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support Infinity and NaN in SBML values and MathML #1381

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merged 4 commits into from
Nov 15, 2024
Merged

support Infinity and NaN in SBML values and MathML #1381

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8acdb85
support Infinity and NaN in SBML values and MathML
jcschaff Nov 14, 2024
355c69e
add unit test for infinity and NaN from MathML
jcschaff Nov 15, 2024
a539a5d
new failure mode for SBML test suite model 696 after supporting NaN
jcschaff Nov 15, 2024
5c6cbd4
SBML Test suite model 952 works now that NaN supported
jcschaff Nov 15, 2024
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25 changes: 21 additions & 4 deletions vcell-core/src/main/java/org/vcell/sbml/vcell/SBMLImporter.java
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Expand Up @@ -2975,18 +2975,35 @@ private static void addOutputFunctions(org.sbml.jsbml.Model sbmlModel, BioModel
private static void applySavedExpressions(org.sbml.jsbml.Model sbmlModel, SBMLSymbolMapping sbmlSymbolMapping, VCLogger vcLogger) throws Exception{
for(SBase sbmlValueTargetSbase : sbmlSymbolMapping.getSbmlValueTargets()){
Double sbmlValue = sbmlSymbolMapping.getSbmlValue(sbmlValueTargetSbase);
if(sbmlValue != null && !sbmlValue.isInfinite() && !sbmlValue.isNaN()){
final Expression sbmlValueExp;
if (sbmlValue != null) {
if (sbmlValue.isInfinite() && sbmlValue > 0) {
sbmlValueExp = new Expression(Double.MAX_VALUE);
logger.debug("setting infinite value for SBML id " + sbmlValueTargetSbase.getId() + " to " + Double.MAX_VALUE);
} else if (sbmlValue.isInfinite() && sbmlValue < 0){
sbmlValueExp = new Expression(-Double.MAX_VALUE);
logger.debug("setting infinite value for SBML id " + sbmlValueTargetSbase.getId() + " to " + -Double.MAX_VALUE);
} else if (sbmlValue.isNaN()){
sbmlValueExp = new Expression("0/0");
logger.debug("setting NaN value for SBML id " + sbmlValueTargetSbase.getId() + " to 0/0");
} else {
sbmlValueExp = new Expression(sbmlValue);
}
} else {
sbmlValueExp = null;
}
if(sbmlValueExp != null){
EditableSymbolTableEntry targetSte = sbmlSymbolMapping.getInitialSte(sbmlValueTargetSbase);
try {
if(targetSte != null){
if(targetSte.isExpressionEditable()){
targetSte.setExpression(new Expression(sbmlValue));
targetSte.setExpression(sbmlValueExp);
}
} else {
targetSte = sbmlSymbolMapping.getRuntimeSte(sbmlValueTargetSbase);
if(targetSte != null){
if(targetSte.isExpressionEditable()){
targetSte.setExpression(new Expression(sbmlValue));
targetSte.setExpression(sbmlValueExp);
}
} else {
logger.error("couldn't find vcell object mapped to sbml object: " + sbmlValueTargetSbase);
Expand All @@ -2998,7 +3015,7 @@ private static void applySavedExpressions(org.sbml.jsbml.Model sbmlModel, SBMLSy
vcLogger.sendMessage(VCLogger.Priority.HighPriority, VCLogger.ErrorType.OverallWarning, msg);
}
} else {
String msg = "missing or unexpected value attribute '" + sbmlValue + "' for SBML object id " + sbmlValueTargetSbase.getId();
String msg = "missing value attribute for SBML object id " + sbmlValueTargetSbase.getId();
logger.error(msg);
vcLogger.sendMessage(VCLogger.Priority.HighPriority, VCLogger.ErrorType.OverallWarning, msg);
}
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3 changes: 1 addition & 2 deletions vcell-core/src/test/java/org/vcell/sbml/BMDB_SBMLImportTest.java
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Expand Up @@ -157,7 +157,7 @@ public static Map<Integer, SBMLTestSuiteTest.FAULT> knownFaults() {
faults.put(627, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Metabolite_123' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that y
faults.put(628, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Metabolite_8' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that you
faults.put(632, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'k4b' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that you have pro
faults.put(696, SBMLTestSuiteTest.FAULT.MATHML_PARSING); // cause: Error adding Lambda function UnsupportedConstruct: error parsing expression ' <math><notanumber/></math>': node type 'notanumber' not supported yet
faults.put(696, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Metabolite_16' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that yo
faults.put(705, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Metabolite_21' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that yo
faults.put(706, SBMLTestSuiteTest.FAULT.UNCATEGORIZED); // cause: found more than one SBase match for sid=v, matched [org.vcell.sbml.vcell.SBMLSymbolMapping$SBaseWrapper@67cc48df, org.vcell.sbml.vcell.SBMLSymbolMapping$SBaseWrapper@483ac21f]
