Examples with ModelPropertyVetoException cbit.vcell.model.ModelPropertyVetoException used on opensource projects

Example 1 with ModelPropertyVetoException

use of cbit.vcell.model.ModelPropertyVetoException in project vcell by virtualcell.

the class SBMLImporter method addReactions.

/**
 * addReactions:
 */
protected void addReactions(VCMetaData metaData) {
    if (sbmlModel == null) {
        throw new SBMLImportException("SBML model is NULL");
    }
    ListOf<Reaction> reactions = sbmlModel.getListOfReactions();
    final int numReactions = reactions.size();
    if (numReactions == 0) {
        lg.info("No Reactions");
        return;
    }
    // all reactions
    ArrayList<ReactionStep> vcReactionList = new ArrayList<>();
    // just the fast ones
    ArrayList<ReactionStep> fastReactionList = new ArrayList<>();
    Model vcModel = vcBioModel.getSimulationContext(0).getModel();
    ModelUnitSystem vcModelUnitSystem = vcModel.getUnitSystem();
    SpeciesContext[] vcSpeciesContexts = vcModel.getSpeciesContexts();
    try {
        for (Reaction sbmlRxn : reactions) {
            ReactionStep vcReaction = null;
            String rxnName = sbmlRxn.getId();
            boolean bReversible = true;
            if (sbmlRxn.isSetReversible()) {
                bReversible = sbmlRxn.getReversible();
            }
            // Check of reaction annotation is present; if so, does it have
            // an embedded element (flux or simpleRxn).
            // Create a fluxReaction or simpleReaction accordingly.
            Element sbmlImportRelatedElement = sbmlAnnotationUtil.readVCellSpecificAnnotation(sbmlRxn);
            Structure reactionStructure = getReactionStructure(sbmlRxn, vcSpeciesContexts, sbmlImportRelatedElement);
            if (sbmlImportRelatedElement != null) {
                Element embeddedRxnElement = getEmbeddedElementInAnnotation(sbmlImportRelatedElement, REACTION);
                if (embeddedRxnElement != null) {
                    if (embeddedRxnElement.getName().equals(XMLTags.FluxStepTag)) {
                        // If embedded element is a flux reaction, set flux
                        // reaction's strucure, flux carrier, physicsOption
                        // from the element attributes.
                        String structName = embeddedRxnElement.getAttributeValue(XMLTags.StructureAttrTag);
                        CastInfo<Membrane> ci = SBMLHelper.getTypedStructure(Membrane.class, vcModel, structName);
                        if (!ci.isGood()) {
                            throw new SBMLImportException("Appears that the flux reaction is occuring on " + ci.actualName() + ", not a membrane.");
                        }
                        vcReaction = new FluxReaction(vcModel, ci.get(), null, rxnName, bReversible);
                        vcReaction.setModel(vcModel);
                        // Set the fluxOption on the flux reaction based on
                        // whether it is molecular, molecular & electrical,
                        // electrical.
                        String fluxOptionStr = embeddedRxnElement.getAttributeValue(XMLTags.FluxOptionAttrTag);
                        if (fluxOptionStr.equals(XMLTags.FluxOptionMolecularOnly)) {
                            ((FluxReaction) vcReaction).setPhysicsOptions(ReactionStep.PHYSICS_MOLECULAR_ONLY);
                        } else if (fluxOptionStr.equals(XMLTags.FluxOptionMolecularAndElectrical)) {
                            ((FluxReaction) vcReaction).setPhysicsOptions(ReactionStep.PHYSICS_MOLECULAR_AND_ELECTRICAL);
                        } else if (fluxOptionStr.equals(XMLTags.FluxOptionElectricalOnly)) {
                            ((FluxReaction) vcReaction).setPhysicsOptions(ReactionStep.PHYSICS_ELECTRICAL_ONLY);
                        } else {
                            localIssueList.add(new Issue(vcReaction, issueContext, IssueCategory.SBMLImport_Reaction, "Unknown FluxOption : " + fluxOptionStr + " for SBML reaction : " + rxnName, Issue.SEVERITY_WARNING));
                        // logger.sendMessage(VCLogger.Priority.MediumPriority,
                        // VCLogger.ErrorType.ReactionError,
                        // "Unknown FluxOption : " + fluxOptionStr +
                        // " for SBML reaction : " + rxnName);
                        }
                    } else if (embeddedRxnElement.getName().equals(XMLTags.SimpleReactionTag)) {
                        // if embedded element is a simple reaction, set
                        // simple reaction's structure from element
                        // attributes
                        vcReaction = new SimpleReaction(vcModel, reactionStructure, rxnName, bReversible);
                    }
                } else {
                    vcReaction = new SimpleReaction(vcModel, reactionStructure, rxnName, bReversible);
                }
            } else {
                vcReaction = new SimpleReaction(vcModel, reactionStructure, rxnName, bReversible);
            }
            // set annotations and notes on vcReactions[i]
