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

Example 51 with BioModel

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

the class BatchTester method batchScanBioModels.

@SuppressWarnings("static-access")
public void batchScanBioModels(VCMultiBioVisitor databaseVisitor, String statusTable, int chunkSize) throws DataAccessException, XmlParseException, SQLException, IOException {
    PrintStream current = System.out;
    // System.setOut(new PrintStream(new NullStream()));
    try {
        String processHostId = ManagementFactory.getRuntimeMXBean().getName();
        String filename = processHostId + ".txt";
        FileOutputStream fos = new FileOutputStream(filename);
        System.setOut(new PrintStream(fos));
        OutputStreamWriter writer = new OutputStreamWriter(fos);
        // autoflush
        PrintWriter printWriter = new PrintWriter(writer, true);
        Connection conn = connFactory.getConnection(null);
        conn.setAutoCommit(true);
        printWriter.println("reserving slots");
        try (Statement statement = conn.createStatement()) {
            String query = "Update " + statusTable + " set scan_process = '" + processHostId + "', log_file = '" + filename + "' where scanned = 0 and scan_process is null and rownum <= " + chunkSize;
            int uCount = statement.executeUpdate(query);
            if (uCount > chunkSize) {
                throw new Error("logic / SQL bad");
            }
            if (uCount == 0) {
                printWriter.println("No models to scan, exiting");
                System.exit(100);
            }
        }
        printWriter.println("finding  ours");
        ArrayList<BioModelIdent> models = new ArrayList<BatchTester.BioModelIdent>();
        try (Statement statement = conn.createStatement()) {
            String query = "Select id, user_id, model_id from " + statusTable + " where scan_process ='" + processHostId + "' and scanned = 0";
            ResultSet rs = statement.executeQuery(query);
            while (rs.next()) {
                BioModelIdent mi = new BioModelIdent(rs);
                models.add(mi);
                printWriter.println("claiming " + mi.statusId);
            }
        }
        try {
            // start visiting models and writing log
            printWriter.println("Start scanning bio-models......");
            printWriter.println("\n");
            PreparedStatement ps = conn.prepareStatement("Update " + statusTable + " set scanned = 1, good = ? , exception_type = ?, exception = ?, scan_process = null where id = ?");
            for (BioModelIdent modelIdent : models) {
                ScanStatus scanStatus = ScanStatus.PASS;
                String exceptionMessage = null;
                String exceptionClass = null;
                try {
                    User user = new User("", convert(modelIdent.userId));
                    KeyValue modelKey = convert(modelIdent.modelId);
                    BigString bioModelXML = null;
                    // seconds
                    long dbSleepTime = 10;
                    while (bioModelXML == null) {
                        try {
                            bioModelXML = dbServerImpl.getBioModelXML(user, modelKey);
                        } catch (DataAccessException dae) {
                            Throwable cause = dae.getCause();
                            if (cause.getClass().getSimpleName().equals("UniversalConnectionPoolException")) {
                                printWriter.println("No db connection for  " + modelIdent.statusId + ", sleeping " + dbSleepTime + " seconds");
                                Thread.currentThread().sleep(dbSleepTime * 1000);
                                // wait a little longer next time
                                dbSleepTime *= 1.5;
                            } else {
                                // other exception, just rethrow
                                throw dae;
                            }
                        }
                    }
                    BioModel storedModel = cbit.vcell.xml.XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
                    if (databaseVisitor.filterBioModel(storedModel)) {
                        storedModel.refreshDependencies();
                        boolean goodModel = verifyMathDescriptionsUnchanged(storedModel, printWriter);
                        if (goodModel) {
                            printWriter.println("Model for " + modelIdent.statusId + " good");
                            databaseVisitor.setBioModel(storedModel, printWriter);
                            for (BioModel bioModel : databaseVisitor) {
                                SimulationContext[] simContexts = bioModel.getSimulationContexts();
                                for (SimulationContext sc : simContexts) {
                                    // try {
                                    // long start = System.currentTimeMillis();
                                    sc.createNewMathMapping().getMathDescription();
                                // long end = System.currentTimeMillis();
                                // printWriter.println("mapping took " + (end - start)/1000.0 + " sec ");
                                /*
									} catch (Exception e) {
										//printWriter.println("\t " + bioModel.getName() + " :: " + sc.getName() + " ----> math regeneration failed.s");
										// e.printStackTrace();
									}
											 */
                                }
                            }
                        } else {
                            throw new MathRegenFail();
                        }
                    } else {
                        scanStatus = ScanStatus.FILTERED;
                    }
                } catch (Exception e) {
                    lg.error(e.getMessage(), e);
                    scanStatus = ScanStatus.FAIL;
                    exceptionClass = e.getClass().getName();
                    exceptionMessage = e.getMessage();
                    printWriter.println("failed " + modelIdent.statusId);
                    e.printStackTrace(printWriter);
                }
                ps.setInt(1, scanStatus.code);
                ps.setString(2, exceptionClass);
                ps.setString(3, exceptionMessage);
                ps.setLong(4, modelIdent.statusId);
                boolean estat = ps.execute();
                if (estat) {
                    throw new Error("logic");
                }
                int uc = ps.getUpdateCount();
                if (uc != 1) {
                    throw new Error("logic / sql ");
                }
            }
        } catch (Exception e) {
            e.printStackTrace(printWriter);
        }
        printWriter.close();
    } finally {
        System.setOut(current);
    }
}

