Examples with BigString org.vcell.util.BigString used on opensource projects

Example 21 with BigString

use of org.vcell.util.BigString in project vcell by virtualcell.

the class ClientTopicMessageCollector method onTopicMessage.

/**
 * Insert the method's description here.
 * Creation date: (10/23/2001 3:58:52 PM)
 * @param message javax.jms.Message
 * @throws VCMessagingException
 */
public void onTopicMessage(VCMessage message, VCMessageSession session) {
    if (message == null) {
        return;
    }
    try {
        if (message.getObjectContent() == null) {
            throw new Exception(this.getClass().getName() + ".onTopicMessage: unimplemented message class " + message.show());
        }
        setTimeSinceLastMessage(System.currentTimeMillis());
        String msgType = message.getStringProperty(VCMessagingConstants.MESSAGE_TYPE_PROPERTY);
        if (msgType == null) {
            throw new Exception(this.getClass().getName() + ".onTopicMessage: message type NULL for message " + message);
        }
        if (msgType.equals(MessageConstants.MESSAGE_TYPE_SIMSTATUS_VALUE)) {
            String messageUserName = message.getStringProperty(VCMessagingConstants.USERNAME_PROPERTY);
            StatusMessage statusMessage = new StatusMessage(message);
            String userName = VCMessagingConstants.USERNAME_PROPERTY_VALUE_ALL;
            if (message.propertyExists(VCMessagingConstants.USERNAME_PROPERTY)) {
                userName = message.getStringProperty(VCMessagingConstants.USERNAME_PROPERTY);
            }
            SimulationJobStatus newJobStatus = statusMessage.getJobStatus();
            if (newJobStatus == null) {
                return;
            }
            VCSimulationIdentifier vcSimID = newJobStatus.getVCSimulationIdentifier();
            Double progress = statusMessage.getProgress();
            Double timePoint = statusMessage.getTimePoint();
            fireSimulationJobStatusEvent(new SimulationJobStatusEvent(this, vcSimID.getID(), newJobStatus, progress, timePoint, messageUserName));
        } else if (msgType.equals(MessageConstants.MESSAGE_TYPE_EXPORT_EVENT_VALUE)) {
            String messageUserName = message.getStringProperty(VCMessagingConstants.USERNAME_PROPERTY);
            ExportEvent event = (ExportEvent) message.getObjectContent();
            fireExportEvent(event);
        } else if (msgType.equals(MessageConstants.MESSAGE_TYPE_DATA_EVENT_VALUE)) {
            String messageUserName = message.getStringProperty(VCMessagingConstants.USERNAME_PROPERTY);
            DataJobEvent event = (DataJobEvent) message.getObjectContent();
            fireMessageEvent(event);
        } else if (msgType.equals(MessageConstants.MESSAGE_TYPE_BROADCASTMESSAGE_VALUE)) {
            String messageUserName = message.getStringProperty(VCMessagingConstants.USERNAME_PROPERTY);
            fireMessageEvent(new VCellMessageEvent(this, System.currentTimeMillis() + "", new MessageData((BigString) message.getObjectContent()), VCellMessageEvent.VCELL_MESSAGEEVENT_TYPE_BROADCAST, messageUserName));
        } else {
            throw new Exception(this.getClass().getName() + ".onControlTopicMessage: Unimplemented message " + message.show());
        }
    } catch (Exception e) {
        e.printStackTrace();
        lg.error(e.getMessage(), e);
    }
}

Example 22 with BigString

use of org.vcell.util.BigString in project vcell by virtualcell.

the class RestDatabaseService method query.

