Example 1 with FakeSeedSpeciesInitialConditionsParameter
use of org.vcell.model.rbm.FakeSeedSpeciesInitialConditionsParameter in project vcell by virtualcell.
the class NetworkTransformer method transform.
private void transform(SimulationContext simContext, SimulationContext transformedSimulationContext, ArrayList<ModelEntityMapping> entityMappings, MathMappingCallback mathMappingCallback, NetworkGenerationRequirements networkGenerationRequirements) {
String msg = "Generating network: flattening...";
mathMappingCallback.setMessage(msg);
TaskCallbackMessage tcm = new TaskCallbackMessage(TaskCallbackStatus.Clean, "");
simContext.appendToConsole(tcm);
tcm = new TaskCallbackMessage(TaskCallbackStatus.TaskStart, msg);
simContext.appendToConsole(tcm);
long startTime = System.currentTimeMillis();
System.out.println("Convert to bngl, execute BNG, retrieve the results.");
try {
BNGOutputSpec outputSpec = generateNetwork(simContext, mathMappingCallback, networkGenerationRequirements);
if (mathMappingCallback.isInterrupted()) {
msg = "Canceled by user.";
tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, msg);
simContext.appendToConsole(tcm);
throw new UserCancelException(msg);
}
long endTime = System.currentTimeMillis();
long elapsedTime = endTime - startTime;
System.out.println(" " + elapsedTime + " milliseconds");
Model model = transformedSimulationContext.getModel();
ReactionContext reactionContext = transformedSimulationContext.getReactionContext();
// ---- Parameters -----------------------------------------------------------------------------------------------
startTime = System.currentTimeMillis();
for (int i = 0; i < outputSpec.getBNGParams().length; i++) {
BNGParameter p = outputSpec.getBNGParams()[i];
// System.out.println(i+1 + ":\t\t"+ p.toString());
if (model.getRbmModelContainer().getParameter(p.getName()) != null) {
// if it's already there we don't try to add it again; this should be true for all of them!
continue;
}
String s = p.getName();
FakeSeedSpeciesInitialConditionsParameter fakeICParam = FakeSeedSpeciesInitialConditionsParameter.fromString(s);
if (speciesEquivalenceMap.containsKey(fakeICParam)) {
// we get rid of the fake parameters we use as keys
continue;
}
FakeReactionRuleRateParameter fakeKineticParam = FakeReactionRuleRateParameter.fromString(s);
if (fakeKineticParam != null) {
System.out.println("found fakeKineticParam " + fakeKineticParam.fakeParameterName);
// we get rid of the fake parameters we use as keys
continue;
}
throw new RuntimeException("unexpected parameter " + p.getName() + " in internal BNG processing");
// Expression exp = new Expression(p.getValue());
// exp.bindExpression(model.getRbmModelContainer().getSymbolTable());
// model.getRbmModelContainer().addParameter(p.getName(), exp, model.getUnitSystem().getInstance_TBD());
}
endTime = System.currentTimeMillis();
elapsedTime = endTime - startTime;
msg = "Adding " + outputSpec.getBNGParams().length + " parameters to model, " + elapsedTime + " ms";
System.out.println(msg);
// ---- Species ------------------------------------------------------------------------------------------------------------
mathMappingCallback.setMessage("generating network: adding species...");
mathMappingCallback.setProgressFraction(progressFractionQuota / 4.0f);
startTime = System.currentTimeMillis();
System.out.println("\nSpecies :");
// the reactions will need this map to recover the names of species knowing only the networkFileIndex
HashMap<Integer, String> speciesMap = new HashMap<Integer, String>();
LinkedHashMap<String, Species> sMap = new LinkedHashMap<String, Species>();
LinkedHashMap<String, SpeciesContext> scMap = new LinkedHashMap<String, SpeciesContext>();
LinkedHashMap<String, BNGSpecies> crossMap = new LinkedHashMap<String, BNGSpecies>();
List<SpeciesContext> noMapForThese = new ArrayList<SpeciesContext>();
// final int decimalTickCount = Math.max(outputSpec.getBNGSpecies().length/10, 1);
for (int i = 0; i < outputSpec.getBNGSpecies().length; i++) {
BNGSpecies s = outputSpec.getBNGSpecies()[i];
// System.out.println(i+1 + ":\t\t"+ s.toString());
String key = s.getConcentration().infix();
FakeSeedSpeciesInitialConditionsParameter fakeParam = FakeSeedSpeciesInitialConditionsParameter.fromString(key);
if (fakeParam != null) {
Pair<SpeciesContext, Expression> value = speciesEquivalenceMap.get(fakeParam);
// the species context of the original model
SpeciesContext originalsc = value.one;
Expression initial = value.two;
// replace the fake initial condition with the real one
s.setConcentration(initial);
// we'll have to find the species context from the cloned model which correspond to the original species
SpeciesContext sc = model.getSpeciesContext(originalsc.getName());
// System.out.println(sc.getName() + ", " + sc.getSpecies().getCommonName() + " ...is one of the original seed species.");
// existing name
speciesMap.put(s.getNetworkFileIndex(), sc.getName());
sMap.put(sc.getName(), sc.getSpecies());
scMap.put(sc.getName(), sc);
crossMap.put(sc.getName(), s);
noMapForThese.add(sc);
continue;
}
// all these species are new!
