AbstractSqlEamDb.java

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/*
 * Central Repository
 *
 * Copyright 2015-2019 Basis Technology Corp.
 * Contact: carrier <at> sleuthkit <dot> org
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package org.sleuthkit.autopsy.centralrepository.datamodel;

import com.google.common.cache.Cache;
import com.google.common.cache.CacheBuilder;
import com.google.common.cache.CacheLoader;
import java.net.UnknownHostException;
import java.util.ArrayList;
import java.util.List;
import java.util.Collection;
import java.util.LinkedHashSet;
import java.util.stream.Collectors;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.sql.Types;
import java.time.LocalDate;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.TimeUnit;
import java.util.logging.Level;
import org.openide.util.NbBundle.Messages;
import org.sleuthkit.autopsy.casemodule.Case;
import static org.sleuthkit.autopsy.centralrepository.datamodel.EamDbUtil.updateSchemaVersion;
import org.sleuthkit.autopsy.coreutils.Logger;
import org.sleuthkit.autopsy.healthmonitor.HealthMonitor;
import org.sleuthkit.autopsy.healthmonitor.TimingMetric;
import org.sleuthkit.datamodel.CaseDbSchemaVersionNumber;
import org.sleuthkit.datamodel.TskData;

abstract class AbstractSqlEamDb implements EamDb {

    private final static Logger logger = Logger.getLogger(AbstractSqlEamDb.class.getName());
    static final String SCHEMA_MAJOR_VERSION_KEY = "SCHEMA_VERSION";
    static final String SCHEMA_MINOR_VERSION_KEY = "SCHEMA_MINOR_VERSION";
    static final String CREATION_SCHEMA_MAJOR_VERSION_KEY = "CREATION_SCHEMA_MAJOR_VERSION";
    static final String CREATION_SCHEMA_MINOR_VERSION_KEY = "CREATION_SCHEMA_MINOR_VERSION";
    static final CaseDbSchemaVersionNumber SOFTWARE_CR_DB_SCHEMA_VERSION = new CaseDbSchemaVersionNumber(1, 3);

    protected final List<CorrelationAttributeInstance.Type> defaultCorrelationTypes;

    private int bulkArtifactsCount;
    protected int bulkArtifactsThreshold;
    private final Map<String, Collection<CorrelationAttributeInstance>> bulkArtifacts;
    private static final int CASE_CACHE_TIMEOUT = 5;
    private static final int DATA_SOURCE_CACHE_TIMEOUT = 5;
    private static final Cache<Integer, CorrelationAttributeInstance.Type> typeCache = CacheBuilder.newBuilder().build();
    private static final Cache<String, CorrelationCase> caseCacheByUUID = CacheBuilder.newBuilder()
            .expireAfterWrite(CASE_CACHE_TIMEOUT, TimeUnit.MINUTES).
            build();
    private static final Cache<Integer, CorrelationCase> caseCacheById = CacheBuilder.newBuilder()
            .expireAfterWrite(CASE_CACHE_TIMEOUT, TimeUnit.MINUTES).
            build();
    private static final Cache<String, CorrelationDataSource> dataSourceCacheByDsObjectId = CacheBuilder.newBuilder()
            .expireAfterWrite(DATA_SOURCE_CACHE_TIMEOUT, TimeUnit.MINUTES).
            build();
    private static final Cache<String, CorrelationDataSource> dataSourceCacheById = CacheBuilder.newBuilder()
            .expireAfterWrite(DATA_SOURCE_CACHE_TIMEOUT, TimeUnit.MINUTES).
            build();
    // Maximum length for the value column in the instance tables
    static final int MAX_VALUE_LENGTH = 256;

    // number of instances to keep in bulk queue before doing an insert.
    // Update Test code if this changes.  It's hard coded there.
    static final int DEFAULT_BULK_THRESHHOLD = 1000;

    protected AbstractSqlEamDb() throws EamDbException {
        bulkArtifactsCount = 0;
        bulkArtifacts = new HashMap<>();

        defaultCorrelationTypes = CorrelationAttributeInstance.getDefaultCorrelationTypes();
        defaultCorrelationTypes.forEach((type) -> {
            bulkArtifacts.put(EamDbUtil.correlationTypeToInstanceTableName(type), new ArrayList<>());
        });
    }

    protected abstract Connection connect(boolean foreignKeys) throws EamDbException;

    protected abstract Connection connect() throws EamDbException;

    @Override
    public void newDbInfo(String name, String value) throws EamDbException {
        Connection conn = connect();

        PreparedStatement preparedStatement = null;
        String sql = "INSERT INTO db_info (name, value) VALUES (?, ?) "
                + getConflictClause();
        try {
            preparedStatement = conn.prepareStatement(sql);
            preparedStatement.setString(1, name);
            preparedStatement.setString(2, value);
            preparedStatement.executeUpdate();
        } catch (SQLException ex) {
            throw new EamDbException("Error adding new name/value pair to db_info.", ex);
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeConnection(conn);
        }

    }

    @Override
    public void addDataSourceObjectId(int rowId, long dataSourceObjectId) throws EamDbException {
        Connection conn = connect();
        PreparedStatement preparedStatement = null;
        String sql = "UPDATE data_sources SET datasource_obj_id=? WHERE id=?";
        try {
            preparedStatement = conn.prepareStatement(sql);
            preparedStatement.setLong(1, dataSourceObjectId);
            preparedStatement.setInt(2, rowId);
            preparedStatement.executeUpdate();
        } catch (SQLException ex) {
            throw new EamDbException("Error updating data source object id for data_sources row " + rowId, ex);
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public String getDbInfo(String name) throws EamDbException {
        Connection conn = connect();

        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;
        String value = null;
        String sql = "SELECT value FROM db_info WHERE name=?";
        try {
            preparedStatement = conn.prepareStatement(sql);
            preparedStatement.setString(1, name);
            resultSet = preparedStatement.executeQuery();
            if (resultSet.next()) {
                value = resultSet.getString("value");
            }
        } catch (SQLException ex) {
            throw new EamDbException("Error getting value for name.", ex);
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }

        return value;
    }

    protected final void clearCaches() {
        typeCache.invalidateAll();
        caseCacheByUUID.invalidateAll();
        caseCacheById.invalidateAll();
        dataSourceCacheByDsObjectId.invalidateAll();
        dataSourceCacheById.invalidateAll();
    }

    @Override
    public void updateDbInfo(String name, String value) throws EamDbException {
        Connection conn = connect();

        PreparedStatement preparedStatement = null;
        String sql = "UPDATE db_info SET value=? WHERE name=?";
        try {
            preparedStatement = conn.prepareStatement(sql);
            preparedStatement.setString(1, value);
            preparedStatement.setString(2, name);
            preparedStatement.executeUpdate();
        } catch (SQLException ex) {
            throw new EamDbException("Error updating value for name.", ex);
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public synchronized CorrelationCase newCase(CorrelationCase eamCase) throws EamDbException {

        if (eamCase.getCaseUUID() == null) {
            throw new EamDbException("Case UUID is null");
        }

        // check if there is already an existing CorrelationCase for this Case
        CorrelationCase cRCase = getCaseByUUID(eamCase.getCaseUUID());
        if (cRCase != null) {
            return cRCase;
        }

        Connection conn = connect();
        PreparedStatement preparedStatement = null;

        String sql = "INSERT INTO cases(case_uid, org_id, case_name, creation_date, case_number, "
                + "examiner_name, examiner_email, examiner_phone, notes) "
                + "VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?) "
                + getConflictClause();
        ResultSet resultSet = null;
        try {
            preparedStatement = conn.prepareStatement(sql, Statement.RETURN_GENERATED_KEYS);

            preparedStatement.setString(1, eamCase.getCaseUUID());
            if (null == eamCase.getOrg()) {
                preparedStatement.setNull(2, Types.INTEGER);
            } else {
                preparedStatement.setInt(2, eamCase.getOrg().getOrgID());
            }
            preparedStatement.setString(3, eamCase.getDisplayName());
            preparedStatement.setString(4, eamCase.getCreationDate());
            if ("".equals(eamCase.getCaseNumber())) {
                preparedStatement.setNull(5, Types.INTEGER);
            } else {
                preparedStatement.setString(5, eamCase.getCaseNumber());
            }
            if ("".equals(eamCase.getExaminerName())) {
                preparedStatement.setNull(6, Types.INTEGER);
            } else {
                preparedStatement.setString(6, eamCase.getExaminerName());
            }
            if ("".equals(eamCase.getExaminerEmail())) {
                preparedStatement.setNull(7, Types.INTEGER);
            } else {
                preparedStatement.setString(7, eamCase.getExaminerEmail());
            }
            if ("".equals(eamCase.getExaminerPhone())) {
                preparedStatement.setNull(8, Types.INTEGER);
            } else {
                preparedStatement.setString(8, eamCase.getExaminerPhone());
            }
            if ("".equals(eamCase.getNotes())) {
                preparedStatement.setNull(9, Types.INTEGER);
            } else {
                preparedStatement.setString(9, eamCase.getNotes());
            }

            preparedStatement.executeUpdate();
            //update the case in the caches
            resultSet = preparedStatement.getGeneratedKeys();
            if (!resultSet.next()) {
                throw new EamDbException(String.format("Failed to INSERT case %s in central repo", eamCase.getCaseUUID()));
            }
            int caseID = resultSet.getInt(1); //last_insert_rowid()    
            CorrelationCase correlationCase = new CorrelationCase(caseID, eamCase.getCaseUUID(), eamCase.getOrg(),
                    eamCase.getDisplayName(), eamCase.getCreationDate(), eamCase.getCaseNumber(), eamCase.getExaminerName(),
                    eamCase.getExaminerEmail(), eamCase.getExaminerPhone(), eamCase.getNotes());
            caseCacheByUUID.put(eamCase.getCaseUUID(), correlationCase);
            caseCacheById.put(caseID, correlationCase);
        } catch (SQLException ex) {
            throw new EamDbException("Error inserting new case.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeConnection(conn);
        }

        // get a new version with the updated ID
        return getCaseByUUID(eamCase.getCaseUUID());
    }

    @Override
    public CorrelationCase newCase(Case autopsyCase) throws EamDbException {
        if (autopsyCase == null) {
            throw new EamDbException("Case is null");
        }

        CorrelationCase curCeCase = new CorrelationCase(
                -1,
                autopsyCase.getName(), // unique case ID
                EamOrganization.getDefault(),
                autopsyCase.getDisplayName(),
                autopsyCase.getCreatedDate(),
                autopsyCase.getNumber(),
                autopsyCase.getExaminer(),
                autopsyCase.getExaminerEmail(),
                autopsyCase.getExaminerPhone(),
                autopsyCase.getCaseNotes());
        return newCase(curCeCase);
    }

    @Override
    public CorrelationCase getCase(Case autopsyCase) throws EamDbException {
        return getCaseByUUID(autopsyCase.getName());
    }

    @Override
    public void updateCase(CorrelationCase eamCase) throws EamDbException {
        if (eamCase == null) {
            throw new EamDbException("Correlation case is null");
        }

        Connection conn = connect();

        PreparedStatement preparedStatement = null;
        String sql = "UPDATE cases "
                + "SET org_id=?, case_name=?, creation_date=?, case_number=?, examiner_name=?, examiner_email=?, examiner_phone=?, notes=? "
                + "WHERE case_uid=?";

        try {
            preparedStatement = conn.prepareStatement(sql);

            if (null == eamCase.getOrg()) {
                preparedStatement.setNull(1, Types.INTEGER);
            } else {
                preparedStatement.setInt(1, eamCase.getOrg().getOrgID());
            }
            preparedStatement.setString(2, eamCase.getDisplayName());
            preparedStatement.setString(3, eamCase.getCreationDate());

            if ("".equals(eamCase.getCaseNumber())) {
                preparedStatement.setNull(4, Types.INTEGER);
            } else {
                preparedStatement.setString(4, eamCase.getCaseNumber());
            }
            if ("".equals(eamCase.getExaminerName())) {
                preparedStatement.setNull(5, Types.INTEGER);
            } else {
                preparedStatement.setString(5, eamCase.getExaminerName());
            }
            if ("".equals(eamCase.getExaminerEmail())) {
                preparedStatement.setNull(6, Types.INTEGER);
            } else {
                preparedStatement.setString(6, eamCase.getExaminerEmail());
            }
            if ("".equals(eamCase.getExaminerPhone())) {
                preparedStatement.setNull(7, Types.INTEGER);
            } else {
                preparedStatement.setString(7, eamCase.getExaminerPhone());
            }
            if ("".equals(eamCase.getNotes())) {
                preparedStatement.setNull(8, Types.INTEGER);
            } else {
                preparedStatement.setString(8, eamCase.getNotes());
            }

            preparedStatement.setString(9, eamCase.getCaseUUID());

            preparedStatement.executeUpdate();
            //update the case in the cache
            caseCacheById.put(eamCase.getID(), eamCase);
            caseCacheByUUID.put(eamCase.getCaseUUID(), eamCase);
        } catch (SQLException ex) {
            throw new EamDbException("Error updating case.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public CorrelationCase getCaseByUUID(String caseUUID) throws EamDbException {
        try {
            return caseCacheByUUID.get(caseUUID, () -> getCaseByUUIDFromCr(caseUUID));
        } catch (CacheLoader.InvalidCacheLoadException ignored) {
            //lambda valueloader returned a null value and cache can not store null values this is normal if the case does not exist in the central repo yet
            return null;
        } catch (ExecutionException ex) {
            throw new EamDbException("Error getting autopsy case from Central repo", ex);
        }
    }

    private CorrelationCase getCaseByUUIDFromCr(String caseUUID) throws EamDbException {
        Connection conn = connect();

