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Spring refactor #146

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53bfa17
Update DatabaseConfiguration.java, GaswSpringConfig.java, DAOFactory.…
Jun 5, 2026
bae8483
Update [GASW] : Refactor most classes into Spring framework
Jun 5, 2026
d4f28d3
Update [Comments] : Remove unnecessary comments
Jun 11, 2026
686c213
Update [Spring] : Keep refactoring, remove useless constants
Jun 12, 2026
2799476
Clean [Velocity] : Remove unused dependencies and velocity tests, fil…
Jun 15, 2026
911bbbd
Update [Spring] : keep refactoring, add tests
Jul 3, 2026
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88 changes: 52 additions & 36 deletions pom.xml
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Expand Up @@ -14,6 +14,8 @@
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>21</maven.compiler.source>
<maven.compiler.target>21</maven.compiler.target>

<spring-framework.version>6.2.10</spring-framework.version>
</properties>

<licenses>
Expand Down Expand Up @@ -50,6 +52,19 @@
</executions>
</plugin>

<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.13.0</version>
<configuration>
<compilerArgs>
<arg>-parameters</arg>
<arg>-Xlint:deprecation</arg>
<arg>-Werror</arg>
</compilerArgs>
</configuration>
</plugin>

<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
Expand Down Expand Up @@ -102,66 +117,67 @@
</dependency>

<dependency>
<groupId>commons-configuration</groupId>
<artifactId>commons-configuration</artifactId>
<version>1.9</version>
<exclusions>
<exclusion>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
</exclusion>
</exclusions>
<groupId>org.hibernate.orm</groupId>
<artifactId>hibernate-core</artifactId>
<version>6.6.0.Final</version>
</dependency>

<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
<version>2.0.17</version>
<groupId>org.mockito</groupId>
<artifactId>mockito-junit-jupiter</artifactId>
<version>5.13.0</version>
<scope>test</scope>
</dependency>

<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.17.0</version>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter</artifactId>
<version>5.11.0</version>
<scope>test</scope>
</dependency>

<dependency>
<groupId>code.google.com</groupId>
<artifactId>jspf.core</artifactId>
<version>1.0.2</version>
<groupId>com.h2database</groupId>
<artifactId>h2</artifactId>
<version>2.3.232</version>
<scope>test</scope>
</dependency>

<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>6.6.0.Final</version>
<groupId>org.springframework</groupId>
<artifactId>spring-test</artifactId>
<version>${spring-framework.version}</version>
<scope>test</scope>
</dependency>

<dependency>
<groupId>org.apache.velocity</groupId>
<artifactId>velocity</artifactId>
<version>1.7</version>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
<version>${spring-framework.version}</version>
</dependency>

<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-api</artifactId>
<version>5.11.3</version>
<scope>test</scope>
<groupId>org.springframework</groupId>
<artifactId>spring-jdbc</artifactId>
<version>${spring-framework.version}</version>
</dependency>

<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-junit-jupiter</artifactId>
<version>5.13.0</version>
<scope>test</scope>
<groupId>org.springframework</groupId>
<artifactId>spring-orm</artifactId>
<version>${spring-framework.version}</version>
</dependency>

<dependency>
<groupId>com.h2database</groupId>
<artifactId>h2</artifactId>
<version>2.3.232</version>
<scope>test</scope>
<groupId>jakarta.annotation</groupId>
<artifactId>jakarta.annotation-api</artifactId>
<version>3.0.0</version>
</dependency>

<dependency>
<groupId>com.zaxxer</groupId>
<artifactId>HikariCP</artifactId>
<version>7.0.2</version>
</dependency>
</dependencies>

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69 changes: 69 additions & 0 deletions src/main/java/fr/insalyon/creatis/gasw/DatabaseConfiguration.java
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@@ -0,0 +1,69 @@
package fr.insalyon.creatis.gasw;

import com.zaxxer.hikari.HikariDataSource;
import fr.insalyon.creatis.gasw.plugin.DatabasePlugin;
import jakarta.persistence.EntityManagerFactory;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.orm.jpa.vendor.HibernateJpaVendorAdapter;
import org.springframework.transaction.PlatformTransactionManager;

import javax.sql.DataSource;
import java.util.Properties;

@Configuration
public class DatabaseConfiguration {

private final Logger logger = LoggerFactory.getLogger(getClass());

private final DatabasePlugin dbPlugin;

public DatabaseConfiguration(DatabasePlugin dbPlugin) {

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MethodArgumentCouldBeFinal (Priority: 3, Ruleset: Code Style)
https://docs.pmd-code.org/snapshot/pmd_rules_java_codestyle.html#methodargumentcouldbefinal
this.dbPlugin = dbPlugin;
}

@Bean
public DataSource dataSource() {
logger.info("Loading database plugin '{}' version '{}'",
dbPlugin.getName(), dbPlugin.getClass().getPackage().getImplementationVersion());

HikariDataSource dataSource = new HikariDataSource();

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dataSource.setDriverClassName(dbPlugin.getDriverClass());
dataSource.setUsername(dbPlugin.getUserName());
dataSource.setPassword(dbPlugin.getPassword());
dataSource.setJdbcUrl(dbPlugin.getConnectionUrl());
return dataSource;
}

@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory(DataSource dataSource) {

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It will also ignore the parameters of abstract methods.

