Example 1 with VariableComparisonSummary
use of cbit.vcell.solver.test.VariableComparisonSummary in project vcell by virtualcell.
the class MathTestingReportGenerator method main.
public static void main(String[] args) {
ClientServerManager clientServerManager = null;
try {
if (args.length != 3) {
System.out.println("usage: MathTestingReportGenerator apihost apiport password");
System.exit(1);
}
String userid = "vcelltestaccount";
String apihost = args[0];
Integer apiport = Integer.parseInt(args[1]);
String password = args[2];
clientServerManager = ClientFactory.createRemoteClientServerManager(apihost, apiport, userid, password);
DocumentManager documentManager = clientServerManager.getDocumentManager();
TestSuiteInfoNew[] testSuiteInfos = documentManager.getTestSuiteInfos();
for (TestSuiteInfoNew testSuiteInfo : testSuiteInfos) {
System.out.println(testSuiteInfo.toShortString());
}
//
// sorted by TSKey
//
Arrays.sort(testSuiteInfos, new Comparator<TestSuiteInfoNew>() {
@Override
public int compare(TestSuiteInfoNew o1, TestSuiteInfoNew o2) {
return o1.getTSKey().compareTo(o2.getTSKey());
}
});
//
// print out details of the last one.
//
TestSuiteNew testSuite = documentManager.getTestSuite(testSuiteInfos[testSuiteInfos.length - 1].getTSKey());
for (TestCaseNew testCase : testSuite.getTestCases()) {
System.out.println("TEST CASE: " + testCase.getAnnotation());
TestCriteriaNew[] testCriterias = testCase.getTestCriterias();
for (TestCriteriaNew testCriteria : testCriterias) {
System.out.println(" CRITERIA: " + testCriteria.getReportStatusMessage());
for (VariableComparisonSummary summary : testCriteria.getVarComparisonSummaries()) {
System.out.println(" SUMMARY: " + summary.toShortString());
}
}
}
} catch (Exception e) {
e.printStackTrace(System.out);
} finally {
if (clientServerManager != null) {
clientServerManager.cleanup();
}
}
}
Also used :
DocumentManager(cbit.vcell.clientdb.DocumentManager)
ClientServerManager(cbit.vcell.client.server.ClientServerManager)
VariableComparisonSummary(cbit.vcell.solver.test.VariableComparisonSummary)
Example 2 with VariableComparisonSummary
use of cbit.vcell.solver.test.VariableComparisonSummary 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 3 with VariableComparisonSummary
use of cbit.vcell.solver.test.VariableComparisonSummary in project vcell by virtualcell.
the class BiomodelsDB_TestSuite method main.
public static void main(String[] args) {
try {
Logging.init();
/*sanity check -- we currently only have a copasi_java dll for 32-bit, so let's make sure
* we're running on the right JVM. (Note we can run this on 64 bit machine, just have to install
* a 32 bit JVM...)
*/
OperatingSystemInfo osi = OperatingSystemInfo.getInstance();
if (!osi.isWindows() || osi.is64bit()) {
System.err.println("run on 32 bit JVM");
System.exit(99);
}
// following are set in command line processing
SortedSet<BiomodelsNetEntry> modelIDs = new TreeSet<BiomodelsNetEntry>();
BioModelsWebServices service = null;
File outDir = null;
boolean isDetailed;
{
// scope for command line processing
Options commandOptions = new Options();
Option help = new Option("help", false, "show help");
commandOptions.addOption(help);
Option detailed = new Option("detailed", false, "record detailed information");
commandOptions.addOption(detailed);
Option output = new Option("output", true, "output directory");
output.setRequired(true);
commandOptions.addOption(output);
OptionGroup primary = new OptionGroup();
LOption min = new LOption("min", true, "minimum number of model to import", true);
min.setType(Number.class);
LOption only = new LOption("only", true, "run only this model", false);
only.setType(Number.class);
LOption include = new LOption("include", true, "run on models in specified file", false);
include.setType(String.class);
LOption exclude = new LOption("exclude", true, "exclude models in specified file", true);
exclude.setType(String.class);
primary.addOption(min).addOption(only).addOption(include).addOption(exclude);
for (Object obj : primary.getOptions()) {
// CLI old, non-generic API
commandOptions.addOption((Option) obj);
}
CommandLine cmdLine = null;
try {
CommandLineParser parser = new DefaultParser();
cmdLine = parser.parse(commandOptions, args);
} catch (ParseException e1) {
e1.printStackTrace();
HelpFormatter hf = new HelpFormatter();
hf.printHelp("BiomodelsDB_TestSuite", commandOptions);
System.exit(2);
}
Option[] present = cmdLine.getOptions();
Set<Option> optionSet = new HashSet<Option>(Arrays.asList(present));
if (optionSet.contains(help)) {
HelpFormatter hf = new HelpFormatter();
hf.printHelp("BiomodelsDB_TestSuite", commandOptions);
System.exit(0);
}
// placeholder, avoid messing with nulls
LOption primaryOpt = new LOption("", false, "", true);
@SuppressWarnings("unchecked") Collection<? extends Option> priOpts = primary.getOptions();
priOpts.retainAll(optionSet);
if (!priOpts.isEmpty()) {
assert (priOpts.size() == 1);
primaryOpt = (LOption) priOpts.iterator().next();
}
outDir = new File(cmdLine.getOptionValue(output.getOpt()));
if (!outDir.exists()) {
outDir.mkdirs();
}
isDetailed = optionSet.contains(detailed);
BioModelsWebServicesServiceLocator locator = new BioModelsWebServicesServiceLocator();
service = locator.getBioModelsWebServices();
if (primaryOpt.downloads) {
String[] modelStrings = service.getAllCuratedModelsId();
for (String s : modelStrings) {
modelIDs.add(new BiomodelsNetEntry(s));
}
}
if (primaryOpt == only) {
Long only1 = (Long) cmdLine.getParsedOptionValue(only.getOpt());
modelIDs.add(new BiomodelsNetEntry(only1.intValue()));
} else if (primaryOpt == min) {
Long lv = (Long) cmdLine.getParsedOptionValue(min.getOpt());
int minimumModel = lv.intValue();
for (int m = 0; m < minimumModel; m++) {
modelIDs.remove(new BiomodelsNetEntry(m));
}
} else if (primaryOpt == include) {
FileBaseFilter fbf = new FileBaseFilter(cmdLine.getOptionValue(include.getOpt()));
modelIDs.addAll(fbf.models);
} else if (primaryOpt == exclude) {
FileBaseFilter fbf = new FileBaseFilter(cmdLine.getOptionValue(exclude.getOpt()));
modelIDs.removeAll(fbf.models);
}
}
// end command line processing
WriterFlusher flusher = new WriterFlusher(10);
PrintWriter detailWriter;
PrintWriter bngWriter;
PrintWriter sbmlWriter;
SBMLExceptionSorter sbmlExceptions;
if (isDetailed) {
detailWriter = new PrintWriter(new File(outDir, "compareDetail.txt"));
bngWriter = new PrintWriter(new File(outDir, "bngErrors.txt"));
sbmlWriter = new PrintWriter(new File(outDir, "sbmlErrors.txt"));
sbmlExceptions = new LiveSorter();
flusher.add(detailWriter);
flusher.add(bngWriter);
flusher.add(sbmlWriter);
} else {
detailWriter = new PrintWriter(new NullWriter());
bngWriter = new PrintWriter(new NullWriter());
sbmlWriter = new PrintWriter(new NullWriter());
sbmlExceptions = new NullSorter();
}
PropertyLoader.loadProperties();
/**
* example properties
*
* vcell.COPASI.executable = "C:\\Program Files\\COPASI\\bin\\CopasiSE.exe"
* vcell.mathSBML.directory = "c:\\developer\\eclipse\\workspace\\mathsbml\\"
* vcell.mathematica.kernel.executable = "C:\\Program Files\\Wolfram Research\\Mathematica\\7.0\\MathKernel.exe"
*/
ResourceUtil.setNativeLibraryDirectory();
PrintWriter printWriter = new PrintWriter(new FileWriter(new File(outDir, "summary.log"), true));
flusher.add(printWriter);
listModels(printWriter, modelIDs);
// SBMLSolver copasiSBMLSolver = new CopasiSBMLSolver();
SBMLSolver copasiSBMLSolver = new SBMLSolver() {
@Override
public File solve(String filePrefix, File outDir, String sbmlText, SimSpec testSpec) throws IOException, SolverException, SbmlException {
throw new RuntimeException("COPASI SOLVER REMOVED, REIMPLEMENT");
}
@Override
public String getResultsFileColumnDelimiter() {
throw new RuntimeException("COPASI SOLVER REMOVED, REIMPLEMENT");
}
};
try {
printWriter.println(" | *BIOMODEL ID* | *BioModel name* | *PASS* | *Rel Error (VC/COP)(VC/MSBML)(COP/MSBML)* | *Exception* | ");
removeToxic(modelIDs, printWriter);
for (BiomodelsNetEntry modelID : modelIDs) {
String modelName = service.getModelNameById(modelID.toString());
String modelSBML = service.getModelById(modelID.toString());
Element bioModelInfo = new Element(BioModelsNetPanel.BIOMODELINFO_ELEMENT_NAME);
bioModelInfo.setAttribute(BioModelsNetPanel.ID_ATTRIBUTE_NAME, modelID.toString());
bioModelInfo.setAttribute(BioModelsNetPanel.SUPPORTED_ATTRIBUTE_NAME, "false");
bioModelInfo.setAttribute("vcell_ran", "false");
bioModelInfo.setAttribute("COPASI_ran", "false");
bioModelInfo.setAttribute("mSBML_ran", "false");
bioModelInfo.setAttribute(BioModelsNetPanel.MODELNAME_ATTRIBUTE_NAME, modelName);
boolean bUseUTF8 = true;
File sbmlFile = new File(outDir, modelID + ".sbml");
XmlUtil.writeXMLStringToFile(modelSBML, sbmlFile.getAbsolutePath(), bUseUTF8);
PrintStream saved_sysout = System.out;
PrintStream saved_syserr = System.err;
PrintStream new_sysout = null;
PrintStream new_syserr = null;
try {
String filePrefix = modelID.toString();
String sbmlText = modelSBML;
File logFile = new File(outDir, filePrefix + ".log");
new_sysout = new PrintStream(logFile);
new_syserr = new_sysout;
System.setOut(new_sysout);
System.setErr(new_syserr);
StringBuffer combinedErrorBuffer = new StringBuffer();
SimSpec simSpec = SimSpec.fromSBML(modelSBML);
String[] varsToTest = simSpec.getVarsList();
printWriter.print("ModelId: " + modelID + ": ");
// if a model crashes out the libSBML dll, we will terminate abruptly. Flush
// summary log before that happens
printWriter.flush();
try {
//
// get VCell solution with an embedded "ROUND TRIP" (time and species concentrations)
//
ODESolverResultSet vcellResults_RT = null;
try {
VCellSBMLSolver vcellSBMLSolver_RT = new VCellSBMLSolver();
vcellSBMLSolver_RT.setRoundTrip(false);
// TODO try with round-trip later.
