Examples with AnnotatedFunction cbit.vcell.solver.AnnotatedFunction used on opensource projects

Example 21 with AnnotatedFunction

use of cbit.vcell.solver.AnnotatedFunction in project vcell by virtualcell.

the class SimulationData method getVarAndFunctionDataIdentifiers.

/**
 * This method was created in VisualAge.
 * @return java.lang.String[]
 */
public synchronized DataIdentifier[] getVarAndFunctionDataIdentifiers(OutputContext outputContext) throws IOException, DataAccessException {
    // Is this zip format?
    boolean bIsChombo = false;
    try {
        bIsChombo = isChombo();
    } catch (FileNotFoundException e) {
        e.printStackTrace(System.out);
    }
    File zipFile1 = getZipFile(bIsChombo, null);
    File zipFile2 = getZipFile(bIsChombo, 0);
    bZipFormat1 = false;
    bZipFormat2 = false;
    if (zipFile1.exists()) {
        bZipFormat1 = true;
    } else if (zipFile2.exists()) {
        bZipFormat2 = true;
    }
    refreshLogFile();
    if (!isComsol()) {
        try {
            refreshMeshFile();
        } catch (MathException e) {
            e.printStackTrace(System.out);
            throw new DataAccessException(e.getMessage());
        }
    }
    if (!isRulesData && !getIsODEData() && !isComsol() && dataFilenames != null) {
        // read variables only when I have never read the file since variables don't change
        if (dataSetIdentifierList.size() == 0) {
            File file = getPDEDataFile(0.0);
            DataSet dataSet = getPDEDataSet(file, 0.0);
            String[] varNames = dataSet.getDataNames();
            int[] varTypeInts = dataSet.getVariableTypeIntegers();
            if (varNames == null) {
                return null;
            }
            dataSetIdentifierList.clear();
            for (int i = 0; i < varNames.length; i++) {
                VariableType varType = null;
                try {
                    varType = VariableType.getVariableTypeFromInteger(varTypeInts[i]);
                } catch (IllegalArgumentException e) {
                    if (LG.isEnabledFor(Level.WARN)) {
                        LG.warn("Exception typing " + varNames[i] + " has unsupported type " + varTypeInts[i] + ": " + e.getMessage());
                    }
                    varType = SimulationData.getVariableTypeFromLength(mesh, dataSet.getDataLength(varNames[i]));
                }
                Domain domain = Variable.getDomainFromCombinedIdentifier(varNames[i]);
                String varName = Variable.getNameFromCombinedIdentifier(varNames[i]);
                dataSetIdentifierList.addElement(new DataSetIdentifier(varName, varType, domain));
            }
            refreshDataProcessingOutputInfo(outputContext);
            if (dataProcessingOutputInfo != null) {
                for (int i = 0; i < dataProcessingOutputInfo.getVariableNames().length; i++) {
                    if (dataProcessingOutputInfo.getPostProcessDataType(dataProcessingOutputInfo.getVariableNames()[i]).equals(DataProcessingOutputInfo.PostProcessDataType.image)) {
                        dataSetIdentifierList.addElement(new DataSetIdentifier(dataProcessingOutputInfo.getVariableNames()[i], VariableType.POSTPROCESSING, null));
                    }
                }
            }
        }
        // always read functions file since functions might change
        getFunctionDataIdentifiers(outputContext);
    }
    if ((isRulesData || getIsODEData()) && dataSetIdentifierList.size() == 0) {
        ODEDataBlock odeDataBlock = getODEDataBlock();
        if (odeDataBlock == null) {
            throw new DataAccessException("Results are not availabe yet. Please try again later.");
        }
        ODESimData odeSimData = odeDataBlock.getODESimData();
        int colCount = odeSimData.getColumnDescriptionsCount();
        // assume index=0 is time "t"
        int DATA_OFFSET = 1;
        dataSetIdentifierList.clear();
        for (int i = 0; i < (colCount - DATA_OFFSET); i++) {
            String varName = odeSimData.getColumnDescriptions(i + DATA_OFFSET).getDisplayName();
