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

Example 91 with BioModel

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

the class SimulationContext method getUnitInfo.

/**
 * SimulationContext constructor.
 * This constructor differs with the previous one with one more boolean input parameter, which specifies whether
 * the new application is a stochastic application or not.
 */
// @Deprecated
// public SimulationContext(Model model, Geometry geometry, boolean bStoch, boolean bRuleBased) throws PropertyVetoException {
// this(model,geometry,null,null,legacyType(bStoch, bRuleBased));
// }
@Override
public UnitInfo getUnitInfo() throws UnsupportedOperationException {
    if (unitInfo != null) {
        return unitInfo;
    }
    if (bioModel == null) {
        throw new UnsupportedOperationException("bioModel not set yet");
    }
    Model m = bioModel.getModel();
    ModelUnitSystem unitSys = m.getUnitSystem();
    VCUnitDefinition tu = unitSys.getTimeUnit();
    String sym = tu.getSymbol();
    unitInfo = new UnitInfo(sym);
    return unitInfo;
}

Example 92 with BioModel

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

the class TestingFrameworkWindowManager method generateTestCaseReport.

/**
 * Insert the method's description here.
 * Creation date: (8/18/2003 5:36:47 PM)
 */
public String generateTestCaseReport(TestCaseNew testCase, TestCriteriaNew onlyThisTCrit, ClientTaskStatusSupport pp, TFGenerateReport.VCDocumentAndSimInfo userDefinedRefSimInfo) {
    StringBuffer reportTCBuffer = new StringBuffer();
    if (testCase == null) {
        reportTCBuffer.append("\n\tTEST CASE :\tERROR: Test Case is NULL\n");
    } else {
        pp.setMessage(testCase.getVersion().getName() + " " + testCase.getType() + " Getting Simulations");
        // Get the Simulations
        Simulation[] sims = null;
        reportTCBuffer.append("\n\tTEST CASE : " + (testCase.getVersion() != null ? testCase.getVersion().getName() : "Null") + "\n\tAnnotation : " + testCase.getAnnotation() + "\n");
        try {
            if (testCase instanceof TestCaseNewMathModel) {
                MathModelInfo mmInfo = ((TestCaseNewMathModel) testCase).getMathModelInfo();
                MathModel mathModel = getRequestManager().getDocumentManager().getMathModel(mmInfo);
                sims = mathModel.getSimulations();
                reportTCBuffer.append("\tMathModel : " + mmInfo.getVersion().getName() + ", " + mmInfo.getVersion().getDate().toString() + "\n");
            } else if (testCase instanceof TestCaseNewBioModel) {
                TestCaseNewBioModel bioTestCase = (TestCaseNewBioModel) testCase;
                // bioTestCase.
                BioModelInfo bmInfo = bioTestCase.getBioModelInfo();
                BioModel bioModel = getRequestManager().getDocumentManager().getBioModel(bmInfo);
                SimulationContext[] simContextArr = bioModel.getSimulationContexts();
                if (simContextArr != null && simContextArr.length > 0) {
                    SimulationContext simContext = null;
                    for (int i = 0; i < simContextArr.length; i += 1) {
                        if (simContextArr[i].getVersion().getVersionKey().compareEqual(bioTestCase.getSimContextKey())) {
                            simContext = simContextArr[i];
                            break;
                        }
                    }
                    if (simContext != null) {
                        sims = bioModel.getSimulations(simContext);
                        reportTCBuffer.append("\tBioModel : " + bmInfo.getVersion().getName() + ", " + bmInfo.getVersion().getDate().toString() + "\n");
                    }
                }
            }
            if (sims == null || sims.length == 0) {
                reportTCBuffer.append("\tERROR " + "No sims found for TestCase " + (testCase.getVersion() != null ? "name=" + testCase.getVersion().getName() : "key=" + testCase.getTCKey()) + "\n");
            }
            if (testCase.getTestCriterias() == null || sims.length != testCase.getTestCriterias().length) {
                reportTCBuffer.append("\tNote " + "Num sims=" + sims.length + " does not match testCriteria length=" + (testCase.getTestCriterias() != null ? testCase.getTestCriterias().length + "" : "null") + " for TestCase " + (testCase.getVersion() != null ? "name=" + testCase.getVersion().getName() : "key=" + testCase.getTCKey()) + "\n");
            }
            // Sort
            if (sims.length > 0) {
                java.util.Arrays.sort(sims, new java.util.Comparator<Simulation>() {

