Example usage for java.sql SQLException printStackTrace

List of usage examples for java.sql SQLException printStackTrace

  1. HOME
  2. Java
  3. java
  4. java.sql.*
  5. SQLException
  6. printStackTrace

Introduction

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

Prototype

public void printStackTrace()

Source Link

Document

Prints this throwable and its backtrace to the standard error stream.

Usage

From source file:cognition.pipeline.data.helper.ClobHelper.java

private String getString(Object expectedClob) {
    SerializableClobProxy clobProxy = (SerializableClobProxy) Proxy.getInvocationHandler(expectedClob);
    Clob wrappedClob = clobProxy.getWrappedClob();
    try {/*from  w  ww.ja va2 s. c  o m*/
        return wrappedClob.getSubString(1, (int) wrappedClob.length());
    } catch (SQLException e) {
        e.printStackTrace();
        return "error: could not retrieve text";
    }
}

From source file:HSqlManager.java

@SuppressWarnings("Duplicates")
@Deprecated/* ww w  .ja  v  a2s  .  com*/
public static void mycoUniqueDB(Connection connection, int bps) throws ClassNotFoundException, SQLException,
        InstantiationException, IllegalAccessException, IOException {
    long time = System.currentTimeMillis();
    DpalLoad.main(new String[1]);
    HSqlPrimerDesign.Dpal_Inst = DpalLoad.INSTANCE_WIN64;
    String base = new File("").getAbsolutePath();
    if (!written) {
        CSV.makeDirectory(new File(base + "/PhageData"));
        INSTANCE.parseAllPhages(bps);
    }
    Connection db = connection;
    db.setAutoCommit(false);
    Statement stat = db.createStatement();
    PrintWriter log = new PrintWriter(new File("javalog.log"));
    stat.execute("SET FILES LOG FALSE;\n");
    PreparedStatement st = db
            .prepareStatement("UPDATE Primerdb.Primers" + " SET UniqueP = true, Tm = ?, GC =?, Hairpin =?"
                    + "WHERE Cluster = ? and Strain = ? and " + "Sequence = ? and Bp = ?");
    ResultSet call = stat.executeQuery("Select * From Primerdb.Phages;");
    List<String[]> phages = new ArrayList<>();
    String strain = "";
    while (call.next()) {
        String[] r = new String[3];
        r[0] = call.getString("Strain");
        r[1] = call.getString("Cluster");
        r[2] = call.getString("Name");
        phages.add(r);
        if (r[2].equals("xkcd")) {
            strain = r[0];
        }
    }
    call.close();
    String x = strain;
    Set<String> clust = phages.stream().filter(y -> y[0].equals(x)).map(y -> y[1]).collect(Collectors.toSet());
    String[] clusters = clust.toArray(new String[clust.size()]);
    for (String z : clusters) {
        try {
            Set<String> nonclustphages = phages.stream().filter(a -> a[0].equals(x) && !a[1].equals(z))
                    .map(a -> a[2]).collect(Collectors.toSet());
            ResultSet resultSet = stat.executeQuery(
                    "Select Sequence from primerdb.primers" + " where Strain ='" + x + "' and Cluster ='" + z
                            + "' and CommonP = true" + " and Bp = " + Integer.valueOf(bps) + " ");
            Set<CharSequence> primers = Collections.synchronizedSet(new HashSet<>());
            while (resultSet.next()) {
                primers.add(resultSet.getString("Sequence"));
            }
            resultSet.close();
            for (String phage : nonclustphages) {
                //                    String[] seqs = Fasta.parse(base + "/Fastas/" + phage + ".fasta");
                //                    String sequence =seqs[0]+seqs[1];
                //                        Map<String, List<Integer>> seqInd = new HashMap<>();
                //                        for (int i = 0; i <= sequence.length()-bps; i++) {
                //                            String sub=sequence.substring(i,i+bps);
                //                            if(seqInd.containsKey(sub)){
                //                                seqInd.get(sub).add(i);
                //                            }else {
                //                                List<Integer> list = new ArrayList<>();
                //                                list.add(i);
                //                                seqInd.put(sub,list);
                //                            }
                //                        }
                //                    primers = primers.stream().filter(primer->!seqInd.containsKey(primer)).collect(Collectors.toSet());
                //                    primers =Sets.difference(primers,CSV.readCSV(base + "/PhageData/"+Integer.toString(bps)
                //                                    + phage + ".csv"));
                CSV.readCSV(base + "/PhageData/" + Integer.toString(bps) + phage + ".csv").stream()
                        .filter(primers::contains).forEach(primers::remove);
                //                    System.gc();