public SimulationRepresentation query(BiomodelSimulationServerResource resource, User vcellUser) throws SQLException, DataAccessException, ExpressionException, XmlParseException, MappingException, MathException, MatrixException, ModelException {
    if (vcellUser == null) {
        vcellUser = VCellApiApplication.DUMMY_USER;
    }
    ArrayList<String> conditions = new ArrayList<String>();
    String bioModelID = (String) resource.getRequestAttributes().get(VCellApiApplication.BIOMODELID);
    if (bioModelID != null) {
        conditions.add("(" + BioModelTable.table.id.getQualifiedColName() + " = " + bioModelID + ")");
    } else {
        throw new RuntimeException(VCellApiApplication.BIOMODELID + " not specified");
    }
    StringBuffer conditionsBuffer = new StringBuffer();
    for (String condition : conditions) {
        if (conditionsBuffer.length() > 0) {
            conditionsBuffer.append(" AND ");
        }
        conditionsBuffer.append(condition);
    }
    int startRow = 1;
    int maxRows = 1;
    BioModelRep[] bioModelReps = databaseServerImpl.getBioModelReps(vcellUser, conditionsBuffer.toString(), null, startRow, maxRows);
    for (BioModelRep bioModelRep : bioModelReps) {
        KeyValue[] simContextKeys = bioModelRep.getSimContextKeyList();
        for (KeyValue scKey : simContextKeys) {
            SimContextRep scRep = getSimContextRep(scKey);
            if (scRep != null) {
                bioModelRep.addSimContextRep(scRep);
            }
        }
        KeyValue[] simulationKeys = bioModelRep.getSimKeyList();
        for (KeyValue simKey : simulationKeys) {
            SimulationRep simulationRep = getSimulationRep(simKey);
            if (simulationRep != null) {
                bioModelRep.addSimulationRep(simulationRep);
            }
        }
    }
    if (bioModelReps == null || bioModelReps.length != 1) {
        // 
        // try to determine if the current credentials are insufficient, try to fetch BioModel again with administrator privilege.
        // 
        User adminUser = new User(PropertyLoader.ADMINISTRATOR_ACCOUNT, new KeyValue(PropertyLoader.ADMINISTRATOR_ID));
        BioModelRep[] allBioModelReps = databaseServerImpl.getBioModelReps(adminUser, conditionsBuffer.toString(), null, startRow, 1);
        if (allBioModelReps != null && allBioModelReps.length >= 0) {
            throw new PermissionException("insufficient privilege to retrive BioModel " + bioModelID);
        } else {
            throw new RuntimeException("failed to get biomodel");
        }
    }
    String simulationId = (String) resource.getRequestAttributes().get(VCellApiApplication.SIMULATIONID);
    if (simulationId == null) {
        throw new RuntimeException(VCellApiApplication.SIMULATIONID + " not specified");
    }
    SimulationRep simRep = getSimulationRep(new KeyValue(simulationId));
    BigString bioModelXML = databaseServerImpl.getBioModelXML(vcellUser, bioModelReps[0].getBmKey());
    BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
    return new SimulationRepresentation(simRep, bioModel);
}

Example 23 with BigString

use of org.vcell.util.BigString in project vcell by virtualcell.

the class MathVerifier method scan.

