gCubeSystem
/
ecological-engine
16
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngine@150568 82a268e6-3cf1-43bd-a215-b396298e98cf

This commit is contained in:
Lucio Lelii 2017-06-27 13:23:07 +00:00
parent 38ce4eb4b5
commit dbaedc1ce7
6 changed files with 208 additions and 248 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
.classpath
View File

@ -22,7 +22,7 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7">
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
<attributes>
<attribute name="maven.pomderived" value="true"/>
</attributes>

6
.settings/org.eclipse.jdt.core.prefs
View File

@ -1,12 +1,12 @@
eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
org.eclipse.jdt.core.compiler.compliance=1.7
org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.debug.lineNumber=generate
org.eclipse.jdt.core.compiler.debug.localVariable=generate
org.eclipse.jdt.core.compiler.debug.sourceFile=generate
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
org.eclipse.jdt.core.compiler.source=1.7
org.eclipse.jdt.core.compiler.source=1.8

9
pom.xml
View File

@ -67,11 +67,6 @@
<artifactId>commons-logging</artifactId>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>dom4j</groupId>
<artifactId>dom4j</artifactId>
<version>1.6</version>
</dependency>
<dependency>
<groupId>graphlayout</groupId>
<artifactId>graphlayout</artifactId>
@ -233,8 +228,8 @@
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>

58
src/main/java/org/gcube/contentmanagement/lexicalmatcher/utils/DatabaseFactory.java
View File

@ -1,18 +1,13 @@
package org.gcube.contentmanagement.lexicalmatcher.utils;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.InputStream;
import java.util.Iterator;
import java.util.List;
import javax.xml.parsers.DocumentBuilderFactory;
import org.dom4j.Document;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
import org.gcube.contentmanagement.lexicalmatcher.analysis.core.LexicalEngineConfiguration;
import org.hibernate.Query;
import org.hibernate.Session;
@ -30,64 +25,23 @@ public class DatabaseFactory {
return DBSessionFactory;
}
@SuppressWarnings({"unchecked"})
public static SessionFactory initDBConnection(String configurationFile, LexicalEngineConfiguration config) throws Exception {
InputStream stream= null;
try{
if (config==null)
return initDBConnection(configurationFile);
InputStream stream;
try {
File fl = new File(configurationFile);
stream = new FileInputStream(fl);
} catch (Exception e) {
stream = ClassLoader.getSystemResourceAsStream(configurationFile);
}
SAXReader saxReader = new SAXReader();
Document document = saxReader.read(stream);
List<Node> nodes = document.selectNodes("//hibernate-configuration/session-factory/property");
Iterator<Node> nodesIterator = nodes.iterator();
// System.out.println("--- DATABASE Configuration --- ");
while (nodesIterator.hasNext()) {
Node currentnode = nodesIterator.next();
String element = currentnode.valueOf("@name");
if (element.equals("connection.driver_class"))
if (config.getDatabaseDriver() != null){
currentnode.setText(config.getDatabaseDriver());
}
if (element.equals("connection.url")) {
if (config.getDatabaseURL() != null)
currentnode.setText(config.getDatabaseURL());
}
if (element.equals("connection.username")) {
if (config.getDatabaseUserName() != null)
currentnode.setText(config.getDatabaseUserName());
}
if (element.equals("connection.password")) {
if (config.getDatabasePassword() != null)
currentnode.setText(config.getDatabasePassword());
}
if (element.equals("dialect")) {
AnalysisLogger.getLogger().trace("Dialect -> "+config.getDatabaseDialect());
if (config.getDatabaseDialect() != null)
currentnode.setText(config.getDatabaseDialect());
}
if (element.equals("c3p0.idleConnectionTestPeriod")) {
if (config.getDatabaseIdleConnectionTestPeriod() != null)
currentnode.setText(config.getDatabaseIdleConnectionTestPeriod());
}
if (element.equals("c3p0.automaticTestTable")) {
if (config.getDatabaseAutomaticTestTable() != null)
currentnode.setText(config.getDatabaseAutomaticTestTable());
}
}
Configuration cfg = new Configuration();
cfg = cfg.configure(DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(new ByteArrayInputStream(document.asXML().getBytes())));
cfg = cfg.configure(DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(stream));
cfg.setProperty("hibernate.hbm2ddl.auto", "create");
SessionFactory DBSessionFactory = null;
@ -97,6 +51,10 @@ public class DatabaseFactory {
stream.close();
return DBSessionFactory;
}finally{
if (stream!=null)
stream.close();
}
}
@SuppressWarnings({"unchecked"})