            // TODO domain
            Domain domain = null;
            dataSetIdentifierList.addElement(new DataSetIdentifier(varName, VariableType.NONSPATIAL, domain));
        }
    }
    if (isComsol() && dataSetIdentifierList.size() == 0) {
        ComsolSimFiles comsolSimFiles = getComsolSimFiles();
        if (comsolSimFiles.simTaskXMLFile != null) {
            try {
                String xmlString = FileUtils.readFileToString(comsolSimFiles.simTaskXMLFile);
                SimulationTask simTask = XmlHelper.XMLToSimTask(xmlString);
                Enumeration<Variable> variablesEnum = simTask.getSimulation().getMathDescription().getVariables();
                while (variablesEnum.hasMoreElements()) {
                    Variable var = variablesEnum.nextElement();
                    if (var instanceof VolVariable) {
                        dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), VariableType.VOLUME, var.getDomain()));
                    } else if (var instanceof MemVariable) {
                        dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), VariableType.MEMBRANE, var.getDomain()));
                    } else if (var instanceof Function) {
                        VariableType varType = VariableType.UNKNOWN;
                        if (var.getDomain() != null && var.getDomain().getName() != null) {
                            SubDomain subDomain = simTask.getSimulation().getMathDescription().getSubDomain(var.getDomain().getName());
                            if (subDomain instanceof CompartmentSubDomain) {
                                varType = VariableType.VOLUME;
                            } else if (subDomain instanceof MembraneSubDomain) {
                                varType = VariableType.MEMBRANE;
                            } else if (subDomain instanceof FilamentSubDomain) {
                                throw new RuntimeException("filament subdomains not supported");
                            } else if (subDomain instanceof PointSubDomain) {
                                varType = VariableType.POINT_VARIABLE;
                            }
                        }
                        dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), varType, var.getDomain()));
                    } else if (var instanceof Constant) {
                        System.out.println("ignoring Constant " + var.getName());
                    } else if (var instanceof InsideVariable) {
                        System.out.println("ignoring InsideVariable " + var.getName());
                    } else if (var instanceof OutsideVariable) {
                        System.out.println("ignoring OutsideVariable " + var.getName());
                    } else {
                        throw new RuntimeException("unexpected variable " + var.getName() + " of type " + var.getClass().getName());
                    }
                }
            } catch (XmlParseException | ExpressionException e) {
                e.printStackTrace();
                throw new RuntimeException("failed to read sim task file, msg: " + e.getMessage(), e);
            }
        }
    }
    DataIdentifier[] dis = new DataIdentifier[dataSetIdentifierList.size()];
    for (int i = 0; i < dataSetIdentifierList.size(); i++) {
        DataSetIdentifier dsi = (DataSetIdentifier) dataSetIdentifierList.elementAt(i);
        String displayName = dsi.getName();
        if (dsi.isFunction()) {
            AnnotatedFunction f = null;
            for (int j = 0; j < annotatedFunctionList.size(); j++) {
                AnnotatedFunction function = (AnnotatedFunction) annotatedFunctionList.elementAt(j);
                if (function.getName().equals(dsi.getName())) {
                    f = function;
                    break;
                }
            }
            if (f != null) {
                displayName = f.getDisplayName();
            }
        }
        dis[i] = new DataIdentifier(dsi.getName(), dsi.getVariableType(), dsi.getDomain(), dsi.isFunction(), displayName);
    }
    return dis;
}

