This is a C++ project exposes libSBML functionality to JavaScript. Starting with the validation API as well as the conversion API. It uses emscripten to compile the libsbml library and its dependencies, with just a couple of functions being exposed.
Its all encapsulated in scripts
./dev/git-dependencies.sh # clones updates the dependencies
./dev/git-libsbml.sh # clones / updates libsbmlfor building the node.js version
./dev/em-dependencies.sh # builds the dependencies if not done
./dev/em-build.sh # build the code from ./src/
./dev/em-test.sh # runs the test_node after copying to install dirto build the version to be embedded into web sites use
./dev/em-web.shThe following JavaScript methods are available:
- validateSBMLString(content, validationOptions)
Validates an SBML string with optional validation options (as JSON). Returns validation errors as a JSON list. validation options are:
{
"LIBSBML_CAT_GENERAL_CONSISTENCY": true,
"LIBSBML_CAT_IDENTIFIER_CONSISTENCY": true,
"LIBSBML_CAT_UNITS_CONSISTENCY": false,
"LIBSBML_CAT_MATHML_CONSISTENCY": true,
"LIBSBML_CAT_SBO_CONSISTENCY": true,
"LIBSBML_CAT_OVERDETERMINED_MODEL": true,
"LIBSBML_CAT_MODELING_PRACTICE": true,
"LIBSBML_CAT_STRICT_UNITS_CONSISTENCY": false,
}-
getLibSBMLVersion()
Returns the linked libSBML version as a dotted string. -
getAvailableConverters()
Returns a list of the names of all available SBML converters. -
getConverterOptions(converterName)
Returns a JSON object describing the options accepted by a specific converter. Valid names are the ones returned bygetAvailableConverters -
getAllConvertersOptions()
Returns a JSON object listing all converters and their available options. -
convertSBMLString(content, conversionOptions)
Converts the supplied SBML string using the provided options (as JSON). Returns the converted SBML as a string.Valid options are the one returned. For example for the level / version converter:
{
{"main":{"description":"Convert the model to a given Level and Version of SBML","key":"setLevelAndVersion","type":"boolean","value":"true"},"options":[{"description":"Whether default units should be added when converting to L3","key":"addDefaultUnits","type":"boolean","value":"true"},{"description":"Whether validity should be strictly preserved","key":"strict","type":"boolean","value":"true"}],"targetNamespaces":{"level":3,"version":2}}
}but a simplified format is also supported, the simplified format treats
options and targetNamespaces as special symbols all other options
will be passed along:
{
"setLevelAndVersion":"true",
"strict":"false",
"targetNamespaces":{"level":1,"version":2}
}-
getConversionErrors()
Returns any errors collected during the last conversion call, as a JSON list. Will be cleared at the start of the conversion. -
freeConvertersMap()
Frees memory allocated for the internal converter registry. Should be called to clear the static map of converters whenever you are done with them.
Running
node test_convertion.js dimerization-invalid.xmlproduces a json list like:
[
{
"line": 3,
"column": 4,
"message": "A Model object may only have the following attributes, all of which are optional: 'metaid', 'sboTerm', 'id', 'name', 'substanceUnits', 'timeUnits', 'volumeUnits', 'areaUnits', 'lengthUnits', 'extentUnits' and 'conversionFactor'. No other attributes from the SBML Level 3 Core namespace are permitted on a Model object. Reference: L3V1 Section 4.2 Attribute 'invalid' is not part of the definition of an SBML Level 3 Version 1 <model> element. ",
"severity": "error",
"category": "SBML component consistency",
"errorId": 20222,
"package": "core"
}
]Running
node test_conversion.js dimerization.xml
prints several conversions to different SBML Levels and Versions. As well as the list of conversion errors.