44
src/main/java/org/gcube/contentmanagement/lexicalmatcher/utils/FileTools.java
View File

@ -9,29 +9,59 @@ import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.io.StringWriter;
import java.io.UnsupportedEncodingException;
import java.io.Writer;
import org.dom4j.Document;
import org.dom4j.io.SAXReader;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.transform.OutputKeys;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
import org.w3c.dom.Document;
public class FileTools {
public static String readXMLDoc(String xmlFilePath) throws Exception {
String xml = null;
InputStream stream;
InputStream stream = null;
try{
try {
File fl = new File(xmlFilePath);
stream = new FileInputStream(fl);
} catch (Exception e) {
stream = ClassLoader.getSystemResourceAsStream(xmlFilePath);
}
SAXReader saxReader = new SAXReader();
Document document = saxReader.read(stream);
xml = document.asXML();
stream.close();
DocumentBuilder dBuilder = DocumentBuilderFactory.newInstance()
.newDocumentBuilder();
Document doc = dBuilder.parse(stream);
xml = toString(doc);
return xml;
}finally{
if (stream!=null)
stream.close();
}
}
private static String toString(Document doc) {
try {
StringWriter sw = new StringWriter();
TransformerFactory tf = TransformerFactory.newInstance();
Transformer transformer = tf.newTransformer();
transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "no");
transformer.setOutputProperty(OutputKeys.METHOD, "xml");
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
transformer.setOutputProperty(OutputKeys.ENCODING, "UTF-8");
transformer.transform(new DOMSource(doc), new StreamResult(sw));
return sw.toString();
} catch (Exception ex) {
throw new RuntimeException("Error converting to String", ex);
}
}
public static void saveString2File(String filename, String string2save) throws Exception {

127
src/main/java/org/gcube/dataanalysis/ecoengine/utils/DatabaseFactory.java
View File