/**
 * Insert the method's description here.
 * Creation date: (2/2/01 3:40:29 PM)
 */
public void scan(User[] users, boolean bUpdateDatabase, KeyValue[] bioAndMathModelKeys) throws MathException, MappingException, SQLException, DataAccessException, ModelException, ExpressionException {
    // java.util.Calendar calendar = java.util.GregorianCalendar.getInstance();
    // //	calendar.set(2002,java.util.Calendar.MAY,7+1);
    // calendar.set(2002,java.util.Calendar.JULY,1);
    // final java.util.Date fluxCorrectionOrDisablingBugFixDate = calendar.getTime();
    // //	calendar.set(2001,java.util.Calendar.JUNE,13+1);
    // calendar.set(2002,java.util.Calendar.JANUARY,1);
    // final java.util.Date totalVolumeCorrectionFixDate = calendar.getTime();
    KeyValue[] sortedBioAndMathModelKeys = null;
    if (bioAndMathModelKeys != null) {
        sortedBioAndMathModelKeys = bioAndMathModelKeys.clone();
        Arrays.sort(sortedBioAndMathModelKeys, keyValueCpmparator);
    }
    for (int i = 0; i < users.length; i++) {
        User user = users[i];
        BioModelInfo[] bioModelInfos0 = dbServerImpl.getBioModelInfos(user, false);
        MathModelInfo[] mathModelInfos0 = dbServerImpl.getMathModelInfos(user, false);
        if (lg.isTraceEnabled())
            lg.trace("Testing user '" + user + "'");
        Vector<VCDocumentInfo> userBioAndMathModelInfoV = new Vector<VCDocumentInfo>();
        userBioAndMathModelInfoV.addAll(Arrays.asList(bioModelInfos0));
        userBioAndMathModelInfoV.addAll(Arrays.asList(mathModelInfos0));
        // 
        for (int j = 0; j < userBioAndMathModelInfoV.size(); j++) {
            // 
            // if certain Bio or Math models are requested, then filter all else out
            // 
            VCDocumentInfo documentInfo = userBioAndMathModelInfoV.elementAt(j);
            KeyValue versionKey = documentInfo.getVersion().getVersionKey();
            if (sortedBioAndMathModelKeys != null) {
                int srch = Arrays.binarySearch(sortedBioAndMathModelKeys, versionKey, keyValueCpmparator);
                if (srch < 0) {
                    continue;
                }
            }
            if (!(documentInfo instanceof BioModelInfo)) {
                continue;
            }
            // 
            if (skipHash.contains(versionKey)) {
                System.out.println("skipping " + (documentInfo instanceof BioModelInfo ? "BioModel" : "MathModel") + " with key '" + versionKey + "'");
                continue;
            }
            try {
                // 
                // read in the BioModel and MathModel from the database
                // 
                VCDocument vcDocumentFromDBCache = null;
                BigString vcDocumentXMLFromDBCache = null;
                try {
                    long startTime = System.currentTimeMillis();
                    if (documentInfo instanceof BioModelInfo) {
                        vcDocumentXMLFromDBCache = new BigString(dbServerImpl.getServerDocumentManager().getBioModelXML(new QueryHashtable(), user, versionKey, false));
                        vcDocumentFromDBCache = XmlHelper.XMLToBioModel(new XMLSource(vcDocumentXMLFromDBCache.toString()));
                    } else {
                        vcDocumentXMLFromDBCache = new BigString(dbServerImpl.getServerDocumentManager().getMathModelXML(new QueryHashtable(), user, versionKey, false));
                        vcDocumentFromDBCache = XmlHelper.XMLToMathModel(new XMLSource(vcDocumentXMLFromDBCache.toString()));
                    }
                    if (bUpdateDatabase && testFlag.equals(MathVerifier.MV_LOAD_XML)) {
                        updateLoadModelsStatTable_LoadTest(System.currentTimeMillis() - startTime, versionKey, null);
                    }
                } catch (Exception e) {
                    lg.error(e.getMessage(), e);
                    if (bUpdateDatabase && testFlag.equals(MathVerifier.MV_LOAD_XML)) {
                        updateLoadModelsStatTable_LoadTest(0, versionKey, e);
                    }
                }
                if (testFlag.equals(MathVerifier.MV_LOAD_XML)) {
                    // 
                    if (vcDocumentXMLFromDBCache != null) {
                        testDocumentLoad(bUpdateDatabase, user, documentInfo, vcDocumentFromDBCache);
                    }
                } else if (testFlag.equals(MathVerifier.MV_DEFAULT)) {
                    // 
                    if (vcDocumentFromDBCache instanceof BioModel) {
                        BioModel bioModel = (BioModel) vcDocumentFromDBCache;
                        checkMathForBioModel(vcDocumentXMLFromDBCache, bioModel, user, bUpdateDatabase);
                    }
                }
            } catch (Throwable e) {
                // exception in whole BioModel
                lg.error(e.getMessage(), e);
            // can't update anything in database, since we don't know what simcontexts are involved
            }
        }
    }
}

Example 24 with BigString

use of org.vcell.util.BigString in project vcell by virtualcell.

the class MathVerifier method testMathGeneration.

