Example usage for java.sql ResultSet getFloat

List of usage examples for java.sql ResultSet getFloat

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Introduction

In this page you can find the example usage for java.sql ResultSet getFloat.

Prototype

float getFloat(String columnLabel) throws SQLException;

Source Link

Document

Retrieves the value of the designated column in the current row of this ResultSet object as a float in the Java programming language.

Usage

From source file:com.draagon.meta.manager.db.driver.GenericSQLDriver.java

protected void parseField(Object o, MetaField f, ResultSet rs, int j) throws SQLException {
    switch (f.getType()) {
    case MetaField.BOOLEAN: {
        boolean bv = rs.getBoolean(j);
        if (rs.wasNull()) {
            f.setBoolean(o, null);//from  w  ww  .java2 s . c  o  m
        } else {
            f.setBoolean(o, new Boolean(bv));
        }
    }
        break;

    case MetaField.BYTE: {
        byte bv = rs.getByte(j);
        if (rs.wasNull()) {
            f.setByte(o, null);
        } else {
            f.setByte(o, new Byte(bv));
        }
    }
        break;

    case MetaField.SHORT: {
        short sv = rs.getShort(j);
        if (rs.wasNull()) {
            f.setShort(o, null);
        } else {
            f.setShort(o, new Short(sv));
        }
    }
        break;

    case MetaField.INT: {
        int iv = rs.getInt(j);
        if (rs.wasNull()) {
            f.setInt(o, null);
        } else {
            f.setInt(o, new Integer(iv));
        }
    }
        break;

    case MetaField.DATE: {
        Timestamp tv = rs.getTimestamp(j);
        if (rs.wasNull()) {
            f.setDate(o, null);
        } else {
            f.setDate(o, new java.util.Date(tv.getTime()));
        }
    }
        break;

    case MetaField.LONG: {
        long lv = rs.getLong(j);
        if (rs.wasNull()) {
            f.setLong(o, null);
        } else {
            f.setLong(o, new Long(lv));
        }
    }
        break;

    case MetaField.FLOAT: {
        float fv = rs.getFloat(j);
        if (rs.wasNull()) {
            f.setFloat(o, null);
        } else {
            f.setFloat(o, new Float(fv));
        }
    }
        break;

    case MetaField.DOUBLE: {
        double dv = rs.getDouble(j);
        if (rs.wasNull()) {
            f.setDouble(o, null);
        } else {
            f.setDouble(o, new Double(dv));
        }
    }
        break;

    case MetaField.STRING:
        f.setString(o, rs.getString(j));
        break;

    case MetaField.OBJECT:
        f.setObject(o, rs.getObject(j));
        break;
    }
}

From source file:oscar.oscarRx.data.RxPrescriptionData.java

private Prescription getPrescriptionFromRS(ResultSet rs, int demographicNo) throws SQLException {
    Prescription p = new Prescription(rs.getInt("drugid"), oscar.Misc.getString(rs, "provider_no"),
            demographicNo);//  w w  w  . j a va  2 s .com
    p.setRxCreatedDate(rs.getDate("create_date"));
    p.setRxDate(rs.getDate("rx_date"));
    p.setEndDate(rs.getDate("end_date"));
    p.setWrittenDate(rs.getDate("written_date"));
    p.setBrandName(oscar.Misc.getString(rs, "BN"));
    p.setGCN_SEQNO(rs.getInt("GCN_SEQNO"));
    p.setCustomName(oscar.Misc.getString(rs, "customName"));
    p.setTakeMin(rs.getFloat("takemin"));
    p.setTakeMax(rs.getFloat("takemax"));
    p.setFrequencyCode(oscar.Misc.getString(rs, "freqcode"));
    p.setDuration(oscar.Misc.getString(rs, "duration"));
    p.setDurationUnit(oscar.Misc.getString(rs, "durunit"));
    p.setQuantity(oscar.Misc.getString(rs, "quantity"));
    p.setRepeat(rs.getInt("repeat"));
    p.setLastRefillDate(rs.getDate("last_refill_date"));
    p.setNosubs(rs.getInt("nosubs"));
    p.setPrn(rs.getInt("prn"));
    p.setSpecial(oscar.Misc.getString(rs, "special"));
    p.setArchived(oscar.Misc.getString(rs, "archived"));
    p.setGenericName(oscar.Misc.getString(rs, "GN"));
    p.setAtcCode(oscar.Misc.getString(rs, "ATC"));
    p.setScript_no(oscar.Misc.getString(rs, "script_no"));
    p.setRegionalIdentifier(oscar.Misc.getString(rs, "regional_identifier"));
    p.setUnit(oscar.Misc.getString(rs, "unit"));
    p.setUnitName(oscar.Misc.getString(rs, "unitName"));
    p.setMethod(oscar.Misc.getString(rs, "method"));
    p.setRoute(oscar.Misc.getString(rs, "route"));
    p.setDrugForm(oscar.Misc.getString(rs, "drug_form"));
    p.setCustomInstr(rs.getBoolean("custom_instructions"));
    p.setDosage(oscar.Misc.getString(rs, "dosage"));
    p.setLongTerm(rs.getBoolean("long_term"));
    p.setCustomNote(rs.getBoolean("custom_note"));
    p.setPastMed(rs.getBoolean("past_med"));
    p.setStartDateUnknown(rs.getBoolean("start_date_unknown"));
    p.setComment(rs.getString("comment"));
    if (rs.getObject("patient_compliance") == null)
        p.setPatientCompliance(null);
    else
        p.setPatientCompliance(rs.getBoolean("patient_compliance"));
    p.setOutsideProviderName(oscar.Misc.getString(rs, "outside_provider_name"));
    p.setOutsideProviderOhip(oscar.Misc.getString(rs, "outside_provider_ohip"));
    p.setPickupDate(rs.getDate("pickup_datetime"));
    p.setPickupTime(rs.getDate("pickup_datetime"));
    p.setETreatmentType(rs.getString("eTreatmentType"));
    p.setRxStatus(rs.getString("rxStatus"));
    if (rs.getObject("dispense_interval") != null)
        p.setDispenseInterval(rs.getInt("dispense_interval"));
    if (rs.getObject("refill_duration") != null)
        p.setRefillDuration(rs.getInt("refill_duration"));
    if (rs.getObject("refill_quantity") != null)
        p.setRefillQuantity(rs.getInt("refill_quantity"));

    // String datesRePrinted = oscar.Misc.getString(rs,"dates_reprinted");
    // if( datesRePrinted != null && datesRePrinted.length() > 0 ) {
    // p.setNumPrints(datesRePrinted.split(",").length + 1);
    // }
    // else {
    // p.setNumPrints(1);
    // }
    return p;

