Example 6 with TestCriteriaNewMathModel
use of cbit.vcell.numericstest.TestCriteriaNewMathModel in project vcell by virtualcell.
the class EditTestCriteriaPanel method applyTestCriteriaInfo.
/**
* Comment
*/
private void applyTestCriteriaInfo() {
TestCriteriaNew newTestCriteria = null;
Double relErr = Double.valueOf(getRelErrTextField().getText());
Double absErr = Double.valueOf(getAbsErrTextField().getText());
if (getSolutionType().equals(TestCaseNew.REGRESSION)) {
// newTestCriteria = new TestCriteriaNew(null, getExistingTestCriteria().getSimInfo(), getReferenceMathModelInfo(), getReferenceSimInfo(), relErr, absErr, null);
if (getExistingTestCriteria() instanceof TestCriteriaNewMathModel) {
newTestCriteria = new TestCriteriaNewMathModel(null, getExistingTestCriteria().getSimInfo(), getReferenceMathModelInfo(), getReferenceSimInfo(), relErr, absErr, null, TestCriteriaNew.TCRIT_STATUS_NEEDSREPORT, null);
} else if (getExistingTestCriteria() instanceof TestCriteriaNewBioModel) {
newTestCriteria = new TestCriteriaNewBioModel(null, getExistingTestCriteria().getSimInfo(), getbioModelInfo(), getappName(), getbmAppSimInfo(), relErr, absErr, null, TestCriteriaNew.TCRIT_STATUS_NEEDSREPORT, null);
}
} else {
// CONSTRUCTED SOLN OR EXACT SOLUTION
if (getExistingTestCriteria() instanceof TestCriteriaNewMathModel) {
newTestCriteria = new TestCriteriaNewMathModel(null, getExistingTestCriteria().getSimInfo(), null, null, relErr, absErr, null, TestCriteriaNew.TCRIT_STATUS_NEEDSREPORT, null);
} else if (getExistingTestCriteria() instanceof TestCriteriaNewBioModel) {
newTestCriteria = new TestCriteriaNewBioModel(null, getExistingTestCriteria().getSimInfo(), null, null, null, relErr, absErr, null, TestCriteriaNew.TCRIT_STATUS_NEEDSREPORT, null);
}
}
setNewTestCriteria(newTestCriteria);
}
Also used :
TestCriteriaNewMathModel(cbit.vcell.numericstest.TestCriteriaNewMathModel)
TestCriteriaNewBioModel(cbit.vcell.numericstest.TestCriteriaNewBioModel)
TestCriteriaNew(cbit.vcell.numericstest.TestCriteriaNew)
Example 7 with TestCriteriaNewMathModel
use of cbit.vcell.numericstest.TestCriteriaNewMathModel 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();
}
Also used :
MathModel(cbit.vcell.mathmodel.MathModel)
AddTestCasesOPMathModel(cbit.vcell.numericstest.AddTestCasesOPMathModel)
TestCaseNewMathModel(cbit.vcell.numericstest.TestCaseNewMathModel)
TestCriteriaNewMathModel(cbit.vcell.numericstest.TestCriteriaNewMathModel)
EditTestCriteriaOPMathModel(cbit.vcell.numericstest.EditTestCriteriaOPMathModel)
AddTestCriteriaOPMathModel(cbit.vcell.numericstest.AddTestCriteriaOPMathModel)
SolverDescription(cbit.vcell.solver.SolverDescription)
TestCriteriaNewBioModel(cbit.vcell.numericstest.TestCriteriaNewBioModel)
NonspatialStochSimOptions(cbit.vcell.solver.NonspatialStochSimOptions)
ClientDocumentManager(cbit.vcell.clientdb.ClientDocumentManager)
TFGenerateReport(cbit.vcell.client.task.TFGenerateReport)
TestCaseNewBioModel(cbit.vcell.numericstest.TestCaseNewBioModel)
RemoveTestResultsOP(cbit.vcell.numericstest.RemoveTestResultsOP)
TestCriteriaNewMathModel(cbit.vcell.numericstest.TestCriteriaNewMathModel)
AddTestResultsOP(cbit.vcell.numericstest.AddTestResultsOP)
SimulationComparisonSummary(cbit.vcell.solver.test.SimulationComparisonSummary)
ODESolverResultSet(cbit.vcell.solver.ode.ODESolverResultSet)
VariableComparisonSummary(cbit.vcell.solver.test.VariableComparisonSummary)
SolverTaskDescription(cbit.vcell.solver.SolverTaskDescription)
EditTestCriteriaOPReportStatus(cbit.vcell.numericstest.EditTestCriteriaOPReportStatus)
VCDocument(org.vcell.util.document.VCDocument)
SimulationSymbolTable(cbit.vcell.solver.SimulationSymbolTable)
BioModelInfo(org.vcell.util.document.BioModelInfo)
PDEDataManager(cbit.vcell.simdata.PDEDataManager)
ODEDataManager(cbit.vcell.simdata.ODEDataManager)
DataManager(cbit.vcell.simdata.DataManager)
MathModelInfo(org.vcell.util.document.MathModelInfo)
VCSimulationDataIdentifier(cbit.vcell.solver.VCSimulationDataIdentifier)