            sbmlAnnotationUtil.readAnnotation(vcReaction, sbmlRxn);
            sbmlAnnotationUtil.readNotes(vcReaction, sbmlRxn);
            // the limit on the reactionName length.
            if (rxnName.length() > 64) {
                String freeTextAnnotation = metaData.getFreeTextAnnotation(vcReaction);
                if (freeTextAnnotation == null) {
                    freeTextAnnotation = "";
                }
                StringBuffer oldRxnAnnotation = new StringBuffer(freeTextAnnotation);
                oldRxnAnnotation.append("\n\n" + rxnName);
                metaData.setFreeTextAnnotation(vcReaction, oldRxnAnnotation.toString());
            }
            // Now add the reactants, products, modifiers as specified by
            // the sbmlRxn
            addReactionParticipants(sbmlRxn, vcReaction);
            KineticLaw kLaw = sbmlRxn.getKineticLaw();
            Kinetics kinetics = null;
            if (kLaw != null) {
                // Convert the formula from kineticLaw into MathML and then
                // to an expression (infix) to be used in VCell kinetics
                ASTNode sbmlRateMath = kLaw.getMath();
                Expression kLawRateExpr = getExpressionFromFormula(sbmlRateMath);
                Expression vcRateExpression = new Expression(kLawRateExpr);
                // modifier (catalyst) to the reaction.
                for (int k = 0; k < vcSpeciesContexts.length; k++) {
                    if (vcRateExpression.hasSymbol(vcSpeciesContexts[k].getName())) {
                        if ((vcReaction.getReactant(vcSpeciesContexts[k].getName()) == null) && (vcReaction.getProduct(vcSpeciesContexts[k].getName()) == null) && (vcReaction.getCatalyst(vcSpeciesContexts[k].getName()) == null)) {
                            // This means that the speciesContext is not a
                            // reactant, product or modifier : it has to be
                            // added to the VC Rxn as a catalyst
                            vcReaction.addCatalyst(vcSpeciesContexts[k]);
                        }
                    }
                }
                // set kinetics on VCell reaction
                if (bSpatial) {
                    // if spatial SBML ('isSpatial' attribute set), create
                    // DistributedKinetics)
                    SpatialReactionPlugin ssrplugin = (SpatialReactionPlugin) sbmlRxn.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
                    // 'spatial'
                    if (ssrplugin != null && ssrplugin.getIsLocal()) {
                        kinetics = new GeneralKinetics(vcReaction);
                    } else {
                        kinetics = new GeneralLumpedKinetics(vcReaction);
                    }
                } else {
                    kinetics = new GeneralLumpedKinetics(vcReaction);
                }
                // set kinetics on vcReaction
                vcReaction.setKinetics(kinetics);
                // If the name of the rate parameter has been changed by
                // user, or matches with global/local param,
                // it has to be changed.
                resolveRxnParameterNameConflicts(sbmlRxn, kinetics, sbmlImportRelatedElement);
                /**
                 * Now, based on the kinetic law expression, see if the rate
                 * is expressed in concentration/time or substance/time : If
                 * the compartment_id of the compartment corresponding to
                 * the structure in which the reaction takes place occurs in
                 * the rate law expression, it is in concentration/time;
                 * divide it by the compartment size and bring in the rate
                 * law as 'Distributed' kinetics. If not, the rate law is in
                 * substance/time; bring it in (as is) as 'Lumped' kinetics.
                 */
                ListOf<LocalParameter> localParameters = kLaw.getListOfLocalParameters();
                for (LocalParameter p : localParameters) {
                    String paramName = p.getId();
                    KineticsParameter kineticsParameter = kinetics.getKineticsParameter(paramName);
                    if (kineticsParameter == null) {
                        // add unresolved for now to prevent errors in kinetics.setParameterValue(kp,vcRateExpression) below
                        kinetics.addUnresolvedParameter(paramName);
                    }
                }
                KineticsParameter kp = kinetics.getAuthoritativeParameter();
                if (lg.isDebugEnabled()) {
                    lg.debug("Setting " + kp.getName() + ":  " + vcRateExpression.infix());
                }
                kinetics.setParameterValue(kp, vcRateExpression);
                // If there are any global parameters used in the kinetics,
                // and if they have species,
                // check if the species are already reactionParticipants in
                // the reaction. If not, add them as catalysts.
                KineticsProxyParameter[] kpps = kinetics.getProxyParameters();