}

From source file:it.greenvulcano.gvesb.datahandling.dbo.utils.ExtendedRowSetBuilder.java

public int build(Document doc, String id, ResultSet rs, Set<Integer> keyField,
        Map<String, FieldFormatter> fieldNameToFormatter, Map<String, FieldFormatter> fieldIdToFormatter)
        throws Exception {
    if (rs == null) {
        return 0;
    }//w w w  . j  ava 2  s.  c  o m
    int rowCounter = 0;
    Element docRoot = doc.getDocumentElement();
    ResultSetMetaData metadata = rs.getMetaData();
    buildFormatterAndNamesArray(metadata, fieldNameToFormatter, fieldIdToFormatter);

    boolean noKey = ((keyField == null) || keyField.isEmpty());
    boolean isKeyCol = false;

    boolean isNull = false;
    Element data = null;
    Element row = null;
    Element col = null;
    Text text = null;
    String textVal = null;
    String precKey = null;
    String colKey = null;
    Map<String, Element> keyCols = new TreeMap<String, Element>();
    while (rs.next()) {
        if (rowCounter % 10 == 0) {
            ThreadUtils.checkInterrupted(getClass().getSimpleName(), name, logger);
        }
        row = parser.createElementNS(doc, AbstractDBO.ROW_NAME, NS);

        parser.setAttribute(row, AbstractDBO.ID_NAME, id);
        for (int j = 1; j <= metadata.getColumnCount(); j++) {
            FieldFormatter fF = fFormatters[j];
            String colName = colNames[j];

            isKeyCol = (!noKey && keyField.contains(new Integer(j)));
            isNull = false;
            col = parser.createElementNS(doc, colName, NS);
            if (isKeyCol) {
                parser.setAttribute(col, AbstractDBO.ID_NAME, String.valueOf(j));
            }
            switch (metadata.getColumnType(j)) {
            case Types.DATE:
            case Types.TIME:
            case Types.TIMESTAMP: {
                parser.setAttribute(col, AbstractDBO.TYPE_NAME, AbstractDBO.TIMESTAMP_TYPE);
                Timestamp dateVal = rs.getTimestamp(j);
                isNull = dateVal == null;
                parser.setAttribute(col, AbstractDBO.NULL_NAME, String.valueOf(isNull));
                if (isNull) {
                    parser.setAttribute(col, AbstractDBO.FORMAT_NAME, AbstractDBO.DEFAULT_DATE_FORMAT);
                    textVal = "";
                } else {
                    if (fF != null) {
                        parser.setAttribute(col, AbstractDBO.FORMAT_NAME, fF.getDateFormat());
                        textVal = fF.formatDate(dateVal);
                    } else {
                        parser.setAttribute(col, AbstractDBO.FORMAT_NAME, AbstractDBO.DEFAULT_DATE_FORMAT);
                        textVal = dateFormatter.format(dateVal);
                    }
                }
            }
                break;
            case Types.DOUBLE:
            case Types.FLOAT:
            case Types.REAL: {
                parser.setAttribute(col, AbstractDBO.TYPE_NAME, AbstractDBO.FLOAT_TYPE);
                float numVal = rs.getFloat(j);
                parser.setAttribute(col, AbstractDBO.NULL_NAME, "false");
                if (fF != null) {
                    parser.setAttribute(col, AbstractDBO.FORMAT_NAME, fF.getNumberFormat());
                    parser.setAttribute(col, AbstractDBO.GRP_SEPARATOR_NAME, fF.getGroupSeparator());
                    parser.setAttribute(col, AbstractDBO.DEC_SEPARATOR_NAME, fF.getDecSeparator());
                    textVal = fF.formatNumber(numVal);
                } else {
                    parser.setAttribute(col, AbstractDBO.FORMAT_NAME, numberFormat);
                    parser.setAttribute(col, AbstractDBO.GRP_SEPARATOR_NAME, groupSeparator);
                    parser.setAttribute(col, AbstractDBO.DEC_SEPARATOR_NAME, decSeparator);
                    textVal = numberFormatter.format(numVal);
                }
            }
                break;
            case Types.BIGINT:
            case Types.INTEGER:
            case Types.NUMERIC:
            case Types.SMALLINT:
            case Types.TINYINT: {
                BigDecimal bigdecimal = rs.getBigDecimal(j);
                isNull = bigdecimal == null;
                parser.setAttribute(col, AbstractDBO.NULL_NAME, String.valueOf(isNull));
                if (isNull) {
                    if (metadata.getScale(j) > 0) {
                        parser.setAttribute(col, AbstractDBO.TYPE_NAME, AbstractDBO.FLOAT_TYPE);
                    } else {
                        parser.setAttribute(col, AbstractDBO.TYPE_NAME, AbstractDBO.NUMERIC_TYPE);
                    }
                    textVal = "";
                } else {
                    if (fF != null) {
                        parser.setAttribute(col, AbstractDBO.TYPE_NAME, AbstractDBO.FLOAT_TYPE);
                        parser.setAttribute(col, AbstractDBO.FORMAT_NAME, fF.getNumberFormat());
                        parser.setAttribute(col, AbstractDBO.GRP_SEPARATOR_NAME, fF.getGroupSeparator());
                        parser.setAttribute(col, AbstractDBO.DEC_SEPARATOR_NAME, fF.getDecSeparator());
                        textVal = fF.formatNumber(bigdecimal);
                    } else if (metadata.getScale(j) > 0) {
                        parser.setAttribute(col, AbstractDBO.TYPE_NAME, AbstractDBO.FLOAT_TYPE);
                        parser.setAttribute(col, AbstractDBO.FORMAT_NAME, numberFormat);
                        parser.setAttribute(col, AbstractDBO.GRP_SEPARATOR_NAME, groupSeparator);
                        parser.setAttribute(col, AbstractDBO.DEC_SEPARATOR_NAME, decSeparator);
                        textVal = numberFormatter.format(bigdecimal);
                    } else {
                        parser.setAttribute(col, AbstractDBO.TYPE_NAME, AbstractDBO.NUMERIC_TYPE);
                        textVal = bigdecimal.toString();
                    }
                }
            }
                break;
            case Types.NCHAR:
            case Types.NVARCHAR: {
                parser.setAttribute(col, AbstractDBO.TYPE_NAME, AbstractDBO.NSTRING_TYPE);
                textVal = rs.getNString(j);
                isNull = textVal == null;
                parser.setAttribute(col, AbstractDBO.NULL_NAME, String.valueOf(isNull));
                if (isNull) {
                    textVal = "";
                }
            }
                break;
            case Types.CHAR:
            case Types.VARCHAR: {
                parser.setAttribute(col, AbstractDBO.TYPE_NAME, AbstractDBO.STRING_TYPE);
                textVal = rs.getString(j);
                isNull = textVal == null;
                parser.setAttribute(col, AbstractDBO.NULL_NAME, String.valueOf(isNull));
                if (isNull) {
                    textVal = "";
                }
            }
                break;
            case Types.NCLOB: {
                parser.setAttribute(col, AbstractDBO.TYPE_NAME, AbstractDBO.LONG_NSTRING_TYPE);
                NClob clob = rs.getNClob(j);
                isNull = clob == null;
                parser.setAttribute(col, AbstractDBO.NULL_NAME, String.valueOf(isNull));
                if (isNull) {
                    textVal = "";
                } else {
                    Reader is = clob.getCharacterStream();
                    StringWriter str = new StringWriter();

                    IOUtils.copy(is, str);
                    is.close();
                    textVal = str.toString();
                }
            }
                break;
            case Types.CLOB: {
                parser.setAttribute(col, AbstractDBO.TYPE_NAME, AbstractDBO.LONG_STRING_TYPE);
                Clob clob = rs.getClob(j);
                isNull = clob == null;
                parser.setAttribute(col, AbstractDBO.NULL_NAME, String.valueOf(isNull));
                if (isNull) {
                    textVal = "";
                } else {
                    Reader is = clob.getCharacterStream();
                    StringWriter str = new StringWriter();