ObjectNotFoundException(org.vcell.util.ObjectNotFoundException)
DataAccessException(org.vcell.util.DataAccessException)
UserCancelException(org.vcell.util.UserCancelException)
Simulation(cbit.vcell.solver.Simulation)
PDEDataManager(cbit.vcell.simdata.PDEDataManager)
TestCaseNewBioModel(cbit.vcell.numericstest.TestCaseNewBioModel)
TestCriteriaNewBioModel(cbit.vcell.numericstest.TestCriteriaNewBioModel)
AddTestCasesOPBioModel(cbit.vcell.numericstest.AddTestCasesOPBioModel)
BioModel(cbit.vcell.biomodel.BioModel)
EditTestCriteriaOPBioModel(cbit.vcell.numericstest.EditTestCriteriaOPBioModel)
AddTestCriteriaOPBioModel(cbit.vcell.numericstest.AddTestCriteriaOPBioModel)
TestCaseNewMathModel(cbit.vcell.numericstest.TestCaseNewMathModel)
ODEDataManager(cbit.vcell.simdata.ODEDataManager)
VCDataIdentifier(org.vcell.util.document.VCDataIdentifier)
DefaultOutputTimeSpec(cbit.vcell.solver.DefaultOutputTimeSpec)
SimulationInfo(cbit.vcell.solver.SimulationInfo)
Example 8 with TestCriteriaNewMathModel
use of cbit.vcell.numericstest.TestCriteriaNewMathModel in project vcell by virtualcell.
the class TestingFrmwkTreeModel method createTestCaseSubTree.
/**
* Insert the method's description here.
* Creation date: (11/28/00 1:06:51 PM)
* @return cbit.vcell.desktop.BioModelNode
* @param docManager cbit.vcell.clientdb.DocumentManager
*/
private BioModelNode createTestCaseSubTree(TestCaseNew testCase) throws DataAccessException {
//
// add 'test case' node
//
BioModelNode testCaseNode = new BioModelNode(testCase, true);
TestCriteriaNew[] tCriteria = testCase.getTestCriterias();
// Sort
if (tCriteria != null && tCriteria.length > 0) {
java.util.Arrays.sort(tCriteria, new java.util.Comparator<TestCriteriaNew>() {
public int compare(TestCriteriaNew tc1, TestCriteriaNew tc2) {
return tc1.getSimInfo().getVersion().getName().compareTo(tc2.getSimInfo().getVersion().getName());
}
public boolean equals(Object obj) {
return false;
}
});
//
// False => sim has not been run; True => for a regression test, the ref SimInfo is not set.
boolean bRefSimNull = false;
for (int t = 0; t < tCriteria.length; t += 1) {
TestCriteriaNew tcInfo = tCriteria[t];
BioModelNode simInfoNode = new BioModelNode(tcInfo, true);
String tcInfoStr = null;
if (tcInfo != null) {
tcInfoStr = "TestCriteria : LimitAbsError = " + tcInfo.getMaxAbsError() + "; LimitRelError = " + tcInfo.getMaxRelError() + "; ";
if (testCase.getType().equals(TestCaseNew.REGRESSION)) {
if (tcInfo.getRegressionSimInfo() != null) {
SimulationInfo refSimInfo = tcInfo.getRegressionSimInfo();
if (refSimInfo != null) {
if (tcInfo instanceof TestCriteriaNewMathModel) {
tcInfoStr = tcInfoStr + "MathModel : " + ((TestCriteriaNewMathModel) tcInfo).getRegressionMathModelInfo().getVersion().getName() + "; ";
tcInfoStr = tcInfoStr + "SimInfo : " + refSimInfo.getName();
} else if (tcInfo instanceof TestCriteriaNewBioModel) {
tcInfoStr = tcInfoStr + "BioModel : " + ((TestCriteriaNewBioModel) tcInfo).getRegressionBioModelInfo().getVersion().getName() + "; ";
tcInfoStr = tcInfoStr + "SimInfo : " + refSimInfo.getName();
}
}
} else {
tcInfoStr = tcInfoStr + " REFERENCE SIMULATION NOT SET YET";
bRefSimNull = true;
}
}
BioModelNode testCriteriaNode = new BioModelNode(tcInfoStr, false);
simInfoNode.add(testCriteriaNode);
}
// Add sim results if present (by adding the reportInfo subtree ...)
BioModelNode reportInfoNode = createSimulationSubTree(tcInfo, simInfoNode, bRefSimNull);
if (reportInfoNode != null) {
simInfoNode.add(reportInfoNode);
}
testCaseNode.add(simInfoNode);
}
}
return testCaseNode;
}
Also used :
TestCriteriaNewMathModel(cbit.vcell.numericstest.TestCriteriaNewMathModel)
TestCriteriaNewBioModel(cbit.vcell.numericstest.TestCriteriaNewBioModel)
TestCriteriaNew(cbit.vcell.numericstest.TestCriteriaNew)
BioModelNode(cbit.vcell.desktop.BioModelNode)
SimulationInfo(cbit.vcell.solver.SimulationInfo)
Example 9 with TestCriteriaNewMathModel
use of cbit.vcell.numericstest.TestCriteriaNewMathModel in project vcell by virtualcell.
the class DbDriver method testSuiteGet.