// generate unique name for the species
int count = 0;
String speciesName = null;
String nameRoot = "s";
String speciesPatternNameString = s.extractName();
while (true) {
speciesName = nameRoot + count;
if (Model.isNameUnused(speciesName, model) && !sMap.containsKey(speciesName) && !scMap.containsKey(speciesName)) {
break;
}
count++;
}
// newly created name
speciesMap.put(s.getNetworkFileIndex(), speciesName);
SpeciesContext speciesContext;
if (s.hasCompartment()) {
String speciesPatternCompartmentString = s.extractCompartment();
speciesContext = new SpeciesContext(new Species(speciesName, s.getName()), model.getStructure(speciesPatternCompartmentString), null);
} else {
speciesContext = new SpeciesContext(new Species(speciesName, s.getName()), model.getStructure(0), null);
}
speciesContext.setName(speciesName);
try {
if (speciesPatternNameString != null) {
SpeciesPattern sp = RbmUtils.parseSpeciesPattern(speciesPatternNameString, model);
speciesContext.setSpeciesPattern(sp);
}
} catch (ParseException e) {
e.printStackTrace();
throw new RuntimeException("Bad format for species pattern string: " + e.getMessage());
}
// speciesContext.setSpeciesPatternString(speciesPatternString);
// model.addSpecies(speciesContext.getSpecies());
// model.addSpeciesContext(speciesContext);
sMap.put(speciesName, speciesContext.getSpecies());
scMap.put(speciesName, speciesContext);
crossMap.put(speciesName, s);
// }
if (mathMappingCallback.isInterrupted()) {
msg = "Canceled by user.";
tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, msg);
simContext.appendToConsole(tcm);
throw new UserCancelException(msg);
}
// if(i%50 == 0) {
// System.out.println(i+"");
// }
// if(i%decimalTickCount == 0) {
// int multiplier = i/decimalTickCount;
// float progress = progressFractionQuota/4.0f + progressFractionQuotaSpecies*multiplier;
// mathMappingCallback.setProgressFraction(progress);
// }
}
for (SpeciesContext sc1 : model.getSpeciesContexts()) {
boolean found = false;
for (Map.Entry<String, SpeciesContext> entry : scMap.entrySet()) {
SpeciesContext sc2 = entry.getValue();
if (sc1.getName().equals(sc2.getName())) {
found = true;
// System.out.println("found species context " + sc1.getName() + " of species " + sc1.getSpecies().getCommonName() + " // " + sc2.getSpecies().getCommonName());
break;
}
}
if (found == false) {
// we add to the map the species context and the species which exist in the model but which are not in the map yet
// the only ones in this situation should be plain species which were not given to bngl for flattening (they are flat already)
// System.out.println("species context " + sc1.getName() + " not found in the map. Adding it.");
scMap.put(sc1.getName(), sc1);
sMap.put(sc1.getName(), sc1.getSpecies());
noMapForThese.add(sc1);
}
}
for (Species s1 : model.getSpecies()) {
boolean found = false;
for (Map.Entry<String, Species> entry : sMap.entrySet()) {
Species s2 = entry.getValue();
if (s1.getCommonName().equals(s2.getCommonName())) {
found = true;
// System.out.println("found species " + s1.getCommonName());
break;
}
}
if (found == false) {
System.err.println("species " + s1.getCommonName() + " not found in the map!");
}
}
SpeciesContext[] sca = new SpeciesContext[scMap.size()];
scMap.values().toArray(sca);
Species[] sa = new HashSet<Species>(sMap.values()).toArray(new Species[0]);
model.setSpecies(sa);
model.setSpeciesContexts(sca);
boolean isSpatial = transformedSimulationContext.getGeometry().getDimension() > 0;
for (SpeciesContext sc : sca) {
if (noMapForThese.contains(sc)) {
continue;
}
SpeciesContextSpec scs = reactionContext.getSpeciesContextSpec(sc);
Parameter param = scs.getParameter(SpeciesContextSpec.ROLE_InitialConcentration);
BNGSpecies s = crossMap.get(sc.getName());
param.setExpression(s.getConcentration());
SpeciesContext origSpeciesContext = simContext.getModel().getSpeciesContext(s.getName());
if (origSpeciesContext != null) {
ModelEntityMapping em = new ModelEntityMapping(origSpeciesContext, sc);
entityMappings.add(em);
} else {
ModelEntityMapping em = new ModelEntityMapping(new GeneratedSpeciesSymbolTableEntry(sc), sc);
if (isSpatial) {
scs.initializeForSpatial();
}
entityMappings.add(em);
}
}
// for(SpeciesContext sc : sca) { // clean all the species patterns from the flattened species, we have no sp now
// sc.setSpeciesPattern(null);
// }
endTime = System.currentTimeMillis();
elapsedTime = endTime - startTime;
msg = "Adding " + outputSpec.getBNGSpecies().length + " species to model, " + elapsedTime + " ms";
System.out.println(msg);
// ---- Reactions -----------------------------------------------------------------------------------------------------
mathMappingCallback.setMessage("generating network: adding reactions...");
mathMappingCallback.setProgressFraction(progressFractionQuota / 4.0f * 3.0f);
startTime = System.currentTimeMillis();
System.out.println("\nReactions :");
Map<String, HashSet<String>> ruleKeyMap = new HashMap<String, HashSet<String>>();
Map<String, BNGReaction> directBNGReactionsMap = new HashMap<String, BNGReaction>();
Map<String, BNGReaction> reverseBNGReactionsMap = new HashMap<String, BNGReaction>();
for (int i = 0; i < outputSpec.getBNGReactions().length; i++) {
BNGReaction r = outputSpec.getBNGReactions()[i];
if (!r.isRuleReversed()) {
// direct
directBNGReactionsMap.put(r.getKey(), r);
} else {
reverseBNGReactionsMap.put(r.getKey(), r);
}
//
// for each rule name, store set of keySets (number of unique keysets are number of generated reactions from this ruleName).