            }
            int i = 0;
            for (CharSequence a : primers) {
                try {
                    st.setDouble(1, HSqlPrimerDesign.primerTm(a, 0, 800, 1.5, 0.2));
                    st.setDouble(2, HSqlPrimerDesign.gcContent(a));
                    st.setBoolean(3, HSqlPrimerDesign.calcHairpin((String) a, 4));
                    st.setString(4, z);
                    st.setString(5, x);
                    st.setString(6, a.toString());
                    st.setInt(7, bps);
                    st.addBatch();
                } catch (SQLException e) {
                    e.printStackTrace();
                    System.out.println("Error occurred at " + x + " " + z);
                }
                i++;
                if (i == 1000) {
                    i = 0;
                    st.executeBatch();
                    db.commit();
                }
            }
            if (i > 0) {
                st.executeBatch();
                db.commit();
            }
        } catch (SQLException e) {
            e.printStackTrace();
            System.out.println("Error occurred at " + x + " " + z);
        }
        log.println(z);
        log.flush();
        System.gc();
    }
    stat.execute("SET FILES LOG TRUE\n");
    st.close();
    stat.close();
    System.out.println("Unique Updated");
    System.out.println((System.currentTimeMillis() - time) / Math.pow(10, 3) / 60);
}

From source file:Data.java

/**
 * Creates a dataset, consisting of two series of monthly data.
 *
 * @return The dataset.//from  w w w  .  j a  v  a2  s .com
 * @throws ClassNotFoundException 
 */
private static XYDataset createDataset(Statement stmt) throws ClassNotFoundException {

    TimeSeries s1 = new TimeSeries("Humidit");
    TimeSeries s2 = new TimeSeries("Temprature");
    ResultSet rs = null;

    try {
        String sqlRequest = "SELECT * FROM `t_temphum`";
        rs = stmt.executeQuery(sqlRequest);
        Double hum;
        Double temp;
        Timestamp date;

        while (rs.next()) {
            hum = rs.getDouble("tmp_humidity");
            temp = rs.getDouble("tmp_temperature");
            date = rs.getTimestamp("tmp_date");

            if (tempUnit == "F") {
                temp = celsiusToFahrenheit(temp.toString());
            }

            if (date != null) {
                s1.add(new Second(date), hum);
                s2.add(new Second(date), temp);
            } else {
                JOptionPane.showMessageDialog(panelPrincipal, "Il manque une date dans la dase de donne",
                        "Date null", JOptionPane.WARNING_MESSAGE);
            }
        }

        rs.close();
    } catch (SQLException e) {
        String exception = e.toString();

        if (e.getErrorCode() == 0) {
            JOptionPane.showMessageDialog(panelPrincipal,
                    "Le serveur met trop de temps  rpondre ! Veuillez rssayer plus tard ou contacter un administrateur",
                    "Connection timed out", JOptionPane.ERROR_MESSAGE);
        } else {
            JOptionPane.showMessageDialog(panelPrincipal, "Voici l'exception : " + exception,
                    "Titre : exception", JOptionPane.ERROR_MESSAGE);
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    } catch (Exception e) {
        String exception = e.toString();
        JOptionPane.showMessageDialog(panelPrincipal, "Voici l'exception : " + exception, "Titre : exception",
                JOptionPane.ERROR_MESSAGE);
        e.printStackTrace();
    }

    // ******************************************************************
    //  More than 150 demo applications are included with the JFreeChart
    //  Developer Guide...for more information, see:
    //
    //  >   http://www.object-refinery.com/jfreechart/guide.html
    //
    // ******************************************************************

    TimeSeriesCollection dataset = new TimeSeriesCollection();
    dataset.addSeries(s1);
    dataset.addSeries(s2);

    return dataset;

