Example usage for java.sql SQLException getStackTrace

List of usage examples for java.sql SQLException getStackTrace

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Introduction

In this page you can find the example usage for java.sql SQLException getStackTrace.

Prototype

public StackTraceElement[] getStackTrace()

Source Link

Document

Provides programmatic access to the stack trace information printed by #printStackTrace() .

Usage

From source file:com.taobao.tddl.jdbc.group.util.ExceptionUtils.java

public static SQLException mergeException(List<SQLException> exceptions) {
    //      return new OneToManySQLExceptionsWrapper(exceptions);
    SQLException first = exceptions.get(0);
    List<StackTraceElement> stes = new ArrayList<StackTraceElement>(30 * exceptions.size());
    //stes.addAll(Arrays.asList(first.getStackTrace()));
    boolean hasSplit = false;
    for (StackTraceElement ste : first.getStackTrace()) {
        stes.add(ste);/*ww w . ja v  a2 s.  c o  m*/
        if (ste == split) {
            hasSplit = true;
        }
    }
    if (!hasSplit) {
        stes.add(split);
    }
    SQLException current = null;
    for (int i = 1, n = exceptions.size(); i < n; i++) {
        //newEx.setNextException(exceptions.get(i));
        //         current.setNextException(exceptions.get(i));
        current = exceptions.get(i);
        //stes.addAll(Arrays.asList(exceptions.get(i).getStackTrace()));
        hasSplit = false;
        for (StackTraceElement ste : current.getStackTrace()) {
            stes.add(ste);
            if (ste == split) {
                hasSplit = true;
            }
        }
        if (!hasSplit) {
            stes.add(split);
        }
    }
    //newEx.getCause();
    first.setStackTrace(stes.toArray(new StackTraceElement[stes.size()]));
    return first;
}

From source file:com.wso2telco.dep.reportingservice.dao.TaxDAO.java

/**
 * Gets the taxes for subscription.//w  w w  . j  av  a 2 s . c o m
 *
 * @param applicationId the application id
 * @param apiId the api id
 * @return the taxes for subscription
 * @throws Exception the exception
 */
public List<Tax> getTaxesForSubscription(int applicationId, int apiId) throws Exception {
    Connection connection = null;
    PreparedStatement ps = null;
    ResultSet results = null;
    String sql = "SELECT type,effective_from,effective_to,value FROM " + ReportingTable.TAX + ", "
            + ReportingTable.SUBSCRIPTION_TAX
            + "WHERE subscription_tax.application_id=? AND subscription_tax.api_id=? AND tax.type=subscription_tax.tax_type ";

    List<Tax> taxes = new ArrayList<Tax>();
    try {
        connection = DbUtils.getDbConnection(DataSourceNames.WSO2AM_STATS_DB);
        ps = connection.prepareStatement(sql);
        log.debug("getTaxesForSubscription for applicationId---> " + applicationId + " apiId--> " + apiId);
        ps.setInt(1, applicationId);
        ps.setInt(2, apiId);
        log.debug("SQL (PS) ---> " + ps.toString());
        results = ps.executeQuery();
        while (results.next()) {
            Tax tax = new Tax();
            tax.setType(results.getString("type"));
            tax.setEffective_from(results.getDate("effective_from"));
            tax.setEffective_to(results.getDate("effective_to"));
            tax.setValue(results.getBigDecimal("value"));
            taxes.add(tax);
        }
    } catch (SQLException e) {
        log.error("SQL Error in getTaxesForSubscription");
        log.error(e.getStackTrace());
        handleException("Error occurred while getting Taxes for Subscription", e);
    } finally {
        DbUtils.closeAllConnections(ps, connection, results);
    }
    return taxes;
}

From source file:com.wso2telco.dep.reportingservice.dao.TaxDAO.java

/**
 * Gets the taxes for tax list./*from ww w  . ja  v  a  2  s  .  c o m*/
 *
 * @param taxList the tax list
 * @return the taxes for tax list
 * @throws Exception the exception
 */
public List<Tax> getTaxesForTaxList(List<String> taxList) throws Exception {
    Connection connection = null;
    Statement st = null;
    ResultSet results = null;

    List<Tax> taxes = new ArrayList<Tax>();

    if (taxList == null || taxList.isEmpty()) {
        return taxes;
    }

    // CSV format surrounded by single quote
    String taxListStr = taxList.toString().replace("[", "'").replace("]", "'").replace(", ", "','");

    String sql = "SELECT type,effective_from,effective_to,value FROM " + ReportingTable.TAX + " WHERE type IN ("
            + taxListStr + ")";

    try {
        connection = DbUtils.getDbConnection(DataSourceNames.WSO2AM_STATS_DB);
        st = connection.createStatement();
        log.debug("In getTaxesForTaxList");
        log.debug("SQL (PS) ---> " + st.toString());
        results = st.executeQuery(sql);
        while (results.next()) {
            Tax tax = new Tax();
            tax.setType(results.getString("type"));
            tax.setEffective_from(results.getDate("effective_from"));
            tax.setEffective_to(results.getDate("effective_to"));
            tax.setValue(results.getBigDecimal("value"));
            taxes.add(tax);
        }
        st.close();
    } catch (SQLException e) {
        log.error("SQL Error in getTaxesForTaxList");
        log.error(e.getStackTrace());
        handleException("Error occurred while getting Taxes for Tax List", e);
    } finally {
        DbUtils.closeAllConnections(null, connection, results);
    }
    return taxes;
}

