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Merge branch 'master' into Container-deploy-fixes
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@CodeByDrescher
CodeByDrescher committed Nov 15, 2024
2 parents a6380cf + 09470a2 commit 796e148
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Showing 8 changed files with 163 additions and 89 deletions.
5 changes: 0 additions & 5 deletions ...nt/src/main/java/cbit/vcell/client/desktop/biomodel/ReactionRulePropertiesTableModel.java
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Expand Up @@ -310,11 +310,6 @@ public void propertyChange(java.beans.PropertyChangeEvent evt) {
}
}

/**
* Sets the geometry property (cbit.vcell.geometry.Geometry) value.
* @param geometry The new value for the property.
* @see #getGeometry
*/
public void setReactionRule(ReactionRule newValue) {
ReactionRule oldValue = reactionRule;
reactionRule = newValue;
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140 changes: 73 additions & 67 deletions vcell-core/src/main/java/cbit/vcell/mapping/NetworkTransformer.java
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43 changes: 35 additions & 8 deletions vcell-core/src/main/java/cbit/vcell/model/Model.java
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Expand Up @@ -1572,7 +1572,10 @@ public ReactionRule createReactionRule(String label, Structure structure, boolea
return new ReactionRule(Model.this, label, structure, bReversible);
}

public final void setObservableList(List<RbmObservable> newValue) throws PropertyVetoException{
public final void setObservableList(List<RbmObservable> newValue) throws PropertyVetoException {
setObservableList(newValue, PropertyNotificationMode.Loud);
}
public final void setObservableList(List<RbmObservable> newValue, PropertyNotificationMode mode) throws PropertyVetoException{
List<RbmObservable> oldValue = observableList;
fireVetoableChange(RbmModelContainer.PROPERTY_NAME_OBSERVABLE_LIST, oldValue, newValue);
if(oldValue != null){
Expand All @@ -1590,7 +1593,9 @@ public final void setObservableList(List<RbmObservable> newValue) throws Propert
mt.setModel(Model.this);
}
}
firePropertyChange(RbmModelContainer.PROPERTY_NAME_OBSERVABLE_LIST, oldValue, newValue);
if(mode == PropertyNotificationMode.Loud) {
firePropertyChange(RbmModelContainer.PROPERTY_NAME_OBSERVABLE_LIST, oldValue, newValue);
}
}

public List<MolecularType> getMolecularTypeList(){
Expand All @@ -1610,8 +1615,14 @@ public Parameter addFunction(String name, Expression expression, VCUnitDefinitio
return Model.this.addModelParameter(new ModelParameter(name, expression, ROLE_UserDefined, unitDefinition));
}

public Parameter addParameter(String name, Expression expression, VCUnitDefinition unitDefinition, PropertyNotificationMode mode) throws ModelException, PropertyVetoException {
ModelParameter mp = new ModelParameter(name, expression, ROLE_UserDefined, unitDefinition);
return Model.this.addModelParameter(mp, mode);

}
public Parameter addParameter(String name, Expression expression, VCUnitDefinition unitDefinition) throws ModelException, PropertyVetoException{
return Model.this.addModelParameter(new ModelParameter(name, expression, ROLE_UserDefined, unitDefinition));
Parameter ret = addParameter(name, expression, unitDefinition, PropertyNotificationMode.Loud);
return ret;
}

public RbmObservable getObservable(String obName){
Expand Down Expand Up @@ -1639,12 +1650,16 @@ public Parameter getParameter(String obName){
}

public boolean removeObservable(RbmObservable observable) throws PropertyVetoException{
boolean ret = removeObservable(observable, PropertyNotificationMode.Loud);
return ret;
}
public boolean removeObservable(RbmObservable observable, PropertyNotificationMode mode) throws PropertyVetoException{
if(!observableList.contains(observable)){
return false;
}
ArrayList<RbmObservable> newValue = new ArrayList<RbmObservable>(observableList);
newValue.remove(observable);
setObservableList(newValue);
setObservableList(newValue, mode);
return true;
}

Expand Down Expand Up @@ -1957,6 +1972,11 @@ public void adjustRulesPatterns(MolecularType mt, MolecularComponent mc){
}
}

public enum PropertyNotificationMode {
Silent,
Loud
}

public Model(Version argVersion){
this(argVersion, ModelUnitSystem.createDefaultVCModelUnitSystem());
}
Expand Down Expand Up @@ -2052,11 +2072,14 @@ private ReservedSymbol[] createReservedSymbols(){
// ModelParameter modelParameter = new ModelParameter(name, expr, role, units);
// return modelParameter;
//}

public ModelParameter addModelParameter(Model.ModelParameter modelParameter) throws PropertyVetoException{
ModelParameter ret = addModelParameter(modelParameter, PropertyNotificationMode.Loud);
return ret;
}
public ModelParameter addModelParameter(Model.ModelParameter modelParameter, PropertyNotificationMode mode) throws PropertyVetoException{
// if (!contains(modelParameter)){
Model.ModelParameter[] newModelParameters = ArrayUtils.addElement(fieldModelParameters, modelParameter);
setModelParameters(newModelParameters);
setModelParameters(newModelParameters, mode);
// }
return modelParameter;
}
Expand Down Expand Up @@ -3721,12 +3744,16 @@ public void setDiagrams(int index, Diagram diagrams){
;
}


public void setModelParameters(ModelParameter[] modelParameters) throws java.beans.PropertyVetoException{
setModelParameters(modelParameters, PropertyNotificationMode.Loud);
}
public void setModelParameters(ModelParameter[] modelParameters, PropertyNotificationMode mode) throws java.beans.PropertyVetoException{
ModelParameter[] oldValue = fieldModelParameters;
fireVetoableChange(Model.PROPERTY_NAME_MODEL_PARAMETERS, oldValue, modelParameters);
fieldModelParameters = modelParameters;
firePropertyChange(Model.PROPERTY_NAME_MODEL_PARAMETERS, oldValue, modelParameters);
if(mode == PropertyNotificationMode.Loud) {
firePropertyChange(Model.PROPERTY_NAME_MODEL_PARAMETERS, oldValue, modelParameters);
}

//System.out.print("vcModel model parameters [");
//for (ModelParameter p : oldValue){
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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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Original file line number Diff line number Diff line change
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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Original file line number Diff line number Diff line change
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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Original file line number Diff line number Diff line change
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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Original file line number Diff line number Diff line change
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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Original file line number Diff line number Diff line change
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

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