Example 52 with BioModel

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

the class DisplayBioModel method compute0.

@Override
protected void compute0(TaskContext context, final ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    // get input
    BioModel biomodel = context.getData(bioModel);
    // do op
    DisplayBioModelOp op = new DisplayBioModelOp();
    op.displayBioModel(biomodel);
    // set output
    context.setData(displayed, true);
}

Example 53 with BioModel

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

the class Generate2DSimBioModel method compute0.

@Override
protected void compute0(TaskContext context, final ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    // get inputs
    Extent extent = context.getData(this.extent);
    ROI cellROI_2D = context.getData(this.cellROI_2D);
    double[] timeStamps = context.getData(this.timeStamps);
    Integer indexFirstPostbleach = context.getData(this.indexFirstPostbleach);
    double primaryDiffusionRate = context.getData(this.primaryDiffusionRate);
    double primaryFraction = context.getData(this.primaryFraction);
    double bleachMonitorRate = context.getData(this.bleachMonitorRate);
    Double secondaryDiffusionRate = context.getData(this.secondaryDiffusionRate);
    double secondaryFraction = context.getData(this.secondaryFraction);
    double bindingSiteConcentration = context.getData(this.bindingSiteConcentration);
    double bindingOnRate = context.getData(this.bindingOnRate);
    double bindingOffRate = context.getData(this.bindingOffRate);
    String extracellularName = context.getData(this.extracellularName);
    String cytosolName = context.getData(this.cytosolName);
    User owner = context.getData(this.owner);
    KeyValue simKey = context.getData(this.simKey);
    // do op
    Generate2DSimBioModelOp op = new Generate2DSimBioModelOp();
    BioModel bioModel = op.generateBioModel(extent, cellROI_2D, timeStamps, indexFirstPostbleach, primaryDiffusionRate, primaryFraction, bleachMonitorRate, secondaryDiffusionRate, secondaryFraction, bindingSiteConcentration, bindingOnRate, bindingOffRate, extracellularName, cytosolName, owner, simKey);
    // set output
    context.setData(this.bioModel_2D, bioModel);
}

Example 54 with BioModel

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

the class Generate2DExpModelOpAbstract method generateModel.

