opencsv upgraded

pom.xml

@@ -325,11 +325,6 @@
 			<scope>runtime</scope>
 		</dependency>
 
-		<dependency>
-			<groupId>net.sf.opencsv</groupId>
-			<artifactId>opencsv</artifactId>
-			<version>2.3</version>
-		</dependency>
 		<dependency>
 			<groupId>org.sitemesh</groupId>
 			<artifactId>sitemesh</artifactId>
@@ -502,6 +497,11 @@
 			<artifactId>jsoup</artifactId>
 			<version>1.8.2</version>
 		</dependency>
+		<dependency>
+			<groupId>com.opencsv</groupId>
+			<artifactId>opencsv</artifactId>
+			<version>3.7</version>
+		</dependency>
 	</dependencies>
 
 	<build>

src/main/java/org/genesys2/server/service/impl/CSVResultSetHelper.java

@@ -2,22 +2,18 @@ package org.genesys2.server.service.impl;
 
 import java.io.IOException;
 import java.io.Reader;
-import java.math.BigDecimal;
 import java.sql.Clob;
 import java.sql.ResultSet;
 import java.sql.ResultSetMetaData;
 import java.sql.SQLException;
-import java.sql.Time;
-import java.sql.Timestamp;
 import java.sql.Types;
-import java.text.SimpleDateFormat;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.UUID;
 
 import org.genesys2.util.NumberUtils;
 
-import au.com.bytecode.opencsv.ResultSetHelperService;
+import com.opencsv.ResultSetHelperService;
 
 /**
  * This class extends {@link ResultSetHelperService} by adding support for UUID.
@@ -34,56 +30,43 @@ public class CSVResultSetHelper extends ResultSetHelperService {
 	private static final int LONGNVARCHAR = -16;
 	private static final int NCLOB = 2011;
 
-	/// Copied straight from superclass
+	/**
+	 * Get all the column values from the result set.
+	 * 
+	 * @param rs
+	 *            - the ResultSet containing the values.
+	 * @param trim
+	 *            - values should have white spaces trimmed.
+	 * @param dateFormatString
+	 *            - format String for dates.
+	 * @param timeFormatString
+	 *            - format String for timestamps.
+	 * @return - String array containing all the column values.
+	 * @throws SQLException
+	 *             - thrown by the result set.
+	 * @throws IOException
+	 *             - thrown by the result set.
+	 */
 	@Override
-	public String[] getColumnValues(ResultSet rs) throws SQLException, IOException {
-
+	public String[] getColumnValues(ResultSet rs, boolean trim, String dateFormatString, String timeFormatString) throws SQLException, IOException {
 		List<String> values = new ArrayList<String>();
 		ResultSetMetaData metadata = rs.getMetaData();
 
 		for (int i = 0; i < metadata.getColumnCount(); i++) {
-			values.add(getColumnValue(rs, metadata.getColumnType(i + 1), i + 1));
+			values.add(getColumnValue(rs, metadata.getColumnType(i + 1), i + 1, trim, dateFormatString, timeFormatString));
 		}
 
 		String[] valueArray = new String[values.size()];
 		return values.toArray(valueArray);
 	}
 
-	private String handleObject(Object obj) {
-		return obj == null ? "" : String.valueOf(obj);
-	}
-
-	private String handleBigDecimal(BigDecimal decimal) {
-		return decimal == null ? "" : decimal.toString();
-	}
-
-	private String handleLong(ResultSet rs, int columnIndex) throws SQLException {
-		long lv = rs.getLong(columnIndex);
-		return rs.wasNull() ? "" : Long.toString(lv);
-	}
-
-	private String handleInteger(ResultSet rs, int columnIndex) throws SQLException {
-		int i = rs.getInt(columnIndex);
-		return rs.wasNull() ? "" : Integer.toString(i);
-	}
-
-	private String handleDate(ResultSet rs, int columnIndex) throws SQLException {
-		java.sql.Date date = rs.getDate(columnIndex);
-		String value = null;
-		if (date != null) {
-			SimpleDateFormat dateFormat = new SimpleDateFormat("dd-MMM-yyyy");
-			value = dateFormat.format(date);
-		}
-		return value;
-	}
-
 	private String handleBinary(ResultSet rs, int colIndex) throws SQLException {
 		byte[] bs = rs.getBytes(colIndex);
 