String columnDelimiter = vcellSBMLSolver_RT.getResultsFileColumnDelimiter();
File resultFile = vcellSBMLSolver_RT.solve(filePrefix, outDir, sbmlFile.getAbsolutePath(), simSpec);
vcellResults_RT = readResultFile(resultFile, columnDelimiter);
bioModelInfo.setAttribute("vcell_ran", "true");
} catch (BNGException e) {
bngWriter.println(modelID + " " + e.getMessage());
throw e;
} catch (SBMLImportException e) {
ModelException me = new ModelException(modelID, e);
write(sbmlWriter, me);
sbmlExceptions.add(me);
throw e;
} catch (Exception e) {
printWriter.println("vcell solve(roundtrip=true) failed");
e.printStackTrace(printWriter);
System.out.println("vcell solve(roundtrip=true) failed");
e.printStackTrace(System.out);
combinedErrorBuffer.append(" *VCELL_RT* _" + e.getMessage() + "_ ");
Element vcellSolverReport = new Element("SolverReport");
vcellSolverReport.setAttribute("solverName", "vcell");
vcellSolverReport.setAttribute("errorMessage", e.getMessage());
bioModelInfo.addContent(vcellSolverReport);
bioModelInfo.setAttribute("vcell_ran", "false");
}
//
// get COPASI solution (time and species concentrations)
//
ODESolverResultSet copasiResults = null;
try {
String columnDelimiter = copasiSBMLSolver.getResultsFileColumnDelimiter();
File resultFile = copasiSBMLSolver.solve(filePrefix, outDir, sbmlText, simSpec);
copasiResults = readResultFile(resultFile, columnDelimiter);
bioModelInfo.setAttribute("COPASI_ran", "true");
} catch (Exception e) {
printWriter.println("Copasi solve() failed");
e.printStackTrace(printWriter);
System.out.println("Copasi solve() failed");
e.printStackTrace(System.out);
combinedErrorBuffer.append(" *COPASI* _" + e.getMessage() + "_ ");
Element copasiSolverReport = new Element("SolverReport");
copasiSolverReport.setAttribute("solverName", "COPASI");
copasiSolverReport.setAttribute("errorMessage", e.getMessage());
bioModelInfo.addContent(copasiSolverReport);
bioModelInfo.setAttribute("COPASI_ran", "false");
}
//
// get mSBML solution (time and species concentrations)
//
/*
ODESolverResultSet mSBMLResults = null;
if (idInt != 246 && idInt != 250 && idInt != 285 && idInt != 301) {
try {
MathSBMLSolver mSBMLSolver = new MathSBMLSolver();
String columnDelimiter = mSBMLSolver.getResultsFileColumnDelimiter();
org.sbml.libsbml.SBMLDocument sbmlDocument = new SBMLReader().readSBML(sbmlFile.getAbsolutePath());
long level = sbmlDocument.getLevel();
long version = sbmlDocument.getVersion();
String mathsbmlFilePrefix = filePrefix;
if (level!=2 || (level==2 && version>3)){
// sbmlDocument.setConsistencyChecksForConversion(libsbmlConstants.LIBSBML_CAT_MODELING_PRACTICE, false);
long numErrors = sbmlDocument.checkL2v3Compatibility();
if (numErrors==0){
boolean bConversionWorked = sbmlDocument.setLevelAndVersion(2, 3, false);
SBMLDocument doc = new SBMLDocument(sbmlDocument);
doc.setLevelAndVersion(2,3,false);
if (bConversionWorked){
mathsbmlFilePrefix = filePrefix+"_L2V3";
long newVersion = doc.getVersion();
SBMLWriter sbmlWriter = new SBMLWriter();
sbmlText = sbmlWriter.writeToString(doc);
try {
XmlUtil.writeXMLStringToFile(sbmlText, mathsbmlFilePrefix+".sbml", true);
} catch (IOException e1) {
e1.printStackTrace(System.out);
}
}else{
throw new RuntimeException("couldn't convert SBML from L"+level+"V"+version+" to L2V3");
}
}else{
throw new RuntimeException("couldn't convert SBML from L"+level+"V"+version+" to L2V3, not compatible: "+sbmlDocument.getError(0));
}
}
File resultFile = mSBMLSolver.solve(mathsbmlFilePrefix, outDir, sbmlText, simSpec);
mSBMLResults = readResultFile(resultFile, columnDelimiter);
bioModelInfo.setAttribute("mSBML_ran","true");
}catch (Exception e){
printWriter.println("mSBML solve() failed");
e.printStackTrace(printWriter);
System.out.println("mSBML solve() failed");
e.printStackTrace(System.out);
combinedErrorBuffer.append(" *mSBML* _"+e.getMessage()+"_ ");
Element mSBMLSolverReport = new Element("SolverReport");
mSBMLSolverReport.setAttribute("solverName","mSBML");
mSBMLSolverReport.setAttribute("errorMessage",e.getMessage());
bioModelInfo.addContent(mSBMLSolverReport);
bioModelInfo.setAttribute("mSBML_ran","false");
}
}
*/
//
// compare results from COPASI and VCELL_RT
//
Boolean bCOPASI_VCELL_matched = null;
if (copasiResults != null && vcellResults_RT != null) {
try {
SimulationComparisonSummary summary = MathTestingUtilities.compareResultSets(copasiResults, vcellResults_RT, varsToTest, TestCaseNew.REGRESSION, 1e-5, 1e-5);
double maxRelError = summary.getMaxRelativeError();
bioModelInfo.setAttribute("COPASI_VCELL_maxRelErr", Double.toString(maxRelError));
if (maxRelError < 1) {
bCOPASI_VCELL_matched = true;
} else {
detailWriter.println(modelID + " " + modelName);
bCOPASI_VCELL_matched = false;
Element solverComparison = new Element("SolverComparison");
solverComparison.setAttribute("solver1", "vcell");
solverComparison.setAttribute("solver2", "COPASI");
VariableComparisonSummary[] failedVCSummaries = summary.getFailingVariableComparisonSummaries(1e-5, 1e-5);
for (VariableComparisonSummary vcSummary : failedVCSummaries) {
Element failedVariableSummary = getVariableSummary(vcSummary);
solverComparison.addContent(failedVariableSummary);
String ss = vcSummary.toShortString();
detailWriter.print('\t');
detailWriter.println(ss);
System.out.println(ss);
}
detailWriter.println();
bioModelInfo.addContent(solverComparison);
}
} catch (Exception e) {
printWriter.println("COMPARE VC/COPASI failed");
e.printStackTrace(printWriter);
System.out.println("COMPARE VC/COPASI failed");
e.printStackTrace(System.out);
combinedErrorBuffer.append(" *COMPARE VC/COPASI* _" + e.getMessage() + "_ ");
Element solverComparison = new Element("SolverComparison");
solverComparison.setAttribute("solver1", "vcell");
solverComparison.setAttribute("solver2", "COPASI");
solverComparison.setAttribute("error", e.getMessage());
bioModelInfo.addContent(solverComparison);
}
}
/*
Boolean bmSBML_VCELL_matched = null;
if (mSBMLResults!=null && vcellResults_RT!=null){
try {
SimulationComparisonSummary summary = MathTestingUtilities.compareUnEqualResultSets(mSBMLResults, vcellResults_RT, varsToTest, 1e-5, 1e-5, 1);
double maxRelError = summary.getMaxRelativeError();
bioModelInfo.setAttribute("mSBML_VCELL_maxRelErr", Double.toString(maxRelError));
if (maxRelError<1){
bmSBML_VCELL_matched = true;
}else{
bmSBML_VCELL_matched = false;
Element solverComparison = new Element("SolverComparison");
solverComparison.setAttribute("solver1","vcell");
solverComparison.setAttribute("solver2","mSBML");
VariableComparisonSummary[] failedVCSummaries = summary.getFailingVariableComparisonSummaries(1e-5, 1e-5);
for (VariableComparisonSummary vcSummary : failedVCSummaries){
Element failedVariableSummary = getVariableSummary(vcSummary);
solverComparison.addContent(failedVariableSummary);
System.out.println(vcSummary.toShortString());
}
bioModelInfo.addContent(solverComparison);
}
} catch (Exception e) {
printWriter.println("COMPARE VCRT/mSBML failed");
e.printStackTrace(printWriter);
System.out.println("COMPARE VCRT/mSBML failed");
e.printStackTrace(System.out);
combinedErrorBuffer.append(" *COMPARE VCRT/mSBML* _"+e.getMessage()+"_ ");
Element solverComparison = new Element("SolverComparison");
solverComparison.setAttribute("solver1","vcell");
solverComparison.setAttribute("solver2","mSBML");
solverComparison.setAttribute("error",e.getMessage());
bioModelInfo.addContent(solverComparison);
}
}
//
// compare results from COPASI and mSBML
//
Boolean bCOPASI_mSBML_matched = null;
if (copasiResults!=null && mSBMLResults!=null){
try {
SimulationComparisonSummary summary = MathTestingUtilities.compareUnEqualResultSets(copasiResults, mSBMLResults, varsToTest, 1e-5, 1e-5, 1);
double maxRelError = summary.getMaxRelativeError();
bioModelInfo.setAttribute("COPASI_mSBML_maxRelErr", Double.toString(maxRelError));
if (maxRelError<1){
bCOPASI_mSBML_matched = true;
}else{
bCOPASI_mSBML_matched = false;
Element solverComparison = new Element("SolverComparison");
solverComparison.setAttribute("solver1","COPASI");
solverComparison.setAttribute("solver2","mSBML");
solverComparison.setAttribute("result","failed");
VariableComparisonSummary[] vcSummaries = summary.getVariableComparisonSummaries();
for (VariableComparisonSummary vcSummary : vcSummaries){
Element failedVariableSummary = getVariableSummary(vcSummary);
solverComparison.addContent(failedVariableSummary);
System.out.println(vcSummary.toShortString());
}
bioModelInfo.addContent(solverComparison);
}
} catch (Exception e) {
printWriter.println("COMPARE COPASI/mSBML failed");
e.printStackTrace(printWriter);
System.out.println("COMPARE COPASI/mSBML failed");
e.printStackTrace(System.out);
combinedErrorBuffer.append(" *COMPARE COPASI/mSBML* _"+e.getMessage()+"_ ");
Element solverComparison = new Element("SolverComparison");
solverComparison.setAttribute("solver1","COPASI");
solverComparison.setAttribute("solver2","mSBML");
solverComparison.setAttribute("error",e.getMessage());
}
}
*/
if ((bCOPASI_VCELL_matched != null && bCOPASI_VCELL_matched.booleanValue())) {
// || /*(bmSBML_VCELL_matched!=null && bmSBML_VCELL_matched.booleanValue()) */ )
bioModelInfo.setAttribute(BioModelsNetPanel.SUPPORTED_ATTRIBUTE_NAME, "true");
printWriter.println("PASS");
} else {
bioModelInfo.setAttribute(BioModelsNetPanel.SUPPORTED_ATTRIBUTE_NAME, "false");
printWriter.println("FAIL");
}
} catch (Exception e) {
e.printStackTrace(printWriter);
combinedErrorBuffer.append(" *UNKNOWN* _" + e.getMessage() + "_ ");
bioModelInfo.setAttribute(BioModelsNetPanel.SUPPORTED_ATTRIBUTE_NAME, "false");
bioModelInfo.setAttribute("exception", e.getMessage());
}
printWriter.flush();
// write for each model just in case files get corrupted (it happened).
write(bioModelInfo, new File(outDir, modelID + "_report.xml"));
} finally {
if (new_sysout != null) {
new_sysout.close();
new_sysout = null;
}
if (new_syserr != null) {
new_syserr.close();
new_syserr = null;
}
System.setOut(saved_sysout);
System.setOut(saved_syserr);
}
}
// this writes out the SBML import exceptions grouped by type
if (!sbmlExceptions.isEmpty()) {
Map<Category, Collection<ModelException>> map = sbmlExceptions.getMap();
try (PrintWriter pw = new PrintWriter(new File(outDir, "sbmlSorted.txt"))) {
// SBMLImportException.Category
for (Category c : Category.values()) {
Collection<ModelException> meCollection = map.get(c);
for (ModelException me : meCollection) {
write(pw, me);
}
}
}
}
} finally {
printWriter.close();
detailWriter.close();
bngWriter.close();
}
} catch (Throwable e) {
e.printStackTrace(System.out);
e.printStackTrace(System.err);
}
System.exit(0);
}
Also used :
BNGException(cbit.vcell.server.bionetgen.BNGException)
HelpFormatter(org.apache.commons.cli.HelpFormatter)
TreeSet(java.util.TreeSet)
SBMLSolver(org.vcell.sbml.SBMLSolver)
VariableComparisonSummary(cbit.vcell.solver.test.VariableComparisonSummary)
BioModelsWebServicesServiceLocator(uk.ac.ebi.www.biomodels_main.services.BioModelsWebServices.BioModelsWebServicesServiceLocator)
Collection(java.util.Collection)
Option(org.apache.commons.cli.Option)
File(java.io.File)
Options(org.apache.commons.cli.Options)
SortedSet(java.util.SortedSet)
Set(java.util.Set)
ODESolverResultSet(cbit.vcell.solver.ode.ODESolverResultSet)
TreeSet(java.util.TreeSet)
HashSet(java.util.HashSet)
Category(org.vcell.sbml.vcell.SBMLImportException.Category)
OperatingSystemInfo(cbit.vcell.resource.OperatingSystemInfo)
FileWriter(java.io.FileWriter)
Element(org.jdom.Element)
NullWriter(org.apache.commons.io.output.NullWriter)
OptionGroup(org.apache.commons.cli.OptionGroup)
ODESolverResultSet(cbit.vcell.solver.ode.ODESolverResultSet)
SimulationComparisonSummary(cbit.vcell.solver.test.SimulationComparisonSummary)
CommandLineParser(org.apache.commons.cli.CommandLineParser)
DefaultParser(org.apache.commons.cli.DefaultParser)
PrintWriter(java.io.PrintWriter)
PrintStream(java.io.PrintStream)
SBMLImportException(org.vcell.sbml.vcell.SBMLImportException)
SimSpec(org.vcell.sbml.SimSpec)
SbmlException(org.vcell.sbml.SbmlException)
FileNotFoundException(java.io.FileNotFoundException)
BNGException(cbit.vcell.server.bionetgen.BNGException)
SBMLImportException(org.vcell.sbml.vcell.SBMLImportException)
ParseException(org.apache.commons.cli.ParseException)
SolverException(cbit.vcell.solver.SolverException)
IOException(java.io.IOException)
BioModelsWebServices(uk.ac.ebi.www.biomodels_main.services.BioModelsWebServices.BioModelsWebServices)
CommandLine(org.apache.commons.cli.CommandLine)
ParseException(org.apache.commons.cli.ParseException)
Example 4 with VariableComparisonSummary
use of cbit.vcell.solver.test.VariableComparisonSummary in project vcell by virtualcell.
the class TestingFrmwkTreeModel method createSimulationSubTree.
/**
* 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 createSimulationSubTree(TestCriteriaNew tcInfo, BioModelNode simInfoNode, boolean refSimNull) throws DataAccessException {
//
// add 'reportInfo' node (with nodes for status and comparison summaries for variables) - sim results
//
VariableComparisonSummary[] varCompSummaries = tcInfo.getVarComparisonSummaries();
BioModelNode reportInfoNode = null;
boolean hasFailedVars = false;
if (tcInfo != null) {
// Calculate actual MAE,MRE
double actualMAE = Double.NEGATIVE_INFINITY;
double actualMRE = Double.NEGATIVE_INFINITY;
if (varCompSummaries != null) {
for (int i = 0; i < varCompSummaries.length; i++) {
VariableComparisonSummary var1 = varCompSummaries[i];
actualMAE = Math.max(actualMAE, var1.getAbsoluteError().doubleValue());
actualMRE = Math.max(actualMRE, var1.getRelativeError().doubleValue());
}
reportInfoNode = new BioModelNode("Report Info: maxActualMAE=" + actualMAE + " maxActualMRE=" + actualMRE, true);
// reportInfoNode.add(new BioModelNode("TBI", false));
for (int i = 0; i < varCompSummaries.length; i++) {
// For each Variable, get the corresponding varComparisonSummary,
// Create a node varNode for varName, minRef,maxRef.
// Create nodes for errors and add them as children to varNode
// To enhance readability of errors in ResultSetsubtree on panel ...
