Examples with BioModelInfo org.vcell.util.document.BioModelInfo used on opensource projects

Example 16 with BioModelInfo

use of org.vcell.util.document.BioModelInfo in project vcell by virtualcell.

the class BioModelDbTreePanel method documentManager_DatabaseUpdate.

/**
 * Comment
 */
protected void documentManager_DatabaseUpdate(DatabaseEvent event) {
    if (event.getNewVersionInfo() instanceof BioModelInfo && getSelectedVersionInfo() instanceof BioModelInfo) {
        BioModelInfo selectedBMInfo = (BioModelInfo) getSelectedVersionInfo();
        BioModelInfo eventBMInfo = (BioModelInfo) event.getNewVersionInfo();
        if (eventBMInfo.getVersion().getVersionKey().equals(selectedBMInfo.getVersion().getVersionKey())) {
            setSelectedVersionInfo(event.getNewVersionInfo());
        }
    }
}

Example 17 with BioModelInfo

use of org.vcell.util.document.BioModelInfo in project vcell by virtualcell.

the class BioModelMetaDataPanel method setBioModelInfo.

/**
 * Sets the bioModelInfo property (cbit.vcell.biomodel.BioModelInfo) value.
 * @param bioModelInfo The new value for the property.
 * @see #getBioModelInfo
 */
public void setBioModelInfo(BioModelInfo bioModelInfo) {
    BioModelInfo oldValue = fieldBioModelInfo;
    fieldBioModelInfo = bioModelInfo;
    firePropertyChange("bioModelInfo", oldValue, bioModelInfo);
}

Example 18 with BioModelInfo

use of org.vcell.util.document.BioModelInfo in project vcell by virtualcell.

the class EditTestCriteriaPanel method resetTextFields.