 		if (bs == null) {
 			return null;
 		}
-		
+
 		if (bs.length == 16) {
 			// UUID?
 			UUID uuid = NumberUtils.toUUID(bs);
@@ -94,16 +77,19 @@ public class CSVResultSetHelper extends ResultSetHelperService {
 		}
 	}
 
-	private String handleTime(Time time) {
-		return time == null ? null : time.toString();
-	}
-
-	private String handleTimestamp(Timestamp timestamp) {
-		SimpleDateFormat timeFormat = new SimpleDateFormat("dd-MMM-yyyy HH:mm:ss");
-		return timestamp == null ? null : timeFormat.format(timestamp);
+	private static String read(Clob c) throws SQLException, IOException {
+		StringBuilder sb = new StringBuilder((int) c.length());
+		Reader r = c.getCharacterStream();
+		char[] cbuf = new char[CLOBBUFFERSIZE];
+		int n;
+		while ((n = r.read(cbuf, 0, cbuf.length)) != -1) {
+			sb.append(cbuf, 0, n);
+		}
+		return sb.toString();
 	}
 
-	private String getColumnValue(ResultSet rs, int colType, int colIndex) throws SQLException, IOException {
+	private String getColumnValue(ResultSet rs, int colType, int colIndex, boolean trim, String dateFormatString, String timestampFormatString)
+			throws SQLException, IOException {
 
 		String value = "";
 
@@ -127,25 +113,29 @@ public class CSVResultSetHelper extends ResultSetHelperService {
 			value = handleLong(rs, colIndex);
 			break;
 		case Types.DECIMAL:
-		case Types.DOUBLE:
-		case Types.FLOAT:
 		case Types.REAL:
 		case Types.NUMERIC:
 			value = handleBigDecimal(rs.getBigDecimal(colIndex));
 			break;
+		case Types.DOUBLE:
+			value = handleDouble(rs.getDouble(colIndex));
+			break;
+		case Types.FLOAT:
+			value = handleFloat(rs.getFloat(colIndex));
+			break;
 		case Types.INTEGER:
 		case Types.TINYINT:
 		case Types.SMALLINT:
 			value = handleInteger(rs, colIndex);
 			break;
 		case Types.DATE:
-			value = handleDate(rs, colIndex);
+			value = handleDate(rs, colIndex, dateFormatString);
 			break;
 		case Types.TIME:
 			value = handleTime(rs.getTime(colIndex));
 			break;
 		case Types.TIMESTAMP:
-			value = handleTimestamp(rs.getTimestamp(colIndex));
+			value = handleTimestamp(rs.getTimestamp(colIndex), timestampFormatString);
 			break;
 		case NVARCHAR: // todo : use rs.getNString
 		case NCHAR: // todo : use rs.getNString
@@ -153,13 +143,17 @@ public class CSVResultSetHelper extends ResultSetHelperService {
 		case Types.LONGVARCHAR:
 		case Types.VARCHAR:
 		case Types.CHAR:
-			value = rs.getString(colIndex);
+			String columnValue = rs.getString(colIndex);
+			if (trim && columnValue != null) {
+				value = columnValue.trim();
+			} else {
+				value = columnValue;
+			}
 			break;
 		case Types.BINARY:
 			value = handleBinary(rs, colIndex);
 			break;
 		default:
-//			System.err.println("SQLType not handled " + colType);
 			value = "";
 		}
 
