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ecological-engine
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git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngine@150851 82a268e6-3cf1-43bd-a215-b396298e98cf

This commit is contained in:
Lucio Lelii 2017-07-06 16:16:42 +00:00
parent dbaedc1ce7
commit 86460bc7a4
2 changed files with 86 additions and 29 deletions
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78
src/main/java/org/gcube/dataanalysis/ecoengine/utils/DatabaseFactory.java
View File

@ -4,11 +4,15 @@ package org.gcube.dataanalysis.ecoengine.utils;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.Statement;
import java.util.ArrayList;
import java.util.List;
import java.util.Map.Entry;
import java.util.Properties;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.SAXParser;
@ -23,14 +27,19 @@ import org.hibernate.Query;
import org.hibernate.Session;
import org.hibernate.SessionFactory;
import org.hibernate.cfg.Configuration;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.xml.sax.Attributes;
import org.xml.sax.SAXException;
import org.xml.sax.helpers.DefaultHandler;
public class DatabaseFactory{
private static final Logger LOGGER = LoggerFactory.getLogger(DatabaseFactory.class);
public static SessionFactory initDBConnection(String configurationFile) throws Exception {
String xml = FileTools.readXMLDoc(configurationFile);
LOGGER.debug("initialising DB Connection with conf: {} ",xml);
SessionFactory DBSessionFactory = null;
Configuration cfg = new Configuration();
cfg = cfg.configure(DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(new ByteArrayInputStream(xml.getBytes())));
@ -43,6 +52,8 @@ public class DatabaseFactory{
final List<StatisticalType> defaultconfig = new ArrayList<StatisticalType>();
LOGGER.debug("reading default DB configuration from {}",configurationFile);
// take the configuration file
File fl = new File(configurationFile);
FileInputStream stream = new FileInputStream(fl);
@ -99,27 +110,70 @@ public class DatabaseFactory{
return defaultconfig;
}
@SuppressWarnings({"unchecked"})
public static SessionFactory initDBConnection(String configurationFile, LexicalEngineConfiguration config) throws Exception {
LOGGER.debug("init DB configuration from {}",configurationFile);
if (config==null)
return initDBConnection(configurationFile);
// take the configuration file
File fl = new File(configurationFile);
FileInputStream stream = new FileInputStream(fl);
Configuration cfg = new Configuration();
cfg = cfg.configure(DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(stream));
cfg.setProperty("hibernate.hbm2ddl.auto", "create");
try(FileInputStream stream = new FileInputStream(new File(configurationFile))){
cfg = cfg.configure(DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(stream));
}
if ((config.getDatabaseDriver() != null)&&(config.getDatabaseDriver().length()>0))
cfg.setProperty("hibernate.connection.driver_class",config.getDatabaseDriver());
else
config.setDatabaseDriver(cfg.getProperty("connection.driver_class"));
if ((config.getDatabaseURL() != null)&&(config.getDatabaseURL().length()>0))
cfg.setProperty("hibernate.connection.url",config.getDatabaseURL());
else
config.setDatabaseURL(cfg.getProperty("connection.url"));
if ((config.getDatabaseUserName() != null)&&(config.getDatabaseUserName().length()>0))
cfg.setProperty("hibernate.connection.username", config.getDatabaseUserName());
else
config.setDatabaseUserName(cfg.getProperty("connection.username"));
if ((config.getDatabasePassword() != null)&&(config.getDatabasePassword().length()>0))
cfg.setProperty("hibernate.connection.password", config.getDatabasePassword());
else
config.setDatabasePassword(cfg.getProperty("connection.password"));
if ((config.getDatabaseDialect() != null)&&(config.getDatabaseDialect().length()>0))
cfg.setProperty("hibernate.dialect", config.getDatabaseDialect());
else
config.setDatabaseDialect(cfg.getProperty("dialect"));
if (config.getDatabaseIdleConnectionTestPeriod() != null)
cfg.setProperty("hibernate.c3p0.idleConnectionTestPeriod",config.getDatabaseIdleConnectionTestPeriod());
else
config.setDatabaseIdleConnectionTestPeriod(cfg.getProperty("c3p0.idleConnectionTestPeriod"));
if (config.getDatabaseAutomaticTestTable() != null)
cfg.setProperty("hibernate.c3p0.automaticTestTable",config.getDatabaseAutomaticTestTable());
else
config.setDatabaseAutomaticTestTable(cfg.getProperty("c3p0.automaticTestTable"));
cfg.setProperty("hibernate.hbm2ddl.auto", "create");
Properties props = cfg.getProperties();
/* LOGGER.debug("retrieving property for connection:");
for (Entry<Object, Object> propEntry : props.entrySet()){
LOGGER.debug("----- property {} -> {} ",propEntry.getKey(), propEntry.getValue());
}*/
SessionFactory DBSessionFactory = null;
DBSessionFactory = cfg.buildSessionFactory();
// close stream
stream.close();
return DBSessionFactory;
}
@ -228,7 +282,7 @@ public class DatabaseFactory{
try {
ss = DBSessionFactory.getCurrentSession();
ss = DBSessionFactory.getCurrentSession();
// System.out.println("executing query");
ss.beginTransaction();
Query qr = null;