        CorrelationCase eamCaseResult = null;
        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;

        String sql = "SELECT cases.id as case_id, case_uid, case_name, creation_date, case_number, examiner_name, "
                + "examiner_email, examiner_phone, notes, organizations.id as org_id, org_name, poc_name, poc_email, poc_phone "
                + "FROM cases "
                + "LEFT JOIN organizations ON cases.org_id=organizations.id "
                + "WHERE case_uid=?";

        try {
            preparedStatement = conn.prepareStatement(sql);
            preparedStatement.setString(1, caseUUID);
            resultSet = preparedStatement.executeQuery();
            if (resultSet.next()) {
                eamCaseResult = getEamCaseFromResultSet(resultSet);
            }
            if (eamCaseResult != null) {
                //Update the version in the other cache
                caseCacheById.put(eamCaseResult.getID(), eamCaseResult);
            }
        } catch (SQLException ex) {
            throw new EamDbException("Error getting case details.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }

        return eamCaseResult;
    }

    @Override
    public CorrelationCase getCaseById(int caseId) throws EamDbException {
        try {
            return caseCacheById.get(caseId, () -> getCaseByIdFromCr(caseId));
        } catch (CacheLoader.InvalidCacheLoadException ignored) {
            //lambda valueloader returned a null value and cache can not store null values this is normal if the case does not exist in the central repo yet
            return null;
        } catch (ExecutionException ex) {
            throw new EamDbException("Error getting autopsy case from Central repo", ex);
        }
    }

    private CorrelationCase getCaseByIdFromCr(int caseId) throws EamDbException {
        Connection conn = connect();

        CorrelationCase eamCaseResult = null;
        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;

        String sql = "SELECT cases.id as case_id, case_uid, case_name, creation_date, case_number, examiner_name, "
                + "examiner_email, examiner_phone, notes, organizations.id as org_id, org_name, poc_name, poc_email, poc_phone "
                + "FROM cases "
                + "LEFT JOIN organizations ON cases.org_id=organizations.id "
                + "WHERE cases.id=?";
        try {
            preparedStatement = conn.prepareStatement(sql);
            preparedStatement.setInt(1, caseId);
            resultSet = preparedStatement.executeQuery();
            if (resultSet.next()) {
                eamCaseResult = getEamCaseFromResultSet(resultSet);
            }
            if (eamCaseResult != null) {
                //Update the version in the other cache
                caseCacheByUUID.put(eamCaseResult.getCaseUUID(), eamCaseResult);
            }
        } catch (SQLException ex) {
            throw new EamDbException("Error getting case details.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }

        return eamCaseResult;
    }

    @Override
    public List<CorrelationCase> getCases() throws EamDbException {
        Connection conn = connect();

        List<CorrelationCase> cases = new ArrayList<>();
        CorrelationCase eamCaseResult;
        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;

        String sql = "SELECT cases.id as case_id, case_uid, case_name, creation_date, case_number, examiner_name, "
                + "examiner_email, examiner_phone, notes, organizations.id as org_id, org_name, poc_name, poc_email, poc_phone "
                + "FROM cases "
                + "LEFT JOIN organizations ON cases.org_id=organizations.id";

        try {
            preparedStatement = conn.prepareStatement(sql);
            resultSet = preparedStatement.executeQuery();
            while (resultSet.next()) {
                eamCaseResult = getEamCaseFromResultSet(resultSet);
                cases.add(eamCaseResult);
            }
        } catch (SQLException ex) {
            throw new EamDbException("Error getting all cases.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }

        return cases;
    }

    private static String getDataSourceByDSObjectIdCacheKey(int caseId, Long dataSourceObjectId) {
        return "Case" + caseId + "DsObjectId" + dataSourceObjectId; //NON-NLS
    }

    private static String getDataSourceByIdCacheKey(int caseId, int dataSourceId) {
        return "Case" + caseId + "Id" + dataSourceId; //NON-NLS
    }

    @Override
    public CorrelationDataSource newDataSource(CorrelationDataSource eamDataSource) throws EamDbException {
        if (eamDataSource.getCaseID() == -1) {
            throw new EamDbException("Case ID is -1");
        }
        if (eamDataSource.getDeviceID() == null) {
            throw new EamDbException("Device ID is null");
        }
        if (eamDataSource.getName() == null) {
            throw new EamDbException("Name is null");
        }
        if (eamDataSource.getID() != -1) {
            // This data source is already in the central repo
            return eamDataSource;
        }

        Connection conn = connect();

        PreparedStatement preparedStatement = null;
        //The conflict clause exists in case multiple nodes are trying to add the data source because it did not exist at the same time
        String sql = "INSERT INTO data_sources(device_id, case_id, name, datasource_obj_id, md5, sha1, sha256) VALUES (?, ?, ?, ?, ?, ?, ?) "
                + getConflictClause();
        ResultSet resultSet = null;
        try {
            preparedStatement = conn.prepareStatement(sql, Statement.RETURN_GENERATED_KEYS);

            preparedStatement.setString(1, eamDataSource.getDeviceID());
            preparedStatement.setInt(2, eamDataSource.getCaseID());
            preparedStatement.setString(3, eamDataSource.getName());
            preparedStatement.setLong(4, eamDataSource.getDataSourceObjectID());
            preparedStatement.setString(5, eamDataSource.getMd5());
            preparedStatement.setString(6, eamDataSource.getSha1());
            preparedStatement.setString(7, eamDataSource.getSha256());

            preparedStatement.executeUpdate();
            resultSet = preparedStatement.getGeneratedKeys();
            if (!resultSet.next()) {
                /*
                 * If nothing was inserted, then return the data source that
                 * exists in the Central Repository.
                 *
                 * This is expected to occur with PostgreSQL Central Repository
                 * databases.
                 */
                try {
                    return dataSourceCacheByDsObjectId.get(getDataSourceByDSObjectIdCacheKey(
                            eamDataSource.getCaseID(), eamDataSource.getDataSourceObjectID()),
                            () -> getDataSourceFromCr(eamDataSource.getCaseID(), eamDataSource.getDataSourceObjectID()));
                } catch (CacheLoader.InvalidCacheLoadException | ExecutionException getException) {
                    throw new EamDbException(String.format("Unable to to INSERT or get data source %s in central repo:", eamDataSource.getName()), getException);
                }
            } else {
                //if a new data source was added to the central repository update the caches to include it and return it
                int dataSourceId = resultSet.getInt(1); //last_insert_rowid()
                CorrelationDataSource dataSource = new CorrelationDataSource(eamDataSource.getCaseID(), dataSourceId, eamDataSource.getDeviceID(), eamDataSource.getName(), eamDataSource.getDataSourceObjectID(), eamDataSource.getMd5(), eamDataSource.getSha1(), eamDataSource.getSha256());
                dataSourceCacheByDsObjectId.put(getDataSourceByDSObjectIdCacheKey(dataSource.getCaseID(), dataSource.getDataSourceObjectID()), dataSource);
                dataSourceCacheById.put(getDataSourceByIdCacheKey(dataSource.getCaseID(), dataSource.getID()), dataSource);
                return dataSource;
            }

        } catch (SQLException insertException) {
            /*
             * If an exception was thrown causing us to not return a new data
             * source, attempt to get an existing data source with the same case
             * ID and data source object ID.
             *
             * This exception block is expected to occur with SQLite Central
             * Repository databases.
             */
            try {
                return dataSourceCacheByDsObjectId.get(getDataSourceByDSObjectIdCacheKey(
                        eamDataSource.getCaseID(), eamDataSource.getDataSourceObjectID()),
                        () -> getDataSourceFromCr(eamDataSource.getCaseID(), eamDataSource.getDataSourceObjectID()));
            } catch (CacheLoader.InvalidCacheLoadException | ExecutionException getException) {
                throw new EamDbException(String.format("Unable to to INSERT or get data source %s in central repo, insert failed due to Exception: %s", eamDataSource.getName(), insertException.getMessage()), getException);
            }
        } finally {
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public CorrelationDataSource getDataSource(CorrelationCase correlationCase, Long dataSourceObjectId) throws EamDbException {

        if (correlationCase == null) {
            throw new EamDbException("Correlation case is null");
        }
        try {
            return dataSourceCacheByDsObjectId.get(getDataSourceByDSObjectIdCacheKey(correlationCase.getID(), dataSourceObjectId), () -> getDataSourceFromCr(correlationCase.getID(), dataSourceObjectId));
        } catch (CacheLoader.InvalidCacheLoadException ignored) {
            //lambda valueloader returned a null value and cache can not store null values this is normal if the dataSource does not exist in the central repo yet
            return null;
        } catch (ExecutionException ex) {
            throw new EamDbException("Error getting data source from central repository", ex);
        }
    }

    private CorrelationDataSource getDataSourceFromCr(int correlationCaseId, Long dataSourceObjectId) throws EamDbException {
        Connection conn = connect();

        CorrelationDataSource eamDataSourceResult = null;
        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;

        String sql = "SELECT * FROM data_sources WHERE datasource_obj_id=? AND case_id=?"; // NON-NLS

        try {
            preparedStatement = conn.prepareStatement(sql);
            preparedStatement.setLong(1, dataSourceObjectId);
            preparedStatement.setInt(2, correlationCaseId);
            resultSet = preparedStatement.executeQuery();
            if (resultSet.next()) {
                eamDataSourceResult = getEamDataSourceFromResultSet(resultSet);
            }
            if (eamDataSourceResult != null) {
                dataSourceCacheById.put(getDataSourceByIdCacheKey(correlationCaseId, eamDataSourceResult.getID()), eamDataSourceResult);
            }
        } catch (SQLException ex) {
            throw new EamDbException("Error getting data source.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }

        return eamDataSourceResult;
    }

    @Override
    public CorrelationDataSource getDataSourceById(CorrelationCase correlationCase, int dataSourceId) throws EamDbException {
        if (correlationCase == null) {
            throw new EamDbException("Correlation case is null");
        }
        try {
            return dataSourceCacheById.get(getDataSourceByIdCacheKey(correlationCase.getID(), dataSourceId), () -> getDataSourceByIdFromCr(correlationCase, dataSourceId));
        } catch (CacheLoader.InvalidCacheLoadException ignored) {
            //lambda valueloader returned a null value and cache can not store null values this is normal if the dataSource does not exist in the central repo yet
            return null;
        } catch (ExecutionException ex) {
            throw new EamDbException("Error getting data source from central repository", ex);
        }
    }

    private CorrelationDataSource getDataSourceByIdFromCr(CorrelationCase correlationCase, int dataSourceId) throws EamDbException {
        Connection conn = connect();

        CorrelationDataSource eamDataSourceResult = null;
        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;

        String sql = "SELECT * FROM data_sources WHERE id=? AND case_id=?"; // NON-NLS

        try {
            preparedStatement = conn.prepareStatement(sql);
            preparedStatement.setInt(1, dataSourceId);
            preparedStatement.setInt(2, correlationCase.getID());
            resultSet = preparedStatement.executeQuery();
            if (resultSet.next()) {
                eamDataSourceResult = getEamDataSourceFromResultSet(resultSet);
            }
            if (eamDataSourceResult != null) {
                dataSourceCacheByDsObjectId.put(getDataSourceByDSObjectIdCacheKey(correlationCase.getID(), eamDataSourceResult.getDataSourceObjectID()), eamDataSourceResult);
            }
        } catch (SQLException ex) {
            throw new EamDbException("Error getting data source.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }

        return eamDataSourceResult;
    }

    @Override
    public List<CorrelationDataSource> getDataSources() throws EamDbException {
        Connection conn = connect();

        List<CorrelationDataSource> dataSources = new ArrayList<>();
        CorrelationDataSource eamDataSourceResult;
        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;

        String sql = "SELECT * FROM data_sources";

        try {
            preparedStatement = conn.prepareStatement(sql);
            resultSet = preparedStatement.executeQuery();
            while (resultSet.next()) {
                eamDataSourceResult = getEamDataSourceFromResultSet(resultSet);
                dataSources.add(eamDataSourceResult);
            }
        } catch (SQLException ex) {
            throw new EamDbException("Error getting all data sources.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }

        return dataSources;
    }

    @Override
    public void updateDataSourceMd5Hash(CorrelationDataSource eamDataSource) throws EamDbException {
        updateDataSourceStringValue(eamDataSource, "md5", eamDataSource.getMd5());
    }

    @Override
    public void updateDataSourceSha1Hash(CorrelationDataSource eamDataSource) throws EamDbException {
        updateDataSourceStringValue(eamDataSource, "sha1", eamDataSource.getSha1());
    }

    @Override
    public void updateDataSourceSha256Hash(CorrelationDataSource eamDataSource) throws EamDbException {
        updateDataSourceStringValue(eamDataSource, "sha256", eamDataSource.getSha256());
    }

    private void updateDataSourceStringValue(CorrelationDataSource eamDataSource, String column, String value) throws EamDbException {
        if (eamDataSource == null) {
            throw new EamDbException("Correlation data source is null");
        }

        Connection conn = connect();

        PreparedStatement preparedStatement = null;
        String sql = "UPDATE data_sources "
                + "SET " + column + "=? "
                + "WHERE id=?";

        try {
            preparedStatement = conn.prepareStatement(sql);

            preparedStatement.setString(1, value);
            preparedStatement.setInt(2, eamDataSource.getID());

            preparedStatement.executeUpdate();
            //update the case in the cache
            dataSourceCacheByDsObjectId.put(getDataSourceByDSObjectIdCacheKey(eamDataSource.getCaseID(), eamDataSource.getDataSourceObjectID()), eamDataSource);
            dataSourceCacheById.put(getDataSourceByIdCacheKey(eamDataSource.getCaseID(), eamDataSource.getID()), eamDataSource);
        } catch (SQLException ex) {
            throw new EamDbException(String.format("Error updating data source (obj_id=%d).", eamDataSource.getDataSourceObjectID()), ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public void updateDataSourceName(CorrelationDataSource eamDataSource, String newName) throws EamDbException {