VariableComparisonSummary var1 = varCompSummaries[i];
TestCriteriaVarUserObj tcritVarUserObj = new TestCriteriaVarUserObj(tcInfo, var1);
// String varInfo = "Var = " + var1.getName() + " MAE = " + var1.getAbsoluteError() + " MRE = " + var1.getRelativeError();
BioModelNode varInfoNode = new BioModelNode(tcritVarUserObj, true);
if (VariableComparisonSummary.isFailed(var1)) {
varInfoNode.setRenderHint(FAILED_VARIABLE_MAE_MRE, Boolean.TRUE);
hasFailedVars = true;
}
String varInfo = "Mean Square Error = " + var1.getMeanSqError();
varInfoNode.add(new cbit.vcell.desktop.BioModelNode(varInfo, false));
varInfo = "minRef = " + var1.getMinRef();
varInfoNode.add(new cbit.vcell.desktop.BioModelNode(varInfo, false));
varInfo = "maxRef = " + var1.getMaxRef();
varInfoNode.add(new cbit.vcell.desktop.BioModelNode(varInfo, false));
varInfo = "timeAbsError = " + var1.getTimeAbsoluteError();
varInfoNode.add(new cbit.vcell.desktop.BioModelNode(varInfo, false));
varInfo = "indexAbsError = " + var1.getIndexAbsoluteError();
varInfoNode.add(new cbit.vcell.desktop.BioModelNode(varInfo, false));
varInfo = "timeRelError = " + var1.getTimeRelativeError();
varInfoNode.add(new cbit.vcell.desktop.BioModelNode(varInfo, false));
varInfo = "indexRelError = " + var1.getIndexRelativeError();
varInfoNode.add(new cbit.vcell.desktop.BioModelNode(varInfo, false));
reportInfoNode.add(varInfoNode);
}
if (hasFailedVars) {
reportInfoNode.insert(new BioModelNode("FAILED", false), 0);
} else {
reportInfoNode.insert(new BioModelNode("PASSED", false), 0);
}
} else {
String status = "NO DATA";
if (refSimNull) {
status = status + " : REFERENCE SIMULATION NOT SPECIFIED";
}
reportInfoNode = new BioModelNode(status, false);
reportInfoNode.setRenderHint(SIMULATIONS_NO_REPORT, Boolean.TRUE);
}
}
if (hasFailedVars) {
simInfoNode.setRenderHint(FAILED_VARIABLE_MAE_MRE, Boolean.TRUE);
} else {
simInfoNode.setRenderHint(FAILED_VARIABLE_MAE_MRE, Boolean.FALSE);
}
return reportInfoNode;
}
Also used :
BioModelNode(cbit.vcell.desktop.BioModelNode)
BioModelNode(cbit.vcell.desktop.BioModelNode)
VariableComparisonSummary(cbit.vcell.solver.test.VariableComparisonSummary)
Example 5 with VariableComparisonSummary
use of cbit.vcell.solver.test.VariableComparisonSummary in project vcell by virtualcell.
the class DbDriver method testSuiteOP.
/**
* Insert the method's description here.
* Creation date: (10/19/2004 6:55:36 AM)
* @return cbit.vcell.numericstest.TestSuiteNew
* @param tsop cbit.vcell.numericstest.TestSuiteOP
*/
public static TestSuiteOPResults testSuiteOP(TestSuiteOP tsop, Connection con, User user, KeyFactory keyFactory) throws SQLException, DataAccessException {
java.util.TreeSet<BigDecimal> changedTestSuiteKeys = new java.util.TreeSet<BigDecimal>();
String sql = null;
Statement stmt = null;
try {
if (tsop instanceof ModelGeometryOP) {
ModelGeometryOP modelGeometryOP = (ModelGeometryOP) tsop;
if (modelGeometryOP.getVCDocumentInfo() instanceof BioModelInfo) {
BioModelInfo bioModelInfo = (BioModelInfo) modelGeometryOP.getVCDocumentInfo();
sql = "SELECT " + SimContextTable.table.geometryRef.getQualifiedColName() + " FROM " + SimContextTable.table.getTableName() + "," + BioModelSimContextLinkTable.table.getTableName() + " WHERE " + SimContextTable.table.name.getQualifiedColName() + " = '" + modelGeometryOP.getBioModelApplicationName() + "'" + " AND " + BioModelSimContextLinkTable.table.simContextRef.getQualifiedColName() + " = " + SimContextTable.table.id.getQualifiedColName() + " AND " + BioModelSimContextLinkTable.table.bioModelRef.getQualifiedColName() + " = " + bioModelInfo.getVersion().getVersionKey().toString();
} else if (modelGeometryOP.getVCDocumentInfo() instanceof MathModelInfo) {
MathModelInfo mathModelInfo = (MathModelInfo) modelGeometryOP.getVCDocumentInfo();
sql = "SELECT " + MathDescTable.table.geometryRef.getQualifiedColName() + " FROM " + MathDescTable.table.getTableName() + "," + MathModelTable.table.getTableName() + " WHERE " + MathModelTable.table.id.getQualifiedColName() + " = " + mathModelInfo.getVersion().getVersionKey().toString() + " AND " + MathModelTable.table.mathRef.getQualifiedColName() + " = " + MathDescTable.table.id.getQualifiedColName();
} else {
throw new IllegalArgumentException("UnImplemented VCDocumentInfo type=" + modelGeometryOP.getVCDocumentInfo().getClass().getName());
}
stmt = con.createStatement();
ResultSet rset = stmt.executeQuery(sql);
BigDecimal geometryKey = null;
if (rset.next()) {
geometryKey = rset.getBigDecimal(1);
if (rset.next()) {
throw new DataAccessException("Expecting only 1 Geometry but found at least 2");
}
} else {
throw new DataAccessException("No Geometry found using criteria");
}
rset.close();
stmt.close();
return new ModelGeometryOPResults(new KeyValue(geometryKey));
} else //
if (tsop instanceof LoadTestInfoOP) {
//
if (((LoadTestInfoOP) tsop).getLoadTestOpFlag() == LoadTestOpFlag.delete) {
// Delete before return details
LoadTestSoftwareVersionTimeStamp[] deleteTheseVersTimeStamps = ((LoadTestInfoOP) tsop).getLoadTestSoftwareVersionTimeStamps();
for (int i = 0; i < deleteTheseVersTimeStamps.length; i++) {
sql = "DELETE FROM " + LoadModelsStatTable.table.getTableName() + " WHERE " + LoadModelsStatTable.table.softwareVers + " = " + "'" + deleteTheseVersTimeStamps[i].getSoftwareVersion() + "'" + " AND " + LoadModelsStatTable.table.timeStamp + " = " + "'" + deleteTheseVersTimeStamps[i].getRunTimeStamp() + "'";
DbDriver.updateCleanSQL(con, sql);
}
return null;
}
// Check if Date info is requested
if (((LoadTestInfoOP) tsop).getLoadTestOpFlag() == LoadTestOpFlag.info && ((LoadTestInfoOP) tsop).getBeginDate() != null) {
final String YMD_FORMAT_STRING = "yyyy-MM-dd";
SimpleDateFormat simpleDateFormat = new SimpleDateFormat(YMD_FORMAT_STRING);
final String BETWEEN_CONDITION = " BETWEEN " + " TO_DATE('" + simpleDateFormat.format(((LoadTestInfoOP) tsop).getBeginDate()) + " 00:00:00', '" + YMD_FORMAT_STRING + " HH24:MI:SS') " + " AND " + " TO_DATE('" + simpleDateFormat.format(((LoadTestInfoOP) tsop).getEndDate()) + " 23:59:59', '" + YMD_FORMAT_STRING + " HH24:MI:SS') ";
sql = "SELECT " + BioModelTable.table.id.getQualifiedColName() + "," + UserTable.table.userid.getUnqualifiedColName() + " FROM " + BioModelTable.table.getTableName() + "," + UserTable.table.getTableName() + " WHERE " + UserTable.table.id.getQualifiedColName() + " = " + BioModelTable.table.ownerRef.getQualifiedColName() + " AND " + BioModelTable.table.versionDate.getQualifiedColName() + BETWEEN_CONDITION + " UNION " + "SELECT " + MathModelTable.table.id.getQualifiedColName() + "," + UserTable.table.userid.getUnqualifiedColName() + " FROM " + MathModelTable.table.getTableName() + "," + UserTable.table.getTableName() + " WHERE " + UserTable.table.id.getQualifiedColName() + " = " + MathModelTable.table.ownerRef.getQualifiedColName() + " AND " + MathModelTable.table.versionDate.getQualifiedColName() + BETWEEN_CONDITION;
stmt = con.createStatement();
ResultSet rset = stmt.executeQuery(sql);
TreeSet<String> uniqueUserIDTreeSet = new TreeSet<String>();
Vector<KeyValue> keyValuesBetweenDatesV = new Vector<KeyValue>();
while (rset.next()) {
uniqueUserIDTreeSet.add(rset.getString(UserTable.table.userid.getUnqualifiedColName()));
keyValuesBetweenDatesV.add(new KeyValue(rset.getBigDecimal(1)));
}
rset.close();
stmt.close();
return new LoadTestInfoOpResults(((LoadTestInfoOP) tsop).getBeginDate(), ((LoadTestInfoOP) tsop).getEndDate(), keyValuesBetweenDatesV.toArray(new KeyValue[0]), uniqueUserIDTreeSet.toArray(new String[0]));
}
//
// Get LoadTest Info
//
// Get existing SoftwareVersion-Timestamp count
//
Vector<Integer> loadTestInfoCountV = new Vector<Integer>();
stmt = con.createStatement();
sql = "SELECT COUNT(*)," + LoadModelsStatTable.table.softwareVers.getUnqualifiedColName() + "," + LoadModelsStatTable.table.timeStamp.getUnqualifiedColName() + " FROM " + LoadModelsStatTable.table.getTableName() + " GROUP BY " + LoadModelsStatTable.table.softwareVers.getUnqualifiedColName() + "," + LoadModelsStatTable.table.timeStamp.getUnqualifiedColName();
Vector<LoadTestInfoOpResults.LoadTestSoftwareVersionTimeStamp> loadTestSoftwareVersionTimeStampsExistingV = new Vector<LoadTestInfoOpResults.LoadTestSoftwareVersionTimeStamp>();
ResultSet rset = stmt.executeQuery(sql);
while (rset.next()) {
String softwareVersion = TokenMangler.getSQLRestoredString(rset.getString(LoadModelsStatTable.table.softwareVers.getUnqualifiedColName()));
String runTimeStamp = rset.getString(LoadModelsStatTable.table.timeStamp.getUnqualifiedColName());
loadTestSoftwareVersionTimeStampsExistingV.add(new LoadTestInfoOpResults.LoadTestSoftwareVersionTimeStamp(softwareVersion, runTimeStamp));
loadTestInfoCountV.add(rset.getInt(1));
}
rset.close();
stmt.close();
//
// Get empty test info count (models that haven't been checked yet during a test run)
//
stmt = con.createStatement();
sql = "SELECT COUNT(*)," + LoadModelsStatTable.table.softwareVers.getUnqualifiedColName() + "," + LoadModelsStatTable.table.timeStamp.getUnqualifiedColName() + " FROM " + LoadModelsStatTable.table.getTableName() + " WHERE " + LoadModelsStatTable.table.resultFlag.getUnqualifiedColName() + " IS NULL" + " GROUP BY " + LoadModelsStatTable.table.softwareVers.getUnqualifiedColName() + "," + LoadModelsStatTable.table.timeStamp.getUnqualifiedColName();
Vector<LoadTestInfoOpResults.LoadTestSoftwareVersionTimeStamp> loadTestSoftwareVersionTimeStampsEmptyV = new Vector<LoadTestInfoOpResults.LoadTestSoftwareVersionTimeStamp>();
rset = stmt.executeQuery(sql);
Integer[] loadTestInfoCountEmptyArr = new Integer[loadTestInfoCountV.size()];
while (rset.next()) {
String softwareVersion = TokenMangler.getSQLRestoredString(rset.getString(LoadModelsStatTable.table.softwareVers.getUnqualifiedColName()));
String runTimeStamp = rset.getString(LoadModelsStatTable.table.timeStamp.getUnqualifiedColName());
loadTestSoftwareVersionTimeStampsEmptyV.add(new LoadTestInfoOpResults.LoadTestSoftwareVersionTimeStamp(softwareVersion, runTimeStamp));
// match to existing array index so full and empty match
for (int i = 0; i < loadTestSoftwareVersionTimeStampsExistingV.size(); i++) {
if (loadTestSoftwareVersionTimeStampsExistingV.elementAt(i).getSoftwareVersion().equals(softwareVersion) && loadTestSoftwareVersionTimeStampsExistingV.elementAt(i).getRunTimeStamp().equals(runTimeStamp)) {
loadTestInfoCountEmptyArr[i] = rset.getInt(1);
}
}
}
rset.close();
stmt.close();
//
// Get total Math and Bio model count
//
int totalBioMathModelCount = 0;
stmt = con.createStatement();
sql = "SELECT COUNT(*) FROM " + BioModelTable.table.getTableName() + " UNION " + "SELECT COUNT(*) FROM " + MathModelTable.table.getTableName();
rset = stmt.executeQuery(sql);
if (rset.next()) {
totalBioMathModelCount = rset.getInt(1);
if (rset.next()) {
totalBioMathModelCount += rset.getInt(1);
} else {
totalBioMathModelCount = 0;
}
}
if (totalBioMathModelCount == 0) {
throw new DataAccessException("No results when querying bio and Mathmodel count");
}
rset.close();
stmt.close();
//
// Get slow Loads
//
Object loadTestSlowHash = null;
if (((LoadTestInfoOP) tsop).getSlowLoadThresholdMilliSec() != null) {
Integer slowLoaderThreshold = ((LoadTestInfoOP) tsop).getSlowLoadThresholdMilliSec();
loadTestSlowHash = getLoadTestDetails(con, slowLoaderThreshold, null);
}
//
// Get failed loads
//
Object loadTestFailHash = getLoadTestDetails(con, null, null);
//
// Get user specified query info.
