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

Example 26 with SimulationInfo

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

the class VCellBasicCellRenderer method getTreeCellRendererComponent.

/**
 * Insert the method's description here.
 * Creation date: (7/27/2000 6:41:57 PM)
 * @return java.awt.Component
 */
public java.awt.Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) {
    JLabel component = (JLabel) super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus);
    // 
    if (!leaf && expanded) {
        setIcon(fieldFolderOpenIcon);
    } else if (!leaf && !expanded) {
        setIcon(fieldFolderClosedIcon);
    }
    try {
        if (value instanceof BioModelNode) {
            BioModelNode node = (BioModelNode) value;
            boolean bLoaded = false;
            // 
            // Check if node is a SolverResultSetInfo
            // 
            Object userObject = node.getUserObject();
            if (userObject instanceof SimulationInfo) {
                // 
                // Check if node is a SimulationInfo
                // 
                setComponentProperties(component, (SimulationInfo) userObject);
                int maxErrorLevel = getMaxErrorLevel(node);
                if (maxErrorLevel == BioModelNode.ERROR_POSSIBLE) {
                    setIcon(fieldSimulationWarningIcon);
                    component.setToolTipText("Simulation contains possibly invalid results");
                } else if (maxErrorLevel == BioModelNode.ERROR_CONFIRMED) {
                    setIcon(fieldSimulationErrorIcon);
                    component.setToolTipText("Simulation contains invalid results");
                }
            } else if (userObject instanceof String && node.getChildCount() == 0) {
                component.setToolTipText(null);
                component.setText((String) userObject);
            } else if (userObject instanceof BioModelInfo) {
                // 
                // Check if node is a BioModelInfo
                // 
                setComponentProperties(component, (BioModelInfo) userObject);
                bLoaded = isLoaded((BioModelInfo) userObject);
                int maxErrorLevel = getMaxErrorLevel(node);
                if (maxErrorLevel == BioModelNode.ERROR_POSSIBLE) {
                    setIcon(fieldBioModelWarningIcon);
                    component.setToolTipText("BioModel version: Has possibly invalid simulation results");
                } else if (maxErrorLevel == BioModelNode.ERROR_CONFIRMED) {
                    setIcon(fieldBioModelErrorIcon);
                    component.setToolTipText("BioModel version: Has invalid simulation results");
                }
            } else if (userObject instanceof String && node.getChildCount() > 0 && ((BioModelNode) node.getChildAt(0)).getUserObject() instanceof BioModelInfo) {
                // 
                // Check if node is a BioModelName (String), with children (at least one version of biomodel), and if the child is a
                // BioModelInfo node
                // 
                String label = (String) userObject;
                component.setToolTipText("BioModel");
                component.setText(label);
                // 
                // check if child is loaded
                // 
                int maxErrorLevel = BioModelNode.ERROR_NONE;
                for (int i = 0; i < node.getChildCount(); i++) {
                    maxErrorLevel = Math.max(maxErrorLevel, getMaxErrorLevel((BioModelNode) node.getChildAt(i)));
                }
                if (maxErrorLevel == BioModelNode.ERROR_POSSIBLE) {
                    if (!leaf && expanded) {
                        setIcon(fieldFolderOpenWarningIcon);
                    } else if (!leaf && !expanded) {
                        setIcon(fieldFolderClosedWarningIcon);
                    }
                    component.setToolTipText("BioModel: one or more versions may have invalid simulation results");
                } else if (maxErrorLevel == BioModelNode.ERROR_CONFIRMED) {
                    if (!leaf && expanded) {
                        setIcon(fieldFolderOpenErrorIcon);
                    } else if (!leaf && !expanded) {
                        setIcon(fieldFolderClosedErrorIcon);
                    }
                    component.setToolTipText("BioModel: one or more versions have invalid simulation results");
                }
                // 
                for (int i = 0; i < node.getChildCount(); i++) {
                    BioModelInfo bioModelInfo = (BioModelInfo) ((BioModelNode) node.getChildAt(i)).getUserObject();
                    if (isLoaded(bioModelInfo)) {
                        bLoaded = true;
                    }
                }
            } else if (userObject instanceof User && node.getChildCount() > 0 && (((BioModelNode) node.getChildAt(0)).getUserObject() instanceof String) && ((BioModelNode) (node.getChildAt(0).getChildAt(0))).getUserObject() instanceof BioModelInfo) {
                // 
                // Check if node is a User, with at least one child which is a string (BioModel name)
                // and if the child's child is a BioModelInfo node
                // 
                String label = ((User) userObject).getName();
                component.setToolTipText("User Name");
                component.setText(label);
                if (isLoaded((User) userObject)) {
                    bLoaded = true;
                }
            } else if (userObject instanceof MathModelInfo) {
                // 
                // Check if node is a MathModelInfo node
                // 
                setComponentProperties(component, (MathModelInfo) userObject);
                bLoaded = isLoaded((MathModelInfo) userObject);
            } else if (userObject instanceof String && node.getChildCount() > 0 && ((BioModelNode) node.getChildAt(0)).getUserObject() instanceof MathModelInfo) {
                // 
                // Check if node is a MathModel name (String), with children (at least one version of mathmodel), and
                // if the child is a MathModelInfo node
                // 
                String label = (String) userObject;
                component.setToolTipText("Mathematical Model");
                component.setText(label);
                // 
                for (int i = 0; i < node.getChildCount(); i++) {
                    MathModelInfo mathModelInfo = (MathModelInfo) ((BioModelNode) node.getChildAt(i)).getUserObject();
                    if (isLoaded(mathModelInfo)) {
                        bLoaded = true;
                    }
                }
            } else if (userObject instanceof User && node.getChildCount() > 0 && (((BioModelNode) node.getChildAt(0)).getUserObject() instanceof String) && ((BioModelNode) (node.getChildAt(0).getChildAt(0))).getUserObject() instanceof MathModelInfo) {
                // 
                // Check if node is a User, with at least one child which is a string (Mathmodel name)
                // and if the child's child is a MathModelInfo node
                // 
                String label = ((User) userObject).getName();
                component.setToolTipText("User Name");
                component.setText(label);
                if (isLoaded((User) userObject)) {
                    bLoaded = true;
                }
            } else if (userObject instanceof cbit.vcell.geometry.GeometryInfo) {
                // 
                // Check if node is a GeometryInfo
                // 
                setComponentProperties(component, (GeometryInfo) userObject);
                bLoaded = isLoaded((GeometryInfo) userObject);
            } else if (userObject instanceof String && node.getChildCount() > 0 && ((BioModelNode) node.getChildAt(0)).getUserObject() instanceof GeometryInfo) {
                // 
                // Check if node is a Geometry name (String), with children (at least one version of Geometry), and
                // if the child is a GeometryInfo node
                // 
                String label = (String) userObject;
                component.setToolTipText("Geometry");
                component.setText(label);
                // 
                for (int i = 0; i < node.getChildCount(); i++) {
                    GeometryInfo geometryInfo = (GeometryInfo) ((BioModelNode) node.getChildAt(i)).getUserObject();
                    if (isLoaded(geometryInfo)) {
                        bLoaded = true;
                    }
                }
            } else if (userObject instanceof User && node.getChildCount() > 0 && (((BioModelNode) node.getChildAt(0)).getUserObject() instanceof String) && ((BioModelNode) (node.getChildAt(0).getChildAt(0))).getUserObject() instanceof GeometryInfo) {
                // 
                // Check if node is a User, with at least one child which is a string (Geometry name)
                // and if the child's child is a GeometryInfo node
                // 
                String label = ((User) userObject).getName();
                component.setToolTipText("User Name");
                component.setText(label);
                if (isLoaded((User) userObject)) {
                    bLoaded = true;
                }
            } else if (userObject instanceof String && node.getChildCount() > 0) {
                component.setToolTipText(null);
                component.setText((String) userObject);
            // }else if (node.getUserObject() instanceof MathInfo) {
            // setComponentProperties(component,(MathInfo)node.getUserObject());
            } else if (userObject instanceof VCImageInfo) {
                setComponentProperties(component, (VCImageInfo) userObject);
            } else if (userObject instanceof Extent) {
                setComponentProperties(component, (Extent) userObject);
            } else if (userObject instanceof Annotation) {
                setComponentProperties(component, (Annotation) userObject);
            } else if (userObject instanceof MathModel) {
                setComponentProperties(component, (MathModel) userObject);
            } else if (userObject instanceof BioModel) {
                setComponentProperties(component, (BioModel) userObject);
            } else if (userObject instanceof SimulationContext) {
                setComponentProperties(component, (SimulationContext) userObject);
                bLoaded = isLoaded((SimulationContext) userObject);
            } else if (userObject instanceof Simulation) {
                setComponentProperties(component, (Simulation) userObject);
            } else if (userObject instanceof MathDescription) {
                setComponentProperties(component, (MathDescription) userObject);
            } else if (userObject instanceof Geometry) {
                setComponentProperties(component, (Geometry) userObject);
            } else if (userObject instanceof User) {
                setComponentProperties(component, (User) userObject);
            } else {
                setComponentProperties(component, userObject);
            }
            if (selectedFont == null && component.getFont() != null) {
                selectedFont = component.getFont().deriveFont(Font.BOLD);
            }
            if (unselectedFont == null && component.getFont() != null) {
                unselectedFont = component.getFont().deriveFont(Font.PLAIN);
            }
            if (bLoaded) {
                component.setFont(selectedFont);
            } else {
                component.setFont(unselectedFont);
            }
        }
    } catch (Throwable e) {
        e.printStackTrace(System.out);
    }
    // 
    return component;
}