        Connection conn = connect();

        PreparedStatement preparedStatement = null;

        String sql = "UPDATE data_sources SET name = ? WHERE id = ?";

        try {
            preparedStatement = conn.prepareStatement(sql);
            preparedStatement.setString(1, newName);
            preparedStatement.setInt(2, eamDataSource.getID());
            preparedStatement.executeUpdate();

            CorrelationDataSource updatedDataSource = new CorrelationDataSource(
                    eamDataSource.getCaseID(),
                    eamDataSource.getID(),
                    eamDataSource.getDeviceID(),
                    newName,
                    eamDataSource.getDataSourceObjectID(),
                    eamDataSource.getMd5(),
                    eamDataSource.getSha1(),
                    eamDataSource.getSha256());

            dataSourceCacheByDsObjectId.put(getDataSourceByDSObjectIdCacheKey(updatedDataSource.getCaseID(), updatedDataSource.getDataSourceObjectID()), updatedDataSource);
            dataSourceCacheById.put(getDataSourceByIdCacheKey(updatedDataSource.getCaseID(), updatedDataSource.getID()), updatedDataSource);
        } catch (SQLException ex) {
            throw new EamDbException("Error updating name of data source with ID " + eamDataSource.getDataSourceObjectID()
                    + " to " + newName, ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public void addArtifactInstance(CorrelationAttributeInstance eamArtifact) throws EamDbException {
        checkAddArtifactInstanceNulls(eamArtifact);

        Connection conn = connect();

        PreparedStatement preparedStatement = null;

        // @@@ We should cache the case and data source IDs in memory
        String tableName = EamDbUtil.correlationTypeToInstanceTableName(eamArtifact.getCorrelationType());
        String sql
                = "INSERT INTO "
                + tableName
                + "(case_id, data_source_id, value, file_path, known_status, comment, file_obj_id) "
                + "VALUES (?, ?, ?, ?, ?, ?, ?) "
                + getConflictClause();

        try {
            preparedStatement = conn.prepareStatement(sql);

            if (!eamArtifact.getCorrelationValue().isEmpty()) {
                preparedStatement.setInt(1, eamArtifact.getCorrelationCase().getID());
                preparedStatement.setInt(2, eamArtifact.getCorrelationDataSource().getID());
                preparedStatement.setString(3, eamArtifact.getCorrelationValue());
                preparedStatement.setString(4, eamArtifact.getFilePath().toLowerCase());
                preparedStatement.setByte(5, eamArtifact.getKnownStatus().getFileKnownValue());

                if ("".equals(eamArtifact.getComment())) {
                    preparedStatement.setNull(6, Types.INTEGER);
                } else {
                    preparedStatement.setString(6, eamArtifact.getComment());
                }
                preparedStatement.setLong(7, eamArtifact.getFileObjectId());

                preparedStatement.executeUpdate();
            }

        } catch (SQLException ex) {
            throw new EamDbException("Error inserting new artifact into artifacts table.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeConnection(conn);
        }
    }

    private void checkAddArtifactInstanceNulls(CorrelationAttributeInstance eamArtifact) throws EamDbException {
        if (eamArtifact == null) {
            throw new EamDbException("CorrelationAttribute is null");
        }
        if (eamArtifact.getCorrelationType() == null) {
            throw new EamDbException("Correlation type is null");
        }
        if (eamArtifact.getCorrelationValue() == null) {
            throw new EamDbException("Correlation value is null");
        }
        if (eamArtifact.getCorrelationValue().length() >= MAX_VALUE_LENGTH) {
            throw new EamDbException("Artifact value too long for central repository."
                    + "\nCorrelationArtifact ID: " + eamArtifact.getID()
                    + "\nCorrelationArtifact Type: " + eamArtifact.getCorrelationType().getDisplayName()
                    + "\nCorrelationArtifact Value: " + eamArtifact.getCorrelationValue());

        }
        if (eamArtifact.getCorrelationCase() == null) {
            throw new EamDbException("CorrelationAttributeInstance case is null");
        }
        if (eamArtifact.getCorrelationDataSource() == null) {
            throw new EamDbException("CorrelationAttributeInstance data source is null");
        }
        if (eamArtifact.getKnownStatus() == null) {
            throw new EamDbException("CorrelationAttributeInstance known status is null");
        }
    }

    @Override
    public List<CorrelationAttributeInstance> getArtifactInstancesByTypeValue(CorrelationAttributeInstance.Type aType, String value) throws EamDbException, CorrelationAttributeNormalizationException {
        if (value == null) {
            throw new CorrelationAttributeNormalizationException("Cannot get artifact instances for null value");
        }
        return getArtifactInstancesByTypeValues(aType, Arrays.asList(value));
    }

    @Override
    public List<CorrelationAttributeInstance> getArtifactInstancesByTypeValues(CorrelationAttributeInstance.Type aType, List<String> values) throws EamDbException, CorrelationAttributeNormalizationException {
        if (aType == null) {
            throw new CorrelationAttributeNormalizationException("Cannot get artifact instances for null type");
        }
        if (values == null || values.isEmpty()) {
            throw new CorrelationAttributeNormalizationException("Cannot get artifact instances without specified values");
        }
        return getArtifactInstances(prepareGetInstancesSql(aType, values), aType);
    }

    @Override
    public List<CorrelationAttributeInstance> getArtifactInstancesByTypeValuesAndCases(CorrelationAttributeInstance.Type aType, List<String> values, List<Integer> caseIds) throws EamDbException, CorrelationAttributeNormalizationException {
        if (aType == null) {
            throw new CorrelationAttributeNormalizationException("Cannot get artifact instances for null type");
        }
        if (values == null || values.isEmpty()) {
            throw new CorrelationAttributeNormalizationException("Cannot get artifact instances without specified values");
        }
        if (caseIds == null || caseIds.isEmpty()) {
            throw new CorrelationAttributeNormalizationException("Cannot get artifact instances without specified cases");
        }
        String tableName = EamDbUtil.correlationTypeToInstanceTableName(aType);
        String sql
                = " and "
                + tableName
                + ".case_id in ('";
        StringBuilder inValuesBuilder = new StringBuilder(prepareGetInstancesSql(aType, values));
        inValuesBuilder.append(sql);
        inValuesBuilder.append(caseIds.stream().map(String::valueOf).collect(Collectors.joining("', '")));
        inValuesBuilder.append("')");
        return getArtifactInstances(inValuesBuilder.toString(), aType);
    }

    private String prepareGetInstancesSql(CorrelationAttributeInstance.Type aType, List<String> values) throws CorrelationAttributeNormalizationException {
        String tableName = EamDbUtil.correlationTypeToInstanceTableName(aType);
        String sql
                = "SELECT "
                + tableName
                + ".id as instance_id,"
                + tableName
                + ".value,"
                + tableName
                + ".file_obj_id,"
                + " cases.*, organizations.org_name, organizations.poc_name, organizations.poc_email, organizations.poc_phone, data_sources.id AS data_source_id, data_sources.name, device_id, file_path, known_status, comment, data_sources.datasource_obj_id, data_sources.md5, data_sources.sha1, data_sources.sha256 FROM "
                + tableName
                + " LEFT JOIN cases ON "
                + tableName
                + ".case_id=cases.id"
                + " LEFT JOIN organizations ON cases.org_id=organizations.id"
                + " LEFT JOIN data_sources ON "
                + tableName
                + ".data_source_id=data_sources.id"
                + " WHERE value IN (";
        StringBuilder inValuesBuilder = new StringBuilder(sql);
        for (String value : values) {
            if (value != null) {
                inValuesBuilder.append("'");
                inValuesBuilder.append(CorrelationAttributeNormalizer.normalize(aType, value));
                inValuesBuilder.append("',");
            }
        }
        inValuesBuilder.deleteCharAt(inValuesBuilder.length() - 1); //delete last comma
        inValuesBuilder.append(")");
        return inValuesBuilder.toString();
    }

    private List<CorrelationAttributeInstance> getArtifactInstances(String sql, CorrelationAttributeInstance.Type aType) throws CorrelationAttributeNormalizationException, EamDbException {
        Connection conn = connect();
        List<CorrelationAttributeInstance> artifactInstances = new ArrayList<>();
        CorrelationAttributeInstance artifactInstance;
        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;
        try {
            preparedStatement = conn.prepareStatement(sql);
            resultSet = preparedStatement.executeQuery();
            while (resultSet.next()) {
                artifactInstance = getEamArtifactInstanceFromResultSet(resultSet, aType);
                artifactInstances.add(artifactInstance);
            }
        } catch (SQLException ex) {
            throw new EamDbException("Error getting artifact instances by artifactType and artifactValue.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }
        return artifactInstances;
    }

    @Override
    public Long getCountArtifactInstancesByTypeValue(CorrelationAttributeInstance.Type aType, String value) throws EamDbException, CorrelationAttributeNormalizationException {
        String normalizedValue = CorrelationAttributeNormalizer.normalize(aType, value);

        Connection conn = connect();

        Long instanceCount = 0L;
        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;

        String tableName = EamDbUtil.correlationTypeToInstanceTableName(aType);
        String sql
                = "SELECT count(*) FROM "
                + tableName
                + " WHERE value=?";

        try {
            preparedStatement = conn.prepareStatement(sql);
            preparedStatement.setString(1, normalizedValue);
            resultSet = preparedStatement.executeQuery();
            resultSet.next();
            instanceCount = resultSet.getLong(1);
        } catch (SQLException ex) {
            throw new EamDbException("Error getting count of artifact instances by artifactType and artifactValue.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }

        return instanceCount;
    }

    @Override
    public int getFrequencyPercentage(CorrelationAttributeInstance corAttr) throws EamDbException, CorrelationAttributeNormalizationException {
        if (corAttr == null) {
            throw new EamDbException("CorrelationAttribute is null");
        }
        Double uniqueTypeValueTuples = getCountUniqueCaseDataSourceTuplesHavingTypeValue(corAttr.getCorrelationType(), corAttr.getCorrelationValue()).doubleValue();
        Double uniqueCaseDataSourceTuples = getCountUniqueDataSources().doubleValue();
        Double commonalityPercentage = uniqueTypeValueTuples / uniqueCaseDataSourceTuples * 100;
        return commonalityPercentage.intValue();
    }

    @Override
    public Long getCountUniqueCaseDataSourceTuplesHavingTypeValue(CorrelationAttributeInstance.Type aType, String value) throws EamDbException, CorrelationAttributeNormalizationException {
        String normalizedValue = CorrelationAttributeNormalizer.normalize(aType, value);

        Connection conn = connect();

        Long instanceCount = 0L;
        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;

        String tableName = EamDbUtil.correlationTypeToInstanceTableName(aType);
        String sql
                = "SELECT count(*) FROM (SELECT DISTINCT case_id, data_source_id FROM "
                + tableName
                + " WHERE value=?) AS "
                + tableName
                + "_distinct_case_data_source_tuple";

        try {
            preparedStatement = conn.prepareStatement(sql);
            preparedStatement.setString(1, normalizedValue);
            resultSet = preparedStatement.executeQuery();
            resultSet.next();
            instanceCount = resultSet.getLong(1);
        } catch (SQLException ex) {
            throw new EamDbException("Error counting unique caseDisplayName/dataSource tuples having artifactType and artifactValue.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }

        return instanceCount;
    }

    @Override
    public Long getCountUniqueDataSources() throws EamDbException {
        Connection conn = connect();

        Long instanceCount = 0L;
        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;

        String stmt = "SELECT count(*) FROM data_sources";

        try {
            preparedStatement = conn.prepareStatement(stmt);
            resultSet = preparedStatement.executeQuery();
            resultSet.next();
            instanceCount = resultSet.getLong(1);
        } catch (SQLException ex) {
            throw new EamDbException("Error counting data sources.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }

        return instanceCount;
    }

    @Override
    public Long getCountArtifactInstancesByCaseDataSource(CorrelationDataSource correlationDataSource) throws EamDbException {
        Connection conn = connect();

        Long instanceCount = 0L;
        List<CorrelationAttributeInstance.Type> artifactTypes = getDefinedCorrelationTypes();
        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;

        //Create query to get count of all instances in the database for the specified case specific data source
        String sql = "SELECT 0 ";

        for (CorrelationAttributeInstance.Type type : artifactTypes) {
            String table_name = EamDbUtil.correlationTypeToInstanceTableName(type);
            sql
                    += "+ (SELECT count(*) FROM "
                    + table_name
                    + " WHERE data_source_id=" + correlationDataSource.getID() + ")";
        }
        try {
            preparedStatement = conn.prepareStatement(sql);

            resultSet = preparedStatement.executeQuery();
            resultSet.next();
            instanceCount = resultSet.getLong(1);
        } catch (SQLException ex) {
            throw new EamDbException("Error counting artifact instances by caseName/dataSource.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }

        return instanceCount;
    }

    @Override
    public void addAttributeInstanceBulk(CorrelationAttributeInstance eamArtifact) throws EamDbException {

        if (eamArtifact.getCorrelationType() == null) {
            throw new EamDbException("Correlation type is null");
        }

        synchronized (bulkArtifacts) {
            bulkArtifacts.get(EamDbUtil.correlationTypeToInstanceTableName(eamArtifact.getCorrelationType())).add(eamArtifact);
            bulkArtifactsCount++;

            if (bulkArtifactsCount >= bulkArtifactsThreshold) {
                commitAttributeInstancesBulk();
            }
        }
    }

    protected abstract String getConflictClause();