}

From source file:com.musala.core.RssManager.java

@PostConstruct
public void startServer() {
    //TODO For testing purposes only, to be deleted
    Server server = null;/*from   w  ww.j  a v  a 2  s .c om*/
    try {
        server = Server.createTcpServer().start();
    } catch (SQLException e) {
        e.printStackTrace();
    }

    logger.info("Server started and connection is open.");
    logger.info("URL: jdbc:h2:" + server.getURL() + "/mem:test");
}

From source file:ca.qc.adinfo.rouge.server.DBManager.java

public void disconnect() {

    try {/*from ww w  .ja  v  a 2 s.c om*/
        this.dataSource.close();
    } catch (SQLException e) {
        e.printStackTrace();
    }
}

From source file:cognition.pipeline.data.helper.BlobHelper.java

private byte[] getBytesFromSerializableBlob(Object serializableBlobProxy) {
    SerializableBlobProxy blobProxy = (SerializableBlobProxy) Proxy.getInvocationHandler(serializableBlobProxy);
    Blob wrappedBlob = blobProxy.getWrappedBlob();
    try {//from   w w  w  . j ava2s .  c o m
        byte[] bytes = wrappedBlob.getBytes(1, (int) wrappedBlob.length());
        if (bytes != null) {
            if (bytes.length == 0) {
                return null;
            }
        }
        return bytes;
    } catch (SQLException e) {
        e.printStackTrace();
    }
    return null;
}