From source file:org.metis.push.PusherBean.java

/**
 * Called by Spring after all of this bean's properties have been set.
 *//*w  w  w .  j a v  a2s.c o m*/
public void afterPropertiesSet() throws Exception {

    // create the session registry
    setWdsSessions(new Hashtable<String, WdsSocketSession>(getInitCapacity()));

    // log info for the jdbc driver being used
    // this will also attempt to open connection
    // with jdbc driver
    try {
        Connection con = getDataSource().getConnection();
        if (con != null) {
            DatabaseMetaData dbmd = con.getMetaData();
            setDbConnectionAcquired(true);
            if (dbmd != null) {
                setDriverName(dbmd.getDriverName().trim().toLowerCase());
                // record the URL to the DB
                setDbUrl(dbmd.getURL().trim());
                isOracle = (getDriverName() != null && getDriverName().indexOf(ORACLE_STR) >= 0) ? true : false;
                LOG.info(getBeanName() + ":Is Oracle JDBC Driver = " + isOracle);
                LOG.info(getBeanName() + ":JDBC Driver name = " + getDriverName());
                LOG.info(getBeanName() + ":JDBC Driver version = " + dbmd.getDriverVersion().trim());
                LOG.info(getBeanName() + ":JDBC Driver product name = " + dbmd.getDatabaseProductName().trim());
                LOG.info(getBeanName() + ":JDBC URL = " + getDbUrl());
                LOG.info(getBeanName() + ":JDBC Driver database product version = "
                        + dbmd.getDatabaseProductVersion().trim());
                con.close();
            } else {
                LOG.info(getBeanName() + ": Unable to get JDBC driver meta data");
            }
        } else {
            LOG.info(getBeanName() + ": Unable to get JDBC connection");
        }
    } catch (SQLException exc) {
        LOG.error(getBeanName() + ": got this exception when trying to " + "get driver meta data: "
                + exc.toString());
        LOG.error(getBeanName() + ": exception stack trace follows:");
        dumpStackTrace(exc.getStackTrace());
        LOG.error(getBeanName() + ": Caused by " + exc.getCause().toString());
        LOG.error(getBeanName() + ": causing exception stack trace follows:");
        dumpStackTrace(exc.getCause().getStackTrace());
    }

    // bean must be assigned a JDBC DataSource
    if (getDataSource() == null) {
        throw new Exception(
                getBeanName() + ".afterPropertiesSet: this bean has not been " + "assigned a JDBC DataSource");
    }

    // do some validation
    if (getSqls4Get() == null) {
        throw new Exception("The PusherBean must be assigned at least one SQL statement");
    }

    // create and validate the injected SQL statements

    sqlStmnts4Get = new ArrayList<SqlStmnt>();
    for (String sql : getSqls4Get()) {
        // get the frequency settings
        Map<String, Long> map = Utils.parseTimeInterval(sql);
        sql = Utils.stripTimeInterval(sql);
        sql = Utils.stripCall(sql);
        SqlStmnt stmt = getSQLStmnt(this, sql, getJdbcTemplate());

        if (stmt.isEqual(sqlStmnts4Get)) {
            throw new Exception("Injected SQL statements for GET are not distinct");
        }
        // set the frequency
        stmt.setIntervalTime(map.get(TIME_INTERVAL));
        if (map.get(TIME_INTERVAL_MAX) != null) {
            stmt.setIntervalMax(map.get(TIME_INTERVAL_MAX));
        }
        if (map.get(TIME_INTERVAL_STEP) != null) {
            stmt.setIntervalStep(map.get(TIME_INTERVAL_STEP));
        }
        sqlStmnts4Get.add(stmt);
    }
    if (LOG.isDebugEnabled()) {
        for (SqlStmnt sqlstmnt : sqlStmnts4Get) {
            LOG.debug(getBeanName() + ": SQL for GET = " + sqlstmnt.getOriginal());
            LOG.debug(getBeanName() + ": Parameterized SQL for GET = " + sqlstmnt.getPrepared());
        }
    }

    if (getHazelcastInstance() != null) {
        LOG.debug(getBeanName() + ": My Hazelcast Instance Name = " + getHazelcastInstance().getName());
        ;
    }
}

From source file:org.metis.pull.WdsResourceBean.java

/**
 * Called by Spring after all of this bean's properties have been set.
 *///from w  ww .  j a  va  2s . c o  m
public void afterPropertiesSet() throws Exception {