Example 22 with AnnotatedFunction

use of cbit.vcell.solver.AnnotatedFunction in project vcell by virtualcell.

the class SimulationData method refreshDataProcessingOutputInfo.

private void refreshDataProcessingOutputInfo(OutputContext outputContext) throws DataAccessException {
    File dataProcessingOutputFile = getDataProcessingOutputSourceFileHDF5();
    if (dataProcessingOutputInfo == null && !dataProcessingOutputFile.exists()) {
        return;
    }
    AnnotatedFunction[] lastFunctions = (lastOutputContext == null ? null : lastOutputContext.getOutputFunctions());
    AnnotatedFunction[] currentFunctions = (outputContext == null ? null : outputContext.getOutputFunctions());
    boolean bFunctionsEqual = Compare.isEqualOrNull(lastFunctions, currentFunctions);
    if (!bFunctionsEqual || dataProcessingOutputInfo == null || lastDataProcessingOutputInfoTime != dataProcessingOutputFile.lastModified()) {
        lastDataProcessingOutputInfoTime = dataProcessingOutputFile.lastModified();
        lastOutputContext = outputContext;
        DataProcessingOutputInfoOP dataProcessingOutputInfoOP = new DataProcessingOutputInfoOP(vcDataId, false, outputContext);
        try {
            dataProcessingOutputInfo = (DataProcessingOutputInfo) DataSetControllerImpl.getDataProcessingOutput(dataProcessingOutputInfoOP, dataProcessingOutputFile);
        } catch (Exception e) {
            throw new DataAccessException(e.getMessage(), (e.getCause() == null ? e : e.getCause()));
        }
    }
}