                for (int j = 0; j < kpps.length; j++) {
                    if (kpps[j].getTarget() instanceof ModelParameter) {
                        ModelParameter mp = (ModelParameter) kpps[j].getTarget();
                        HashSet<String> refSpeciesNameHash = new HashSet<String>();
                        getReferencedSpeciesInExpr(mp.getExpression(), refSpeciesNameHash);
                        java.util.Iterator<String> refSpIterator = refSpeciesNameHash.iterator();
                        while (refSpIterator.hasNext()) {
                            String spName = refSpIterator.next();
                            org.sbml.jsbml.Species sp = sbmlModel.getSpecies(spName);
                            ArrayList<ReactionParticipant> rpArray = getVCReactionParticipantsFromSymbol(vcReaction, sp.getId());
                            if (rpArray == null || rpArray.size() == 0) {
                                // This means that the speciesContext is not
                                // a reactant, product or modifier : it has
                                // to be added as a catalyst
                                vcReaction.addCatalyst(vcModel.getSpeciesContext(sp.getId()));
                            }
                        }
                    }
                }
                // model - local params cannot be defined by rules.
                for (LocalParameter param : localParameters) {
                    String paramName = param.getId();
                    Expression exp = new Expression(param.getValue());
                    String unitString = param.getUnits();
                    VCUnitDefinition paramUnit = sbmlUnitIdentifierHash.get(unitString);
                    if (paramUnit == null) {
                        paramUnit = vcModelUnitSystem.getInstance_TBD();
                    }
                    // check if sbml local param is in kinetic params list;
                    // if so, add its value.
                    boolean lpSet = false;
                    KineticsParameter kineticsParameter = kinetics.getKineticsParameter(paramName);
                    if (kineticsParameter != null) {
                        if (lg.isDebugEnabled()) {
                            lg.debug("Setting local " + kineticsParameter.getName() + ":  " + exp.infix());
                        }
                        kineticsParameter.setExpression(exp);
                        kineticsParameter.setUnitDefinition(paramUnit);
                        lpSet = true;
                    } else {
                        UnresolvedParameter ur = kinetics.getUnresolvedParameter(paramName);
                        if (ur != null) {
                            kinetics.addUserDefinedKineticsParameter(paramName, exp, paramUnit);
                            lpSet = true;
                        }
                    }
                    if (!lpSet) {
                        // check if it is a proxy parameter (specifically,
                        // speciesContext or model parameter (structureSize
                        // too)).
                        KineticsProxyParameter kpp = kinetics.getProxyParameter(paramName);
                        // and units to local param values
                        if (kpp != null && kpp.getTarget() instanceof ModelParameter) {
                            kinetics.convertParameterType(kpp, false);
                            kineticsParameter = kinetics.getKineticsParameter(paramName);
                            kinetics.setParameterValue(kineticsParameter, exp);
                            kineticsParameter.setUnitDefinition(paramUnit);
                        }
                    }
                }
            } else {
                // sbmlKLaw was null, so creating a GeneralKinetics with 0.0
                // as rate.
                kinetics = new GeneralKinetics(vcReaction);
            }
            // end - if-else KLaw != null
            // set the reaction kinetics, and add reaction to the vcell
            // model.
            kinetics.resolveUndefinedUnits();
            // System.out.println("ADDED SBML REACTION : \"" + rxnName +
            // "\" to VCModel");
            vcReactionList.add(vcReaction);
            if (sbmlRxn.isSetFast() && sbmlRxn.getFast()) {
                fastReactionList.add(vcReaction);
            }
        }
        // end - for vcReactions
        ReactionStep[] array = vcReactionList.toArray(new ReactionStep[vcReactionList.size()]);
        vcModel.setReactionSteps(array);
        final ReactionContext rc = vcBioModel.getSimulationContext(0).getReactionContext();
        for (ReactionStep frs : fastReactionList) {
            final ReactionSpec rs = rc.getReactionSpec(frs);
            rs.setReactionMapping(ReactionSpec.FAST);
        }
    } catch (ModelPropertyVetoException mpve) {
        throw new SBMLImportException(mpve.getMessage(), mpve);
    } catch (Exception e1) {
        e1.printStackTrace(System.out);
        throw new SBMLImportException(e1.getMessage(), e1);
    }
}