public final GeneratedModelResults generateModel(double deltaX, double bleachRadius, double cellRadius, double bleachDuration, double bleachRate, double postbleachDelay, double postbleachDuration, double psfSigma, double outputTimeStep, double primaryDiffusionRate, double primaryFraction, double bleachMonitorRate, double secondaryDiffusionRate, double secondaryFraction, String extracellularName, String cytosolName, Context context) throws PropertyVetoException, ExpressionException, GeometryException, ImageException, ModelException, MappingException, MathException, MatrixException {
    double domainSize = 2.2 * cellRadius;
    Extent extent = new Extent(domainSize, domainSize, 1.0);
    Origin origin = new Origin(-extent.getX() / 2.0, -extent.getY() / 2.0, -extent.getZ() / 2.0);
    String EXTRACELLULAR_NAME = extracellularName;
    String CYTOSOL_NAME = cytosolName;
    AnalyticSubVolume cytosolSubVolume = new AnalyticSubVolume(CYTOSOL_NAME, new Expression("pow(x,2)+pow(y,2)<pow(" + cellRadius + ",2)"));
    AnalyticSubVolume extracellularSubVolume = new AnalyticSubVolume(EXTRACELLULAR_NAME, new Expression(1.0));
    Geometry geometry = new Geometry("geometry", 2);
    geometry.getGeometrySpec().setExtent(extent);
    geometry.getGeometrySpec().setOrigin(origin);
    geometry.getGeometrySpec().addSubVolume(extracellularSubVolume);
    geometry.getGeometrySpec().addSubVolume(cytosolSubVolume, true);
    geometry.getGeometrySurfaceDescription().updateAll();
    BioModel bioModel = new BioModel(null);
    bioModel.setName("unnamed");
    Model model = new Model("model");
    bioModel.setModel(model);
    model.addFeature(EXTRACELLULAR_NAME);
    Feature extracellular = (Feature) model.getStructure(EXTRACELLULAR_NAME);
    model.addFeature(CYTOSOL_NAME);
    Feature cytosol = (Feature) model.getStructure(CYTOSOL_NAME);
    SpeciesContext immobileSC = model.createSpeciesContext(cytosol);
    SpeciesContext primarySC = model.createSpeciesContext(cytosol);
    SpeciesContext secondarySC = model.createSpeciesContext(cytosol);
    // 
    // common bleaching rate for all species
    // 
    double bleachStart = 10 * outputTimeStep - bleachDuration - postbleachDelay;
    double bleachEnd = bleachStart + bleachDuration;
    Expression bleachRateExp = createBleachExpression(bleachRadius, bleachRate, bleachMonitorRate, bleachStart, bleachEnd);
    {
        SimpleReaction immobileBWM = model.createSimpleReaction(cytosol);
        GeneralKinetics immobileBWMKinetics = new GeneralKinetics(immobileBWM);
        immobileBWM.setKinetics(immobileBWMKinetics);
        immobileBWM.addReactant(immobileSC, 1);
        immobileBWMKinetics.getReactionRateParameter().setExpression(Expression.mult(bleachRateExp, new Expression(immobileSC.getName())));
    }
    {
        SimpleReaction primaryBWM = model.createSimpleReaction(cytosol);
        GeneralKinetics primaryBWMKinetics = new GeneralKinetics(primaryBWM);
        primaryBWM.setKinetics(primaryBWMKinetics);
        primaryBWM.addReactant(primarySC, 1);
        primaryBWMKinetics.getReactionRateParameter().setExpression(Expression.mult(bleachRateExp, new Expression(primarySC.getName())));
    }
    {
        SimpleReaction secondaryBWM = model.createSimpleReaction(cytosol);
        GeneralKinetics secondaryBWMKinetics = new GeneralKinetics(secondaryBWM);
        secondaryBWM.setKinetics(secondaryBWMKinetics);
        secondaryBWM.addReactant(secondarySC, 1);
        secondaryBWMKinetics.getReactionRateParameter().setExpression(Expression.mult(bleachRateExp, new Expression(secondarySC.getName())));
    }
    // create simulation context
    SimulationContext simContext = bioModel.addNewSimulationContext("simContext", SimulationContext.Application.NETWORK_DETERMINISTIC);
    simContext.setGeometry(geometry);
    FeatureMapping cytosolFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(cytosol);
    FeatureMapping extracellularFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(extracellular);
    SubVolume cytSubVolume = geometry.getGeometrySpec().getSubVolume(CYTOSOL_NAME);
    SubVolume exSubVolume = geometry.getGeometrySpec().getSubVolume(EXTRACELLULAR_NAME);
    // unused? SurfaceClass pmSurfaceClass = geometry.getGeometrySurfaceDescription().getSurfaceClass(exSubVolume, cytSubVolume);
    cytosolFeatureMapping.setGeometryClass(cytSubVolume);
    extracellularFeatureMapping.setGeometryClass(exSubVolume);
    cytosolFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    extracellularFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    double fixedFraction = 1.0 - primaryFraction - secondaryFraction;