/**
* Insert the method's description here.
* Creation date: (10/16/2004 2:39:49 PM)
* @return cbit.vcell.numericstest.TestSuiteInfoNew[]
*/
public static TestSuiteNew testSuiteGet(BigDecimal getThisTS, Connection con, User user, DatabaseSyntax dbSyntax) throws SQLException, DataAccessException {
if (!user.isTestAccount()) {
throw new PermissionException("User=" + user.getName() + " not allowed TestSuiteInfo");
}
// if(testSuiteHash.containsKey(getThisTS)){
// return (cbit.vcell.numericstest.TestSuiteNew)testSuiteHash.get(getThisTS);
// }
Hashtable simulationInfoH = new Hashtable();
Hashtable mathModelInfoH = new Hashtable();
Hashtable bioModelInfoH = new Hashtable();
Statement stmt = null;
ResultSet rset = null;
String sql = null;
Level origLogLevel = DatabasePolicySQL.lg.getLevel();
try {
DatabasePolicySQL.lg.setLevel(Level.WARN);
// double begTime=System.currentTimeMillis();
// int counter = 0;
stmt = con.createStatement();
// Get VariableComparisonSummaries
Hashtable vcsH = new Hashtable();
{
sql = "SELECT " + TFTestResultTable.table.getTableName() + ".*" + " FROM " + TFTestResultTable.table.getTableName() + "," + TFTestCriteriaTable.table.getTableName() + "," + TFTestCaseTable.table.getTableName() + "," + TFTestSuiteTable.table.getTableName() + " WHERE " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + getThisTS + " AND " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + TFTestCaseTable.table.testSuiteRef.getQualifiedColName() + " AND " + TFTestCaseTable.table.id.getQualifiedColName() + "=" + TFTestCriteriaTable.table.testCaseRef.getQualifiedColName() + " AND " + TFTestCriteriaTable.table.id.getQualifiedColName() + "=" + TFTestResultTable.table.testCriteriaRef.getQualifiedColName() + " ORDER BY UPPER(" + TFTestResultTable.table.varName.getQualifiedColName() + ")";
rset = stmt.executeQuery(sql);
while (rset.next()) {
BigDecimal tcritRef = rset.getBigDecimal(TFTestResultTable.table.testCriteriaRef.getUnqualifiedColName());
String varName = rset.getString(TFTestResultTable.table.varName.getUnqualifiedColName());
double absError = rset.getDouble(TFTestResultTable.table.absError.getUnqualifiedColName());
double relError = rset.getDouble(TFTestResultTable.table.relError.getUnqualifiedColName());
double maxRef = rset.getDouble(TFTestResultTable.table.maxRef.getUnqualifiedColName());
double minRef = rset.getDouble(TFTestResultTable.table.minRef.getUnqualifiedColName());
double mse = rset.getDouble(TFTestResultTable.table.meanSqrError.getUnqualifiedColName());
double timeAbsError = rset.getDouble(TFTestResultTable.table.timeAbsError.getUnqualifiedColName());
int indexAbsError = rset.getInt(TFTestResultTable.table.indexAbsError.getUnqualifiedColName());
double timeRelError = rset.getDouble(TFTestResultTable.table.timeRelError.getUnqualifiedColName());
int indexRelError = rset.getInt(TFTestResultTable.table.indexRelError.getUnqualifiedColName());
Vector v = (Vector) vcsH.get(tcritRef);
if (v == null) {
v = new Vector();
vcsH.put(tcritRef, v);
}
v.add(new VariableComparisonSummary(varName, minRef, maxRef, absError, relError, mse, timeAbsError, indexAbsError, timeRelError, indexRelError));
// counter+= 1;
}
// System.out.println("VCS count="+counter+" time="+((System.currentTimeMillis()-begTime)/1000));
rset.close();
}
// begTime=System.currentTimeMillis();
// counter = 0;
// Get TestCriteria for mathModel based TestCases
Hashtable tcritH = new Hashtable();
{
sql = "SELECT " + TFTestCriteriaTable.table.getTableName() + ".*" + "," + MathModelSimulationLinkTable.table.getTableName() + ".*" + " FROM " + TFTestCriteriaTable.table.getTableName() + "," + TFTestCaseTable.table.getTableName() + "," + TFTestSuiteTable.table.getTableName() + "," + MathModelSimulationLinkTable.table.getTableName() + "," + SimulationTable.table.getTableName() + " WHERE " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + getThisTS + " AND " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + TFTestCaseTable.table.testSuiteRef.getQualifiedColName() + " AND " + TFTestCaseTable.table.id.getQualifiedColName() + "=" + TFTestCriteriaTable.table.testCaseRef.getQualifiedColName() + " AND " + TFTestCaseTable.table.mathModelRef.getQualifiedColName() + " IS NOT NULL " + " AND " + TFTestCriteriaTable.table.simulationRef.getQualifiedColName() + "=" + SimulationTable.table.id.getQualifiedColName() + " AND " + TFTestCriteriaTable.table.regressionMMSimRef.getQualifiedColName() + "=" + MathModelSimulationLinkTable.table.id.getQualifiedColName() + "(+)" + " ORDER BY UPPER(" + SimulationTable.table.name.getQualifiedColName() + ")";