//
HashSet<String> keySet = ruleKeyMap.get(r.getRuleName());
if (keySet == null) {
keySet = new HashSet<String>();
ruleKeyMap.put(r.getRuleName(), keySet);
}
keySet.add(r.getKey());
}
Map<String, ReactionStep> reactionStepMap = new HashMap<String, ReactionStep>();
for (int i = 0; i < outputSpec.getBNGReactions().length; i++) {
BNGReaction bngReaction = outputSpec.getBNGReactions()[i];
// System.out.println(i+1 + ":\t\t"+ r.writeReaction());
String baseName = bngReaction.getRuleName();
String reactionName = null;
HashSet<String> keySetsForThisRule = ruleKeyMap.get(bngReaction.getRuleName());
if (keySetsForThisRule.size() == 1 && model.getReactionStep(bngReaction.getRuleName()) == null && !reactionStepMap.containsKey(bngReaction.getRuleName())) {
// we can reuse the reaction rule labels
reactionName = bngReaction.getRuleName();
} else {
reactionName = bngReaction.getRuleName() + "_0";
while (true) {
if (model.getReactionStep(reactionName) == null && !reactionStepMap.containsKey(reactionName)) {
// we can reuse the reaction rule labels
break;
}
reactionName = TokenMangler.getNextEnumeratedToken(reactionName);
}
}
//
if (directBNGReactionsMap.containsValue(bngReaction)) {
BNGReaction forwardBNGReaction = bngReaction;
BNGReaction reverseBNGReaction = reverseBNGReactionsMap.get(bngReaction.getKey());
String name = forwardBNGReaction.getRuleName();
if (name.endsWith(ReactionRule.DirectHalf)) {
name = name.substring(0, name.indexOf(ReactionRule.DirectHalf));
}
if (name.endsWith(ReactionRule.InverseHalf)) {
name = name.substring(0, name.indexOf(ReactionRule.InverseHalf));
}
ReactionRule rr = model.getRbmModelContainer().getReactionRule(name);
Structure structure = rr.getStructure();
boolean bReversible = reverseBNGReaction != null;
SimpleReaction sr = new SimpleReaction(model, structure, reactionName, bReversible);
for (int j = 0; j < forwardBNGReaction.getReactants().length; j++) {
BNGSpecies s = forwardBNGReaction.getReactants()[j];
String scName = speciesMap.get(s.getNetworkFileIndex());
SpeciesContext sc = model.getSpeciesContext(scName);
Reactant reactant = sr.getReactant(scName);
if (reactant == null) {
int stoichiometry = 1;
sr.addReactant(sc, stoichiometry);
} else {
int stoichiometry = reactant.getStoichiometry();
stoichiometry += 1;
reactant.setStoichiometry(stoichiometry);
}
}
for (int j = 0; j < forwardBNGReaction.getProducts().length; j++) {
BNGSpecies s = forwardBNGReaction.getProducts()[j];
String scName = speciesMap.get(s.getNetworkFileIndex());
SpeciesContext sc = model.getSpeciesContext(scName);
Product product = sr.getProduct(scName);
if (product == null) {
int stoichiometry = 1;
sr.addProduct(sc, stoichiometry);
} else {
int stoichiometry = product.getStoichiometry();
stoichiometry += 1;
product.setStoichiometry(stoichiometry);
}
}
MassActionKinetics targetKinetics = new MassActionKinetics(sr);
sr.setKinetics(targetKinetics);
KineticsParameter kforward = targetKinetics.getForwardRateParameter();
KineticsParameter kreverse = targetKinetics.getReverseRateParameter();
String kforwardNewName = rr.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MassActionForwardRate).getName();
if (!kforward.getName().equals(kforwardNewName)) {
targetKinetics.renameParameter(kforward.getName(), kforwardNewName);
kforward = targetKinetics.getForwardRateParameter();
}
final String kreverseNewName = rr.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate).getName();
if (!kreverse.getName().equals(kreverseNewName)) {
targetKinetics.renameParameter(kreverse.getName(), kreverseNewName);
kreverse = targetKinetics.getReverseRateParameter();
}
applyKineticsExpressions(forwardBNGReaction, kforward, targetKinetics);
if (reverseBNGReaction != null) {
applyKineticsExpressions(reverseBNGReaction, kreverse, targetKinetics);
}
// String fieldParameterName = kforward.getName();
// fieldParameterName += "_" + r.getRuleName();
// kforward.setName(fieldParameterName);
reactionStepMap.put(reactionName, sr);
} else if (reverseBNGReactionsMap.containsValue(bngReaction) && !directBNGReactionsMap.containsKey(bngReaction.getKey())) {
// reverse only (must be irreversible)
BNGReaction reverseBNGReaction = reverseBNGReactionsMap.get(bngReaction.getKey());
ReactionRule rr = model.getRbmModelContainer().getReactionRule(reverseBNGReaction.extractRuleName());
Structure structure = rr.getStructure();
boolean bReversible = false;
SimpleReaction sr = new SimpleReaction(model, structure, reactionName, bReversible);
for (int j = 0; j < reverseBNGReaction.getReactants().length; j++) {
BNGSpecies s = reverseBNGReaction.getReactants()[j];
String scName = speciesMap.get(s.getNetworkFileIndex());
SpeciesContext sc = model.getSpeciesContext(scName);
Reactant reactant = sr.getReactant(scName);
if (reactant == null) {
int stoichiometry = 1;
sr.addReactant(sc, stoichiometry);
} else {
int stoichiometry = reactant.getStoichiometry();
stoichiometry += 1;
reactant.setStoichiometry(stoichiometry);
}
}
for (int j = 0; j < reverseBNGReaction.getProducts().length; j++) {
BNGSpecies s = reverseBNGReaction.getProducts()[j];
String scName = speciesMap.get(s.getNetworkFileIndex());
SpeciesContext sc = model.getSpeciesContext(scName);
Product product = sr.getProduct(scName);
if (product == null) {