    // log info for the jdbc driver being used
    // this will also attempt to open connection
    // with jdbc driver
    try {
        Connection con = getDataSource().getConnection();
        if (con != null) {
            DatabaseMetaData dbmd = con.getMetaData();
            setDbConnectionAcquired(true);
            if (dbmd != null) {
                setDriverName(dbmd.getDriverName().trim().toLowerCase());
                isOracle = (getDriverName() != null && getDriverName().indexOf(ORACLE_STR) >= 0) ? true : false;
                LOG.info(getBeanName() + ":Is Oracle JDBC Driver = " + isOracle);
                LOG.info(getBeanName() + ":JDBC Driver name = " + getDriverName());
                LOG.info(getBeanName() + ":JDBC Driver version = " + dbmd.getDriverVersion().trim());
                LOG.info(getBeanName() + ":JDBC Driver product name = " + dbmd.getDatabaseProductName().trim());
                LOG.info(getBeanName() + ":JDBC Driver database product version = "
                        + dbmd.getDatabaseProductVersion().trim());
                con.close();
            } else {
                LOG.info(getBeanName() + ": Unable to get JDBC driver meta data");
            }
        } else {
            LOG.info(getBeanName() + ": Unable to get JDBC connection");
        }
    } catch (SQLException exc) {
        LOG.error(getBeanName() + ": got this exception when trying to " + "get driver meta data: "
                + exc.toString());
        LOG.error(getBeanName() + ": exception stack trace follows:");
        dumpStackTrace(exc.getStackTrace());
        LOG.error(getBeanName() + ": Caused by " + exc.getCause().toString());
        LOG.error(getBeanName() + ": causing exception stack trace follows:");
        dumpStackTrace(exc.getCause().getStackTrace());
    }

    // bean must be assigned a JDBC DataSource
    if (getDataSource() == null) {
        throw new Exception(
                getBeanName() + ".afterPropertiesSet: this bean has not been " + "assigned a JDBC DataSource");
    }

    // do some validation
    if (getSqls4Get() == null && getSqls4Put() == null && getSqls4Post() == null && getSqls4Delete() == null) {
        throw new Exception("At least one of the WdsResourceBean's http methods has "
                + "not been assigned a SQL statement");
    }

    // create and validate the different SQL statements
    if (getSqls4Get() != null) {
        sqlStmnts4Get = new ArrayList<SqlStmnt>();
        for (String sql : getSqls4Get()) {
            SqlStmnt stmt = getSQLStmnt(this, sql, getJdbcTemplate());
            if (stmt.isEqual(sqlStmnts4Get)) {
                throw new Exception("Injected SQL statements for GET are not distinct");
            }
            sqlStmnts4Get.add(stmt);
        }
        if (LOG.isDebugEnabled()) {
            for (SqlStmnt sqlstmnt : sqlStmnts4Get) {
                LOG.debug(getBeanName() + ": SQL for GET = " + sqlstmnt.getOriginal());
                LOG.debug(getBeanName() + ": Parameterized SQL for GET = " + sqlstmnt.getPrepared());
            }
        }
        allowedMethodsRsp += "GET ";
    }

    if (getSqls4Put() != null) {
        sqlStmnts4Put = new ArrayList<SqlStmnt>();
        for (String sql : getSqls4Put()) {
            SqlStmnt stmt = getSQLStmnt(this, sql, getJdbcTemplate());
            if (stmt.isEqual(sqlStmnts4Put)) {
                throw new Exception("Injected SQL statements for PUT are not distinct");
            }
            sqlStmnts4Put.add(stmt);
        }
        if (LOG.isDebugEnabled()) {
            for (SqlStmnt sqlstmnt : sqlStmnts4Put) {
                LOG.debug(getBeanName() + ": SQL for PUT = " + sqlstmnt.getOriginal());
                LOG.debug(getBeanName() + ": Parameterized SQL for PUT = " + sqlstmnt.getPrepared());
            }
        }
        allowedMethodsRsp += "PUT ";
    }

    if (getSqls4Post() != null) {
        sqlStmnts4Post = new ArrayList<SqlStmnt>();
        for (String sql : getSqls4Post()) {
            SqlStmnt stmt = getSQLStmnt(this, sql, getJdbcTemplate());
            if (stmt.isEqual(sqlStmnts4Post)) {
                throw new Exception("Injected SQL statements for POST are not distinct");
            }
            sqlStmnts4Post.add(stmt);
        }
        if (LOG.isDebugEnabled()) {
            for (SqlStmnt sqlstmnt : sqlStmnts4Post) {
                LOG.debug(getBeanName() + ": SQL for POST = " + sqlstmnt.getOriginal());
                LOG.debug(getBeanName() + ": Parameterized SQL for POST = " + sqlstmnt.getPrepared());
            }
        }
        allowedMethodsRsp += "POST ";
    }

    if (getSqls4Delete() != null) {
        sqlStmnts4Delete = new ArrayList<SqlStmnt>();
        for (String sql : getSqls4Delete()) {
            SqlStmnt stmt = getSQLStmnt(this, sql, getJdbcTemplate());
            if (stmt.isEqual(sqlStmnts4Delete)) {
                throw new Exception("Injected SQL statements for DELETE are not distinct");
            }
            sqlStmnts4Delete.add(stmt);
        }
        if (LOG.isDebugEnabled()) {
            for (SqlStmnt sqlstmnt : sqlStmnts4Delete) {
                LOG.debug(getBeanName() + ": SQL for DELETE = " + sqlstmnt.getOriginal());
                LOG.debug(getBeanName() + ": Parameterized SQL for DELETE = " + sqlstmnt.getPrepared());
            }
        }
        allowedMethodsRsp += "DELETE";
    }