                    IOUtils.copy(is, str);
                    is.close();
                    textVal = str.toString();
                }
            }
                break;
            case Types.BLOB: {
                parser.setAttribute(col, AbstractDBO.TYPE_NAME, AbstractDBO.BASE64_TYPE);
                Blob blob = rs.getBlob(j);
                isNull = blob == null;
                parser.setAttribute(col, AbstractDBO.NULL_NAME, String.valueOf(isNull));
                if (isNull) {
                    textVal = "";
                } else {
                    InputStream is = blob.getBinaryStream();
                    ByteArrayOutputStream baos = new ByteArrayOutputStream();
                    IOUtils.copy(is, baos);
                    is.close();
                    try {
                        byte[] buffer = Arrays.copyOf(baos.toByteArray(), (int) blob.length());
                        textVal = Base64.getEncoder().encodeToString(buffer);
                    } catch (SQLFeatureNotSupportedException exc) {
                        textVal = Base64.getEncoder().encodeToString(baos.toByteArray());
                    }
                }
            }
                break;
            default: {
                parser.setAttribute(col, AbstractDBO.TYPE_NAME, AbstractDBO.DEFAULT_TYPE);
                textVal = rs.getString(j);
                isNull = textVal == null;
                parser.setAttribute(col, AbstractDBO.NULL_NAME, String.valueOf(isNull));
                if (isNull) {
                    textVal = "";
                }
            }
            }
            if (textVal != null) {
                text = doc.createTextNode(textVal);
                col.appendChild(text);
            }
            if (isKeyCol) {
                if (textVal != null) {
                    if (colKey == null) {
                        colKey = textVal;
                    } else {
                        colKey += "##" + textVal;
                    }
                    keyCols.put(String.valueOf(j), col);
                }
            } else {
                row.appendChild(col);
            }
        }
        if (noKey) {
            if (data == null) {
                data = parser.createElementNS(doc, AbstractDBO.DATA_NAME, NS);
                parser.setAttribute(data, AbstractDBO.ID_NAME, id);
            }
        } else if ((colKey != null) && !colKey.equals(precKey)) {
            if (data != null) {
                docRoot.appendChild(data);
            }
            data = parser.createElementNS(doc, AbstractDBO.DATA_NAME, NS);
            parser.setAttribute(data, AbstractDBO.ID_NAME, id);
            Element key = parser.createElementNS(doc, AbstractDBO.KEY_NAME, NS);
            data.appendChild(key);
            for (Entry<String, Element> keyColsEntry : keyCols.entrySet()) {
                key.appendChild(keyColsEntry.getValue());
            }
            keyCols.clear();
            precKey = colKey;
        }
        colKey = null;
        data.appendChild(row);
        rowCounter++;
    }
    if (data != null) {
        docRoot.appendChild(data);
    }

    return rowCounter;
}

From source file:oscar.oscarRx.data.RxPrescriptionData.java

public Prescription[] getPrescriptionsByPatientHideDeleted(int demographicNo) {
    Prescription[] arr = {};//from w  w w . j a  v a2s . co m
    ArrayList lst = new ArrayList();

    String sql = "SELECT * FROM drugs WHERE archived = 0 AND " + "demographic_no = " + demographicNo + " "
            + "ORDER BY position, rx_date DESC, drugId DESC";

    try {
        // Get Prescription from database

        ResultSet rs;

        Prescription p;

        rs = DBHandler.GetSQL(sql);

        while (rs.next()) {
            p = new Prescription(rs.getInt("drugid"), oscar.Misc.getString(rs, "provider_no"), demographicNo);
            p.setRxCreatedDate(rs.getDate("create_date"));
            p.setRxDate(rs.getDate("rx_date"));
            p.setEndDate(rs.getDate("end_date"));
            p.setWrittenDate(rs.getDate("written_date"));
            p.setBrandName(oscar.Misc.getString(rs, "BN"));
            p.setGCN_SEQNO(rs.getInt("GCN_SEQNO"));
            p.setCustomName(oscar.Misc.getString(rs, "customName"));
            p.setTakeMin(rs.getFloat("takemin"));
            p.setTakeMax(rs.getFloat("takemax"));
            p.setFrequencyCode(oscar.Misc.getString(rs, "freqcode"));
            p.setDuration(oscar.Misc.getString(rs, "duration"));
            p.setDurationUnit(oscar.Misc.getString(rs, "durunit"));
            p.setQuantity(oscar.Misc.getString(rs, "quantity"));
            p.setRepeat(rs.getInt("repeat"));
            p.setLastRefillDate(rs.getDate("last_refill_date"));
            p.setNosubs(rs.getInt("nosubs"));
            p.setPrn(rs.getInt("prn"));
            p.setSpecial(oscar.Misc.getString(rs, "special"));
            p.setGenericName(oscar.Misc.getString(rs, "GN"));
            p.setAtcCode(oscar.Misc.getString(rs, "ATC"));
            p.setScript_no(oscar.Misc.getString(rs, "script_no"));
            p.setRegionalIdentifier(oscar.Misc.getString(rs, "regional_identifier"));
            p.setUnit(oscar.Misc.getString(rs, "unit"));
            p.setUnitName(oscar.Misc.getString(rs, "unitName"));
            p.setMethod(oscar.Misc.getString(rs, "method"));
            p.setRoute(oscar.Misc.getString(rs, "route"));
            p.setDrugForm(oscar.Misc.getString(rs, "drug_form"));
            p.setCustomInstr(rs.getBoolean("custom_instructions"));
            p.setDosage(oscar.Misc.getString(rs, "dosage"));
            p.setLongTerm(rs.getBoolean("long_term"));
            p.setCustomNote(rs.getBoolean("custom_note"));
            p.setPastMed(rs.getBoolean("past_med"));
            p.setStartDateUnknown(rs.getBoolean("start_date_unknown"));
            p.setComment(rs.getString("comment"));
            if (rs.getObject("patient_compliance") == null)
                p.setPatientCompliance(null);
            else
                p.setPatientCompliance(rs.getBoolean("patient_compliance"));
            p.setOutsideProviderName(oscar.Misc.getString(rs, "outside_provider_name"));
            p.setOutsideProviderOhip(oscar.Misc.getString(rs, "outside_provider_ohip"));
            p.setPickupDate(rs.getDate("pickup_datetime"));
            p.setPickupTime(rs.getDate("pickup_datetime"));
            p.setETreatmentType(rs.getString("eTreatmentType"));
            p.setRxStatus(rs.getString("rxStatus"));
            if (rs.getObject("dispense_interval") != null)
                p.setDispenseInterval(rs.getInt("dispense_interval"));
            if (rs.getObject("refill_duration") != null)
                p.setRefillDuration(rs.getInt("refill_duration"));
            if (rs.getObject("refill_quantity") != null)
                p.setRefillQuantity(rs.getInt("refill_quantity"));
            lst.add(p);
        }

        rs.close();

        arr = (Prescription[]) lst.toArray(arr);

    } catch (SQLException e) {
        logger.error(sql, e);
    } finally {
        DbConnectionFilter.releaseThreadLocalDbConnection();
    }

    return arr;
}

From source file:oscar.oscarRx.data.RxPrescriptionData.java

public Prescription[] getPrescriptionsByPatient(int demographicNo) {
    Prescription[] arr = {};/*from   w w  w.jav a 2  s.  c  om*/
    ArrayList lst = new ArrayList();