int stoichiometry = 1;
sr.addProduct(sc, stoichiometry);
} else {
int stoichiometry = product.getStoichiometry();
stoichiometry += 1;
product.setStoichiometry(stoichiometry);
}
}
MassActionKinetics k = new MassActionKinetics(sr);
sr.setKinetics(k);
KineticsParameter kforward = k.getForwardRateParameter();
KineticsParameter kreverse = k.getReverseRateParameter();
String kforwardNewName = rr.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MassActionForwardRate).getName();
if (!kforward.getName().equals(kforwardNewName)) {
k.renameParameter(kforward.getName(), kforwardNewName);
kforward = k.getForwardRateParameter();
}
final String kreverseNewName = rr.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate).getName();
if (!kreverse.getName().equals(kreverseNewName)) {
k.renameParameter(kreverse.getName(), kreverseNewName);
kreverse = k.getReverseRateParameter();
}
applyKineticsExpressions(reverseBNGReaction, kforward, k);
// String fieldParameterName = kforward.getName();
// fieldParameterName += "_" + r.getRuleName();
// kforward.setName(fieldParameterName);
reactionStepMap.put(reactionName, sr);
}
}
for (ReactionStep rs : model.getReactionSteps()) {
reactionStepMap.put(rs.getName(), rs);
}
ReactionStep[] reactionSteps = new ReactionStep[reactionStepMap.size()];
reactionStepMap.values().toArray(reactionSteps);
model.setReactionSteps(reactionSteps);
if (mathMappingCallback.isInterrupted()) {
msg = "Canceled by user.";
tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, msg);
simContext.appendToConsole(tcm);
throw new UserCancelException(msg);
}
endTime = System.currentTimeMillis();
elapsedTime = endTime - startTime;
msg = "Adding " + outputSpec.getBNGReactions().length + " reactions to model, " + elapsedTime + " ms";
System.out.println(msg);
// clean all the reaction rules
model.getRbmModelContainer().getReactionRuleList().clear();
// ---- Observables -------------------------------------------------------------------------------------------------
mathMappingCallback.setMessage("generating network: adding observables...");
mathMappingCallback.setProgressFraction(progressFractionQuota / 8.0f * 7.0f);
startTime = System.currentTimeMillis();
System.out.println("\nObservables :");
RbmModelContainer rbmmc = model.getRbmModelContainer();
for (int i = 0; i < outputSpec.getObservableGroups().length; i++) {
ObservableGroup o = outputSpec.getObservableGroups()[i];
if (rbmmc.getParameter(o.getObservableGroupName()) != null) {
System.out.println(" ...already exists.");
// if it's already there we don't try to add it again; this should be true for all of them!
continue;
}
ArrayList<Expression> terms = new ArrayList<Expression>();
for (int j = 0; j < o.getListofSpecies().length; j++) {
Expression term = Expression.mult(new Expression(o.getSpeciesMultiplicity()[j]), new Expression(speciesMap.get(o.getListofSpecies()[j].getNetworkFileIndex())));
terms.add(term);
}
Expression exp = Expression.add(terms.toArray(new Expression[terms.size()])).flatten();
exp.bindExpression(rbmmc.getSymbolTable());
RbmObservable originalObservable = rbmmc.getObservable(o.getObservableGroupName());
VCUnitDefinition observableUnitDefinition = originalObservable.getUnitDefinition();
rbmmc.removeObservable(originalObservable);
Parameter newParameter = rbmmc.addParameter(o.getObservableGroupName(), exp, observableUnitDefinition);
RbmObservable origObservable = simContext.getModel().getRbmModelContainer().getObservable(o.getObservableGroupName());
ModelEntityMapping em = new ModelEntityMapping(origObservable, newParameter);
entityMappings.add(em);
}
if (mathMappingCallback.isInterrupted()) {
msg = "Canceled by user.";
tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, msg);
simContext.appendToConsole(tcm);
throw new UserCancelException(msg);
}
endTime = System.currentTimeMillis();
elapsedTime = endTime - startTime;
msg = "Adding " + outputSpec.getObservableGroups().length + " observables to model, " + elapsedTime + " ms";
System.out.println(msg);
} catch (PropertyVetoException ex) {
ex.printStackTrace(System.out);
throw new RuntimeException(ex.getMessage());
} catch (ExpressionBindingException ex) {
ex.printStackTrace(System.out);
throw new RuntimeException(ex.getMessage());
} catch (ModelException ex) {
ex.printStackTrace(System.out);
throw new RuntimeException(ex.getMessage());
} catch (ExpressionException ex) {
ex.printStackTrace(System.out);
throw new RuntimeException(ex.getMessage());
} catch (ClassNotFoundException ex) {
throw new RuntimeException(ex.getMessage());
} catch (IOException ex) {
throw new RuntimeException(ex.getMessage());
}
System.out.println("Done transforming");
msg = "Generating math...";
System.out.println(msg);
mathMappingCallback.setMessage(msg);
mathMappingCallback.setProgressFraction(progressFractionQuota);
}
Also used :
HashMap(java.util.HashMap)
LinkedHashMap(java.util.LinkedHashMap)
UserCancelException(org.vcell.util.UserCancelException)
ArrayList(java.util.ArrayList)
Product(cbit.vcell.model.Product)
SpeciesContext(cbit.vcell.model.SpeciesContext)
FakeSeedSpeciesInitialConditionsParameter(org.vcell.model.rbm.FakeSeedSpeciesInitialConditionsParameter)
Reactant(cbit.vcell.model.Reactant)
BNGOutputSpec(cbit.vcell.bionetgen.BNGOutputSpec)