// System.out.println(sql);
rset = stmt.executeQuery(sql);
while (rset.next()) {
BigDecimal tcritKey = rset.getBigDecimal(TFTestCriteriaTable.table.id.getUnqualifiedColName());
BigDecimal tcaseRef = rset.getBigDecimal(TFTestCriteriaTable.table.testCaseRef.getUnqualifiedColName());
BigDecimal simRef = rset.getBigDecimal(TFTestCriteriaTable.table.simulationRef.getUnqualifiedColName());
BigDecimal simRegrRef = rset.getBigDecimal(MathModelSimulationLinkTable.table.simRef.getUnqualifiedColName());
if (rset.wasNull()) {
simRegrRef = null;
}
BigDecimal mathRegrRef = rset.getBigDecimal(MathModelSimulationLinkTable.table.mathModelRef.getUnqualifiedColName());
if (rset.wasNull()) {
mathRegrRef = null;
}
Double maxRelError = null;
double dtemp = rset.getDouble(TFTestCriteriaTable.table.maxRelError.getUnqualifiedColName());
if (rset.wasNull()) {
maxRelError = null;
} else {
maxRelError = new Double(dtemp);
}
Double maxAbsError = null;
dtemp = rset.getDouble(TFTestCriteriaTable.table.maxAbsError.getUnqualifiedColName());
if (rset.wasNull()) {
maxAbsError = null;
} else {
maxAbsError = new Double(dtemp);
}
String reportStatus = rset.getString(TFTestCriteriaTable.table.reportStatus.getUnqualifiedColName());
if (rset.wasNull()) {
reportStatus = TestCriteriaNew.TCRIT_STATUS_NEEDSREPORT;
}
String reportStatusMessage = rset.getString(TFTestCriteriaTable.table.reportMessage.getUnqualifiedColName());
if (rset.wasNull()) {
reportStatusMessage = null;
}
if (reportStatusMessage != null && reportStatusMessage.length() > 0) {
reportStatusMessage = TokenMangler.getSQLRestoredString(reportStatusMessage);
}
Vector v = (Vector) tcritH.get(tcaseRef);
if (v == null) {
v = new Vector();
tcritH.put(tcaseRef, v);
}
SimulationInfo simInfo = (SimulationInfo) simulationInfoH.get(simRef);
if (simInfo == null) {
Vector<VersionInfo> simVector = getVersionableInfos(con, user, VersionableType.Simulation, false, new KeyValue(simRef), false, dbSyntax);
if (simVector != null && simVector.size() > 0) {
simInfo = (SimulationInfo) simVector.firstElement();
simulationInfoH.put(simRef, simInfo);
}
}
SimulationInfo regrSimInfo = null;
MathModelInfo regrMathModelInfo = null;
if (simRegrRef != null) {
regrSimInfo = (SimulationInfo) simulationInfoH.get(simRegrRef);
if (regrSimInfo == null) {
Vector<VersionInfo> regSimVector = getVersionableInfos(con, user, VersionableType.Simulation, false, new KeyValue(simRegrRef), false, dbSyntax);
if (regSimVector != null && regSimVector.size() > 0) {
regrSimInfo = (SimulationInfo) regSimVector.firstElement();
simulationInfoH.put(simRegrRef, regrSimInfo);
}
}
regrMathModelInfo = (MathModelInfo) mathModelInfoH.get(mathRegrRef);
if (regrMathModelInfo == null) {
Vector<VersionInfo> regMathVector = getVersionableInfos(con, user, VersionableType.MathModelMetaData, false, new KeyValue(mathRegrRef), false, dbSyntax);
if (regMathVector != null && regMathVector.size() > 0) {
regrMathModelInfo = (MathModelInfo) regMathVector.firstElement();
mathModelInfoH.put(mathRegrRef, regrMathModelInfo);
}
}
}
//
VariableComparisonSummary[] neededVCSArr = null;
Vector vcsV = (Vector) vcsH.get(tcritKey);
if (vcsV != null) {
neededVCSArr = new VariableComparisonSummary[vcsV.size()];
vcsV.copyInto(neededVCSArr);
}
//
TestCriteriaNew tcn = null;
if (simInfo != null) {
tcn = new TestCriteriaNewMathModel(tcritKey, simInfo, regrMathModelInfo, regrSimInfo, maxRelError, maxAbsError, neededVCSArr, reportStatus, reportStatusMessage);