    @Override
    public void commitAttributeInstancesBulk() throws EamDbException {
        List<CorrelationAttributeInstance.Type> artifactTypes = getDefinedCorrelationTypes();

        Connection conn = connect();
        PreparedStatement bulkPs = null;

        try {
            synchronized (bulkArtifacts) {
                if (bulkArtifactsCount == 0) {
                    return;
                }

                for (String tableName : bulkArtifacts.keySet()) {

                    String sql
                            = "INSERT INTO "
                            + tableName
                            + " (case_id, data_source_id, value, file_path, known_status, comment, file_obj_id) "
                            + "VALUES ((SELECT id FROM cases WHERE case_uid=? LIMIT 1), "
                            + "(SELECT id FROM data_sources WHERE datasource_obj_id=? AND case_id=? LIMIT 1), ?, ?, ?, ?, ?) "
                            + getConflictClause();

                    bulkPs = conn.prepareStatement(sql);

                    Collection<CorrelationAttributeInstance> eamArtifacts = bulkArtifacts.get(tableName);
                    for (CorrelationAttributeInstance eamArtifact : eamArtifacts) {

                        if (!eamArtifact.getCorrelationValue().isEmpty()) {

                            if (eamArtifact.getCorrelationCase() == null) {
                                throw new EamDbException("CorrelationAttributeInstance case is null for: "
                                        + "\n\tCorrelationArtifact ID: " + eamArtifact.getID()
                                        + "\n\tCorrelationArtifact Type: " + eamArtifact.getCorrelationType().getDisplayName()
                                        + "\n\tCorrelationArtifact Value: " + eamArtifact.getCorrelationValue());
                            }
                            if (eamArtifact.getCorrelationDataSource() == null) {
                                throw new EamDbException("CorrelationAttributeInstance data source is null for: "
                                        + "\n\tCorrelationArtifact ID: " + eamArtifact.getID()
                                        + "\n\tCorrelationArtifact Type: " + eamArtifact.getCorrelationType().getDisplayName()
                                        + "\n\tCorrelationArtifact Value: " + eamArtifact.getCorrelationValue());
                            }
                            if (eamArtifact.getKnownStatus() == null) {
                                throw new EamDbException("CorrelationAttributeInstance known status is null for: "
                                        + "\n\tCorrelationArtifact ID: " + eamArtifact.getID()
                                        + "\n\tCorrelationArtifact Type: " + eamArtifact.getCorrelationType().getDisplayName()
                                        + "\n\tCorrelationArtifact Value: " + eamArtifact.getCorrelationValue()
                                        + "\n\tEam Instance: "
                                        + "\n\t\tCaseId: " + eamArtifact.getCorrelationDataSource().getCaseID()
                                        + "\n\t\tDeviceID: " + eamArtifact.getCorrelationDataSource().getDeviceID());
                            }

                            if (eamArtifact.getCorrelationValue().length() < MAX_VALUE_LENGTH) {
                                bulkPs.setString(1, eamArtifact.getCorrelationCase().getCaseUUID());
                                bulkPs.setLong(2, eamArtifact.getCorrelationDataSource().getDataSourceObjectID());
                                bulkPs.setInt(3, eamArtifact.getCorrelationDataSource().getCaseID());
                                bulkPs.setString(4, eamArtifact.getCorrelationValue());
                                bulkPs.setString(5, eamArtifact.getFilePath());
                                bulkPs.setByte(6, eamArtifact.getKnownStatus().getFileKnownValue());
                                if ("".equals(eamArtifact.getComment())) {
                                    bulkPs.setNull(7, Types.INTEGER);
                                } else {
                                    bulkPs.setString(7, eamArtifact.getComment());
                                }
                                bulkPs.setLong(8, eamArtifact.getFileObjectId());
                                bulkPs.addBatch();
                            } else {
                                logger.log(Level.WARNING, ("Artifact value too long for central repository."
                                        + "\n\tCorrelationArtifact ID: " + eamArtifact.getID()
                                        + "\n\tCorrelationArtifact Type: " + eamArtifact.getCorrelationType().getDisplayName()
                                        + "\n\tCorrelationArtifact Value: " + eamArtifact.getCorrelationValue())
                                        + "\n\tEam Instance: "
                                        + "\n\t\tCaseId: " + eamArtifact.getCorrelationDataSource().getCaseID()
                                        + "\n\t\tDeviceID: " + eamArtifact.getCorrelationDataSource().getDeviceID()
                                        + "\n\t\tFilePath: " + eamArtifact.getFilePath());
                            }
                        }

                    }

                    bulkPs.executeBatch();
                    bulkArtifacts.get(tableName).clear();
                }

                TimingMetric timingMetric = HealthMonitor.getTimingMetric("Correlation Engine: Bulk insert");
                HealthMonitor.submitTimingMetric(timingMetric);

                // Reset state
                bulkArtifactsCount = 0;
            }
        } catch (SQLException ex) {
            throw new EamDbException("Error inserting bulk artifacts.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(bulkPs);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public void bulkInsertCases(List<CorrelationCase> cases) throws EamDbException {
        if (cases == null) {
            throw new EamDbException("cases argument is null");
        }

        if (cases.isEmpty()) {
            return;
        }

        Connection conn = connect();

        int counter = 0;
        PreparedStatement bulkPs = null;
        try {
            String sql = "INSERT INTO cases(case_uid, org_id, case_name, creation_date, case_number, "
                    + "examiner_name, examiner_email, examiner_phone, notes) "
                    + "VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?) "
                    + getConflictClause();
            bulkPs = conn.prepareStatement(sql);

            for (CorrelationCase eamCase : cases) {
                bulkPs.setString(1, eamCase.getCaseUUID());
                if (null == eamCase.getOrg()) {
                    bulkPs.setNull(2, Types.INTEGER);
                } else {
                    bulkPs.setInt(2, eamCase.getOrg().getOrgID());
                }
                bulkPs.setString(3, eamCase.getDisplayName());
                bulkPs.setString(4, eamCase.getCreationDate());

                if ("".equals(eamCase.getCaseNumber())) {
                    bulkPs.setNull(5, Types.INTEGER);
                } else {
                    bulkPs.setString(5, eamCase.getCaseNumber());
                }
                if ("".equals(eamCase.getExaminerName())) {
                    bulkPs.setNull(6, Types.INTEGER);
                } else {
                    bulkPs.setString(6, eamCase.getExaminerName());
                }
                if ("".equals(eamCase.getExaminerEmail())) {
                    bulkPs.setNull(7, Types.INTEGER);
                } else {
                    bulkPs.setString(7, eamCase.getExaminerEmail());
                }
                if ("".equals(eamCase.getExaminerPhone())) {
                    bulkPs.setNull(8, Types.INTEGER);
                } else {
                    bulkPs.setString(8, eamCase.getExaminerPhone());
                }
                if ("".equals(eamCase.getNotes())) {
                    bulkPs.setNull(9, Types.INTEGER);
                } else {
                    bulkPs.setString(9, eamCase.getNotes());
                }

                bulkPs.addBatch();

                counter++;

                // limit a batch's max size to bulkArtifactsThreshold
                if (counter >= bulkArtifactsThreshold) {
                    bulkPs.executeBatch();
                    counter = 0;
                }
            }
            // send the remaining batch records
            bulkPs.executeBatch();
        } catch (SQLException ex) {
            throw new EamDbException("Error inserting bulk cases.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(bulkPs);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public void updateAttributeInstanceComment(CorrelationAttributeInstance eamArtifact) throws EamDbException {

        if (eamArtifact == null) {
            throw new EamDbException("CorrelationAttributeInstance is null");
        }
        if (eamArtifact.getCorrelationCase() == null) {
            throw new EamDbException("Correlation case is null");
        }
        if (eamArtifact.getCorrelationDataSource() == null) {
            throw new EamDbException("Correlation data source is null");
        }
        Connection conn = connect();
        PreparedStatement preparedQuery = null;
        String tableName = EamDbUtil.correlationTypeToInstanceTableName(eamArtifact.getCorrelationType());
        String sqlUpdate
                = "UPDATE "
                + tableName
                + " SET comment=? "
                + "WHERE case_id=? "
                + "AND data_source_id=? "
                + "AND value=? "
                + "AND file_path=?";

        try {
            preparedQuery = conn.prepareStatement(sqlUpdate);
            preparedQuery.setString(1, eamArtifact.getComment());
            preparedQuery.setInt(2, eamArtifact.getCorrelationCase().getID());
            preparedQuery.setInt(3, eamArtifact.getCorrelationDataSource().getID());
            preparedQuery.setString(4, eamArtifact.getCorrelationValue());
            preparedQuery.setString(5, eamArtifact.getFilePath().toLowerCase());
            preparedQuery.executeUpdate();
        } catch (SQLException ex) {
            throw new EamDbException("Error getting/setting artifact instance comment=" + eamArtifact.getComment(), ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedQuery);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public CorrelationAttributeInstance getCorrelationAttributeInstance(CorrelationAttributeInstance.Type type, CorrelationCase correlationCase,
            CorrelationDataSource correlationDataSource, long objectID) throws EamDbException, CorrelationAttributeNormalizationException {

        if (correlationCase == null) {
            throw new EamDbException("Correlation case is null");
        }

        Connection conn = connect();

        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;
        CorrelationAttributeInstance correlationAttributeInstance = null;

        try {

            String tableName = EamDbUtil.correlationTypeToInstanceTableName(type);
            String sql
                    = "SELECT id, value, file_path, known_status, comment FROM "
                    + tableName
                    + " WHERE case_id=?"
                    + " AND file_obj_id=?";

            preparedStatement = conn.prepareStatement(sql);
            preparedStatement.setInt(1, correlationCase.getID());
            preparedStatement.setInt(2, (int) objectID);
            resultSet = preparedStatement.executeQuery();
            if (resultSet.next()) {
                int instanceId = resultSet.getInt(1);
                String value = resultSet.getString(2);
                String filePath = resultSet.getString(3);
                int knownStatus = resultSet.getInt(4);
                String comment = resultSet.getString(5);

                correlationAttributeInstance = new CorrelationAttributeInstance(type, value,
                        instanceId, correlationCase, correlationDataSource, filePath, comment, TskData.FileKnown.valueOf((byte) knownStatus), objectID);
            }
        } catch (SQLException ex) {
            throw new EamDbException("Error getting notable artifact instances.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }

        return correlationAttributeInstance;
    }

    @Override
    public CorrelationAttributeInstance getCorrelationAttributeInstance(CorrelationAttributeInstance.Type type, CorrelationCase correlationCase,
            CorrelationDataSource correlationDataSource, String value, String filePath) throws EamDbException, CorrelationAttributeNormalizationException {

        if (correlationCase == null) {
            throw new EamDbException("Correlation case is null");
        }
        if (correlationDataSource == null) {
            throw new EamDbException("Correlation data source is null");
        }
        if (filePath == null) {
            throw new EamDbException("Correlation file path is null");
        }

        Connection conn = connect();

        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;
        CorrelationAttributeInstance correlationAttributeInstance = null;

        try {
            String normalizedValue = CorrelationAttributeNormalizer.normalize(type, value);

            String tableName = EamDbUtil.correlationTypeToInstanceTableName(type);
            String sql
                    = "SELECT id, known_status, comment FROM "
                    + tableName
                    + " WHERE case_id=?"
                    + " AND data_source_id=?"
                    + " AND value=?"
                    + " AND file_path=?";

            preparedStatement = conn.prepareStatement(sql);
            preparedStatement.setInt(1, correlationCase.getID());
            preparedStatement.setInt(2, correlationDataSource.getID());
            preparedStatement.setString(3, normalizedValue);
            preparedStatement.setString(4, filePath.toLowerCase());
            resultSet = preparedStatement.executeQuery();
            if (resultSet.next()) {
                int instanceId = resultSet.getInt(1);
                int knownStatus = resultSet.getInt(2);
                String comment = resultSet.getString(3);
                //null objectId used because we only fall back to using this method when objectID was not available
                correlationAttributeInstance = new CorrelationAttributeInstance(type, value,
                        instanceId, correlationCase, correlationDataSource, filePath, comment, TskData.FileKnown.valueOf((byte) knownStatus), null);
            }
        } catch (SQLException ex) {
            throw new EamDbException("Error getting notable artifact instances.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }

        return correlationAttributeInstance;
    }

    @Override
    public void setAttributeInstanceKnownStatus(CorrelationAttributeInstance eamArtifact, TskData.FileKnown knownStatus) throws EamDbException {
        if (eamArtifact == null) {
            throw new EamDbException("CorrelationAttribute is null");
        }
        if (knownStatus == null) {
            throw new EamDbException("Known status is null");
        }

        if (eamArtifact.getCorrelationCase() == null) {
            throw new EamDbException("Correlation case is null");
        }
        if (eamArtifact.getCorrelationDataSource() == null) {
            throw new EamDbException("Correlation data source is null");
        }

        Connection conn = connect();

        PreparedStatement preparedUpdate = null;
        PreparedStatement preparedQuery = null;
        ResultSet resultSet = null;

        String tableName = EamDbUtil.correlationTypeToInstanceTableName(eamArtifact.getCorrelationType());

        String sqlQuery
                = "SELECT id FROM "
                + tableName
                + " WHERE case_id=? "
                + "AND data_source_id=? "
                + "AND value=? "
                + "AND file_path=?";