    LOG.debug(getBeanName() + ": allowedMethodsRsp string = " + allowedMethodsRsp);

    // tell our parent what methods this RDB will support
    setSupportedMethods(allowedMethodsRsp.split(SPACE_CHR_STR));

    if (LOG.isDebugEnabled() && getAllowedAgents() != null) {
        if (!getAllowedAgents().isEmpty()) {
            LOG.debug(getBeanName() + ": agents allowed =  " + getAllowedAgents());
        } else {
            LOG.debug(getBeanName() + ": agents not allowed =  " + getNotAllowedAgents());
        }
    }

}

From source file:massbank.DatabaseManager.java

public void persistAccessionFile(Record acc, boolean bulk) {
    //      this.openConnection();
    //      String insertCompound = "INSERT INTO COMPOUND VALUES(?,?,?,?,?,?,?,?)";
    //      PreparedStatement stmnt = con.prepareStatement(insertCompound);

    Integer conId = -1;/*from  w w  w  .j a v  a 2s.co m*/
    try {
        String sql = "SELECT ID FROM CONTRIBUTOR WHERE SHORT_NAME = ?";
        PreparedStatement stmnt = con.prepareStatement(sql);
        stmnt.setString(1, acc.CONTRIBUTOR());
        ResultSet res = stmnt.executeQuery();
        if (res.next()) {
            conId = res.getInt(1);
        }
    } catch (SQLException e1) {
        e1.printStackTrace();
    }

    if (conId == -1) {
        try {
            String sql = "INSERT INTO CONTRIBUTOR (ACRONYM, SHORT_NAME, FULL_NAME) VALUES (NULL,?,NULL)";
            PreparedStatement stmnt = con.prepareStatement(sql);
            stmnt.setString(1, acc.CONTRIBUTOR());
            stmnt.executeUpdate();
        } catch (SQLException e1) {
            e1.printStackTrace();
        }

        try {
            String sql = "SELECT ID FROM CONTRIBUTOR WHERE SHORT_NAME = ?";
            PreparedStatement stmnt = con.prepareStatement(sql);
            stmnt.setString(1, acc.CONTRIBUTOR());
            ResultSet res = stmnt.executeQuery();
            if (res.next()) {
                conId = res.getInt(1);
            }
        } catch (SQLException e1) {
            e1.printStackTrace();
        }
    }

    try {
        //System.out.println(System.nanoTime());
        statementInsertCompound.setNull(1, java.sql.Types.INTEGER);
        statementInsertCompound.setString(2, acc.CH_FORMULA());
        statementInsertCompound.setDouble(3, acc.CH_EXACT_MASS());
        statementInsertCompound.setString(4, acc.CH_SMILES());
        statementInsertCompound.setString(5, acc.CH_IUPAC());

        // TODO support CH$CDK_DEPICT_SMILES
        // TODO support CH$CDK_DEPICT_GENERIC_SMILES
        // TODO support CH$CDK_DEPICT_STRUCTURE_SMILES
        //      if (acc.get("CH$CDK_DEPICT_SMILES").size() != 0) {
        //         statementInsertCompound.setString(6, acc.get("CH$CDK_DEPICT_SMILES").get(0)[2]);
        //      } else {
        statementInsertCompound.setNull(6, java.sql.Types.VARCHAR);
        //      }
        //      if (acc.get("CH$CDK_DEPICT_GENERIC_SMILES").size() != 0) {
        //         statementInsertCompound.setString(7, acc.get("CH$CDK_DEPICT_GENERIC_SMILES").get(0)[2]);
        //      } else {
        statementInsertCompound.setNull(7, java.sql.Types.VARCHAR);
        //      }
        //      if (acc.get("CH$CDK_DEPICT_STRUCTURE_SMILES").size() != 0) {
        //         statementInsertCompound.setString(8, acc.get("CH$CDK_DEPICT_STRUCTURE_SMILES").get(0)[2]);
        //      } else {
        statementInsertCompound.setNull(8, java.sql.Types.VARCHAR);
        //      }
        statementInsertCompound.executeUpdate();
        ResultSet set = statementInsertCompound.getGeneratedKeys();
        set.next();
        int compoundId = set.getInt("ID");

        //System.out.println(System.nanoTime());
        int compoundClassId;
        //      String insertCompoundClass = "INSERT INTO COMPOUND_CLASS VALUES(?,?,?,?)";
        //      stmnt = con.prepareStatement(insertCompoundClass);
        for (String el : acc.CH_COMPOUND_CLASS()) {
            statementInsertCompound_Class.setNull(1, java.sql.Types.INTEGER);
            statementInsertCompound_Class.setString(2, null);
            statementInsertCompound_Class.setString(3, null);
            statementInsertCompound_Class.setString(4, el);
            statementInsertCompound_Class.executeUpdate();
            set = statementInsertCompound_Class.getGeneratedKeys();
            set.next();
            compoundClassId = set.getInt("ID");

            //         String insertCompoundCompoundClass = "INSERT INTO COMPOUND_COMPOUND_CLASS VALUES(?,?)";
            //         stmnt = con.prepareStatement(insertCompoundCompoundClass);
            statementInsertCompound_Compound_Class.setInt(1, compoundId);
            statementInsertCompound_Compound_Class.setInt(2, compoundClassId);
            statementInsertCompound_Compound_Class.executeUpdate();
        }