//
Object loadTestUserQueryHash = null;
if (((LoadTestInfoOP) tsop).getUserQueryCondition() != null) {
loadTestUserQueryHash = getLoadTestDetails(con, null, ((LoadTestInfoOP) tsop).getUserQueryCondition());
}
return new LoadTestInfoOpResults(loadTestInfoCountV.toArray(new Integer[0]), loadTestInfoCountEmptyArr, totalBioMathModelCount, loadTestSoftwareVersionTimeStampsExistingV.toArray(new LoadTestInfoOpResults.LoadTestSoftwareVersionTimeStamp[0]), (Hashtable<LoadTestInfoOpResults.LoadTestSoftwareVersionTimeStamp, Vector<LoadTestInfoOpResults.LoadTestFailDetails>>) loadTestFailHash, (Hashtable<LoadTestInfoOpResults.LoadTestSoftwareVersionTimeStamp, Vector<LoadTestInfoOpResults.LoadTestSlowDetails>>) loadTestSlowHash, (Hashtable<LoadTestInfoOpResults.LoadTestSoftwareVersionTimeStamp, Vector<LoadTestInfoOpResults.LoadTestDetails>>) loadTestUserQueryHash, ((LoadTestInfoOP) tsop).getSlowLoadThresholdMilliSec());
}
//
// TestSuite operations ---------------------------------------------------------------------------------------------------
//
stmt = con.createStatement();
if (tsop instanceof AddTestSuiteOP) {
AddTestSuiteOP addts_tsop = (AddTestSuiteOP) tsop;
String annotation = addts_tsop.getTestSuiteAnnotation();
if (annotation != null) {
if (annotation.length() == 0) {
annotation = null;
} else {
annotation = TokenMangler.getSQLEscapedString(annotation);
}
}
BigDecimal changedTSKey = keyFactory.getUniqueBigDecimal(con);
final int NOT_LOCKED = 0;
sql = "INSERT INTO " + TFTestSuiteTable.table.getTableName() + " VALUES(" + changedTSKey + ",'" + addts_tsop.getTestSuiteVersionID() + "'," + "'" + addts_tsop.getVCellBuildVersionID() + "'" + "," + "'" + addts_tsop.getNumericsBuildVersionID() + "'" + "," + "current_timestamp,current_timestamp," + (annotation == null ? "NULL" : "'" + annotation + "'") + "," + NOT_LOCKED + ")";
stmt.executeUpdate(sql);
if (addts_tsop.getAddTestCasesOPs() != null) {
for (int i = 0; i < addts_tsop.getAddTestCasesOPs().length; i += 1) {
// Set new TSKey and do child OPs
AddTestCasesOP atcOP = addts_tsop.getAddTestCasesOPs()[i];
if (atcOP instanceof AddTestCasesOPMathModel) {
testSuiteOP(new AddTestCasesOPMathModel(changedTSKey, ((AddTestCasesOPMathModel) atcOP).getMathModelKey(), atcOP.getTestCaseType(), atcOP.getAnnotation(), ((AddTestCasesOPMathModel) atcOP).getAddTestCriteriaOPsMathModel()), con, user, keyFactory);
} else if (atcOP instanceof AddTestCasesOPBioModel) {
testSuiteOP(new AddTestCasesOPBioModel(changedTSKey, ((AddTestCasesOPBioModel) atcOP).getBioModelKey(), ((AddTestCasesOPBioModel) atcOP).getSimContextKey(), atcOP.getTestCaseType(), atcOP.getAnnotation(), ((AddTestCasesOPBioModel) atcOP).getAddTestCriteriaOPsBioModel()), con, user, keyFactory);
}
}
}
changedTestSuiteKeys.add(changedTSKey);
} else if (tsop instanceof AddTestCasesOPBioModel) {
AddTestCasesOPBioModel addtc_tsop = (AddTestCasesOPBioModel) tsop;
//
BigDecimal bmSimContextLinkRef = null;
// Convert BioModelKey and SimContextKey to bmsimcontext key
sql = "SELECT " + BioModelSimContextLinkTable.table.id.getQualifiedColName() + " FROM " + BioModelSimContextLinkTable.table.getTableName() + " WHERE " + BioModelSimContextLinkTable.table.bioModelRef.getQualifiedColName() + "=" + addtc_tsop.getBioModelKey().toString() + " AND " + BioModelSimContextLinkTable.table.simContextRef.getQualifiedColName() + "=" + addtc_tsop.getSimContextKey().toString();
ResultSet rset = stmt.executeQuery(sql);
if (rset.next()) {
bmSimContextLinkRef = rset.getBigDecimal(BioModelSimContextLinkTable.table.id.getUnqualifiedColName());
if (rset.next()) {
throw new DataAccessException("Too many MathModelSimLink found for bmKey=" + addtc_tsop.getBioModelKey() + " simContextKey=" + addtc_tsop.getSimContextKey());
}
} else {
throw new DataAccessException("No BioModelSimcontextLink found for bmKey=" + addtc_tsop.getBioModelKey() + " simContextKey=" + addtc_tsop.getSimContextKey());
}
rset.close();
//
BigDecimal tcKey = keyFactory.getUniqueBigDecimal(con);
String annotation = addtc_tsop.getAnnotation();
if (annotation != null) {
annotation = TokenMangler.getSQLEscapedString(annotation);
}
stmt.executeUpdate("INSERT INTO " + TFTestCaseTable.table.getTableName() + " VALUES(" + tcKey.toString() + "," + addtc_tsop.getTestSuiteKey().toString() + ",NULL," + "'" + addtc_tsop.getTestCaseType() + "'" + "," + "'" + annotation + "'" + "," + "current_timestamp" + "," + bmSimContextLinkRef.toString() + ")");
if (addtc_tsop.getAddTestCriteriaOPsBioModel() != null) {
for (int i = 0; i < addtc_tsop.getAddTestCriteriaOPsBioModel().length; i += 1) {
// Set new TSKey,TCaseKey and do child OPs
AddTestCriteriaOPBioModel atcritOP = addtc_tsop.getAddTestCriteriaOPsBioModel()[i];
testSuiteOP(new AddTestCriteriaOPBioModel(tcKey, atcritOP.getBioModelSimKey(), atcritOP.getRegressionBioModelKey(), atcritOP.getRegressionBioModelSimKey(), atcritOP.getMaxAbsoluteError(), atcritOP.getMaxRelativeError(), atcritOP.getAddTestResultsOP()), con, user, keyFactory);
}
}
changedTestSuiteKeys.add(addtc_tsop.getTestSuiteKey());
} else if (tsop instanceof AddTestCasesOPMathModel) {
AddTestCasesOPMathModel addtc_tsop = (AddTestCasesOPMathModel) tsop;
BigDecimal tcKey = keyFactory.getUniqueBigDecimal(con);
KeyValue mmKey = addtc_tsop.getMathModelKey();
String annotation = addtc_tsop.getAnnotation();
if (annotation != null) {
annotation = TokenMangler.getSQLEscapedString(annotation);
}
stmt.executeUpdate("INSERT INTO " + TFTestCaseTable.table.getTableName() + " VALUES(" + tcKey.toString() + "," + addtc_tsop.getTestSuiteKey().toString() + "," + mmKey.toString() + "," + "'" + addtc_tsop.getTestCaseType() + "'" + "," + "'" + annotation + "'" + "," + "current_timestamp" + ",NULL)");
if (addtc_tsop.getAddTestCriteriaOPsMathModel() != null) {
for (int i = 0; i < addtc_tsop.getAddTestCriteriaOPsMathModel().length; i += 1) {
// Set new TSKey,TCaseKey and do child OPs
AddTestCriteriaOPMathModel atcritOP = addtc_tsop.getAddTestCriteriaOPsMathModel()[i];
testSuiteOP(new AddTestCriteriaOPMathModel(tcKey, atcritOP.getMathModelSimKey(), atcritOP.getRegressionMathModelKey(), atcritOP.getRegressionMathModelSimKey(), atcritOP.getMaxAbsoluteError(), atcritOP.getMaxRelativeError(), atcritOP.getAddTestResultsOP()), con, user, keyFactory);
}
}
changedTestSuiteKeys.add(addtc_tsop.getTestSuiteKey());
} else if (tsop instanceof RemoveTestCasesOP) {
RemoveTestCasesOP removetc_tsop = (RemoveTestCasesOP) tsop;
StringBuffer sb = new StringBuffer();
for (int i = 0; i < removetc_tsop.getTestCasesKeys().length; i += 1) {
if (i != 0) {
sb.append(",");
}
sb.append(removetc_tsop.getTestCasesKeys()[i].toString());
}
ResultSet rset = stmt.executeQuery("SELECT DISTINCT " + TFTestSuiteTable.table.id.getQualifiedColName() + " FROM " + TFTestSuiteTable.table.getTableName() + "," + TFTestCaseTable.table.getTableName() + " WHERE " + TFTestCaseTable.table.id.getQualifiedColName() + " IN (" + sb.toString() + ")" + " AND " + TFTestCaseTable.table.testSuiteRef.getQualifiedColName() + "=" + TFTestSuiteTable.table.id.getQualifiedColName());
while (rset.next()) {
changedTestSuiteKeys.add(rset.getBigDecimal(TFTestSuiteTable.table.id.getUnqualifiedColName()));
}
rset.close();
int numRowsUpdated = stmt.executeUpdate("DELETE FROM " + TFTestCaseTable.table.getTableName() + " WHERE " + TFTestCaseTable.table.id.getUnqualifiedColName() + " IN (" + sb.toString() + ")");
if (numRowsUpdated != removetc_tsop.getTestCasesKeys().length) {
throw new DataAccessException("Remove TestCase keys=" + sb.toString() + " from TSKey=" + removetc_tsop.getTestSuiteKey() + " removed row count=" + numRowsUpdated + " expected " + removetc_tsop.getTestCasesKeys().length);
}
} else if (tsop instanceof AddTestCriteriaOPMathModel) {
AddTestCriteriaOPMathModel addtcrit_tsop = (AddTestCriteriaOPMathModel) tsop;
BigDecimal tcritKey = keyFactory.getUniqueBigDecimal(con);
BigDecimal tcKey = addtcrit_tsop.getTestCaseKey();
KeyValue simKey = addtcrit_tsop.getMathModelSimKey();
// Check that there is a single mathmodel associated with simkey and parentsimref is null
sql = "SELECT " + MathModelSimulationLinkTable.table.id.getQualifiedColName() + " FROM " + MathModelSimulationLinkTable.table.getTableName() + "," + SimulationTable.table.getTableName() + " WHERE " + MathModelSimulationLinkTable.table.simRef.getQualifiedColName() + "=" + simKey.toString() + " AND " + MathModelSimulationLinkTable.table.simRef.getQualifiedColName() + "=" + SimulationTable.table.id.getQualifiedColName() + " AND " + SimulationTable.table.getTableName() + "." + SimulationTable.versionParentSimRef_ColumnName + " IS NULL";
ResultSet rset = stmt.executeQuery(sql);
if (rset.next()) {
if (rset.next()) {
throw new DataAccessException("Too many MathModelSimulationLink found for simKey=" + simKey);
}
} else {
throw new DataAccessException("No MathModelSimulationLink found for simKey=" + simKey);
}
rset.close();
// //
// //Make sure TestCase type and regressionRef match
// sql = "SELECT "+TFTestCaseTable.table.id.getQualifiedColName()+
// " FROM "+TFTestCaseTable.table.getTableName()+
// " WHERE "+
// TFTestCaseTable.table.id.getQualifiedColName()+"="+tcKey.toString()+
// " AND "+
// TFTestCaseTable.table.tcSolutionType.getQualifiedColName()+
// (regrSimKey != null?"=":"!=")+
// "'"+cbit.vcell.numericstest.TestCaseNew.REGRESSION+"'";
// rset = stmt.executeQuery(sql);
// if(!rset.next()){
// throw new DataAccessException("TestCase type not compatible with regressionSimKey");
// }
// rset.close();
//
//
// Get simDataRef from simKey
BigDecimal simDataRef = null;
// sql =
// "SELECT "+ResultSetMetaDataTable.table.id.getQualifiedColName()+
// " FROM " +ResultSetMetaDataTable.table.getTableName()+
// " WHERE "+
// ResultSetMetaDataTable.table.simRef.getQualifiedColName()+"="+simKey.toString();
// rset = stmt.executeQuery(sql);
// if(rset.next()){
// simDataRef = rset.getBigDecimal(MathModelSimulationLinkTable.table.id.getUnqualifiedColName());
// if(rset.next()){
// throw new DataAccessException("Too many ResultSetMetaData found for simKey="+simKey);
// }
// }
// else{
// throw new DataAccessException("No ResultSetMetaData found for simKey="+simKey);
// }
rset.close();
//
// Insert TestCriteria
sql = "INSERT INTO " + TFTestCriteriaTable.table.getTableName() + " VALUES(" + tcritKey.toString() + "," + tcKey.toString() + "," + simKey.toString() + "," + (simDataRef != null ? simDataRef.toString() : null) + "," + "NULL" + "," + (addtcrit_tsop.getMaxRelativeError() != null ? "TO_NUMBER('" + addtcrit_tsop.getMaxRelativeError().toString() + "')" : "null") + "," + (addtcrit_tsop.getMaxAbsoluteError() != null ? "TO_NUMBER('" + addtcrit_tsop.getMaxAbsoluteError().toString() + "')" : "null") + "," + "NULL,NULL," + "'" + TestCriteriaNew.TCRIT_STATUS_NEEDSREPORT + "'" + ",null" + ")";
stmt.executeUpdate(sql);
if (addtcrit_tsop.getRegressionMathModelSimKey() != null) {
testSuiteOP(new EditTestCriteriaOPMathModel(tcritKey, addtcrit_tsop.getRegressionMathModelKey(), addtcrit_tsop.getRegressionMathModelSimKey(), addtcrit_tsop.getMaxAbsoluteError(), addtcrit_tsop.getMaxRelativeError()), con, user, keyFactory);
}
if (addtcrit_tsop.getAddTestResultsOP() != null) {
AddTestResultsOP atrOP = addtcrit_tsop.getAddTestResultsOP();
// Set new TSKey,TCritKey and do child OPs
testSuiteOP(new AddTestResultsOP(tcritKey, atrOP.getVariableComparisonSummaries()), con, user, keyFactory);
}