v.add(tcn);
}
// counter+= 1;
}
// System.out.println("TCrit count="+counter+" time="+((System.currentTimeMillis()-begTime)/1000));
rset.close();
}
// Get TestCriteria for bioModel based TestCases
// Hashtable tcritH = new Hashtable();
{
final String REGRSIMREF = "REGRSIMREF";
final String SCNAME = "SCNAME";
sql = "SELECT " + TFTestCriteriaTable.table.getTableName() + ".*" + "," + BioModelSimContextLinkTable.table.bioModelRef.getQualifiedColName() + "," + BioModelSimulationLinkTable.table.simRef.getQualifiedColName() + " " + REGRSIMREF + "," + SimContextTable.table.name.getQualifiedColName() + " " + SCNAME + " FROM " + TFTestCriteriaTable.table.getTableName() + "," + TFTestCaseTable.table.getTableName() + "," + TFTestSuiteTable.table.getTableName() + "," + BioModelSimContextLinkTable.table.getTableName() + "," + SimContextTable.table.getTableName() + "," + BioModelSimulationLinkTable.table.getTableName() + // SimulationTable.table.getTableName()+
" WHERE " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + getThisTS + " AND " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + TFTestCaseTable.table.testSuiteRef.getQualifiedColName() + " AND " + TFTestCaseTable.table.id.getQualifiedColName() + "=" + TFTestCriteriaTable.table.testCaseRef.getQualifiedColName() + " AND " + TFTestCaseTable.table.bmAppRef.getQualifiedColName() + " IS NOT NULL " + " AND " + TFTestCriteriaTable.table.regressionBMAPPRef.getQualifiedColName() + "=" + BioModelSimContextLinkTable.table.id.getQualifiedColName() + "(+)" + " AND " + BioModelSimContextLinkTable.table.simContextRef + " = " + SimContextTable.table.id.getQualifiedColName() + "(+)" + // SimContextTable.table.mathRef.getQualifiedColName()+" = "+SimulationTable.table.mathRef.getQualifiedColName()+"(+)" +
" AND " + TFTestCriteriaTable.table.regressionBMSimRef.getQualifiedColName() + " = " + BioModelSimulationLinkTable.table.id.getQualifiedColName() + "(+)";
// System.out.println(sql);
rset = stmt.executeQuery(sql);
while (rset.next()) {
BigDecimal tcritKey = rset.getBigDecimal(TFTestCriteriaTable.table.id.getUnqualifiedColName());
BigDecimal tcaseRef = rset.getBigDecimal(TFTestCriteriaTable.table.testCaseRef.getUnqualifiedColName());
BigDecimal tcSimRef = rset.getBigDecimal(TFTestCriteriaTable.table.simulationRef.getUnqualifiedColName());
BigDecimal regrSimRef = rset.getBigDecimal(REGRSIMREF);
// BigDecimal regrSimRef = rset.getBigDecimal(SimulationTable.table.id.getUnqualifiedColName());
if (rset.wasNull()) {
regrSimRef = null;
}
BigDecimal regrBioModelRef = rset.getBigDecimal(BioModelSimContextLinkTable.table.bioModelRef.getUnqualifiedColName());
if (rset.wasNull()) {
regrBioModelRef = null;
}
String regrSCName = rset.getString(SCNAME);
if (rset.wasNull()) {
regrSCName = null;
}
Double maxRelError = null;
double dtemp = rset.getDouble(TFTestCriteriaTable.table.maxRelError.getUnqualifiedColName());
if (rset.wasNull()) {
maxRelError = null;
} else {
maxRelError = new Double(dtemp);
}
Double maxAbsError = null;
dtemp = rset.getDouble(TFTestCriteriaTable.table.maxAbsError.getUnqualifiedColName());
if (rset.wasNull()) {
maxAbsError = null;
} else {
maxAbsError = new Double(dtemp);
}
String reportStatus = rset.getString(TFTestCriteriaTable.table.reportStatus.getUnqualifiedColName());
if (rset.wasNull()) {
reportStatus = TestCriteriaNew.TCRIT_STATUS_NEEDSREPORT;
}
String reportStatusMessage = rset.getString(TFTestCriteriaTable.table.reportMessage.getUnqualifiedColName());
if (rset.wasNull()) {
reportStatusMessage = null;
}
if (reportStatusMessage != null && reportStatusMessage.length() > 0) {
reportStatusMessage = TokenMangler.getSQLRestoredString(reportStatusMessage);
}
Vector v = (Vector) tcritH.get(tcaseRef);
if (v == null) {
v = new Vector();
tcritH.put(tcaseRef, v);
}
SimulationInfo simInfo = (SimulationInfo) simulationInfoH.get(tcSimRef);
if (simInfo == null) {
Vector<VersionInfo> simVector = getVersionableInfos(con, user, VersionableType.Simulation, false, new KeyValue(tcSimRef), false, dbSyntax);
