Examples with BioModel cbit.vcell.biomodel.BioModel used on opensource projects

Example 36 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class BNGExecutorServiceMultipass method preprocessInput.

// parse the compartmental bngl file and produce the "trick"
// where each molecule has an extra Site with the compartments as possible States
// a reserved name will be used for this Site
// 
private String preprocessInput(String cBngInputString) throws ParseException, PropertyVetoException, ExpressionBindingException {
    // take the cBNGL file (as string), parse it to recover the rules (we'll need them later)
    // and create the bngl string with the extra, fake site for the compartments
    BioModel bioModel = new BioModel(null);
    bioModel.setName("BngBioModel");
    model = new Model("model");
    bioModel.setModel(model);
    model.createFeature();
    simContext = bioModel.addNewSimulationContext("BioNetGen app", SimulationContext.Application.NETWORK_DETERMINISTIC);
    List<SimulationContext> appList = new ArrayList<SimulationContext>();
    appList.add(simContext);
    // set convention for initial conditions in generated application for seed species (concentration or count)
    BngUnitSystem bngUnitSystem = new BngUnitSystem(BngUnitOrigin.DEFAULT);
    InputStream is = new ByteArrayInputStream(cBngInputString.getBytes());
    BufferedReader br = new BufferedReader(new InputStreamReader(is));
    ASTModel astModel = RbmUtils.importBnglFile(br);
    if (astModel.hasCompartments()) {
        Structure struct = model.getStructure(0);
        if (struct != null) {
            try {
                model.removeStructure(struct);
            } catch (PropertyVetoException e) {
                e.printStackTrace();
            }
        }
    }
    BnglObjectConstructionVisitor constructionVisitor = null;
    constructionVisitor = new BnglObjectConstructionVisitor(model, appList, bngUnitSystem, true);
    astModel.jjtAccept(constructionVisitor, model.getRbmModelContainer());
    int numCompartments = model.getStructures().length;
    if (numCompartments == 0) {
        throw new RuntimeException("No structure present in the bngl file.");
    } else if (numCompartments == 1) {
        // for single compartment we don't need the 'trick'
        compartmentMode = CompartmentMode.hide;
    } else {
        compartmentMode = CompartmentMode.asSite;
    }
    // extract all polymer observables for special treatment at the end
    for (RbmObservable oo : model.getRbmModelContainer().getObservableList()) {
        if (oo.getSequence() == RbmObservable.Sequence.PolymerLengthEqual) {
            polymerEqualObservables.add(oo);
        } else if (oo.getSequence() == RbmObservable.Sequence.PolymerLengthGreater) {
            polymerGreaterObservables.add(oo);
        }
    }
    for (RbmObservable oo : polymerEqualObservables) {
        model.getRbmModelContainer().removeObservable(oo);
    }
    for (RbmObservable oo : polymerGreaterObservables) {
        model.getRbmModelContainer().removeObservable(oo);
    }
    // replace all reversible rules with 2 direct rules
    List<ReactionRule> newRRList = new ArrayList<>();
    for (ReactionRule rr : model.getRbmModelContainer().getReactionRuleList()) {
        if (rr.isReversible()) {
            ReactionRule rr1 = ReactionRule.deriveDirectRule(rr);
            newRRList.add(rr1);
            ReactionRule rr2 = ReactionRule.deriveInverseRule(rr);
            newRRList.add(rr2);
        } else {
            newRRList.add(rr);
        }
        model.getRbmModelContainer().removeReactionRule(rr);
    }
    // model.getRbmModelContainer().getReactionRuleList().clear();
    model.getRbmModelContainer().setReactionRules(newRRList);
    StringWriter bnglStringWriter = new StringWriter();
    PrintWriter writer = new PrintWriter(bnglStringWriter);
    writer.println(RbmNetworkGenerator.BEGIN_MODEL);
    writer.println();
    // RbmNetworkGenerator.writeCompartments(writer, model, null);