faults.put(710, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Metabolite_0_0' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that y
Expand All @@ -179,7 +179,6 @@ public static Map<Integer, SBMLTestSuiteTest.FAULT> knownFaults() {
faults.put(872, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'beta' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that you have pr
faults.put(908, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Metabolite_2' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that you
faults.put(925, SBMLTestSuiteTest.FAULT.UNCATEGORIZED); // cause: OverallWarning: missing or unexpected value attribute '-Infinity' for SBML object id log_time
faults.put(952, SBMLTestSuiteTest.FAULT.MATHML_PARSING); // cause: Error adding Lambda function UnsupportedConstruct: error parsing expression ' <math><notanumber/></math>': node type 'notanumber' not supported yet
faults.put(956, SBMLTestSuiteTest.FAULT.MATHML_PARSING); // cause: Error adding Lambda function UnsupportedConstruct: error parsing expression ' <math><notanumber/></math>': node type 'notanumber' not supported yet
faults.put(961, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'rateOf_re15' to model: 're15' is either not found in your model or is not allowed to be used in the current context. Check that you have provided t
faults.put(969, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Metabolite_11' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that yo
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2 changes: 0 additions & 2 deletions vcell-core/src/test/java/org/vcell/sbml/SBMLTestSuiteTest.java
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Expand Up @@ -374,8 +374,6 @@ public static Collection<Integer> testCases() {
faults.put(943, FAULT.DELAY);
faults.put(945, FAULT.STRUCTURE_SIZE_IN_ASSIGNMENT_RULE);
faults.put(947, FAULT.STRUCTURE_SIZE_IN_ASSIGNMENT_RULE);
faults.put(950, FAULT.VALUE_NAN_INF_OR_MISSING);
faults.put(951, FAULT.VALUE_NAN_INF_OR_MISSING);
faults.put(957, FAULT.XOR_MISSING);
faults.put(958, FAULT.XOR_MISSING);
faults.put(959, FAULT.INCONSISTENT_UNIT_SYSTEM);
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14 changes: 13 additions & 1 deletion vcell-math/src/main/java/cbit/vcell/parser/ExpressionMathMLParser.java
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Expand Up @@ -497,7 +497,19 @@ private SimpleNode getRootNode(Element nodeMathML, String timeSymbol) throws Exp
} else {
throw new ExpressionException("csymbol node type "+nodeMathML.getAttributeValue(MathMLTags.DEFINITIONURL)+" not supported yet");
}
} else{
} else if (nodeMathML.getName().equals(MathMLTags.NOT_A_NUMBER)){
ASTFloatNode zeroNode = new ASTFloatNode(0.0);
ASTFloatNode zeroNode2 = new ASTFloatNode(0.0);
ASTInvertTermNode invNode = new ASTInvertTermNode();
invNode.jjtAddChild(zeroNode2);
ASTMultNode multNode = new ASTMultNode();
multNode.jjtAddChild(zeroNode);
multNode.jjtAddChild(invNode);
return multNode;
} else if (nodeMathML.getName().equals(MathMLTags.INFINITY)) {
ASTFloatNode infNode = new ASTFloatNode(Double.MAX_VALUE);
return infNode;
}else{
throw new ExpressionException("node type '"+nodeMathML.getName()+"' not supported yet");
}
}
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20 changes: 20 additions & 0 deletions vcell-math/src/test/java/cbit/vcell/parser/MathMLTest.java
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Expand Up @@ -80,6 +80,26 @@ public void testMathMLParsing_XOR() throws IOException, ExpressionException {
assertTrue(equiv, msg);
}

@Test
public void testNaN_MathmlParsing() throws ExpressionException {
String nanMathML = "<notanumber/>";
Expression exp = new ExpressionMathMLParser(null).fromMathML(nanMathML, "t");
Expression expectedExp = new Expression("0/0");
boolean equiv = ExpressionUtils.functionallyEquivalent(exp, expectedExp, true);
String msg = "not equivalent: origExp='"+exp.infix()+"', expMathML='"+expectedExp.infix()+"'";
assertTrue(equiv, msg);
}

@Test
public void testInfinity_MathmlParsing() throws ExpressionException {
String nanMathML = "<infinity/>";
Expression exp = new ExpressionMathMLParser(null).fromMathML(nanMathML, "t");
Expression expectedExp = new Expression(Double.MAX_VALUE);
boolean equiv = ExpressionUtils.functionallyEquivalent(exp, expectedExp, true);
String msg = "not equivalent: origExp='"+exp.infix()+"', expMathML='"+expectedExp.infix()+"'";
assertTrue(equiv, msg);
}


@ParameterizedTest
@MethodSource("testCases")
Expand Down