ExpressionException(cbit.vcell.parser.ExpressionException)
LinkedHashMap(java.util.LinkedHashMap)
FakeReactionRuleRateParameter(org.vcell.model.rbm.FakeReactionRuleRateParameter)
KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter)
RbmModelContainer(cbit.vcell.model.Model.RbmModelContainer)
Species(cbit.vcell.model.Species)
BNGSpecies(cbit.vcell.bionetgen.BNGSpecies)
HashSet(java.util.HashSet)
BNGParameter(cbit.vcell.bionetgen.BNGParameter)
ModelException(cbit.vcell.model.ModelException)
ObservableGroup(cbit.vcell.bionetgen.ObservableGroup)
RbmObservable(cbit.vcell.model.RbmObservable)
PropertyVetoException(java.beans.PropertyVetoException)
BNGReaction(cbit.vcell.bionetgen.BNGReaction)
VCUnitDefinition(cbit.vcell.units.VCUnitDefinition)
ReactionStep(cbit.vcell.model.ReactionStep)
Map(java.util.Map)
HashMap(java.util.HashMap)
LinkedHashMap(java.util.LinkedHashMap)
SpeciesPattern(org.vcell.model.rbm.SpeciesPattern)
Structure(cbit.vcell.model.Structure)
SimpleReaction(cbit.vcell.model.SimpleReaction)
ReactionRule(cbit.vcell.model.ReactionRule)
IOException(java.io.IOException)
ExpressionBindingException(cbit.vcell.parser.ExpressionBindingException)
Expression(cbit.vcell.parser.Expression)
Model(cbit.vcell.model.Model)
FakeSeedSpeciesInitialConditionsParameter(org.vcell.model.rbm.FakeSeedSpeciesInitialConditionsParameter)
Parameter(cbit.vcell.model.Parameter)
KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter)
LocalParameter(cbit.vcell.mapping.ParameterContext.LocalParameter)
BNGParameter(cbit.vcell.bionetgen.BNGParameter)
FakeReactionRuleRateParameter(org.vcell.model.rbm.FakeReactionRuleRateParameter)
MassActionKinetics(cbit.vcell.model.MassActionKinetics)
ParseException(org.vcell.model.bngl.ParseException)
BNGSpecies(cbit.vcell.bionetgen.BNGSpecies)
Example 2 with FakeSeedSpeciesInitialConditionsParameter
use of org.vcell.model.rbm.FakeSeedSpeciesInitialConditionsParameter in project vcell by virtualcell.
the class RulebasedTransformer method generateNetwork.
private void generateNetwork(SimulationContext simContext, Set<ReactionRule> fromReactions, MathMappingCallback mathMappingCallback) throws ClassNotFoundException, IOException {
TaskCallbackMessage tcm;
BNGOutputSpec outputSpec;
speciesEquivalenceMap.clear();
kineticsParameterMap.clear();
NetworkGenerationRequirements networkGenerationRequirements = NetworkGenerationRequirements.ComputeFullStandardTimeout;
String input = convertToBngl(simContext, true, mathMappingCallback, networkGenerationRequirements);
// System.out.println(input); // TODO: uncomment to see the xml string
for (Map.Entry<FakeSeedSpeciesInitialConditionsParameter, Pair<SpeciesContext, Expression>> entry : speciesEquivalenceMap.entrySet()) {
FakeSeedSpeciesInitialConditionsParameter key = entry.getKey();
Pair<SpeciesContext, Expression> value = entry.getValue();
SpeciesContext sc = value.one;
Expression initial = value.two;
System.out.println("key: " + key.fakeParameterName + ", species: " + sc.getName() + ", initial: " + initial.infix());
}
BNGInput bngInput = new BNGInput(input);
BNGOutput bngOutput = null;
try {
// for the writeXML command we don't want to run iteration by iteration - it wouldn't even make sense since we don't flatten anything
// so we run bionetgen the "old" way
final BNGExecutorService bngService = BNGExecutorService.getInstanceOld(bngInput, networkGenerationRequirements.timeoutDurationMS);
bngOutput = bngService.executeBNG();
} catch (RuntimeException ex) {
ex.printStackTrace(System.out);
// rethrow without losing context
throw ex;
} catch (Exception ex) {
ex.printStackTrace(System.out);
throw new RuntimeException(ex.getMessage());
}
simContext.setInsufficientIterations(false);
simContext.setInsufficientMaxMolecules(false);
String bngConsoleString = bngOutput.getConsoleOutput();
tcm = new TaskCallbackMessage(TaskCallbackStatus.DetailBatch, bngConsoleString);
// simContext.appendToConsole(tcm);
// String bngNetString = bngOutput.getNetFileContent();
// outputSpec = BNGOutputFileParser.createBngOutputSpec(bngNetString);
// //BNGOutputFileParser.printBNGNetOutput(outputSpec); // prints all output to console
//
// if (mathMappingCallback.isInterrupted()){
// String msg = "Canceled by user.";
// // tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, msg);
// // simContext.appendToConsole(tcm);
// // simContext.setMd5hash(null); // clean the cache if the user interrupts
// throw new UserCancelException(msg);
// }
// if(outputSpec.getBNGSpecies().length > SimulationConsolePanel.speciesLimit) {
// String message = SimulationConsolePanel.getSpeciesLimitExceededMessage(outputSpec);
// // tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, message);
// // simContext.appendToConsole(tcm);
// // simContext.setMd5hash(null);
// throw new RuntimeException(message);
// }
// if(outputSpec.getBNGReactions().length > SimulationConsolePanel.reactionsLimit) {
// String message = SimulationConsolePanel.getReactionsLimitExceededMessage(outputSpec);
// // tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, message);
// // simContext.appendToConsole(tcm);
// // simContext.setMd5hash(null);
// throw new RuntimeException(message);
// }
// TODO: uncomment here to parse the xml file!!!