                    public int compare(Simulation si1, Simulation si2) {
                        return si1.getName().compareTo(si2.getName());
                    }

                    public boolean equals(Object obj) {
                        return false;
                    }
                });
            }
            TestCriteriaNew[] testCriterias = (onlyThisTCrit != null ? new TestCriteriaNew[] { onlyThisTCrit } : testCase.getTestCriterias());
            for (int k = 0; k < sims.length; k++) {
                TestCriteriaNew testCriteria = getMatchingTestCriteria(sims[k], testCriterias);
                if (testCriteria != null) {
                    pp.setMessage((testCase instanceof TestCaseNewMathModel ? "(MM)" : "(BM)") + " " + (onlyThisTCrit == null ? "sim " + (k + 1) + " of " + sims.length : "sim=" + onlyThisTCrit.getSimInfo().getName()) + "  " + testCase.getVersion().getName() + " " + testCase.getType());
                    reportTCBuffer.append(generateTestCriteriaReport(testCase, testCriteria, sims[k], userDefinedRefSimInfo));
                }
            }
        } catch (UserCancelException e) {
            throw e;
        } catch (Throwable e) {
            e.printStackTrace();
            reportTCBuffer.append("\tERROR " + e.getClass().getName() + " mesg=" + e.getMessage() + "\n");
            try {
                if (onlyThisTCrit != null) {
                    updateTCritStatus(onlyThisTCrit, TestCriteriaNew.TCRIT_STATUS_RPERROR, "TestCase Error " + e.getClass().getName() + " " + e.getMessage());
                } else if (testCase.getTestCriterias() != null) {
                    for (int i = 0; i < testCase.getTestCriterias().length; i += 1) {
                        updateTCritStatus(testCase.getTestCriterias()[i], TestCriteriaNew.TCRIT_STATUS_RPERROR, "TestCase Error " + e.getClass().getName() + " " + e.getMessage());
                    }
                }
            } catch (Throwable e2) {
            // 
            }
        }
    }
    return reportTCBuffer.toString();
}

Example 93 with BioModel

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

the class TestingFrameworkWindowManager method getUserSelectedRefSimInfo.