    RbmNetworkGenerator.writeParameters(writer, model.getRbmModelContainer(), false);
    RbmNetworkGenerator.writeMolecularTypes(writer, model, compartmentMode);
    RbmNetworkGenerator.writeSpeciesSortedAlphabetically(writer, model, simContext, compartmentMode);
    RbmNetworkGenerator.writeObservables(writer, model.getRbmModelContainer(), compartmentMode);
    // RbmNetworkGenerator.writeFunctions(writer, rbmModelContainer, ignoreFunctions);
    RbmNetworkGenerator.writeReactions(writer, model.getRbmModelContainer(), null, false, compartmentMode);
    writer.println(RbmNetworkGenerator.END_MODEL);
    writer.println();
    // we parse the real numbers from the bngl file provided by the caller, the nc in the simContext has the default ones
    NetworkConstraints realNC = extractNetworkConstraints(cBngInputString);
    simContext.getNetworkConstraints().setMaxMoleculesPerSpecies(realNC.getMaxMoleculesPerSpecies());
    simContext.getNetworkConstraints().setMaxIteration(realNC.getMaxIteration());
    RbmNetworkGenerator.generateNetworkEx(1, simContext.getNetworkConstraints().getMaxMoleculesPerSpecies(), writer, model.getRbmModelContainer(), simContext, NetworkGenerationRequirements.AllowTruncatedStandardTimeout);
    String sInputString = bnglStringWriter.toString();
    return sInputString;
}

Example 37 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class XmlHelper method applyOverridesForSBML.

/**
 * applyOverrides: private method to apply overrides from the simulation in 'simJob' to simContext, if any.
 * 				Start off by cloning biomodel, since all the references are required in cloned simContext and is
 * 				best retained by cloning biomodel.
 * @param bm - biomodel to be cloned
 * @param sc - simulationContext to be cloned and overridden using math overrides in simulation
 * @param simJob - simulationJob from where simulation with overrides is obtained.
 * @return
 */
public static SimulationContext applyOverridesForSBML(BioModel bm, SimulationContext sc, SimulationJob simJob) {
    SimulationContext overriddenSimContext = sc;
    if (simJob != null) {
        Simulation sim = simJob.getSimulation();
        // need to clone Biomodel, simContext, etc. only if simulation has override(s)
        try {
            if (sim != null && sim.getMathOverrides().hasOverrides()) {
                // BioModel clonedBM = (BioModel)BeanUtils.cloneSerializable(bm);
                BioModel clonedBM = XMLToBioModel(new XMLSource(bioModelToXML(bm)));
                clonedBM.refreshDependencies();
                // get the simContext in cloned Biomodel that corresponds to 'sc'
                SimulationContext[] simContexts = clonedBM.getSimulationContexts();
                for (int i = 0; i < simContexts.length; i++) {
                    if (simContexts[i].getName().equals(sc.getName())) {
                        overriddenSimContext = simContexts[i];
                        break;
                    }
                }
                // 
                overriddenSimContext.getModel().refreshDependencies();
                overriddenSimContext.refreshDependencies();
                MathMapping mathMapping = overriddenSimContext.createNewMathMapping();
                MathSymbolMapping msm = mathMapping.getMathSymbolMapping();
                MathOverrides mathOverrides = sim.getMathOverrides();
                String[] moConstNames = mathOverrides.getOverridenConstantNames();
                for (int i = 0; i < moConstNames.length; i++) {
                    cbit.vcell.math.Constant overriddenConstant = mathOverrides.getConstant(moConstNames[i]);
                    // Expression overriddenExpr = mathOverrides.getActualExpression(moConstNames[i], 0);
                    Expression overriddenExpr = mathOverrides.getActualExpression(moConstNames[i], simJob.getJobIndex());
                    // The above constant (from mathoverride) is not the same instance as the one in the MathSymbolMapping hash.
