value for attribute 'substanceUnits' on KineticLaw object | ||||||||
TimeUnitsAllowedInKL | Disallowed value for attribute 'timeUnits' on KineticLaw object | ||||||||
FormulaInLevel1KL | Only predefined functions are allowed in SBML Level 1 formulas | ||||||||
L3SubstanceUnitsOnModel | Invalid 'substanceUnits' attribute value | ||||||||
StoichiometryMathMissingMath | The <stoichiometryMath> element must contain a <math> element | ||||||||
TimeUnitsRemoved | This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects | ||||||||
BadMathML | Invalid MathML expression | ||||||||
FailedMathMLReadOfDouble | Missing or invalid floating-point number in MathML expression | ||||||||
FailedMathMLReadOfInteger | Missing or invalid integer in MathML expression | ||||||||
FailedMathMLReadOfExponential | Missing or invalid exponential expression in MathML | ||||||||
FailedMathMLReadOfRational | Missing or invalid rational expression in MathML | ||||||||
BadMathMLNodeType | Invalid MathML element | ||||||||
InvalidMathMLAttribute | Invalid MathML attribute | ||||||||
NoTimeSymbolInFunctionDef | Use of <csymbol> for 'time' not allowed within FunctionDefinition objects | ||||||||
NoBodyInFunctionDef | There must be a <lambda> body within the <math> element of a FunctionDefinition object | ||||||||
DanglingUnitSIdRef | Units must refer to valid unit or unitDefinition | ||||||||
RDFMissingAboutTag | RDF missing the <about> tag | ||||||||
RDFEmptyAboutTag | RDF empty <about> tag | ||||||||
RDFAboutTagNotMetaid | RDF <about> tag is not metaid | ||||||||
RDFNotCompleteModelHistory | RDF does not contain valid ModelHistory | ||||||||
RDFNotModelHistory | RDF does not result in a ModelHistory | ||||||||
AnnotationNotElement | Annotation must contain element | ||||||||
NestedAnnotationNotAllowed | Nested annotations not allowed | ||||||||
UndeclaredUnits | Missing unit declarations on parameters or literal numbers in expression | ||||||||
UndeclaredTimeUnitsL3 | Unable to verify consistency of units: the unit of time has not been declared | ||||||||
UndeclaredExtentUnitsL3 | Unable to verify consistency of units: the units of reaction extent have not been declared | ||||||||
UndeclaredObjectUnitsL3 | Unable to verify consistency of units: encountered a model entity with no declared units | ||||||||
CannotVerifyUnitsObjectNoMath | Unable to verify consistency of units: encountered an object with no <math> element | ||||||||
UnrecognisedSBOTerm | Unrecognized 'sboTerm' attribute value | ||||||||
ObseleteSBOTerm | Obsolete 'sboTerm' attribute value | ||||||||
IncorrectCompartmentSpatialDimensions | In SBML Level 1, only three-dimensional compartments are allowed | ||||||||
CompartmentTypeNotValidAttribute | CompartmentType objects are not available in this Level+Version of SBML | ||||||||
ConstantNotValidAttribute | This Level+Version of SBML does not support the 'constant' attribute on this component | ||||||||
MetaIdNotValidAttribute | Attribute 'metaid' is not available in SBML Level 1 | ||||||||
SBOTermNotValidAttributeBeforeL2V3 | The 'sboTerm' attribute is not available on this component before SBML Level 2 Version 3 | ||||||||
InvalidL1CompartmentUnits | Invalid units for a compartment in SBML Level 1 | ||||||||
L1V1CompartmentVolumeReqd | In SBML Level 1, a compartment's volume must be specified | ||||||||
CompartmentTypeNotValidComponent | CompartmentType objects are not available in this Level+Version of SBML | ||||||||
ConstraintNotValidComponent | Constraint objects are not available in this Level+Version of SBML | ||||||||
EventNotValidComponent | Event objects are not available in this Level+Version of SBML | ||||||||
SBOTermNotValidAttributeBeforeL2V2 | The 'sboTerm' attribute is invalid for this component before Level 2 Version 2 | ||||||||
FuncDefNotValidComponent | FunctionDefinition objects are not available in this Level+Version of SBML | ||||||||
InitialAssignNotValidComponent | InitialAssignment objects are not available in this Level+Version of SBML | ||||||||
VariableNotValidAttribute | Attribute 'variable' is not available on this component in this Level+Version of SBML | ||||||||
UnitsNotValidAttribute | Attribute 'units' is not available on this component in this Level+Version of SBML | ||||||||
ConstantSpeciesNotValidAttribute | Attribute 'constant' is not available on Species objects in SBML Level 1 | ||||||||
SpatialSizeUnitsNotValidAttribute | Attribute 'spatialSizeUnits' is not available on Species objects in SBML Level 1 | ||||||||
SpeciesTypeNotValidAttribute | Attribute 'speciesType' is not available on Species objects in SBML Level 1 | ||||||||
HasOnlySubsUnitsNotValidAttribute | Attribute 'hasOnlySubstanceUnits' is not available on Species objects in SBML Level 1 | ||||||||
IdNotValidAttribute | Attribute 'id' is not available on SpeciesReference objects in SBML Level 1 | ||||||||
NameNotValidAttribute | Attribute 'name' is not available on SpeciesReference objects in SBML Level 1 | ||||||||
SpeciesTypeNotValidComponent | The SpeciesType object is not supported in SBML Level 1 | ||||||||
StoichiometryMathNotValidComponent | The StoichiometryMath object is not supported in SBML Level 1 | ||||||||
MultiplierNotValidAttribute | Attribute 'multiplier' on Unit objects is not supported in SBML Level 1 | ||||||||
OffsetNotValidAttribute | Attribute 'offset' on Unit objects is only available in SBML Level 2 Version 1 | ||||||||
L3SpatialDimensionsUnset | No value given for 'spatialDimensions' attribute; assuming a value of 3 | ||||||||
PackageConversionNotSupported | Conversion of SBML Level 3 package constructs is not yet supported | ||||||||
InvalidTargetLevelVersion | The requested SBML Level/Version combination is not known to exist | ||||||||
L3NotSupported | SBML Level 3 is not yet supported | ||||||||
CompUnknown | |||||||||
CompNSUndeclared | The comp ns is not correctly declared | ||||||||
CompElementNotInNs | Element not in comp namespace | ||||||||
CompDuplicateComponentId | Duplicate 'id' attribute value | ||||||||
CompUniqueModelIds | Model and ExternalModelDefinitions must have unique ids | ||||||||
CompUniquePortIds | Ports must have unique ids | ||||||||
CompInvalidSIdSyntax | Invalid SId syntax | ||||||||
CompInvalidSubmodelRefSyntax | Invalid submodelRef syntax | ||||||||
CompInvalidDeletionSyntax | Invalid deletion syntax | ||||||||
CompInvalidConversionFactorSyntax | Invalid conversionFactor syntax | ||||||||
CompInvalidNameSyntax | Invalid name syntax | ||||||||
CompReplacedUnitsShouldMatch | Units of replaced elements should match replacement units. | ||||||||
CompOneListOfReplacedElements | Only one <listOfReplacedElements> allowed. | ||||||||
CompLOReplaceElementsAllowedElements | Allowed children of <listOfReplacedElements> | ||||||||
CompLOReplacedElementsAllowedAttribs | Allowed <listOfReplacedElements> attributes | ||||||||
CompEmptyLOReplacedElements | <listOfReplacedElements> must not be empty | ||||||||
CompOneReplacedByElement | Only one <replacedBy> object allowed. | ||||||||
CompAttributeRequiredMissing | Required comp:required attribute on <sbml> | ||||||||