From source file:HSqlPrimerDesign.java

@SuppressWarnings("Duplicates")
public static void locations(Connection connection) throws ClassNotFoundException, SQLException,
        InstantiationException, IllegalAccessException, IOException {
    long time = System.nanoTime();
    String base = new File("").getAbsolutePath();
    DpalLoad.main(new String[0]);
    Dpal_Inst = DpalLoad.INSTANCE_WIN64;
    System.out.println(Dpal_Inst);
    Connection db = connection;/*from  w  w w . j av  a  2  s.  c  o m*/
    db.setAutoCommit(false);
    Statement stat = db.createStatement();
    PrintWriter log = new PrintWriter(new File("javalog.log"));
    stat.execute("SET FILES LOG FALSE;");
    PreparedStatement st = db.prepareStatement("INSERT INTO Primerdb.MatchedPrimers("
            + "Primer, PrimerMatch, Comp,FragAVG,FragVAR,H2SD,L2SD, Cluster, Strain)"
            + "Values(?,?,?,?,?,?,?,?,?)");
    ResultSet call = stat.executeQuery("Select * From Primerdb.Phages;");
    List<String[]> phages = new ArrayList<>();
    while (call.next()) {
        String[] r = new String[3];
        r[0] = call.getString("Strain");
        r[1] = call.getString("Cluster");
        r[2] = call.getString("Name");
        phages.add(r);
        //            if(strain.equals("-myco")) {
        //                if (r[2].equals("xkcd")) {
        //                    strain = r[0];
        //                }
        //            }else if(strain.equals("-arthro")){
        //                if (r[2].equals("ArV1")) {
        //                    strain = r[0];
        //                }
        //            }
    }
    call.close();
    Set<String> strains = phages.stream().map(y -> y[0]).collect(Collectors.toSet());
    for (String x : strains) {
        Set<String> clust = phages.stream().filter(y -> y[0].equals(x)).map(y -> y[1])
                .collect(Collectors.toSet());
        String[] clusters = clust.toArray(new String[clust.size()]);
        //        String z ="A1";
        for (String z : clusters) {
            System.out.println("Starting:" + z);
            List<Primer> primers = new ArrayList<>();
            Set<Matches> matched = new HashSet<>();
            Set<String> clustphage = phages.stream().filter(a -> a[0].equals(x) && a[1].equals(z))
                    .map(a -> a[2]).collect(Collectors.toSet());
            String[] clustphages = clustphage.toArray(new String[clustphage.size()]);
            if (clustphages.length > 1) {
                try {
                    ResultSet resultSet = stat
                            .executeQuery("Select * from primerdb.primers" + " where Strain ='" + x
                                    + "' and Cluster ='" + z + "' and UniqueP = true" + " and Hairpin = false");
                    while (resultSet.next()) {
                        Primer primer = new Primer(resultSet.getString("Sequence"));
                        primer.setTm(resultSet.getDouble("Tm"));
                        primers.add(primer);
                    }
                    resultSet.close();
                } catch (SQLException e) {
                    e.printStackTrace();
                    System.out.println("Error occurred at " + x + " " + z);
                }
                System.out.println(primers.size());
                Set<Primer> primerlist2 = primers.stream().collect(Collectors.toSet());
                Primer[] primers2 = primerlist2.toArray(new Primer[primerlist2.size()]);
                Map<String, Map<CharSequence, List<Integer>>> locations = Collections
                        .synchronizedMap(new HashMap<>());
                clustphage.stream().forEach(phage -> {
                    String[] seqs = Fasta.parse(base + "/Fastas/" + phage + ".fasta");
                    String sequence = seqs[0] + seqs[1];
                    Map<String, List<Integer>> seqInd = new HashMap<>();
                    for (int i = 0; i <= sequence.length() - 10; i++) {
                        String sub = sequence.substring(i, i + 10);
                        if (seqInd.containsKey(sub)) {
                            seqInd.get(sub).add(i);
                        } else {
                            List<Integer> list = new ArrayList<>();
                            list.add(i);
                            seqInd.put(sub, list);
                        }
                    }
                    Map<CharSequence, List<Integer>> alllocs = new HashMap<>();
                    for (Primer primer : primers2) {
                        List<Integer> locs = new ArrayList<>();
                        String sequence1 = primer.getSequence();
                        String frag = sequence1.substring(0, 10);
                        List<Integer> integers = seqInd.get(frag);
                        if (integers != null) {
                            for (Integer i : integers) {
                                if ((sequence1.length() + i) < sequence.length()
                                        && sequence.substring(i, sequence1.length() + i).equals(sequence1)) {
                                    locs.add(i);
                                }
                            }
                        }
                        alllocs.put(sequence1, locs);
                    }
                    locations.put(phage, alllocs);
                });
                System.out.println("locations found");
                System.out.println((System.nanoTime() - time) / Math.pow(10, 9) / 60.0);
                final int[] k = new int[] { 0 };
                primerlist2.parallelStream().forEach(a -> {
                    int matches = 0;
                    int i = 0;
                    while (primers2[i] != a) {
                        i++;
                    }
                    for (int j = i + 1; j < primers2.length; j++) {
                        double[] frags = new double[clustphages.length];
                        int phageCounter = 0;
                        Primer b = primers2[j];
                        boolean match = true;
                        if (matches > 0) {
                            break;
                        }
                        if (Math.abs(a.getTm() - b.getTm()) > 5.0 || a.getSequence().equals(b.getSequence())) {
                            continue;
                        }
                        for (String phage : clustphages) {
                            List<Integer> loc1 = locations.get(phage).get(a.getSequence());
                            List<Integer> loc2 = locations.get(phage).get(b.getSequence());
                            //                            if(loc1.size()==0){
                            //                                System.out.println(phage+" "+a.getSequence());
                            //                            }
                            if (loc1.size() == 0 || loc2.size() == 0) {
                                //                                if (loc1.size()!=1||loc2.size()!=1){
                                match = false;
                                break;
                            }
                            boolean found = false;
                            int fragCount = 0;
                            int l1 = loc1.get(0);
                            int l2 = loc2.get(0);
                            int count1 = 0;
                            int count2 = 0;
                            int frag = Math.abs(l1 - l2);
                            while (!found) {
                                if (frag >= 500 && frag <= 2000) {
                                    fragCount++;
                                    if (++count1 < loc1.size())
                                        l1 = loc1.get(count1);
                                    else if (++count2 < loc2.size())
                                        l2 = loc2.get(count2);
                                } else if (l1 < l2 && frag < 500) {
                                    count2++;
                                } else if (l1 > l2 && frag < 500) {
                                    count1++;
                                } else if (l1 > l2 && frag > 2000) {
                                    count2++;
                                } else if (l1 < l2 && frag > 2000) {
                                    count1++;
                                } else {
                                    break;
                                }
                                if (count1 < loc1.size() && count2 < loc2.size()) {
                                    l1 = loc1.get(count1);
                                    l2 = loc2.get(count2);
                                    frag = Math.abs(l1 - l2);
                                } else {
                                    if (fragCount == 1) {
                                        found = true;
                                        frags[phageCounter++] = frag + 0.0;
                                    } else {
                                        break;
                                    }
                                }
                            }
                            if (!found) {
                                match = false;
                                break;
                            }