37
src/main/java/org/gcube/dataanalysis/ecoengine/utils/DatabaseUtils.java
View File

@ -5,14 +5,17 @@ import java.io.FileWriter;
import java.sql.Connection;
import java.util.List;
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
import org.hibernate.SessionFactory;
import org.postgresql.copy.CopyManager;
import org.postgresql.core.BaseConnection;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class DatabaseUtils {
private static Logger LOGGER = LoggerFactory.getLogger(DatabaseUtils.class);
static String queryDesc = "SELECT column_name,data_type, character_maximum_length, is_nullable FROM information_schema.COLUMNS WHERE table_name ='%1$s'";
static String queryColumns = "SELECT column_name FROM information_schema.COLUMNS WHERE table_name ='%1$s'";
static String queryForKeys = "SELECT b.column_name as name, a.constraint_type as type FROM information_schema.table_constraints as a join information_schema.key_column_usage as b on a.table_name ='%1$s' and a.constraint_name = b.constraint_name";
@ -35,7 +38,7 @@ public class DatabaseUtils {
private String primaryK;
private String primaryKColName;
public static long estimateNumberofRows(String table, SessionFactory dbconnection) throws Exception{
List<Object> explain = DatabaseFactory.executeSQLQuery("EXPLAIN SELECT * FROM "+table, dbconnection);
String explained = "" + explain.get(0);
@ -43,7 +46,7 @@ public class DatabaseUtils {
explained = explained.substring(explained.indexOf('=') + 1, explained.indexOf(' '));
return Long.parseLong(explained);
}
private void getPrimaryKeys(List<Object> keys, String table) {
int keynum = 0;
if (keys != null)
@ -177,9 +180,9 @@ public class DatabaseUtils {
public static void insertChunksIntoTable(String table, String columnsNames, List<String[]> values, int chunkSize,SessionFactory dbconnection) throws Exception{
insertChunksIntoTable(table, columnsNames, values, chunkSize,dbconnection, true) ;
}
public static void insertChunksIntoTable(String table, String columnsNames, List<String[]> values, int chunkSize,SessionFactory dbconnection, boolean correctApos) throws Exception{
int valuesize = values.size();
StringBuffer sb = new StringBuffer();
int stopIndex =0;
@ -206,23 +209,23 @@ public class DatabaseUtils {
else if (i<valuesize-1)
sb.append(",");
}
if (stopIndex<valuesize-1){
if (sb.length()>0){
// System.out.println(sb);
// System.out.println(sb);
try{
DatabaseFactory.executeSQLUpdate(insertFromBuffer(table, columnsNames, sb), dbconnection);
}catch(Exception e){
System.out.println("Query:"+sb);
throw e;
}
}
}
}
public static String insertFromString(String table, String columnsNames, String values) {
return "insert into " + table + " (" + columnsNames + ") values " + values;
@ -287,12 +290,12 @@ public class DatabaseUtils {
public static void createBigTable(boolean createTable, String table, String dbdriver, String dbuser, String dbpassword, String dburl, String creationStatement, SessionFactory dbHibConnection) throws Exception {
if (createTable) {
try {
AnalysisLogger.getLogger().debug("Dropping previous table if exists");
LOGGER.debug("Dropping previous table if exists");
DatabaseFactory.executeSQLUpdate("drop table " + table, dbHibConnection);
} catch (Exception e) {
// e.printStackTrace();
}
AnalysisLogger.getLogger().debug("Creating Big Table");
LOGGER.debug("Creating Big Table");
DatabaseFactory.executeUpdateNoTransaction(creationStatement, dbdriver, dbuser, dbpassword, dburl, true);
}
}
@ -327,13 +330,13 @@ public class DatabaseUtils {
config.setDatabaseUserName(config.getParam("DatabaseUserName"));
config.setDatabasePassword(config.getParam("DatabasePassword"));
config.setDatabaseURL(config.getParam("DatabaseURL"));
LOGGER.trace("initializing DB session {} {} ",config.getParam("DatabaseUserName"), config.getParam("DatabaseURL"));
dbHibConnection = DatabaseFactory.initDBConnection(defaultDatabaseFile, config);
}
} catch (Exception e) {
System.out.println("ERROR IN DB INITIALIZATION : " + e.getLocalizedMessage());
e.printStackTrace();
// AnalysisLogger.getLogger().trace(e);
LOGGER.error("ERROR IN DB INITIALIZATION",e);
}
return dbHibConnection;
}