CompAttributeRequiredMustBeBoolean | The comp:required attribute must be Boolean | ||||||||
CompRequiredTrueIfElementsRemain | The comp:required attribute must be 'true' if math changes | ||||||||
CompRequiredFalseIfAllElementsReplaced | The comp:required attribute must be 'false' if math does not change | ||||||||
CompOneListOfModelDefinitions | Only one <listOfModelDefinitions> allowed. | ||||||||
CompEmptyLOModelDefs | <listOfModelDefinitions> and <listOfExternalModelDefinitions> must not be empty | ||||||||
CompLOModelDefsAllowedElements | Only <modelDefinitions> in <listOfModelDefinitions> | ||||||||
CompLOExtModelDefsAllowedElements | Only <externalModelDefinitions> in <listOfExternalModelDefinitions> | ||||||||
CompLOModelDefsAllowedAttributes | Allowed <listOfModelDefinitions> attributes | ||||||||
CompLOExtModDefsAllowedAttributes | Allowed <listOfExternalModelDefinitions> attributes | ||||||||
CompOneListOfExtModelDefinitions | Only one <listOfExternalModelDefinitions> allowed. | ||||||||
CompAttributeRequiredMustBeTrue | The comp:required attribute must be 'true' | ||||||||
CompExtModDefAllowedCoreAttributes | Allowed <externalModelDefinitions> core attributes | ||||||||
CompExtModDefAllowedElements | Allowed <externalModelDefinitions> elements | ||||||||
CompExtModDefAllowedAttributes | Allowed <externalModelDefinitions> attributes | ||||||||
CompReferenceMustBeL3 | External models must be L3 | ||||||||
CompModReferenceMustIdOfModel | 'modelRef' must be the 'id' of a model in the 'source' document | ||||||||
CompExtModMd5DoesNotMatch | MD5 checksum does not match the 'source' document | ||||||||
CompInvalidSourceSyntax | The 'comp:source' attribute must be of type 'anyURI' | ||||||||
CompInvalidModelRefSyntax | The 'comp:modelRef' attribute must have the syntax of 'SId' | ||||||||
CompInvalidMD5Syntax | The 'comp:md5' attribute must have the syntax of 'string' | ||||||||
CompCircularExternalModelReference | Circular reference in <externalModelDefinitiongt; | ||||||||
CompOneListOfOnModel | Only one <listOfSubmodels> and one <listOfPorts> allowed | ||||||||
CompNoEmptyListOfOnModel | No empty listOf elements allowed | ||||||||
CompLOSubmodelsAllowedElements | Allowed elements on <listOfSubmodels> | ||||||||
CompLOPortsAllowedElements | Allowed elements on <listOfPorts> | ||||||||
CompLOSubmodelsAllowedAttributes | Allowed attributes on <listOfSubmodels> | ||||||||
CompLOPortsAllowedAttributes | Allowed attributes on <listOfPorts> | ||||||||
CompSubmodelAllowedCoreAttributes | Allowed core attributes on <submodel> | ||||||||
CompSubmodelAllowedElements | Allowed elements on <submodel> | ||||||||
CompOneListOfDeletionOnSubmodel | Only one <listOfDeletions> on a <submodel> allowed | ||||||||
CompSubmodelNoEmptyLODeletions | No empty listOfDeletions elements allowed | ||||||||
CompLODeletionsAllowedElements | Allowed elements on <listOfDeletions> | ||||||||
CompLODeletionAllowedAttributes | Allowed <listOfDeletions> attributes | ||||||||
CompSubmodelAllowedAttributes | Allowed <submodel> attributes | ||||||||
CompModReferenceSyntax | 'comp:modelRef' must conform to SId syntax | ||||||||
CompInvalidTimeConvFactorSyntax | 'comp:timeConversionFactor' must conform to SId syntax | ||||||||
CompInvalidExtentConvFactorSyntax | 'comp:extentConversionFactor' must conform to SId syntax | ||||||||
CompSubmodelMustReferenceModel | The 'comp:modelRef' attribute must reference a model | ||||||||
CompSubmodelCannotReferenceSelf | The 'comp:modelRef' attribute cannot reference own model | ||||||||
CompModCannotCircularlyReferenceSelf | <model> may not reference <submodel> that references itself. | ||||||||
CompTimeConversionMustBeParameter | The 'comp:timeConversionFactor' must reference a parameter | ||||||||
CompExtentConversionMustBeParameter | The 'comp:extentConversionFactor' must reference a parameter | ||||||||
CompPortRefMustReferencePort | The 'comp:portRef' attribute must be the 'id' of a <port> | ||||||||
CompIdRefMustReferenceObject | The 'comp:idRef' attribute must be the 'id' of a model element | ||||||||
CompUnitRefMustReferenceUnitDef | The 'comp:unitRef' attribute must be the 'id' of a UnitDefinition | ||||||||
CompMetaIdRefMustReferenceObject | The 'comp:metaIdRef' attribute must be the 'metaid' of an object | ||||||||
CompParentOfSBRefChildMustBeSubmodel | If <sBaseRef> has a child <sBaseRef> its parent must be a <submodel> | ||||||||
CompInvalidPortRefSyntax | The 'comp:portRef' attribute must have the syntax of an SBML SId | ||||||||
CompInvalidIdRefSyntax | The 'comp:idRef' attribute must have the syntax of an SBML SId | ||||||||
CompInvalidUnitRefSyntax | The 'comp:unitRef' attribute must have the syntax of an SBML SId | ||||||||
CompInvalidMetaIdRefSyntax | The 'comp:metaIdRef' attribute must have the syntax of an XML ID | ||||||||
CompOneSBaseRefOnly | Only one <sbaseRef> | ||||||||
CompDeprecatedSBaseRefSpelling | The spelling 'sbaseRef' is deprecated | ||||||||
CompSBaseRefMustReferenceObject | An SBaseRef must reference an object. | ||||||||
CompSBaseRefMustReferenceOnlyOneObject | An SBaseRef must reference only one other object. | ||||||||
CompNoMultipleReferences | Objects may not be referenced by mutiple SBaseRef constructs. | ||||||||
CompPortMustReferenceObject | Port must reference an object | ||||||||
CompPortMustReferenceOnlyOneObject | Port must reference only one other object. | ||||||||
CompPortAllowedAttributes | Allowed attributes on a Port | ||||||||
CompPortReferencesUnique | Port definitions must be unique. | ||||||||
CompDeletionMustReferenceObject | Deletion must reference an object | ||||||||
CompDeletionMustReferOnlyOneObject | Deletion must reference only one other object. | ||||||||
CompDeletionAllowedAttributes | Allowed attributes on a Deletion | ||||||||
CompReplacedElementMustRefObject | ReplacedElement must reference an object | ||||||||
CompReplacedElementMustRefOnlyOne | ReplacedElement must reference only one other object. | ||||||||
CompReplacedElementAllowedAttributes | Allowed attributes on <replacedElement> | ||||||||
CompReplacedElementSubModelRef | The 'comp:submodelRef' attribute must point to a <submodel> | ||||||||
CompReplacedElementDeletionRef | The 'comp:deletion' attribute must point to a <deletion> | ||||||||
CompReplacedElementConvFactorRef | The 'comp:conversionFactor attribute must point to a <parameter> | ||||||||
CompReplacedElementSameReference | No <replacedElement> refer to same object | ||||||||
CompReplacedElementNoDelAndConvFact | No <replacedElement> with deletion and conversionfactor | ||||||||
CompReplacedByMustRefObject | ReplacedBy must reference an object | ||||||||
CompReplacedByMustRefOnlyOne | ReplacedBy must reference only one other object. | ||||||||
CompReplacedByAllowedAttributes | Allowed attributes on <replacedBy> | ||||||||
CompReplacedBySubModelRef | The 'comp:submodelRef' attribute must point to a <submodel> | ||||||||
CompMustReplaceSameClass | Replaced classes must match. | ||||||||
CompMustReplaceIDs | Replaced IDs must be replaced with IDs. | ||||||||