        String sqlUpdate
                = "UPDATE "
                + tableName
                + " SET known_status=?, comment=? "
                + "WHERE id=?";

        try {
            preparedQuery = conn.prepareStatement(sqlQuery);
            preparedQuery.setInt(1, eamArtifact.getCorrelationCase().getID());
            preparedQuery.setInt(2, eamArtifact.getCorrelationDataSource().getID());
            preparedQuery.setString(3, eamArtifact.getCorrelationValue());
            preparedQuery.setString(4, eamArtifact.getFilePath());
            resultSet = preparedQuery.executeQuery();
            if (resultSet.next()) {
                int instance_id = resultSet.getInt("id");
                preparedUpdate = conn.prepareStatement(sqlUpdate);

                preparedUpdate.setByte(1, knownStatus.getFileKnownValue());
                // NOTE: if the user tags the same instance as BAD multiple times,
                // the comment from the most recent tagging is the one that will
                // prevail in the DB.
                if ("".equals(eamArtifact.getComment())) {
                    preparedUpdate.setNull(2, Types.INTEGER);
                } else {
                    preparedUpdate.setString(2, eamArtifact.getComment());
                }
                preparedUpdate.setInt(3, instance_id);

                preparedUpdate.executeUpdate();
            } else {
                // In this case, the user is tagging something that isn't in the database,
                // which means the case and/or datasource may also not be in the database.
                // We could improve effiency by keeping a list of all datasources and cases
                // in the database, but we don't expect the user to be tagging large numbers
                // of items (that didn't have the CE ingest module run on them) at once.
                CorrelationCase correlationCaseWithId = getCaseByUUID(eamArtifact.getCorrelationCase().getCaseUUID());
                if (null == getDataSource(correlationCaseWithId, eamArtifact.getCorrelationDataSource().getDataSourceObjectID())) {
                    newDataSource(eamArtifact.getCorrelationDataSource());
                }
                eamArtifact.setKnownStatus(knownStatus);
                addArtifactInstance(eamArtifact);
            }

        } catch (SQLException ex) {
            throw new EamDbException("Error getting/setting artifact instance knownStatus=" + knownStatus.getName(), ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedUpdate);
            EamDbUtil.closeStatement(preparedQuery);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public Long getCountArtifactInstancesKnownBad(CorrelationAttributeInstance.Type aType, String value) throws EamDbException, CorrelationAttributeNormalizationException {

        String normalizedValue = CorrelationAttributeNormalizer.normalize(aType, value);

        Connection conn = connect();

        Long badInstances = 0L;
        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;

        String tableName = EamDbUtil.correlationTypeToInstanceTableName(aType);
        String sql
                = "SELECT count(*) FROM "
                + tableName
                + " WHERE value=? AND known_status=?";

        try {
            preparedStatement = conn.prepareStatement(sql);
            preparedStatement.setString(1, normalizedValue);
            preparedStatement.setByte(2, TskData.FileKnown.BAD.getFileKnownValue());
            resultSet = preparedStatement.executeQuery();
            resultSet.next();
            badInstances = resultSet.getLong(1);
        } catch (SQLException ex) {
            throw new EamDbException("Error getting count of notable artifact instances.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }

        return badInstances;
    }

    @Override
    public List<String> getListCasesHavingArtifactInstancesKnownBad(CorrelationAttributeInstance.Type aType, String value) throws EamDbException, CorrelationAttributeNormalizationException {

        String normalizedValue = CorrelationAttributeNormalizer.normalize(aType, value);

        Connection conn = connect();

        Collection<String> caseNames = new LinkedHashSet<>();

        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;

        String tableName = EamDbUtil.correlationTypeToInstanceTableName(aType);
        String sql
                = "SELECT DISTINCT case_name FROM "
                + tableName
                + " INNER JOIN cases ON "
                + tableName
                + ".case_id=cases.id WHERE "
                + tableName
                + ".value=? AND "
                + tableName
                + ".known_status=?";

        try {
            preparedStatement = conn.prepareStatement(sql);
            preparedStatement.setString(1, normalizedValue);
            preparedStatement.setByte(2, TskData.FileKnown.BAD.getFileKnownValue());
            resultSet = preparedStatement.executeQuery();
            while (resultSet.next()) {
                caseNames.add(resultSet.getString("case_name"));
            }
        } catch (SQLException ex) {
            throw new EamDbException("Error getting notable artifact instances.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }

        return caseNames.stream().collect(Collectors.toList());
    }

    @Override
    public void deleteReferenceSet(int referenceSetID) throws EamDbException {
        deleteReferenceSetEntries(referenceSetID);
        deleteReferenceSetEntry(referenceSetID);
    }

    private void deleteReferenceSetEntry(int referenceSetID) throws EamDbException {
        Connection conn = connect();

        PreparedStatement preparedStatement = null;
        String sql = "DELETE FROM reference_sets WHERE id=?";

        try {
            preparedStatement = conn.prepareStatement(sql);
            preparedStatement.setInt(1, referenceSetID);
            preparedStatement.executeUpdate();
        } catch (SQLException ex) {
            throw new EamDbException("Error deleting reference set " + referenceSetID, ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeConnection(conn);
        }
    }

    private void deleteReferenceSetEntries(int referenceSetID) throws EamDbException {
        Connection conn = connect();

        PreparedStatement preparedStatement = null;
        String sql = "DELETE FROM %s WHERE reference_set_id=?";

        // When other reference types are added, this will need to loop over all the tables
        String fileTableName = EamDbUtil.correlationTypeToReferenceTableName(getCorrelationTypeById(CorrelationAttributeInstance.FILES_TYPE_ID));

        try {
            preparedStatement = conn.prepareStatement(String.format(sql, fileTableName));
            preparedStatement.setInt(1, referenceSetID);
            preparedStatement.executeUpdate();
        } catch (SQLException ex) {
            throw new EamDbException("Error deleting files from reference set " + referenceSetID, ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public boolean referenceSetIsValid(int referenceSetID, String setName, String version) throws EamDbException {
        EamGlobalSet refSet = this.getReferenceSetByID(referenceSetID);
        if (refSet == null) {
            return false;
        }

        return (refSet.getSetName().equals(setName) && refSet.getVersion().equals(version));
    }

    @Override
    public boolean isFileHashInReferenceSet(String hash, int referenceSetID) throws EamDbException, CorrelationAttributeNormalizationException {
        return isValueInReferenceSet(hash, referenceSetID, CorrelationAttributeInstance.FILES_TYPE_ID);
    }

    @Override
    public boolean isValueInReferenceSet(String value, int referenceSetID, int correlationTypeID) throws EamDbException, CorrelationAttributeNormalizationException {

        String normalizeValued = CorrelationAttributeNormalizer.normalize(this.getCorrelationTypeById(correlationTypeID), value);

        Connection conn = connect();

        Long matchingInstances = 0L;
        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;
        String sql = "SELECT count(*) FROM %s WHERE value=? AND reference_set_id=?";

        String fileTableName = EamDbUtil.correlationTypeToReferenceTableName(getCorrelationTypeById(correlationTypeID));

        try {
            preparedStatement = conn.prepareStatement(String.format(sql, fileTableName));
            preparedStatement.setString(1, normalizeValued);
            preparedStatement.setInt(2, referenceSetID);
            resultSet = preparedStatement.executeQuery();
            resultSet.next();
            matchingInstances = resultSet.getLong(1);
        } catch (SQLException ex) {
            throw new EamDbException("Error determining if value (" + normalizeValued + ") is in reference set " + referenceSetID, ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }

        return 0 < matchingInstances;
    }

    @Override
    public boolean isArtifactKnownBadByReference(CorrelationAttributeInstance.Type aType, String value) throws EamDbException, CorrelationAttributeNormalizationException {

        //this should be done here so that we can be certain that aType and value are valid before we proceed
        String normalizeValued = CorrelationAttributeNormalizer.normalize(aType, value);

        // TEMP: Only support file correlation type
        if (aType.getId() != CorrelationAttributeInstance.FILES_TYPE_ID) {
            return false;
        }

        Connection conn = connect();

        Long badInstances = 0L;
        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;
        String sql = "SELECT count(*) FROM %s WHERE value=? AND known_status=?";

        try {
            preparedStatement = conn.prepareStatement(String.format(sql, EamDbUtil.correlationTypeToReferenceTableName(aType)));
            preparedStatement.setString(1, normalizeValued);
            preparedStatement.setByte(2, TskData.FileKnown.BAD.getFileKnownValue());
            resultSet = preparedStatement.executeQuery();
            resultSet.next();
            badInstances = resultSet.getLong(1);
        } catch (SQLException ex) {
            throw new EamDbException("Error determining if artifact is notable by reference.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }

        return 0 < badInstances;
    }

    @Override
    public void processInstanceTable(CorrelationAttributeInstance.Type type, InstanceTableCallback instanceTableCallback) throws EamDbException {
        if (type == null) {
            throw new EamDbException("Correlation type is null");
        }

        if (instanceTableCallback == null) {
            throw new EamDbException("Callback interface is null");
        }

        Connection conn = connect();
        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;
        String tableName = EamDbUtil.correlationTypeToInstanceTableName(type);
        StringBuilder sql = new StringBuilder();
        sql.append("select * from ");
        sql.append(tableName);

        try {
            preparedStatement = conn.prepareStatement(sql.toString());
            resultSet = preparedStatement.executeQuery();
            instanceTableCallback.process(resultSet);
        } catch (SQLException ex) {
            throw new EamDbException("Error getting all artifact instances from instances table", ex);
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public void processInstanceTableWhere(CorrelationAttributeInstance.Type type, String whereClause, InstanceTableCallback instanceTableCallback) throws EamDbException {
        if (type == null) {
            throw new EamDbException("Correlation type is null");
        }

        if (instanceTableCallback == null) {
            throw new EamDbException("Callback interface is null");
        }

        if (whereClause == null) {
            throw new EamDbException("Where clause is null");
        }

        Connection conn = connect();
        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;
        String tableName = EamDbUtil.correlationTypeToInstanceTableName(type);
        StringBuilder sql = new StringBuilder(300);
        sql.append("select * from ")
                .append(tableName)
                .append(" WHERE ")
                .append(whereClause);

        try {
            preparedStatement = conn.prepareStatement(sql.toString());
            resultSet = preparedStatement.executeQuery();
            instanceTableCallback.process(resultSet);
        } catch (SQLException ex) {
            throw new EamDbException("Error getting all artifact instances from instances table", ex);
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public EamOrganization newOrganization(EamOrganization eamOrg) throws EamDbException {
        if (eamOrg == null) {
            throw new EamDbException("EamOrganization is null");
        } else if (eamOrg.getOrgID() != -1) {
            throw new EamDbException("EamOrganization already has an ID");
        }

        Connection conn = connect();
        ResultSet generatedKeys = null;
        PreparedStatement preparedStatement = null;
        String sql = "INSERT INTO organizations(org_name, poc_name, poc_email, poc_phone) VALUES (?, ?, ?, ?) "
                + getConflictClause();

        try {
            preparedStatement = conn.prepareStatement(sql, Statement.RETURN_GENERATED_KEYS);
            preparedStatement.setString(1, eamOrg.getName());
            preparedStatement.setString(2, eamOrg.getPocName());
            preparedStatement.setString(3, eamOrg.getPocEmail());
            preparedStatement.setString(4, eamOrg.getPocPhone());

            preparedStatement.executeUpdate();
            generatedKeys = preparedStatement.getGeneratedKeys();
            if (generatedKeys.next()) {
                eamOrg.setOrgID((int) generatedKeys.getLong(1));
                return eamOrg;
            } else {
                throw new SQLException("Creating user failed, no ID obtained.");
            }
        } catch (SQLException ex) {
            throw new EamDbException("Error inserting new organization.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(generatedKeys);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public List<EamOrganization> getOrganizations() throws EamDbException {
        Connection conn = connect();

        List<EamOrganization> orgs = new ArrayList<>();
        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;
        String sql = "SELECT * FROM organizations";

        try {
            preparedStatement = conn.prepareStatement(sql);
            resultSet = preparedStatement.executeQuery();
            while (resultSet.next()) {
                orgs.add(getEamOrganizationFromResultSet(resultSet));
            }
            return orgs;

        } catch (SQLException ex) {
            throw new EamDbException("Error getting all organizations.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public EamOrganization getOrganizationByID(int orgID) throws EamDbException {
        Connection conn = connect();

        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;
        String sql = "SELECT * FROM organizations WHERE id=?";

        try {
            preparedStatement = conn.prepareStatement(sql);
            preparedStatement.setInt(1, orgID);
            resultSet = preparedStatement.executeQuery();
            resultSet.next();
            return getEamOrganizationFromResultSet(resultSet);

        } catch (SQLException ex) {
            throw new EamDbException("Error getting organization by id.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public EamOrganization getReferenceSetOrganization(int referenceSetID) throws EamDbException {

        EamGlobalSet globalSet = getReferenceSetByID(referenceSetID);
        if (globalSet == null) {
            throw new EamDbException("Reference set with ID " + referenceSetID + " not found");
        }
        return (getOrganizationByID(globalSet.getOrgID()));
    }

    private void testArgument(EamOrganization org) throws EamDbException {
        if (org == null) {
            throw new EamDbException("EamOrganization is null");
        } else if (org.getOrgID() == -1) {
            throw new EamDbException("Organization  has -1 row ID");
        }
    }

    @Override
    public void updateOrganization(EamOrganization updatedOrganization) throws EamDbException {
        testArgument(updatedOrganization);