Example 27 with SimulationInfo

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

the class BioModelWindowManager method updateSimulationDataViewers.

/**
 * Insert the method's description here.
 * Creation date: (7/20/2004 1:13:06 PM)
 */
private void updateSimulationDataViewers(ApplicationComponents appComponents, SimulationContext found) {
    SimulationWindow[] simWindows = appComponents.getSimulationWindows();
    Simulation[] sims = found.getSimulations();
    Hashtable<VCSimulationIdentifier, Simulation> hash = new Hashtable<VCSimulationIdentifier, Simulation>();
    for (int i = 0; i < sims.length; i++) {
        SimulationInfo simInfo = sims[i].getSimulationInfo();
        if (simInfo != null) {
            VCSimulationIdentifier vcSimulationIdentifier = simInfo.getAuthoritativeVCSimulationIdentifier();
            hash.put(vcSimulationIdentifier, sims[i]);
        }
    }
    for (int i = 0; i < simWindows.length; i++) {
        SimulationWindow sw = simWindows[i];
        if (hash.containsKey(simWindows[i].getVcSimulationIdentifier())) {
            sw.resetSimulation((Simulation) hash.get(sw.getVcSimulationIdentifier()));
        } else if (sw.isShowingLocalSimulation()) {
            sw.setLocalState(LocalState.LOCAL_SIMMODFIED);
        } else {
            ChildWindowManager childWindowManager = ChildWindowManager.findChildWindowManager(getJPanel());
            ChildWindow childWindow = childWindowManager.getChildWindowFromContext(sw);
            if (childWindow != null) {
                childWindowManager.closeChildWindow(childWindow);
            }
        }
    }
}

Example 28 with SimulationInfo

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

the class SimulationDispatcherEngine method onStartRequest.