                    // Hence retreive the correct instance from mathSymbolMapping (mathMapping -> mathDescription) and use it to
                    // retrieve its value (symbolTableEntry) from hash.
                    cbit.vcell.math.Variable overriddenVar = msm.findVariableByName(overriddenConstant.getName());
                    cbit.vcell.parser.SymbolTableEntry[] stes = msm.getBiologicalSymbol(overriddenVar);
                    if (stes == null) {
                        throw new NullPointerException("No matching biological symbol for : " + overriddenConstant.getName());
                    }
                    if (stes.length > 1) {
                        throw new RuntimeException("Cannot have more than one mapping entry for constant : " + overriddenConstant.getName());
                    }
                    if (stes[0] instanceof Parameter) {
                        Parameter param = (Parameter) stes[0];
                        if (param.isExpressionEditable()) {
                            if (param instanceof Kinetics.KineticsParameter) {
                                // Kinetics param has to be set separately for the integrity of the kinetics object
                                Kinetics.KineticsParameter kinParam = (Kinetics.KineticsParameter) param;
                                ReactionStep[] rs = overriddenSimContext.getModel().getReactionSteps();
                                for (int j = 0; j < rs.length; j++) {
                                    if (rs[j].getNameScope().getName().equals(kinParam.getNameScope().getName())) {
                                        rs[j].getKinetics().setParameterValue(kinParam, overriddenExpr);
                                    }
                                }
                            } else if (param instanceof cbit.vcell.model.ExpressionContainer) {
                                // If it is any other editable param, set its expression with the
                                ((cbit.vcell.model.ExpressionContainer) param).setExpression(overriddenExpr);
                            }
                        }
                    }
                // end - if (stes[0] is Parameter)
                }
            // end  - for moConstNames
            }
        // end if (sim has MathOverrides)
        } catch (Exception e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Could not apply overrides from simulation to application parameters : " + e.getMessage());
        }
    }
    // end if (simJob != null)
    return overriddenSimContext;
}

Example 38 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class XmlHelper method sedmlToBioModel.

public static VCDocument sedmlToBioModel(VCLogger transLogger, ExternalDocInfo externalDocInfo, SedML sedml, AbstractTask selectedTask) throws Exception {
    if (sedml.getModels().isEmpty()) {
        return null;
    }
    VCDocument doc = null;
    try {
        // extract the path only from the sedml file
        String fullPath = FileUtils.getFullPath(externalDocInfo.getFile().getAbsolutePath());
        // Namespace namespace = sedml.getNamespace();
        // iterate through all the elements and show them at the console
        List<org.jlibsedml.Model> mmm = sedml.getModels();
        for (Model mm : mmm) {
            System.out.println(mm.toString());
        }
        List<org.jlibsedml.Simulation> sss = sedml.getSimulations();
        for (org.jlibsedml.Simulation ss : sss) {
            System.out.println(ss.toString());
        }
        List<AbstractTask> ttt = sedml.getTasks();
        for (AbstractTask tt : ttt) {
            System.out.println(tt.toString());
        }
        List<DataGenerator> ddd = sedml.getDataGenerators();
        for (DataGenerator dd : ddd) {
            System.out.println(dd.toString());
        }
        List<Output> ooo = sedml.getOutputs();
        for (Output oo : ooo) {
            System.out.println(oo.toString());
        }
        KisaoTerm sedmlKisao = null;
        // this will become the vCell simulation
        org.jlibsedml.Simulation sedmlSimulation = null;
        // the "original" model referred to by the task
        org.jlibsedml.Model sedmlOriginalModel = null;
        String sedmlOriginalModelName = null;
        if (selectedTask == null) {
            // no task, just pick the Model and find its sbml file
            sedmlOriginalModelName = SEDMLUtil.getName(mmm.get(0));
        } else {
            if (selectedTask instanceof Task) {
                sedmlOriginalModel = sedml.getModelWithId(selectedTask.getModelReference());
                sedmlSimulation = sedml.getSimulation(selectedTask.getSimulationReference());
            } else if (selectedTask instanceof RepeatedTask) {
                RepeatedTask rt = (RepeatedTask) selectedTask;
                assert (rt.getSubTasks().size() == 1);
                // first (and only) subtask
                SubTask st = rt.getSubTasks().entrySet().iterator().next().getValue();
                String taskId = st.getTaskId();
                AbstractTask t = sedml.getTaskWithId(taskId);
                // get model and simulation from subtask
                sedmlOriginalModel = sedml.getModelWithId(t.getModelReference());
                sedmlSimulation = sedml.getSimulation(t.getSimulationReference());
            } else {
                throw new RuntimeException("Unexpected task " + selectedTask);
            }
            sedmlOriginalModelName = sedmlOriginalModel.getId();
            sedmlKisao = KisaoOntology.getInstance().getTermById(sedmlSimulation.getAlgorithm().getKisaoID());
        }