Example 2 with ModelPropertyVetoException

use of cbit.vcell.model.ModelPropertyVetoException in project vcell by virtualcell.

the class SBMLImporter method addSpecies.

protected void addSpecies(VCMetaData metaData) {
    if (sbmlModel == null) {
        throw new SBMLImportException("SBML model is NULL");
    }
    ListOf listOfSpecies = sbmlModel.getListOfSpecies();
    if (listOfSpecies == null) {
        System.out.println("No Spcecies");
        return;
    }
    HashMap<String, Species> vcSpeciesHash = new HashMap<String, Species>();
    HashMap<Species, org.sbml.jsbml.Species> vc_sbmlSpeciesHash = new HashMap<Species, org.sbml.jsbml.Species>();
    SpeciesContext[] vcSpeciesContexts = new SpeciesContext[(int) sbmlModel.getNumSpecies()];
    // Get species from SBMLmodel; Add/get speciesContext
    try {
        // First pass - add the speciesContexts
        for (int i = 0; i < sbmlModel.getNumSpecies(); i++) {
            org.sbml.jsbml.Species sbmlSpecies = (org.sbml.jsbml.Species) listOfSpecies.get(i);
            // Sometimes, the species name can be null or a blank string; in
            // that case, use species id as the name.
            String speciesName = sbmlSpecies.getId();
            Species vcSpecies = null;
            // create a species with speciesName as commonName. If it is
            // different in the annotation, can change it later
            Element sbmlImportRelatedElement = sbmlAnnotationUtil.readVCellSpecificAnnotation(sbmlSpecies);
            if (sbmlImportRelatedElement != null) {
                Element embeddedElement = getEmbeddedElementInAnnotation(sbmlImportRelatedElement, SPECIES_NAME);
                if (embeddedElement != null) {
                    // species.
                    if (embeddedElement.getName().equals(XMLTags.SpeciesTag)) {
                        String vcSpeciesName = embeddedElement.getAttributeValue(XMLTags.NameAttrTag);
                        vcSpecies = vcSpeciesHash.get(vcSpeciesName);
                        if (vcSpecies == null) {
                            vcSpecies = new Species(vcSpeciesName, vcSpeciesName);
                            vcSpeciesHash.put(vcSpeciesName, vcSpecies);
                        }
                    }
                // if embedded element is not speciesTag, do I have to
                // do something?
                } else {
                    // Annotation element is present, but doesn't contain
                    // the species element.
                    vcSpecies = new Species(speciesName, speciesName);
                    vcSpeciesHash.put(speciesName, vcSpecies);
                }
            } else {
                vcSpecies = new Species(speciesName, speciesName);
                vcSpeciesHash.put(speciesName, vcSpecies);
            }
            // store vc & sbml species in hash to read in annotation later
            vc_sbmlSpeciesHash.put(vcSpecies, sbmlSpecies);
            // Get matching compartment name (of sbmlSpecies[i]) from
            // feature list
            String compartmentId = sbmlSpecies.getCompartment();
            Structure spStructure = vcBioModel.getSimulationContext(0).getModel().getStructure(compartmentId);
            vcSpeciesContexts[i] = new SpeciesContext(vcSpecies, spStructure);
            vcSpeciesContexts[i].setName(speciesName);
            // Adjust units of species, convert to VC units.
            // Units in SBML, compute this using some of the attributes of
            // sbmlSpecies
            Compartment sbmlCompartment = sbmlModel.getCompartment(sbmlSpecies.getCompartment());
            int dimension = 3;
            if (sbmlCompartment.isSetSpatialDimensions()) {
                dimension = (int) sbmlCompartment.getSpatialDimensions();
            }
            if (dimension == 0 || dimension == 1) {
                logger.sendMessage(VCLogger.Priority.HighPriority, VCLogger.ErrorType.UnitError, dimension + " dimensional compartment " + compartmentId + " not supported");
            }
        }
        // end - for sbmlSpecies
        // set the species & speciesContexts on model
        Model vcModel = vcBioModel.getSimulationContext(0).getModel();
        vcModel.setSpecies(vcSpeciesHash.values().toArray(new Species[0]));
        vcModel.setSpeciesContexts(vcSpeciesContexts);
        // Set annotations and notes from SBML to VCMetadata
        Species[] vcSpeciesArray = vc_sbmlSpeciesHash.keySet().toArray(new Species[0]);
        for (Species vcSpecies : vcSpeciesArray) {
            org.sbml.jsbml.Species sbmlSpecies = vc_sbmlSpeciesHash.get(vcSpecies);
            sbmlAnnotationUtil.readAnnotation(vcSpecies, sbmlSpecies);
            sbmlAnnotationUtil.readNotes(vcSpecies, sbmlSpecies);
        }
    } catch (ModelPropertyVetoException e) {
        throw new SBMLImportException("Error adding species context; " + e.getMessage(), e);
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new SBMLImportException("Error adding species context; " + e.getMessage(), e);
    }
}