/**
 * @param vcMessage
 * @param session
 * @throws VCMessagingException
 * @throws SQLException
 * @throws DataAccessException
 */
public void onStartRequest(VCSimulationIdentifier vcSimID, User user, int simulationScanCount, SimulationDatabase simulationDatabase, VCMessageSession session, VCMessageSession dispatcherQueueSession) throws VCMessagingException, DataAccessException, SQLException {
    KeyValue simKey = vcSimID.getSimulationKey();
    SimulationInfo simulationInfo = null;
    try {
        simulationInfo = simulationDatabase.getSimulationInfo(user, simKey);
    } catch (DataAccessException ex) {
        if (lg.isWarnEnabled())
            lg.warn("Bad simulation " + vcSimID);
        StatusMessage message = new StatusMessage(new SimulationJobStatus(VCellServerID.getSystemServerID(), vcSimID, -1, null, SchedulerStatus.FAILED, 0, SimulationMessage.workerFailure("Failed to dispatch simulation: " + ex.getMessage()), null, null), user.getName(), null, null);
        message.sendToClient(session);
        return;
    }
    if (simulationInfo == null) {
        if (lg.isWarnEnabled())
            lg.warn("Can't start, simulation [" + vcSimID + "] doesn't exist in database");
        StatusMessage message = new StatusMessage(new SimulationJobStatus(VCellServerID.getSystemServerID(), vcSimID, -1, null, SchedulerStatus.FAILED, 0, SimulationMessage.workerFailure("Can't start, simulation [" + vcSimID + "] doesn't exist"), null, null), user.getName(), null, null);
        message.sendToClient(session);
        return;
    }
    if (simulationScanCount > Integer.parseInt(cbit.vcell.resource.PropertyLoader.getRequiredProperty(cbit.vcell.resource.PropertyLoader.maxJobsPerScan))) {
        if (lg.isWarnEnabled())
            lg.warn("Too many simulations (" + simulationScanCount + ") for parameter scan." + vcSimID);
        StatusMessage message = new StatusMessage(new SimulationJobStatus(VCellServerID.getSystemServerID(), vcSimID, -1, null, SchedulerStatus.FAILED, 0, SimulationMessage.workerFailure("Too many simulations (" + simulationScanCount + ") for parameter scan."), null, null), user.getName(), null, null);
        message.sendToClient(session);
        return;
    }
    for (int jobIndex = 0; jobIndex < simulationScanCount; jobIndex++) {
        SimulationStateMachine simStateMachine = getSimulationStateMachine(simKey, jobIndex);
        try {
            simStateMachine.onStartRequest(user, vcSimID, simulationDatabase, session);
        } catch (UpdateSynchronizationException e) {
            simStateMachine.onStartRequest(user, vcSimID, simulationDatabase, session);
        }
    }
}

Example 29 with SimulationInfo

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

the class DbDriver method testSuiteGet.