rset = stmt.executeQuery("SELECT DISTINCT " + TFTestSuiteTable.table.id.getQualifiedColName() + " FROM " + TFTestSuiteTable.table.getTableName() + "," + TFTestCaseTable.table.getTableName() + "," + TFTestCriteriaTable.table.getTableName() + " WHERE " + TFTestCaseTable.table.id.getQualifiedColName() + "=" + TFTestCriteriaTable.table.testCaseRef.getQualifiedColName() + " AND " + TFTestCriteriaTable.table.id.getQualifiedColName() + "=" + tcritKey.toString() + " AND " + TFTestCaseTable.table.testSuiteRef.getQualifiedColName() + "=" + TFTestSuiteTable.table.id.getQualifiedColName());
while (rset.next()) {
changedTestSuiteKeys.add(rset.getBigDecimal(TFTestSuiteTable.table.id.getUnqualifiedColName()));
}
rset.close();
} else if (tsop instanceof AddTestCriteriaOPBioModel) {
AddTestCriteriaOPBioModel addtcrit_tsop = (AddTestCriteriaOPBioModel) tsop;
BigDecimal tcritKey = keyFactory.getUniqueBigDecimal(con);
BigDecimal tcKey = addtcrit_tsop.getTestCaseKey();
KeyValue simKey = addtcrit_tsop.getBioModelSimKey();
// Check that there is a single biomodel associated with simkey and parentsimref is null
sql = "SELECT " + BioModelSimulationLinkTable.table.id.getQualifiedColName() + " FROM " + BioModelSimulationLinkTable.table.getTableName() + "," + SimulationTable.table.getTableName() + " WHERE " + BioModelSimulationLinkTable.table.simRef.getQualifiedColName() + "=" + simKey.toString() + " AND " + BioModelSimulationLinkTable.table.simRef.getQualifiedColName() + "=" + SimulationTable.table.id.getQualifiedColName() + " AND " + SimulationTable.table.getTableName() + "." + SimulationTable.versionParentSimRef_ColumnName + " IS NULL";
ResultSet rset = stmt.executeQuery(sql);
if (rset.next()) {
if (rset.next()) {
throw new DataAccessException("Too many BioModelSimulationLink found for simKey=" + simKey);
}
} else {
throw new DataAccessException("No BioModelSimulationLink found for simKey=" + simKey);
}
rset.close();
// //
// //Make sure TestCase type and regressionRef match
// sql = "SELECT "+TFTestCaseTable.table.id.getQualifiedColName()+
// " FROM "+TFTestCaseTable.table.getTableName()+
// " WHERE "+
// TFTestCaseTable.table.id.getQualifiedColName()+"="+tcKey.toString()+
// " AND "+
// TFTestCaseTable.table.tcSolutionType.getQualifiedColName()+
// (regrSimKey != null?"=":"!=")+
// "'"+cbit.vcell.numericstest.TestCaseNew.REGRESSION+"'";
// rset = stmt.executeQuery(sql);
// if(!rset.next()){
// throw new DataAccessException("TestCase type not compatible with regressionSimKey");
// }
// rset.close();
//
//
// Get simDataRef from simKey
BigDecimal simDataRef = null;
// sql =
// "SELECT "+ResultSetMetaDataTable.table.id.getQualifiedColName()+
// " FROM " +ResultSetMetaDataTable.table.getTableName()+
// " WHERE "+
// ResultSetMetaDataTable.table.simRef.getQualifiedColName()+"="+simKey.toString();
// rset = stmt.executeQuery(sql);
// if(rset.next()){
// simDataRef = rset.getBigDecimal(BioModelSimulationLinkTable.table.id.getUnqualifiedColName());
// if(rset.next()){
// throw new DataAccessException("Too many ResultSetMetaData found for simKey="+simKey);
// }
// }
// else{
// throw new DataAccessException("No ResultSetMetaData found for simKey="+simKey);
// }
rset.close();
//
// Insert TestCriteria
sql = "INSERT INTO " + TFTestCriteriaTable.table.getTableName() + " VALUES(" + tcritKey.toString() + "," + tcKey.toString() + "," + simKey.toString() + "," + (simDataRef != null ? simDataRef.toString() : null) + "," + "null" + "," + (addtcrit_tsop.getMaxRelativeError() != null ? "TO_NUMBER('" + addtcrit_tsop.getMaxRelativeError().toString() + "')" : "null") + "," + (addtcrit_tsop.getMaxAbsoluteError() != null ? "TO_NUMBER('" + addtcrit_tsop.getMaxAbsoluteError().toString() + "')" : "null") + "," + "NULL,NULL," + "'" + TestCriteriaNew.TCRIT_STATUS_NEEDSREPORT + "'" + ",null" + ")";
stmt.executeUpdate(sql);
if (addtcrit_tsop.getRegressionBioModelSimKey() != null) {
testSuiteOP(new EditTestCriteriaOPBioModel(tcritKey, addtcrit_tsop.getRegressionBioModelKey(), addtcrit_tsop.getRegressionBioModelSimKey(), addtcrit_tsop.getMaxAbsoluteError(), addtcrit_tsop.getMaxRelativeError()), con, user, keyFactory);
}
if (addtcrit_tsop.getAddTestResultsOP() != null) {
AddTestResultsOP atrOP = addtcrit_tsop.getAddTestResultsOP();
// Set new TSKey,TCritKey and do child OPs
testSuiteOP(new AddTestResultsOP(tcritKey, atrOP.getVariableComparisonSummaries()), con, user, keyFactory);
}
rset = stmt.executeQuery("SELECT DISTINCT " + TFTestSuiteTable.table.id.getQualifiedColName() + " FROM " + TFTestSuiteTable.table.getTableName() + "," + TFTestCaseTable.table.getTableName() + "," + TFTestCriteriaTable.table.getTableName() + " WHERE " + TFTestCaseTable.table.id.getQualifiedColName() + "=" + TFTestCriteriaTable.table.testCaseRef.getQualifiedColName() + " AND " + TFTestCriteriaTable.table.id.getQualifiedColName() + "=" + tcritKey.toString() + " AND " + TFTestCaseTable.table.testSuiteRef.getQualifiedColName() + "=" + TFTestSuiteTable.table.id.getQualifiedColName());
while (rset.next()) {
changedTestSuiteKeys.add(rset.getBigDecimal(TFTestSuiteTable.table.id.getUnqualifiedColName()));
}
rset.close();
} else if (tsop instanceof RemoveTestCriteriaOP) {
RemoveTestCriteriaOP removetcrit_tsop = (RemoveTestCriteriaOP) tsop;
StringBuffer sb = new StringBuffer();
for (int i = 0; i < removetcrit_tsop.getTestCriterias().length; i += 1) {
if (i != 0) {
sb.append(",");
}
sb.append(removetcrit_tsop.getTestCriterias()[i].getTCritKey().toString());
}
ResultSet rset = stmt.executeQuery("SELECT DISTINCT " + TFTestSuiteTable.table.id.getQualifiedColName() + " FROM " + TFTestSuiteTable.table.getTableName() + "," + TFTestCaseTable.table.getTableName() + "," + TFTestCriteriaTable.table.getTableName() + " WHERE " + TFTestCaseTable.table.id.getQualifiedColName() + "=" + TFTestCriteriaTable.table.testCaseRef.getQualifiedColName() + " AND " + TFTestCriteriaTable.table.id.getQualifiedColName() + " IN (" + sb.toString() + ")" + " AND " + TFTestCaseTable.table.testSuiteRef.getQualifiedColName() + "=" + TFTestSuiteTable.table.id.getQualifiedColName());
while (rset.next()) {
changedTestSuiteKeys.add(rset.getBigDecimal(TFTestSuiteTable.table.id.getUnqualifiedColName()));
}
rset.close();
int numRowsUpdated = stmt.executeUpdate("DELETE FROM " + TFTestCriteriaTable.table.getTableName() + " WHERE " + TFTestCriteriaTable.table.id.getUnqualifiedColName() + " IN (" + sb.toString() + ")");
if (numRowsUpdated != removetcrit_tsop.getTestCriterias().length) {
throw new DataAccessException("Remove TestCriteria keys=" + sb.toString() + " removed row count=" + numRowsUpdated + " expected " + removetcrit_tsop.getTestCriterias().length);
}
} else if (tsop instanceof RemoveTestSuiteOP) {
RemoveTestSuiteOP removets_tsop = (RemoveTestSuiteOP) tsop;
int numRowsUpdated = stmt.executeUpdate("DELETE FROM " + TFTestSuiteTable.table.getTableName() + " WHERE " + TFTestSuiteTable.table.id.getUnqualifiedColName() + "=" + removets_tsop.getTestSuiteKey().toString());
if (numRowsUpdated != 1) {
throw new DataAccessException("Remove SINGLE TestSuite - key=" + removets_tsop.getTestSuiteKey().toString() + " removed row count=" + numRowsUpdated);
}
changedTestSuiteKeys.add(removets_tsop.getTestSuiteKey());
} else if (tsop instanceof AddTestResultsOP) {
AddTestResultsOP addtr_tsop = (AddTestResultsOP) tsop;
VariableComparisonSummary[] vcs = addtr_tsop.getVariableComparisonSummaries();
if (vcs == null || vcs.length == 0) {
throw new DataAccessException(RemoveTestCasesOP.class.getName() + " had no TestResults");
}
for (int i = 0; i < vcs.length; i += 1) {
if (vcs[i] == null) {
throw new DataAccessException(RemoveTestCasesOP.class.getName() + " Array element was null");
}
}
ResultSet rset = stmt.executeQuery("SELECT " + TFTestResultTable.table.id.getUnqualifiedColName() + " FROM " + TFTestResultTable.table.getTableName() + " WHERE " + TFTestResultTable.table.testCriteriaRef.getUnqualifiedColName() + "=" + addtr_tsop.getTestCriteriaKey().toString());
if (rset.next()) {
throw new DataAccessException("AddTestResultsOP Criteria key=" + addtr_tsop.getTestCriteriaKey() + " has results");
}
rset.close();
for (int i = 0; i < vcs.length; i += 1) {
sql = "INSERT INTO " + TFTestResultTable.table.getTableName() + " VALUES(" + "NEWSEQ.NEXTVAL" + "," + addtr_tsop.getTestCriteriaKey().toString() + "," + "'" + vcs[i].getName() + "'" + "," + "TO_NUMBER('" + vcs[i].getAbsoluteError() + "')" + "," + "TO_NUMBER('" + vcs[i].getRelativeError() + "')" + "," + "TO_NUMBER('" + vcs[i].getMaxRef() + "')" + "," + "TO_NUMBER('" + vcs[i].getMinRef() + "')" + "," + "TO_NUMBER('" + vcs[i].getMeanSqError() + "')" + "," + "TO_NUMBER('" + vcs[i].getTimeAbsoluteError() + "')" + "," + "TO_NUMBER('" + vcs[i].getIndexAbsoluteError() + "')" + "," + "TO_NUMBER('" + vcs[i].getTimeRelativeError() + "')" + "," + "TO_NUMBER('" + vcs[i].getIndexRelativeError() + "')" + ")";
stmt.executeUpdate(sql);
}
rset = stmt.executeQuery("SELECT DISTINCT " + TFTestSuiteTable.table.id.getQualifiedColName() + " FROM " + TFTestSuiteTable.table.getTableName() + "," + TFTestCaseTable.table.getTableName() + "," + TFTestCriteriaTable.table.getTableName() + " WHERE " + TFTestCaseTable.table.id.getQualifiedColName() + "=" + TFTestCriteriaTable.table.testCaseRef.getQualifiedColName() + " AND " + TFTestCriteriaTable.table.id.getQualifiedColName() + "=" + addtr_tsop.getTestCriteriaKey().toString() + " AND " + TFTestCaseTable.table.testSuiteRef.getQualifiedColName() + "=" + TFTestSuiteTable.table.id.getQualifiedColName());
while (rset.next()) {
changedTestSuiteKeys.add(rset.getBigDecimal(TFTestSuiteTable.table.id.getUnqualifiedColName()));
}
rset.close();
} else if (tsop instanceof RemoveTestResultsOP) {
RemoveTestResultsOP removetr_tsop = (RemoveTestResultsOP) tsop;
StringBuffer sb = new StringBuffer();
for (int i = 0; i < removetr_tsop.getTestCriteriaKeys().length; i += 1) {
if (i != 0) {
sb.append(",");
}
sb.append(removetr_tsop.getTestCriteriaKeys()[i].toString());
stmt.executeUpdate("DELETE FROM " + TFTestResultTable.table.getTableName() + " WHERE " + TFTestResultTable.table.testCriteriaRef.getUnqualifiedColName() + "=" + removetr_tsop.getTestCriteriaKeys()[i].toString());
}
ResultSet rset = stmt.executeQuery("SELECT DISTINCT " + TFTestSuiteTable.table.id.getQualifiedColName() + " FROM " + TFTestSuiteTable.table.getTableName() + "," + TFTestCaseTable.table.getTableName() + "," + TFTestCriteriaTable.table.getTableName() + " WHERE " + TFTestCaseTable.table.id.getQualifiedColName() + "=" + TFTestCriteriaTable.table.testCaseRef.getQualifiedColName() + " AND " + TFTestCriteriaTable.table.id.getQualifiedColName() + " IN (" + sb.toString() + ")" + " AND " + TFTestCaseTable.table.testSuiteRef.getQualifiedColName() + "=" + TFTestSuiteTable.table.id.getQualifiedColName());
while (rset.next()) {
changedTestSuiteKeys.add(rset.getBigDecimal(TFTestSuiteTable.table.id.getUnqualifiedColName()));
}
rset.close();
} else if (tsop instanceof EditTestCriteriaOPReportStatus) {
EditTestCriteriaOPReportStatus edittcrit_tsop = (EditTestCriteriaOPReportStatus) tsop;
BigDecimal tcritKey = edittcrit_tsop.getTestCriteriaKey();
if (tcritKey == null) {
throw new DataAccessException(tsop.getClass().getName() + " had no TestCriteria keys");
}
String newRS = edittcrit_tsop.getNewReportStatus();