Example 23 with AnnotatedFunction

use of cbit.vcell.solver.AnnotatedFunction in project vcell by virtualcell.

the class DisplayTimeSeriesOp method getDataSetControllerProvider.

private DataSetControllerProvider getDataSetControllerProvider(final ImageTimeSeries<? extends Image> imageTimeSeries, final PDEDataViewer pdeDataViewer) throws ImageException, IOException {
    ISize size = imageTimeSeries.getISize();
    int dimension = (size.getZ() > 0) ? (3) : (2);
    Extent extent = imageTimeSeries.getExtent();
    Origin origin = imageTimeSeries.getAllImages()[0].getOrigin();
    // don't care ... no surfaces
    double filterCutoffFrequency = 0.5;
    VCImage vcImage = new VCImageUncompressed(null, new byte[size.getXYZ()], extent, size.getX(), size.getY(), size.getZ());
    RegionImage regionImage = new RegionImage(vcImage, dimension, extent, origin, filterCutoffFrequency);
    final CartesianMesh mesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, size, regionImage);
    final DataIdentifier dataIdentifier = new DataIdentifier("var", VariableType.VOLUME, new Domain("domain"), false, "var");
    final DataSetController dataSetController = new DataSetController() {

        @Override
        public ExportEvent makeRemoteFile(OutputContext outputContext, ExportSpecs exportSpecs) throws DataAccessException, RemoteProxyException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public TimeSeriesJobResults getTimeSeriesValues(OutputContext outputContext, VCDataIdentifier vcdataID, TimeSeriesJobSpec timeSeriesJobSpec) throws RemoteProxyException, DataAccessException {
            pdeDataViewer.dataJobMessage(new DataJobEvent(timeSeriesJobSpec.getVcDataJobID(), MessageEvent.DATA_START, vcdataID.getDataKey(), vcdataID.getID(), new Double(0)));
            if (!timeSeriesJobSpec.isCalcSpaceStats() && !timeSeriesJobSpec.isCalcTimeStats()) {
                int[][] indices = timeSeriesJobSpec.getIndices();
                double[] timeStamps = imageTimeSeries.getImageTimeStamps();
                // [var][dataindex+1][timeindex]
                double[][][] dataValues = new double[1][indices[0].length + 1][timeStamps.length];
                for (int timeIndex = 0; timeIndex < timeStamps.length; timeIndex++) {
                    // index 0 is time
                    dataValues[0][0][timeIndex] = timeStamps[timeIndex];
                }
                for (int timeIndex = 0; timeIndex < timeStamps.length; timeIndex++) {
                    float[] pixelValues = imageTimeSeries.getAllImages()[timeIndex].getFloatPixels();
                    for (int samplePointIndex = 0; samplePointIndex < indices[0].length; samplePointIndex++) {
                        int pixelIndex = indices[0][samplePointIndex];
                        dataValues[0][samplePointIndex + 1][timeIndex] = pixelValues[pixelIndex];
                    }
                }
                TSJobResultsNoStats timeSeriesJobResults = new TSJobResultsNoStats(new String[] { "var" }, indices, timeStamps, dataValues);
                pdeDataViewer.dataJobMessage(new DataJobEvent(timeSeriesJobSpec.getVcDataJobID(), MessageEvent.DATA_COMPLETE, vcdataID.getDataKey(), vcdataID.getID(), new Double(0)));
                return timeSeriesJobResults;
            }
            return null;
        }