/**
 * Insert the method's description here.
 * Creation date: (10/16/2004 2:39:49 PM)
 * @return cbit.vcell.numericstest.TestSuiteInfoNew[]
 */
public static TestSuiteNew testSuiteGet(BigDecimal getThisTS, Connection con, User user, DatabaseSyntax dbSyntax) throws SQLException, DataAccessException {
    if (!user.isTestAccount()) {
        throw new PermissionException("User=" + user.getName() + " not allowed TestSuiteInfo");
    }
    // if(testSuiteHash.containsKey(getThisTS)){
    // return (cbit.vcell.numericstest.TestSuiteNew)testSuiteHash.get(getThisTS);
    // }
    Hashtable simulationInfoH = new Hashtable();
    Hashtable mathModelInfoH = new Hashtable();
    Hashtable bioModelInfoH = new Hashtable();
    Statement stmt = null;
    ResultSet rset = null;
    String sql = null;
    Level origLogLevel = DatabasePolicySQL.lg.getLevel();
    try {
        DatabasePolicySQL.lg.setLevel(Level.WARN);
        // double begTime=System.currentTimeMillis();
        // int counter = 0;
        stmt = con.createStatement();
        // Get VariableComparisonSummaries
        Hashtable vcsH = new Hashtable();
        {
            sql = "SELECT " + TFTestResultTable.table.getTableName() + ".*" + " FROM " + TFTestResultTable.table.getTableName() + "," + TFTestCriteriaTable.table.getTableName() + "," + TFTestCaseTable.table.getTableName() + "," + TFTestSuiteTable.table.getTableName() + " WHERE " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + getThisTS + " AND " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + TFTestCaseTable.table.testSuiteRef.getQualifiedColName() + " AND " + TFTestCaseTable.table.id.getQualifiedColName() + "=" + TFTestCriteriaTable.table.testCaseRef.getQualifiedColName() + " AND " + TFTestCriteriaTable.table.id.getQualifiedColName() + "=" + TFTestResultTable.table.testCriteriaRef.getQualifiedColName() + " ORDER BY UPPER(" + TFTestResultTable.table.varName.getQualifiedColName() + ")";
            rset = stmt.executeQuery(sql);
            while (rset.next()) {
                BigDecimal tcritRef = rset.getBigDecimal(TFTestResultTable.table.testCriteriaRef.getUnqualifiedColName());
                String varName = rset.getString(TFTestResultTable.table.varName.getUnqualifiedColName());
                double absError = rset.getDouble(TFTestResultTable.table.absError.getUnqualifiedColName());
                double relError = rset.getDouble(TFTestResultTable.table.relError.getUnqualifiedColName());
                double maxRef = rset.getDouble(TFTestResultTable.table.maxRef.getUnqualifiedColName());
                double minRef = rset.getDouble(TFTestResultTable.table.minRef.getUnqualifiedColName());
                double mse = rset.getDouble(TFTestResultTable.table.meanSqrError.getUnqualifiedColName());
                double timeAbsError = rset.getDouble(TFTestResultTable.table.timeAbsError.getUnqualifiedColName());
                int indexAbsError = rset.getInt(TFTestResultTable.table.indexAbsError.getUnqualifiedColName());
                double timeRelError = rset.getDouble(TFTestResultTable.table.timeRelError.getUnqualifiedColName());
                int indexRelError = rset.getInt(TFTestResultTable.table.indexRelError.getUnqualifiedColName());
                Vector v = (Vector) vcsH.get(tcritRef);
                if (v == null) {
                    v = new Vector();
                    vcsH.put(tcritRef, v);
                }
                v.add(new VariableComparisonSummary(varName, minRef, maxRef, absError, relError, mse, timeAbsError, indexAbsError, timeRelError, indexRelError));
            // counter+= 1;
            }
            // System.out.println("VCS count="+counter+" time="+((System.currentTimeMillis()-begTime)/1000));
            rset.close();
        }
        // begTime=System.currentTimeMillis();
        // counter = 0;
        // Get TestCriteria for mathModel based TestCases
        Hashtable tcritH = new Hashtable();
        {
            sql = "SELECT " + TFTestCriteriaTable.table.getTableName() + ".*" + "," + MathModelSimulationLinkTable.table.getTableName() + ".*" + " FROM " + TFTestCriteriaTable.table.getTableName() + "," + TFTestCaseTable.table.getTableName() + "," + TFTestSuiteTable.table.getTableName() + "," + MathModelSimulationLinkTable.table.getTableName() + "," + SimulationTable.table.getTableName() + " WHERE " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + getThisTS + " AND " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + TFTestCaseTable.table.testSuiteRef.getQualifiedColName() + " AND " + TFTestCaseTable.table.id.getQualifiedColName() + "=" + TFTestCriteriaTable.table.testCaseRef.getQualifiedColName() + " AND " + TFTestCaseTable.table.mathModelRef.getQualifiedColName() + " IS NOT NULL " + " AND " + TFTestCriteriaTable.table.simulationRef.getQualifiedColName() + "=" + SimulationTable.table.id.getQualifiedColName() + " AND " + TFTestCriteriaTable.table.regressionMMSimRef.getQualifiedColName() + "=" + MathModelSimulationLinkTable.table.id.getQualifiedColName() + "(+)" + " ORDER BY UPPER(" + SimulationTable.table.name.getQualifiedColName() + ")";
            // System.out.println(sql);
            rset = stmt.executeQuery(sql);
            while (rset.next()) {
                BigDecimal tcritKey = rset.getBigDecimal(TFTestCriteriaTable.table.id.getUnqualifiedColName());
                BigDecimal tcaseRef = rset.getBigDecimal(TFTestCriteriaTable.table.testCaseRef.getUnqualifiedColName());
                BigDecimal simRef = rset.getBigDecimal(TFTestCriteriaTable.table.simulationRef.getUnqualifiedColName());
                BigDecimal simRegrRef = rset.getBigDecimal(MathModelSimulationLinkTable.table.simRef.getUnqualifiedColName());