public MathGenerationResults testMathGeneration(KeyValue simContextKey) throws SQLException, ObjectNotFoundException, DataAccessException, XmlParseException, MappingException, MathException, MatrixException, ExpressionException, ModelException, PropertyVetoException {
    User adminUser = new User(PropertyLoader.ADMINISTRATOR_ACCOUNT, new org.vcell.util.document.KeyValue(PropertyLoader.ADMINISTRATOR_ID));
    if (lg.isTraceEnabled())
        lg.trace("Testing SimContext with key '" + simContextKey + "'");
    // get biomodel refs
    java.sql.Connection con = null;
    java.sql.Statement stmt = null;
    con = conFactory.getConnection(new Object());
    cbit.vcell.modeldb.BioModelSimContextLinkTable bmscTable = cbit.vcell.modeldb.BioModelSimContextLinkTable.table;
    cbit.vcell.modeldb.BioModelTable bmTable = cbit.vcell.modeldb.BioModelTable.table;
    cbit.vcell.modeldb.UserTable userTable = cbit.vcell.modeldb.UserTable.table;
    String sql = "SELECT " + bmscTable.bioModelRef.getQualifiedColName() + "," + bmTable.ownerRef.getQualifiedColName() + "," + userTable.userid.getQualifiedColName() + " FROM " + bmscTable.getTableName() + "," + bmTable.getTableName() + "," + userTable.getTableName() + " WHERE " + bmscTable.simContextRef.getQualifiedColName() + " = " + simContextKey + " AND " + bmTable.id.getQualifiedColName() + " = " + bmscTable.bioModelRef.getQualifiedColName() + " AND " + bmTable.ownerRef.getQualifiedColName() + " = " + userTable.id.getQualifiedColName();
    ArrayList<KeyValue> bioModelKeys = new ArrayList<KeyValue>();
    stmt = con.createStatement();
    User owner = null;
    try {
        ResultSet rset = stmt.executeQuery(sql);
        while (rset.next()) {
            KeyValue key = new KeyValue(rset.getBigDecimal(bmscTable.bioModelRef.getUnqualifiedColName()));
            bioModelKeys.add(key);
            KeyValue ownerRef = new KeyValue(rset.getBigDecimal(bmTable.ownerRef.getUnqualifiedColName()));
            String userid = rset.getString(userTable.userid.getUnqualifiedColName());
            owner = new User(userid, ownerRef);
        }
    } finally {
        if (stmt != null) {
            stmt.close();
        }
        con.close();
    }
    // use the first biomodel...
    if (bioModelKeys.size() == 0) {
        throw new RuntimeException("zombie simContext ... no biomodels");
    }
    BioModelInfo bioModelInfo = dbServerImpl.getBioModelInfo(owner, bioModelKeys.get(0));
    // 
    // read in the BioModel from the database
    // 
    BigString bioModelXML = dbServerImpl.getBioModelXML(owner, bioModelInfo.getVersion().getVersionKey());
    BioModel bioModelFromDB = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
    BioModel bioModelNewMath = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
    bioModelFromDB.refreshDependencies();
    bioModelNewMath.refreshDependencies();
    // 
    // get all Simulations for this model
    // 
    Simulation[] modelSimsFromDB = bioModelFromDB.getSimulations();
    // 
    // ---> only for the SimContext we started with...
    // recompute mathDescription, and verify it is equivalent
    // then check each associated simulation to ensure math overrides are applied in an equivalent manner also.
    // 
    SimulationContext[] simContextsFromDB = bioModelFromDB.getSimulationContexts();
    SimulationContext[] simContextsNewMath = bioModelNewMath.getSimulationContexts();
    SimulationContext simContextFromDB = null;
    SimulationContext simContextNewMath = null;
    for (int k = 0; k < simContextsFromDB.length; k++) {
        // find it...
        if (simContextsFromDB[k].getKey().equals(simContextKey)) {
            simContextFromDB = simContextsFromDB[k];
            simContextNewMath = simContextsNewMath[k];
            break;
        }
    }
    if (simContextFromDB == null) {
        throw new RuntimeException("BioModel referred to by this SimContext does not contain this SimContext");
    } else {
        MathDescription origMathDesc = simContextFromDB.getMathDescription();
        // 
        try {
            if (simContextNewMath.getGeometry().getDimension() > 0 && simContextNewMath.getGeometry().getGeometrySurfaceDescription().getGeometricRegions() == null) {
                simContextNewMath.getGeometry().getGeometrySurfaceDescription().updateAll();
            }
        } catch (Exception e) {
            e.printStackTrace(System.out);
        }
        // 
        // updated mathDescription loaded into copy of bioModel, then test for equivalence.
        // 
        cbit.vcell.mapping.MathMapping mathMapping = simContextNewMath.createNewMathMapping();
        MathDescription mathDesc_latest = mathMapping.getMathDescription();
        MathMapping_4_8 mathMapping_4_8 = new MathMapping_4_8(simContextNewMath);
        MathDescription mathDesc_4_8 = mathMapping_4_8.getMathDescription();
        String issueString = null;
        org.vcell.util.Issue[] issues = mathMapping.getIssues();
        if (issues != null && issues.length > 0) {
            StringBuffer buffer = new StringBuffer("Issues(" + issues.length + "):\n");
            for (int l = 0; l < issues.length; l++) {
                buffer.append(" <<" + issues[l].toString() + ">>\n");
            }
            issueString = buffer.toString();
        }
        simContextNewMath.setMathDescription(mathDesc_latest);
        MathCompareResults mathCompareResults_latest = MathDescription.testEquivalency(SimulationSymbolTable.createMathSymbolTableFactory(), origMathDesc, mathDesc_latest);
        MathCompareResults mathCompareResults_4_8 = null;
        try {
            mathCompareResults_4_8 = MathDescription.testEquivalency(SimulationSymbolTable.createMathSymbolTableFactory(), origMathDesc, mathDesc_4_8);
        } catch (Exception e) {
            e.printStackTrace(System.out);
            mathCompareResults_4_8 = new MathCompareResults(Decision.MathDifferent_FAILURE_UNKNOWN, e.getMessage());
        }
        return new MathGenerationResults(bioModelFromDB, simContextFromDB, origMathDesc, mathDesc_latest, mathCompareResults_latest, mathDesc_4_8, mathCompareResults_4_8);
    }
}