CompMustReplaceMetaIDs | Replaced metaids must be replaced with metaids. | ||||||||
CompMustReplacePackageIDs | Replaced package IDs must be replaced with package IDs. | ||||||||
CompUnresolvedReference | Unresolved reference. | ||||||||
CompNoModelInReference | No model in referenced document. | ||||||||
CompExtModDefBad | Referenced <externalModelDefinitiongt; unresolvable. | ||||||||
CompModelFlatteningFailed | Model failed to flatten. | ||||||||
CompFlatModelNotValid | Flat model not valid. | ||||||||
CompLineNumbersUnreliable | Line numbers unreliable. | ||||||||
CompFlatteningNotRecognisedReqd | Flattening not implemented for required package. | ||||||||
CompFlatteningNotRecognisedNotReqd | Flattening not implemented for unrequired package. | ||||||||
CompFlatteningNotImplementedNotReqd | Flattening not implemented for unrequired package. | ||||||||
CompFlatteningNotImplementedReqd | Flattening not implemented for required package. | ||||||||
CompFlatteningWarning | Flattening reference may come from package. | ||||||||
CompDeprecatedDeleteFunction | The performDeletions functions is deprecated. | ||||||||
CompDeprecatedReplaceFunction | The performReplacementsAndConversions fuctions is deprecated. | ||||||||
CompDeletedReplacement | Element deleted before a subelement could be replaced. | ||||||||
CompIdRefMayReferenceUnknownPackage | The 'comp:idRef' attribute must be the 'id' of a model element | ||||||||
CompMetaIdRefMayReferenceUnknownPkg | The 'comp:metaIdRef' attribute must be the 'metaid' of a model element | ||||||||
FbcUnknown | |||||||||
FbcNSUndeclared | The fbc ns is not correctly declared | ||||||||
FbcElementNotInNs | Element not in fbc namespace | ||||||||
FbcDuplicateComponentId | Duplicate 'id' attribute value | ||||||||
FbcSBMLSIdSyntax | Invalid 'id' attribute | ||||||||
FbcAttributeRequiredMissing | Required fbc:required attribute on <sbml> | ||||||||
FbcAttributeRequiredMustBeBoolean | The fbc:required attribute must be Boolean | ||||||||
FbcRequiredFalse | The fbc:required attribute must be 'false' | ||||||||
FbcOnlyOneEachListOf | One of each list of allowed | ||||||||
FbcNoEmptyListOfs | ListOf elements cannot be empty | ||||||||
FbcLOFluxBoundsAllowedElements | Allowed elements on ListOfFluxBounds | ||||||||
FbcLOObjectivesAllowedElements | Allowed elements on ListOfObjectives | ||||||||
FbcLOFluxBoundsAllowedAttributes | Allowed attributes on ListOfFluxBounds | ||||||||
FbcLOObjectivesAllowedAttributes | Allowed attributes on ListOfObjectives | ||||||||
FbcActiveObjectiveSyntax | Type of activeObjective attribute | ||||||||
FbcActiveObjectiveRefersObjective | ActiveObjective must reference Objective | ||||||||
FbcModelMustHaveStrict | 'Strict' attribute required on <model> | ||||||||
FbcModelStrictMustBeBoolean | 'Strict' attribute must be Boolean | ||||||||
FbcLOGeneProductsAllowedElements | Allowed elements on ListOfGeneProducts | ||||||||
FbcLOGeneProductsAllowedAttributes | Allowed attributes on ListOfGeneProducts | ||||||||
FbcSpeciesAllowedL3Attributes | Species allowed attributes | ||||||||
FbcSpeciesChargeMustBeInteger | Charge must be integer | ||||||||
FbcSpeciesFormulaMustBeString | Chemical formula must be string | ||||||||
FbcFluxBoundAllowedL3Attributes | <fluxBound> may only have 'metaId' and 'sboTerm' from L3 namespace | ||||||||
FbcFluxBoundAllowedElements | <fluxBound> may only have <notes> and <annotations> from L3 Core | ||||||||
FbcFluxBoundRequiredAttributes | Invalid attribute found on <fluxBound> object | ||||||||
FbcFluxBoundRectionMustBeSIdRef | Datatype for 'fbc:reaction' must be SIdRef | ||||||||
FbcFluxBoundNameMustBeString | The attribute 'fbc:name' must be of the data type string | ||||||||
FbcFluxBoundOperationMustBeEnum | The attribute 'fbc:operation' must be of data type FbcOperation | ||||||||
FbcFluxBoundValueMustBeDouble | The attribute 'fbc:value' must be of the data type float | ||||||||
FbcFluxBoundReactionMustExist | 'fbc:reaction' must refer to valid reaction | ||||||||
FbcFluxBoundsForReactionConflict | Conflicting set of FluxBounds for a reaction | ||||||||
FbcObjectiveAllowedL3Attributes | <objective> may only have 'metaId' and 'sboTerm' from L3 namespace | ||||||||
FbcObjectiveAllowedElements | <objective> may only have <notes> and <annotations> from L3 Core | ||||||||
FbcObjectiveRequiredAttributes | Invalid attribute found on <objective> object | ||||||||
FbcObjectiveNameMustBeString | The attribute 'fbc:name' must be of the data type string | ||||||||
FbcObjectiveTypeMustBeEnum | The attribute 'fbc:type' must be of data type FbcType. | ||||||||
FbcObjectiveOneListOfObjectives | An <objective> must have one <listOfFluxObjectives> . | ||||||||
FbcObjectiveLOFluxObjMustNotBeEmpty | <listOfFluxObjectives> subobject must not be empty | ||||||||
FbcObjectiveLOFluxObjOnlyFluxObj | Invalid element found in <listOfFluxObjectives> | ||||||||
FbcObjectiveLOFluxObjAllowedAttribs | <listOfFluxObjectives> may only have 'metaId' and 'sboTerm' from L3 core | ||||||||
FbcFluxObjectAllowedL3Attributes | <fluxObjectivegt; may only have 'metaId' and 'sboTerm' from L3 namespace | ||||||||
FbcFluxObjectAllowedElements | <fluxObjectivegt; may only have <notes> and <annotations> from L3 Core | ||||||||
FbcFluxObjectRequiredAttributes | Invalid attribute found on <fluxObjectivegt; object | ||||||||
FbcFluxObjectNameMustBeString | The attribute 'fbc:name' must be of the data type string | ||||||||
FbcFluxObjectReactionMustBeSIdRef | Datatype for 'fbc:reaction' must be SIdRef | ||||||||
FbcFluxObjectReactionMustExist | 'fbc:reaction' must refer to valid reaction | ||||||||
FbcFluxObjectCoefficientMustBeDouble | The attribute 'fbc:coefficient' must be of the data type float | ||||||||
FbcFluxObjectCoefficientWhenStrict | The 'fbc:coefficient' must be declared when strict | ||||||||
FbcReactionOnlyOneGeneProdAss | One GeneProductAssociation in a Reaction | ||||||||
FbcReactionAllowedAttributes | Fbc attributes on a Reaction | ||||||||
FbcReactionLwrBoundSIdRef | LowerBound must be SIdRef | ||||||||
FbcReactionUpBoundSIdRef | UpperBound must be SIdRef | ||||||||
FbcReactionLwrBoundRefExists | LowerBound must point to Parameter | ||||||||
FbcReactionUpBoundRefExists | UpperBound must point to Parameter | ||||||||
FbcReactionMustHaveBoundsStrict | Reaction must have bounds when strict | ||||||||
FbcReactionConstantBoundsStrict | Reaction bounds constant when strict | ||||||||
FbcReactionBoundsMustHaveValuesStrict | Reaction bounds must have values when strict | ||||||||
FbcReactionBoundsNotAssignedStrict | Reaction bounds not assigned when strict | ||||||||
FbcReactionLwrBoundNotInfStrict | LowerBound cannot be INF when strict | ||||||||
FbcReactionUpBoundNotNegInfStrict | UpperBound cannot be -INF when strict | ||||||||
FbcReactionLwrLessThanUpStrict | LowerBound less than upperBound when strict | ||||||||
FbcSpeciesReferenceConstantStrict | SpeciesReferences must be constant when strict | ||||||||
FbcSpeciesRefsStoichMustBeRealStrict | Stoichiometry of SpeciesReferences must be real valued when strict | ||||||||