                if (rset.wasNull()) {
                    simRegrRef = null;
                }
                BigDecimal mathRegrRef = rset.getBigDecimal(MathModelSimulationLinkTable.table.mathModelRef.getUnqualifiedColName());
                if (rset.wasNull()) {
                    mathRegrRef = null;
                }
                Double maxRelError = null;
                double dtemp = rset.getDouble(TFTestCriteriaTable.table.maxRelError.getUnqualifiedColName());
                if (rset.wasNull()) {
                    maxRelError = null;
                } else {
                    maxRelError = new Double(dtemp);
                }
                Double maxAbsError = null;
                dtemp = rset.getDouble(TFTestCriteriaTable.table.maxAbsError.getUnqualifiedColName());
                if (rset.wasNull()) {
                    maxAbsError = null;
                } else {
                    maxAbsError = new Double(dtemp);
                }
                String reportStatus = rset.getString(TFTestCriteriaTable.table.reportStatus.getUnqualifiedColName());
                if (rset.wasNull()) {
                    reportStatus = TestCriteriaNew.TCRIT_STATUS_NEEDSREPORT;
                }
                String reportStatusMessage = rset.getString(TFTestCriteriaTable.table.reportMessage.getUnqualifiedColName());
                if (rset.wasNull()) {
                    reportStatusMessage = null;
                }
                if (reportStatusMessage != null && reportStatusMessage.length() > 0) {
                    reportStatusMessage = TokenMangler.getSQLRestoredString(reportStatusMessage);
                }
                Vector v = (Vector) tcritH.get(tcaseRef);
                if (v == null) {
                    v = new Vector();
                    tcritH.put(tcaseRef, v);
                }
                SimulationInfo simInfo = (SimulationInfo) simulationInfoH.get(simRef);
                if (simInfo == null) {
                    Vector<VersionInfo> simVector = getVersionableInfos(con, user, VersionableType.Simulation, false, new KeyValue(simRef), false, dbSyntax);
                    if (simVector != null && simVector.size() > 0) {
                        simInfo = (SimulationInfo) simVector.firstElement();
                        simulationInfoH.put(simRef, simInfo);
                    }
                }
                SimulationInfo regrSimInfo = null;
                MathModelInfo regrMathModelInfo = null;
                if (simRegrRef != null) {
                    regrSimInfo = (SimulationInfo) simulationInfoH.get(simRegrRef);
                    if (regrSimInfo == null) {
                        Vector<VersionInfo> regSimVector = getVersionableInfos(con, user, VersionableType.Simulation, false, new KeyValue(simRegrRef), false, dbSyntax);
                        if (regSimVector != null && regSimVector.size() > 0) {
                            regrSimInfo = (SimulationInfo) regSimVector.firstElement();
                            simulationInfoH.put(simRegrRef, regrSimInfo);
                        }
                    }
                    regrMathModelInfo = (MathModelInfo) mathModelInfoH.get(mathRegrRef);
                    if (regrMathModelInfo == null) {
                        Vector<VersionInfo> regMathVector = getVersionableInfos(con, user, VersionableType.MathModelMetaData, false, new KeyValue(mathRegrRef), false, dbSyntax);
                        if (regMathVector != null && regMathVector.size() > 0) {
                            regrMathModelInfo = (MathModelInfo) regMathVector.firstElement();
                            mathModelInfoH.put(mathRegrRef, regrMathModelInfo);
                        }
                    }
                }
                // 
                VariableComparisonSummary[] neededVCSArr = null;
                Vector vcsV = (Vector) vcsH.get(tcritKey);
                if (vcsV != null) {
                    neededVCSArr = new VariableComparisonSummary[vcsV.size()];
                    vcsV.copyInto(neededVCSArr);
                }
                // 
                TestCriteriaNew tcn = null;
                if (simInfo != null) {
                    tcn = new TestCriteriaNewMathModel(tcritKey, simInfo, regrMathModelInfo, regrSimInfo, maxRelError, maxAbsError, neededVCSArr, reportStatus, reportStatusMessage);
                    v.add(tcn);
                }
            // counter+= 1;
            }
            // System.out.println("TCrit count="+counter+" time="+((System.currentTimeMillis()-begTime)/1000));
            rset.close();
        }
        // Get TestCriteria for bioModel based TestCases
        // Hashtable tcritH = new Hashtable();
        {
            final String REGRSIMREF = "REGRSIMREF";
            final String SCNAME = "SCNAME";
            sql = "SELECT " + TFTestCriteriaTable.table.getTableName() + ".*" + "," + BioModelSimContextLinkTable.table.bioModelRef.getQualifiedColName() + "," + BioModelSimulationLinkTable.table.simRef.getQualifiedColName() + " " + REGRSIMREF + "," + SimContextTable.table.name.getQualifiedColName() + " " + SCNAME + " FROM " + TFTestCriteriaTable.table.getTableName() + "," + TFTestCaseTable.table.getTableName() + "," + TFTestSuiteTable.table.getTableName() + "," + BioModelSimContextLinkTable.table.getTableName() + "," + SimContextTable.table.getTableName() + "," + BioModelSimulationLinkTable.table.getTableName() + // SimulationTable.table.getTableName()+