        // UniformTimeCourse [initialTime=0.0, numberOfPoints=1000, outputEndTime=1.0, outputStartTime=0.0,
        // Algorithm [kisaoID=KISAO:0000019], getId()=SimSlow]
        // identify the vCell solvers that would match best the sedml solver kisao id
        List<SolverDescription> solverDescriptions = new ArrayList<>();
        for (SolverDescription sd : SolverDescription.values()) {
            KisaoTerm solverKisaoTerm = KisaoOntology.getInstance().getTermById(sd.getKisao());
            if (solverKisaoTerm == null) {
                break;
            }
            boolean isExactlySame = solverKisaoTerm.equals(sedmlKisao);
            if (isExactlySame && !solverKisaoTerm.isObsolete()) {
                // we make a list with all the solvers that match the kisao
                solverDescriptions.add(sd);
            }
        }
        // from the list of vcell solvers that match the sedml kisao we select the ones that have a matching time step
        SolverDescription solverDescription = null;
        for (SolverDescription sd : solverDescriptions) {
            if (true) {
                solverDescription = sd;
                break;
            }
        }
        // find out everything else we need about the application we're going to use,
        // some of the info will be needed when we parse the sbml file
        boolean bSpatial = false;
        Application appType = Application.NETWORK_DETERMINISTIC;
        Set<SolverDescription.SolverFeature> sfList = solverDescription.getSupportedFeatures();
        for (SolverDescription.SolverFeature sf : sfList) {
            switch(sf) {
                case Feature_Rulebased:
                    appType = Application.RULE_BASED_STOCHASTIC;
                    break;
                case Feature_Stochastic:
                    appType = Application.NETWORK_STOCHASTIC;
                    break;
                case Feature_Deterministic:
                    appType = Application.NETWORK_DETERMINISTIC;
                    break;
                case Feature_Spatial:
                    bSpatial = true;
                    break;
                default:
                    break;
            }
        }
        // -------------------------------------------------------------------------------------------
        // extract bioModel name from sedx (or sedml) file
        String bioModelName = FileUtils.getBaseName(externalDocInfo.getFile().getAbsolutePath());
        // if we have repeated task, we ignore them, we just use the normal resolvers for archive and changes
        // once the application and simulation are built, we iterate through the repeated tasks and
        // add math overrides to the simulation for each repeated task
        ArchiveComponents ac = null;
        if (externalDocInfo.getFile().getPath().toLowerCase().endsWith("sedx") || externalDocInfo.getFile().getPath().toLowerCase().endsWith("omex")) {
            ac = Libsedml.readSEDMLArchive(new FileInputStream(externalDocInfo.getFile().getPath()));
        }
        ModelResolver resolver = new ModelResolver(sedml);
        if (ac != null) {
            resolver.add(new ArchiveModelResolver(ac));
        }
        resolver.add(new FileModelResolver());
        resolver.add(new RelativeFileModelResolver(fullPath));
        String newMdl = resolver.getModelString(sedmlOriginalModel);
        // sbmlSource with all the changes applied
        XMLSource sbmlSource = new XMLSource(newMdl);
        doc = XmlHelper.importSBML(transLogger, sbmlSource, bSpatial);
        BioModel bioModel = (BioModel) doc;
        bioModel.setName(bioModelName);
        // we already have an application loaded from the sbml file, with initial conditions and stuff
        // which may be not be suitable because the sedml kisao may need a different app type
        // so we do a "copy as" to the right type and then delete the original we loaded from the sbml file
        // the new application we're making from the old one
        SimulationContext newSimulationContext = null;
        if (bioModel.getSimulationContexts().length == 1) {
            SimulationContext oldSimulationContext = bioModel.getSimulationContext(0);
            newSimulationContext = SimulationContext.copySimulationContext(oldSimulationContext, sedmlOriginalModelName, bSpatial, appType);
            bioModel.removeSimulationContext(oldSimulationContext);
            bioModel.addSimulationContext(newSimulationContext);
        } else {
            // length == 0
            newSimulationContext = bioModel.addNewSimulationContext(sedmlOriginalModelName, appType);
        }
        // making the new vCell simulation based on the sedml simulation
        newSimulationContext.refreshDependencies();
        MathMappingCallback callback = new MathMappingCallbackTaskAdapter(null);
        newSimulationContext.refreshMathDescription(callback, NetworkGenerationRequirements.ComputeFullStandardTimeout);
        Simulation newSimulation = new Simulation(newSimulationContext.getMathDescription());
        newSimulation.setName(SEDMLUtil.getName(sedmlSimulation));
        // TODO: make sure that everything has proper names
        // we check the repeated tasks, if any, and add to the list of math overrides
        // if(selectedTask instanceof RepeatedTask) {
        // for(Change change : ((RepeatedTask) selectedTask).getChanges()) {
        // if(!(change instanceof SetValue)) {
        // throw new RuntimeException("Only 'SetValue' changes are supported for repeated tasks.");
        // }
        // SetValue setValue = (SetValue)change;
        // // TODO: extract target from XPath
        // // ......