if (newRS == null || (!newRS.equals(TestCriteriaNew.TCRIT_STATUS_NEEDSREPORT) && !newRS.equals(TestCriteriaNew.TCRIT_STATUS_FAILEDVARS) && !newRS.equals(TestCriteriaNew.TCRIT_STATUS_NODATA) && !newRS.equals(TestCriteriaNew.TCRIT_STATUS_NOREFREGR) && !newRS.equals(TestCriteriaNew.TCRIT_STATUS_PASSED) && !newRS.equals(TestCriteriaNew.TCRIT_STATUS_RPERROR) && !newRS.equals(TestCriteriaNew.TCRIT_STATUS_SIMFAILED) && !newRS.equals(TestCriteriaNew.TCRIT_STATUS_SIMRUNNING) && !newRS.equals(TestCriteriaNew.TCRIT_STATUS_SIMNOTRUNFAILDONE))) {
throw new DataAccessException("Unsupported ReportStatus=" + edittcrit_tsop.getNewReportStatus());
}
String reportStatusMessage = edittcrit_tsop.getNewReportStatusMessage();
if (reportStatusMessage != null) {
reportStatusMessage = TokenMangler.getSQLEscapedString(reportStatusMessage);
reportStatusMessage = reportStatusMessage.substring(0, Math.min(TFTestCriteriaTable.MAX_MESSAGE_SIZE, reportStatusMessage.length()));
}
stmt.executeUpdate("UPDATE " + TFTestCriteriaTable.table.getTableName() + " SET " + TFTestCriteriaTable.table.reportStatus.getQualifiedColName() + "=" + (newRS != null ? "'" + newRS + "'" : "null") + "," + TFTestCriteriaTable.table.reportMessage.getQualifiedColName() + "=" + (reportStatusMessage != null ? "'" + reportStatusMessage + "'" : "null") + " WHERE " + TFTestCriteriaTable.table.id.getQualifiedColName() + "=" + tcritKey.toString());
if (newRS.equals(TestCriteriaNew.TCRIT_STATUS_NEEDSREPORT)) {
testSuiteOP(new RemoveTestResultsOP(new BigDecimal[] { tcritKey }), con, user, keyFactory);
}
ResultSet rset = stmt.executeQuery("SELECT DISTINCT " + TFTestSuiteTable.table.id.getQualifiedColName() + " FROM " + TFTestSuiteTable.table.getTableName() + "," + TFTestCaseTable.table.getTableName() + "," + TFTestCriteriaTable.table.getTableName() + " WHERE " + TFTestCaseTable.table.id.getQualifiedColName() + "=" + TFTestCriteriaTable.table.testCaseRef.getQualifiedColName() + " AND " + TFTestCriteriaTable.table.id.getQualifiedColName() + " = " + tcritKey.toString() + " AND " + TFTestCaseTable.table.testSuiteRef.getQualifiedColName() + "=" + TFTestSuiteTable.table.id.getQualifiedColName());
while (rset.next()) {
changedTestSuiteKeys.add(rset.getBigDecimal(TFTestSuiteTable.table.id.getUnqualifiedColName()));
}
rset.close();
} else if (tsop instanceof EditTestCriteriaOPMathModel) {
EditTestCriteriaOPMathModel edittcrit_tsop = (EditTestCriteriaOPMathModel) tsop;
BigDecimal tcritKey = edittcrit_tsop.getTestCriteriaKey();
if (tcritKey == null) {
throw new DataAccessException(tsop.getClass().getName() + " had no TestCriteria keys");
}
if ((edittcrit_tsop.getMathModelRegressionRef() == null && edittcrit_tsop.getMathModelRegressionSimRef() != null) || (edittcrit_tsop.getMathModelRegressionRef() != null && edittcrit_tsop.getMathModelRegressionSimRef() == null)) {
throw new DataAccessException(tsop.getClass().getName() + " MathRef and SimRef must both be null or both not null");
}
Double maxAbsError = edittcrit_tsop.getNewMaxAbsError();
Double maxRelError = edittcrit_tsop.getNewMaxRelError();
KeyValue regrSimRef = edittcrit_tsop.getMathModelRegressionSimRef();
// Convert regrSimKey to regrMathModelSimLinkKey
BigDecimal regrMathModelSimLink = null;
if (regrSimRef != null) {
sql = "SELECT " + MathModelSimulationLinkTable.table.id.getQualifiedColName() + " FROM " + MathModelSimulationLinkTable.table.getTableName() + " WHERE " + MathModelSimulationLinkTable.table.simRef.getQualifiedColName() + "=" + regrSimRef.toString();
ResultSet rset = stmt.executeQuery(sql);
if (rset.next()) {
regrMathModelSimLink = rset.getBigDecimal(MathModelSimulationLinkTable.table.id.getUnqualifiedColName());
if (rset.next()) {
throw new DataAccessException("Too many MathModelSimLink found for regrSimKey=" + regrSimRef);
}
} else {
throw new DataAccessException("No MathModelSimLink found for regrSimKey=" + regrSimRef);
}
rset.close();
}
stmt.executeUpdate("UPDATE " + TFTestCriteriaTable.table.getTableName() + " SET " + TFTestCriteriaTable.table.maxAbsError.getQualifiedColName() + "=" + (maxAbsError != null ? "TO_NUMBER(" + maxAbsError.toString() + ")" : "null") + "," + TFTestCriteriaTable.table.maxRelError.getQualifiedColName() + "=" + (maxRelError != null ? "TO_NUMBER(" + maxRelError.toString() + ")" : "null") + "," + TFTestCriteriaTable.table.regressionMMSimRef.getQualifiedColName() + "=" + (regrMathModelSimLink != null ? regrMathModelSimLink.toString() : "null") + " WHERE " + TFTestCriteriaTable.table.id.getQualifiedColName() + "=" + tcritKey.toString());
testSuiteOP(new EditTestCriteriaOPReportStatus(tcritKey, TestCriteriaNew.TCRIT_STATUS_NEEDSREPORT, null), con, user, keyFactory);
ResultSet rset = stmt.executeQuery("SELECT DISTINCT " + TFTestSuiteTable.table.id.getQualifiedColName() + " FROM " + TFTestSuiteTable.table.getTableName() + "," + TFTestCaseTable.table.getTableName() + "," + TFTestCriteriaTable.table.getTableName() + " WHERE " + TFTestCaseTable.table.id.getQualifiedColName() + "=" + TFTestCriteriaTable.table.testCaseRef.getQualifiedColName() + " AND " + TFTestCriteriaTable.table.id.getQualifiedColName() + " = " + tcritKey.toString() + " AND " + TFTestCaseTable.table.testSuiteRef.getQualifiedColName() + "=" + TFTestSuiteTable.table.id.getQualifiedColName());
while (rset.next()) {
changedTestSuiteKeys.add(rset.getBigDecimal(TFTestSuiteTable.table.id.getUnqualifiedColName()));
}
rset.close();
} else if (tsop instanceof EditTestCriteriaOPBioModel) {
EditTestCriteriaOPBioModel edittcrit_tsop = (EditTestCriteriaOPBioModel) tsop;
BigDecimal tcritKey = edittcrit_tsop.getTestCriteriaKey();
if (tcritKey == null) {
throw new DataAccessException(tsop.getClass().getName() + " had no TestCriteria keys");
}
if ((edittcrit_tsop.getBioModelRegressionRef() == null && edittcrit_tsop.getBioModelRegressionSimRef() != null) || (edittcrit_tsop.getBioModelRegressionRef() != null && edittcrit_tsop.getBioModelRegressionSimRef() == null)) {
throw new DataAccessException(tsop.getClass().getName() + " ApplicationRef and SimRef must both be null or both not null");
}
Double maxAbsError = edittcrit_tsop.getNewMaxAbsError();
Double maxRelError = edittcrit_tsop.getNewMaxRelError();
BigDecimal bmscAppKey = null;
BigDecimal bmsltSimKey = null;
final String BMSLT = "BMSLT";
if (edittcrit_tsop.getBioModelRegressionSimRef() != null) {
sql = "SELECT " + BioModelSimContextLinkTable.table.id.getQualifiedColName() + "," + BioModelSimulationLinkTable.table.id.getQualifiedColName() + " " + BMSLT + " FROM " + BioModelSimContextLinkTable.table.getTableName() + "," + SimContextTable.table.getTableName() + "," + SimulationTable.table.getTableName() + "," + BioModelSimulationLinkTable.table.getTableName() + " WHERE " + BioModelSimContextLinkTable.table.bioModelRef.getQualifiedColName() + "=" + edittcrit_tsop.getBioModelRegressionRef() + " AND " + BioModelSimContextLinkTable.table.simContextRef.getQualifiedColName() + "=" + SimContextTable.table.id.getQualifiedColName() + " AND " + SimContextTable.table.mathRef.getQualifiedColName() + "=" + SimulationTable.table.mathRef.getQualifiedColName() + " AND " + SimulationTable.table.id.getQualifiedColName() + "=" + edittcrit_tsop.getBioModelRegressionSimRef().toString() + " AND " + BioModelSimulationLinkTable.table.bioModelRef.getQualifiedColName() + " = " + BioModelSimContextLinkTable.table.bioModelRef.getQualifiedColName() + " AND " + BioModelSimulationLinkTable.table.simRef.getQualifiedColName() + " = " + SimulationTable.table.id.getQualifiedColName();
ResultSet rset = stmt.executeQuery(sql);
if (rset.next()) {
bmscAppKey = rset.getBigDecimal(BioModelSimContextLinkTable.table.id.getUnqualifiedColName());
bmsltSimKey = rset.getBigDecimal(BMSLT);
if (rset.next()) {
throw new DataAccessException("Too many ResultSetMetaData found for simKey=" + edittcrit_tsop.getBioModelRegressionSimRef());
}
}
rset.close();
}
stmt.executeUpdate("UPDATE " + TFTestCriteriaTable.table.getTableName() + " SET " + TFTestCriteriaTable.table.maxAbsError.getQualifiedColName() + "=" + (maxAbsError != null ? "TO_NUMBER(" + maxAbsError.toString() + ")" : "null") + "," + TFTestCriteriaTable.table.maxRelError.getQualifiedColName() + "=" + (maxRelError != null ? "TO_NUMBER(" + maxRelError.toString() + ")" : "null") + "," + TFTestCriteriaTable.table.regressionBMAPPRef.getQualifiedColName() + "=" + (bmscAppKey != null ? bmscAppKey.toString() : "NULL") + "," + TFTestCriteriaTable.table.regressionBMSimRef.getQualifiedColName() + "=" + (bmsltSimKey != null ? bmsltSimKey.toString() : "NULL") + " WHERE " + TFTestCriteriaTable.table.id.getQualifiedColName() + "=" + tcritKey.toString());
testSuiteOP(new EditTestCriteriaOPReportStatus(tcritKey, TestCriteriaNew.TCRIT_STATUS_NEEDSREPORT, null), con, user, keyFactory);
ResultSet rset = stmt.executeQuery("SELECT DISTINCT " + TFTestSuiteTable.table.id.getQualifiedColName() + " FROM " + TFTestSuiteTable.table.getTableName() + "," + TFTestCaseTable.table.getTableName() + "," + TFTestCriteriaTable.table.getTableName() + " WHERE " + TFTestCaseTable.table.id.getQualifiedColName() + "=" + TFTestCriteriaTable.table.testCaseRef.getQualifiedColName() + " AND " + TFTestCriteriaTable.table.id.getQualifiedColName() + " = " + tcritKey.toString() + " AND " + TFTestCaseTable.table.testSuiteRef.getQualifiedColName() + "=" + TFTestSuiteTable.table.id.getQualifiedColName());
while (rset.next()) {
changedTestSuiteKeys.add(rset.getBigDecimal(TFTestSuiteTable.table.id.getUnqualifiedColName()));
}
rset.close();
} else if (tsop instanceof ChangeTestCriteriaErrorLimitOP) {
ChangeTestCriteriaErrorLimitOP edittcrit_tsop = (ChangeTestCriteriaErrorLimitOP) tsop;
BigDecimal[] tcritKeyArr = edittcrit_tsop.getTestCriteriaKeys();
double[] maxAbsErrorArr = edittcrit_tsop.getAbsErrorLimits();
double[] maxRelErrorArr = edittcrit_tsop.getRelErrorLimits();
if (tcritKeyArr == null || (maxAbsErrorArr != null && maxAbsErrorArr.length != tcritKeyArr.length) || (maxAbsErrorArr != null && maxRelErrorArr.length != tcritKeyArr.length)) {
throw new DataAccessException(tsop.getClass().getName() + " Improper arguments.");
}
StringBuffer tcritList = new StringBuffer();
for (int i = 0; i < tcritKeyArr.length; i++) {
if (i != 0) {
tcritList.append(",");
}
tcritList.append(tcritKeyArr[i]);
stmt.executeUpdate("UPDATE " + TFTestCriteriaTable.table.getTableName() + " SET " + (maxAbsErrorArr != null ? TFTestCriteriaTable.table.maxAbsError.getQualifiedColName() + "=" + maxAbsErrorArr[i] : "") + (maxAbsErrorArr != null && maxRelErrorArr != null ? "," : "") + (maxRelErrorArr != null ? TFTestCriteriaTable.table.maxRelError.getQualifiedColName() + "=" + maxRelErrorArr[i] : "") + " WHERE " + TFTestCriteriaTable.table.id.getQualifiedColName() + "=" + tcritKeyArr[i].toString());
testSuiteOP(new EditTestCriteriaOPReportStatus(tcritKeyArr[i], TestCriteriaNew.TCRIT_STATUS_NEEDSREPORT, null), con, user, keyFactory);
}
ResultSet rset = stmt.executeQuery("SELECT DISTINCT " + TFTestSuiteTable.table.id.getQualifiedColName() + " FROM " + TFTestSuiteTable.table.getTableName() + "," + TFTestCaseTable.table.getTableName() + "," + TFTestCriteriaTable.table.getTableName() + " WHERE " + TFTestCaseTable.table.id.getQualifiedColName() + "=" + TFTestCriteriaTable.table.testCaseRef.getQualifiedColName() + " AND " + TFTestCriteriaTable.table.id.getQualifiedColName() + " IN (" + tcritList.toString() + ")" + " AND " + TFTestCaseTable.table.testSuiteRef.getQualifiedColName() + "=" + TFTestSuiteTable.table.id.getQualifiedColName());
while (rset.next()) {
changedTestSuiteKeys.add(rset.getBigDecimal(TFTestSuiteTable.table.id.getUnqualifiedColName()));
}
} else if (tsop instanceof EditTestCasesOP) {