    String sql = "SELECT * FROM drugs WHERE  " + "demographic_no = " + demographicNo + " "
            + "ORDER BY position, rx_date DESC, drugId DESC";

    try {
        // Get Prescription from database

        ResultSet rs;

        Prescription p;

        rs = DBHandler.GetSQL(sql);

        while (rs.next()) {
            p = new Prescription(rs.getInt("drugid"), oscar.Misc.getString(rs, "provider_no"), demographicNo);
            p.setRxCreatedDate(rs.getDate("create_date"));
            p.setRxDate(rs.getDate("rx_date"));
            p.setEndDate(rs.getDate("end_date"));
            p.setWrittenDate(rs.getDate("written_date"));
            p.setBrandName(oscar.Misc.getString(rs, "BN"));
            p.setGCN_SEQNO(rs.getInt("GCN_SEQNO"));
            p.setCustomName(oscar.Misc.getString(rs, "customName"));
            p.setTakeMin(rs.getFloat("takemin"));
            p.setTakeMax(rs.getFloat("takemax"));
            p.setFrequencyCode(oscar.Misc.getString(rs, "freqcode"));
            p.setDuration(oscar.Misc.getString(rs, "duration"));
            p.setDurationUnit(oscar.Misc.getString(rs, "durunit"));
            p.setQuantity(oscar.Misc.getString(rs, "quantity"));
            p.setRepeat(rs.getInt("repeat"));
            p.setLastRefillDate(rs.getDate("last_refill_date"));
            p.setNosubs(rs.getInt("nosubs"));
            p.setPrn(rs.getInt("prn"));
            p.setSpecial(oscar.Misc.getString(rs, "special"));
            p.setSpecialInstruction(oscar.Misc.getString(rs, "special_instruction"));
            p.setArchived(oscar.Misc.getString(rs, "archived"));
            p.setGenericName(oscar.Misc.getString(rs, "GN"));
            p.setAtcCode(oscar.Misc.getString(rs, "ATC"));
            p.setScript_no(oscar.Misc.getString(rs, "script_no"));
            p.setRegionalIdentifier(oscar.Misc.getString(rs, "regional_identifier"));
            p.setUnit(oscar.Misc.getString(rs, "unit"));
            p.setUnitName(oscar.Misc.getString(rs, "unitName"));
            p.setMethod(oscar.Misc.getString(rs, "method"));
            p.setRoute(oscar.Misc.getString(rs, "route"));
            p.setDrugForm(oscar.Misc.getString(rs, "drug_form"));
            p.setCustomInstr(rs.getBoolean("custom_instructions"));
            p.setDosage(oscar.Misc.getString(rs, "dosage"));
            p.setLongTerm(rs.getBoolean("long_term"));
            p.setCustomNote(rs.getBoolean("custom_note"));
            p.setPastMed(rs.getBoolean("past_med"));
            p.setStartDateUnknown(rs.getBoolean("start_date_unknown"));
            p.setComment(rs.getString("comment"));
            if (rs.getObject("patient_compliance") == null)
                p.setPatientCompliance(null);
            else
                p.setPatientCompliance(rs.getBoolean("patient_compliance"));
            p.setOutsideProviderName(oscar.Misc.getString(rs, "outside_provider_name"));
            p.setOutsideProviderOhip(oscar.Misc.getString(rs, "outside_provider_ohip"));
            p.setPickupDate(rs.getDate("pickup_datetime"));
            p.setPickupTime(rs.getDate("pickup_datetime"));
            p.setETreatmentType(rs.getString("eTreatmentType"));
            p.setRxStatus(rs.getString("rxStatus"));
            if (rs.getObject("dispense_interval") != null)
                p.setDispenseInterval(rs.getInt("dispense_interval"));
            if (rs.getObject("refill_duration") != null)
                p.setRefillDuration(rs.getInt("refill_duration"));
            if (rs.getObject("refill_quantity") != null)
                p.setRefillQuantity(rs.getInt("refill_quantity"));
            lst.add(p);
        }

        rs.close();

        arr = (Prescription[]) lst.toArray(arr);

    } catch (SQLException e) {
        logger.error(sql, e);
    } finally {
        DbConnectionFilter.releaseThreadLocalDbConnection();
    }

    return arr;
}

From source file:piramide.interaction.reasoner.db.deploy.DatabaseMigrator.java

/**
* Given the Downloaded table, we populate the Devices and Trends tables.
*///from ww w. java  2s.c o m
public void populateTables() {
    int invalidData = 0;

    try {
        final Connection con = DriverManager.getConnection(CONNECTION_URL, USERNAME, PASSWORD);

        final Statement stmtClearTrends = con.createStatement();
        stmtClearTrends.execute("DELETE FROM Trends");
        stmtClearTrends.close();

        final Statement stmtClearDevices = con.createStatement();
        stmtClearDevices.execute("DELETE FROM Devices");
        stmtClearDevices.close();

        con.setAutoCommit(false);

        final Statement stmtDownloaded = con.createStatement();
        final ResultSet rsDownloaded = stmtDownloaded
                .executeQuery("SELECT device_name, wurfl_id, marketing_name, brand_name, model_name, "
                        + "real_height, real_width, reso_height, "
                        + "reso_width, value, region FROM Downloaded");
        final List<String> deviceNames = new Vector<String>();
        final PreparedStatement stmtDevices = con.prepareStatement(
                "" + "INSERT INTO Devices(device_name, wurfl_id, marketing_name, brand_name, model_name, "
                        + "real_height, real_width, real_size, reso_height, reso_width, reso_size) "
                        + "Values(?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? )");
        final PreparedStatement stmtTrends = con.prepareStatement(
                "" + "INSERT INTO Trends( device_name, region, month, year, value, error_margin ) "
                        + "Values(?, ?, ?, ?, ?, ? )");
        final Map<String, Integer> month2month = new HashMap<String, Integer>();
        month2month.put("Jan", Integer.valueOf(1));
        month2month.put("Feb", Integer.valueOf(2));
        month2month.put("Mar", Integer.valueOf(3));
        month2month.put("Apr", Integer.valueOf(4));
        month2month.put("May", Integer.valueOf(5));
        month2month.put("Jun", Integer.valueOf(6));
        month2month.put("Jul", Integer.valueOf(7));
        month2month.put("Aug", Integer.valueOf(8));
        month2month.put("Sep", Integer.valueOf(9));
        month2month.put("Oct", Integer.valueOf(10));
        month2month.put("Nov", Integer.valueOf(11));
        month2month.put("Dec", Integer.valueOf(12));

        int counter = 0;
        final Set<String> badOnes = new HashSet<String>();

        while (rsDownloaded.next()) {
            ++counter;

            if (counter % 100 == 0) {
                System.out.println("committed... " + counter);
                con.commit();
            }

            final String deviceName = rsDownloaded.getString("device_name");

            if (deviceName.equals("htc x7500") || deviceName.equals("samsung sgh-m300")
                    || deviceName.equals("nokia verizon") || deviceName.equals("kddi a1407pt")
                    || deviceName.equals("nokia thr880i") || deviceName.equals("softbank softbank 910t")
                    || deviceName.equals("nokia 8860") || deviceName.equals("sony ericsson w580i")
                    || deviceName.equals("motorola c139") || deviceName.equals("samsung stripe")
                    || deviceName.equals("samsung sgh-c414") || deviceName.equals("samsung gt-e2121l")
                    || deviceName.equals("samsung sgh-z400") || deviceName.equals("i-mobile 606")
                    || deviceName.equals("softbank v302sh") || deviceName.equals("motorola krzr k1c"))
                continue;