        Connection conn = connect();
        PreparedStatement preparedStatement = null;
        String sql = "UPDATE organizations SET org_name = ?, poc_name = ?, poc_email = ?, poc_phone = ? WHERE id = ?";
        try {
            preparedStatement = conn.prepareStatement(sql);
            preparedStatement.setString(1, updatedOrganization.getName());
            preparedStatement.setString(2, updatedOrganization.getPocName());
            preparedStatement.setString(3, updatedOrganization.getPocEmail());
            preparedStatement.setString(4, updatedOrganization.getPocPhone());
            preparedStatement.setInt(5, updatedOrganization.getOrgID());
            preparedStatement.executeUpdate();
        } catch (SQLException ex) {
            throw new EamDbException("Error updating organization.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public void deleteOrganization(EamOrganization organizationToDelete) throws EamDbException {
        testArgument(organizationToDelete);

        Connection conn = connect();
        PreparedStatement checkIfUsedStatement = null;
        ResultSet resultSet = null;
        String checkIfUsedSql = "SELECT (select count(*) FROM cases WHERE org_id=?) + (select count(*) FROM reference_sets WHERE org_id=?)";
        PreparedStatement deleteOrgStatement = null;
        String deleteOrgSql = "DELETE FROM organizations WHERE id=?";
        try {
            checkIfUsedStatement = conn.prepareStatement(checkIfUsedSql);
            checkIfUsedStatement.setInt(1, organizationToDelete.getOrgID());
            checkIfUsedStatement.setInt(2, organizationToDelete.getOrgID());
            resultSet = checkIfUsedStatement.executeQuery();
            resultSet.next();
            if (resultSet.getLong(1) > 0) {
                throw new EamDbException("Can not delete organization which is currently in use by a case or reference set in the central repository.");
            }
            deleteOrgStatement = conn.prepareStatement(deleteOrgSql);
            deleteOrgStatement.setInt(1, organizationToDelete.getOrgID());
            deleteOrgStatement.executeUpdate();
        } catch (SQLException ex) {
            throw new EamDbException("Error executing query when attempting to delete organization by id.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(checkIfUsedStatement);
            EamDbUtil.closeStatement(deleteOrgStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public int newReferenceSet(EamGlobalSet eamGlobalSet) throws EamDbException {
        if (eamGlobalSet == null) {
            throw new EamDbException("EamGlobalSet is null");
        }

        if (eamGlobalSet.getFileKnownStatus() == null) {
            throw new EamDbException("File known status on the EamGlobalSet is null");
        }

        if (eamGlobalSet.getType() == null) {
            throw new EamDbException("Type on the EamGlobalSet is null");
        }

        Connection conn = connect();

        PreparedStatement preparedStatement1 = null;
        PreparedStatement preparedStatement2 = null;
        ResultSet resultSet = null;
        String sql1 = "INSERT INTO reference_sets(org_id, set_name, version, known_status, read_only, type, import_date) VALUES (?, ?, ?, ?, ?, ?, ?) "
                + getConflictClause();
        String sql2 = "SELECT id FROM reference_sets WHERE org_id=? AND set_name=? AND version=? AND import_date=? LIMIT 1";

        try {
            preparedStatement1 = conn.prepareStatement(sql1);
            preparedStatement1.setInt(1, eamGlobalSet.getOrgID());
            preparedStatement1.setString(2, eamGlobalSet.getSetName());
            preparedStatement1.setString(3, eamGlobalSet.getVersion());
            preparedStatement1.setInt(4, eamGlobalSet.getFileKnownStatus().getFileKnownValue());
            preparedStatement1.setBoolean(5, eamGlobalSet.isReadOnly());
            preparedStatement1.setInt(6, eamGlobalSet.getType().getId());
            preparedStatement1.setString(7, eamGlobalSet.getImportDate().toString());

            preparedStatement1.executeUpdate();

            preparedStatement2 = conn.prepareStatement(sql2);
            preparedStatement2.setInt(1, eamGlobalSet.getOrgID());
            preparedStatement2.setString(2, eamGlobalSet.getSetName());
            preparedStatement2.setString(3, eamGlobalSet.getVersion());
            preparedStatement2.setString(4, eamGlobalSet.getImportDate().toString());

            resultSet = preparedStatement2.executeQuery();
            resultSet.next();
            return resultSet.getInt("id");

        } catch (SQLException ex) {
            throw new EamDbException("Error inserting new global set.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement1);
            EamDbUtil.closeStatement(preparedStatement2);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public EamGlobalSet getReferenceSetByID(int referenceSetID) throws EamDbException {
        Connection conn = connect();

        PreparedStatement preparedStatement1 = null;
        ResultSet resultSet = null;
        String sql1 = "SELECT * FROM reference_sets WHERE id=?";

        try {
            preparedStatement1 = conn.prepareStatement(sql1);
            preparedStatement1.setInt(1, referenceSetID);
            resultSet = preparedStatement1.executeQuery();
            if (resultSet.next()) {
                return getEamGlobalSetFromResultSet(resultSet);
            } else {
                return null;
            }

        } catch (SQLException ex) {
            throw new EamDbException("Error getting reference set by id.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement1);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public List<EamGlobalSet> getAllReferenceSets(CorrelationAttributeInstance.Type correlationType) throws EamDbException {

        if (correlationType == null) {
            throw new EamDbException("Correlation type is null");
        }

        List<EamGlobalSet> results = new ArrayList<>();
        Connection conn = connect();

        PreparedStatement preparedStatement1 = null;
        ResultSet resultSet = null;
        String sql1 = "SELECT * FROM reference_sets WHERE type=" + correlationType.getId();

        try {
            preparedStatement1 = conn.prepareStatement(sql1);
            resultSet = preparedStatement1.executeQuery();
            while (resultSet.next()) {
                results.add(getEamGlobalSetFromResultSet(resultSet));
            }

        } catch (SQLException ex) {
            throw new EamDbException("Error getting reference sets.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement1);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }
        return results;
    }

    @Override
    public void addReferenceInstance(EamGlobalFileInstance eamGlobalFileInstance, CorrelationAttributeInstance.Type correlationType) throws EamDbException {
        if (eamGlobalFileInstance.getKnownStatus() == null) {
            throw new EamDbException("Known status of EamGlobalFileInstance is null");
        }
        if (correlationType == null) {
            throw new EamDbException("Correlation type is null");
        }

        Connection conn = connect();

        PreparedStatement preparedStatement = null;

        String sql = "INSERT INTO %s(reference_set_id, value, known_status, comment) VALUES (?, ?, ?, ?) "
                + getConflictClause();

        try {
            preparedStatement = conn.prepareStatement(String.format(sql, EamDbUtil.correlationTypeToReferenceTableName(correlationType)));
            preparedStatement.setInt(1, eamGlobalFileInstance.getGlobalSetID());
            preparedStatement.setString(2, eamGlobalFileInstance.getMD5Hash());
            preparedStatement.setByte(3, eamGlobalFileInstance.getKnownStatus().getFileKnownValue());
            preparedStatement.setString(4, eamGlobalFileInstance.getComment());
            preparedStatement.executeUpdate();
        } catch (SQLException ex) {
            throw new EamDbException("Error inserting new reference instance into reference_ table.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public boolean referenceSetExists(String referenceSetName, String version) throws EamDbException {
        Connection conn = connect();

        PreparedStatement preparedStatement1 = null;
        ResultSet resultSet = null;
        String sql1 = "SELECT * FROM reference_sets WHERE set_name=? AND version=?";

        try {
            preparedStatement1 = conn.prepareStatement(sql1);
            preparedStatement1.setString(1, referenceSetName);
            preparedStatement1.setString(2, version);
            resultSet = preparedStatement1.executeQuery();
            return (resultSet.next());

        } catch (SQLException ex) {
            throw new EamDbException("Error testing whether reference set exists (name: " + referenceSetName
                    + " version: " + version, ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement1);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public void bulkInsertReferenceTypeEntries(Set<EamGlobalFileInstance> globalInstances, CorrelationAttributeInstance.Type contentType) throws EamDbException {
        if (contentType == null) {
            throw new EamDbException("Correlation type is null");
        }
        if (globalInstances == null) {
            throw new EamDbException("Null set of EamGlobalFileInstance");
        }

        Connection conn = connect();

        PreparedStatement bulkPs = null;
        try {
            conn.setAutoCommit(false);

            // FUTURE: have a separate global_files table for each Type.
            String sql = "INSERT INTO %s(reference_set_id, value, known_status, comment) VALUES (?, ?, ?, ?) "
                    + getConflictClause();

            bulkPs = conn.prepareStatement(String.format(sql, EamDbUtil.correlationTypeToReferenceTableName(contentType)));

            for (EamGlobalFileInstance globalInstance : globalInstances) {
                if (globalInstance.getKnownStatus() == null) {
                    throw new EamDbException("EamGlobalFileInstance with value " + globalInstance.getMD5Hash() + " has null known status");
                }

                bulkPs.setInt(1, globalInstance.getGlobalSetID());
                bulkPs.setString(2, globalInstance.getMD5Hash());
                bulkPs.setByte(3, globalInstance.getKnownStatus().getFileKnownValue());
                bulkPs.setString(4, globalInstance.getComment());
                bulkPs.addBatch();
            }

            bulkPs.executeBatch();
            conn.commit();
        } catch (SQLException | EamDbException ex) {
            try {
                conn.rollback();
            } catch (SQLException ex2) {
                // We're alredy in an error state
            }
            throw new EamDbException("Error inserting bulk artifacts.", ex); // NON-NLS           
        } finally {
            EamDbUtil.closeStatement(bulkPs);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public List<EamGlobalFileInstance> getReferenceInstancesByTypeValue(CorrelationAttributeInstance.Type aType, String aValue) throws EamDbException, CorrelationAttributeNormalizationException {
        String normalizeValued = CorrelationAttributeNormalizer.normalize(aType, aValue);

        Connection conn = connect();

        List<EamGlobalFileInstance> globalFileInstances = new ArrayList<>();
        PreparedStatement preparedStatement1 = null;
        ResultSet resultSet = null;
        String sql1 = "SELECT * FROM %s WHERE value=?";

        try {
            preparedStatement1 = conn.prepareStatement(String.format(sql1, EamDbUtil.correlationTypeToReferenceTableName(aType)));
            preparedStatement1.setString(1, normalizeValued);
            resultSet = preparedStatement1.executeQuery();
            while (resultSet.next()) {
                globalFileInstances.add(getEamGlobalFileInstanceFromResultSet(resultSet));
            }

        } catch (SQLException ex) {
            throw new EamDbException("Error getting reference instances by type and value.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement1);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }

        return globalFileInstances;
    }

    @Override
    public int newCorrelationType(CorrelationAttributeInstance.Type newType) throws EamDbException {
        if (newType == null) {
            throw new EamDbException("Correlation type is null");
        }
        int typeId;
        if (-1 == newType.getId()) {
            typeId = newCorrelationTypeNotKnownId(newType);
        } else {
            typeId = newCorrelationTypeKnownId(newType);
        }

        return typeId;
    }

    public int newCorrelationTypeNotKnownId(CorrelationAttributeInstance.Type newType) throws EamDbException {
        Connection conn = connect();

        PreparedStatement preparedStatement = null;
        PreparedStatement preparedStatementQuery = null;
        ResultSet resultSet = null;
        int typeId = 0;
        String insertSql;
        String querySql;
        // if we have a known ID, use it, if not (is -1) let the db assign it.
        insertSql = "INSERT INTO correlation_types(display_name, db_table_name, supported, enabled) VALUES (?, ?, ?, ?) " + getConflictClause();

        querySql = "SELECT * FROM correlation_types WHERE display_name=? AND db_table_name=?";

        try {
            preparedStatement = conn.prepareStatement(insertSql);

            preparedStatement.setString(1, newType.getDisplayName());
            preparedStatement.setString(2, newType.getDbTableName());
            preparedStatement.setInt(3, newType.isSupported() ? 1 : 0);
            preparedStatement.setInt(4, newType.isEnabled() ? 1 : 0);

            preparedStatement.executeUpdate();

            preparedStatementQuery = conn.prepareStatement(querySql);
            preparedStatementQuery.setString(1, newType.getDisplayName());
            preparedStatementQuery.setString(2, newType.getDbTableName());

            resultSet = preparedStatementQuery.executeQuery();
            if (resultSet.next()) {
                CorrelationAttributeInstance.Type correlationType = getCorrelationTypeFromResultSet(resultSet);
                typeId = correlationType.getId();
            }
        } catch (SQLException ex) {
            throw new EamDbException("Error inserting new correlation type.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeStatement(preparedStatementQuery);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }
        return typeId;
    }

    private int newCorrelationTypeKnownId(CorrelationAttributeInstance.Type newType) throws EamDbException {
        Connection conn = connect();

        PreparedStatement preparedStatement = null;
        PreparedStatement preparedStatementQuery = null;
        ResultSet resultSet = null;
        int typeId = 0;
        String insertSql;
        String querySql;
        // if we have a known ID, use it, if not (is -1) let the db assign it.
        insertSql = "INSERT INTO correlation_types(id, display_name, db_table_name, supported, enabled) VALUES (?, ?, ?, ?, ?) " + getConflictClause();

        querySql = "SELECT * FROM correlation_types WHERE display_name=? AND db_table_name=?";

        try {
            preparedStatement = conn.prepareStatement(insertSql);

            preparedStatement.setInt(1, newType.getId());
            preparedStatement.setString(2, newType.getDisplayName());
            preparedStatement.setString(3, newType.getDbTableName());
            preparedStatement.setInt(4, newType.isSupported() ? 1 : 0);
            preparedStatement.setInt(5, newType.isEnabled() ? 1 : 0);

            preparedStatement.executeUpdate();

            preparedStatementQuery = conn.prepareStatement(querySql);
            preparedStatementQuery.setString(1, newType.getDisplayName());
            preparedStatementQuery.setString(2, newType.getDbTableName());

            resultSet = preparedStatementQuery.executeQuery();
            if (resultSet.next()) {
                CorrelationAttributeInstance.Type correlationType = getCorrelationTypeFromResultSet(resultSet);
                typeId = correlationType.getId();
            }
        } catch (SQLException ex) {
            throw new EamDbException("Error inserting new correlation type.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeStatement(preparedStatementQuery);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }
        return typeId;
    }