        //System.out.println(System.nanoTime());
        int nameId;
        //      String insertName = "INSERT INTO NAME VALUES(?,?)";
        //      stmnt = con.prepareStatement(insertName);
        for (String el : acc.CH_NAME()) {
            statementInsertName.setNull(1, java.sql.Types.INTEGER);
            statementInsertName.setString(2, el);
            try {
                statementInsertName.executeUpdate();
                set = statementInsertName.getGeneratedKeys();
                set.next();
                nameId = set.getInt("ID");

                //            String insertCompoundName = "INSERT INTO COMPOUND_NAME VALUES(?,?)";
                //            stmnt = con.prepareStatement(insertCompoundName);
                statementInsertCompound_Name.setInt(1, compoundId);
                statementInsertCompound_Name.setInt(2, nameId);
                statementInsertCompound_Name.executeUpdate();
            } catch (SQLException e) {
                if (e.getErrorCode() == 1062) {
                    PreparedStatement retrieveIdForName = con
                            .prepareStatement("SELECT ID FROM NAME WHERE CH_NAME = ?");
                    retrieveIdForName.setString(1, el);
                    set = retrieveIdForName.executeQuery();
                    set.next();
                    nameId = set.getInt("ID");
                    statementInsertCompound_Name.setInt(1, compoundId);
                    statementInsertCompound_Name.setInt(2, nameId);
                    statementInsertCompound_Name.executeUpdate();
                } else {
                    this.closeConnection();
                    throw e;
                    //               e.printStackTrace();
                    //               nameId = -1;
                }
            }
        }

        //System.out.println(System.nanoTime());
        //      String insertChLink = "INSERT INTO CH_LINK VALUES(?,?,?)";
        //      stmnt = con.prepareStatement(insertChLink);
        for (Pair<String, String> el : acc.CH_LINK()) {
            statementInsertCH_LINK.setInt(1, compoundId);
            statementInsertCH_LINK.setString(2, el.getLeft());
            statementInsertCH_LINK.setString(3, el.getRight());
            //         statementInsertCH_LINK.executeUpdate();
            statementInsertCH_LINK.addBatch();
        }
        if (!bulk) {
            statementInsertCH_LINK.executeBatch();
        }

        //System.out.println(System.nanoTime());
        int sampleId = -1;
        statementInsertSAMPLE.setNull(1, java.sql.Types.INTEGER);
        if (acc.SP_SCIENTIFIC_NAME() != null) {
            statementInsertSAMPLE.setString(2, acc.SP_SCIENTIFIC_NAME());
        } else {
            statementInsertSAMPLE.setNull(2, java.sql.Types.VARCHAR);
        }
        if (acc.SP_LINEAGE() != null) {
            statementInsertSAMPLE.setString(3, acc.SP_LINEAGE());
        } else {
            statementInsertSAMPLE.setNull(3, java.sql.Types.VARCHAR);
        }
        if (acc.SP_SCIENTIFIC_NAME() != null && acc.SP_LINEAGE() != null) {
            statementInsertSAMPLE.executeUpdate();
            set = statementInsertSAMPLE.getGeneratedKeys();
            set.next();
            sampleId = set.getInt("ID");
        }

        //System.out.println(System.nanoTime());
        for (Pair<String, String> el : acc.SP_LINK()) {
            statementInsertSP_LINK.setInt(1, sampleId);
            statementInsertSP_LINK.setString(2, el.getLeft() + " " + el.getRight());
            //         statementInsertSP_LINK.executeUpdate();
            statementInsertSP_LINK.addBatch();
        }
        if (!bulk) {
            statementInsertSP_LINK.executeBatch();
        }

        //System.out.println(System.nanoTime());
        for (String el : acc.SP_SAMPLE()) {
            statementInsertSP_SAMPLE.setInt(1, sampleId);
            statementInsertSP_SAMPLE.setString(2, el);
            //         statementInsertSP_SAMPLE.executeUpdate();
            statementInsertSP_SAMPLE.addBatch();
        }
        if (!bulk) {
            statementInsertSP_SAMPLE.executeBatch();
        }

        //System.out.println(System.nanoTime());
        statementInsertINSTRUMENT.setNull(1, java.sql.Types.INTEGER);
        statementInsertINSTRUMENT.setString(2, acc.AC_INSTRUMENT());
        statementInsertINSTRUMENT.setString(3, acc.AC_INSTRUMENT_TYPE());
        statementInsertINSTRUMENT.executeUpdate();
        set = statementInsertINSTRUMENT.getGeneratedKeys();
        set.next();
        int instrumentId = set.getInt("ID");