public SimulationInfo getUserSelectedRefSimInfo(RequestManager currentRequstManager, VCDocumentInfo vcDocInfo) throws Exception {
    final int MODELTYPE_INDEX = 0;
    final int MODELKEY_INDEX = 2;
    final int SIMNAME_INDEX = 5;
    final String[] ROWDATACOLNAMES = new String[] { "Type", "Model", "Model Key", "Owner", "App", "Sim", "Date" };
    Vector<Object[]> simInfoV = new Vector<Object[]>();
    // BioModelMetaData[] bmMetaDataArr = getRequestManager().getDocumentManager().getSessionManager().getUserMetaDbServer().getBioModelMetaDatas(true);
    // bmMetaDataArr[0].
    BioModelInfo[] bioModelInfoArr = null;
    if (vcDocInfo == null) {
        bioModelInfoArr = currentRequstManager.getDocumentManager().getBioModelInfos();
    } else if (vcDocInfo instanceof BioModelInfo) {
        bioModelInfoArr = new BioModelInfo[] { (BioModelInfo) vcDocInfo };
    }
    for (int i = 0; bioModelInfoArr != null && i < bioModelInfoArr.length; i++) {
        if (bioModelInfoArr[i].getBioModelChildSummary() != null) {
            String[] bmSimContextNamesArr = bioModelInfoArr[i].getBioModelChildSummary().getSimulationContextNames();
            for (int j = 0; bmSimContextNamesArr != null && j < bmSimContextNamesArr.length; j++) {
                String[] bmSimNamesArr = bioModelInfoArr[i].getBioModelChildSummary().getSimulationNames(bmSimContextNamesArr[j]);
                for (int k = 0; bmSimNamesArr != null && k < bmSimNamesArr.length; k++) {
                    // System.out.println("BM "+
                    // bioModelInfoArr[i].getVersion().getOwner().getName()+" "+
                    // bioModelInfoArr[i].getVersion().getName()+
                    // " app="+bmSimContextNamesArr[j]+
                    // " sim="+bmSimNamesArr[k]);
                    simInfoV.add(new Object[] { "BM", bioModelInfoArr[i].getVersion().getName(), bioModelInfoArr[i].getVersion().getVersionKey(), bioModelInfoArr[i].getVersion().getOwner().getName(), bmSimContextNamesArr[j], bmSimNamesArr[k], bioModelInfoArr[i].getVersion().getDate() });
                }
            }
        }
    }
    MathModelInfo[] mathModelInfoArr = null;
    if (vcDocInfo == null) {
        mathModelInfoArr = currentRequstManager.getDocumentManager().getMathModelInfos();
    } else if (vcDocInfo instanceof MathModelInfo) {
        mathModelInfoArr = new MathModelInfo[] { (MathModelInfo) vcDocInfo };
    }
    for (int i = 0; mathModelInfoArr != null && i < mathModelInfoArr.length; i++) {
        if (mathModelInfoArr[i].getMathModelChildSummary() != null) {
            String[] mathSimNamesArr = mathModelInfoArr[i].getMathModelChildSummary().getSimulationNames();
            for (int j = 0; mathSimNamesArr != null && j < mathSimNamesArr.length; j++) {
                // System.out.println("MM "+
                // mathModelInfoArr[i].getVersion().getOwner().getName()+" "+
                // mathModelInfoArr[i].getVersion().getName()+
                // " sim="+mathSimNamesArr[j]);
                simInfoV.add(new Object[] { "MM", mathModelInfoArr[i].getVersion().getName(), mathModelInfoArr[i].getVersion().getVersionKey(), mathModelInfoArr[i].getVersion().getOwner().getName(), null, mathSimNamesArr[j], mathModelInfoArr[i].getVersion().getDate() });
            }
        }
    }
    Object[][] rowData = new Object[simInfoV.size()][ROWDATACOLNAMES.length];
    simInfoV.copyInto(rowData);
    int[] simSelection = DialogUtils.showComponentOKCancelTableList(getComponent(), "Choose Ref Simulation", ROWDATACOLNAMES, rowData, ListSelectionModel.SINGLE_SELECTION);
    if (simSelection == null || simSelection.length == 0) {
        throw UserCancelException.CANCEL_GENERIC;
    }
    Simulation[] simArr = null;
    if (rowData[simSelection[0]][MODELTYPE_INDEX].equals("BM")) {
        BioModel bm = currentRequstManager.getDocumentManager().getBioModel((KeyValue) rowData[simSelection[0]][MODELKEY_INDEX]);
        simArr = bm.getSimulations();
    } else {
        MathModel mm = currentRequstManager.getDocumentManager().getMathModel((KeyValue) rowData[simSelection[0]][MODELKEY_INDEX]);
        simArr = mm.getSimulations();
    }
    for (int i = 0; simArr != null && i < simArr.length; i++) {
        if (simArr[i].getName().equals(rowData[simSelection[0]][SIMNAME_INDEX])) {
            return simArr[i].getSimulationInfo();
        }
    }
    throw new Exception("Couldn't find selected simulation");
}

Example 94 with BioModel

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

the class TestingFrameworkWindowManager method generateTestCriteriaReport.