To get the conversion options:
// either get individual converters
var converters = instance.getAvailableConverters();
for (var i = 0; i < converters.size(); i++) {
console.log(converters.get(i));
// and their options
console.log(instance.getConverterOptions(converters.get(i)));
}which produces an output like:
SBML Function Definition Converter
{"main":{"description":"Expand all function definitions in the model","key":"expandFunctionDefinitions","type":"boolean","value":"true"},"options":[{"description":"Comma separated list of ids to skip during expansion","key":"skipIds","type":"string","value":""}]}or
console.log(instance.getAllConvertersOptions());which produces a complete list of all converters and their options:
{
"Layout Converter L2 <=> L3": {
"main": {
"description": "convert the layout to the given namespaces",
"key": "convert layout",
"type": "boolean",
"value": "true"
},
"options": []
},
"SBML COBRA to FBC Converter": {
"main": {
"description": "convert cobra sbml to fbc",
"key": "convert cobra",
"type": "boolean",
"value": "true"
},
"options": [
{
"description": "checks level/version compatibility",
"key": "checkCompatibility",
"type": "boolean",
"value": "false"
},
{
"description": "removes unit definitions",
"key": "removeUnits",
"type": "boolean",
"value": "false"
}
]
},
"SBML Comp Flattening Converter": {
"main": {
"description": "flatten comp",
"key": "flatten comp",
"type": "boolean",
"value": "true"
},
"options": [
{
"description": "specify whether to abort if any unflattenable packages are encountered",
"key": "abortIfUnflattenable",
"type": "string",
"value": "requiredOnly"
},
{
"description": "the base directory in which to search for external references",
"key": "basePath",
"type": "string",
"value": "."
},
{
"description": "any packages that cannot be flattened should be stripped (note: this option replaced by 'stripUnflattenablePackages').",
"key": "ignorePackages",
"type": "boolean",
"value": "true"
},
{
"description": "unused ports should be listed in the flattened model",
"key": "leavePorts",
"type": "boolean",
"value": "false"
},
{
"description": "all model definitions and external model definitions should remain in the SBMLDocument",
"key": "listModelDefinitions",
"type": "boolean",
"value": "false"
},
{
"description": "perform validation before and after trying to flatten",
"key": "performValidation",
"type": "boolean",
"value": "true"
},
{
"description": "comma separated list of packages to be stripped before flattening is attempted",
"key": "stripPackages",
"type": "string",
"value": ""
},
{
"description": "specify whether to strip any unflattenable packages ignored by 'abortIfUnflattenable'",
"key": "stripUnflattenablePackages",
"type": "boolean",
"value": "true"
}
]
},
"SBML Distributions Annotations Converter": {
"main": {
"description": "convert distrib to annotations",
"key": "convert distrib to annotations",
"type": "boolean",
"value": "true"
},
"options": [
{
"description": "Use the UncertML namespace for the annotation instead of Wikipedia ones",
"key": "useUncertMLNamespaces",
"type": "boolean",
"value": "false"
},
{
"description": "Created functions return means of distributions instead of NaN",
"key": "writeMeans",
"type": "boolean",
"value": "false"
}
]
},
"SBML FBC to COBRA Converter": {
"main": {
"description": "convert FBC L3V1 to SBML L2V4 with COBRA annotation",
"key": "convert fbc to cobra",
"type": "boolean",
"value": "true"
},
"options": [
{
"description": "write gene association into reaction notes, even if the reaction has notes already",
"key": "overwriteReactionNotes",
"type": "boolean",
"value": "false"
}
]
},
"SBML FBC v1 to FBC v2 Converter": {
"main": {
"description": "convert fbc v1 to fbc v2",
"key": "convert fbc v1 to fbc v2",
"type": "boolean",
"value": "true"
},
"options": [
{
"description": "should the model be a strict one (i.e.: all non-specified bounds will be filled)",
"key": "strict",
"type": "boolean",
"value": "true"
}
]
},
"SBML FBC v2 to FBC v1 Converter": {
"main": {
"description": "convert fbc v2 to fbc v1",
"key": "convert fbc v2 to fbc v1",
"type": "boolean",
"value": "true"
},
"options": []
},
"SBML Function Definition Converter": {
"main": {
"description": "Expand all function definitions in the model",
"key": "expandFunctionDefinitions",
"type": "boolean",
"value": "true"
},
"options": [
{