            " WHERE " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + getThisTS + " AND " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + TFTestCaseTable.table.testSuiteRef.getQualifiedColName() + " AND " + TFTestCaseTable.table.id.getQualifiedColName() + "=" + TFTestCriteriaTable.table.testCaseRef.getQualifiedColName() + " AND " + TFTestCaseTable.table.bmAppRef.getQualifiedColName() + " IS NOT NULL " + " AND " + TFTestCriteriaTable.table.regressionBMAPPRef.getQualifiedColName() + "=" + BioModelSimContextLinkTable.table.id.getQualifiedColName() + "(+)" + " AND " + BioModelSimContextLinkTable.table.simContextRef + " = " + SimContextTable.table.id.getQualifiedColName() + "(+)" + // SimContextTable.table.mathRef.getQualifiedColName()+" = "+SimulationTable.table.mathRef.getQualifiedColName()+"(+)" +
            " AND " + TFTestCriteriaTable.table.regressionBMSimRef.getQualifiedColName() + " = " + BioModelSimulationLinkTable.table.id.getQualifiedColName() + "(+)";
            // System.out.println(sql);
            rset = stmt.executeQuery(sql);
            while (rset.next()) {
                BigDecimal tcritKey = rset.getBigDecimal(TFTestCriteriaTable.table.id.getUnqualifiedColName());
                BigDecimal tcaseRef = rset.getBigDecimal(TFTestCriteriaTable.table.testCaseRef.getUnqualifiedColName());
                BigDecimal tcSimRef = rset.getBigDecimal(TFTestCriteriaTable.table.simulationRef.getUnqualifiedColName());
                BigDecimal regrSimRef = rset.getBigDecimal(REGRSIMREF);
                // BigDecimal regrSimRef = rset.getBigDecimal(SimulationTable.table.id.getUnqualifiedColName());
                if (rset.wasNull()) {
                    regrSimRef = null;
                }
                BigDecimal regrBioModelRef = rset.getBigDecimal(BioModelSimContextLinkTable.table.bioModelRef.getUnqualifiedColName());
                if (rset.wasNull()) {
                    regrBioModelRef = null;
                }
                String regrSCName = rset.getString(SCNAME);
                if (rset.wasNull()) {
                    regrSCName = null;
                }
                Double maxRelError = null;
                double dtemp = rset.getDouble(TFTestCriteriaTable.table.maxRelError.getUnqualifiedColName());
                if (rset.wasNull()) {
                    maxRelError = null;
                } else {
                    maxRelError = new Double(dtemp);
                }
                Double maxAbsError = null;
                dtemp = rset.getDouble(TFTestCriteriaTable.table.maxAbsError.getUnqualifiedColName());
                if (rset.wasNull()) {
                    maxAbsError = null;
                } else {
                    maxAbsError = new Double(dtemp);
                }
                String reportStatus = rset.getString(TFTestCriteriaTable.table.reportStatus.getUnqualifiedColName());
                if (rset.wasNull()) {
                    reportStatus = TestCriteriaNew.TCRIT_STATUS_NEEDSREPORT;
                }
                String reportStatusMessage = rset.getString(TFTestCriteriaTable.table.reportMessage.getUnqualifiedColName());
                if (rset.wasNull()) {
                    reportStatusMessage = null;
                }
                if (reportStatusMessage != null && reportStatusMessage.length() > 0) {
                    reportStatusMessage = TokenMangler.getSQLRestoredString(reportStatusMessage);
                }
                Vector v = (Vector) tcritH.get(tcaseRef);
                if (v == null) {
                    v = new Vector();
                    tcritH.put(tcaseRef, v);
                }
                SimulationInfo simInfo = (SimulationInfo) simulationInfoH.get(tcSimRef);
                if (simInfo == null) {
                    Vector<VersionInfo> simVector = getVersionableInfos(con, user, VersionableType.Simulation, false, new KeyValue(tcSimRef), false, dbSyntax);
                    if (simVector != null && simVector.size() == 1) {
                        simInfo = (SimulationInfo) simVector.firstElement();
                        simulationInfoH.put(tcSimRef, simInfo);
                    } else {
                        throw new DataAccessException("Found more than 1 versionable for tcsimRef=" + tcSimRef);
                    }
                }
                SimulationInfo regrSimInfo = null;
                BioModelInfo regrBioModelInfo = null;
                if (regrSimRef != null) {
                    regrSimInfo = (SimulationInfo) simulationInfoH.get(regrSimRef);
                    if (regrSimInfo == null) {
                        Vector<VersionInfo> regSimVector = getVersionableInfos(con, user, VersionableType.Simulation, false, new KeyValue(regrSimRef), false, dbSyntax);
                        if (regSimVector != null && regSimVector.size() == 1) {
                            regrSimInfo = (SimulationInfo) regSimVector.firstElement();
                            simulationInfoH.put(regrSimRef, regrSimInfo);
                        } else {
                            throw new DataAccessException("Found more than 1 versionable for simregRef=" + regrSimRef);
                        }
                    }
                    regrBioModelInfo = (BioModelInfo) mathModelInfoH.get(regrBioModelRef);
                    if (regrBioModelInfo == null) {
                        Vector<VersionInfo> regBioModelVector = getVersionableInfos(con, user, VersionableType.BioModelMetaData, false, new KeyValue(regrBioModelRef), false, dbSyntax);
                        if (regBioModelVector != null && regBioModelVector.size() == 1) {
                            regrBioModelInfo = (BioModelInfo) regBioModelVector.firstElement();
                            mathModelInfoH.put(regrBioModelRef, regrBioModelInfo);
                        } else {