    SpeciesContextSpec immobileSCS = simContext.getReactionContext().getSpeciesContextSpec(immobileSC);
    immobileSCS.getInitialConditionParameter().setExpression(new Expression(fixedFraction));
    immobileSCS.getDiffusionParameter().setExpression(new Expression(0.0));
    SpeciesContextSpec primarySCS = simContext.getReactionContext().getSpeciesContextSpec(primarySC);
    primarySCS.getInitialConditionParameter().setExpression(new Expression(primaryFraction));
    primarySCS.getDiffusionParameter().setExpression(new Expression(primaryDiffusionRate));
    SpeciesContextSpec secondarySCS = simContext.getReactionContext().getSpeciesContextSpec(secondarySC);
    secondarySCS.getInitialConditionParameter().setExpression(new Expression(secondaryFraction));
    secondarySCS.getDiffusionParameter().setExpression(new Expression(secondaryDiffusionRate));
    simContext.getMicroscopeMeasurement().addFluorescentSpecies(immobileSC);
    simContext.getMicroscopeMeasurement().addFluorescentSpecies(primarySC);
    simContext.getMicroscopeMeasurement().addFluorescentSpecies(secondarySC);
    simContext.getMicroscopeMeasurement().setConvolutionKernel(new GaussianConvolutionKernel(new Expression(psfSigma), new Expression(psfSigma)));
    MathMapping mathMapping = simContext.createNewMathMapping();
    MathDescription mathDesc = mathMapping.getMathDescription();
    simContext.setMathDescription(mathDesc);
    User owner = context.getDefaultOwner();
    int meshSize = (int) (domainSize / deltaX);
    if (meshSize % 2 == 0) {
        // want an odd-sized mesh in x and y ... so centered at the origin.
        meshSize = meshSize + 1;
    }
    TimeBounds timeBounds = new TimeBounds(0.0, postbleachDuration);
    // 
    // simulation to use for data generation (output time steps as recorded by the microscope)
    // 
    double bleachBlackoutBegin = bleachStart - postbleachDelay;
    double bleachBlackoutEnd = bleachEnd + postbleachDelay;
    // ArrayList<Double> times = new ArrayList<Double>();
    // double time = 0;
    // while (time<=timeBounds.getEndingTime()){
    // if (time<=bleachBlackoutBegin || time>bleachBlackoutEnd){
    // // postbleachDelay is the time it takes to switch the filters.
    // times.add(time);
    // }
    // time += outputTimeStep.getData();
    // }
    // double[] timeArray = new double[times.size()];
    // for (int i=0;i<timeArray.length;i++){
    // timeArray[i] = times.get(i);
    // }
    // OutputTimeSpec fakeDataSimOutputTimeSpec = new ExplicitOutputTimeSpec(timeArray);
    OutputTimeSpec fakeDataSimOutputTimeSpec = new UniformOutputTimeSpec(outputTimeStep);
    KeyValue fakeDataSimKey = context.createNewKeyValue();
    SimulationVersion fakeDataSimVersion = new SimulationVersion(fakeDataSimKey, "fakeDataSim", owner, new GroupAccessNone(), new KeyValue("0"), new BigDecimal(0), new Date(), VersionFlag.Current, "", null);
    Simulation fakeDataSim = new Simulation(fakeDataSimVersion, mathDesc);
    simContext.addSimulation(fakeDataSim);
    fakeDataSim.getSolverTaskDescription().setTimeBounds(timeBounds);
    fakeDataSim.getMeshSpecification().setSamplingSize(new ISize(meshSize, meshSize, 1));
    fakeDataSim.getSolverTaskDescription().setSolverDescription(SolverDescription.SundialsPDE);
    fakeDataSim.getSolverTaskDescription().setOutputTimeSpec(fakeDataSimOutputTimeSpec);
    // 
    // simulation to use for viewing the protocol (output time steps to understand the physics)
    // 
    KeyValue fullExperimentSimKey = context.createNewKeyValue();
    SimulationVersion fullExperimentSimVersion = new SimulationVersion(fullExperimentSimKey, "fullExperiment", owner, new GroupAccessNone(), new KeyValue("0"), new BigDecimal(0), new Date(), VersionFlag.Current, "", null);
    Simulation fullExperimentSim = new Simulation(fullExperimentSimVersion, mathDesc);
    simContext.addSimulation(fullExperimentSim);
    OutputTimeSpec fullExperimentOutputTimeSpec = new UniformOutputTimeSpec(outputTimeStep / 10.0);
    fullExperimentSim.getSolverTaskDescription().setTimeBounds(timeBounds);
    fullExperimentSim.getMeshSpecification().setSamplingSize(new ISize(meshSize, meshSize, 1));
    fullExperimentSim.getSolverTaskDescription().setSolverDescription(SolverDescription.SundialsPDE);
    fullExperimentSim.getSolverTaskDescription().setOutputTimeSpec(fullExperimentOutputTimeSpec);
    GeneratedModelResults results = new GeneratedModelResults();
    results.bioModel_2D = bioModel;
    results.simulation_2D = fakeDataSim;
    results.bleachBlackoutBeginTime = bleachBlackoutBegin;
    results.bleachBlackoutEndTime = bleachBlackoutEnd;
    return results;
}