            if (!deviceNames.contains(deviceName)) {
                stmtDevices.setString(1, deviceName);
                stmtDevices.setString(2, rsDownloaded.getString("wurfl_id"));
                stmtDevices.setString(3, rsDownloaded.getString("marketing_name"));
                stmtDevices.setString(4, rsDownloaded.getString("brand_name"));
                stmtDevices.setString(5, rsDownloaded.getString("model_name"));
                stmtDevices.setFloat(6, rsDownloaded.getFloat("real_height"));
                stmtDevices.setFloat(7, rsDownloaded.getFloat("real_width"));
                stmtDevices.setFloat(8,
                        rsDownloaded.getFloat("real_height") * rsDownloaded.getFloat("real_width"));
                stmtDevices.setInt(9, rsDownloaded.getInt("reso_height"));
                stmtDevices.setInt(10, rsDownloaded.getInt("reso_width"));
                stmtDevices.setInt(11, rsDownloaded.getInt("reso_height") * rsDownloaded.getInt("reso_width"));
                stmtDevices.execute();
                deviceNames.add(deviceName);
            }

            final String base64csv = rsDownloaded.getString("value");

            final CsvReader csvReader2 = buildCSVReader(base64csv);
            if (!csvReader2.readRecord() && base64csv.length() != 924) {
                final byte[] binaryCSV = new Base64().decode(base64csv);
                final String stringCSV = new String(binaryCSV, "utf-8");
                if (stringCSV.contains("could not be interpreted")) {
                    badOnes.add(rsDownloaded.getString("region") + "@" + deviceName);
                }
            }

            final CsvReader csvReader = buildCSVReader(base64csv);

            int previousMonth = 0;
            int previousYear = 0;
            float currentValue = 0.0f;
            String currentErrorMargin = "";

            boolean executed = false;
            while (csvReader.readRecord()) {
                executed = true;
                final String week = csvReader.get(0);
                final float value = Float.parseFloat(csvReader.get(1));
                final String errorMargin = csvReader.get(2);

                final String[] weekParts = week.split(" ");
                final Integer monthString = month2month.get(weekParts[0]);
                if (monthString == null) {
                    System.err.println("Failed to load device: " + deviceName);
                    continue;
                }
                final int month = monthString.intValue();
                final int year = Integer.parseInt(weekParts[2]);

                if (month == previousMonth && year == previousYear) {
                    currentValue += value;
                    currentErrorMargin = currentErrorMargin + "; " + errorMargin;
                    continue;
                }

                final String region = rsDownloaded.getString("region");

                //System.out.println(deviceName + " " + region + " " + month + " " + year);

                stmtTrends.setString(1, deviceName);
                stmtTrends.setString(2, region);
                stmtTrends.setInt(3, previousMonth);
                stmtTrends.setInt(4, previousYear);
                stmtTrends.setFloat(5, currentValue);
                stmtTrends.setString(6, currentErrorMargin);
                stmtTrends.execute();

                currentValue = value;
                currentErrorMargin = errorMargin;
                previousMonth = month;
                previousYear = year;
            }
            if (!executed) {
                invalidData++;
                badOnes.add(rsDownloaded.getString("region") + "@" + deviceName);
            }
        }

        con.commit();

        stmtDevices.close();
        stmtTrends.close();
        stmtDownloaded.close();

        System.out.println("Counter: " + counter);
        System.out.println("Invalid data: " + invalidData);

        if (invalidData > 0) {
            final StringBuilder builder = new StringBuilder();
            for (String badOne : badOnes) {
                builder.append(badOne);
                builder.append("\n");
            }

            FileUtils.writeStringToFile(new File(INVALID_FILE_PATH), builder.toString());

            System.err.println("Warning: data of " + invalidData
                    + " mobile devices is wrong. Check which devices at " + INVALID_FILE_PATH);
        }

    } catch (Exception e) {
        e.printStackTrace();
    }
}

From source file:oscar.oscarRx.data.RxPrescriptionData.java

public ArrayList<Prescription> getPrescriptionsByScriptNo(int script_no, int demographicNo) {
    ArrayList<Prescription> lst = new ArrayList<Prescription>();

    String sql = "select drugs.*, p.date_printed, p.dates_reprinted from drugs, prescription p where p.script_no = drugs.script_no and "
            + "drugs.script_no = " + script_no;

    try {//from   w ww.  j a v  a 2 s  .co  m
        // Get Prescription from database

        ResultSet rs;

        Prescription p;
        String datesRePrinted;

        rs = DBHandler.GetSQL(sql);

        while (rs.next()) {
            p = new Prescription(rs.getInt("drugid"), oscar.Misc.getString(rs, "provider_no"), demographicNo);
            p.setRxCreatedDate(rs.getDate("create_date"));
            p.setRxDate(rs.getDate("rx_date"));
            p.setEndDate(rs.getDate("end_date"));
            p.setWrittenDate(rs.getDate("written_date"));
            p.setBrandName(oscar.Misc.getString(rs, "BN"));
            p.setGCN_SEQNO(rs.getInt("GCN_SEQNO"));
            p.setCustomName(oscar.Misc.getString(rs, "customName"));
            p.setTakeMin(rs.getFloat("takemin"));
            p.setTakeMax(rs.getFloat("takemax"));
            p.setFrequencyCode(oscar.Misc.getString(rs, "freqcode"));
            p.setDuration(oscar.Misc.getString(rs, "duration"));
            p.setDurationUnit(oscar.Misc.getString(rs, "durunit"));
            p.setQuantity(oscar.Misc.getString(rs, "quantity"));
            p.setRepeat(rs.getInt("repeat"));
            p.setLastRefillDate(rs.getDate("last_refill_date"));
            p.setNosubs(rs.getInt("nosubs"));
            p.setPrn(rs.getInt("prn"));
            p.setSpecial(oscar.Misc.getString(rs, "special"));
            p.setGenericName(oscar.Misc.getString(rs, "GN"));
            p.setAtcCode(oscar.Misc.getString(rs, "ATC"));
            p.setScript_no(oscar.Misc.getString(rs, "script_no"));
            p.setRegionalIdentifier(oscar.Misc.getString(rs, "regional_identifier"));
            p.setUnit(oscar.Misc.getString(rs, "unit"));
            p.setUnitName(oscar.Misc.getString(rs, "unitName"));
            p.setMethod(oscar.Misc.getString(rs, "method"));
            p.setRoute(oscar.Misc.getString(rs, "route"));
            p.setDrugForm(oscar.Misc.getString(rs, "drug_form"));
            p.setCustomInstr(rs.getBoolean("custom_instructions"));
            p.setDosage(oscar.Misc.getString(rs, "dosage"));
            p.setLongTerm(rs.getBoolean("long_term"));
            p.setCustomNote(rs.getBoolean("custom_note"));
            p.setPastMed(rs.getBoolean("past_med"));
            p.setStartDateUnknown(rs.getBoolean("start_date_unknown"));
            p.setComment(rs.getString("comment"));
            if (rs.getObject("patient_compliance") == null)
                p.setPatientCompliance(null);
            else
                p.setPatientCompliance(rs.getBoolean("patient_compliance"));
            p.setOutsideProviderName(oscar.Misc.getString(rs, "outside_provider_name"));
            p.setOutsideProviderOhip(oscar.Misc.getString(rs, "outside_provider_ohip"));
            p.setPrintDate(rs.getDate("date_printed"));
            p.setPickupDate(rs.getDate("pickup_datetime"));
            p.setPickupTime(rs.getDate("pickup_datetime"));
            p.setETreatmentType(rs.getString("eTreatmentType"));
            p.setRxStatus(rs.getString("rxStatus"));
            if (rs.getObject("dispense_interval") != null)
                p.setDispenseInterval(rs.getInt("dispense_interval"));
            if (rs.getObject("refill_duration") != null)
                p.setRefillDuration(rs.getInt("refill_duration"));
            if (rs.getObject("refill_quantity") != null)
                p.setRefillQuantity(rs.getInt("refill_quantity"));