        @Override
        public SimDataBlock getSimDataBlock(OutputContext outputContext, VCDataIdentifier vcdataID, String varName, double time) throws RemoteProxyException, DataAccessException {
            double timePoint = time;
            double[] timePoints = getDataSetTimes(vcdataID);
            int index = -1;
            for (int i = 0; i < timePoints.length; i++) {
                if (timePoint == timePoints[i]) {
                    index = i;
                    break;
                }
            }
            double[] data = imageTimeSeries.getAllImages()[index].getDoublePixels();
            PDEDataInfo pdeDataInfo = new PDEDataInfo(null, null, varName, time, 0);
            VariableType varType = VariableType.VOLUME;
            return new SimDataBlock(pdeDataInfo, data, varType);
        }

        @Override
        public boolean getParticleDataExists(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
            return false;
        }

        @Override
        public ParticleDataBlock getParticleDataBlock(VCDataIdentifier vcdataID, double time) throws DataAccessException, RemoteProxyException {
            return null;
        }

        @Override
        public ODESimData getODEData(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
            return null;
        }

        @Override
        public CartesianMesh getMesh(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            return mesh;
        }

        @Override
        public PlotData getLineScan(OutputContext outputContext, VCDataIdentifier vcdataID, String variable, double time, SpatialSelection spatialSelection) throws RemoteProxyException, DataAccessException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public AnnotatedFunction[] getFunctions(OutputContext outputContext, VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
            return new AnnotatedFunction[0];
        }

        @Override
        public double[] getDataSetTimes(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            return imageTimeSeries.getImageTimeStamps();
        }

        @Override
        public DataSetTimeSeries getDataSetTimeSeries(VCDataIdentifier vcdataID, String[] variableNames) throws DataAccessException, RemoteProxyException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public DataSetMetadata getDataSetMetadata(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public DataIdentifier[] getDataIdentifiers(OutputContext outputContext, VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            return new DataIdentifier[] { dataIdentifier };
        }

        @Override
        public FieldDataFileOperationResults fieldDataFileOperation(FieldDataFileOperationSpec fieldDataFileOperationSpec) throws RemoteProxyException, DataAccessException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public DataOperationResults doDataOperation(DataOperation dataOperation) throws DataAccessException, RemoteProxyException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public VtuFileContainer getEmptyVtuMeshFiles(VCDataIdentifier vcdataID, int timeIndex) throws RemoteProxyException, DataAccessException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public double[] getVtuTimes(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public double[] getVtuMeshData(OutputContext outputContext, VCDataIdentifier vcdataID, VtuVarInfo var, double time) throws RemoteProxyException, DataAccessException {
            // TODO Auto-generated method stub
            return null;
        }

        @Override
        public VtuVarInfo[] getVtuVarInfos(OutputContext outputContext, VCDataIdentifier vcDataIdentifier) throws DataAccessException, RemoteProxyException {
            // TODO Auto-generated method stub
            return null;
        }

        @Override
        public NFSimMolecularConfigurations getNFSimMolecularConfigurations(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            // TODO Auto-generated method stub
            return null;
        }
    };
    DataSetControllerProvider dataSetControllerProvider = new DataSetControllerProvider() {

        @Override
        public DataSetController getDataSetController() throws DataAccessException {
            return dataSetController;
        }
    };
    return dataSetControllerProvider;
}

Example 24 with AnnotatedFunction

use of cbit.vcell.solver.AnnotatedFunction in project vcell by virtualcell.

the class NagiosVCellMonitor method checkVCell.