/**
 * Insert the method's description here.
 * Creation date: (8/18/2003 5:36:47 PM)
 */
private String generateTestCriteriaReport(TestCaseNew testCase, TestCriteriaNew testCriteria, Simulation testSim, TFGenerateReport.VCDocumentAndSimInfo userSelectedRefSimInfo) /*,VCDocument refDoc,VCDocument testDocument*/
{
    if (testSim.getScanCount() != 1) {
        throw new RuntimeException("paramater scan is not supported in Math Testing Framework");
    }
    SimulationSymbolTable simSymbolTable = new SimulationSymbolTable(testSim, 0);
    String simReportStatus = null;
    String simReportStatusMessage = null;
    StringBuffer reportTCBuffer = new StringBuffer();
    VariableComparisonSummary[] failVarSummaries = null;
    VariableComparisonSummary[] allVarSummaries = null;
    double absErr = 0;
    double relErr = 0;
    if (testCriteria != null) {
        absErr = testCriteria.getMaxAbsError().doubleValue();
        relErr = testCriteria.getMaxRelError().doubleValue();
    }
    try {
        VCDocument testDoc = null;
        if (testCase instanceof TestCaseNewMathModel) {
            MathModelInfo mmInfo = ((TestCaseNewMathModel) testCase).getMathModelInfo();
            MathModel mathModel = getRequestManager().getDocumentManager().getMathModel(mmInfo);
            testDoc = mathModel;
        } else if (testCase instanceof TestCaseNewBioModel) {
            TestCaseNewBioModel bioTestCase = (TestCaseNewBioModel) testCase;
            // bioTestCase.
            BioModelInfo bmInfo = bioTestCase.getBioModelInfo();
            BioModel bioModel = getRequestManager().getDocumentManager().getBioModel(bmInfo);
            testDoc = bioModel;
        }
        TFGenerateReport.VCDocumentAndSimInfo refVCDocumentAndSimInfo = null;
        if (userSelectedRefSimInfo == null) {
            SimulationInfo refSimInfo = testCriteria.getRegressionSimInfo();
            if (refSimInfo != null) {
                VCDocument refDoc = null;
                if (testCriteria instanceof TestCriteriaNewMathModel) {
                    MathModelInfo mmInfo = ((TestCriteriaNewMathModel) testCriteria).getRegressionMathModelInfo();
                    MathModel mathModel = getRequestManager().getDocumentManager().getMathModel(mmInfo);
                    refDoc = mathModel;
                } else if (testCriteria instanceof TestCriteriaNewBioModel) {
                    BioModelInfo bmInfo = ((TestCriteriaNewBioModel) testCriteria).getRegressionBioModelInfo();
                    BioModel bioModel = getRequestManager().getDocumentManager().getBioModel(bmInfo);
                    refDoc = bioModel;
                }
                refVCDocumentAndSimInfo = new TFGenerateReport.VCDocumentAndSimInfo(refSimInfo, refDoc);
            }
            reportTCBuffer.append("\t\t" + testSim.getName() + (refVCDocumentAndSimInfo != null ? " (Using TestCrit RegrRefSim)" : "") + " : " + "\n");
        } else {
            refVCDocumentAndSimInfo = userSelectedRefSimInfo;
            reportTCBuffer.append("\t\t" + testSim.getName() + " (Using UserDefined RegrRefSim '" + userSelectedRefSimInfo.getSimInfo().getAuthoritativeVCSimulationIdentifier() + "') : " + "\n");
        }
        if (testCase.getType().equals(TestCaseNew.REGRESSION) && refVCDocumentAndSimInfo == null) {
            reportTCBuffer.append("\t\t\tNo reference SimInfo, SimInfoKey=" + testCriteria.getSimInfo().getVersion().getName() + ". Cannot perform Regression Test!\n");
            simReportStatus = TestCriteriaNew.TCRIT_STATUS_NOREFREGR;
        } else {
            VCDataIdentifier vcdID = new VCSimulationDataIdentifier(testSim.getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), 0);
            DataManager simDataManager = getRequestManager().getDataManager(null, vcdID, testSim.isSpatial());
            double[] timeArray = null;
            // can be histogram, so there won't be time array
            try {
                timeArray = simDataManager.getDataSetTimes();
            } catch (Exception ex) {
                ex.printStackTrace(System.out);
            }
            NonspatialStochSimOptions stochOpt = testSim.getSolverTaskDescription().getStochOpt();
            if ((stochOpt == null || stochOpt.getNumOfTrials() == 1) && (timeArray == null || timeArray.length == 0)) {
                reportTCBuffer.append("\t\t\tNO DATA : Simulation not run yet.\n");
                simReportStatus = TestCriteriaNew.TCRIT_STATUS_NODATA;
            } else {
                // SPATIAL simulation
                if (testSim.getMathDescription().isSpatial()) {
                    PDEDataManager pdeDataManager = (PDEDataManager) simDataManager;
                    // Get EXACT solution if test case type is EXACT, Compare with numerical
                    if (testCase.getType().equals(TestCaseNew.EXACT) || testCase.getType().equals(TestCaseNew.EXACT_STEADY)) {
                        SimulationComparisonSummary simCompSummary = MathTestingUtilities.comparePDEResultsWithExact(simSymbolTable, pdeDataManager, testCase.getType(), testCriteria.getMaxAbsError(), testCriteria.getMaxRelError());
                        // Failed var summaries
                        failVarSummaries = simCompSummary.getFailingVariableComparisonSummaries(absErr, relErr);
                        allVarSummaries = simCompSummary.getVariableComparisonSummaries();
                        if (failVarSummaries.length > 0) {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_FAILEDVARS;
                            // Failed simulation
                            reportTCBuffer.append("\t\tTolerance test FAILED \n");