            datesRePrinted = oscar.Misc.getString(rs, "dates_reprinted");
            if (datesRePrinted != null && datesRePrinted.length() > 0)
                p.setNumPrints(datesRePrinted.split(",").length + 1);
            else
                p.setNumPrints(1);

            lst.add(p);
        }

        rs.close();
        DbConnectionFilter.getThreadLocalDbConnection().close();

    } catch (SQLException e) {
        logger.error(sql, e);
    }

    return lst;
}

From source file:oscar.oscarRx.data.RxPrescriptionData.java

public Prescription[] getPrescriptionScriptsByPatient(int demographicNo) {
    Prescription[] arr = {};//from   w  w  w.  j  a  v a2s .  c  om
    ArrayList lst = new ArrayList();

    String sql = "SELECT d.*, p.date_printed, p.dates_reprinted FROM drugs d, prescription p WHERE  "
            + "d.demographic_no = " + demographicNo + " and d.script_no = p.script_no "
            + "ORDER BY position DESC" + ", rx_date DESC, drugId ASC";

    try {
        // Get Prescription from database

        ResultSet rs;

        Prescription p;
        String datesRePrinted;

        rs = DBHandler.GetSQL(sql);

        while (rs.next()) {
            p = new Prescription(rs.getInt("drugid"), oscar.Misc.getString(rs, "provider_no"), demographicNo);
            p.setRxCreatedDate(rs.getDate("create_date"));
            p.setRxDate(rs.getDate("rx_date"));
            p.setEndDate(rs.getDate("end_date"));
            p.setWrittenDate(rs.getDate("written_date"));
            p.setBrandName(oscar.Misc.getString(rs, "BN"));
            p.setGCN_SEQNO(rs.getInt("GCN_SEQNO"));
            p.setCustomName(oscar.Misc.getString(rs, "customName"));
            p.setTakeMin(rs.getFloat("takemin"));
            p.setTakeMax(rs.getFloat("takemax"));
            p.setFrequencyCode(oscar.Misc.getString(rs, "freqcode"));
            p.setDuration(oscar.Misc.getString(rs, "duration"));
            p.setDurationUnit(oscar.Misc.getString(rs, "durunit"));
            p.setQuantity(oscar.Misc.getString(rs, "quantity"));
            p.setRepeat(rs.getInt("repeat"));
            p.setLastRefillDate(rs.getDate("last_refill_date"));
            p.setNosubs(rs.getInt("nosubs"));
            p.setPrn(rs.getInt("prn"));
            p.setSpecial(oscar.Misc.getString(rs, "special"));
            p.setArchived(oscar.Misc.getString(rs, "archived"));
            p.setGenericName(oscar.Misc.getString(rs, "GN"));
            p.setAtcCode(oscar.Misc.getString(rs, "ATC"));
            p.setScript_no(oscar.Misc.getString(rs, "script_no"));
            p.setRegionalIdentifier(oscar.Misc.getString(rs, "regional_identifier"));
            p.setUnit(oscar.Misc.getString(rs, "unit"));
            p.setUnitName(oscar.Misc.getString(rs, "unitName"));
            p.setMethod(oscar.Misc.getString(rs, "method"));
            p.setRoute(oscar.Misc.getString(rs, "route"));
            p.setDrugForm(oscar.Misc.getString(rs, "drug_form"));
            p.setCustomInstr(rs.getBoolean("custom_instructions"));
            p.setDosage(oscar.Misc.getString(rs, "dosage"));
            p.setLongTerm(rs.getBoolean("long_term"));
            p.setCustomNote(rs.getBoolean("custom_note"));
            p.setPastMed(rs.getBoolean("past_med"));
            p.setStartDateUnknown(rs.getBoolean("start_date_unknown"));
            p.setComment(rs.getString("comment"));
            if (rs.getObject("patient_compliance") == null)
                p.setPatientCompliance(null);
            else
                p.setPatientCompliance(rs.getBoolean("patient_compliance"));
            p.setOutsideProviderName(oscar.Misc.getString(rs, "outside_provider_name"));
            p.setOutsideProviderOhip(oscar.Misc.getString(rs, "outside_provider_ohip"));
            p.setPickupDate(rs.getDate("pickup_datetime"));
            p.setPickupTime(rs.getDate("pickup_datetime"));
            p.setETreatmentType(rs.getString("eTreatmentType"));
            p.setRxStatus(rs.getString("rxStatus"));
            if (rs.getObject("dispense_interval") != null)
                p.setDispenseInterval(rs.getInt("dispense_interval"));
            if (rs.getObject("refill_duration") != null)
                p.setRefillDuration(rs.getInt("refill_duration"));
            if (rs.getObject("refill_quantity") != null)
                p.setRefillQuantity(rs.getInt("refill_quantity"));

            datesRePrinted = oscar.Misc.getString(rs, "dates_reprinted");
            if (datesRePrinted != null && datesRePrinted.length() > 0) {
                p.setNumPrints(datesRePrinted.split(",").length + 1);
            } else {
                p.setNumPrints(1);
            }
            p.setPrintDate(rs.getDate("date_printed"));
            p.setDatesReprinted(datesRePrinted);
            lst.add(p);
        }

        rs.close();
        DbConnectionFilter.getThreadLocalDbConnection().close();

        arr = (Prescription[]) lst.toArray(arr);