        // //
        // String target = "s0";	// for now we just use a hardcoded thing
        // ConstantArraySpec cas;
        // Range range = ((RepeatedTask) selectedTask).getRange(setValue.getRangeReference());
        // if(range instanceof UniformRange) {
        // cas = ConstantArraySpec.createIntervalSpec(target, ((UniformRange) range).getStart(), ((UniformRange) range).getEnd(),
        // range.getNumElements(), ((UniformRange) range).getType() == UniformRange.UniformType.LOG ? true : false);
        // } else if(range instanceof VectorRange) {
        // //    				List<String> constants = new ArrayList<> ();
        // //    				for(int i=0; i<range.getNumElements(); i++) {
        // //    					constants.add(new Constant(i+"", new Expression(range.getElementAt(i))));
        // //    				}
        // //    				cas = ConstantArraySpec.createListSpec(target, constants);
        // 
        // } else {
        // throw new RuntimeException("Only 'Uniform Range' and 'Vector Range' are supported at this time.");
        // }
        // 
        // }
        // }
        // we identify the type of sedml simulation (uniform time course, etc)
        // and set the vCell simulation parameters accordingly
        SolverTaskDescription simTaskDesc = newSimulation.getSolverTaskDescription();
        TimeBounds timeBounds = new TimeBounds();
        TimeStep timeStep = new TimeStep();
        double outputTimeStep = 0.1;
        if (sedmlSimulation instanceof UniformTimeCourse) {
            // we translate initial time to zero, we provide output for the duration of the simulation
            // because we can't select just an interval the way the SEDML simulation can
            double initialTime = ((UniformTimeCourse) sedmlSimulation).getInitialTime();
            double outputStartTime = ((UniformTimeCourse) sedmlSimulation).getOutputStartTime();
            double outputEndTime = ((UniformTimeCourse) sedmlSimulation).getOutputEndTime();
            double outputNumberOfPoints = ((UniformTimeCourse) sedmlSimulation).getNumberOfPoints();
            outputTimeStep = (outputEndTime - outputStartTime) / outputNumberOfPoints;
            timeBounds = new TimeBounds(0, outputEndTime - initialTime);
        } else if (sedmlSimulation instanceof OneStep) {
        // for anything other than UniformTimeCourse we just ignore
        } else if (sedmlSimulation instanceof SteadyState) {
        } else {
        }
        OutputTimeSpec outputTimeSpec = new UniformOutputTimeSpec(outputTimeStep);
        simTaskDesc.setTimeBounds(timeBounds);
        simTaskDesc.setTimeStep(timeStep);
        simTaskDesc.setOutputTimeSpec(outputTimeSpec);
        newSimulation.setSolverTaskDescription(simTaskDesc);
        bioModel.addSimulation(newSimulation);
        newSimulation.refreshDependencies();
    } catch (Exception e) {
        e.printStackTrace();
        throw new RuntimeException("Unable to initialize bioModel for the given selection.");
    }
    return doc;
}

Example 39 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class XmlHelper method exportSBML.