/**
 * Sets the testSuiteInfo property (cbit.vcell.numericstest.TestSuiteInfo) value.
 * @param testSuiteInfo The new value for the property.
 * @see #getTestSuiteInfo
 */
public void resetTextFields() {
    // If the chosen simInfo already has test criteria defined, set the fields with the appropriate values
    // Else set them to blank.
    getRelErrTextField().setText("");
    getAbsErrTextField().setText("");
    if (getExistingTestCriteria() != null) {
        Double relErr = getExistingTestCriteria().getMaxRelError();
        Double absErr = getExistingTestCriteria().getMaxAbsError();
        getRelErrTextField().setText((relErr != null ? relErr.toString() : null));
        getAbsErrTextField().setText((absErr != null ? absErr.toString() : null));
    }
    // Depending on test case soultion type (which is set by testingFrameworkWindowManager based on the test case
    // the simulation belongs to), enable apprpriate (ref MathModel, ref simInfo buttons) fields.
    // if (!getSolutionType().equals(TestCaseNew.REGRESSION)) {
    getRefMathModelLabel().setText(null);
    getRefSimLabel().setText(null);
    getBioModelAppLabel().setText(null);
    getBmAppSimLabel().setText(null);
    getRefMathModelButton().setEnabled(false);
    getRefMathModelLabel().setEnabled(false);
    getRefSimButton().setEnabled(false);
    getRefSimLabel().setEnabled(false);
    getSelectRefBMAppJButton().setEnabled(false);
    getBioModelAppLabel().setEnabled(false);
    getSelectRefSimJButton().setEnabled(false);
    getBmAppSimLabel().setEnabled(false);
    // } else {
    if (getExistingTestCriteria() instanceof TestCriteriaNewMathModel && getSolutionType().equals(TestCaseNew.REGRESSION)) {
        getRefMathModelButton().setEnabled(true);
        getRefMathModelLabel().setEnabled(true);
        getRefSimButton().setEnabled(true);
        getRefSimLabel().setEnabled(true);
    } else if (getExistingTestCriteria() instanceof TestCriteriaNewBioModel && getSolutionType().equals(TestCaseNew.REGRESSION)) {
        getSelectRefBMAppJButton().setEnabled(true);
        getBioModelAppLabel().setEnabled(true);
        getSelectRefSimJButton().setEnabled(true);
        getBmAppSimLabel().setEnabled(true);
    }
    if (getExistingTestCriteria() != null && getExistingTestCriteria().getRegressionSimInfo() != null) {
        if (getExistingTestCriteria() instanceof TestCriteriaNewMathModel) {
            MathModelInfo refMMInfo = ((TestCriteriaNewMathModel) getExistingTestCriteria()).getRegressionMathModelInfo();
            if (refMMInfo == null) {
                PopupGenerator.showErrorDialog(this, "No MathModelInfo found for SimInfo Key " + getExistingTestCriteria().getRegressionSimInfo().getVersion().getVersionKey());
            }
            SimulationInfo refSimInfo = null;
            refSimInfo = getExistingTestCriteria().getRegressionSimInfo();
            if (refSimInfo == null) {
                PopupGenerator.showErrorDialog(this, "No SimulationInfo found for simInfo Key " + getExistingTestCriteria().getRegressionSimInfo().getVersion().getVersionKey());
            }
            setReferenceMathModelInfo(refMMInfo);
            setReferenceSimInfo(refSimInfo);
            getRefMathModelLabel().setText("<html>" + refMMInfo.getVersion().getName() + "<br>(MathModelKey=" + refMMInfo.getVersion().getVersionKey() + ")<br>" + refMMInfo.getVersion().getDate() + "<html>");
            getRefSimLabel().setText("<html>" + refSimInfo.getVersion().getName() + "<br>(SimulationKey:" + refSimInfo.getVersion().getVersionKey() + ")</html>");
        } else if (getExistingTestCriteria() instanceof TestCriteriaNewBioModel) {
            BioModelInfo refBMInfo = ((TestCriteriaNewBioModel) getExistingTestCriteria()).getRegressionBioModelInfo();
            if (refBMInfo == null) {
                PopupGenerator.showErrorDialog(this, "No bioModelInfo found for SimInfo Key " + getExistingTestCriteria().getRegressionSimInfo().getVersion().getVersionKey());
            }
            SimulationInfo refSimInfo = null;
            refSimInfo = getExistingTestCriteria().getRegressionSimInfo();
            if (refSimInfo == null) {
                PopupGenerator.showErrorDialog(this, "No SimulationInfo found for simInfo Key " + getExistingTestCriteria().getRegressionSimInfo().getVersion().getVersionKey());
            }
            setbioModelInfo(refBMInfo);
            setbmAppSimInfo(refSimInfo);
            setappName(((TestCriteriaNewBioModel) getExistingTestCriteria()).getRegressionApplicationName());
            getBioModelAppLabel().setText("<html>" + refBMInfo.getVersion().getName() + "/" + getappName() + "<br>(BioModelKey=" + refBMInfo.getVersion().getVersionKey() + ")<br>" + refBMInfo.getVersion().getDate() + "</html>");
            getBmAppSimLabel().setText("<html>" + refSimInfo.getVersion().getName() + "<br>(SimulationKey:" + refSimInfo.getVersion().getVersionKey() + ")</html>");
        }
    } else {
        setReferenceMathModelInfo(null);
        setReferenceSimInfo(null);
        getRefMathModelLabel().setText("");
        getRefSimLabel().setText("");
        setbioModelInfo(null);
        setbmAppSimInfo(null);
        setappName(null);
        getBioModelAppLabel().setText(null);
        getBmAppSimLabel().setText(null);
    }
// }
}

Example 19 with BioModelInfo

use of org.vcell.util.document.BioModelInfo in project vcell by virtualcell.

the class NagiosVCellMonitor method checkVCell.

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

Example 20 with BioModelInfo

use of org.vcell.util.document.BioModelInfo in project vcell by virtualcell.

the class BioModelMultiVisitor method visitBioModel.

public void visitBioModel(BioModel bioModel, PrintStream logFilePrintStream) {
    KeyValue currentKey = bioModel.getVersion().getVersionKey();
    BioModelInfo bmInfo = bioModelInfoHash.get(currentKey);
    logFilePrintStream.append(" == SUCEEDED IN READING BIOMODEL " + bmInfo.getVersion().getName() + "; key : " + currentKey.toString() + "\n");
    unparsedBioModels.remove(currentKey);
    for (Iterator<KeyValue> iterator = unparsedBioModels.iterator(); iterator.hasNext(); ) {
        KeyValue key = iterator.next();
        bmInfo = bioModelInfoHash.get(key);
        logFilePrintStream.append(" == FAILED TO READ BIOMODEL : " + bmInfo.getVersion().getName() + "; key : " + key.toString() + "\n");
        iterator.remove();
    }
    return;
}