        //System.out.println(System.nanoTime());
        statementInsertRECORD.setString(1, acc.ACCESSION());
        statementInsertRECORD.setString(2, acc.RECORD_TITLE());
        statementInsertRECORD.setDate(3, Date.valueOf(acc.DATE()));
        statementInsertRECORD.setString(4, acc.AUTHORS());
        //      if (acc.get("LICENSE").size() != 0) {
        statementInsertRECORD.setString(5, acc.LICENSE());
        //      } else {
        //         statementInsertRECORD.setNull(5, java.sql.Types.VARCHAR);
        //      }
        if (acc.COPYRIGHT() != null) {
            statementInsertRECORD.setString(6, acc.COPYRIGHT());
        } else {
            statementInsertRECORD.setNull(6, java.sql.Types.VARCHAR);
        }
        if (acc.PUBLICATION() != null) {
            statementInsertRECORD.setString(7, acc.PUBLICATION());
        } else {
            statementInsertRECORD.setNull(7, java.sql.Types.VARCHAR);
        }
        statementInsertRECORD.setInt(8, compoundId);
        if (sampleId > 0) {
            statementInsertRECORD.setInt(9, sampleId);
        } else {
            statementInsertRECORD.setNull(9, java.sql.Types.INTEGER);
        }
        statementInsertRECORD.setInt(10, instrumentId);
        statementInsertRECORD.setString(11, acc.AC_MASS_SPECTROMETRY_MS_TYPE());
        statementInsertRECORD.setString(12, acc.AC_MASS_SPECTROMETRY_ION_MODE());
        statementInsertRECORD.setString(13, acc.PK_SPLASH());
        statementInsertRECORD.setInt(14, conId);
        statementInsertRECORD.executeUpdate();
        //      set = statementInsertRECORD.getGeneratedKeys();
        //      set.next();
        String accession = acc.ACCESSION();

        //System.out.println(System.nanoTime());
        for (String el : acc.COMMENT()) {
            statementInsertCOMMENT.setString(1, accession);
            statementInsertCOMMENT.setString(2, el);
            //         statementInsertCOMMENT.executeUpdate();
            statementInsertCOMMENT.addBatch();
        }
        if (!bulk) {
            statementInsertCOMMENT.executeBatch();
        }

        //System.out.println(System.nanoTime());
        for (Pair<String, String> el : acc.AC_MASS_SPECTROMETRY()) {
            statementInsertAC_MASS_SPECTROMETRY.setString(1, accession);
            statementInsertAC_MASS_SPECTROMETRY.setString(2, el.getLeft());
            statementInsertAC_MASS_SPECTROMETRY.setString(3, el.getRight());
            //         statementInsertAC_MASS_SPECTROMETRY.executeUpdate();
            statementInsertAC_MASS_SPECTROMETRY.addBatch();
        }
        if (!bulk) {
            statementInsertAC_MASS_SPECTROMETRY.executeBatch();
        }

        //System.out.println(System.nanoTime());
        for (Pair<String, String> el : acc.AC_CHROMATOGRAPHY()) {
            statementInsertAC_CHROMATOGRAPHY.setString(1, accession);
            statementInsertAC_CHROMATOGRAPHY.setString(2, el.getLeft());
            statementInsertAC_CHROMATOGRAPHY.setString(3, el.getRight());
            //         statementInsertAC_CHROMATOGRAPHY.executeUpdate();
            statementInsertAC_CHROMATOGRAPHY.addBatch();
        }
        if (!bulk) {
            statementInsertAC_CHROMATOGRAPHY.executeBatch();
        }

        //System.out.println(System.nanoTime());
        for (Pair<String, String> el : acc.MS_FOCUSED_ION()) {
            statementInsertMS_FOCUSED_ION.setString(1, accession);
            statementInsertMS_FOCUSED_ION.setString(2, el.getLeft());
            statementInsertMS_FOCUSED_ION.setString(3, el.getRight());
            //         statementInsertMS_FOCUSED_ION.executeUpdate();
            statementInsertMS_FOCUSED_ION.addBatch();
        }
        if (!bulk) {
            statementInsertMS_FOCUSED_ION.executeBatch();
        }

        //System.out.println(System.nanoTime());
        for (Pair<String, String> el : acc.MS_DATA_PROCESSING()) {
            statementInsertMS_DATA_PROCESSING.setString(1, accession);
            statementInsertMS_DATA_PROCESSING.setString(2, el.getLeft());
            statementInsertMS_DATA_PROCESSING.setString(3, el.getRight());
            //         statementInsertMS_DATA_PROCESSING.executeUpdate();
            statementInsertMS_DATA_PROCESSING.addBatch();
        }
        if (!bulk) {
            statementInsertMS_DATA_PROCESSING.executeBatch();
        }

        //System.out.println(System.nanoTime());
        for (List<Double> peak : acc.PK_PEAK()) {
            statementInsertPEAK.setString(1, accession);
            statementInsertPEAK.setDouble(2, peak.get(0));
            statementInsertPEAK.setFloat(3, (float) (double) peak.get(1));
            statementInsertPEAK.setShort(4, (short) (double) peak.get(2));
            statementInsertPEAK.setNull(5, java.sql.Types.VARCHAR);
            //         statementInsertPEAK.setNull(5, java.sql.Types.VARCHAR);
            //         statementInsertPEAK.setNull(6, java.sql.Types.SMALLINT);
            //         statementInsertPEAK.setNull(7, java.sql.Types.FLOAT);
            //         statementInsertPEAK.setNull(8, java.sql.Types.FLOAT);
            //         statementInsertPEAK.executeUpdate();
            statementInsertPEAK.addBatch();
        }
        if (!bulk) {
            statementInsertPEAK.executeBatch();
        }

