Examples with BioModel cbit.vcell.biomodel.BioModel used on opensource projects

Example 76 with BioModel

use of cbit.vcell.biomodel.BioModel 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 77 with BioModel

use of cbit.vcell.biomodel.BioModel 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();
                }
            }
        }
    }
}

Example 78 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class MathVerifier method checkMathForBioModel.

private void checkMathForBioModel(BigString bioModelXMLFromDB, BioModel bioModelFromDB, User user, boolean bUpdateDatabase) throws Exception {
    BioModel bioModelNewMath = XmlHelper.XMLToBioModel(new XMLSource(bioModelXMLFromDB.toString()));
    bioModelFromDB.refreshDependencies();
    bioModelNewMath.refreshDependencies();
    // 
    // get all Simulations for this model
    // 
    Simulation[] modelSimsFromDB = bioModelFromDB.getSimulations();
    // 
    // for each application, 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();
    for (int k = 0; k < simContextsFromDB.length; k++) {
        SimulationContext simContextFromDB = simContextsFromDB[k];
        Simulation[] appSimsFromDB = simContextFromDB.getSimulations();
        SimulationContext simContextNewMath = simContextsNewMath[k];
        Simulation[] appSimsNewMath = simContextNewMath.getSimulations();
        MathCompareResults mathCompareResults_latest = null;
        MathCompareResults mathCompareResults_4_8 = 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();
            }
            MathCompareResults testIfSameResult = cbit.vcell.math.MathUtilities.testIfSame(SimulationSymbolTable.createMathSymbolTableFactory(), origMathDesc, newMathDesc);
            mathCompareResults_latest = MathDescription.testEquivalency(SimulationSymbolTable.createMathSymbolTableFactory(), origMathDesc, newMathDesc);
            System.out.println(">>>BioModel(" + bioModelFromDB.getVersion().getVersionKey() + ") '" + bioModelFromDB.getName() + "':" + bioModelFromDB.getVersion().getDate() + ", Application(" + simContextFromDB.getKey() + ") '" + simContextFromDB.getName() + "' <<EQUIV=" + mathCompareResults_latest.isEquivalent() + ">>: " + mathCompareResults_latest.toDatabaseStatus());
            MathDescription mathDesc_4_8 = null;
            try {
                mathDesc_4_8 = new MathMapping_4_8(simContextNewMath).getMathDescription();
                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());
            }
            simContextNewMath.setMathDescription(newMathDesc);
            // 
            if (bUpdateDatabase) {
                java.sql.Connection con = null;
                java.sql.Statement 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_latest.isEquivalent() ? (1) : (0)) + ", " + SimContextStat2Table.table.status.getUnqualifiedColName() + " = '" + org.vcell.util.TokenMangler.getSQLEscapedString(mathCompareResults_latest.toDatabaseStatus(), 255) + "', " + SimContextStat2Table.table.equiv_4_8.getUnqualifiedColName() + " = " + (mathCompareResults_4_8.isEquivalent() ? (1) : (0)) + ", " + SimContextStat2Table.table.status_4_8.getUnqualifiedColName() + " = '" + org.vcell.util.TokenMangler.getSQLEscapedString(mathCompareResults_4_8.toDatabaseStatus(), 255) + "'" + // ((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) {
                java.sql.Connection con = null;
                java.sql.Statement 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() + " = 'EXCEPTION: " + org.vcell.util.TokenMangler.getSQLEscapedString(e.toString()) + "'" + " 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_latest);
                if (lg.isTraceEnabled())
                    lg.trace("Application(" + simContextFromDB.getKey() + ") '" + simContextFromDB.getName() + "', " + "Simulation(" + modelSimsFromDB[l].getKey() + ") '" + modelSimsFromDB[l].getName() + "':" + modelSimsFromDB[l].getVersion().getDate() + "mathEquivalency=" + mathCompareResults_latest.isEquivalent() + ", simEquivalency=" + bSimEquivalent);
                // 
                if (bUpdateDatabase) {
                    java.sql.Connection con = null;
                    java.sql.Statement 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_latest.decision.description) + "'" + " 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) {
                    java.sql.Connection con = null;
                    java.sql.Statement stmt = null;
                    try {
                        con = conFactory.getConnection(new Object());
                        stmt = con.createStatement();
                        // KeyValue mathKey = origMathDesc.getKey();
                        String UPDATESTATUS = "UPDATE " + SimStatTable.table.getTableName() + " SET " + SimStatTable.table.status.getUnqualifiedColName() + " = 'EXCEPTION: " + org.vcell.util.TokenMangler.getSQLEscapedString(e.toString()) + "'" + " 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();
                    }
                }
            }
        }
    }
}

Example 79 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class MathVerifier method scanBioModels.