FbcSpeciesRefNotAssignedStrict | SpeciesReference not target of InitialAssignment when strict | ||||||||
FbcGeneProdAssocAllowedCoreAttribs | Allowed core attributes on <GeneProductAssociationgt; | ||||||||
FbcGeneProdAssocAllowedCoreElements | Allowed core elements on <GeneProductAssociationgt; | ||||||||
FbcGeneProdAssocAllowedAttribs | Allowed fbc attributes on <GeneProductAssociationgt; | ||||||||
FbcGeneProdAssocIdSyntax | 'fbc:id' must have SId syntax | ||||||||
FbcGeneProdAssocContainsOneElement | <GeneProductAssociationgt; must contain one concrete object | ||||||||
FbcGeneProdAssocNameMustBeString | 'fbc:name' must be string | ||||||||
FbcGeneProdRefAllowedCoreAttribs | Allowed core attributes on <GeneProductRefgt; | ||||||||
FbcGeneProdRefAllowedCoreElements | Allowed core elements on <GeneProductRefgt; | ||||||||
FbcGeneProdRefAllowedAttribs | Allowed fbc attributes on <GeneProductRefgt; | ||||||||
FbcGeneProdRefGeneProductSIdRef | 'fbc:geneProduct' must be SIdRef | ||||||||
FbcGeneProdRefGeneProductExists | 'fbc:geneProduct' must point to existing <GeneProductgt; | ||||||||
FbcAndAllowedCoreAttributes | Allowed core attributes on <And> | ||||||||
FbcAndAllowedCoreElements | Allowed core attributes on <And> | ||||||||
FbcAndTwoChildren | <And> must have at least two child elements | ||||||||
FbcOrAllowedCoreAttributes | Allowed core attributes on <Or> | ||||||||
FbcOrAllowedCoreElements | Allowed core elements on <Or> | ||||||||
FbcOrTwoChildren | <Or> must have at least two child elements | ||||||||
FbcGeneProductAllowedCoreAttributes | Allowed core attributes on <GeneProductgt; | ||||||||
FbcGeneProductAllowedCoreElements | Allowed core elements on <GeneProductgt; | ||||||||
FbcGeneProductAllowedAttributes | Allowed fbc attributes on <GeneProductgt; | ||||||||
FbcGeneProductLabelMustBeString | 'fbc:label' must be string | ||||||||
FbcGeneProductLabelMustBeUnique | 'fbc:label' must be unique | ||||||||
FbcGeneProductNameMustBeString | 'fbc:name' must be string | ||||||||
FbcGeneProductAssocSpeciesMustExist | 'fbc:associatedSpecies' must point to existing <species> | ||||||||
QualUnknown | |||||||||
QualNSUndeclared | The qual ns is not correctly declared | ||||||||
QualElementNotInNs | Element not in qual namespace | ||||||||
QualFunctionTermBool | FunctionTerm should return Boolean | ||||||||
QualMathCSymbolDisallowed | CSymbol time or delay not allowed | ||||||||
QualDuplicateComponentId | Duplicate 'id' attribute value | ||||||||
QualAttributeRequiredMissing | Required qual:required attribute on <sbml> | ||||||||
QualAttributeRequiredMustBeBoolean | The qual:required attribute must be Boolean | ||||||||
QualRequiredTrueIfTransitions | The qual:required attribute must be 'true' if math changes | ||||||||
QualOneListOfTransOrQS | Only one <listOfTransitions> or <listOfQualitativeSpeciesgt; allowed. | ||||||||
QualEmptyLONotAllowed | Empty <listOfTransitions> or <listOfQualitativeSpeciesgt; not allowed. | ||||||||
QualLOTransitiondAllowedElements | Elements allowed on <listOfTransitions> . | ||||||||
QualLOQualSpeciesAllowedElements | Elements allowed on <listOfTransitions> . | ||||||||
QualLOQualSpeciesAllowedAttributes | Attributes allowed on <listOfQualitativeSpeciesgt; . | ||||||||
QualLOTransitionsAllowedAttributes | Attributes allowed on <listOfTransitions> . | ||||||||
QualQualSpeciesAllowedCoreAttributes | Core attributes allowed on <qualitativeSpeciesgt; . | ||||||||
QualQualSpeciesAllowedElements | Elements allowed on <qualitativeSpeciesgt; . | ||||||||
QualQualSpeciesAllowedAttributes | Attributes allowed on <qualitativeSpeciesgt; . | ||||||||
QualConstantMustBeBool | Attribute 'constant' on <qualitativeSpeciesgt; must be Boolean. | ||||||||
QualNameMustBeString | Attribute 'name' on <qualitativeSpeciesgt; must be string. | ||||||||
QualInitialLevelMustBeInt | Attribute 'initialLevel' on <qualitativeSpeciesgt; must be integer. | ||||||||
QualMaxLevelMustBeInt | Attribute 'maxLevel' on <qualitativeSpeciesgt; must be integer. | ||||||||
QualCompartmentMustReferExisting | Attribute 'compartment' on <qualitativeSpeciesgt; must reference compartment. | ||||||||
QualInitialLevelCannotExceedMax | Attribute 'initialLevel' on <qualitativeSpeciesgt; cannot exceed maxLevel. | ||||||||
QualConstantQSCannotBeOutput | Constant <qualitativeSpeciesgt; cannot be an Output. | ||||||||
QualQSAssignedOnlyOnce | A <qualitativeSpeciesgt; can only be assigned once. | ||||||||
QualInitalLevelNotNegative | Attribute 'initialLevel' on <qualitativeSpeciesgt; cannot be negative. | ||||||||
QualMaxLevelNotNegative | Attribute 'maxLevel' on <qualitativeSpeciesgt; cannot be negative. | ||||||||
QualTransitionAllowedCoreAttributes | Core attributes allowed on <transition> . | ||||||||
QualTransitionAllowedElements | Elements allowed on <transition> . | ||||||||
QualTransitionAllowedAttributes | Attributes allowed on <transition> . | ||||||||
QualTransitionNameMustBeString | Attribute 'name' on <transition> must be string. | ||||||||
QualTransitionLOElements | ListOf elements on <transition> . | ||||||||
QualTransitionEmptyLOElements | ListOf elements on <transition> not empty. | ||||||||
QualTransitionLOInputElements | Elements on <listOfInputs> . | ||||||||
QualTransitionLOOutputElements | Elements on <listOfOutputs> . | ||||||||
QualTransitionLOFuncTermElements | Elements on <listOfFunctionTerms> . | ||||||||
QualTransitionLOInputAttributes | Attributes allowed on <listOfInputs> . | ||||||||
QualTransitionLOOutputAttributes | Attributes allowed on <listOfOutputs> . | ||||||||
QualTransitionLOFuncTermAttributes | Attributes allowed on <listOfFunctionTerms> . | ||||||||
QualTransitionLOFuncTermExceedMax | <listOfFunctionTerms> cannot make qualitativeSpecies exceed maxLevel. | ||||||||
QualTransitionLOFuncTermNegative | <listOfFunctionTerms> cannot make qualitativeSpecies negative. | ||||||||
QualInputAllowedCoreAttributes | Core attributes allowed on <input> . | ||||||||
QualInputAllowedElements | Elements allowed on <input> . | ||||||||
QualInputAllowedAttributes | Attributes allowed on <input> . | ||||||||
QualInputNameMustBeString | Attribute 'name' on <input> must be string. | ||||||||
QualInputSignMustBeSignEnum | Attribute 'sign' on <input> must be enum. | ||||||||
QualInputTransEffectMustBeInputEffect | Attribute 'transitionEffect' on <input> must be enum. | ||||||||
QualInputThreshMustBeInteger | Attribute 'thresholdLevel' on <input> must be non negative integer. | ||||||||
QualInputQSMustBeExistingQS | Attribute 'qualitativeSpecies' on <input> must refer to existing | ||||||||
QualInputConstantCannotBeConsumed | Constant <input> cannot be consumed. | ||||||||
QualInputThreshMustBeNonNegative | Attribute 'thresholdLevel' on <input> must be non negative integer. | ||||||||
QualOutputAllowedCoreAttributes | Core attributes allowed on <output> . | ||||||||
QualOutputAllowedElements | Elements allowed on <output> . | ||||||||
QualOutputAllowedAttributes | Attributes allowed on <output> . | ||||||||