@ -8,14 +8,12 @@ import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.Statement;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.SAXParser;
import javax.xml.parsers.SAXParserFactory;
import org.dom4j.Document;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
import org.gcube.contentmanagement.lexicalmatcher.analysis.core.LexicalEngineConfiguration;
import org.gcube.contentmanagement.lexicalmatcher.utils.FileTools;
import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType;
@ -25,6 +23,9 @@ import org.hibernate.Query;
import org.hibernate.Session;
import org.hibernate.SessionFactory;
import org.hibernate.cfg.Configuration;
import org.xml.sax.Attributes;
import org.xml.sax.SAXException;
import org.xml.sax.helpers.DefaultHandler;
public class DatabaseFactory{
@ -40,32 +41,60 @@ public class DatabaseFactory{
public static List<StatisticalType> getDefaultDatabaseConfiguration(String configurationFile) throws Exception {
List<StatisticalType> defaultconfig = new ArrayList<StatisticalType>();
final List<StatisticalType> defaultconfig = new ArrayList<StatisticalType>();
// take the configuration file
File fl = new File(configurationFile);
FileInputStream stream = new FileInputStream(fl);
SAXReader saxReader = new SAXReader();
Document document = saxReader.read(stream);
List<Node> nodes = document.selectNodes("//hibernate-configuration/session-factory/property");
Iterator<Node> nodesIterator = nodes.iterator();
SAXParser parser = SAXParserFactory.newInstance().newSAXParser();
while (nodesIterator.hasNext()) {
parser.parse(stream, new DefaultHandler(){
Node currentnode = nodesIterator.next();
String element = currentnode.valueOf("@name");
if (element.equals("connection.driver_class"))
defaultconfig.add(new DatabaseType(DatabaseParameters.DATABASEDRIVER, "DatabaseDriver", "db driver",currentnode.getText()));
if (element.equals("connection.url"))
defaultconfig.add(new DatabaseType(DatabaseParameters.DATABASEURL, "DatabaseURL", "db url",currentnode.getText()));
if (element.equals("connection.username"))
defaultconfig.add(new DatabaseType(DatabaseParameters.DATABASEUSERNAME, "DatabaseUserName", "db user name",currentnode.getText()));
if (element.equals("connection.password"))
defaultconfig.add(new DatabaseType(DatabaseParameters.DATABASEPASSWORD, "DatabasePassword", "db password",currentnode.getText()));
if (element.equals("dialect"))
defaultconfig.add(new DatabaseType(DatabaseParameters.DATABASEDIALECT, "DatabaseDialect", "db dialect",currentnode.getText()));
private DatabaseParameters actualparameter = null;
private String actualParameterDescription= null;
@Override
public void startElement(String uri, String localName,
String qName, Attributes attributes) throws SAXException {
if (localName.equals("property")){
String element = attributes.getValue("name");
if (element.equals("connection.driver_class")){
actualparameter = DatabaseParameters.DATABASEDRIVER;
actualParameterDescription = "DatabaseDriver";
}else if (element.equals("connection.url")) {
actualparameter = DatabaseParameters.DATABASEURL;
actualParameterDescription = "DatabaseURL";
}else if (element.equals("connection.username")){
actualparameter = DatabaseParameters.DATABASEUSERNAME;
actualParameterDescription = "DatabaseUserName";
}else if (element.equals("connection.password")){
actualparameter = DatabaseParameters.DATABASEPASSWORD;
actualParameterDescription = "DATABASEPASSWORD";
}else if (element.equals("dialect")){
actualparameter = DatabaseParameters.DATABASEDIALECT;
actualParameterDescription = "DATABASEDIALECT";
}
}
}
@Override
public void characters(char ch[], int start, int length) throws SAXException {
if (actualParameterDescription!=null){
defaultconfig.add(new DatabaseType(actualparameter, actualParameterDescription, actualParameterDescription, new String(ch, start, length)));
actualparameter = null;
actualParameterDescription= null;
}
}
});
return defaultconfig;
}
@ -82,60 +111,8 @@ public class DatabaseFactory{
File fl = new File(configurationFile);
FileInputStream stream = new FileInputStream(fl);
SAXReader saxReader = new SAXReader();
Document document = saxReader.read(stream);
List<Node> nodes = document.selectNodes("//hibernate-configuration/session-factory/property");
Iterator<Node> nodesIterator = nodes.iterator();
while (nodesIterator.hasNext()) {
Node currentnode = nodesIterator.next();
String element = currentnode.valueOf("@name");
if (element.equals("connection.driver_class")){
if ((config.getDatabaseDriver() != null)&&(config.getDatabaseDriver().length()>0))
currentnode.setText(config.getDatabaseDriver());
else
config.setDatabaseDriver(currentnode.getText());
}
if (element.equals("connection.url")) {
if ((config.getDatabaseURL() != null)&&(config.getDatabaseURL().length()>0))
currentnode.setText(config.getDatabaseURL());
else
config.setDatabaseURL(currentnode.getText());
}
if (element.equals("connection.username")) {
if ((config.getDatabaseUserName() != null)&&(config.getDatabaseUserName().length()>0))
currentnode.setText(config.getDatabaseUserName());
else
config.setDatabaseUserName(currentnode.getText());
}
if (element.equals("connection.password")) {
if ((config.getDatabasePassword() != null)&&(config.getDatabasePassword().length()>0))
currentnode.setText(config.getDatabasePassword());
else
config.setDatabasePassword(currentnode.getText());
}
if (element.equals("dialect")) {
if ((config.getDatabaseDialect() != null)&&(config.getDatabaseDialect().length()>0))
currentnode.setText(config.getDatabaseDialect());
else
config.setDatabaseDialect(currentnode.getText());
}
if (element.equals("c3p0.idleConnectionTestPeriod")) {
if (config.getDatabaseIdleConnectionTestPeriod() != null)
currentnode.setText(config.getDatabaseIdleConnectionTestPeriod());
else
config.setDatabaseIdleConnectionTestPeriod(currentnode.getText());
}
if (element.equals("c3p0.automaticTestTable")) {
if (config.getDatabaseAutomaticTestTable() != null)
currentnode.setText(config.getDatabaseAutomaticTestTable());
else
config.setDatabaseAutomaticTestTable(currentnode.getText());
}
}
Configuration cfg = new Configuration();
cfg = cfg.configure(DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(new ByteArrayInputStream(document.asXML().getBytes())));
cfg = cfg.configure(DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(stream));
cfg.setProperty("hibernate.hbm2ddl.auto", "create");
SessionFactory DBSessionFactory = null;