Example 25 with BigString

use of org.vcell.util.BigString in project vcell by virtualcell.

the class MathVerifier method scanSimContexts.

/**
 * Insert the method's description here.
 * Creation date: (2/2/01 3:40:29 PM)
 */
public void scanSimContexts(boolean bUpdateDatabase, KeyValue[] simContextKeys) throws MathException, MappingException, SQLException, DataAccessException, ModelException, ExpressionException {
    java.util.Calendar calendar = java.util.GregorianCalendar.getInstance();
    // calendar.set(2002,java.util.Calendar.MAY,7+1);
    calendar.set(2002, java.util.Calendar.JULY, 1);
    final java.util.Date fluxCorrectionOrDisablingBugFixDate = calendar.getTime();
    // calendar.set(2001,java.util.Calendar.JUNE,13+1);
    calendar.set(2002, java.util.Calendar.JANUARY, 1);
    final java.util.Date totalVolumeCorrectionFixDate = calendar.getTime();
    User user = new User(PropertyLoader.ADMINISTRATOR_ACCOUNT, new KeyValue(PropertyLoader.ADMINISTRATOR_ID));
    for (int i = 0; i < simContextKeys.length; i++) {
        if (lg.isTraceEnabled())
            lg.trace("Testing SimContext with key '" + simContextKeys[i] + "'");
        // get biomodel refs
        java.sql.Connection con = null;
        java.sql.Statement stmt = null;
        con = conFactory.getConnection(new Object());
        cbit.vcell.modeldb.BioModelSimContextLinkTable bmscTable = cbit.vcell.modeldb.BioModelSimContextLinkTable.table;
        String sql = "SELECT " + bmscTable.bioModelRef.getQualifiedColName() + " FROM " + bmscTable.getTableName() + " WHERE " + bmscTable.simContextRef.getQualifiedColName() + " = " + simContextKeys[i];
        java.util.Vector keys = new java.util.Vector();
        stmt = con.createStatement();
        try {
            ResultSet rset = stmt.executeQuery(sql);
            while (rset.next()) {
                KeyValue key = new KeyValue(rset.getBigDecimal(bmscTable.bioModelRef.getUnqualifiedColName()));
                keys.addElement(key);
            }
        } finally {
            if (stmt != null) {
                stmt.close();
            }
            con.close();
        }
        KeyValue[] bmKeys = (org.vcell.util.document.KeyValue[]) org.vcell.util.BeanUtils.getArray(keys, org.vcell.util.document.KeyValue.class);
        try {
            // use the first biomodel...
            BioModelInfo bioModelInfo = dbServerImpl.getBioModelInfo(user, bmKeys[0]);
            // 
            // read in the BioModel from the database
            // 
            BigString bioModelXML = dbServerImpl.getBioModelXML(user, bioModelInfo.getVersion().getVersionKey());
            BioModel bioModelFromDB = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
            BioModel bioModelNewMath = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
            bioModelFromDB.refreshDependencies();
            bioModelNewMath.refreshDependencies();
            // 
            // get all Simulations for this model
            // 
            Simulation[] modelSimsFromDB = bioModelFromDB.getSimulations();
            // 
            // ---> only for the SimContext we started with...
            // recompute mathDescription, and verify it is equivalent
            // then check each associated simulation to ensure math overrides are applied in an equivalent manner also.
            // 
            SimulationContext[] simContextsFromDB = bioModelFromDB.getSimulationContexts();
            SimulationContext[] simContextsNewMath = bioModelNewMath.getSimulationContexts();
            SimulationContext simContextFromDB = null;
            SimulationContext simContextNewMath = null;
            for (int k = 0; k < simContextsFromDB.length; k++) {
                // find it...
                if (simContextsFromDB[k].getKey().equals(simContextKeys[i])) {
                    simContextFromDB = simContextsFromDB[k];
                    simContextNewMath = simContextsNewMath[k];
                    break;
                }
            }
            if (simContextFromDB == null) {
                throw new RuntimeException("BioModel referred to by this SimContext does not contain this SimContext");
            } else {
                Simulation[] appSimsFromDB = simContextFromDB.getSimulations();
                Simulation[] appSimsNewMath = simContextNewMath.getSimulations();
                MathCompareResults mathCompareResults = null;
                try {
                    MathDescription origMathDesc = simContextFromDB.getMathDescription();
                    // 