QualOutputNameMustBeString | Attribute 'name' on <output> must be string. | ||||||||
QualOutputTransEffectMustBeOutput | Attribute 'transitionEffect' on <output> must be enum. | ||||||||
QualOutputLevelMustBeInteger | Attribute 'outputLevel' on <output> must be non negative integer. | ||||||||
QualOutputQSMustBeExistingQS | Attribute 'qualitativeSpecies' on <output> must refer to existing | ||||||||
QualOutputConstantMustBeFalse | Constant 'qualitativeSpecies' cannot be <output> | ||||||||
QualOutputProductionMustHaveLevel | <output> being produced must have level | ||||||||
QualOutputLevelMustBeNonNegative | Attribute 'outputLevel' on <output> must be non negative integer. | ||||||||
QualDefaultTermAllowedCoreAttributes | Core attributes allowed on <defaultTerm> . | ||||||||
QualDefaultTermAllowedElements | Elements allowed on <defaultTerm> . | ||||||||
QualDefaultTermAllowedAttributes | Attributes allowed on <defaultTerm> . | ||||||||
QualDefaultTermResultMustBeInteger | Attribute 'resultLevel' on <defaultTerm> must be non negative integer. | ||||||||
QualDefaultTermResultMustBeNonNeg | Attribute 'resultLevel' on <defaultTerm> must be non negative integer. | ||||||||
QualFuncTermAllowedCoreAttributes | Core attributes allowed on <functionTerm> . | ||||||||
QualFuncTermAllowedElements | Elements allowed on <functionTerm> . | ||||||||
QualFuncTermAllowedAttributes | Attributes allowed on <functionTerm> . | ||||||||
QualFuncTermOnlyOneMath | Only one <math> on <functionTerm> . | ||||||||
QualFuncTermResultMustBeInteger | Attribute 'resultLevel' on <functionTerm> must be non negative integer. | ||||||||
QualFuncTermResultMustBeNonNeg | Attribute 'resultLevel' on <functionTerm> must be non negative integer. | ||||||||
GroupsUnknown | |||||||||
GroupsNSUndeclared | The Groups namespace is not correctly declared. | ||||||||
GroupsElementNotInNs | Element not in Groups namespace | ||||||||
GroupsDuplicateComponentId | Duplicate 'id' attribute value | ||||||||
GroupsIdSyntaxRule | Invalid SId syntax | ||||||||
GroupsAttributeRequiredMissing | Required groups:required attribute on <sbml> | ||||||||
GroupsAttributeRequiredMustBeBoolean | The groups:required attribute must be Boolean | ||||||||
GroupsAttributeRequiredMustHaveValue | The groups:required attribute must be 'false' | ||||||||
GroupsModelAllowedElements | Elements allowed on <model> . | ||||||||
GroupsModelEmptyLOElements | No Empty ListOf elements allowed on <Modelgt; . | ||||||||
GroupsModelLOGroupsAllowedCoreElements | Core elements allowed on <model> . | ||||||||
GroupsModelLOGroupsAllowedCoreAttributes | Core attributes allowed on <model> . | ||||||||
GroupsGroupAllowedCoreAttributes | Core attributes allowed on <group> . | ||||||||
GroupsGroupAllowedCoreElements | Core elements allowed on <group> . | ||||||||
GroupsGroupAllowedAttributes | Attributes allowed on <group> . | ||||||||
GroupsGroupAllowedElements | Elements allowed on <group> . | ||||||||
GroupsGroupKindMustBeGroupKindEnum | Kind attribute must be GroupKind. | ||||||||
GroupsGroupNameMustBeString | Name attribute must be String. | ||||||||
GroupsGroupEmptyLOElements | No Empty ListOf elements allowed on <group> . | ||||||||
GroupsGroupLOMembersAllowedCoreElements | Core elements allowed on <listOfMembers> . | ||||||||
GroupsGroupLOMembersAllowedCoreAttributes | Core attributes allowed on <listOfMembers> . | ||||||||
GroupsGroupLOMembersAllowedAttributes | Attributes allowed on <listOfMembers> . | ||||||||
GroupsLOMembersNameMustBeString | Name attribute must be String. | ||||||||
GroupsLOMembersConsistentReferences | Consistent references by multiple <member> objects. | ||||||||
GroupsNotCircularReferences | Circular references by multiple <member> objects. | ||||||||
GroupsMemberAllowedCoreAttributes | Core attributes allowed on <member> . | ||||||||
GroupsMemberAllowedCoreElements | Core elements allowed on <member> . | ||||||||
GroupsMemberAllowedAttributes | Attributes allowed on <member> . | ||||||||
GroupsMemberNameMustBeString | Name attribute must be String. | ||||||||
GroupsMemberIdRefMustBeSBase | Attribute 'idRef' must point to SBase object. | ||||||||
GroupsMemberMetaIdRefMustBeSBase | Attribute 'metaIdRef' must point to SBase object. | ||||||||
GroupsMemberIdRefMustBeSId | Attribute 'idRef' must be type 'SId'. | ||||||||
GroupsMemberMetaIdRefMustBeID | Attribute 'metaIdRef' must be type 'ID'. | ||||||||
LayoutUnknownError | |||||||||
LayoutNSUndeclared | The layout ns is not correctly declared | ||||||||
LayoutElementNotInNs | Element not in layout namespace | ||||||||
LayoutDuplicateComponentId | Duplicate 'id' attribute value | ||||||||
LayoutSIdSyntax | 'id' attribute incorrect syntax | ||||||||
LayoutXsiTypeAllowedLocations | 'xsi:type' allowed locations | ||||||||
LayoutXsiTypeSyntax | 'xsi:type' attribute incorrect syntax | ||||||||
LayoutAttributeRequiredMissing | Required layout:required attribute on <sbml> | ||||||||
LayoutAttributeRequiredMustBeBoolean | The layout:required attribute must be Boolean | ||||||||
LayoutRequiredFalse | The layout:required attribute must be 'false' | ||||||||
LayoutOnlyOneLOLayouts | Only one listOfLayouts on <model> | ||||||||
LayoutLOLayoutsNotEmpty | ListOf elements cannot be empty | ||||||||
LayoutLOLayoutsAllowedElements | Allowed elements on ListOfLayouts | ||||||||
LayoutLOLayoutsAllowedAttributes | Allowed attributes on ListOfLayouts | ||||||||
LayoutLayoutAllowedElements | Allowed elements on Layout | ||||||||
LayoutLayoutAllowedCoreAttributes | Allowed core attributes on Layout | ||||||||
LayoutOnlyOneEachListOf | Only one each listOf on <layout> | ||||||||
LayoutNoEmptyListOfs | ListOf elements cannot be empty | ||||||||
LayoutLayoutAllowedAttributes | <layout> must have 'id' and may have 'name' | ||||||||
LayoutLayoutNameMustBeString | 'name' must be string | ||||||||
LayoutLOCompGlyphAllowedAttributes | Attributes allowed on <listOfCompartmentGlyphs> . | ||||||||
LayoutLOCompGlyphAllowedElements | Elements allowed on <listOfCompartmentGlyphs> . | ||||||||
LayoutLOSpeciesGlyphAllowedAttributes | Attributes allowed on <listOfSpeciesGlyphs> . | ||||||||
LayoutLOSpeciesGlyphAllowedElements | Elements allowed on <listOfSpeciesGlyphs> . | ||||||||
LayoutLORnGlyphAllowedAttributes | Attributes allowed on <listOfReactionGlyphs> . | ||||||||
LayoutLORnGlyphAllowedElements | Elements allowed on <listOfReactionGlyphs> . | ||||||||
LayoutLOAddGOAllowedAttribut | Attributes allowed on <listOfAdditionalGraphicalObjectGlyphs> . | ||||||||
LayoutLOAddGOAllowedElements | Elements allowed on <listOfAdditionalGraphicalObjectGlyphs> . | ||||||||
LayoutLayoutMustHaveDimensions | Layout must have <dimensions> . | ||||||||
LayoutLOTextGlyphAllowedAttributes | Attributes allowed on <listOfTextGlyphs> . | ||||||||
LayoutLOTextGlyphAllowedElements | Elements allowed on <listOfTextGlyphs> . | ||||||||
LayoutGOAllowedCoreElements | Core elements allowed on <graphicalObject> . | ||||||||
LayoutGOAllowedCoreAttributes | Core attributes allowed on <graphicalObject> . | ||||||||