        //System.out.println(System.nanoTime());
        List<List<String>> annotation = acc.PK_ANNOTATION();
        if (annotation.size() != 0) {
            statementInsertANNOTATION_HEADER.setString(1, accession);
            statementInsertANNOTATION_HEADER.setString(2, String.join(" ", annotation.get(0)));
            statementInsertANNOTATION_HEADER.executeUpdate();
        }
        for (int i = 1; i < annotation.size(); i++) {
            String values = String.join(" ", annotation.get(i));
            Float mz = Float.parseFloat(annotation.get(i).get(0));
            //         values = values.substring(values.indexOf(" ")+1, values.length());
            statementUpdatePEAKs.setString(1, values);
            statementUpdatePEAKs.setString(2, accession);
            statementUpdatePEAKs.setFloat(3, mz);
            //         statementUpdatePEAK.setString(1, values.substring(0, values.indexOf(" ")));
            //         values = values.substring(values.indexOf(" ")+1, values.length());
            //         statementUpdatePEAK.setShort(2, Short.parseShort(values.substring(0, values.indexOf(" "))));
            //         values = values.substring(values.indexOf(" ")+1, values.length());
            //         statementUpdatePEAK.setFloat(3, Float.parseFloat(values.substring(0, values.indexOf(" "))));
            //         values = values.substring(values.indexOf(" ")+1, values.length());
            //         statementUpdatePEAK.setFloat(4, Float.parseFloat(values.substring(0, values.length())));
            //         statementUpdatePEAK.setString(5, accession);
            //         statementUpdatePEAK.setFloat(6, mz);
            //         statementUpdatePEAK.executeUpdate();
            statementUpdatePEAKs.addBatch();
        }
        if (!bulk) {
            statementUpdatePEAKs.executeBatch();
        }

        //System.out.println(System.nanoTime());
        con.commit();
        //System.out.println(System.nanoTime());

    } catch (SQLException e) {
        StringBuilder tmp = new StringBuilder();
        tmp.append(e.getMessage());
        tmp.append("\n");
        for (StackTraceElement el : e.getStackTrace()) {
            tmp.append(el.toString());
            tmp.append("\n");
        }
        DevLogger.printToDBLog("DB ERROR " + tmp + " for accession: " + acc.ACCESSION());
        //         try {
        //            e.printStackTrace(new PrintStream(new FileOutputStream("/Users/laptop/Desktop/errors/" + acc.ACCESSION() + ".txt")));
        //         } catch (FileNotFoundException e1) {
        //            //e1.printStackTrace();
        //         }
        this.closeConnection();
    } catch (IndexOutOfBoundsException e) {
        StringBuilder tmp = new StringBuilder();
        tmp.append(e.getMessage());
        tmp.append("\n");
        for (StackTraceElement el : e.getStackTrace()) {
            tmp.append(el.toString());
            tmp.append("\n");
        }
        DevLogger.printToDBLog("DB ERROR " + tmp + " for accession: " + acc.ACCESSION());
        //         System.out.println(acc.ACCESSION());
        //         System.out.println(acc.get("PK$PEAK").size());
        //         System.out.println(acc.get("PK$ANNOTATION").size());
        //         try {
        //            e.printStackTrace(new PrintStream(new FileOutputStream("/Users/laptop/Desktop/errors/" + acc.ACCESSION() + ".txt")));
        //         } catch (FileNotFoundException e1) {
        //            //e1.printStackTrace();
        //         }
    } catch (Exception e) {
        StringBuilder tmp = new StringBuilder();
        tmp.append(e.getMessage());
        tmp.append("\n");
        for (StackTraceElement el : e.getStackTrace()) {
            tmp.append(el.toString());
            tmp.append("\n");
        }
        DevLogger.printToDBLog("DB ERROR " + tmp + " for accession: " + acc.ACCESSION());
        //         try {
        //            e.printStackTrace(new PrintStream(new FileOutputStream("/Users/laptop/Desktop/errors/" + acc.ACCESSION() + ".txt")));
        //         } catch (FileNotFoundException e1) {
        //            //e1.printStackTrace();
        //         }
        this.closeConnection();
    }
    //      this.closeConnection();
}

From source file:org.air.standard.security.UserDetailsServiceImpl.java

@Override
public Object loadUserBySAML(final SAMLCredential samlCred) throws UsernameNotFoundException {

    CoreStandardSbacUser user = null;/*from w  w w.j a  v a2  s . c  o m*/
    try {
        final String[] pipeDelimitedChain = samlCred.getAttributeAsStringArray(SBAC_TENANCY_CHAIN_KEY);
        System.out.println("tenant chain:" + pipeDelimitedChain);

        final Map<String, String> userAtts = extractUserAttributes(samlCred);
        user = (CoreStandardSbacUser) rolesAndPermissionsService.createUser(pipeDelimitedChain, userAtts,
                CoreStandardSbacUser.class);