                            reportTCBuffer.append("\t\tFailed Variables : \n");
                            for (int m = 0; m < failVarSummaries.length; m++) {
                                reportTCBuffer.append("\t\t\t" + failVarSummaries[m].toShortString() + "\n");
                            }
                        } else {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_PASSED;
                            reportTCBuffer.append("\t\tTolerance test PASSED \n");
                        }
                        reportTCBuffer.append("\t\tPassed Variables : \n");
                        // Check if varSummary exists in failed summaries list. If not, simulation passed.
                        for (int m = 0; m < allVarSummaries.length; m++) {
                            if (!BeanUtils.arrayContains(failVarSummaries, allVarSummaries[m])) {
                                reportTCBuffer.append("\t\t\t" + allVarSummaries[m].toShortString() + "\n");
                            }
                        }
                    // Get CONSTRUCTED solution if test case type is CONSTRUCTED, Compare with numerical
                    } else if (testCase.getType().equals(TestCaseNew.CONSTRUCTED)) {
                        SimulationComparisonSummary simCompSummary = MathTestingUtilities.comparePDEResultsWithExact(simSymbolTable, pdeDataManager, testCase.getType(), testCriteria.getMaxAbsError(), testCriteria.getMaxRelError());
                        // Failed var summaries
                        failVarSummaries = simCompSummary.getFailingVariableComparisonSummaries(absErr, relErr);
                        allVarSummaries = simCompSummary.getVariableComparisonSummaries();
                        if (failVarSummaries.length > 0) {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_FAILEDVARS;
                            // Failed simulation
                            reportTCBuffer.append("\t\tTolerance test FAILED \n");
                            reportTCBuffer.append("\t\tFailed Variables : \n");
                            for (int m = 0; m < failVarSummaries.length; m++) {
                                reportTCBuffer.append("\t\t\t" + failVarSummaries[m].toShortString() + "\n");
                            }
                        } else {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_PASSED;
                            reportTCBuffer.append("\t\tTolerance test PASSED \n");
                        }
                        reportTCBuffer.append("\t\tPassed Variables : \n");
                        // Check if varSummary exists in failed summaries list. If not, simulation passed.
                        for (int m = 0; m < allVarSummaries.length; m++) {
                            if (!BeanUtils.arrayContains(failVarSummaries, allVarSummaries[m])) {
                                reportTCBuffer.append("\t\t\t" + allVarSummaries[m].toShortString() + "\n");
                            }
                        }
                    } else if (testCase.getType().equals(TestCaseNew.REGRESSION)) {
                        Simulation refSim = ((ClientDocumentManager) getRequestManager().getDocumentManager()).getSimulation(refVCDocumentAndSimInfo.getSimInfo());
                        VCDataIdentifier refVcdID = new VCSimulationDataIdentifier(refVCDocumentAndSimInfo.getSimInfo().getAuthoritativeVCSimulationIdentifier(), 0);
                        PDEDataManager refDataManager = (PDEDataManager) getRequestManager().getDataManager(null, refVcdID, refSim.isSpatial());
                        if (refSim.getScanCount() != 1) {
                            throw new RuntimeException("paramater scan is not supported in Math Testing Framework");
                        }
                        SimulationSymbolTable refSimSymbolTable = new SimulationSymbolTable(refSim, 0);
                        String[] varsToCompare = getVariableNamesToCompare(simSymbolTable, refSimSymbolTable);
                        SimulationComparisonSummary simCompSummary = MathTestingUtilities.comparePDEResults(simSymbolTable, pdeDataManager, refSimSymbolTable, refDataManager, varsToCompare, testCriteria.getMaxAbsError(), testCriteria.getMaxRelError(), refVCDocumentAndSimInfo.getVCDocument(), getDataInfoProvider(refVCDocumentAndSimInfo.getVCDocument(), refDataManager.getPDEDataContext(), refSim.getName()), testDoc, getDataInfoProvider(testDoc, pdeDataManager.getPDEDataContext(), testSim.getName()));
                        // Failed var summaries
                        failVarSummaries = simCompSummary.getFailingVariableComparisonSummaries(absErr, relErr);
                        allVarSummaries = simCompSummary.getVariableComparisonSummaries();
                        if (failVarSummaries.length > 0) {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_FAILEDVARS;
                            // Failed simulation
                            reportTCBuffer.append("\t\tTolerance test FAILED \n");
                            reportTCBuffer.append("\t\tFailed Variables : \n");
                            for (int m = 0; m < failVarSummaries.length; m++) {
                                reportTCBuffer.append("\t\t\t" + failVarSummaries[m].toShortString() + "\n");
                            }
                        } else {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_PASSED;
                            reportTCBuffer.append("\t\tTolerance test PASSED \n");
                        }
                        reportTCBuffer.append("\t\tPassed Variables : \n");