LayoutGOAllowedElements | Layout elements allowed on <graphicalObject> . | ||||||||
LayoutGOAllowedAttributes | Layout attributes allowed on <graphicalObject> . | ||||||||
LayoutGOMetaIdRefMustBeIDREF | Layout 'metaidRef' must be IDREF. | ||||||||
LayoutGOMetaIdRefMustReferenceObject | Layout 'metaidRef' must reference existing object. | ||||||||
LayoutGOMustContainBoundingBox | A <graphicalObject> must contain a <boundingBox> . | ||||||||
LayoutCGAllowedCoreElements | Core elements allowed on <compartmentGlyph> . | ||||||||
LayoutCGAllowedCoreAttributes | Core attributes allowed on <compartmentGlyph> . | ||||||||
LayoutCGAllowedElements | Layout elements allowed on <compartmentGlyph> . | ||||||||
LayoutCGAllowedAttributes | Layout attributes allowed on <compartmentGlyph> . | ||||||||
LayoutCGMetaIdRefMustBeIDREF | Layout 'metaidRef' must be IDREF. | ||||||||
LayoutCGMetaIdRefMustReferenceObject | Layout 'metaidRef' must reference existing object. | ||||||||
LayoutCGCompartmentSyntax | CompartmentGlyph 'compartment' must have SIdRef syntax. | ||||||||
LayoutCGCompartmentMustRefComp | CompartmentGlyph compartment must reference existing compartment. | ||||||||
LayoutCGNoDuplicateReferences | CompartmentGlyph cannot reference two objects. | ||||||||
LayoutCGOrderMustBeDouble | CompartmentGlyph order must be float. | ||||||||
LayoutSGAllowedCoreElements | Core elements allowed on <speciesGlyph> . | ||||||||
LayoutSGAllowedCoreAttributes | Core attributes allowed on <speciesGlyph> . | ||||||||
LayoutSGAllowedElements | Layout elements allowed on <speciesGlyph> . | ||||||||
LayoutSGAllowedAttributes | Layout attributes allowed on <speciesGlyph> . | ||||||||
LayoutSGMetaIdRefMustBeIDREF | Layout 'metaidRef' must be IDREF. | ||||||||
LayoutSGMetaIdRefMustReferenceObject | Layout 'metaidRef' must reference existing object. | ||||||||
LayoutSGSpeciesSyntax | SpeciesGlyph 'species' must have SIdRef syntax. | ||||||||
LayoutSGSpeciesMustRefSpecies | SpeciesGlyph species must reference existing species. | ||||||||
LayoutSGNoDuplicateReferences | SpeciesGlyph cannot reference two objects. | ||||||||
LayoutRGAllowedCoreElements | Core elements allowed on <reactionGlyph> . | ||||||||
LayoutRGAllowedCoreAttributes | Core attributes allowed on <reactionGlyph> . | ||||||||
LayoutRGAllowedElements | Layout elements allowed on <reactionGlyph> . | ||||||||
LayoutRGAllowedAttributes | Layout attributes allowed on <reactionGlyph> . | ||||||||
LayoutRGMetaIdRefMustBeIDREF | Layout 'metaidRef' must be IDREF. | ||||||||
LayoutRGMetaIdRefMustReferenceObject | Layout 'metaidRef' must reference existing object. | ||||||||
LayoutRGReactionSyntax | ReactionGlyph 'reaction' must have SIdRef syntax. | ||||||||
LayoutRGReactionMustRefReaction | ReactionGlyph reaction must reference existing reaction. | ||||||||
LayoutRGNoDuplicateReferences | ReactionGlyph cannot reference two objects. | ||||||||
LayoutLOSpeciesRefGlyphAllowedElements | Allowed elements on ListOfSpeciesReferenceGlyphs | ||||||||
LayoutLOSpeciesRefGlyphAllowedAttribs | Allowed attributes on ListOfSpeciesReferenceGlyphs | ||||||||
LayoutLOSpeciesRefGlyphNotEmpty | ListOfSpeciesReferenceGlyphs not empty | ||||||||
LayoutGGAllowedCoreElements | Core elements allowed on <generalGlyph> . | ||||||||
LayoutGGAllowedCoreAttributes | Core attributes allowed on <generalGlyph> . | ||||||||
LayoutGGAllowedElements | Layout elements allowed on <generalGlyph> . | ||||||||
LayoutGGAllowedAttributes | Layout attributes allowed on <generalGlyph> . | ||||||||
LayoutGGMetaIdRefMustBeIDREF | Layout 'metaidRef' must be IDREF. | ||||||||
LayoutGGMetaIdRefMustReferenceObject | Layout 'metaidRef' must reference existing object. | ||||||||
LayoutGGReferenceSyntax | GeneralGlyph 'reference' must have SIdRef syntax. | ||||||||
LayoutGGReferenceMustRefObject | GeneralGlyph 'reference' must reference existing element. | ||||||||
LayoutGGNoDuplicateReferences | GeneralGlyph cannot reference two objects. | ||||||||
LayoutLOReferenceGlyphAllowedElements | Allowed elements on ListOfReferenceGlyphs | ||||||||
LayoutLOReferenceGlyphAllowedAttribs | Allowed attributes on ListOfReferenceGlyphs | ||||||||
LayoutLOSubGlyphAllowedElements | |||||||||
LayoutLOSubGlyphAllowedAttribs | Allowed attributes on ListOfSubGlyphs | ||||||||
LayoutTGAllowedCoreElements | Core elements allowed on <textGlyph> . | ||||||||
LayoutTGAllowedCoreAttributes | Core attributes allowed on <textGlyph> . | ||||||||
LayoutTGAllowedElements | Layout elements allowed on <textGlyph> . | ||||||||
LayoutTGAllowedAttributes | Layout attributes allowed on <textGlyph> . | ||||||||
LayoutTGMetaIdRefMustBeIDREF | Layout 'metaidRef' must be IDREF. | ||||||||
LayoutTGMetaIdRefMustReferenceObject | Layout 'metaidRef' must reference existing object. | ||||||||
LayoutTGOriginOfTextSyntax | TextGlyph 'originOfText' must have SIdRef syntax. | ||||||||
LayoutTGOriginOfTextMustRefObject | TextGlyph 'originOfText' must reference existing element. | ||||||||
LayoutTGNoDuplicateReferences | TextGlyph cannot reference two objects. | ||||||||
LayoutTGGraphicalObjectSyntax | TextGlyph 'graphicalObject' must have SIdRef syntax. | ||||||||
LayoutTGGraphicalObjectMustRefObject | TextGlyph 'graphicalObject' must reference existing element. | ||||||||
LayoutTGTextMustBeString | TextGlyph 'text' must be string. | ||||||||
LayoutSRGAllowedCoreElements | Core elements allowed on <speciesReferenceGlyphgt; . | ||||||||
LayoutSRGAllowedCoreAttributes | Core attributes allowed on <speciesReferenceGlyphgt; . | ||||||||
LayoutSRGAllowedElements | Layout elements allowed on <speciesReferenceGlyphgt; . | ||||||||
LayoutSRGAllowedAttributes | Layout attributes allowed on <speciesReferenceGlyphgt; . | ||||||||
LayoutSRGMetaIdRefMustBeIDREF | Layout 'metaidRef' must be IDREF. | ||||||||
LayoutSRGMetaIdRefMustReferenceObject | Layout 'metaidRef' must reference existing object. | ||||||||
LayoutSRGSpeciesReferenceSyntax | SpeciesReferenceGlyph 'speciesReference' must have SIdRef syntax. | ||||||||
LayoutSRGSpeciesRefMustRefObject | SpeciesReferenceGlyph 'speciesReference' must reference existing element. | ||||||||
LayoutSRGNoDuplicateReferences | SpeciesReferenceGlyph cannot reference two objects. | ||||||||
LayoutSRGSpeciesGlyphSyntax | SpeciesReferenceGlyph 'speciesGlyph' must have SIdRef syntax. | ||||||||
LayoutSRGSpeciesGlyphMustRefObject | SpeciesReferenceGlyph 'speciesGlyph' must reference existing element. | ||||||||
LayoutSRGRoleSyntax | SpeciesReferenceGlyph 'role' must be string from enumeration. | ||||||||
LayoutREFGAllowedCoreElements | Core elements allowed on <referenceGlyph> . | ||||||||
LayoutREFGAllowedCoreAttributes | Core attributes allowed on <referenceGlyph> . | ||||||||
LayoutREFGAllowedElements | Layout elements allowed on <referenceGlyph> . | ||||||||
LayoutREFGAllowedAttributes | Layout attributes allowed on <referenceGlyph> . | ||||||||
LayoutREFGMetaIdRefMustBeIDREF | Layout 'metaidRef' must be IDREF. | ||||||||
LayoutREFGMetaIdRefMustReferenceObject | Layout 'metaidRef' must reference existing object. | ||||||||