EditTestCasesOP edittc_tsop = (EditTestCasesOP) tsop;
BigDecimal[] tcaseKeys = edittc_tsop.getTestCasesKeys();
String[] annots = edittc_tsop.getNewAnnotations();
boolean[] newSteadyStates = edittc_tsop.getNewSteadyStates();
if (tcaseKeys == null || tcaseKeys.length == 0) {
throw new DataAccessException(tsop.getClass().getName() + " had no TestCase keys");
}
StringBuffer sb = new StringBuffer();
for (int i = 0; i < tcaseKeys.length; i += 1) {
if (i != 0) {
sb.append(",");
}
sb.append(tcaseKeys[i].toString());
if (annots != null) {
String annotation = annots[i];
if (annotation != null) {
if (annotation.length() == 0) {
annotation = null;
} else {
annotation = TokenMangler.getSQLEscapedString(annotation);
}
}
stmt.executeUpdate("UPDATE " + TFTestCaseTable.table.getTableName() + " SET " + TFTestCaseTable.table.tcAnnotation.getQualifiedColName() + "=" + (annotation == null ? "NULL" : "'" + annotation + "'") + " WHERE " + TFTestCaseTable.table.id.getQualifiedColName() + "=" + tcaseKeys[i].toString());
}
if (newSteadyStates != null) {
// Make sure the change is for EXACT type
ResultSet rset = stmt.executeQuery("SELECT DISTINCT " + TFTestCriteriaTable.table.id.getQualifiedColName() + " FROM " + TFTestCaseTable.table.getTableName() + "," + TFTestCriteriaTable.table.getTableName() + " WHERE " + TFTestCaseTable.table.id.getQualifiedColName() + "=" + tcaseKeys[i].toString() + " AND " + "(" + TFTestCaseTable.table.tcSolutionType.getQualifiedColName() + "='" + TestCaseNew.EXACT + "'" + " OR " + TFTestCaseTable.table.tcSolutionType.getQualifiedColName() + "='" + TestCaseNew.EXACT_STEADY + "'" + ")" + " AND " + TFTestCriteriaTable.table.testCaseRef + "=" + TFTestCaseTable.table.id.getQualifiedColName());
// Get TestCriteria Keys for Test case
Vector<BigDecimal> tcritKeyV = new Vector<BigDecimal>();
while (rset.next()) {
tcritKeyV.add(rset.getBigDecimal(TFTestCriteriaTable.table.id.getUnqualifiedColName()));
}
if (tcritKeyV.size() == 0) {
throw new DataAccessException("Updating SteadyState on TestCase that is not EXACT is NOT allowed.");
}
rset.close();
// Change SteadyState type for TestCase
boolean newSteadyState = newSteadyStates[i];
stmt.executeUpdate("UPDATE " + TFTestCaseTable.table.getTableName() + " SET " + TFTestCaseTable.table.tcSolutionType.getQualifiedColName() + "=" + (newSteadyState ? "'" + TestCaseNew.EXACT_STEADY + "'" : "'" + TestCaseNew.EXACT + "'") + " WHERE " + TFTestCaseTable.table.id.getQualifiedColName() + "=" + tcaseKeys[i].toString());
// Change Report status
for (int j = 0; j < tcritKeyV.size(); j++) {
EditTestCriteriaOPReportStatus etcors = new EditTestCriteriaOPReportStatus(tcritKeyV.elementAt(j), TestCriteriaNew.TCRIT_STATUS_NEEDSREPORT, null);
testSuiteOP(etcors, con, user, keyFactory);
}
}
}
ResultSet rset = stmt.executeQuery("SELECT DISTINCT " + TFTestSuiteTable.table.id.getQualifiedColName() + " FROM " + TFTestSuiteTable.table.getTableName() + "," + TFTestCaseTable.table.getTableName() + " WHERE " + TFTestCaseTable.table.id.getQualifiedColName() + " IN (" + sb.toString() + ")" + " AND " + TFTestCaseTable.table.testSuiteRef.getQualifiedColName() + "=" + TFTestSuiteTable.table.id.getQualifiedColName());
while (rset.next()) {
changedTestSuiteKeys.add(rset.getBigDecimal(TFTestSuiteTable.table.id.getUnqualifiedColName()));
}
rset.close();
} else if (tsop instanceof EditTestSuiteOP) {
EditTestSuiteOP editts_tsop = (EditTestSuiteOP) tsop;
BigDecimal[] tsKeys = editts_tsop.getTestSuiteKeys();
String[] annots = editts_tsop.getNewAnnotations();
if (tsKeys == null || tsKeys.length == 0) {
throw new DataAccessException(tsop.getClass().getName() + " had no TestSuite keys");
}
StringBuffer sb = new StringBuffer();
for (int i = 0; i < tsKeys.length; i += 1) {
if (i != 0) {
sb.append(",");
}
sb.append(tsKeys[i].toString());
if (editts_tsop.isLock() != null) {
stmt.executeUpdate("UPDATE " + TFTestSuiteTable.table.getTableName() + " SET " + TFTestSuiteTable.table.isLocked.getQualifiedColName() + "= 1" + " WHERE " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + tsKeys[i].toString());
} else {
if (annots != null) {
String annotation = annots[i];
if (annotation != null) {
if (annotation.length() == 0) {
annotation = null;
} else {
annotation = TokenMangler.getSQLEscapedString(annotation);
}
}
stmt.executeUpdate("UPDATE " + TFTestSuiteTable.table.getTableName() + " SET " + TFTestSuiteTable.table.tsAnnotation.getQualifiedColName() + "=" + (annotation == null ? "NULL" : "'" + annotation + "'") + " WHERE " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + tsKeys[i].toString());
}
}
}
ResultSet rset = stmt.executeQuery("SELECT DISTINCT " + TFTestSuiteTable.table.id.getQualifiedColName() + " FROM " + TFTestSuiteTable.table.getTableName() + " WHERE " + TFTestSuiteTable.table.id.getQualifiedColName() + " IN (" + sb.toString() + ")");
while (rset.next()) {
changedTestSuiteKeys.add(rset.getBigDecimal(TFTestSuiteTable.table.id.getUnqualifiedColName()));
}
rset.close();
} else if (tsop instanceof QueryTestCriteriaCrossRefOP) {
QueryTestCriteriaCrossRefOP qtcritxr_tsop = (QueryTestCriteriaCrossRefOP) tsop;
Vector<TestCriteriaCrossRefOPResults.CrossRefData> crossRefV = new Vector<TestCriteriaCrossRefOPResults.CrossRefData>();
//
// BioModel query
//
String TSID = "tsid";
String TCID = "tcid";
String TCRID = "tcrid";
String BMNAME = "bmname";
String SCNAME = "scname";
String SIMNAME = "simname";
String TSALT = "TSALT";
String TCALT = "TCALT";
String TCRALT = "TCRALT";
String BSCALT = "BSCALT";
String MMSIMALT = "MMSIMALT";
String MODELID = "MODELID";
String REFTSUITEKEY = "REFTSUITEKEY";
String REFTCASEKEY = "REFTCASEKEY";
String REFTCRITKEY = "REFTCRITKEY";
// String TCRALT2 = "TCRALT2";
// String SIM2 = "SIM2";
sql = "SELECT DISTINCT " + TFTestSuiteTable.table.tsVersion.getQualifiedColName() + "," + TFTestSuiteTable.table.id.getQualifiedColName() + " " + TSID + "," + TFTestCaseTable.table.id.getQualifiedColName() + " " + TCID + "," + TFTestCriteriaTable.table.id.getQualifiedColName() + " " + TCRID + "," + BioModelTable.table.name.getQualifiedColName() + " " + BMNAME + "," + SimContextTable.table.name.getQualifiedColName() + " " + SCNAME + "," + SimulationTable.table.name.getQualifiedColName() + " " + SIMNAME + "," + TFTestCriteriaTable.table.maxAbsError.getQualifiedColName() + "," + TFTestCriteriaTable.table.maxRelError.getQualifiedColName() + "," + TFTestResultTable.table.varName.getQualifiedColName() + "," + TFTestResultTable.table.minRef.getQualifiedColName() + "," + TFTestResultTable.table.maxRef.getQualifiedColName() + "," + TFTestResultTable.table.absError.getQualifiedColName() + "," + TFTestResultTable.table.relError.getQualifiedColName() + "," + TFTestResultTable.table.meanSqrError.getQualifiedColName() + "," + TFTestResultTable.table.timeAbsError.getQualifiedColName() + "," + TFTestResultTable.table.indexAbsError.getQualifiedColName() + "," + TFTestResultTable.table.timeRelError.getQualifiedColName() + "," + TFTestResultTable.table.indexRelError.getQualifiedColName() + "," + TSALT + "." + TFTestSuiteTable.table.tsVersion.getUnqualifiedColName() + "," + BSCALT + "." + BioModelSimContextLinkTable.table.bioModelRef.getUnqualifiedColName() + "," + TFTestCaseTable.table.tcSolutionType.getQualifiedColName() + "," + BioModelTable.table.id.getQualifiedColName() + " " + MODELID + "," + TSALT + "." + TFTestSuiteTable.table.id.getUnqualifiedColName() + " " + REFTSUITEKEY + "," + TCALT + "." + TFTestCaseTable.table.id.getUnqualifiedColName() + " " + REFTCASEKEY + "," + "NULL " + // TCRALT2+"."+TFTestCriteriaTable.table.id.getUnqualifiedColName() +" "+REFTCRITKEY +
REFTCRITKEY + " FROM " + TFTestSuiteTable.table.getTableName() + "," + TFTestCaseTable.table.getTableName() + "," + TFTestCriteriaTable.table.getTableName() + "," + TFTestResultTable.table.getTableName() + "," + BioModelSimContextLinkTable.table.getTableName() + "," + BioModelTable.table.getTableName() + "," + SimContextTable.table.getTableName() + "," + SimulationTable.table.getTableName() + "," + BioModelSimulationLinkTable.table.getTableName() + "," + TFTestSuiteTable.table.getTableName() + " " + TSALT + "," + TFTestCaseTable.table.getTableName() + " " + TCALT + "," + TFTestCriteriaTable.table.getTableName() + " " + TCRALT + "," + BioModelSimContextLinkTable.table.getTableName() + " " + BSCALT + // ","+TFTestCriteriaTable.table.getTableName()+" "+TCRALT2+
" WHERE " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + TFTestCaseTable.table.testSuiteRef.getQualifiedColName() + " AND " + TFTestCriteriaTable.table.testCaseRef.getQualifiedColName() + "=" + TFTestCaseTable.table.id.getQualifiedColName() + " AND " + TFTestResultTable.table.testCriteriaRef.getQualifiedColName() + "(+)" + "=" + TFTestCriteriaTable.table.id.getQualifiedColName() + (qtcritxr_tsop.getVarName() != null ? " AND " + TFTestResultTable.table.varName.getQualifiedColName() + "(+)" + "=" + "'" + qtcritxr_tsop.getVarName() + "'" : "") + " AND " + TFTestCaseTable.table.bmAppRef.getQualifiedColName() + "=" + BioModelSimContextLinkTable.table.id.getQualifiedColName() + " AND " + BioModelSimContextLinkTable.table.bioModelRef.getQualifiedColName() + "=" + BioModelTable.table.id.getQualifiedColName() + " AND " + BioModelSimContextLinkTable.table.simContextRef.getQualifiedColName() + "=" + SimContextTable.table.id.getQualifiedColName() + " AND " + BioModelSimulationLinkTable.table.bioModelRef.getQualifiedColName() + "=" + BioModelTable.table.id.getQualifiedColName() + " AND " + BioModelSimulationLinkTable.table.simRef.getQualifiedColName() + "=" + SimulationTable.table.id.getQualifiedColName() + " AND " + BioModelTable.table.versionBranchID.getQualifiedColName() + "=" + "(" + "SELECT DISTINCT " + BioModelTable.table.versionBranchID.getQualifiedColName() + " FROM " + TFTestCaseTable.table.getTableName() + "," + TFTestCriteriaTable.table.getTableName() + "," + BioModelSimContextLinkTable.table.getTableName() + "," + BioModelTable.table.getTableName() + " WHERE " + TFTestCriteriaTable.table.id.getQualifiedColName() + "=" + qtcritxr_tsop.getTestCriterium() + " AND " + TFTestCriteriaTable.table.testCaseRef.getQualifiedColName() + "=" + TFTestCaseTable.table.id.getQualifiedColName() + " AND " + TFTestCaseTable.table.bmAppRef.getQualifiedColName() + "=" + BioModelSimContextLinkTable.table.id.getQualifiedColName() + " AND " + BioModelSimContextLinkTable.table.bioModelRef.getQualifiedColName() + "=" + BioModelTable.table.id.getQualifiedColName() + ")" + " AND " + SimContextTable.table.name.getQualifiedColName() + "=" + "(" + "SELECT DISTINCT " + SimContextTable.table.name.getQualifiedColName() + " FROM " + TFTestCaseTable.table.getTableName() + "," + TFTestCriteriaTable.table.getTableName() + "," + BioModelSimContextLinkTable.table.getTableName() + "," + SimContextTable.table.getTableName() + " WHERE " + TFTestCriteriaTable.table.id.getQualifiedColName() + "=" + qtcritxr_tsop.getTestCriterium() + " AND " + TFTestCriteriaTable.table.testCaseRef.getQualifiedColName() + "=" + TFTestCaseTable.table.id.getQualifiedColName() + " AND " + TFTestCaseTable.table.bmAppRef.getQualifiedColName() + "=" + BioModelSimContextLinkTable.table.id.getQualifiedColName() + " AND " + BioModelSimContextLinkTable.table.simContextRef.getQualifiedColName() + "=" + SimContextTable.table.id.getQualifiedColName() + ")" + " AND " + SimulationTable.table.name.getQualifiedColName() + "=" + "(" + "SELECT DISTINCT " + SimulationTable.table.name.getQualifiedColName() + " FROM " + TFTestCriteriaTable.table.getTableName() + "," + SimulationTable.table.getTableName() + " WHERE " + TFTestCriteriaTable.table.id.getQualifiedColName() + "=" + qtcritxr_tsop.getTestCriterium() + " AND " + TFTestCriteriaTable.table.simulationRef.getQualifiedColName() + "=" + SimulationTable.table.id.getQualifiedColName() + ")" + // reference info