parseBngOutput(simContext, fromReactions, bngOutput);
//
// Saving the observables, as produced by bionetgen
// in debug configurations add to command line -Ddebug.user=danv
//
// String debugUser = PropertyLoader.getProperty("debug.user", "not_defined");
// if (debugUser.equals("danv") || debugUser.equals("mblinov")){
// System.out.println("Saving their observables");
// parseObservablesBngOutput(simContext, bngOutput);
// }
// compareOutputs(simContext);
}
Also used :
SpeciesContext(cbit.vcell.model.SpeciesContext)
BNGExecutorService(cbit.vcell.server.bionetgen.BNGExecutorService)
BNGOutput(cbit.vcell.server.bionetgen.BNGOutput)
FakeSeedSpeciesInitialConditionsParameter(org.vcell.model.rbm.FakeSeedSpeciesInitialConditionsParameter)
BNGOutputSpec(cbit.vcell.bionetgen.BNGOutputSpec)
PropertyVetoException(java.beans.PropertyVetoException)
ModelException(cbit.vcell.model.ModelException)
IOException(java.io.IOException)
ExpressionException(cbit.vcell.parser.ExpressionException)
Expression(cbit.vcell.parser.Expression)
NetworkGenerationRequirements(cbit.vcell.mapping.SimulationContext.NetworkGenerationRequirements)
BNGInput(cbit.vcell.server.bionetgen.BNGInput)
Map(java.util.Map)
LinkedHashMap(java.util.LinkedHashMap)
Pair(org.vcell.util.Pair)
Example 3 with FakeSeedSpeciesInitialConditionsParameter
use of org.vcell.model.rbm.FakeSeedSpeciesInitialConditionsParameter in project vcell by virtualcell.
the class GeneratedSpeciesTableModel method refreshData.
private void refreshData() {
allGeneratedSpeciesList = new ArrayList<>();
networkFileIndexToNameMap = new HashMap<>();
LinkedHashMap<String, String> scMap = new LinkedHashMap<>();
for (int i = 0; i < speciess.length; i++) {
BNGSpecies species = speciess[i];
String key = species.getConcentration().infix();
String originalName = "";
FakeSeedSpeciesInitialConditionsParameter fakeParam = FakeSeedSpeciesInitialConditionsParameter.fromString(key);
if (fakeParam != null) {
originalName = fakeParam.speciesContextName;
System.out.println(originalName);
scMap.put(originalName, originalName);
GeneratedSpeciesTableRow newRow = createTableRow(species, i + 1, originalName, species.toStringShort());
allGeneratedSpeciesList.add(newRow);
networkFileIndexToNameMap.put(species.getNetworkFileIndex(), originalName);
}
}
for (int i = 0; i < speciess.length; i++) {
BNGSpecies species = speciess[i];
String key = species.getConcentration().infix();
FakeSeedSpeciesInitialConditionsParameter fakeParam = FakeSeedSpeciesInitialConditionsParameter.fromString(key);
if (fakeParam != null) {
// we already dealt with these
continue;
} else {
// generate unique name for the species
int count = 0;
String speciesName = null;
String nameRoot = "s";
while (true) {
speciesName = nameRoot + count;
if (Model.isNameUnused(speciesName, model) && !scMap.containsKey(speciesName)) {
break;
}
count++;
}
scMap.put(speciesName, speciesName);
GeneratedSpeciesTableRow newRow = createTableRow(species, i + 1, speciesName, species.toStringShort());
allGeneratedSpeciesList.add(newRow);
networkFileIndexToNameMap.put(species.getNetworkFileIndex(), speciesName);
}
}
// apply text search function for particular columns
List<GeneratedSpeciesTableRow> speciesObjectList = new ArrayList<>();
if (searchText == null || searchText.length() == 0) {
speciesObjectList.addAll(allGeneratedSpeciesList);
} else {
String lowerCaseSearchText = searchText.toLowerCase();
for (GeneratedSpeciesTableRow rs : allGeneratedSpeciesList) {
boolean added = false;
if (rs.getExpression().toLowerCase().contains(lowerCaseSearchText)) {
speciesObjectList.add(rs);
added = true;
}
if (!added && rs.getOriginalName().toLowerCase().contains(lowerCaseSearchText)) {
speciesObjectList.add(rs);
added = true;
}
}
}
setData(speciesObjectList);
GuiUtils.flexResizeTableColumns(ownerTable);
}
Also used :
ArrayList(java.util.ArrayList)
FakeSeedSpeciesInitialConditionsParameter(org.vcell.model.rbm.FakeSeedSpeciesInitialConditionsParameter)
LinkedHashMap(java.util.LinkedHashMap)
BNGSpecies(cbit.vcell.bionetgen.BNGSpecies)
Example 4 with FakeSeedSpeciesInitialConditionsParameter
use of org.vcell.model.rbm.FakeSeedSpeciesInitialConditionsParameter in project vcell by virtualcell.
the class GeneratedSpeciesTableModel2 method refreshData.