/**
 * Insert the method's description here.
 * Creation date: (2/2/01 3:40:29 PM)
 */
public void scanBioModels(boolean bUpdateDatabase, KeyValue[] bioModelKeys) 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 < bioModelKeys.length; i++) {
        BioModelInfo bioModelInfo = dbServerImpl.getBioModelInfo(user, bioModelKeys[i]);
        if (lg.isTraceEnabled())
            lg.trace("Testing bioModel with key '" + bioModelKeys[i] + "'");
        java.sql.Connection con = null;
        java.sql.Statement stmt = null;
        try {
            // 
            // 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();
            // 
            // for each application, 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();
            for (int k = 0; k < simContextsFromDB.length; k++) {
                SimulationContext simContextFromDB = simContextsFromDB[k];
                Simulation[] appSimsFromDB = simContextFromDB.getSimulations();
                SimulationContext simContextNewMath = simContextsNewMath[k];
                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.decision.description) + "'" + " 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);
        // can't update anything in database, since we don't know what simcontexts are involved
        }
    }
}

Example 80 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class ServerDocumentManager method getBioModelUnresolved.

/**
 * Insert the method's description here.
 * Creation date: (11/14/00 4:02:44 PM)
 * @return cbit.vcell.biomodel.BioModel
 * @param bioModelInfo cbit.vcell.biomodel.BioModelInfo
 */
// 
// this returns a BioModel that contains multiple instances of objects.
// 
public String getBioModelUnresolved(QueryHashtable dbc, User user, KeyValue bioModelKey) throws DataAccessException, XmlParseException, java.sql.SQLException {
    // 
    // get meta data associated with BioModel
    // 
    BioModelMetaData bioModelMetaData = dbServer.getDBTopLevel().getBioModelMetaData(dbc, user, bioModelKey);
    // 
    // get list of appropriate child components
    // 
    KeyValue modelKey = bioModelMetaData.getModelKey();
    KeyValue[] simKeys = getKeyArrayFromEnumeration(bioModelMetaData.getSimulationKeys());
    KeyValue[] scKeys = getKeyArrayFromEnumeration(bioModelMetaData.getSimulationContextKeys());
    Model model = dbServer.getDBTopLevel().getModel(dbc, user, modelKey);
    Simulation[] simArray = new Simulation[simKeys.length];
    for (int i = 0; i < simKeys.length; i++) {
        Simulation sim = dbServer.getDBTopLevel().getSimulation(dbc, user, simKeys[i]);
        // 
        try {
            simArray[i] = (Simulation) BeanUtils.cloneSerializable(sim);
        } catch (Throwable e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("exception cloning Simulation: " + e.getMessage());
        }
    }
    SimulationContext[] scArray = new SimulationContext[scKeys.length];
    for (int i = 0; i < scKeys.length; i++) {
        SimulationContext sc = dbServer.getDBTopLevel().getSimulationContext(dbc, user, scKeys[i]);
        // 
        try {
            scArray[i] = (SimulationContext) BeanUtils.cloneSerializable(sc);
            scArray[i].getModel().refreshDependencies();
            scArray[i].refreshDependencies();
            scArray[i].setModel(model);
        } catch (Throwable e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("exception cloning Application: " + e.getMessage());
        }
        if (!scArray[i].getModel().getKey().compareEqual(modelKey)) {
            // throw new DataAccessException("simulationContext("+scKeys[i]+").model = "+scArray[i].getModel().getKey()+", BioModel.model = "+modelKey);
            System.out.println("simulationContext(" + scKeys[i] + ").model = " + scArray[i].getModel().getKey() + ", BioModel.model = " + modelKey);
        }
    }
    // 
    // create new BioModel according to loaded BioModelMetaData
    // 
    BioModel newBioModel = new BioModel(bioModelMetaData.getVersion());
    try {
        // newBioModel.setMIRIAMAnnotation(bioModelMetaData.getMIRIAMAnnotation());
        System.err.println("< < < < NEED TO GET VCMETADATA FROM METADATA TABLE ... METADATA IS EMPTY. > > > >");
        newBioModel.setModel(model);
        newBioModel.setSimulationContexts(scArray);
        // 
        for (int i = 0; i < simArray.length; i++) {
            boolean bMathFound = false;
            for (int j = 0; j < scArray.length; j++) {
                if (simArray[i].getMathDescription().getVersion().getVersionKey().compareEqual(scArray[j].getMathDescription().getVersion().getVersionKey())) {
                    simArray[i].setMathDescription(scArray[j].getMathDescription());
                    bMathFound = true;
                    break;
                }
            }
            if (!bMathFound) {
                System.out.println("<<<<WARNING>>>>> ClientDocumentManager.getBioModel(), Simulation " + simArray[i].getName() + " is orphaned, Math(" + simArray[i].getMathDescription().getName() + ") not found in Applications");
                simArray = (Simulation[]) BeanUtils.removeElement(simArray, simArray[i]);
                i--;
            }
        }
        newBioModel.setSimulations(simArray);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException("PropertyVetoException caught " + e.getMessage());
    }
    // 
    // The BioModel is no longer cloned because the reference to this BioModel is no longer returned to the calling method.
    // the only possible side effect is the "BioModel:refreshDependencies()" method call.
    // this will reconnect internal listeners and other transient fields, and is not going to harm the cache integrity.
    // 
    // //
    // // clone BioModel (so that children can't be corrupted in the cache)
    // //
    // try {
    // newBioModel = (BioModel)BeanUtils.cloneSerializable(newBioModel);
    // }catch (Exception e){
    // e.printStackTrace(System.out);
    // throw new DataAccessException("BioModel clone failed: "+e.getMessage());
    // }
    newBioModel.refreshDependencies();
    // 
    return cbit.vcell.xml.XmlHelper.bioModelToXML(newBioModel);
}