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

Example 96 with KeyValue

use of org.vcell.util.document.KeyValue 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 97 with KeyValue

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

the class ModelDbDriver method getSpeciesContext.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.model.SpeciesContext
 * @param rset java.sql.ResultSet
 */
private SpeciesContext getSpeciesContext(QueryHashtable dbc, Connection con, ResultSet rset) throws SQLException, DataAccessException {
    // 
    // if in object cache, no need to create it
    // 
    KeyValue scKey = new KeyValue(rset.getBigDecimal(SpeciesContextModelTable.table.id.toString()));
    SpeciesContext speciesContext = (SpeciesContext) dbc.get(scKey);
    if (speciesContext != null) {
        return speciesContext;
    }
    // 
    // get foreign keys
    // 
    KeyValue structKey = new KeyValue(rset.getBigDecimal(SpeciesContextModelTable.table.structRef.toString()));
    KeyValue speciesKey = new KeyValue(rset.getBigDecimal(SpeciesContextModelTable.table.speciesRef.toString()));
    // 
    // get object (ignoring foreign keys)
    // 
    speciesContext = speciesContextModelTable.getSpeciesContext(rset, scKey);
    String speciesPatternString = speciesContext.getSpeciesPatternString();
    // 
    // add objects corresponding to foreign keys
    // 
    Structure structure = reactStepDB.getStructure(dbc, con, structKey);
    Species species = reactStepDB.getSpecies(dbc, con, speciesKey);
    speciesContext = new SpeciesContext(scKey, speciesContext.getName(), species, structure);
    speciesContext.setSpeciesPatternString(speciesPatternString);
    // 
    // put SpeciesContext into object cache
    // 
    dbc.put(scKey, speciesContext);
    return speciesContext;
}

Example 98 with KeyValue

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

the class ModelDbDriver method getModel.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.model.Model
 * @param rset java.sql.ResultSet
 */
private Model getModel(QueryHashtable dbc, ResultSet rset, Connection con, User user) throws SQLException, DataAccessException {
    // User owner = new User(ownerName, ownerRef);
    try {
        Model model = modelTable.getModel(rset, con);
        // model.setOwner(owner);
        KeyValue modelKey = model.getVersion().getVersionKey();
        // 
        // set structures for this model
        // 
        StructureTopology structureTopology = model.getStructureTopology();
        Structure[] structures = reactStepDB.getStructuresFromModel(dbc, con, modelKey);
        if (structures != null && structures.length > 0) {
            model.setStructures(structures);
        }
        HashMap<KeyValue, StructureKeys> structureKeysMap = reactStepDB.getStructureParentMapByModel(dbc, con, modelKey);
        ReactStepDbDriver.populateStructureAndElectricalTopology(model, structureKeysMap);
        // 
        // set species for this model
        // 
        SpeciesContext[] speciesContexts = getSpeciesContextFromModel(dbc, con, user, modelKey, structureTopology);
        if (speciesContexts != null) {
            Vector<Species> speciesList = new Vector<Species>();
            for (int i = 0; i < speciesContexts.length; i++) {
                if (!speciesList.contains(speciesContexts[i].getSpecies())) {
                    speciesList.addElement(speciesContexts[i].getSpecies());
                }
            }
            Species[] speciesArray = new Species[speciesList.size()];
            speciesList.copyInto(speciesArray);
            model.setSpecies(speciesArray);
        }
        // 
        if (speciesContexts != null) {
            model.setSpeciesContexts(speciesContexts);
        }
        // 
        // Add global parameters to the model
        // 
        GlobalModelParameterTable.table.setModelParameters(con, model);
        // 
        // add reactionSteps for this model
        // 
        ReactionStep[] reactSteps = reactStepDB.getReactionStepsFromModel(dbc, con, model, modelKey);
        if (reactSteps != null) {
            model.setReactionSteps(reactSteps);
            for (int i = 0; i < reactSteps.length; i++) {
                try {
                    // 
                    // fix any improperly defined reactionSteps (which have parameters that should be catalysts)
                    // name space of kinetic parameters should be unique with respect to SpeciesContexts (so if they overlap, should be a catalyst).
                    // 
                    Kinetics.KineticsParameter[] params = reactSteps[i].getKinetics().getKineticsParameters();
                    for (int j = 0; j < params.length; j++) {
                        SpeciesContext speciesContext = model.getSpeciesContext(params[j].getName());
                        if (speciesContext != null) {
                            reactSteps[i].addCatalyst(speciesContext);
                            if (lg.isWarnEnabled())
                                lg.warn("ModelDbDriver.getModel(), Parameter '" + params[j].getName() + "' in Reaction " + reactSteps[i].getName() + " in Model(" + model.getKey() + ") conflicts with SpeciesContext, added as a catalyst");
                        }
                    }
                } catch (Throwable e) {
                    lg.error(e.getMessage(), e);
                }
                try {
                    reactSteps[i].rebindAllToModel(model);
                } catch (cbit.vcell.parser.ExpressionBindingException e) {
                    throw new DataAccessException("bindingException: " + e.getMessage());
                } catch (cbit.vcell.parser.ExpressionException e) {
                    throw new DataAccessException(e.getMessage());
                } catch (PropertyVetoException e) {
                    throw new DataAccessException("PropertyVetoException: " + e.getMessage());
                } catch (cbit.vcell.model.ModelException e) {
                    throw new DataAccessException(e.getMessage());
                }
            }
        }
        // 
        // add diagrams for this model
        // 
        Diagram[] diagrams = getDiagramsFromModel(dbc, con, modelKey, structureTopology, dbSyntax);
        model.setDiagrams(diagrams);
        // 
        // add rbm
        // 
        ModelTable.readRbmElement(con, model, dbSyntax);
        if (!model.getRbmModelContainer().isEmpty()) {
            for (SpeciesContext sc : model.getSpeciesContexts()) {
                sc.parseSpeciesPatternString(model);
            }
        }
        return model;
    } catch (PropertyVetoException e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException(e.getMessage());
    }
}