/**
 * Exports VCML format to another supported format (currently: SBML or CellML). It allows
 *   choosing a specific Simulation Spec to export.
 * Creation date: (4/8/2003 12:30:27 PM)
 * @return java.lang.String
 */
public static String exportSBML(VCDocument vcDoc, int level, int version, int pkgVersion, boolean isSpatial, SimulationContext simContext, SimulationJob simJob) throws XmlParseException {
    if (vcDoc == null) {
        throw new XmlParseException("Invalid arguments for exporting SBML.");
    }
    if (vcDoc instanceof BioModel) {
        try {
            // check if model to be exported to SBML has units compatible with SBML default units (default units in SBML can be assumed only until SBML Level2)
            ModelUnitSystem forcedModelUnitSystem = simContext.getModel().getUnitSystem();
            if (level < 3 && !ModelUnitSystem.isCompatibleWithDefaultSBMLLevel2Units(forcedModelUnitSystem)) {
                forcedModelUnitSystem = ModelUnitSystem.createDefaultSBMLLevel2Units();
            }
            // create new Biomodel with new (SBML compatible)  unit system
            BioModel modifiedBiomodel = ModelUnitConverter.createBioModelWithNewUnitSystem(simContext.getBioModel(), forcedModelUnitSystem);
            // extract the simContext from new Biomodel. Apply overrides to *this* modified simContext
            SimulationContext simContextFromModifiedBioModel = modifiedBiomodel.getSimulationContext(simContext.getName());
            SimulationContext clonedSimContext = applyOverridesForSBML(modifiedBiomodel, simContextFromModifiedBioModel, simJob);
            // extract sim (in simJob) from modified Biomodel, if not null
            SimulationJob modifiedSimJob = null;
            if (simJob != null) {
                Simulation simFromModifiedBiomodel = clonedSimContext.getSimulation(simJob.getSimulation().getName());
                modifiedSimJob = new SimulationJob(simFromModifiedBiomodel, simJob.getJobIndex(), null);
            }
            SBMLExporter sbmlExporter = new SBMLExporter(modifiedBiomodel, level, version, isSpatial);
            sbmlExporter.setSelectedSimContext(simContextFromModifiedBioModel);
            sbmlExporter.setSelectedSimulationJob(modifiedSimJob);
            return sbmlExporter.getSBMLFile();
        } catch (ExpressionException | SbmlException | SBMLException | XMLStreamException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException(e);
        }
    } else if (vcDoc instanceof MathModel) {
        try {
            return MathModel_SBMLExporter.getSBMLString((MathModel) vcDoc, level, version);
        } catch (ExpressionException | IOException | SBMLException | XMLStreamException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException(e);
        }
    } else {
        throw new RuntimeException("unsupported Document Type " + vcDoc.getClass().getName() + " for SBML export");
    }
}

Example 40 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class ChooseFile method run.

/**
 * Insert the method's description here.
 * Creation date: (5/31/2004 6:04:14 PM)
 * @param hashTable java.util.Hashtable
 * @param clientWorker cbit.vcell.desktop.controls.ClientWorker
 */
public void run(Hashtable<String, Object> hashTable) throws java.lang.Exception {
    VCDocument documentToExport = fetch(hashTable, DocumentToExport.EXPORT_DOCUMENT, VCDocument.class, true);
    File exportFile = null;
    if (documentToExport instanceof BioModel) {
        exportFile = showBioModelXMLFileChooser(hashTable);
    } else if (documentToExport instanceof MathModel) {
        exportFile = showMathModelXMLFileChooser(hashTable);
    } else if (documentToExport instanceof Geometry) {
        exportFile = showGeometryModelXMLFileChooser(hashTable);
    } else {
        throw new Exception("Unsupported document type for XML export: " + documentToExport.getClass());
    }
    // check to see if we've changed extension from what user entered
    if (extensionUserProvided != null && !extensionUserProvided.isEmpty()) {
        String fp = exportFile.getAbsolutePath();
        String currentExt = FilenameUtils.getExtension(fp);
        if (!extensionUserProvided.equals(currentExt)) {
            hashTable.put(RENAME_KEY, fp);
        }
    }
    hashTable.put(EXPORT_FILE, exportFile);
}