                        // Check if varSummary exists in failed summaries list. If not, simulation passed.
                        for (int m = 0; m < allVarSummaries.length; m++) {
                            if (!BeanUtils.arrayContains(failVarSummaries, allVarSummaries[m])) {
                                reportTCBuffer.append("\t\t\t" + allVarSummaries[m].toShortString() + "\n");
                            }
                        }
                    }
                } else {
                    // NON-SPATIAL CASE
                    ODEDataManager odeDataManager = (ODEDataManager) simDataManager;
                    ODESolverResultSet numericalResultSet = odeDataManager.getODESolverResultSet();
                    // Get EXACT result set if test case type is EXACT, Compare with numerical
                    if (testCase.getType().equals(TestCaseNew.EXACT) || testCase.getType().equals(TestCaseNew.EXACT_STEADY)) {
                        ODESolverResultSet exactResultSet = MathTestingUtilities.getExactResultSet(testSim.getMathDescription(), timeArray, testSim.getSolverTaskDescription().getSensitivityParameter());
                        String[] varsToCompare = getVariableNamesToCompare(simSymbolTable, simSymbolTable);
                        SimulationComparisonSummary simCompSummary_exact = MathTestingUtilities.compareResultSets(numericalResultSet, exactResultSet, varsToCompare, testCase.getType(), testCriteria.getMaxAbsError(), testCriteria.getMaxRelError());
                        // Get all the variable comparison summaries and the failed ones to print out report for EXACT solution comparison.
                        failVarSummaries = simCompSummary_exact.getFailingVariableComparisonSummaries(absErr, relErr);
                        allVarSummaries = simCompSummary_exact.getVariableComparisonSummaries();
                        if (failVarSummaries.length > 0) {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_FAILEDVARS;
                            // Failed simulation
                            reportTCBuffer.append("\t\tTolerance test FAILED \n");
                            reportTCBuffer.append("\t\tFailed Variables : \n");
                            for (int m = 0; m < failVarSummaries.length; m++) {
                                reportTCBuffer.append("\t\t\t" + failVarSummaries[m].toShortString() + "\n");
                            }
                        } else {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_PASSED;
                            reportTCBuffer.append("\t\tTolerance test PASSED \n");
                        }
                        reportTCBuffer.append("\t\tPassed Variables : \n");
                        // Check if varSummary exists in failed summaries list. If not, simulation passed.
                        for (int m = 0; m < allVarSummaries.length; m++) {
                            if (!BeanUtils.arrayContains(failVarSummaries, allVarSummaries[m])) {
                                reportTCBuffer.append("\t\t\t" + allVarSummaries[m].toShortString() + "\n");
                            }
                        }
                    // Get CONSTRUCTED result set if test case type is CONSTRUCTED , compare with numerical
                    } else if (testCase.getType().equals(TestCaseNew.CONSTRUCTED)) {
                        ODESolverResultSet constructedResultSet = MathTestingUtilities.getConstructedResultSet(testSim.getMathDescription(), timeArray);
                        String[] varsToCompare = getVariableNamesToCompare(simSymbolTable, simSymbolTable);
                        SimulationComparisonSummary simCompSummary_constr = MathTestingUtilities.compareResultSets(numericalResultSet, constructedResultSet, varsToCompare, testCase.getType(), testCriteria.getMaxAbsError(), testCriteria.getMaxRelError());
                        // Get all the variable comparison summaries and the failed ones to print out report for CONSTRUCTED solution comparison.
                        failVarSummaries = simCompSummary_constr.getFailingVariableComparisonSummaries(absErr, relErr);
                        allVarSummaries = simCompSummary_constr.getVariableComparisonSummaries();
                        if (failVarSummaries.length > 0) {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_FAILEDVARS;
                            // Failed simulation
                            reportTCBuffer.append("\t\tTolerance test FAILED \n");
                            reportTCBuffer.append("\t\tFailed Variables : \n");
                            for (int m = 0; m < failVarSummaries.length; m++) {
                                reportTCBuffer.append("\t\t\t" + failVarSummaries[m].toShortString() + "\n");
                            }
                        } else {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_PASSED;
                            reportTCBuffer.append("\t\tTolerance test PASSED \n");
                        }
                        reportTCBuffer.append("\t\tPassed Variables : \n");
                        // Check if varSummary exists in failed summaries list. If not, simulation passed.
                        for (int m = 0; m < allVarSummaries.length; m++) {
                            if (!BeanUtils.arrayContains(failVarSummaries, allVarSummaries[m])) {
                                reportTCBuffer.append("\t\t\t" + allVarSummaries[m].toShortString() + "\n");
                            }
                        }
                    } else if (testCase.getType().equals(TestCaseNew.REGRESSION)) {