" AND " + TSALT + "." + TFTestSuiteTable.table.id.getUnqualifiedColName() + "(+)" + "=" + TCALT + "." + TFTestCaseTable.table.testSuiteRef.getUnqualifiedColName() + " AND " + BSCALT + "." + BioModelSimContextLinkTable.table.id.getUnqualifiedColName() + "(+)" + "=" + TCRALT + "." + TFTestCriteriaTable.table.regressionBMAPPRef.getUnqualifiedColName() + " AND " + TCALT + "." + TFTestCaseTable.table.bmAppRef.getUnqualifiedColName() + "(+)" + "=" + TCRALT + "." + TFTestCriteriaTable.table.regressionBMAPPRef.getUnqualifiedColName() + " AND " + TCRALT + "." + TFTestCriteriaTable.table.id.getUnqualifiedColName() + "=" + TFTestCriteriaTable.table.id.getQualifiedColName() + // SIM2+"."+SimulationTable.table.name.getUnqualifiedColName()+"="+SimulationTable.table.name.getQualifiedColName()+
" ORDER BY " + TSID;
ResultSet rset = stmt.executeQuery(sql);
while (rset.next()) {
crossRefV.add(new TestCriteriaCrossRefOPResults.CrossRefData(rset, true));
}
rset.close();
//
// MathModel query
//
String MMNAME = "mmname";
sql = "SELECT DISTINCT " + TFTestSuiteTable.table.tsVersion.getQualifiedColName() + "," + TFTestSuiteTable.table.id.getQualifiedColName() + " " + TSID + "," + TFTestCaseTable.table.id.getQualifiedColName() + " " + TCID + "," + TFTestCriteriaTable.table.id.getQualifiedColName() + " " + TCRID + "," + MathModelTable.table.name.getQualifiedColName() + " " + MMNAME + "," + SimulationTable.table.name.getQualifiedColName() + " " + SIMNAME + "," + TFTestCriteriaTable.table.maxAbsError.getQualifiedColName() + "," + TFTestCriteriaTable.table.maxRelError.getQualifiedColName() + "," + TFTestResultTable.table.varName.getQualifiedColName() + "," + TFTestResultTable.table.minRef.getQualifiedColName() + "," + TFTestResultTable.table.maxRef.getQualifiedColName() + "," + TFTestResultTable.table.absError.getQualifiedColName() + "," + TFTestResultTable.table.relError.getQualifiedColName() + "," + TFTestResultTable.table.meanSqrError.getQualifiedColName() + "," + TFTestResultTable.table.timeAbsError.getQualifiedColName() + "," + TFTestResultTable.table.indexAbsError.getQualifiedColName() + "," + TFTestResultTable.table.timeRelError.getQualifiedColName() + "," + TFTestResultTable.table.indexRelError.getQualifiedColName() + "," + TSALT + "." + TFTestSuiteTable.table.tsVersion.getUnqualifiedColName() + "," + MMSIMALT + "." + MathModelSimulationLinkTable.table.mathModelRef.getUnqualifiedColName() + "," + TFTestCaseTable.table.tcSolutionType.getQualifiedColName() + "," + MathModelTable.table.id.getQualifiedColName() + " " + MODELID + "," + TSALT + "." + TFTestSuiteTable.table.id.getUnqualifiedColName() + " " + REFTSUITEKEY + "," + TCALT + "." + TFTestCaseTable.table.id.getUnqualifiedColName() + " " + REFTCASEKEY + "," + "NULL " + // TCRALT2+"."+TFTestCriteriaTable.table.id.getUnqualifiedColName() +" "+REFTCRITKEY +
REFTCRITKEY + " FROM " + TFTestSuiteTable.table.getTableName() + "," + TFTestCaseTable.table.getTableName() + "," + TFTestCriteriaTable.table.getTableName() + "," + TFTestResultTable.table.getTableName() + "," + MathModelTable.table.getTableName() + "," + SimulationTable.table.getTableName() + "," + MathModelSimulationLinkTable.table.getTableName() + "," + TFTestSuiteTable.table.getTableName() + " " + TSALT + "," + TFTestCaseTable.table.getTableName() + " " + TCALT + "," + TFTestCriteriaTable.table.getTableName() + " " + TCRALT + "," + MathModelSimulationLinkTable.table.getTableName() + " " + MMSIMALT + // ","+TFTestCriteriaTable.table.getTableName()+" "+TCRALT2+
" WHERE " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + TFTestCaseTable.table.testSuiteRef.getQualifiedColName() + " AND " + TFTestCriteriaTable.table.testCaseRef.getQualifiedColName() + "=" + TFTestCaseTable.table.id.getQualifiedColName() + " AND " + TFTestResultTable.table.testCriteriaRef.getQualifiedColName() + "(+)" + "=" + TFTestCriteriaTable.table.id.getQualifiedColName() + (qtcritxr_tsop.getVarName() != null ? " AND " + TFTestResultTable.table.varName.getQualifiedColName() + "(+)" + "=" + "'" + qtcritxr_tsop.getVarName() + "'" : "") + " AND " + TFTestCaseTable.table.mathModelRef.getQualifiedColName() + "=" + MathModelTable.table.id.getQualifiedColName() + " AND " + TFTestCriteriaTable.table.simulationRef.getQualifiedColName() + "=" + SimulationTable.table.id.getQualifiedColName() + " AND " + MathModelSimulationLinkTable.table.mathModelRef.getQualifiedColName() + "=" + MathModelTable.table.id.getQualifiedColName() + " AND " + MathModelSimulationLinkTable.table.simRef.getQualifiedColName() + "=" + SimulationTable.table.id.getQualifiedColName() + " AND " + MathModelTable.table.versionBranchID.getQualifiedColName() + "=" + "(" + "SELECT DISTINCT " + MathModelTable.table.versionBranchID.getQualifiedColName() + " FROM " + TFTestCaseTable.table.getTableName() + "," + TFTestCriteriaTable.table.getTableName() + "," + MathModelTable.table.getTableName() + " WHERE " + TFTestCriteriaTable.table.id.getQualifiedColName() + "=" + qtcritxr_tsop.getTestCriterium() + " AND " + TFTestCriteriaTable.table.testCaseRef.getQualifiedColName() + "=" + TFTestCaseTable.table.id.getQualifiedColName() + " AND " + TFTestCaseTable.table.mathModelRef.getQualifiedColName() + "=" + MathModelTable.table.id.getQualifiedColName() + ")" + " AND " + SimulationTable.table.name.getQualifiedColName() + "=" + "(" + "SELECT DISTINCT " + SimulationTable.table.name.getQualifiedColName() + " FROM " + TFTestCriteriaTable.table.getTableName() + "," + SimulationTable.table.getTableName() + " WHERE " + TFTestCriteriaTable.table.id.getQualifiedColName() + "=" + qtcritxr_tsop.getTestCriterium() + " AND " + TFTestCriteriaTable.table.simulationRef.getQualifiedColName() + "=" + SimulationTable.table.id.getQualifiedColName() + ")" + // reference info
" AND " + TSALT + "." + TFTestSuiteTable.table.id.getUnqualifiedColName() + "(+)" + "=" + TCALT + "." + TFTestCaseTable.table.testSuiteRef.getUnqualifiedColName() + " AND " + TCALT + "." + TFTestCaseTable.table.mathModelRef.getUnqualifiedColName() + "(+)" + "=" + MMSIMALT + "." + MathModelSimulationLinkTable.table.mathModelRef.getUnqualifiedColName() + " AND " + TCRALT + "." + TFTestCriteriaTable.table.regressionMMSimRef.getUnqualifiedColName() + "=" + MMSIMALT + "." + MathModelSimulationLinkTable.table.id.getUnqualifiedColName() + "(+)" + " AND " + TCRALT + "." + TFTestCriteriaTable.table.id.getUnqualifiedColName() + "=" + TFTestCriteriaTable.table.id.getQualifiedColName() + // SIM2+"."+SimulationTable.table.name.getUnqualifiedColName()+"="+SimulationTable.table.name.getQualifiedColName()+
" ORDER BY " + TSID;
rset = stmt.executeQuery(sql);
while (rset.next()) {
crossRefV.add(new TestCriteriaCrossRefOPResults.CrossRefData(rset, false));
}
rset.close();
return new TestCriteriaCrossRefOPResults(qtcritxr_tsop.getTestSuiteKey(), qtcritxr_tsop.getTestCriterium(), crossRefV);
} else {
throw new IllegalArgumentException("Unsupported OP+" + tsop);
}
} finally {
if (stmt != null) {
stmt.close();
}
}
Object[] changedTSKeys = changedTestSuiteKeys.toArray();
for (int i = 0; i < changedTSKeys.length; i += 1) {
System.out.println("TestSuite " + changedTSKeys[i].toString() + " changed");
// testSuiteHash.remove(changedTSKeys[i]);
}
return new TestSuiteOPResults(null);
}
Also used :
AddTestCriteriaOPBioModel(cbit.vcell.numericstest.AddTestCriteriaOPBioModel)
AddTestCasesOPBioModel(cbit.vcell.numericstest.AddTestCasesOPBioModel)
LoadTestInfoOpResults(cbit.vcell.numericstest.LoadTestInfoOpResults)
LoadTestSoftwareVersionTimeStamp(cbit.vcell.numericstest.LoadTestInfoOpResults.LoadTestSoftwareVersionTimeStamp)
AddTestResultsOP(cbit.vcell.numericstest.AddTestResultsOP)
TreeSet(java.util.TreeSet)
ResultSet(java.sql.ResultSet)
TestSuiteOPResults(cbit.vcell.numericstest.TestSuiteOPResults)
EditTestCriteriaOPBioModel(cbit.vcell.numericstest.EditTestCriteriaOPBioModel)
VariableComparisonSummary(cbit.vcell.solver.test.VariableComparisonSummary)
Vector(java.util.Vector)
TestCriteriaCrossRefOPResults(cbit.vcell.numericstest.TestCriteriaCrossRefOPResults)
RemoveTestCasesOP(cbit.vcell.numericstest.RemoveTestCasesOP)
AddTestCriteriaOPMathModel(cbit.vcell.numericstest.AddTestCriteriaOPMathModel)
ModelGeometryOPResults(cbit.vcell.numericstest.ModelGeometryOPResults)
RemoveTestSuiteOP(cbit.vcell.numericstest.RemoveTestSuiteOP)
KeyValue(org.vcell.util.document.KeyValue)
LoadTestInfoOP(cbit.vcell.numericstest.LoadTestInfoOP)
AddTestCasesOP(cbit.vcell.numericstest.AddTestCasesOP)
EditTestSuiteOP(cbit.vcell.numericstest.EditTestSuiteOP)
RemoveTestResultsOP(cbit.vcell.numericstest.RemoveTestResultsOP)
RemoveTestCriteriaOP(cbit.vcell.numericstest.RemoveTestCriteriaOP)
EditTestCriteriaOPMathModel(cbit.vcell.numericstest.EditTestCriteriaOPMathModel)
AddTestSuiteOP(cbit.vcell.numericstest.AddTestSuiteOP)
AddTestCasesOPMathModel(cbit.vcell.numericstest.AddTestCasesOPMathModel)
DataAccessException(org.vcell.util.DataAccessException)
EditTestCriteriaOPReportStatus(cbit.vcell.numericstest.EditTestCriteriaOPReportStatus)
ModelGeometryOP(cbit.vcell.numericstest.ModelGeometryOP)
QueryTestCriteriaCrossRefOP(cbit.vcell.numericstest.QueryTestCriteriaCrossRefOP)
PreparedStatement(java.sql.PreparedStatement)
Statement(java.sql.Statement)
Hashtable(java.util.Hashtable)
InsertHashtable(cbit.sql.InsertHashtable)
BioModelInfo(org.vcell.util.document.BioModelInfo)
MathModelInfo(org.vcell.util.document.MathModelInfo)
BigDecimal(java.math.BigDecimal)
EditTestCasesOP(cbit.vcell.numericstest.EditTestCasesOP)
ChangeTestCriteriaErrorLimitOP(cbit.vcell.numericstest.ChangeTestCriteriaErrorLimitOP)
SimpleDateFormat(java.text.SimpleDateFormat)
Aggregations
VariableComparisonSummary (cbit.vcell.solver.test.VariableComparisonSummary)6
DataAccessException (org.vcell.util.DataAccessException)3
BioModelInfo (org.vcell.util.document.BioModelInfo)3
MathModelInfo (org.vcell.util.document.MathModelInfo)3
InsertHashtable (cbit.sql.InsertHashtable)2
AddTestCasesOPBioModel (cbit.vcell.numericstest.AddTestCasesOPBioModel)2
AddTestCasesOPMathModel (cbit.vcell.numericstest.AddTestCasesOPMathModel)2
AddTestCriteriaOPBioModel (cbit.vcell.numericstest.AddTestCriteriaOPBioModel)2
AddTestCriteriaOPMathModel (cbit.vcell.numericstest.AddTestCriteriaOPMathModel)2
AddTestResultsOP (cbit.vcell.numericstest.AddTestResultsOP)2
EditTestCriteriaOPBioModel (cbit.vcell.numericstest.EditTestCriteriaOPBioModel)2
EditTestCriteriaOPMathModel (cbit.vcell.numericstest.EditTestCriteriaOPMathModel)2
EditTestCriteriaOPReportStatus (cbit.vcell.numericstest.EditTestCriteriaOPReportStatus)2
RemoveTestResultsOP (cbit.vcell.numericstest.RemoveTestResultsOP)2
TestCaseNewBioModel (cbit.vcell.numericstest.TestCaseNewBioModel)2
TestCaseNewMathModel (cbit.vcell.numericstest.TestCaseNewMathModel)2
TestCriteriaNewBioModel (cbit.vcell.numericstest.TestCriteriaNewBioModel)2
TestCriteriaNewMathModel (cbit.vcell.numericstest.TestCriteriaNewMathModel)2
SimulationInfo (cbit.vcell.solver.SimulationInfo)2
ODESolverResultSet (cbit.vcell.solver.ode.ODESolverResultSet)2