LayoutREFGReferenceSyntax | ReferenceGlyph 'reference' must have SIdRef syntax. | ||||||||
LayoutREFGReferenceMustRefObject | ReferenceGlyph 'reference' must reference existing element. | ||||||||
LayoutREFGNoDuplicateReferences | ReferenceGlyph cannot reference two objects. | ||||||||
LayoutREFGGlyphSyntax | ReferenceGlyph 'glyph' must have SIdRef syntax. | ||||||||
LayoutREFGGlyphMustRefObject | ReferenceGlyph 'glyph' must reference existing element. | ||||||||
LayoutREFGRoleSyntax | ReferenceGlyph 'role' must be string. | ||||||||
LayoutPointAllowedCoreElements | Core elements allowed on <pointgt; . | ||||||||
LayoutPointAllowedCoreAttributes | Core attributes allowed on <pointgt; . | ||||||||
LayoutPointAllowedAttributes | Layout attributes allowed on <pointgt; . | ||||||||
LayoutPointAttributesMustBeDouble | Layout 'x', 'y' and 'z' must be float. | ||||||||
LayoutBBoxAllowedCoreElements | Core elements allowed on <boundingBox> . | ||||||||
LayoutBBoxAllowedCoreAttributes | Core attributes allowed on <boundingBox> . | ||||||||
LayoutBBoxAllowedElements | Layout elements allowed on <boundingBox> . | ||||||||
LayoutBBoxAllowedAttributes | Layout attributes allowed on <boundingBox> . | ||||||||
LayoutBBoxConsistent3DDefinition | Layout consistent dimensions on a <boundingBox> | ||||||||
LayoutCurveAllowedCoreElements | Core elements allowed on <curve> . | ||||||||
LayoutCurveAllowedCoreAttributes | Core attributes allowed on <curve> . | ||||||||
LayoutCurveAllowedElements | Layout elements allowed on <curve> . | ||||||||
LayoutCurveAllowedAttributes | Layout attributes allowed on <curve> . | ||||||||
LayoutLOCurveSegsAllowedAttributes | Allowed attributes on ListOfCurveSegments | ||||||||
LayoutLOCurveSegsAllowedElements | Allowed elements on ListOfCurveSegments | ||||||||
LayoutLOCurveSegsNotEmpty | No empty ListOfCurveSegments | ||||||||
LayoutLSegAllowedCoreElements | Core elements allowed on <lineSegment> . | ||||||||
LayoutLSegAllowedCoreAttributes | Core attributes allowed on <lineSegment> . | ||||||||
LayoutLSegAllowedElements | Layout elements allowed on <lineSegment> . | ||||||||
LayoutLSegAllowedAttributes | Layout attributes allowed on <lineSegment> . | ||||||||
LayoutCBezAllowedCoreElements | Core elements allowed on <cubicBezier> . | ||||||||
LayoutCBezAllowedCoreAttributes | Core attributes allowed on <cubicBezier> . | ||||||||
LayoutCBezAllowedElements | Layout elements allowed on <cubicBezier> . | ||||||||
LayoutCBezAllowedAttributes | Layout attributes allowed on <cubicBezier> . | ||||||||
LayoutDimsAllowedCoreElements | Core elements allowed on <dimensions> . | ||||||||
LayoutDimsAllowedCoreAttributes | Core attributes allowed on <dimensions> . | ||||||||
LayoutDimsAllowedAttributes | Layout attributes allowed on <dimensions> . | ||||||||
LayoutDimsAttributesMustBeDouble | Layout 'width', 'height' and 'depth' must be float. |
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 Versions 1–2 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 Versions 1–2 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 Versions 1–2 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 Versions 1–2 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 Versions 1–2 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 Versions 1–2 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. |
In libSBML version 5.18.0 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 | __init__ (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | getCategory (self) |
Returns the category of this error. More... | |
def | getCategoryAsString (self) |
Returns a string describing the category of this error. More... | |
def | getColumn (self) |
Returns the column number in the XML input near where the error, warning or other diagnostic occurred. More... | |
def | getErrorId (self) |
Returns the identifier of this error. More... | |
def | getErrorIdOffset (self) |
Returns libSBML's internal numerical offset for the error code associated with this error. More... | |
def | getLine (self) |
Returns the line number in the XML input near where the error, warning or other diagnostic occurred. More... | |
def | getMessage (self) |
Returns the message text of this error. More... | |
def | getPackage (self) |
Returns the SBML Level 3 package extension (if any) that logged this error. More... | |
def | getSeverity (self) |
Returns the severity of this error. More... | |
def | getSeverityAsString (self) |
Returns a string describing the severity level of this error. More... | |
def | getShortMessage (self) |
Returns a brief message for this error. More... | |
def | getStandardMessage (code) |
Returns a copy of the message string associated with the given predefined XMLError code. More... | |
def | isError (self) |
Predicate returning True or False depending on whether this error is a significant error. More... | |
def | isFatal (self) |
Predicate returning True or False depending on whether this error is a fatal run-time error. More... | |
def | isInfo (self) |
Predicate returning True or False depending on whether this error object is for information purposes only. More... | |
def | isInternal (self) |
Predicate returning True or False depending on whether this error resulted from an internal program error. More... | |
def | isSystem (self) |
Predicate returning True or False depending on whether this error was generated by the operating system. More... | |
def | isValid (self) |
Predicate returning True or False depending on whether this error resulted from a problem or whether it was logged as an unknown error. More... | |
def | isWarning (self) |
Predicate returning True or False depending on whether this error object is a warning. More... | |
def | isXML (self) |
def | setColumn (self, column) |
Sets the column number where this error occurred. More... | |
def | setLine (self, line) |
Sets the line number where this error occurred. More... | |
def libsbml.SBMLError.__init__ | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
__init__(long errorId=0, long level, long version, string details, long line=0, long column=0, long severity, long category, string package, long pkgVersion=1) SBMLError __init__(long errorId=0, long level, long version, string details, long line=0, long column=0, long severity, long category, string package) SBMLError __init__(long errorId=0, long level, long version, string details, long line=0, long column=0, long severity, long category) SBMLError __init__(long errorId=0, long level, long version, string details, long line=0, long column=0, long severity) SBMLError __init__(long errorId=0, long level, long version, string details, long line=0, long column=0) SBMLError __init__(long errorId=0, long level, long version, string details, long line=0) SBMLError __init__(long errorId=0, long level, long version, string details) SBMLError __init__(long errorId=0, long level, long version) SBMLError __init__(long errorId=0, long level) SBMLError __init__(long errorId=0) SBMLError __init__() SBMLError __init__(SBMLError orig) SBMLError
Each variant is described separately below.