Example 55 with BioModel

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

the class RuleBasedTest method main.

public static void main(String[] args) {
    try {
        PropertyLoader.loadProperties();
    } catch (Exception e) {
        e.printStackTrace();
    }
    final int numTrials = 40;
    VCDatabaseVisitor vcDatabaseVisitor = new VCDatabaseVisitor() {

        @Override
        public void visitMathModel(MathModel mathModel, PrintStream logFilePrintStream) {
            throw new IllegalArgumentException("Not Implemented");
        }

        @Override
        public void visitGeometry(Geometry geometry, PrintStream logFilePrintStream) {
            throw new IllegalArgumentException("Not Implemented");
        }

        @Override
        public void visitBioModel(BioModel bioModel, PrintStream logFilePrintStream) {
            SimulationContext[] simulationContexts = bioModel.getSimulationContexts();
            for (SimulationContext simContext : simulationContexts) {
                if ((simContext.getApplicationType() == Application.NETWORK_STOCHASTIC) && simContext.getGeometry().getDimension() == 0) {
                    File baseDirectory = createDirFile(simContext);
                    try {
                        checkNonspatialStochasticSimContext(simContext, baseDirectory, numTrials);
                    } catch (Exception e) {
                        e.printStackTrace();
                        if (!e.getMessage().contains("Only Mass Action Kinetics supported ")) {
                            writeMessageTofile(baseDirectory, e.getMessage());
                        }
                    }
                }
            }
        }

        @Override
        public boolean filterMathModel(MathModelInfo mathModelInfo) {
            return false;
        }

        @Override
        public boolean filterGeometry(GeometryInfo geometryInfo) {
            return false;
        }

        @Override
        public boolean filterBioModel(BioModelInfo bioModelInfo) {
            return // bioModelInfo.getVersion().getName().equals("model");
            bioModelInfo.getVersion().getName().equals("simpleModel_Network_orig");
        }
    };
    String currentUserID = "schaff";
    String[] allUsers = new String[] { /*-all*/
    currentUserID, "-" };
    VCDatabaseScanner.scanBioModels(allUsers, vcDatabaseVisitor, false);
}