private CheckResults checkVCell(VCELL_CHECK_LEVEL checkLevel, String rmiHostName, int rmiPort, String rmiBootstrapStubName, String vcellNagiosPassword, int criticalTimeout, int monitorPort) throws Exception {
    SimulationStatusPersistent lastSimStatus = null;
    String vcellVersion = null;
    TreeMap<VCELL_CHECK_LEVEL, Long> levelTimesMillisec = new TreeMap<NagiosVCellMonitor.VCELL_CHECK_LEVEL, Long>();
    long startTime = System.currentTimeMillis();
    VCellConnection vcellConnection = null;
    try {
        if (rmiHostName == null || rmiPort == -1) {
            throw new UnexpectedTestStateException("Host name/ip and rmiPort required for testing, rmihostname=" + rmiHostName + " rmiport=" + rmiPort);
        }
        String rmiUrl = "//" + rmiHostName + ":" + rmiPort + "/" + rmiBootstrapStubName;
        VCellBootstrap vcellBootstrap = null;
        try {
            vcellBootstrap = (VCellBootstrap) Naming.lookup(rmiUrl);
        } catch (Exception e) {
            throw new UnexpectedTestStateException("Error during bootstrap lookup, " + e.getClass().getSimpleName() + " " + e.getMessage());
        }
        vcellVersion = vcellBootstrap.getVCellSoftwareVersion();
        levelTimesMillisec.put(VCELL_CHECK_LEVEL.RMI_ONLY_0, System.currentTimeMillis() - startTime);
        if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.CONNECT_1.ordinal()) {
            if (vcellNagiosPassword == null) {
                throw new UnexpectedTestStateException("vcellNagios Password required for " + VCELL_CHECK_LEVEL.CONNECT_1.toString() + " and above");
            }
            UserLoginInfo userLoginInfo = new UserLoginInfo(VCELL_NAGIOS_USER, new DigestedPassword(vcellNagiosPassword));
            vcellConnection = vcellBootstrap.getVCellConnection(userLoginInfo);
            levelTimesMillisec.put(VCELL_CHECK_LEVEL.CONNECT_1, System.currentTimeMillis() - startTime - levelTimesMillisec.get(VCELL_CHECK_LEVEL.RMI_ONLY_0));
            if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.INFOS_2.ordinal()) {
                VCInfoContainer vcInfoContainer = vcellConnection.getUserMetaDbServer().getVCInfoContainer();
                levelTimesMillisec.put(VCELL_CHECK_LEVEL.INFOS_2, System.currentTimeMillis() - startTime - levelTimesMillisec.get(VCELL_CHECK_LEVEL.CONNECT_1));
                if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.LOAD_3.ordinal()) {
                    KeyValue bioModelKey = null;
                    final String testModelName = "Solver Suite 5.1 (BETA only ode)";
                    for (BioModelInfo bioModelInfo : vcInfoContainer.getBioModelInfos()) {
                        if (userLoginInfo.getUserName().equals(bioModelInfo.getVersion().getOwner().getName()) && bioModelInfo.getVersion().getName().equals(testModelName)) {
                            bioModelKey = bioModelInfo.getVersion().getVersionKey();
                            break;
                        }
                    }
                    BigString bioModelXML = vcellConnection.getUserMetaDbServer().getBioModelXML(bioModelKey);
                    BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
                    bioModel.refreshDependencies();
                    levelTimesMillisec.put(VCELL_CHECK_LEVEL.LOAD_3, System.currentTimeMillis() - startTime - levelTimesMillisec.get(VCELL_CHECK_LEVEL.INFOS_2));
                    if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.DATA_4.ordinal()) {
                        final String testSimContextName = "non-spatial ODE";
                        SimulationContext simulationContext = bioModel.getSimulationContext(testSimContextName);
                        final String testSimName = "Copy of combined ida/cvode";
                        Simulation simulation = simulationContext.getSimulation(testSimName);
                        if (simulation == null) {
                            throw new UnexpectedTestStateException("Couldn't find sim '" + testSimName + "' for " + checkLevel.toString());
                        }
                        VCSimulationDataIdentifier vcSimulationDataIdentifier = new VCSimulationDataIdentifier(simulation.getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), 0);
                        ArrayList<AnnotatedFunction> outputFunctionsList = simulationContext.getOutputFunctionContext().getOutputFunctionsList();
                        OutputContext outputContext = new OutputContext(outputFunctionsList.toArray(new AnnotatedFunction[outputFunctionsList.size()]));
                        double[] times = vcellConnection.getDataSetController().getDataSetTimes(vcSimulationDataIdentifier);
                        ODESimData odeSimData = vcellConnection.getDataSetController().getODEData(vcSimulationDataIdentifier);
                        levelTimesMillisec.put(VCELL_CHECK_LEVEL.DATA_4, System.currentTimeMillis() - startTime - levelTimesMillisec.get(VCELL_CHECK_LEVEL.LOAD_3));
                        if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.RUN_5.ordinal()) {
                            KeyValue copy1Key = null;
                            KeyValue copy2Key = null;
                            VCSimulationIdentifier testRunSimID = null;
                            try {
                                if (simulationContext.getSimulations().length != 1) {
                                    throw new UnexpectedTestStateException("Expecting only 1 sim to be copied for " + checkLevel.toString());
                                }
                                SimulationStatusPersistent simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(simulation.getVersion().getVersionKey());
                                if (!simulationStatus.isCompleted()) {
                                    throw new UnexpectedTestStateException("Expecting completed sim to copy for " + checkLevel.toString());
                                }
                                String copyModelName = testModelName + "_" + rmiHostName + "_rmi" + rmiPort + "_siteprt" + monitorPort;
                                boolean bForceCleanup = true;
                                while (true) {
                                    boolean bMessy = false;
                                    for (BioModelInfo bioModelInfo : vcInfoContainer.getBioModelInfos()) {
                                        if (userLoginInfo.getUserName().equals(bioModelInfo.getVersion().getOwner().getName()) && bioModelInfo.getVersion().getName().equals(copyModelName)) {
                                            bMessy = true;
                                            if (bForceCleanup) {