if (simVector != null && simVector.size() == 1) {
simInfo = (SimulationInfo) simVector.firstElement();
simulationInfoH.put(tcSimRef, simInfo);
} else {
throw new DataAccessException("Found more than 1 versionable for tcsimRef=" + tcSimRef);
}
}
SimulationInfo regrSimInfo = null;
BioModelInfo regrBioModelInfo = null;
if (regrSimRef != null) {
regrSimInfo = (SimulationInfo) simulationInfoH.get(regrSimRef);
if (regrSimInfo == null) {
Vector<VersionInfo> regSimVector = getVersionableInfos(con, user, VersionableType.Simulation, false, new KeyValue(regrSimRef), false, dbSyntax);
if (regSimVector != null && regSimVector.size() == 1) {
regrSimInfo = (SimulationInfo) regSimVector.firstElement();
simulationInfoH.put(regrSimRef, regrSimInfo);
} else {
throw new DataAccessException("Found more than 1 versionable for simregRef=" + regrSimRef);
}
}
regrBioModelInfo = (BioModelInfo) mathModelInfoH.get(regrBioModelRef);
if (regrBioModelInfo == null) {
Vector<VersionInfo> regBioModelVector = getVersionableInfos(con, user, VersionableType.BioModelMetaData, false, new KeyValue(regrBioModelRef), false, dbSyntax);
if (regBioModelVector != null && regBioModelVector.size() == 1) {
regrBioModelInfo = (BioModelInfo) regBioModelVector.firstElement();
mathModelInfoH.put(regrBioModelRef, regrBioModelInfo);
} else {
throw new DataAccessException("Found more than 1 versionable for reegrbiomodelRef=" + regrBioModelRef);
}
}
}
//
VariableComparisonSummary[] neededVCSArr = null;
Vector vcsV = (Vector) vcsH.get(tcritKey);
if (vcsV != null) {
neededVCSArr = new VariableComparisonSummary[vcsV.size()];
vcsV.copyInto(neededVCSArr);
}
//
TestCriteriaNew tcn = null;
if (simInfo != null) {
tcn = new TestCriteriaNewBioModel(tcritKey, simInfo, regrBioModelInfo, regrSCName, regrSimInfo, maxRelError, maxAbsError, neededVCSArr, reportStatus, reportStatusMessage);
v.add(tcn);
}
// counter+= 1;
}
// System.out.println("TCrit count="+counter+" time="+((System.currentTimeMillis()-begTime)/1000));
rset.close();
}
// Get TestCases
Vector tcV = new Vector();
// begTime=System.currentTimeMillis();
// counter = 0;
{
// final String BMSCL = "bmscl";
final String OBTCTYPECOLUMN = "OBTCTYPECOLUMN";
final String OBNAMECOLUMN = "OBNAMECOLUMN";
final String BMSCBMRNAME = "BMSCBMRNAME";
final String BMSCSCRNAME = "BMSCSCRNAME";
final String SCNAME = "SCNAME";
final String SORTHELP1 = "SORTHELP1";
final String SORTHELP2 = "SORTHELP2";
sql = "SELECT " + "UPPER(" + MathModelTable.table.name.getQualifiedColName() + ") " + SORTHELP1 + "," + "TO_CHAR(NULL) " + SORTHELP2 + "," + TFTestCaseTable.table.getTableName() + ".*" + "," + "TO_NUMBER(NULL) " + BMSCBMRNAME + "," + "TO_NUMBER(NULL) " + BMSCSCRNAME + "," + "TO_CHAR(NULL) " + SCNAME + "," + "'MM' " + OBTCTYPECOLUMN + "," + MathModelTable.table.name.getQualifiedColName() + " " + OBNAMECOLUMN + " FROM " + TFTestCaseTable.table.getTableName() + "," + TFTestSuiteTable.table.getTableName() + "," + MathModelTable.table.getTableName() + " WHERE " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + getThisTS + " AND " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + TFTestCaseTable.table.testSuiteRef.getQualifiedColName() + " AND " + TFTestCaseTable.table.mathModelRef.getQualifiedColName() + " IS NOT NULL" + " AND " + TFTestCaseTable.table.mathModelRef.getQualifiedColName() + " = " + MathModelTable.table.id.getQualifiedColName() + " UNION " + "SELECT " + "UPPER(" + BioModelTable.table.name.getQualifiedColName() + ") " + SORTHELP1 + ",UPPER(" + SimContextTable.table.name.getQualifiedColName() + ") " + SORTHELP2 + "," + TFTestCaseTable.table.getTableName() + ".