    } catch (SQLException e) {
        logger.error(sql, e);
    }

    return arr;
}

From source file:massbank.DatabaseManager.java

public Record getAccessionData(String accessionId, String contributor) {
    Record acc = new Record(contributor);
    try {//  w  w w  .ja  v  a 2s. c o  m
        this.statementRECORD.setString(1, accessionId);
        ResultSet set = this.statementRECORD.executeQuery();
        int compoundID = -1;
        int sampleID = -1;
        int instrumentID = -1;
        if (set.next()) {
            acc.ACCESSION(set.getString("ACCESSION"));
            acc.RECORD_TITLE(set.getString("RECORD_TITLE"));
            acc.DATE(set.getDate("DATE").toLocalDate());
            acc.AUTHORS(set.getString("AUTHORS"));
            acc.LICENSE(set.getString("LICENSE"));
            acc.COPYRIGHT(set.getString("COPYRIGHT"));
            acc.PUBLICATION(set.getString("PUBLICATION"));
            compoundID = set.getInt("CH");
            sampleID = set.getInt("SP");
            instrumentID = set.getInt("AC_INSTRUMENT");
            acc.AC_MASS_SPECTROMETRY_MS_TYPE(set.getString("AC_MASS_SPECTROMETRY_MS_TYPE"));
            acc.AC_MASS_SPECTROMETRY_ION_MODE(set.getString("AC_MASS_SPECTROMETRY_ION_MODE"));
            acc.PK_SPLASH(set.getString("PK_SPLASH"));
            this.statementAC_CHROMATOGRAPHY.setString(1, set.getString("ACCESSION"));
            this.statementAC_MASS_SPECTROMETRY.setString(1, set.getString("ACCESSION"));
            this.statementMS_DATA_PROCESSING.setString(1, set.getString("ACCESSION"));
            this.statementMS_FOCUSED_ION.setString(1, set.getString("ACCESSION"));
            this.statementCOMMENT.setString(1, set.getString("ACCESSION"));
            this.statementPEAK.setString(1, set.getString("ACCESSION"));
            this.statementPK_NUM_PEAK.setString(1, set.getString("ACCESSION"));
            this.statementANNOTATION_HEADER.setString(1, accessionId);

            ResultSet tmp = this.statementAC_CHROMATOGRAPHY.executeQuery();
            List<Pair<String, String>> tmpList = new ArrayList<Pair<String, String>>();
            while (tmp.next())
                tmpList.add(Pair.of(tmp.getString("SUBTAG"), tmp.getString("VALUE")));
            acc.AC_CHROMATOGRAPHY(tmpList);

            tmp = this.statementAC_MASS_SPECTROMETRY.executeQuery();
            tmpList.clear();
            while (tmp.next())
                tmpList.add(Pair.of(tmp.getString("SUBTAG"), tmp.getString("VALUE")));
            acc.AC_MASS_SPECTROMETRY(tmpList);

            tmp = this.statementMS_DATA_PROCESSING.executeQuery();
            tmpList.clear();
            while (tmp.next())
                tmpList.add(Pair.of(tmp.getString("SUBTAG"), tmp.getString("VALUE")));
            acc.MS_DATA_PROCESSING(tmpList);

            tmp = this.statementMS_FOCUSED_ION.executeQuery();
            tmpList.clear();
            while (tmp.next())
                tmpList.add(Pair.of(tmp.getString("SUBTAG"), tmp.getString("VALUE")));
            acc.MS_FOCUSED_ION(tmpList);

            tmp = this.statementCOMMENT.executeQuery();
            List<String> tmpList2 = new ArrayList<String>();
            while (tmp.next())
                tmpList2.add(tmp.getString("COMMENT"));
            acc.COMMENT(tmpList2);

            tmp = this.statementANNOTATION_HEADER.executeQuery();
            //            int PK_ANNOTATION_HEADER_numberOfTokens   = -1;
            if (tmp.next()) {
                String PK_ANNOTATION_HEADER = tmp.getString("HEADER");
                String[] PK_ANNOTATION_HEADER_tokens = PK_ANNOTATION_HEADER.split(" ");
                acc.PK_ANNOTATION_HEADER(Arrays.asList(PK_ANNOTATION_HEADER_tokens));
                //               PK_ANNOTATION_HEADER_numberOfTokens   = PK_ANNOTATION_HEADER_tokens.length;
            }

            tmp = this.statementPEAK.executeQuery();
            //            acc.add("PK$PEAK", null, "m/z int. rel.int.");
            while (tmp.next()) {
                acc.PK_PEAK_ADD_LINE(Arrays.asList((Double) tmp.getDouble("PK_PEAK_MZ"),
                        (Double) (double) tmp.getFloat("PK_PEAK_INTENSITY"),
                        (Double) (double) tmp.getShort("PK_PEAK_RELATIVE")));
                String PK_ANNOTATION = tmp.getString("PK_ANNOTATION");
                if (PK_ANNOTATION != null)
                    acc.PK_ANNOTATION_ADD_LINE(Arrays.asList(PK_ANNOTATION.split(" ")));
            }
            tmp = this.statementPK_NUM_PEAK.executeQuery();
            while (tmp.next()) {
                acc.PK_NUM_PEAK(Integer.valueOf(tmp.getInt("PK_NUM_PEAK")));
            }
        } else
            throw new IllegalStateException("accessionId '" + accessionId + "' is not in database");
        if (compoundID == -1)
            throw new IllegalStateException("compoundID is not set");
        this.statementCOMPOUND.setInt(1, compoundID);
        set = this.statementCOMPOUND.executeQuery();
        while (set.next()) {
            String formulaString = set.getString("CH_FORMULA");
            IMolecularFormula m = MolecularFormulaManipulator.getMolecularFormula(formulaString,
                    DefaultChemObjectBuilder.getInstance());
            acc.CH_FORMULA(m);
            acc.CH_EXACT_MASS(set.getDouble("CH_EXACT_MASS"));

            String smilesString = set.getString("CH_SMILES");
            if (smilesString.equals("N/A"))
                acc.CH_SMILES(new AtomContainer());
            else {
                IAtomContainer c = new SmilesParser(DefaultChemObjectBuilder.getInstance())
                        .parseSmiles(smilesString);
                acc.CH_SMILES(c);
            }

            String iupacString = set.getString("CH_IUPAC");
            if (iupacString.equals("N/A"))
                acc.CH_IUPAC(new AtomContainer());
            else {
                // Get InChIToStructure
                InChIToStructure intostruct = InChIGeneratorFactory.getInstance()
                        .getInChIToStructure(iupacString, DefaultChemObjectBuilder.getInstance());
                INCHI_RET ret = intostruct.getReturnStatus();
                if (ret == INCHI_RET.WARNING) {
                    // Structure generated, but with warning message
                    System.out.println(acc.ACCESSION() + ": InChI warning: " + intostruct.getMessage());
                } else if (ret != INCHI_RET.OKAY) {
                    // Structure generation failed
                    throw new IllegalArgumentException(
                            "Can not parse INCHI string in \"CH$IUPAC\" field. Structure generation failed: "
                                    + ret.toString() + " [" + intostruct.getMessage() + "] for " + iupacString);
                }
                IAtomContainer iupac = intostruct.getAtomContainer();
                acc.CH_IUPAC(iupac);
            }