                                                try {
                                                    vcellConnection.getUserMetaDbServer().deleteBioModel(bioModelInfo.getVersion().getVersionKey());
                                                } catch (Exception e) {
                                                    e.printStackTrace();
                                                }
                                            } else {
                                                throw new MessyTestEnvironmentException("Messy test environment, not expecting " + copyModelName + " and couldn't cleanup");
                                            }
                                        }
                                    }
                                    if (!bMessy) {
                                        break;
                                    }
                                    // get new vcInfoContainer without cleaned-up model
                                    vcInfoContainer = vcellConnection.getUserMetaDbServer().getVCInfoContainer();
                                    bForceCleanup = false;
                                }
                                BigString copyBioModelXMLStr = vcellConnection.getUserMetaDbServer().saveBioModelAs(bioModelXML, copyModelName, null);
                                BioModel copyBioModel = XmlHelper.XMLToBioModel(new XMLSource(copyBioModelXMLStr.toString()));
                                copy1Key = copyBioModel.getVersion().getVersionKey();
                                copyBioModel.refreshDependencies();
                                Simulation copySim = copyBioModel.getSimulationContext(testSimContextName).copySimulation(copyBioModel.getSimulationContext(testSimContextName).getSimulation(testSimName));
                                final String copyTestSimName = "test";
                                copySim.setName(copyTestSimName);
                                copyBioModel.refreshDependencies();
                                copyBioModelXMLStr = new BigString(XmlHelper.bioModelToXML(copyBioModel));
                                copyBioModelXMLStr = vcellConnection.getUserMetaDbServer().saveBioModel(copyBioModelXMLStr, null);
                                copyBioModel = XmlHelper.XMLToBioModel(new XMLSource(copyBioModelXMLStr.toString()));
                                copy2Key = copyBioModel.getVersion().getVersionKey();
                                copyBioModel.refreshDependencies();
                                Simulation newSimulation = copyBioModel.getSimulationContext(testSimContextName).getSimulation(copyTestSimName);
                                simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(newSimulation.getVersion().getVersionKey());
                                if (simulationStatus != null && !simulationStatus.isNeverRan()) {
                                    throw new UnexpectedTestStateException("Expecting new sim to have 'never ran' status for " + checkLevel.toString());
                                }
                                testRunSimID = new VCSimulationIdentifier(newSimulation.getVersion().getVersionKey(), copyBioModel.getVersion().getOwner());
                                vcellConnection.getSimulationController().startSimulation(testRunSimID, 1);
                                lastSimStatus = simulationStatus;
                                MessageEvent[] messageEvents = null;
                                while (simulationStatus == null || (!simulationStatus.isStopped() && !simulationStatus.isCompleted() && !simulationStatus.isFailed())) {
                                    Thread.sleep(200);
                                    if (((System.currentTimeMillis() - startTime) / 1000) > criticalTimeout) {
                                        vcellConnection.getSimulationController().stopSimulation(testRunSimID);
                                        vcellConnection.getMessageEvents();
                                        break;
                                    }
                                    simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(newSimulation.getVersion().getVersionKey());
                                    if (simulationStatus != null && !simulationStatus.toString().equals((lastSimStatus == null ? null : lastSimStatus.toString()))) {
                                        lastSimStatus = simulationStatus;
                                    }
                                    if (simulationStatus != null && simulationStatus.isFailed()) {
                                        throw new Exception("time " + ((System.currentTimeMillis() - startTime) / 1000) + ", Sim execution failed key:" + testRunSimID.getSimulationKey() + " sim " + newSimulation.getName() + " model " + copyBioModel.getVersion().getName() + " messg " + simulationStatus.getFailedMessage());
                                    }
                                    messageEvents = vcellConnection.getMessageEvents();
                                }
                            } finally {
                                try {
                                    if (copy1Key != null) {
                                        vcellConnection.getUserMetaDbServer().deleteBioModel(copy1Key);
                                    }
                                } catch (Exception e) {
                                    e.printStackTrace();
                                }
                                try {
                                    if (copy2Key != null) {
                                        vcellConnection.getUserMetaDbServer().deleteBioModel(copy2Key);
                                    }
                                } catch (Exception e) {
                                    e.printStackTrace();
                                }
                                if (testRunSimID != null) {
                                    deleteSimData(testRunSimID);
                                }
                            }
                            levelTimesMillisec.put(VCELL_CHECK_LEVEL.RUN_5, System.currentTimeMillis() - startTime - levelTimesMillisec.get(VCELL_CHECK_LEVEL.DATA_4));
                        }
                    }
                }
            }
        }
        return new CheckResults(vcellVersion, levelTimesMillisec, lastSimStatus, System.currentTimeMillis() - startTime, null);
    } catch (Exception e) {
        return new CheckResults(vcellVersion, levelTimesMillisec, lastSimStatus, System.currentTimeMillis() - startTime, e);
    } finally {
        vcellConnection = null;
    }
}