SBMLError(SBMLError orig)
Copy constructor; creates a copy of this SBMLError.
orig | the instance to copy. |
SBMLError(long errorId = 0, long level = SBML_DEFAULT_LEVEL, long version = SBML_DEFAULT_VERSION, string details = '', long line = 0, long column = 0, long severity = LIBSBML_SEV_ERROR, long category = LIBSBML_CAT_SBML, string package = 'core', long pkgVersion = 1)
Creates a new SBMLError to report that something occurred during SBML processing.
When a libSBML operation on SBML content results in a warning, error or other diagnostic, the issue is reported as an SBMLError object. SBMLError objects have identification numbers to indicate the nature of the exception.These numbers are defined as longeger constants in the interface class libsbml. See the top of this documentation page for a table listing the possible values and their meanings. The argument errorId
to this constructor can be (but does not have to be) a value from this set of constants. If it is one of the predefined error identifiers, the SBMLError class assumes the error is a low-level system or SBML layer error and prepends a built-in, predefined error message to any string passed in the argument details
to this constructor. In addition, all the predefined error identifiers have associated values for the severity
and category
codes, and these fields are filled-in using the libSBML defaults for each different error identifier.
If the error identifier errorId
is a number greater than 99999, the SBMLError class assumes the error was generated from another part of the software and does not do additional filling in of values beyond the default in the constructor itself. This allows SBMLError to serve as a base class for other errors, such as for user-defined validation rules (see Validator). Callers should fill in all the parameters with suitable values if generating errors with codes greater than 99999 to make maximum use of the SBMLError facilities.
As mentioned above, there are additional constants defined for standard severity and standard category codes, and every predefined error in libSBML has an associated value for severity and category taken from these predefined sets. These constants have symbol names prefixed with LIBSBML_SEV_
and LIBSBML_CAT_
, respectively. If the value of errorId
is one of the standard error codes, callers do not need to fill in severity
and category
in a call to this constructor. Conversely, if errorId
is not an existing SBML-level error code, callers can use other values for severity
and category
.
Please see the top of the documentation for SBMLError for a longer discussion of the possible error codes, their meanings, and their applicability to different combinations of Level+Version of SBML.
errorId | a long integer, the identification number of the error. |
level | the SBML Level of the SBML model. |
version | the SBML Version within the Level of the SBML model. |
details | a string containing additional details about the error. If the error code in errorId is one that is recognized by SBMLError, the given message is appended to a predefined message associated with the given code. If the error code is not recognized, the message is stored as-is as the text of the error. |
line | a long integer, the line number at which the error occured. |
column | a long integer, the column number at which the error occured. |
severity | an integer indicating severity of the error. |
category | an integer indicating the category to which the error belongs. |
package | the SBML Level package involved. |
pkgVersion | the version of the package . |
parameter
= value
. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.
|
inherited |
Returns the category of this error.
getCategory() long
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.
|
inherited |
Returns a string describing the category of this error.
getCategoryAsString() string
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.
|
inherited |
Returns the column number in the XML input near where the error, warning or other diagnostic occurred.
getColumn() long
We say 'near where the problem occurred', because many factors affect how accurate the line/column information ultimately is. For example, sometimes, the underlying XML parsers can only report such information for the parent XML element where an error occurs, and not for the specific point where the problem occurs. In other situations, some parsers report invalid line and/or column numbers altogether. If this occurs, libSBML sets the line and/or column number in the XMLError object to either 0
or the value of the maximum unsigned long integer representable on the platform where libSBML is running. 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.
|
inherited |
Returns the identifier of this error.
getErrorId() long
|
inherited |
Returns libSBML's internal numerical offset for the error code associated with this error.
getErrorIdOffset() long
In the SBML Level 3 package specifications, package validation rules are identified by 5-digit numbers prefixed with the nickname of the package itself—e.g., “comp-10101”, “fbc-20301”, etc. Historically, libSBML reported error codes as pure integers, and some application software systems make decisions based on the numerical values of the error codes. To permit these applications to continue to function in this fashion, libSBML internally continues to maintain error identifiers as pure integers. To handle the possibility that errors may come from package extensions, libSBML uses numerical offsets added to the internal error codes. These offsets add two leading digits to the regular 5-digit error codes; for example, “comp” error codes are stored as 1010101, 1020102, etc. The offset in this case is 1000000. Another package will have the offset 2000000, yet another will have 3000000, etc.
This method returns the integer offset in this error's error code. Calling applications can get the 5-digit package-specific number for a given error code by subtracting the offset from the value reported by getErrorId():
getErrorId() - getErrorIdOffset()
When libSBML produces error messages, it combines the text string returned by getPackage() with the subtracted value of the error code, to produce a text string of the form “comp-10101”.
|
inherited |
Returns the line number in the XML input near where the error, warning or other diagnostic occurred.
getLine() long
We say 'near where the problem occurred', because many factors affect how accurate the line/column information ultimately is. For example, sometimes, the underlying XML parsers can only report such information for the parent XML element where an error occurs, and not for the specific point where the problem occurs. In other situations, some parsers report invalid line and/or column numbers altogether. If this occurs, libSBML sets the line and/or column number in the XMLError object to either 0
or the value of the maximum unsigned long integer representable on the platform where libSBML is running. 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.
|
inherited |
Returns the message text of this error.
getMessage() string
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.
|
inherited |
Returns the SBML Level 3 package extension (if any) that logged this error.
getPackage() string
Each error logged by an libSBML extension for SBML Level 3 packages includes a record of the package that logged it. The field is a simple text string. If the string is empty or has the value 'core'
, then the error came from libSBML core; otherwise, the string will be the short-form name of the package (e.g., 'comp'
for the Hierarchical Model Composition package).
'core'
.
|
inherited |
Returns the severity of this error.
getSeverity() long
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.
|
inherited |
Returns a string describing the severity level of this error.
getSeverityAsString() string
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.
|
inherited |
Returns a brief message for this error.
getShortMessage() string
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.
|
inherited |
Returns a copy of the message string associated with the given predefined XMLError code.
getStandardMessage(int code) string
code | the error code whose message is sought; it must be a predefined value from the set of predefined error identifiers. |
|
inherited |
Predicate returning True
or False
depending on whether this error is a significant error.
isError() bool
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.
True
if this error is an error, False
otherwise.
|
inherited |
Predicate returning True
or False
depending on whether this error is a fatal run-time error.
isFatal() bool
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.
True
if this error is a fatal error, False
otherwise.
|
inherited |
Predicate returning True
or False
depending on whether this error object is for information purposes only.
isInfo() bool
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.
True
if this XMLError is for informational purposes only, False
otherwise.
|
inherited |
Predicate returning True
or False
depending on whether this error resulted from an internal program error.
isInternal() bool
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.
|
inherited |
Predicate returning True
or False
depending on whether this error was generated by the operating system.
isSystem() bool
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.
|
inherited |
Predicate returning True
or False
depending on whether this error resulted from a problem or whether it was logged as an unknown error.
isValid() bool
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.
True
) or whether it is unknown (False
).
|
inherited |
Predicate returning True
or False
depending on whether this error object is a warning.
isWarning() bool
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.
True
if this error is a warning, False
otherwise.
|
inherited |
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.
|
inherited |
Sets the column number where this error occurred.
setColumn(long column) int
column | a long integer, the column number to set. |
|
inherited |
Sets the line number where this error occurred.
setLine(long line) int
line | a long integer, the line number to set. |