private void refreshData() {
allGeneratedSpeciesList = new ArrayList<>();
networkFileIndexToNameMap = new HashMap<>();
LinkedHashMap<String, String> scMap = new LinkedHashMap<>();
String multiplier = "";
for (int i = 0; i < speciess.length; i++) {
BNGSpecies species = speciess[i];
String key = species.getConcentration().infix();
String originalName = "";
FakeSeedSpeciesInitialConditionsParameter fakeParam = FakeSeedSpeciesInitialConditionsParameter.fromString(key);
if (observableFilter != null) {
int index = 0;
ObservableGroup og = observableFilter.getObservableGroupObject();
if (og.getSpeciesMultiplicity().length > 0) {
multiplier = og.getSpeciesMultiplicity()[index] + "";
}
}
if (fakeParam != null) {
originalName = fakeParam.speciesContextName;
// System.out.println(originalName);
scMap.put(originalName, originalName);
GeneratedSpeciesTableRow newRow = createTableRow(species, i + 1, multiplier, originalName, species.toStringShort());
allGeneratedSpeciesList.add(newRow);
networkFileIndexToNameMap.put(species.getNetworkFileIndex(), originalName);
}
}
for (int i = 0; i < speciess.length; i++) {
BNGSpecies species = speciess[i];
String key = species.getConcentration().infix();
FakeSeedSpeciesInitialConditionsParameter fakeParam = FakeSeedSpeciesInitialConditionsParameter.fromString(key);
if (fakeParam != null) {
// we already dealt with these
continue;
} else {
// generate unique name for the species
int count = 0;
String speciesName = null;
String nameRoot = "s";
while (true) {
speciesName = nameRoot + count;
if (Model.isNameUnused(speciesName, model) && !scMap.containsKey(speciesName)) {
break;
}
count++;
}
scMap.put(speciesName, speciesName);
GeneratedSpeciesTableRow newRow = createTableRow(species, i + 1, multiplier, speciesName, species.toStringShort());
allGeneratedSpeciesList.add(newRow);
networkFileIndexToNameMap.put(species.getNetworkFileIndex(), speciesName);
}
}
// apply text search function for particular columns
List<GeneratedSpeciesTableRow> speciesObjectList = new ArrayList<>();
if (searchText == null || searchText.length() == 0) {
speciesObjectList.addAll(allGeneratedSpeciesList);
} else {
String lowerCaseSearchText = searchText.toLowerCase();
for (GeneratedSpeciesTableRow rs : allGeneratedSpeciesList) {
boolean added = false;
if (rs.getExpression().toLowerCase().contains(lowerCaseSearchText)) {
speciesObjectList.add(rs);
added = true;
}
if (!added && rs.getOriginalName().toLowerCase().contains(lowerCaseSearchText)) {
speciesObjectList.add(rs);
added = true;
}
}
}
List<GeneratedSpeciesTableRow> speciesObjectList2;
if (observableFilter == null) {
speciesObjectList2 = speciesObjectList;
} else {
// extra filtering by observable, if needed
speciesObjectList2 = new ArrayList<>();
ObservableGroup og = observableFilter.getObservableGroupObject();
List<Integer> indexesList = og.getIndexesAsIntegersList();
for (GeneratedSpeciesTableRow rs : speciesObjectList) {
int ourIndex = rs.getSpeciesObject().getNetworkFileIndex();
if (indexesList.contains(ourIndex)) {
speciesObjectList2.add(rs);
}
}
}
if (observableFilter != null) {
// go through each and set the correct multiplier
// key is networkFileIndex, value is multiplicity
Map<Integer, Integer> ogIndexMap = new HashMap<>();
ObservableGroup og = observableFilter.getObservableGroupObject();
for (int i = 0; i < og.getListofSpecies().length; i++) {
int networkFileIndex = og.getListofSpecies()[i].getNetworkFileIndex();
int multiplicity = og.getSpeciesMultiplicity()[i];
ogIndexMap.put(networkFileIndex, multiplicity);
}
for (GeneratedSpeciesTableRow gstr : speciesObjectList2) {
int networkFileIndex = gstr.getSpeciesObject().getNetworkFileIndex();
int multiplicity = ogIndexMap.get(networkFileIndex);
gstr.setMultiplier(multiplicity + "");
}
}
setData(speciesObjectList2);
GuiUtils.flexResizeTableColumns(ownerTable);
}
Also used :
HashMap(java.util.HashMap)
LinkedHashMap(java.util.LinkedHashMap)
ObservableGroup(cbit.vcell.bionetgen.ObservableGroup)
ArrayList(java.util.ArrayList)
FakeSeedSpeciesInitialConditionsParameter(org.vcell.model.rbm.FakeSeedSpeciesInitialConditionsParameter)
LinkedHashMap(java.util.LinkedHashMap)
BNGSpecies(cbit.vcell.bionetgen.BNGSpecies)
Example 5 with FakeSeedSpeciesInitialConditionsParameter
use of org.vcell.model.rbm.FakeSeedSpeciesInitialConditionsParameter in project vcell by virtualcell.
the class NetworkTransformer method generateNetwork.
private BNGOutputSpec generateNetwork(SimulationContext simContext, MathMappingCallback mathMappingCallback, NetworkGenerationRequirements networkGenerationRequirements) throws ClassNotFoundException, IOException {
TaskCallbackMessage tcm;
BNGOutputSpec outputSpec;
speciesEquivalenceMap.clear();
kineticsParameterMap.clear();
String input = convertToBngl(simContext, true, mathMappingCallback, networkGenerationRequirements);
for (Map.Entry<FakeSeedSpeciesInitialConditionsParameter, Pair<SpeciesContext, Expression>> entry : speciesEquivalenceMap.entrySet()) {
FakeSeedSpeciesInitialConditionsParameter key = entry.getKey();
Pair<SpeciesContext, Expression> value = entry.getValue();
SpeciesContext sc = value.one;
Expression initial = value.two;
System.out.println("key: " + key.fakeParameterName + ", species: " + sc.getName() + ", initial: " + initial.infix());
}
String md5hash = MD5.md5(input);
if (isBngHashValid(input, md5hash, simContext)) {
String s = "Previously saved outputSpec is up-to-date, no need to generate network.";
System.out.println(s);
// not an error, we just want to show it in red
tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, s);
simContext.appendToConsole(tcm);
if (simContext.isInsufficientIterations()) {
s = NetworkTransformer.getInsufficientIterationsMessage();
System.out.println(s);
tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, s);
simContext.appendToConsole(tcm);
}