                        Simulation refSim = ((ClientDocumentManager) getRequestManager().getDocumentManager()).getSimulation(testCriteria.getRegressionSimInfo());
                        if (refSim.getScanCount() != 1) {
                            throw new RuntimeException("paramater scan is not supported in Math Testing Framework");
                        }
                        SimulationSymbolTable refSimSymbolTable = new SimulationSymbolTable(refSim, 0);
                        String[] varsToTest = getVariableNamesToCompare(simSymbolTable, refSimSymbolTable);
                        VCDataIdentifier refVcdID = new VCSimulationDataIdentifier(refVCDocumentAndSimInfo.getSimInfo().getAuthoritativeVCSimulationIdentifier(), 0);
                        ODEDataManager refDataManager = (ODEDataManager) getRequestManager().getDataManager(null, refVcdID, refSim.isSpatial());
                        ODESolverResultSet referenceResultSet = refDataManager.getODESolverResultSet();
                        SimulationComparisonSummary simCompSummary_regr = null;
                        int interpolationOrder = 1;
                        SolverTaskDescription solverTaskDescription = refSim.getSolverTaskDescription();
                        if (solverTaskDescription.getOutputTimeSpec().isDefault() && ((DefaultOutputTimeSpec) solverTaskDescription.getOutputTimeSpec()).getKeepEvery() == 1) {
                            SolverDescription solverDescription = solverTaskDescription.getSolverDescription();
                            if ((!solverDescription.supportsAll(SolverDescription.DiscontinutiesFeatures)) || !refSim.getMathDescription().hasDiscontinuities()) {
                                interpolationOrder = solverDescription.getTimeOrder();
                            }
                        }
                        simCompSummary_regr = MathTestingUtilities.compareUnEqualResultSets(numericalResultSet, referenceResultSet, varsToTest, testCriteria.getMaxAbsError(), testCriteria.getMaxRelError(), interpolationOrder);
                        // Get all the variable comparison summaries and the failed ones to print out report for CONSTRUCTED solution comparison.
                        failVarSummaries = simCompSummary_regr.getFailingVariableComparisonSummaries(absErr, relErr);
                        allVarSummaries = simCompSummary_regr.getVariableComparisonSummaries();
                        if (failVarSummaries.length > 0) {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_FAILEDVARS;
                            // Failed simulation
                            reportTCBuffer.append("\t\tTolerance test FAILED \n");
                            reportTCBuffer.append("\t\tFailed Variables : \n");
                            for (int m = 0; m < failVarSummaries.length; m++) {
                                reportTCBuffer.append("\t\t\t" + failVarSummaries[m].toShortString() + "\n");
                            }
                        } else {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_PASSED;
                            reportTCBuffer.append("\t\tTolerance test PASSED \n");
                        }
                        reportTCBuffer.append("\t\tPassed Variables : \n");
                        // Check if varSummary exists in failed summaries list. If not, simulation passed.
                        for (int m = 0; m < allVarSummaries.length; m++) {
                            if (!BeanUtils.arrayContains(failVarSummaries, allVarSummaries[m])) {
                                reportTCBuffer.append("\t\t\t" + allVarSummaries[m].toShortString() + "\n");
                            }
                        }
                    }
                }
            }
        }
    } catch (Throwable e) {
        simReportStatus = TestCriteriaNew.TCRIT_STATUS_RPERROR;
        simReportStatusMessage = e.getClass().getName() + " " + e.getMessage();
        reportTCBuffer.append("\t\t" + simReportStatusMessage + "\n");
        e.printStackTrace(System.out);
    }
    if (userSelectedRefSimInfo == null) {
        try {
            // Remove any test results already present for testCriteria
            RemoveTestResultsOP removeResultsOP = new RemoveTestResultsOP(new BigDecimal[] { testCriteria.getTCritKey() });
            // testResultsOPsVector.add(removeResultsOP);
            getRequestManager().getDocumentManager().doTestSuiteOP(removeResultsOP);
            // Create new AddTestREsultsOP object for the current simulation./testCriteria.
            if (allVarSummaries != null) {
                AddTestResultsOP testResultsOP = new AddTestResultsOP(testCriteria.getTCritKey(), allVarSummaries);
                // testResultsOPsVector.add(testResultsOP);
                // Write the testResults for simulation/TestCriteria into the database ...
                getRequestManager().getDocumentManager().doTestSuiteOP(testResultsOP);
            }
            // Update report status
            updateTCritStatus(testCriteria, simReportStatus, simReportStatusMessage);
        } catch (Throwable e) {
            reportTCBuffer.append("\t\tUpdate DB Results failed. " + e.getClass().getName() + " " + e.getMessage() + "\n");
            try {
                getRequestManager().getDocumentManager().doTestSuiteOP(new EditTestCriteriaOPReportStatus(testCriteria.getTCritKey(), TestCriteriaNew.TCRIT_STATUS_RPERROR, e.getClass().getName() + " " + e.getMessage()));
            } catch (Throwable e2) {
            // Nothing more can be done
            }
        }
    }
    return reportTCBuffer.toString();
}