"description": "Comma separated list of ids to skip during expansion",
"key": "skipIds",
"type": "string",
"value": ""
}
]
},
"SBML Id Converter": {
"main": {
"description": "Rename all SIds specified in the 'currentIds' option to the ones specified in 'newIds'",
"key": "renameSIds",
"type": "boolean",
"value": "true"
},
"options": [
{
"description": "Comma separated list of ids to rename",
"key": "currentIds",
"type": "string",
"value": ""
},
{
"description": "Comma separated list of the new ids",
"key": "newIds",
"type": "string",
"value": ""
}
]
},
"SBML Infer Units Converter": {
"main": {
"description": "Infer the units of Parameters",
"key": "inferUnits",
"type": "boolean",
"value": "true"
},
"options": []
},
"SBML Initial Assignment Converter": {
"main": {
"description": "Expand initial assignments in the model",
"key": "expandInitialAssignments",
"type": "boolean",
"value": "true"
},
"options": []
},
"SBML Level 1 Version 1 Converter": {
"main": {
"description": "convert the document to SBML Level 1 Version 1",
"key": "convertToL1V1",
"type": "boolean",
"value": "true"
},
"options": [
{
"description": "change pow expressions to the (^) hat notation",
"key": "changePow",
"type": "boolean",
"value": "false"
},
{
"description": "if true, occurrances of compartment ids in expressions will be replaced with their initial size",
"key": "inlineCompartmentSizes",
"type": "boolean",
"value": "false"
}
],
"targetNamespaces": { "level": 1, "version": 1 }
},
"SBML Level Version Converter": {
"main": {
"description": "Convert the model to a given Level and Version of SBML",
"key": "setLevelAndVersion",
"type": "boolean",
"value": "true"
},
"options": [
{
"description": "Whether default units should be added when converting to L3",
"key": "addDefaultUnits",
"type": "boolean",
"value": "true"
},
{
"description": "Whether validity should be strictly preserved",
"key": "strict",
"type": "boolean",
"value": "true"
}
],
"targetNamespaces": { "level": 3, "version": 2 }
},
"SBML Local Parameter Converter": {
"main": {
"description": "Promotes all Local Parameters to Global ones",
"key": "promoteLocalParameters",
"type": "boolean",
"value": "true"
},
"options": []
},
"SBML Rate Of Converter": {
"main": {
"description": "Replace rateOf with functionDefinition",
"key": "replaceRateOf",
"type": "boolean",
"value": "true"
},
"options": [
{
"description": "create FunctionDefinition",
"key": "toFunction",
"type": "boolean",
"value": "true"
}
]
},
"SBML RateRule Converter": {
"main": {
"description": "Infer reactions from rateRules in the model",
"key": "inferReactions",
"type": "boolean",
"value": "true"
},
"options": [
{
"description": "Whether the model should be checked for suitability first",
"key": "performSanityCheck",
"type": "boolean",
"value": "true"
},
{
"description": "If a number appears in the math use it as the stoichiometry",
"key": "useStoichiometryFromMath",
"type": "boolean",
"value": "true"
}
]
},
"SBML Reaction Converter": {
"main": {
"description": "Replace reactions with rateRules",
"key": "replaceReactions",
"type": "boolean",
"value": "true"
},
"options": [
{
"description": "make any species into parameters",
"key": "rateRuleVariablesShouldBeParameters",
"type": "boolean",
"value": "false"
}
]
},
"SBML Rule Converter": {
"main": {
"description": "Sort AssignmentRules and InitialAssignments in the model",
"key": "sortRules",
"type": "boolean",
"value": "true"
},
"options": []
},
"SBML Strip Package Converter": {
"main": {
"description": "Strip SBML Level 3 package constructs from the model",
"key": "stripPackage",
"type": "boolean",
"value": "true"
},
"options": [
{
"description": "Name of the SBML Level 3 package to be stripped",
"key": "package",
"type": "string",
"value": ""
},
{
"description": "If set, all unsupported packages will be removed.",
"key": "stripAllUnrecognized",
"type": "boolean",
"value": "false"
}
]
},
"SBML Units Converter": {
"main": {
"description": "Convert units in the model to SI units",
"key": "units",
"type": "boolean",
"value": "true"
},
"options": [
{
"description": "Whether unused UnitDefinition objects should be removed",
"key": "removeUnusedUnits",
"type": "boolean",
"value": "true"
}
]
}
}
This project has been possible thanks to LiBiS, the Baden-Württemberg Institute for Bioinformatics Infrastructure:
and to the BMBF funded de.NBI initiative (031L0104A, W-de.NBI-016)):
BSD 2-Clause License see LICENSE