                    // find out if any simulation belonging to this Application has data
                    // 
                    boolean bApplicationHasData = false;
                    for (int l = 0; l < modelSimsFromDB.length; l++) {
                        SimulationStatusPersistent simulationStatus = dbServerImpl.getSimulationStatus(modelSimsFromDB[l].getKey());
                        if (simulationStatus != null && simulationStatus.getHasData()) {
                            bApplicationHasData = true;
                        }
                    }
                    // 
                    try {
                        if (simContextNewMath.getGeometry().getDimension() > 0 && simContextNewMath.getGeometry().getGeometrySurfaceDescription().getGeometricRegions() == null) {
                            simContextNewMath.getGeometry().getGeometrySurfaceDescription().updateAll();
                        }
                    } catch (Exception e) {
                        e.printStackTrace(System.out);
                    }
                    // 
                    // updated mathdescription loaded into copy of biomodel, then test for equivalence.
                    // 
                    cbit.vcell.mapping.MathMapping mathMapping = simContextNewMath.createNewMathMapping();
                    MathDescription newMathDesc = mathMapping.getMathDescription();
                    String issueString = null;
                    org.vcell.util.Issue[] issues = mathMapping.getIssues();
                    if (issues != null && issues.length > 0) {
                        StringBuffer buffer = new StringBuffer("Issues(" + issues.length + "):");
                        for (int l = 0; l < issues.length; l++) {
                            buffer.append(" <<" + issues[l].toString() + ">>");
                        }
                        issueString = buffer.toString();
                    }
                    simContextNewMath.setMathDescription(newMathDesc);
                    MathCompareResults testIfSameResults = cbit.vcell.math.MathUtilities.testIfSame(SimulationSymbolTable.createMathSymbolTableFactory(), origMathDesc, newMathDesc);
                    mathCompareResults = MathDescription.testEquivalency(SimulationSymbolTable.createMathSymbolTableFactory(), origMathDesc, newMathDesc);
                    StringBuffer buffer = new StringBuffer();
                    buffer.append(">>>BioModel(" + bioModelFromDB.getVersion().getVersionKey() + ") '" + bioModelFromDB.getName() + "':" + bioModelFromDB.getVersion().getDate() + ", Application(" + simContextFromDB.getKey() + ") '" + simContextFromDB.getName() + "' <<EQUIV=" + mathCompareResults.isEquivalent() + ">>: " + mathCompareResults.toDatabaseStatus());
                    // 
                    if (bUpdateDatabase) {
                        con = null;
                        stmt = null;
                        try {
                            con = conFactory.getConnection(new Object());
                            stmt = con.createStatement();
                            // KeyValue mathKey = origMathDesc.getKey();
                            String UPDATESTATUS = "UPDATE " + SimContextStat2Table.table.getTableName() + " SET " + SimContextStat2Table.table.hasData.getUnqualifiedColName() + " = " + ((bApplicationHasData) ? (1) : (0)) + ", " + SimContextStat2Table.table.equiv.getUnqualifiedColName() + " = " + (mathCompareResults.isEquivalent() ? (1) : (0)) + ", " + SimContextStat2Table.table.status.getUnqualifiedColName() + " = '" + org.vcell.util.TokenMangler.getSQLEscapedString(mathCompareResults.toDatabaseStatus()) + "'" + ((issueString != null) ? (", " + SimContextStat2Table.table.comments.getUnqualifiedColName() + " = '" + org.vcell.util.TokenMangler.getSQLEscapedString(issueString, 255) + "'") : ("")) + " WHERE " + SimContextStat2Table.table.simContextRef.getUnqualifiedColName() + " = " + simContextFromDB.getKey();
                            int numRowsChanged = stmt.executeUpdate(UPDATESTATUS);
                            if (numRowsChanged != 1) {
                                System.out.println("failed to update status");
                            }
                            con.commit();
                            if (lg.isTraceEnabled())
                                lg.trace("-------------- Update=true, saved 'newMath' for Application '" + simContextFromDB.getName() + "'");
                        } catch (SQLException e) {
                            lg.error(e.getMessage(), e);