    @Override
    public List<CorrelationAttributeInstance.Type> getDefinedCorrelationTypes() throws EamDbException {
        Connection conn = connect();

        List<CorrelationAttributeInstance.Type> aTypes = new ArrayList<>();
        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;
        String sql = "SELECT * FROM correlation_types";

        try {
            preparedStatement = conn.prepareStatement(sql);
            resultSet = preparedStatement.executeQuery();
            while (resultSet.next()) {
                aTypes.add(getCorrelationTypeFromResultSet(resultSet));
            }
            return aTypes;

        } catch (SQLException ex) {
            throw new EamDbException("Error getting all correlation types.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public List<CorrelationAttributeInstance.Type> getEnabledCorrelationTypes() throws EamDbException {
        Connection conn = connect();

        List<CorrelationAttributeInstance.Type> aTypes = new ArrayList<>();
        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;
        String sql = "SELECT * FROM correlation_types WHERE enabled=1";

        try {
            preparedStatement = conn.prepareStatement(sql);
            resultSet = preparedStatement.executeQuery();
            while (resultSet.next()) {
                aTypes.add(getCorrelationTypeFromResultSet(resultSet));
            }
            return aTypes;

        } catch (SQLException ex) {
            throw new EamDbException("Error getting enabled correlation types.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public List<CorrelationAttributeInstance.Type> getSupportedCorrelationTypes() throws EamDbException {
        Connection conn = connect();

        List<CorrelationAttributeInstance.Type> aTypes = new ArrayList<>();
        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;
        String sql = "SELECT * FROM correlation_types WHERE supported=1";

        try {
            preparedStatement = conn.prepareStatement(sql);
            resultSet = preparedStatement.executeQuery();
            while (resultSet.next()) {
                aTypes.add(getCorrelationTypeFromResultSet(resultSet));
            }
            return aTypes;

        } catch (SQLException ex) {
            throw new EamDbException("Error getting supported correlation types.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }
    }

    @Override
    public void updateCorrelationType(CorrelationAttributeInstance.Type aType) throws EamDbException {
        Connection conn = connect();

        PreparedStatement preparedStatement = null;
        String sql = "UPDATE correlation_types SET display_name=?, db_table_name=?, supported=?, enabled=? WHERE id=?";

        try {
            preparedStatement = conn.prepareStatement(sql);
            preparedStatement.setString(1, aType.getDisplayName());
            preparedStatement.setString(2, aType.getDbTableName());
            preparedStatement.setInt(3, aType.isSupported() ? 1 : 0);
            preparedStatement.setInt(4, aType.isEnabled() ? 1 : 0);
            preparedStatement.setInt(5, aType.getId());
            preparedStatement.executeUpdate();
            typeCache.put(aType.getId(), aType);
        } catch (SQLException ex) {
            throw new EamDbException("Error updating correlation type.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeConnection(conn);
        }

    }

    @Override
    public CorrelationAttributeInstance.Type getCorrelationTypeById(int typeId) throws EamDbException {
        try {
            return typeCache.get(typeId, () -> getCorrelationTypeByIdFromCr(typeId));
        } catch (CacheLoader.InvalidCacheLoadException ignored) {
            //lambda valueloader returned a null value and cache can not store null values this is normal if the correlation type does not exist in the central repo yet
            return null;
        } catch (ExecutionException ex) {
            throw new EamDbException("Error getting correlation type", ex);
        }
    }

    private CorrelationAttributeInstance.Type getCorrelationTypeByIdFromCr(int typeId) throws EamDbException {
        Connection conn = connect();

        CorrelationAttributeInstance.Type aType;
        PreparedStatement preparedStatement = null;
        ResultSet resultSet = null;
        String sql = "SELECT * FROM correlation_types WHERE id=?";

        try {
            preparedStatement = conn.prepareStatement(sql);
            preparedStatement.setInt(1, typeId);
            resultSet = preparedStatement.executeQuery();
            if (resultSet.next()) {
                aType = getCorrelationTypeFromResultSet(resultSet);
                return aType;
            } else {
                throw new EamDbException("Failed to find entry for correlation type ID = " + typeId);
            }

        } catch (SQLException ex) {
            throw new EamDbException("Error getting correlation type by id.", ex); // NON-NLS
        } finally {
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeConnection(conn);
        }
    }

    private CorrelationCase getEamCaseFromResultSet(ResultSet resultSet) throws SQLException {
        if (null == resultSet) {
            return null;
        }

        EamOrganization eamOrg = null;

        resultSet.getInt("org_id");
        if (!resultSet.wasNull()) {

            eamOrg = new EamOrganization(resultSet.getInt("org_id"),
                    resultSet.getString("org_name"),
                    resultSet.getString("poc_name"),
                    resultSet.getString("poc_email"),
                    resultSet.getString("poc_phone"));
        }

        CorrelationCase eamCase = new CorrelationCase(resultSet.getInt("case_id"), resultSet.getString("case_uid"), eamOrg, resultSet.getString("case_name"),
                resultSet.getString("creation_date"), resultSet.getString("case_number"), resultSet.getString("examiner_name"),
                resultSet.getString("examiner_email"), resultSet.getString("examiner_phone"), resultSet.getString("notes"));

        return eamCase;
    }

    private CorrelationDataSource getEamDataSourceFromResultSet(ResultSet resultSet) throws SQLException {
        if (null == resultSet) {
            return null;
        }

        CorrelationDataSource eamDataSource = new CorrelationDataSource(
                resultSet.getInt("case_id"),
                resultSet.getInt("id"),
                resultSet.getString("device_id"),
                resultSet.getString("name"),
                resultSet.getLong("datasource_obj_id"),
                resultSet.getString("md5"),
                resultSet.getString("sha1"),
                resultSet.getString("sha256")
        );

        return eamDataSource;
    }

    private CorrelationAttributeInstance.Type getCorrelationTypeFromResultSet(ResultSet resultSet) throws EamDbException, SQLException {
        if (null == resultSet) {
            return null;
        }

        CorrelationAttributeInstance.Type eamArtifactType = new CorrelationAttributeInstance.Type(
                resultSet.getInt("id"),
                resultSet.getString("display_name"),
                resultSet.getString("db_table_name"),
                resultSet.getBoolean("supported"),
                resultSet.getBoolean("enabled")
        );

        return eamArtifactType;
    }

    private CorrelationAttributeInstance getEamArtifactInstanceFromResultSet(ResultSet resultSet, CorrelationAttributeInstance.Type aType) throws SQLException, EamDbException, CorrelationAttributeNormalizationException {
        if (null == resultSet) {
            return null;
        }

        EamOrganization eamOrg = new EamOrganization(resultSet.getInt("org_id"),
                resultSet.getString("org_name"),
                resultSet.getString("poc_name"),
                resultSet.getString("poc_email"),
                resultSet.getString("poc_phone"));

        return new CorrelationAttributeInstance(
                aType,
                resultSet.getString("value"),
                resultSet.getInt("instance_id"),
                new CorrelationCase(resultSet.getInt("id"), resultSet.getString("case_uid"), eamOrg, resultSet.getString("case_name"),
                        resultSet.getString("creation_date"), resultSet.getString("case_number"), resultSet.getString("examiner_name"),
                        resultSet.getString("examiner_email"), resultSet.getString("examiner_phone"), resultSet.getString("notes")),
                new CorrelationDataSource(
                        resultSet.getInt("id"), resultSet.getInt("data_source_id"), resultSet.getString("device_id"), resultSet.getString("name"),
                        resultSet.getLong("datasource_obj_id"), resultSet.getString("md5"), resultSet.getString("sha1"), resultSet.getString("sha256")),
                resultSet.getString("file_path"),
                resultSet.getString("comment"),
                TskData.FileKnown.valueOf(resultSet.getByte("known_status")),
                resultSet.getLong("file_obj_id"));
    }

    private EamOrganization getEamOrganizationFromResultSet(ResultSet resultSet) throws SQLException {
        if (null == resultSet) {
            return null;
        }

        return new EamOrganization(
                resultSet.getInt("id"),
                resultSet.getString("org_name"),
                resultSet.getString("poc_name"),
                resultSet.getString("poc_email"),
                resultSet.getString("poc_phone")
        );
    }

    private EamGlobalSet getEamGlobalSetFromResultSet(ResultSet resultSet) throws SQLException, EamDbException {
        if (null == resultSet) {
            return null;
        }

        return new EamGlobalSet(
                resultSet.getInt("id"),
                resultSet.getInt("org_id"),
                resultSet.getString("set_name"),
                resultSet.getString("version"),
                TskData.FileKnown.valueOf(resultSet.getByte("known_status")),
                resultSet.getBoolean("read_only"),
                EamDb.getInstance().getCorrelationTypeById(resultSet.getInt("type")),
                LocalDate.parse(resultSet.getString("import_date"))
        );
    }

    private EamGlobalFileInstance getEamGlobalFileInstanceFromResultSet(ResultSet resultSet) throws SQLException, EamDbException, CorrelationAttributeNormalizationException {
        if (null == resultSet) {
            return null;
        }

        return new EamGlobalFileInstance(
                resultSet.getInt("id"),
                resultSet.getInt("reference_set_id"),
                resultSet.getString("value"),
                TskData.FileKnown.valueOf(resultSet.getByte("known_status")),
                resultSet.getString("comment")
        );
    }

    abstract boolean doesColumnExist(Connection conn, String tableName, String columnName) throws SQLException;

    @Messages({"AbstractSqlEamDb.upgradeSchema.incompatible=The selected Central Repository is not compatible with the current version of the application, please upgrade the application if you wish to use this Central Repository."})
    @Override
    public void upgradeSchema() throws EamDbException, SQLException, IncompatibleCentralRepoException {

        ResultSet resultSet = null;
        Statement statement = null;
        PreparedStatement preparedStatement = null;
        Connection conn = null;
        EamDbPlatformEnum selectedPlatform = null;
        try {

            conn = connect(false);
            conn.setAutoCommit(false);
            statement = conn.createStatement();
            selectedPlatform = EamDbPlatformEnum.getSelectedPlatform();
            int minorVersion = 0;
            String minorVersionStr = null;
            resultSet = statement.executeQuery("SELECT value FROM db_info WHERE name='" + AbstractSqlEamDb.SCHEMA_MINOR_VERSION_KEY + "'");
            if (resultSet.next()) {
                minorVersionStr = resultSet.getString("value");
                try {
                    minorVersion = Integer.parseInt(minorVersionStr);
                } catch (NumberFormatException ex) {
                    throw new EamDbException("Bad value for schema minor version (" + minorVersionStr + ") - database is corrupt", ex);
                }
            } else {
                throw new EamDbException("Failed to read schema minor version from db_info table");
            }

            int majorVersion = 0;
            String majorVersionStr = null;
            resultSet = statement.executeQuery("SELECT value FROM db_info WHERE name='" + AbstractSqlEamDb.SCHEMA_MAJOR_VERSION_KEY + "'");
            if (resultSet.next()) {
                majorVersionStr = resultSet.getString("value");
                try {
                    majorVersion = Integer.parseInt(majorVersionStr);
                } catch (NumberFormatException ex) {
                    throw new EamDbException("Bad value for schema version (" + majorVersionStr + ") - database is corrupt", ex);
                }
            } else {
                throw new EamDbException("Failed to read schema major version from db_info table");
            }

            /*
             * IMPORTANT: The code that follows had a bug in it prior to Autopsy
             * 4.10.0. The consequence of the bug is that the schema version
             * number is always reset to 1.0 or 1.1 if a Central Repository is
             * opened by an Autopsy 4.9.1 or earlier client. To cope with this,
             * there is an effort in updates to 1.2 and greater to not retry
             * schema updates that may already have been done once.
             */
            CaseDbSchemaVersionNumber dbSchemaVersion = new CaseDbSchemaVersionNumber(majorVersion, minorVersion);

            //compare the major versions for compatability 
            //we can not use the CaseDbSchemaVersionNumber.isCompatible method 
            //because it is specific to case db schema versions only supporting major versions greater than 1
            if (SOFTWARE_CR_DB_SCHEMA_VERSION.getMajor() < dbSchemaVersion.getMajor()) {
                throw new IncompatibleCentralRepoException(Bundle.AbstractSqlEamDb_upgradeSchema_incompatible());
            }
            if (dbSchemaVersion.equals(SOFTWARE_CR_DB_SCHEMA_VERSION)) {
                logger.log(Level.INFO, "Central Repository is up to date");
                return;
            }
            if (dbSchemaVersion.compareTo(SOFTWARE_CR_DB_SCHEMA_VERSION) > 0) {
                logger.log(Level.INFO, "Central Repository is of newer version than software creates");
                return;
            }

            /*
             * Update to 1.1
             */
            if (dbSchemaVersion.compareTo(new CaseDbSchemaVersionNumber(1, 1)) < 0) {
                statement.execute("ALTER TABLE reference_sets ADD COLUMN known_status INTEGER;"); //NON-NLS
                statement.execute("ALTER TABLE reference_sets ADD COLUMN read_only BOOLEAN;"); //NON-NLS
                statement.execute("ALTER TABLE reference_sets ADD COLUMN type INTEGER;"); //NON-NLS