@@ -168,17 +162,5 @@ public class CSVResultSetHelper extends ResultSetHelperService {
 		}
 
 		return value;
-
-	}
-
-	private static String read(Clob c) throws SQLException, IOException {
-		StringBuilder sb = new StringBuilder((int) c.length());
-		Reader r = c.getCharacterStream();
-		char[] cbuf = new char[CLOBBUFFERSIZE];
-		int n;
-		while ((n = r.read(cbuf, 0, cbuf.length)) != -1) {
-			sb.append(cbuf, 0, n);
-		}
-		return sb.toString();
 	}
 }

src/main/java/org/genesys2/server/service/impl/GenesysServiceImpl.java

@@ -119,9 +119,9 @@ import org.springframework.security.acls.domain.BasePermission;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 
-import au.com.bytecode.opencsv.CSVWriter;
-import au.com.bytecode.opencsv.ResultSetHelper;
-import au.com.bytecode.opencsv.ResultSetHelperService;
+import com.opencsv.CSVWriter;
+import com.opencsv.ResultSetHelper;
+import com.opencsv.ResultSetHelperService;
 
 @Service
 @Transactional(readOnly = true)

src/main/java/org/genesys2/server/service/worker/GeoNamesCountrySource.java

@@ -37,7 +37,7 @@ import org.apache.http.impl.client.HttpClientBuilder;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
-import au.com.bytecode.opencsv.CSVReader;
+import com.opencsv.CSVReader;
 
 /**
  * Fetch and parse country information from

src/main/java/org/genesys2/server/service/worker/ITPGRFAStatusUpdater.java

@@ -43,7 +43,7 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.task.TaskExecutor;
 import org.springframework.stereotype.Component;
 
-import au.com.bytecode.opencsv.CSVReader;
+import com.opencsv.CSVReader;
 
 /**
  * Update country ITPGRFA status by fetching data from

src/main/java/org/genesys2/server/service/worker/InstituteUpdater.java

@@ -46,7 +46,7 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.task.TaskExecutor;
 import org.springframework.stereotype.Component;
 
-import au.com.bytecode.opencsv.CSVReader;
+import com.opencsv.CSVReader;
 
 @Component
 public class InstituteUpdater {
@@ -225,12 +225,6 @@ public class InstituteUpdater {
 					LOG.info("Updating FaoInstitutes: " + toSave.size());
 					instituteService.update(toSave);
 				}
-
-				// try {
-				// Thread.sleep(2000);
-				// } catch (final InterruptedException e) {
-				// LOG.warn(e.getMessage());
-				// }
 			}
 
 			private FaoInstitute insertData(String[] line) {
@@ -267,7 +261,9 @@ public class InstituteUpdater {
 				}
 				faoInstitute.setAcronym(acronym);
 				faoInstitute.setFullName(fullName);
-				LOG.info("Updating: " + instCode + " " + fullName);
+				if (LOG.isTraceEnabled()) {
+					LOG.trace("Updating: code=" + instCode + " fullname='" + fullName + "' acronym=" + acronym);
+				}
 				faoInstitute.setPgrActivity(pgrActivity);
 				faoInstitute.setMaintainsCollection(maintColl);
 				faoInstitute.setEmail(email);

src/main/java/org/genesys2/server/service/worker/SGSVUpdate.java

@@ -38,8 +38,6 @@ import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.SvalbardData;
 import org.genesys2.server.persistence.domain.SvalbardRepository;
 import org.genesys2.server.service.GenesysService;
-import org.genesys2.server.service.GeoService;
-import org.genesys2.server.service.TaxonomyService;
 import org.hibernate.exception.ConstraintViolationException;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.task.TaskExecutor;
@@ -47,7 +45,7 @@ import org.springframework.orm.hibernate3.HibernateOptimisticLockingFailureExcep
 import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.stereotype.Component;
 
-import au.com.bytecode.opencsv.CSVReader;
+import com.opencsv.CSVReader;
 
 @Component
 public class SGSVUpdate {
@@ -71,12 +69,6 @@ public class SGSVUpdate {
 	@Autowired
 	private GenesysService genesysService;
 
-	@Autowired
-	private TaxonomyService taxonomyService;
-
-	@Autowired
-	private GeoService geoService;
-
 	@Autowired
 	private SvalbardRepository svalbardRepository;