if (simContext.isInsufficientMaxMolecules()) {
s = NetworkTransformer.getInsufficientMaxMoleculesMessage();
System.out.println(s);
tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, s);
simContext.appendToConsole(tcm);
}
outputSpec = simContext.getMostRecentlyCreatedOutputSpec();
return (BNGOutputSpec) BeanUtils.cloneSerializable(outputSpec);
}
BNGInput bngInput = new BNGInput(input);
BNGOutput bngOutput = null;
try {
final BNGExecutorService bngService = BNGExecutorService.getInstance(bngInput, networkGenerationRequirements.timeoutDurationMS);
bngService.registerBngUpdaterCallback(simContext);
bngOutput = bngService.executeBNG();
} catch (BNGException ex) {
ex.printStackTrace(System.out);
System.out.println("bionetgen exception");
if (ex.getMessage().contains("was asked to write the network, but no reactions were found")) {
RuntimeException rex = new RuntimeException("Specified species and reaction rules are not sufficient to define reaction network.");
throw rex;
} else {
// rethrow without losing context
throw ex;
}
} catch (RuntimeException ex) {
ex.printStackTrace(System.out);
System.out.println("runtime exception");
throw ex;
} catch (Exception ex) {
ex.printStackTrace(System.out);
System.out.println("other exception");
throw new RuntimeException(ex.getMessage());
}
// simContext.setInsufficientIterations(false);
// simContext.setInsufficientMaxMolecules(false);
String bngConsoleString = bngOutput.getConsoleOutput();
// TODO: this message we check if insufficient iterations / max molecules
// DO IT OUTSIDE (in the bng service), we now can
// tcm = new TaskCallbackMessage(TaskCallbackStatus.DetailBatch, bngConsoleString);
// simContext.appendToConsole(tcm);
tcm = new TaskCallbackMessage(TaskCallbackStatus.TaskEndNotificationOnly, "");
simContext.setNewCallbackMessage(tcm);
tcm = new TaskCallbackMessage(TaskCallbackStatus.TaskEndAdjustSimulationContextFlagsOnly, "");
simContext.setNewCallbackMessage(tcm);
String bngNetString = bngOutput.getNetFileContent();
outputSpec = BNGOutputFileParser.createBngOutputSpec(bngNetString);
// prints all output to console
BNGOutputFileParser.printBNGNetOutput(outputSpec);
if (mathMappingCallback.isInterrupted()) {
String msg = "Canceled by user.";
tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, msg);
simContext.appendToConsole(tcm);
// clean the cache if the user interrupts
simContext.setMd5hash(null);
throw new UserCancelException(msg);
}
if (outputSpec.getBNGSpecies().length > NetworkTransformer.speciesLimit) {
String message = NetworkTransformer.getSpeciesLimitExceededMessage(outputSpec);
tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, message);
simContext.appendToConsole(tcm);
simContext.setMd5hash(null);
message = "Unable to generate Math for Application " + simContext.getName() + ".\n" + message;
throw new RuntimeException(message);
}
if (outputSpec.getBNGReactions().length > NetworkTransformer.reactionsLimit) {
String message = NetworkTransformer.getReactionsLimitExceededMessage(outputSpec);
tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, message);
simContext.appendToConsole(tcm);
simContext.setMd5hash(null);
message = "Unable to generate Math for Application " + simContext.getName() + ".\n" + message;
throw new RuntimeException(message);
}
// System.out.println("old hash: " + simContext.getMd5hash());
if (md5hash != null && md5hash.length() != 0 && outputSpec != null) {
System.out.println("saving hash and output spec");
synchronized (this) {
simContext.setMd5hash(md5hash);
simContext.setMostRecentlyCreatedOutputSpec(outputSpec);
}
} else {
System.out.println("something is wrong with the hash and/or output spec");
}
return (BNGOutputSpec) BeanUtils.cloneSerializable(outputSpec);
}
Also used :
UserCancelException(org.vcell.util.UserCancelException)
SpeciesContext(cbit.vcell.model.SpeciesContext)
BNGExecutorService(cbit.vcell.server.bionetgen.BNGExecutorService)
BNGOutput(cbit.vcell.server.bionetgen.BNGOutput)
FakeSeedSpeciesInitialConditionsParameter(org.vcell.model.rbm.FakeSeedSpeciesInitialConditionsParameter)
BNGOutputSpec(cbit.vcell.bionetgen.BNGOutputSpec)
PropertyVetoException(java.beans.PropertyVetoException)
ExpressionBindingException(cbit.vcell.parser.ExpressionBindingException)
ParseException(org.vcell.model.bngl.ParseException)
BNGException(cbit.vcell.server.bionetgen.BNGException)
ModelException(cbit.vcell.model.ModelException)
IOException(java.io.IOException)
ExpressionException(cbit.vcell.parser.ExpressionException)
UserCancelException(org.vcell.util.UserCancelException)
BNGException(cbit.vcell.server.bionetgen.BNGException)
Expression(cbit.vcell.parser.Expression)
BNGInput(cbit.vcell.server.bionetgen.BNGInput)
Map(java.util.Map)
HashMap(java.util.HashMap)
LinkedHashMap(java.util.LinkedHashMap)
Pair(org.vcell.util.Pair)
Aggregations
LinkedHashMap (java.util.LinkedHashMap)5
FakeSeedSpeciesInitialConditionsParameter (org.vcell.model.rbm.FakeSeedSpeciesInitialConditionsParameter)5
BNGOutputSpec (cbit.vcell.bionetgen.BNGOutputSpec)3
BNGSpecies (cbit.vcell.bionetgen.BNGSpecies)3
ModelException (cbit.vcell.model.ModelException)3
SpeciesContext (cbit.vcell.model.SpeciesContext)3
Expression (cbit.vcell.parser.Expression)3
ExpressionException (cbit.vcell.parser.ExpressionException)3
PropertyVetoException (java.beans.PropertyVetoException)3
IOException (java.io.IOException)3
ArrayList (java.util.ArrayList)3
HashMap (java.util.HashMap)3
Map (java.util.Map)3
ObservableGroup (cbit.vcell.bionetgen.ObservableGroup)2
ExpressionBindingException (cbit.vcell.parser.ExpressionBindingException)2
BNGExecutorService (cbit.vcell.server.bionetgen.BNGExecutorService)2
BNGInput (cbit.vcell.server.bionetgen.BNGInput)2
BNGOutput (cbit.vcell.server.bionetgen.BNGOutput)2
ParseException (org.vcell.model.bngl.ParseException)2
BNGParameter (cbit.vcell.bionetgen.BNGParameter)1