                        }
                        if (match) {
                            matches++;
                            matched.add(new Matches(a, b, frags));
                        }
                    }
                    //                    k[0]++;
                    //                    System.out.println(k[0]);
                });
                System.out.println((System.nanoTime() - time) / Math.pow(10, 9) / 60.0);
                System.out.println("Primers matched");
                int c = 0;
                int i = 0;
                try {
                    for (Matches primerkey : matched) {
                        c++;
                        String primer1 = primerkey.one.getSequence();
                        String primer2 = primerkey.two.getSequence();
                        st.setString(1, primer1);
                        st.setString(2, primer2);
                        st.setDouble(3, complementarity(primer1, primer2, Dpal_Inst));
                        st.setDouble(4, primerkey.stats.getMean());
                        st.setDouble(5, primerkey.stats.getVariance());
                        st.setDouble(6, primerkey.stats.getMean() + 2 * primerkey.stats.getStandardDeviation());
                        st.setDouble(7, primerkey.stats.getMean() - 2 * primerkey.stats.getStandardDeviation());
                        st.setString(8, z);
                        st.setString(9, x);
                        st.addBatch();
                        i++;
                        if (i == 1000) {
                            i = 0;
                            st.executeBatch();
                            db.commit();
                        }
                    }

                    if (i > 0) {
                        st.executeBatch();
                        db.commit();
                    }
                } catch (SQLException e) {
                    e.printStackTrace();
                    System.out.println("Error occurred at " + x + " " + z);
                }
                System.out.println(c);
            }
            log.println(z);
            log.flush();
            System.gc();
        }
    }
    stat.execute("SET FILES LOG TRUE;");
    st.close();
    stat.close();
    System.out.println("Matches Submitted");
}

From source file:com.hendisantika.pasien.domain.PasienIdGenerator.java

public Serializable generate(SessionImplementor session, Object object) throws HibernateException {

    String prefix = "PAS-";
    //        String prefix = "1500";
    Connection connection = session.connection();
    try {//from  ww  w .  jav a  2  s.c o m

        PreparedStatement ps = connection
                .prepareStatement("SELECT MAX(pasien_id) as value from db_pasien.pasien2");

        ResultSet rs = ps.executeQuery();
        if (rs.next()) {
            int id = rs.getInt("value") + 1;
            //                String id = rs.getString("value") + 1;
            String code = prefix + new Integer(id);
            //                String code = prefix + id;

            //                String code = prefix + StringUtils.leftPad("" + id, 3, '0');
            System.out.println("Generated pasienId: " + code);
            return code;
        }
    } catch (SQLException e) {
        e.printStackTrace();
    }
    return null;
}

From source file:gemlite.testing.util.DBManager.java

private boolean checkConnection(BasicDataSource dataSource) {

    try {/*from   www. j a  v a 2s . co m*/
        Connection conn = dataSource.getConnection();
        conn.close();
    } catch (SQLException e) {
        e.printStackTrace();
        return false;
    }

    return true;
}

From source file:com.jp.systemdirector.projectzero.zab01.ap.logicbean.SZAB011CUpdateLogicBean.java

@Transactional
public SZAB011CUpdateResultData execute(ContextData context, SZAB011CUpdateInputData inputData) {

    SZAB011CUpdateResultData resultData = new SZAB011CUpdateResultData();

    SZAB011CUpdateDTO zUpdateDTO = new SZAB011CUpdateDTO();

    // DTO?inputData?
    zUpdateDTO.setIN1(context.getProductCd());
    zUpdateDTO.setQUANTITY(new BigDecimal(context.getQuantity()));

    try {//from  w ww  .ja  va  2s.co  m
        int result = dao.update(zUpdateDTO);

        resultData.setAffectLines(result);
    } catch (SQLException e) {

        e.printStackTrace();
        throw new RuntimeException(e);
    }

    return resultData;
}