                            if (lg.isWarnEnabled())
                                lg.warn("*&*&*&*&*&*&*& Update=true, FAILED TO UPDATE MATH for Application '" + simContextFromDB.getName() + "'");
                        } finally {
                            if (stmt != null) {
                                stmt.close();
                            }
                            con.close();
                        }
                    }
                } catch (Throwable e) {
                    // exception in SimContext
                    lg.error(e.getMessage(), e);
                    if (bUpdateDatabase) {
                        con = null;
                        stmt = null;
                        try {
                            con = conFactory.getConnection(new Object());
                            stmt = con.createStatement();
                            String status = "'EXCEPTION: " + org.vcell.util.TokenMangler.getSQLEscapedString(e.toString()) + "'";
                            if (status.length() > 255)
                                status = status.substring(0, 254) + "'";
                            String UPDATESTATUS = "UPDATE " + SimContextStat2Table.table.getTableName() + " SET " + SimContextStat2Table.table.status.getUnqualifiedColName() + " = " + status + " WHERE " + SimContextStat2Table.table.simContextRef.getUnqualifiedColName() + " = " + simContextFromDB.getKey();
                            int numRowsChanged = stmt.executeUpdate(UPDATESTATUS);
                            if (numRowsChanged != 1) {
                                System.out.println("failed to update status with exception");
                            }
                            con.commit();
                            if (lg.isTraceEnabled())
                                lg.trace("-------------- Update=true, saved exception for Application '" + simContextFromDB.getName() + "'");
                        } catch (SQLException e2) {
                            lg.error(e2.getMessage(), e2);
                            if (lg.isWarnEnabled())
                                lg.warn("*&*&*&*&*&*&*& Update=true, FAILED TO save exception status for Application '" + simContextFromDB.getName() + "'");
                        } finally {
                            if (stmt != null) {
                                stmt.close();
                            }
                            con.close();
                        }
                    }
                }
                // 
                for (int l = 0; l < appSimsFromDB.length; l++) {
                    try {
                        boolean bSimEquivalent = Simulation.testEquivalency(appSimsNewMath[l], appSimsFromDB[l], mathCompareResults);
                        if (lg.isTraceEnabled())
                            lg.trace("Application(" + simContextFromDB.getKey() + ") '" + simContextFromDB.getName() + "', " + "Simulation(" + modelSimsFromDB[l].getKey() + ") '" + modelSimsFromDB[l].getName() + "':" + modelSimsFromDB[l].getVersion().getDate() + "mathEquivalency=" + mathCompareResults.isEquivalent() + ", simEquivalency=" + bSimEquivalent);
                        // 
                        if (bUpdateDatabase) {
                            con = null;
                            stmt = null;
                            try {
                                con = conFactory.getConnection(new Object());
                                stmt = con.createStatement();
                                String UPDATESTATUS = "UPDATE " + SimStatTable.table.getTableName() + " SET " + SimStatTable.table.equiv.getUnqualifiedColName() + " = " + ((bSimEquivalent) ? (1) : (0)) + ", " + SimStatTable.table.status.getUnqualifiedColName() + " = '" + org.vcell.util.TokenMangler.getSQLEscapedString(mathCompareResults.toDatabaseStatus()) + "'" + " WHERE " + SimStatTable.table.simRef.getUnqualifiedColName() + " = " + appSimsFromDB[l].getKey();
                                int numRowsChanged = stmt.executeUpdate(UPDATESTATUS);
                                if (numRowsChanged != 1) {
                                    System.out.println("failed to update status");
                                }
                                con.commit();
                                if (lg.isTraceEnabled())
                                    lg.trace("-------------- Update=true, saved 'simulation status for simulation '" + appSimsFromDB[l].getName() + "'");
                            } catch (SQLException e) {