                            throw new DataAccessException("Found more than 1 versionable for reegrbiomodelRef=" + regrBioModelRef);
                        }
                    }
                }
                // 
                VariableComparisonSummary[] neededVCSArr = null;
                Vector vcsV = (Vector) vcsH.get(tcritKey);
                if (vcsV != null) {
                    neededVCSArr = new VariableComparisonSummary[vcsV.size()];
                    vcsV.copyInto(neededVCSArr);
                }
                // 
                TestCriteriaNew tcn = null;
                if (simInfo != null) {
                    tcn = new TestCriteriaNewBioModel(tcritKey, simInfo, regrBioModelInfo, regrSCName, regrSimInfo, maxRelError, maxAbsError, neededVCSArr, reportStatus, reportStatusMessage);
                    v.add(tcn);
                }
            // counter+= 1;
            }
            // System.out.println("TCrit count="+counter+" time="+((System.currentTimeMillis()-begTime)/1000));
            rset.close();
        }
        // Get TestCases
        Vector tcV = new Vector();
        // begTime=System.currentTimeMillis();
        // counter = 0;
        {
            // final String BMSCL = "bmscl";
            final String OBTCTYPECOLUMN = "OBTCTYPECOLUMN";
            final String OBNAMECOLUMN = "OBNAMECOLUMN";
            final String BMSCBMRNAME = "BMSCBMRNAME";
            final String BMSCSCRNAME = "BMSCSCRNAME";
            final String SCNAME = "SCNAME";
            final String SORTHELP1 = "SORTHELP1";
            final String SORTHELP2 = "SORTHELP2";
            sql = "SELECT " + "UPPER(" + MathModelTable.table.name.getQualifiedColName() + ") " + SORTHELP1 + "," + "TO_CHAR(NULL) " + SORTHELP2 + "," + TFTestCaseTable.table.getTableName() + ".*" + "," + "TO_NUMBER(NULL) " + BMSCBMRNAME + "," + "TO_NUMBER(NULL) " + BMSCSCRNAME + "," + "TO_CHAR(NULL) " + SCNAME + "," + "'MM' " + OBTCTYPECOLUMN + "," + MathModelTable.table.name.getQualifiedColName() + " " + OBNAMECOLUMN + " FROM " + TFTestCaseTable.table.getTableName() + "," + TFTestSuiteTable.table.getTableName() + "," + MathModelTable.table.getTableName() + " WHERE " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + getThisTS + " AND " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + TFTestCaseTable.table.testSuiteRef.getQualifiedColName() + " AND " + TFTestCaseTable.table.mathModelRef.getQualifiedColName() + " IS NOT NULL" + " AND " + TFTestCaseTable.table.mathModelRef.getQualifiedColName() + " = " + MathModelTable.table.id.getQualifiedColName() + " UNION " + "SELECT " + "UPPER(" + BioModelTable.table.name.getQualifiedColName() + ") " + SORTHELP1 + ",UPPER(" + SimContextTable.table.name.getQualifiedColName() + ") " + SORTHELP2 + "," + TFTestCaseTable.table.getTableName() + ".*" + "," + BioModelSimContextLinkTable.table.bioModelRef.getQualifiedColName() + " " + BMSCBMRNAME + "," + BioModelSimContextLinkTable.table.simContextRef.getQualifiedColName() + " " + BMSCSCRNAME + "," + SimContextTable.table.name.getQualifiedColName() + " " + SCNAME + "," + "'BM' " + OBTCTYPECOLUMN + "," + BioModelTable.table.name.getQualifiedColName() + " " + OBNAMECOLUMN + " FROM " + BioModelSimContextLinkTable.table.getTableName() + "," + SimContextTable.table.getTableName() + "," + TFTestCaseTable.table.getTableName() + "," + TFTestSuiteTable.table.getTableName() + "," + BioModelTable.table.getTableName() + " WHERE " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + getThisTS + " AND " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + TFTestCaseTable.table.testSuiteRef.getQualifiedColName() + " AND " + TFTestCaseTable.table.bmAppRef.getQualifiedColName() + " IS NOT NULL" + " AND " + TFTestCaseTable.table.bmAppRef.getQualifiedColName() + " = " + BioModelSimContextLinkTable.table.id.getQualifiedColName() + " AND " + BioModelSimContextLinkTable.table.simContextRef.getQualifiedColName() + " = " + SimContextTable.table.id.getQualifiedColName() + " AND " + BioModelSimContextLinkTable.table.bioModelRef.getQualifiedColName() + "=" + BioModelTable.table.id.getQualifiedColName() + // " ORDER BY 11,"+"UPPER(12)"+","+"UPPER(10)";
            " ORDER BY 13,1,2";
            rset = stmt.executeQuery(sql);
            while (rset.next()) {
                BigDecimal tcaseKey = rset.getBigDecimal(TFTestCaseTable.table.id.getUnqualifiedColName());
                BigDecimal mmRef = rset.getBigDecimal(TFTestCaseTable.table.mathModelRef.getUnqualifiedColName());
                if (rset.wasNull()) {
                    mmRef = null;
                }
                BigDecimal simContextRef = rset.getBigDecimal(BMSCSCRNAME);
                if (rset.wasNull()) {
                    simContextRef = null;
                }
                BigDecimal bioModelRef = rset.getBigDecimal(BMSCBMRNAME);
                if (rset.wasNull()) {
                    bioModelRef = null;
                }
                String simContextName = rset.getString(SCNAME);
                if (rset.wasNull()) {
                    simContextName = null;
                }
                String tcType = rset.getString(TFTestCaseTable.table.tcSolutionType.getUnqualifiedColName());
                String tcAnnot = rset.getString(TFTestCaseTable.table.tcAnnotation.getUnqualifiedColName());
                if (rset.wasNull()) {
                    tcAnnot = "";
                } else {
                    tcAnnot = TokenMangler.getSQLRestoredString(tcAnnot);
                }
                java.util.Date tcDate = VersionTable.getDate(rset, TFTestCaseTable.table.creationDate.getUnqualifiedColName());
                MathModelInfo mmInfo = null;
                BioModelInfo bmInfo = null;