Example 99 with KeyValue

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

the class ReactStepTable method getUserReactionList.

/**
 * Insert the method's description here.
 * Creation date: (7/12/2003 2:59:27 PM)
 * @return java.lang.String
 * @param likeString java.lang.String
 */
public ReactionDescription[] getUserReactionList(java.sql.ResultSet rset) throws java.sql.SQLException {
    java.util.Vector resultV = new java.util.Vector();
    ReactionDescription[] result = null;
    java.util.Vector rxidV = null;
    // 
    java.math.BigDecimal rxid = null;
    ReactionDescription dbfr = null;
    // 
    while (rset.next()) {
        java.math.BigDecimal currRXID = rset.getBigDecimal(ReactStepTable.table.id.toString());
        if (rset.isFirst()) {
            rxid = currRXID;
        }
        if (rxid != null && !rxid.equals(currRXID)) {
            rxid = currRXID;
            dbfr = null;
        }
        // 
        if (dbfr == null) {
            ReactionType rxType = ReactionType.fromDatabaseName(rset.getString(ReactStepTable.table.reactType.toString()));
            String rxName = rset.getString(ReactStepTable.table.name.toString());
            java.math.BigDecimal currBioModelID = rset.getBigDecimal("bmid");
            java.math.BigDecimal currStructID = rset.getBigDecimal(ReactStepTable.table.structRef.toString());
            dbfr = new ReactionDescription(rxName, rxType, new KeyValue(rxid), new KeyValue(currBioModelID), new KeyValue(currStructID));
            resultV.add(dbfr);
        }
        String name = rset.getString(SpeciesTable.table.commonName.toString());
        DBNonFormalUnboundSpecies dbnfu = new DBNonFormalUnboundSpecies(name);
        // 
        String partRole = rset.getString(ReactPartTable.table.role.toString());
        char partRoleType;
        if (partRole.equals("reactant")) {
            partRoleType = ReactionDescription.RX_ELEMENT_REACTANT;
        } else if (partRole.equals("flux")) {
            partRoleType = ReactionDescription.RX_ELEMENT_FLUX;
        } else if (partRole.equals("catalyst")) {
            partRoleType = ReactionDescription.RX_ELEMENT_CATALYST;
        } else if (partRole.equals("product")) {
            partRoleType = ReactionDescription.RX_ELEMENT_PRODUCT;
        } else {
            throw new RuntimeException("Unknown role in UserList Query results");
        }
        // 
        int stoich = rset.getInt(ReactPartTable.table.stoich.toString());
        dbfr.addReactionElement(dbnfu, stoich, partRoleType);
        if (partRole.equals("flux")) {
            dbfr.addReactionElement(new DBNonFormalUnboundSpecies(name), stoich, partRoleType);
        }
    }
    // 
    if (resultV.size() > 0) {
        result = new ReactionDescription[resultV.size()];
        resultV.copyInto(result);
    }
    return result;
}

Example 100 with KeyValue

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

the class ResultSetCrawler method scanUserDirectory.