Example 25 with AnnotatedFunction

use of cbit.vcell.solver.AnnotatedFunction in project vcell by virtualcell.

the class StandaloneRuleBasedTest method checkNonspatialStochasticSimContext.

private static void checkNonspatialStochasticSimContext(SimulationContext srcSimContext, File baseDirectory, int numTrials, long bngTimeoutDuration) throws Exception {
    if (!srcSimContext.getApplicationType().equals(Application.NETWORK_STOCHASTIC) || srcSimContext.getGeometry().getDimension() != 0) {
        throw new RuntimeException("simContext is of type " + srcSimContext.getApplicationType() + " and geometry dimension of " + srcSimContext.getGeometry().getDimension() + ", expecting nonspatial stochastic");
    }
    BioModel origBioModel = srcSimContext.getBioModel();
    BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(XmlHelper.bioModelToXML(origBioModel)));
    bioModel.refreshDependencies();
    // create ODE and RuleBased
    SimulationContext newODEApp = SimulationContext.copySimulationContext(srcSimContext, "aUniqueNewODEApp", false, Application.NETWORK_DETERMINISTIC);
    SimulationContext newRuleBasedApp = SimulationContext.copySimulationContext(srcSimContext, "aUniqueNewRuleBasedApp", false, Application.RULE_BASED_STOCHASTIC);
    newODEApp.setBioModel(bioModel);
    newRuleBasedApp.setBioModel(bioModel);
    ArrayList<AnnotatedFunction> outputFunctionsList = srcSimContext.getOutputFunctionContext().getOutputFunctionsList();
    // OutputContext outputContext = new OutputContext(outputFunctionsList.toArray(new AnnotatedFunction[outputFunctionsList.size()]));
    newODEApp.getOutputFunctionContext().setOutputFunctions(outputFunctionsList);
    newRuleBasedApp.getOutputFunctionContext().setOutputFunctions(outputFunctionsList);
    NetworkGenerationRequirements networkGenRequirements = NetworkGenerationRequirements.getComputeFull(bngTimeoutDuration);
    bioModel.addSimulationContext(newODEApp);
    newODEApp.refreshMathDescription(new MathMappingCallbackTaskAdapter(null), networkGenRequirements);
    bioModel.addSimulationContext(newRuleBasedApp);
    newRuleBasedApp.refreshMathDescription(new MathMappingCallbackTaskAdapter(null), networkGenRequirements);
    srcSimContext.refreshMathDescription(new MathMappingCallbackTaskAdapter(null), networkGenRequirements);
    // Create non-spatialStoch, ODE and RuleBased sims
    Simulation nonspatialStochAppNewSim = srcSimContext.addNewSimulation(STOCH_SIM_NAME, /*SimulationOwner.DEFAULT_SIM_NAME_PREFIX*/
    new MathMappingCallbackTaskAdapter(null), networkGenRequirements);
    Simulation newODEAppNewSim = newODEApp.addNewSimulation(ODE_SIM_NAME, new MathMappingCallbackTaskAdapter(null), networkGenRequirements);
    Simulation newRuleBasedAppNewSim = newRuleBasedApp.addNewSimulation(NFS_SIM_NAME, new MathMappingCallbackTaskAdapter(null), networkGenRequirements);
    nonspatialStochAppNewSim.setSimulationOwner(srcSimContext);
    newODEAppNewSim.setSimulationOwner(newODEApp);
    newRuleBasedAppNewSim.setSimulationOwner(newRuleBasedApp);
    try {
        bioModel.getModel().getSpeciesContexts();
        ArrayList<String> varNameList = new ArrayList<String>();
        for (SpeciesContextSpec scs : srcSimContext.getReactionContext().getSpeciesContextSpecs()) {
            varNameList.add(scs.getSpeciesContext().getName());
        }
        String[] varNames = varNameList.toArray(new String[0]);
        OutputTimeSpec outputTimeSpec = nonspatialStochAppNewSim.getSolverTaskDescription().getOutputTimeSpec();
        ArrayList<Double> sampleTimeList = new ArrayList<Double>();
        if (outputTimeSpec instanceof UniformOutputTimeSpec) {
            double endingTime = nonspatialStochAppNewSim.getSolverTaskDescription().getTimeBounds().getEndingTime();
            double dT = ((UniformOutputTimeSpec) outputTimeSpec).getOutputTimeStep();
            int currTimeIndex = 0;
            while (currTimeIndex * dT <= (endingTime + 1e-8)) {
                sampleTimeList.add(currTimeIndex * dT);
                currTimeIndex++;
            }
        }
        double[] sampleTimes = new double[sampleTimeList.size()];
        for (int i = 0; i < sampleTimes.length; i++) {
            sampleTimes[i] = sampleTimeList.get(i);
        }
        TimeSeriesMultitrialData sampleDataStoch1 = new TimeSeriesMultitrialData("stochastic1", varNames, sampleTimes, numTrials);
        TimeSeriesMultitrialData sampleDataStoch2 = new TimeSeriesMultitrialData("stochastic2", varNames, sampleTimes, numTrials);
        TimeSeriesMultitrialData sampleDataDeterministic = new TimeSeriesMultitrialData("determinstic", varNames, sampleTimes, 1);
        runsolver(nonspatialStochAppNewSim, baseDirectory, numTrials, sampleDataStoch1);
        runsolver(newODEAppNewSim, baseDirectory, 1, sampleDataDeterministic);
        runsolver(newRuleBasedAppNewSim, baseDirectory, numTrials, sampleDataStoch2);
        StochtestFileUtils.writeVarDiffData(new File(baseDirectory, VARDIFF_FILE), sampleDataStoch1, sampleDataStoch2);
        StochtestFileUtils.writeKolmogorovSmirnovTest(new File(baseDirectory, KS_TEST_FILE), sampleDataStoch1, sampleDataStoch2);
        StochtestFileUtils.writeChiSquareTest(new File(baseDirectory, ChiSquared_TEST_FILE), sampleDataStoch1, sampleDataStoch2);
        StochtestFileUtils.writeData(sampleDataStoch1, new File(baseDirectory, "data." + sampleDataStoch1.datasetName + ".json"));
        StochtestFileUtils.writeData(sampleDataStoch2, new File(baseDirectory, "data." + sampleDataStoch2.datasetName + ".json"));
        StochtestFileUtils.writeData(sampleDataDeterministic, new File(baseDirectory, "data." + sampleDataDeterministic.datasetName + ".json"));
    } finally {
        srcSimContext.removeSimulation(nonspatialStochAppNewSim);
        newODEApp.removeSimulation(newODEAppNewSim);
        newRuleBasedApp.removeSimulation(newRuleBasedAppNewSim);
    }
}