*" + "," + BioModelSimContextLinkTable.table.bioModelRef.getQualifiedColName() + " " + BMSCBMRNAME + "," + BioModelSimContextLinkTable.table.simContextRef.getQualifiedColName() + " " + BMSCSCRNAME + "," + SimContextTable.table.name.getQualifiedColName() + " " + SCNAME + "," + "'BM' " + OBTCTYPECOLUMN + "," + BioModelTable.table.name.getQualifiedColName() + " " + OBNAMECOLUMN + " FROM " + BioModelSimContextLinkTable.table.getTableName() + "," + SimContextTable.table.getTableName() + "," + TFTestCaseTable.table.getTableName() + "," + TFTestSuiteTable.table.getTableName() + "," + BioModelTable.table.getTableName() + " WHERE " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + getThisTS + " AND " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + TFTestCaseTable.table.testSuiteRef.getQualifiedColName() + " AND " + TFTestCaseTable.table.bmAppRef.getQualifiedColName() + " IS NOT NULL" + " AND " + TFTestCaseTable.table.bmAppRef.getQualifiedColName() + " = " + BioModelSimContextLinkTable.table.id.getQualifiedColName() + " AND " + BioModelSimContextLinkTable.table.simContextRef.getQualifiedColName() + " = " + SimContextTable.table.id.getQualifiedColName() + " AND " + BioModelSimContextLinkTable.table.bioModelRef.getQualifiedColName() + "=" + BioModelTable.table.id.getQualifiedColName() + // " ORDER BY 11,"+"UPPER(12)"+","+"UPPER(10)";
" ORDER BY 13,1,2";
rset = stmt.executeQuery(sql);
while (rset.next()) {
BigDecimal tcaseKey = rset.getBigDecimal(TFTestCaseTable.table.id.getUnqualifiedColName());
BigDecimal mmRef = rset.getBigDecimal(TFTestCaseTable.table.mathModelRef.getUnqualifiedColName());
if (rset.wasNull()) {
mmRef = null;
}
BigDecimal simContextRef = rset.getBigDecimal(BMSCSCRNAME);
if (rset.wasNull()) {
simContextRef = null;
}
BigDecimal bioModelRef = rset.getBigDecimal(BMSCBMRNAME);
if (rset.wasNull()) {
bioModelRef = null;
}
String simContextName = rset.getString(SCNAME);
if (rset.wasNull()) {
simContextName = null;
}
String tcType = rset.getString(TFTestCaseTable.table.tcSolutionType.getUnqualifiedColName());
String tcAnnot = rset.getString(TFTestCaseTable.table.tcAnnotation.getUnqualifiedColName());
if (rset.wasNull()) {
tcAnnot = "";
} else {
tcAnnot = TokenMangler.getSQLRestoredString(tcAnnot);
}
java.util.Date tcDate = VersionTable.getDate(rset, TFTestCaseTable.table.creationDate.getUnqualifiedColName());
MathModelInfo mmInfo = null;
BioModelInfo bmInfo = null;
if (mmRef != null) {
mmInfo = (MathModelInfo) mathModelInfoH.get(mmRef);
if (mmInfo == null) {
Vector<VersionInfo> mathVector = getVersionableInfos(con, user, VersionableType.MathModelMetaData, false, new KeyValue(mmRef), false, dbSyntax);
if (mathVector != null && mathVector.size() > 0) {
mmInfo = (MathModelInfo) mathVector.firstElement();
mathModelInfoH.put(mmRef, mmInfo);
}
}
} else if (bioModelRef != null) {
bmInfo = (BioModelInfo) bioModelInfoH.get(bioModelRef);
if (bmInfo == null) {
Vector<VersionInfo> bmAppVector = getVersionableInfos(con, user, VersionableType.BioModelMetaData, false, new KeyValue(bioModelRef), false, dbSyntax);
if (bmAppVector != null && bmAppVector.size() > 0) {
bmInfo = (BioModelInfo) bmAppVector.firstElement();
bioModelInfoH.put(bioModelRef, bmInfo);
}
}
} else {
throw new RuntimeException("Test case in DB does not have MathmodelRef or BioModelAppRef");
}
TestCriteriaNew[] neededTcritArr = null;
Vector needTcritV = (Vector) tcritH.get(tcaseKey);
if (needTcritV != null) {
neededTcritArr = new TestCriteriaNew[needTcritV.size()];
needTcritV.copyInto(neededTcritArr);
}
TestCaseNew tcn = null;
if (mmInfo != null) {
tcn = new TestCaseNewMathModel(tcaseKey, mmInfo, tcType, tcAnnot, neededTcritArr);
tcV.add(tcn);
} else if (bmInfo != null) {
tcn = new TestCaseNewBioModel(tcaseKey, bmInfo, simContextName, new KeyValue(simContextRef), tcType, tcAnnot, neededTcritArr);
tcV.add(tcn);
} else {
// throw new RuntimeException("Expected testCase MathModelInfo or BioModelInfo to be not null");
}
// counter+= 1;
}
// System.out.println("TCase count="+counter+" time="+((System.currentTimeMillis()-begTime)/1000));
rset.close();
}
// Get TestSuite
{
TestCaseNew[] tcnArr = null;
if (tcV.size() > 0) {
tcnArr = new TestCaseNew[tcV.size()];
tcV.copyInto(tcnArr);
}
sql = "SELECT " + TFTestSuiteTable.table.getTableName() + ".*" + " FROM " + TFTestSuiteTable.table.getTableName() + " WHERE " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + getThisTS + " ORDER BY UPPER(" + TFTestSuiteTable.table.tsVersion.getQualifiedColName() + ")";