                if (mmRef != null) {
                    mmInfo = (MathModelInfo) mathModelInfoH.get(mmRef);
                    if (mmInfo == null) {
                        Vector<VersionInfo> mathVector = getVersionableInfos(con, user, VersionableType.MathModelMetaData, false, new KeyValue(mmRef), false, dbSyntax);
                        if (mathVector != null && mathVector.size() > 0) {
                            mmInfo = (MathModelInfo) mathVector.firstElement();
                            mathModelInfoH.put(mmRef, mmInfo);
                        }
                    }
                } else if (bioModelRef != null) {
                    bmInfo = (BioModelInfo) bioModelInfoH.get(bioModelRef);
                    if (bmInfo == null) {
                        Vector<VersionInfo> bmAppVector = getVersionableInfos(con, user, VersionableType.BioModelMetaData, false, new KeyValue(bioModelRef), false, dbSyntax);
                        if (bmAppVector != null && bmAppVector.size() > 0) {
                            bmInfo = (BioModelInfo) bmAppVector.firstElement();
                            bioModelInfoH.put(bioModelRef, bmInfo);
                        }
                    }
                } else {
                    throw new RuntimeException("Test case in DB does not have MathmodelRef or BioModelAppRef");
                }
                TestCriteriaNew[] neededTcritArr = null;
                Vector needTcritV = (Vector) tcritH.get(tcaseKey);
                if (needTcritV != null) {
                    neededTcritArr = new TestCriteriaNew[needTcritV.size()];
                    needTcritV.copyInto(neededTcritArr);
                }
                TestCaseNew tcn = null;
                if (mmInfo != null) {
                    tcn = new TestCaseNewMathModel(tcaseKey, mmInfo, tcType, tcAnnot, neededTcritArr);
                    tcV.add(tcn);
                } else if (bmInfo != null) {
                    tcn = new TestCaseNewBioModel(tcaseKey, bmInfo, simContextName, new KeyValue(simContextRef), tcType, tcAnnot, neededTcritArr);
                    tcV.add(tcn);
                } else {
                // throw new RuntimeException("Expected testCase MathModelInfo or BioModelInfo to be not null");
                }
            // counter+= 1;
            }
            // System.out.println("TCase count="+counter+" time="+((System.currentTimeMillis()-begTime)/1000));
            rset.close();
        }
        // Get TestSuite
        {
            TestCaseNew[] tcnArr = null;
            if (tcV.size() > 0) {
                tcnArr = new TestCaseNew[tcV.size()];
                tcV.copyInto(tcnArr);
            }
            sql = "SELECT " + TFTestSuiteTable.table.getTableName() + ".*" + " FROM " + TFTestSuiteTable.table.getTableName() + " WHERE " + TFTestSuiteTable.table.id.getQualifiedColName() + "=" + getThisTS + " ORDER BY UPPER(" + TFTestSuiteTable.table.tsVersion.getQualifiedColName() + ")";
            rset = stmt.executeQuery(sql);
            BigDecimal tsKey = null;
            String tsVersion = null;
            String tsVCBuild = null;
            String tsNumericsBuild = null;
            java.util.Date tsDate = null;
            String tsAnnot = null;
            boolean islocked = true;
            if (rset.next()) {
                tsKey = rset.getBigDecimal(TFTestSuiteTable.table.id.getUnqualifiedColName());
                tsVersion = rset.getString(TFTestSuiteTable.table.tsVersion.getUnqualifiedColName());
                tsVCBuild = rset.getString(TFTestSuiteTable.table.vcBuildVersion.getUnqualifiedColName());
                tsNumericsBuild = rset.getString(TFTestSuiteTable.table.vcNumericsVersion.getUnqualifiedColName());
                tsDate = VersionTable.getDate(rset, TFTestSuiteTable.table.creationDate.getUnqualifiedColName());
                tsAnnot = rset.getString(TFTestSuiteTable.table.tsAnnotation.getUnqualifiedColName());
                islocked = rset.getBoolean(TFTestSuiteTable.table.isLocked.getUnqualifiedColName());
            } else {
                throw new ObjectNotFoundException("TestSuite with key=" + getThisTS + " not found");
            }
            rset.close();
            TestSuiteInfoNew tsiNew = new TestSuiteInfoNew(tsKey, tsVersion, tsVCBuild, tsNumericsBuild, tsDate, tsAnnot, islocked);
            TestSuiteNew tsn = new TestSuiteNew(tsiNew, tcnArr);
            // testSuiteHash.put(tsKey,tsn);
            return tsn;
        }
    } catch (SQLException e) {
        lg.error("failed: (" + sql + "): " + e.getMessage(), e);
        throw e;
    } finally {
        DatabasePolicySQL.lg.setLevel(origLogLevel);
        if (stmt != null) {
            stmt.close();
        }
    }
}

Example 30 with SimulationInfo

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

the class SimulationTable method getInfo.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.geometry.GeometryInfo
 * @param rset java.sql.ResultSet
 * @param log cbit.vcell.server.SessionLog
 */
public VersionInfo getInfo(ResultSet rset, Connection con) throws SQLException, DataAccessException {
    KeyValue mathRef = new KeyValue(rset.getBigDecimal(SimulationTable.table.mathRef.toString()));
    java.math.BigDecimal groupid = rset.getBigDecimal(VersionTable.privacy_ColumnName);
    Version version = getVersion(rset, DbDriver.getGroupAccessFromGroupID(con, groupid));
    SimulationVersion simulationVersion = (SimulationVersion) version;
    String softwareVersion = rset.getString(SoftwareVersionTable.table.softwareVersion.toString());
    return new SimulationInfo(mathRef, simulationVersion, VCellSoftwareVersion.fromString(softwareVersion));
}