                // There's an outide chance that the user has already made an organization with the default name,
                // and the default org being missing will not impact any database operations, so continue on
                // regardless of whether this succeeds.
                EamDbUtil.insertDefaultOrganization(conn);
            }

            /*
             * Update to 1.2
             */
            if (dbSchemaVersion.compareTo(new CaseDbSchemaVersionNumber(1, 2)) < 0) {
                final String addIntegerColumnTemplate = "ALTER TABLE %s ADD COLUMN %s INTEGER;";  //NON-NLS
                final String addSsidTableTemplate;
                final String addCaseIdIndexTemplate;
                final String addDataSourceIdIndexTemplate;
                final String addValueIndexTemplate;
                final String addKnownStatusIndexTemplate;
                final String addObjectIdIndexTemplate;

                final String addAttributeSql;
                //get the data base specific code for creating a new _instance table
                switch (selectedPlatform) {
                    case POSTGRESQL:
                        addAttributeSql = "INSERT INTO correlation_types(id, display_name, db_table_name, supported, enabled) VALUES (?, ?, ?, ?, ?) " + getConflictClause();  //NON-NLS

                        addSsidTableTemplate = PostgresEamDbSettings.getCreateArtifactInstancesTableTemplate();
                        addCaseIdIndexTemplate = PostgresEamDbSettings.getAddCaseIdIndexTemplate();
                        addDataSourceIdIndexTemplate = PostgresEamDbSettings.getAddDataSourceIdIndexTemplate();
                        addValueIndexTemplate = PostgresEamDbSettings.getAddValueIndexTemplate();
                        addKnownStatusIndexTemplate = PostgresEamDbSettings.getAddKnownStatusIndexTemplate();
                        addObjectIdIndexTemplate = PostgresEamDbSettings.getAddObjectIdIndexTemplate();
                        break;
                    case SQLITE:
                        addAttributeSql = "INSERT OR IGNORE INTO correlation_types(id, display_name, db_table_name, supported, enabled) VALUES (?, ?, ?, ?, ?)";  //NON-NLS

                        addSsidTableTemplate = SqliteEamDbSettings.getCreateArtifactInstancesTableTemplate();
                        addCaseIdIndexTemplate = SqliteEamDbSettings.getAddCaseIdIndexTemplate();
                        addDataSourceIdIndexTemplate = SqliteEamDbSettings.getAddDataSourceIdIndexTemplate();
                        addValueIndexTemplate = SqliteEamDbSettings.getAddValueIndexTemplate();
                        addKnownStatusIndexTemplate = SqliteEamDbSettings.getAddKnownStatusIndexTemplate();
                        addObjectIdIndexTemplate = SqliteEamDbSettings.getAddObjectIdIndexTemplate();
                        break;
                    default:
                        throw new EamDbException("Currently selected database platform \"" + selectedPlatform.name() + "\" can not be upgraded.");
                }
                final String dataSourcesTableName = "data_sources";
                final String dataSourceObjectIdColumnName = "datasource_obj_id";
                if (!doesColumnExist(conn, dataSourcesTableName, dataSourceObjectIdColumnName)) {
                    statement.execute(String.format(addIntegerColumnTemplate, dataSourcesTableName, dataSourceObjectIdColumnName)); //NON-NLS
                }
                final String dataSourceObjectIdIndexTemplate = "CREATE INDEX IF NOT EXISTS datasource_object_id ON data_sources (%s)";
                statement.execute(String.format(dataSourceObjectIdIndexTemplate, dataSourceObjectIdColumnName));
                List<String> instaceTablesToAdd = new ArrayList<>();
                //update central repository to be able to store new correlation attributes 
                final String wirelessNetworksDbTableName = "wireless_networks";
                instaceTablesToAdd.add(wirelessNetworksDbTableName + "_instances");
                final String macAddressDbTableName = "mac_address";
                instaceTablesToAdd.add(macAddressDbTableName + "_instances");
                final String imeiNumberDbTableName = "imei_number";
                instaceTablesToAdd.add(imeiNumberDbTableName + "_instances");
                final String iccidNumberDbTableName = "iccid_number";
                instaceTablesToAdd.add(iccidNumberDbTableName + "_instances");
                final String imsiNumberDbTableName = "imsi_number";
                instaceTablesToAdd.add(imsiNumberDbTableName + "_instances");

                //add the wireless_networks attribute to the correlation_types table
                preparedStatement = conn.prepareStatement(addAttributeSql);
                preparedStatement.setInt(1, CorrelationAttributeInstance.SSID_TYPE_ID);
                preparedStatement.setString(2, Bundle.CorrelationType_SSID_displayName());
                preparedStatement.setString(3, wirelessNetworksDbTableName);
                preparedStatement.setInt(4, 1);
                preparedStatement.setInt(5, 1);
                preparedStatement.execute();

                //add the mac_address attribute to the correlation_types table
                preparedStatement = conn.prepareStatement(addAttributeSql);
                preparedStatement.setInt(1, CorrelationAttributeInstance.MAC_TYPE_ID);
                preparedStatement.setString(2, Bundle.CorrelationType_MAC_displayName());
                preparedStatement.setString(3, macAddressDbTableName);
                preparedStatement.setInt(4, 1);
                preparedStatement.setInt(5, 1);
                preparedStatement.execute();

                //add the imei_number attribute to the correlation_types table
                preparedStatement = conn.prepareStatement(addAttributeSql);
                preparedStatement.setInt(1, CorrelationAttributeInstance.IMEI_TYPE_ID);
                preparedStatement.setString(2, Bundle.CorrelationType_IMEI_displayName());
                preparedStatement.setString(3, imeiNumberDbTableName);
                preparedStatement.setInt(4, 1);
                preparedStatement.setInt(5, 1);
                preparedStatement.execute();

                //add the imsi_number attribute to the correlation_types table
                preparedStatement = conn.prepareStatement(addAttributeSql);
                preparedStatement.setInt(1, CorrelationAttributeInstance.IMSI_TYPE_ID);
                preparedStatement.setString(2, Bundle.CorrelationType_IMSI_displayName());
                preparedStatement.setString(3, imsiNumberDbTableName);
                preparedStatement.setInt(4, 1);
                preparedStatement.setInt(5, 1);
                preparedStatement.execute();

                //add the iccid_number attribute to the correlation_types table
                preparedStatement = conn.prepareStatement(addAttributeSql);
                preparedStatement.setInt(1, CorrelationAttributeInstance.ICCID_TYPE_ID);
                preparedStatement.setString(2, Bundle.CorrelationType_ICCID_displayName());
                preparedStatement.setString(3, iccidNumberDbTableName);
                preparedStatement.setInt(4, 1);
                preparedStatement.setInt(5, 1);
                preparedStatement.execute();

                //create a new _instances tables and add indexes for their columns
                for (String tableName : instaceTablesToAdd) {
                    statement.execute(String.format(addSsidTableTemplate, tableName, tableName));
                    statement.execute(String.format(addCaseIdIndexTemplate, tableName, tableName));
                    statement.execute(String.format(addDataSourceIdIndexTemplate, tableName, tableName));
                    statement.execute(String.format(addValueIndexTemplate, tableName, tableName));
                    statement.execute(String.format(addKnownStatusIndexTemplate, tableName, tableName));
                }

                //add file_obj_id column to _instances table which do not already have it
                String instance_type_dbname;
                final String objectIdColumnName = "file_obj_id";
                for (CorrelationAttributeInstance.Type type : CorrelationAttributeInstance.getDefaultCorrelationTypes()) {
                    instance_type_dbname = EamDbUtil.correlationTypeToInstanceTableName(type);
                    if (!doesColumnExist(conn, instance_type_dbname, objectIdColumnName)) {
                        statement.execute(String.format(addIntegerColumnTemplate, instance_type_dbname, objectIdColumnName)); //NON-NLS
                    }
                    statement.execute(String.format(addObjectIdIndexTemplate, instance_type_dbname, instance_type_dbname));
                }

                /*
                 * Add hash columns to the data_sources table.
                 */
                if (!doesColumnExist(conn, dataSourcesTableName, "md5")) {
                    statement.execute("ALTER TABLE data_sources ADD COLUMN md5 TEXT DEFAULT NULL");
                }
                if (!doesColumnExist(conn, dataSourcesTableName, "sha1")) {
                    statement.execute("ALTER TABLE data_sources ADD COLUMN sha1 TEXT DEFAULT NULL");
                }
                if (!doesColumnExist(conn, dataSourcesTableName, "sha256")) {
                    statement.execute("ALTER TABLE data_sources ADD COLUMN sha256 TEXT DEFAULT NULL");
                }

                /*
                 * Drop the db_info table and add it back in with the name
                 * column having a UNIQUE constraint. The name column could now
                 * be used as the primary key, but the essentially useless id
                 * column is retained for the sake of backwards compatibility.
                 * Note that the creation schema version number is set to 0.0 to
                 * indicate that it is unknown.
                 */
                String creationMajorVer;
                resultSet = statement.executeQuery("SELECT value FROM db_info WHERE name = '" + AbstractSqlEamDb.CREATION_SCHEMA_MAJOR_VERSION_KEY + "'");
                if (resultSet.next()) {
                    creationMajorVer = resultSet.getString("value");
                } else {
                    creationMajorVer = "0";
                }
                String creationMinorVer;
                resultSet = statement.executeQuery("SELECT value FROM db_info WHERE name = '" + AbstractSqlEamDb.CREATION_SCHEMA_MINOR_VERSION_KEY + "'");
                if (resultSet.next()) {
                    creationMinorVer = resultSet.getString("value");
                } else {
                    creationMinorVer = "0";
                }
                statement.execute("DROP TABLE db_info");
                if (selectedPlatform == EamDbPlatformEnum.POSTGRESQL) {
                    statement.execute("CREATE TABLE db_info (id SERIAL, name TEXT UNIQUE NOT NULL, value TEXT NOT NULL)");
                } else {
                    statement.execute("CREATE TABLE db_info (id INTEGER PRIMARY KEY, name TEXT UNIQUE NOT NULL, value TEXT NOT NULL)");
                }
                statement.execute("INSERT INTO db_info (name, value) VALUES ('" + AbstractSqlEamDb.SCHEMA_MAJOR_VERSION_KEY + "','" + majorVersionStr + "')");
                statement.execute("INSERT INTO db_info (name, value) VALUES ('" + AbstractSqlEamDb.SCHEMA_MINOR_VERSION_KEY + "','" + minorVersionStr + "')");
                statement.execute("INSERT INTO db_info (name, value) VALUES ('" + AbstractSqlEamDb.CREATION_SCHEMA_MAJOR_VERSION_KEY + "','" + creationMajorVer + "')");
                statement.execute("INSERT INTO db_info (name, value) VALUES ('" + AbstractSqlEamDb.CREATION_SCHEMA_MINOR_VERSION_KEY + "','" + creationMinorVer + "')");
            }
            /*
             * Update to 1.3
             */
            if (dbSchemaVersion.compareTo(new CaseDbSchemaVersionNumber(1, 3)) < 0) {
                switch (selectedPlatform) {
                    case POSTGRESQL:
                        statement.execute("ALTER TABLE data_sources DROP CONSTRAINT datasource_unique");
                        //unique constraint for upgraded data_sources table is purposefully different than new data_sources table
                        statement.execute("ALTER TABLE data_sources ADD CONSTRAINT datasource_unique UNIQUE (case_id, device_id, name, datasource_obj_id)");

                        break;
                    case SQLITE:
                        statement.execute("DROP INDEX IF EXISTS data_sources_name");
                        statement.execute("DROP INDEX IF EXISTS data_sources_object_id");
                        statement.execute("ALTER TABLE data_sources RENAME TO old_data_sources");
                        //unique constraint for upgraded data_sources table is purposefully different than new data_sources table
                        statement.execute("CREATE TABLE IF NOT EXISTS data_sources (id integer primary key autoincrement NOT NULL,"
                                + "case_id integer NOT NULL,device_id text NOT NULL,name text NOT NULL,datasource_obj_id integer,"
                                + "md5 text DEFAULT NULL,sha1 text DEFAULT NULL,sha256 text DEFAULT NULL,"
                                + "foreign key (case_id) references cases(id) ON UPDATE SET NULL ON DELETE SET NULL,"
                                + "CONSTRAINT datasource_unique UNIQUE (case_id, device_id, name, datasource_obj_id))");
                        statement.execute(SqliteEamDbSettings.getAddDataSourcesNameIndexStatement());
                        statement.execute(SqliteEamDbSettings.getAddDataSourcesObjectIdIndexStatement());
                        statement.execute("INSERT INTO data_sources SELECT * FROM old_data_sources");
                        statement.execute("DROP TABLE old_data_sources");
                        break;
                    default:
                        throw new EamDbException("Currently selected database platform \"" + selectedPlatform.name() + "\" can not be upgraded.");
                }
            }
            updateSchemaVersion(conn);
            conn.commit();
            logger.log(Level.INFO, String.format("Central Repository schema updated to version %s", SOFTWARE_CR_DB_SCHEMA_VERSION));

        } catch (SQLException | EamDbException ex) {
            try {
                if (conn != null) {
                    conn.rollback();
                }
            } catch (SQLException ex2) {
                logger.log(Level.SEVERE, String.format("Central Repository rollback of failed schema update to %s failed", SOFTWARE_CR_DB_SCHEMA_VERSION), ex2);
            }
            throw ex;
        } finally {
            EamDbUtil.closeResultSet(resultSet);
            EamDbUtil.closeStatement(preparedStatement);
            EamDbUtil.closeStatement(statement);
            EamDbUtil.closeConnection(conn);
        }
    }

}