    } catch (final Exception e) {
        final String referenceNumber = String.valueOf(RandomUtils.nextInt(MAX_ERROR_CODE));
        _logger.error("failure processing user, reference number: " + referenceNumber, e);
        throw new UsernameNotFoundException("Unable to process user, reference number: " + referenceNumber, e);
    }

    try {
        // lets create a new sessionKey.
        AuthorizationDAO dao = new AuthorizationDAO();

        // generate a unique identifier.
        // todo: not sure if we need to make a DB call for this.
        String sessionKey = dao.generateNewSessionKey();

        // now insert a session into the table for this user.
        // todo: instead of CSR_Administrator we need to insert the
        // appropriate OpenAM roles - one record for each role.
        dao.addSessionForUser(user.getUsername(), sessionKey, "Admin");
        user.setSessionId(sessionKey);
    } catch (SQLException exp) {
        _logger.error(exp.getMessage());
        _logger.error(exp.getStackTrace().toString());
        // todo: Fix this so that it returns a proper message.
    }
    return user;
}

From source file:org.apache.ddlutils.task.DumpMetadataTask.java

/**
 * Adds a property that is represented as a result set to the current element in the given xml writer.
 * /*from   www  .  j  av  a2  s .  c om*/
 * @param xmlWriter The XML writer to write to
 * @param name      The name of the property
 * @param result    The values of the property as a result set
 */
private void addResultSetProperty(PrettyPrintingXmlWriter xmlWriter, String name, ResultSet result) {
    String propName = name;

    if (propName.endsWith("s")) {
        propName = propName.substring(0, propName.length() - 1);
    }

    try {
        ResultSetMetaData metaData = result.getMetaData();

        xmlWriter.writeElementStart(null, propName + "s");
        try {
            while (result.next()) {
                xmlWriter.writeElementStart(null, propName);

                try {
                    for (int idx = 1; idx <= metaData.getColumnCount(); idx++) {
                        Object value = result.getObject(idx);

                        addProperty(xmlWriter, metaData.getColumnLabel(idx), value);
                    }
                } finally {
                    xmlWriter.writeElementEnd();
                }
            }
        } finally {
            xmlWriter.writeElementEnd();
        }
    } catch (SQLException ex) {
        log("Could not read the result set metadata: " + ex.getStackTrace(), Project.MSG_ERR);
    }
}

From source file:org.apache.ddlutils.task.DumpMetadataTask.java

/**
 * Helper method that performs the given operation.
 * //from   ww w . j ava2  s . co  m
 * @param xmlWriter The xml writer that the operation shall write to
 * @param name      The name of the xml element surrounding the operation's output
 * @param op        The operation
 */
private void performResultSetXmlOperation(PrettyPrintingXmlWriter xmlWriter, String name,
        ResultSetXmlOperation op) {
    ResultSet result = null;

    try {
        result = op.getResultSet();

        if (name != null) {
            xmlWriter.writeElementStart(null, name);
        }
        try {
            while (result.next()) {
                op.handleRow(xmlWriter, result);
            }
        } finally {
            if (name != null) {
                xmlWriter.writeElementEnd();
            }
        }
    } catch (SQLException ex) {
        op.handleError(ex);
    } finally {
        if (result != null) {
            try {
                result.close();
            } catch (SQLException ex) {
                log("Could not close a result set: " + ex.getStackTrace(), Project.MSG_ERR);
            }
        }
    }
}

From source file:org.apache.ddlutils.task.DumpMetadataTask.java

/**
 * Dumps the catalogs and schemas of the database.
 * //from w ww .j  ava2s  .  c om
 * @param xmlWriter The xml writer to write to
 * @param metaData  The database meta data
 */
private void dumpCatalogsAndSchemas(PrettyPrintingXmlWriter xmlWriter, final DatabaseMetaData metaData) {
    performResultSetXmlOperation(xmlWriter, "catalogs", new ResultSetXmlOperation() {
        public ResultSet getResultSet() throws SQLException {
            return metaData.getCatalogs();
        }

        public void handleRow(PrettyPrintingXmlWriter xmlWriter, ResultSet result) throws SQLException {
            String catalogName = result.getString("TABLE_CAT");

            if ((catalogName != null) && (catalogName.length() > 0)) {
                xmlWriter.writeElementStart(null, "catalog");
                xmlWriter.writeAttribute(null, "name", catalogName);
                xmlWriter.writeElementEnd();
            }
        }

        public void handleError(SQLException ex) {
            log("Could not read the catalogs from the result set: " + ex.getStackTrace(), Project.MSG_ERR);
        }
    });
    performResultSetXmlOperation(xmlWriter, "schemas", new ResultSetXmlOperation() {
        public ResultSet getResultSet() throws SQLException {
            return metaData.getSchemas();
        }

        public void handleRow(PrettyPrintingXmlWriter xmlWriter, ResultSet result) throws SQLException {
            String schemaName = result.getString("TABLE_SCHEM");

            if ((schemaName != null) && (schemaName.length() > 0)) {
                xmlWriter.writeElementStart(null, "schema");
                xmlWriter.writeAttribute(null, "name", schemaName);
                xmlWriter.writeElementEnd();
            }
        }

        public void handleError(SQLException ex) {
            log("Could not read the schemas from the result set: " + ex.getStackTrace(), Project.MSG_ERR);
        }
    });
}