rset = stmt.executeQuery(sql);
BigDecimal tsKey = null;
String tsVersion = null;
String tsVCBuild = null;
String tsNumericsBuild = null;
java.util.Date tsDate = null;
String tsAnnot = null;
boolean islocked = true;
if (rset.next()) {
tsKey = rset.getBigDecimal(TFTestSuiteTable.table.id.getUnqualifiedColName());
tsVersion = rset.getString(TFTestSuiteTable.table.tsVersion.getUnqualifiedColName());
tsVCBuild = rset.getString(TFTestSuiteTable.table.vcBuildVersion.getUnqualifiedColName());
tsNumericsBuild = rset.getString(TFTestSuiteTable.table.vcNumericsVersion.getUnqualifiedColName());
tsDate = VersionTable.getDate(rset, TFTestSuiteTable.table.creationDate.getUnqualifiedColName());
tsAnnot = rset.getString(TFTestSuiteTable.table.tsAnnotation.getUnqualifiedColName());
islocked = rset.getBoolean(TFTestSuiteTable.table.isLocked.getUnqualifiedColName());
} else {
throw new ObjectNotFoundException("TestSuite with key=" + getThisTS + " not found");
}
rset.close();
TestSuiteInfoNew tsiNew = new TestSuiteInfoNew(tsKey, tsVersion, tsVCBuild, tsNumericsBuild, tsDate, tsAnnot, islocked);
TestSuiteNew tsn = new TestSuiteNew(tsiNew, tcnArr);
// testSuiteHash.put(tsKey,tsn);
return tsn;
}
} catch (SQLException e) {
lg.error("failed: (" + sql + "): " + e.getMessage(), e);
throw e;
} finally {
DatabasePolicySQL.lg.setLevel(origLogLevel);
if (stmt != null) {
stmt.close();
}
}
}
Also used :
PermissionException(org.vcell.util.PermissionException)
KeyValue(org.vcell.util.document.KeyValue)
SQLException(java.sql.SQLException)
TestCriteriaNewBioModel(cbit.vcell.numericstest.TestCriteriaNewBioModel)
TestCaseNewBioModel(cbit.vcell.numericstest.TestCaseNewBioModel)
TestCriteriaNewMathModel(cbit.vcell.numericstest.TestCriteriaNewMathModel)
ResultSet(java.sql.ResultSet)
VariableComparisonSummary(cbit.vcell.solver.test.VariableComparisonSummary)
Vector(java.util.Vector)
DataAccessException(org.vcell.util.DataAccessException)
TestSuiteNew(cbit.vcell.numericstest.TestSuiteNew)
Hashtable(java.util.Hashtable)
InsertHashtable(cbit.sql.InsertHashtable)
PreparedStatement(java.sql.PreparedStatement)
Statement(java.sql.Statement)
BioModelInfo(org.vcell.util.document.BioModelInfo)
MathModelInfo(org.vcell.util.document.MathModelInfo)
TestCaseNew(cbit.vcell.numericstest.TestCaseNew)
BigDecimal(java.math.BigDecimal)
VersionInfo(org.vcell.util.document.VersionInfo)
ObjectNotFoundException(org.vcell.util.ObjectNotFoundException)
TestCriteriaNew(cbit.vcell.numericstest.TestCriteriaNew)
Level(org.apache.log4j.Level)
TestCaseNewMathModel(cbit.vcell.numericstest.TestCaseNewMathModel)
TestSuiteInfoNew(cbit.vcell.numericstest.TestSuiteInfoNew)
SimulationInfo(cbit.vcell.solver.SimulationInfo)
Aggregations
TestCriteriaNewBioModel (cbit.vcell.numericstest.TestCriteriaNewBioModel)9
TestCriteriaNewMathModel (cbit.vcell.numericstest.TestCriteriaNewMathModel)9
TestCriteriaNew (cbit.vcell.numericstest.TestCriteriaNew)5
SimulationInfo (cbit.vcell.solver.SimulationInfo)5
TestCaseNewBioModel (cbit.vcell.numericstest.TestCaseNewBioModel)4
TestCaseNewMathModel (cbit.vcell.numericstest.TestCaseNewMathModel)4
DataAccessException (org.vcell.util.DataAccessException)4
BioModelInfo (org.vcell.util.document.BioModelInfo)4
MathModelInfo (org.vcell.util.document.MathModelInfo)4
EditTestCriteriaOPBioModel (cbit.vcell.numericstest.EditTestCriteriaOPBioModel)3
EditTestCriteriaOPMathModel (cbit.vcell.numericstest.EditTestCriteriaOPMathModel)3
TestCaseNew (cbit.vcell.numericstest.TestCaseNew)3
TestSuiteNew (cbit.vcell.numericstest.TestSuiteNew)3
ObjectNotFoundException (org.vcell.util.ObjectNotFoundException)3
BioModel (cbit.vcell.biomodel.BioModel)2
MathModel (cbit.vcell.mathmodel.MathModel)2
AddTestCasesOPBioModel (cbit.vcell.numericstest.AddTestCasesOPBioModel)2
AddTestCasesOPMathModel (cbit.vcell.numericstest.AddTestCasesOPMathModel)2
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