/**
 * Insert the method's description here.
 * Creation date: (2/2/01 3:40:29 PM)
 */
private static void scanUserDirectory(File userDir, ExternalDataIdentifier[] extDataIDArr, SimulationInfo[] simulationInfos, File outputDir, final boolean bScanOnly, AmplistorUtils.AmplistorCredential amplistorCredential) throws Exception {
    File outputFile = null;
    java.io.PrintWriter writer = null;
    try {
        long timestamp = new Date().getTime();
        outputFile = new File(outputDir, "ResultSetCrawler_" + userDir.getName() + "_" + timestamp + ".txt");
        writer = new java.io.PrintWriter(new java.io.FileOutputStream(outputFile));
        final PrintWriter pw = writer;
        pw.println("scanning directory : " + userDir.getPath());
        if (lg.isTraceEnabled())
            lg.trace("scanning directory : " + userDir.getPath());
        // 
        // gather list of keys that should be retained.
        // 
        final HashSet<KeyValue> referencedKeys = new HashSet<KeyValue>();
        for (ExternalDataIdentifier extDataId : extDataIDArr) {
            referencedKeys.add(extDataId.getKey());
        }
        for (SimulationInfo simulationInfo : simulationInfos) {
            referencedKeys.add(simulationInfo.getSimulationVersion().getVersionKey());
        }
        if (amplistorCredential != null) {
            try {
                if (bScanOnly) {
                    ArrayList<String> shouldBeDeleted = AmplistorUtils.deleteSimFilesNotInHash(AmplistorUtils.DEFAULT_AMPLI_SERVICE_VCELL_URL + userDir.getName(), referencedKeys, bScanOnly, amplistorCredential);
                    for (String fileName : shouldBeDeleted) {
                        pw.println("Should delete Amplistor " + fileName);
                        if (lg.isTraceEnabled())
                            lg.trace("Should delete Amplistor " + fileName);
                    }
                } else {
                    ArrayList<String> wasDeleted = AmplistorUtils.deleteSimFilesNotInHash(AmplistorUtils.DEFAULT_AMPLI_SERVICE_VCELL_URL + userDir.getName(), referencedKeys, bScanOnly, amplistorCredential);
                    for (String fileName : wasDeleted) {
                        pw.println("deleted Amplistor " + fileName);
                        if (lg.isTraceEnabled())
                            lg.trace("deleted Amplistor " + fileName);
                    }
                }
            } catch (Exception e) {
                if (lg.isTraceEnabled())
                    lg.trace("Amplistor delete failed url=" + AmplistorUtils.DEFAULT_AMPLI_SERVICE_VCELL_URL + userDir.getName() + " : " + e.getMessage());
                pw.println("Amplistor delete failed url=" + AmplistorUtils.DEFAULT_AMPLI_SERVICE_VCELL_URL + userDir.getName() + " : " + e.getMessage());
            }
        }
        final HashMap<KeyValue, Integer> deletedKeyMap = new HashMap<KeyValue, Integer>();
        // 
        // visit each file and delete it on the fly (through a FileFilter)
        // 
        FileFilter fileVisitor = new FileFilter() {

            @Override
            public boolean accept(File file) {
                String filename = file.getName();
                String[] parts = filename.split("\\_|\\.");
                if (parts.length > 0 && parts[0].equals("SimID")) {
                    if (parts.length > 1) {
                        String simkeyString = parts[1];
                        try {
                            KeyValue simKey = new KeyValue(simkeyString);
                            if (!referencedKeys.contains(simKey)) {
                                Integer count = deletedKeyMap.get(simKey);
                                if (count == null) {
                                    deletedKeyMap.put(simKey, 1);
                                    count = 1;
                                } else {
                                    deletedKeyMap.put(simKey, 1 + count.intValue());
                                }
                                if (bScanOnly) {
                                    pw.println("Should delete file(" + count + ") with key " + simKey + " : " + file.getPath());
                                    if (lg.isTraceEnabled())
                                        lg.trace("Should delete file(" + count + ") with key " + simKey + " : " + file.getPath());
                                } else {
                                    pw.println("deleted file(" + simKey + ":" + count + ") " + file.getPath());
                                    if (lg.isTraceEnabled())
                                        lg.trace("deleted file(" + simKey + ":" + count + ") " + file.getPath());
                                    file.delete();
                                }
                            }
                        } catch (Exception e) {
                            if (lg.isTraceEnabled())
                                lg.trace("failed to process file " + file.getPath() + ": " + e.getMessage());
                        }
                    }
                }
                return false;
            }
        };
        // 
        // visit all of the files and delete if bScanOnly=false
        // 
        userDir.listFiles(fileVisitor);
        pw.println("done scanning directory : " + userDir.getPath());
        if (lg.isTraceEnabled())
            lg.trace("done scanning directory : " + userDir.getPath());
    } finally {
        if (writer != null) {
            writer.close();
        }
        if (lg.isTraceEnabled())
            lg.trace("User " + userDir.getName() + ", See " + outputFile.getAbsolutePath() + " for details");
    }
}