                                lg.error(e.getMessage(), e);
                                if (lg.isWarnEnabled())
                                    lg.warn("*&*&*&*&*&*&*& Update=true, FAILED TO UPDATE status for simulation '" + appSimsFromDB[l].getName() + "'");
                            } finally {
                                if (stmt != null) {
                                    stmt.close();
                                }
                                con.close();
                            }
                        }
                    } catch (Throwable e) {
                        // exception in SimContext
                        lg.error(e.getMessage(), e);
                        if (bUpdateDatabase) {
                            con = null;
                            stmt = null;
                            try {
                                con = conFactory.getConnection(new Object());
                                stmt = con.createStatement();
                                String status = "'EXCEPTION: " + org.vcell.util.TokenMangler.getSQLEscapedString(e.toString()) + "'";
                                if (status.length() > 255)
                                    status = status.substring(0, 254) + "'";
                                String UPDATESTATUS = "UPDATE " + SimStatTable.table.getTableName() + " SET " + SimStatTable.table.status.getUnqualifiedColName() + " = " + status + " WHERE " + SimStatTable.table.simRef.getUnqualifiedColName() + " = " + appSimsFromDB[l].getKey();
                                int numRowsChanged = stmt.executeUpdate(UPDATESTATUS);
                                if (numRowsChanged != 1) {
                                    System.out.println("failed to update status with exception");
                                }
                                con.commit();
                                if (lg.isTraceEnabled())
                                    lg.trace("-------------- Update=true, saved exception for Simulation '" + appSimsFromDB[l].getName() + "'");
                            } catch (SQLException e2) {
                                lg.error(e2.getMessage(), e2);
                                if (lg.isWarnEnabled())
                                    lg.warn("*&*&*&*&*&*&*& Update=true, FAILED TO save exception status for simulation '" + appSimsFromDB[l].getName() + "'");
                            } finally {
                                if (stmt != null) {
                                    stmt.close();
                                }
                                con.close();
                            }
                        }
                    }
                }
            }
        } catch (Throwable e) {
            // exception in whole BioModel
            lg.error(e.getMessage(), e);
            // update database, since we know the simcontext...
            if (bUpdateDatabase) {
                con = null;
                stmt = null;
                try {
                    con = conFactory.getConnection(new Object());
                    stmt = con.createStatement();
                    // KeyValue mathKey = origMathDesc.getKey();
                    String UPDATESTATUS = "UPDATE " + SimContextStat2Table.table.getTableName() + " SET " + SimContextStat2Table.table.status.getUnqualifiedColName() + " = 'BIOMODEL EXCEPTION: " + org.vcell.util.TokenMangler.getSQLEscapedString(e.toString()) + "'" + " WHERE " + SimContextStat2Table.table.simContextRef.getUnqualifiedColName() + " = " + simContextKeys[i];
                    int numRowsChanged = stmt.executeUpdate(UPDATESTATUS);
                    if (numRowsChanged != 1) {
                        System.out.println("failed to update status with exception");
                    }
                    con.commit();
                    if (lg.isTraceEnabled())
                        lg.trace("-------------- Update=true, saved exception for Application with key '" + simContextKeys[i] + "'");
                } catch (SQLException e2) {
                    lg.error(e2.getMessage(), e2);
                    if (lg.isWarnEnabled())
                        lg.warn("*&*&*&*&*&*&*& Update=true, FAILED TO save exception status for Application with key '" + simContextKeys[i] + "'");
                } finally {
                    if (stmt != null) {
                        stmt.close();
                    }
                    con.close();
                }
            }
        }
    }
}