            // TODO CH$CDK_DEPICT_SMILES
            // TODO CH$CDK_DEPICT_GENERIC_SMILES
            // TODO CH$CDK_DEPICT_STRUCTURE_SMILES
            //            acc.add("CH$CDK_DEPICT_SMILES", null, set.getString("CH_CDK_DEPICT_SMILES"));
            //            acc.add("CH$CDK_DEPICT_GENERIC_SMILES", null, set.getString("CH_CDK_DEPICT_GENERIC_SMILES"));
            //            acc.add("CH$CDK_DEPICT_STRUCTURE_SMILES", null, set.getString("CH_CDK_DEPICT_STRUCTURE_SMILES"));
        }
        this.statementCH_LINK.setInt(1, compoundID);
        set = this.statementCH_LINK.executeQuery();
        List<Pair<String, String>> tmpList = new ArrayList<Pair<String, String>>();
        while (set.next()) {
            tmpList.add(Pair.of(set.getString("DATABASE_NAME"), set.getString("DATABASE_ID")));
        }
        acc.CH_LINK(tmpList);

        this.statementCOMPOUND_COMPOUND_CLASS.setInt(1, compoundID);
        set = this.statementCOMPOUND_COMPOUND_CLASS.executeQuery();
        List<String> tmpList2 = new ArrayList<String>();
        while (set.next()) {
            this.statementCOMPOUND_CLASS.setInt(1, set.getInt("CLASS"));
            ResultSet tmp = this.statementCOMPOUND_CLASS.executeQuery();
            while (tmp.next()) {
                tmpList2.add(tmp.getString("CH_COMPOUND_CLASS"));
            }
        }
        acc.CH_COMPOUND_CLASS(tmpList2);

        this.statementCOMPOUND_NAME.setInt(1, compoundID);
        set = this.statementCOMPOUND_NAME.executeQuery();
        tmpList2.clear();
        while (set.next()) {
            this.statementNAME.setInt(1, set.getInt("NAME"));
            ResultSet tmp = this.statementNAME.executeQuery();
            while (tmp.next()) {
                tmpList2.add(tmp.getString("CH_NAME"));
            }
        }
        acc.CH_NAME(tmpList2);

        this.statementSAMPLE.setInt(1, sampleID);
        set = this.statementSAMPLE.executeQuery();
        if (set.next()) {
            acc.SP_SCIENTIFIC_NAME(set.getString("SP_SCIENTIFIC_NAME"));
            acc.SP_LINEAGE(set.getString("SP_LINEAGE"));

            this.statementSP_LINK.setInt(1, set.getInt("ID"));
            ResultSet tmp = this.statementSP_LINK.executeQuery();
            tmpList.clear();
            while (tmp.next()) {
                String spLink = tmp.getString("SP_LINK");
                String[] tokens = spLink.split(" ");
                tmpList.add(Pair.of(tokens[0], tokens[1]));
            }
            acc.SP_LINK(tmpList);

            this.statementSP_SAMPLE.setInt(1, set.getInt("ID"));
            tmp = this.statementSP_SAMPLE.executeQuery();
            tmpList2.clear();
            while (tmp.next()) {
                tmpList2.add(tmp.getString("SP_SAMPLE"));
            }
            acc.SP_SAMPLE(tmpList2);
        }
        if (instrumentID == -1)
            throw new IllegalStateException("instrumentID is not set");
        this.statementINSTRUMENT.setInt(1, instrumentID);
        set = this.statementINSTRUMENT.executeQuery();
        if (set.next()) {
            acc.AC_INSTRUMENT(set.getString("AC_INSTRUMENT"));
            acc.AC_INSTRUMENT_TYPE(set.getString("AC_INSTRUMENT_TYPE"));
        } else
            throw new IllegalStateException("instrumentID is not in database");
    } catch (Exception e) {
        System.out.println("error: " + accessionId);
        e.printStackTrace();
        return null;
    }
    //      this.openConnection();

    return acc;
}

From source file:org.apache.ddlutils.platform.PlatformImplBase.java

/**
 * This is the core method to retrieve a value for a column from a result set. Its  primary
 * purpose is to call the appropriate method on the result set, and to provide an extension
 * point where database-specific implementations can change this behavior.
 * /*w ww .j a v a2  s .c  om*/
 * @param resultSet  The result set to extract the value from
 * @param columnName The name of the column; can be <code>null</code> in which case the
  *                   <code>columnIdx</code> will be used instead
  * @param columnIdx  The index of the column's value in the result set; is only used if
  *                   <code>columnName</code> is <code>null</code>
 * @param jdbcType   The jdbc type to extract
 * @return The value
 * @throws SQLException If an error occurred while accessing the result set
 */
protected Object extractColumnValue(ResultSet resultSet, String columnName, int columnIdx, int jdbcType)
        throws SQLException {
    boolean useIdx = (columnName == null);
    Object value;

    switch (jdbcType) {
    case Types.CHAR:
    case Types.VARCHAR:
    case Types.LONGVARCHAR:
        value = useIdx ? resultSet.getString(columnIdx) : resultSet.getString(columnName);
        break;
    case Types.NUMERIC:
    case Types.DECIMAL:
        value = useIdx ? resultSet.getBigDecimal(columnIdx) : resultSet.getBigDecimal(columnName);
        break;
    case Types.BIT:
    case Types.BOOLEAN:
        value = new Boolean(useIdx ? resultSet.getBoolean(columnIdx) : resultSet.getBoolean(columnName));
        break;
    case Types.TINYINT:
    case Types.SMALLINT:
    case Types.INTEGER:
        value = new Integer(useIdx ? resultSet.getInt(columnIdx) : resultSet.getInt(columnName));
        break;
    case Types.BIGINT:
        value = new Long(useIdx ? resultSet.getLong(columnIdx) : resultSet.getLong(columnName));
        break;
    case Types.REAL:
        value = new Float(useIdx ? resultSet.getFloat(columnIdx) : resultSet.getFloat(columnName));
        break;
    case Types.FLOAT:
    case Types.DOUBLE:
        value = new Double(useIdx ? resultSet.getDouble(columnIdx) : resultSet.getDouble(columnName));
        break;
    case Types.BINARY:
    case Types.VARBINARY:
    case Types.LONGVARBINARY:
        value = useIdx ? resultSet.getBytes(columnIdx) : resultSet.getBytes(columnName);
        break;
    case Types.DATE:
        value = useIdx ? resultSet.getDate(columnIdx) : resultSet.getDate(columnName);
        break;
    case Types.TIME:
        value = useIdx ? resultSet.getTime(columnIdx) : resultSet.getTime(columnName);
        break;
    case Types.TIMESTAMP:
        value = useIdx ? resultSet.getTimestamp(columnIdx) : resultSet.getTimestamp(columnName);
        break;
    case Types.CLOB:
        Clob clob = useIdx ? resultSet.getClob(columnIdx) : resultSet.getClob(columnName);

        if (clob == null) {
            value = null;
        } else {
            long length = clob.length();

            if (length > Integer.MAX_VALUE) {
                value = clob;
            } else if (length == 0) {
                // the javadoc is not clear about whether Clob.getSubString
                // can be used with a substring length of 0
                // thus we do the safe thing and handle it ourselves
                value = "";
            } else {
                value = clob.getSubString(1l, (int) length);
            }
        }
        break;
    case Types.BLOB:
        Blob blob = useIdx ? resultSet.getBlob(columnIdx) : resultSet.getBlob(columnName);

        if (blob == null) {
            value = null;
        } else {
            long length = blob.length();

            if (length > Integer.MAX_VALUE) {
                value = blob;
            } else if (length == 0) {
                // the javadoc is not clear about whether Blob.getBytes
                // can be used with for 0 bytes to be copied
                // thus we do the safe thing and handle it ourselves
                value = new byte[0];
            } else {
                value = blob.getBytes(1l, (int) length);
            }
        }
        break;
    case Types.ARRAY:
        value = useIdx ? resultSet.getArray(columnIdx) : resultSet.getArray(columnName);
        break;
    case Types.REF:
        value = useIdx ? resultSet.getRef(columnIdx) : resultSet.getRef(columnName);
        break;
    default:
        value = useIdx ? resultSet.getObject(columnIdx) : resultSet.getObject(columnName);
        break;
    }
    return resultSet.wasNull() ? null : value;
}