Example 95 with BioModel

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

the class TestingFrameworkWindowManager method selectRefSimInfo.

/**
 * Insert the method's description here.
 * Creation date: (7/15/2004 4:48:36 PM)
 * @param newTestingFrameworkWindowPanel cbit.vcell.client.desktop.TestingFrameworkWindowPanel
 */
public Object[] selectRefSimInfo(BioModelInfo bmInfo, String appName) throws DataAccessException {
    if (bmInfo == null || appName == null || appName.length() == 0) {
        PopupGenerator.showErrorDialog(TestingFrameworkWindowManager.this, "Selected Reference BioModel is null, choose a reference BioModel before choosing simulation!");
        return null;
    }
    // code for obtaining siminfos from Biomodel and displaying it as a list
    // and displaying the siminfo in the label
    SimulationContext simContext = null;
    BioModel bioModel = getRequestManager().getDocumentManager().getBioModel(bmInfo);
    for (int i = 0; i < bioModel.getSimulationContexts().length; i += 1) {
        if (bioModel.getSimulationContexts()[i].getName().equals(appName)) {
            simContext = bioModel.getSimulationContexts()[i];
            break;
        }
    }
    if (simContext != null) {
        SimulationInfo simInfo = selectSimInfoPrivate(bioModel.getSimulations(simContext));
        return new Object[] { simContext.getName(), simInfo };
    } else {
        PopupGenerator.showErrorDialog(TestingFrameworkWindowManager.this, "No simcontext found for biomodel " + bmInfo + " app=" + appName);
        return null;
    }
}