MethodArgumentCouldBeFinal (Priority: 3, Ruleset: Code Style)
https://docs.pmd-code.org/snapshot/pmd_rules_java_codestyle.html#methodargumentcouldbefinal
LocalContainerEntityManagerFactoryBean emf = new LocalContainerEntityManagerFactoryBean();

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emf.setDataSource(dataSource);
emf.setPackagesToScan(
"fr.insalyon.creatis.gasw.bean",
"fr.insalyon.creatis.gasw.plugin"
);

emf.setJpaVendorAdapter(new HibernateJpaVendorAdapter());
emf.setJpaProperties(hibernateProperties());
return emf;
}

private Properties hibernateProperties() {
Properties properties = new Properties();

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properties.setProperty("hibernate.default_schema", dbPlugin.getSchema());
properties.setProperty("hibernate.hbm2ddl.auto", "update");
properties.setProperty("hibernate.show_sql", "false");
properties.setProperty("hibernate.format_sql", "false");
return properties;
}

@Bean
public PlatformTransactionManager transactionManager(EntityManagerFactory emf) {

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return new JpaTransactionManager(emf);
}
}
153 changes: 113 additions & 40 deletions src/main/java/fr/insalyon/creatis/gasw/Gasw.java
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Expand Up @@ -32,70 +32,143 @@
*/
package fr.insalyon.creatis.gasw;

import fr.insalyon.creatis.gasw.bean.SEEntryPoint;
import fr.insalyon.creatis.gasw.bean.SEEntryPointID;
import fr.insalyon.creatis.gasw.dao.DAOException;
import fr.insalyon.creatis.gasw.dao.SEEntryPointsDAO;
import fr.insalyon.creatis.gasw.execution.ExecutorFactory;
import fr.insalyon.creatis.gasw.execution.FailOver;
import fr.insalyon.creatis.gasw.plugin.ExecutorPlugin;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.net.URI;
import java.net.URISyntaxException;
import java.util.List;

import fr.insalyon.creatis.gasw.plugin.ListenerPlugin;
import jakarta.annotation.PostConstruct;
import jakarta.annotation.PreDestroy;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.context.event.ContextRefreshedEvent;
import org.springframework.context.event.EventListener;
import org.springframework.stereotype.Service;

@Service
public class Gasw {

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private static final Logger logger = LoggerFactory.getLogger(Gasw.class);
private static Gasw instance;
private GaswNotification notification;

/**
* Gets a default instance of GASW.
*
* @return Instance of GASW
*/
public synchronized static Gasw getInstance() throws GaswException {

if (instance == null) {
instance = new Gasw();

private final Logger logger = LoggerFactory.getLogger(getClass());

private final GaswConfiguration config;
private final GaswNotification gaswNotification;
private final ExecutorFactory executorFactory;
private final SEEntryPointsDAO seEntryPointsDAO;
private final List<ExecutorPlugin> executorPlugins;
private final List<ListenerPlugin> listenerPlugins;

public Gasw(GaswConfiguration config, GaswNotification gaswNotification, ExecutorFactory executorFactory,

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SEEntryPointsDAO seEntryPointsDAO, List<ExecutorPlugin> executorPlugins, List<ListenerPlugin> listenerPlugins) {
this.config = config;
this.gaswNotification = gaswNotification;
this.executorFactory = executorFactory;
this.seEntryPointsDAO = seEntryPointsDAO;
this.executorPlugins = executorPlugins;
this.listenerPlugins = listenerPlugins;
}

@PostConstruct
public void init() throws GaswException {
if (config.isFailOverEnabled()) {
loadSEEntryPoints();
}
return instance;
}

private Gasw() throws GaswException {
try {
logger.info("Initializing GASW.");
GaswConfiguration.getInstance().loadHibernate();
// Log loaded plugins after all beans creation
@EventListener(ContextRefreshedEvent.class)
public void logPlugins() {
executorPlugins.forEach(p ->
logger.info("Loaded executor plugin '{}' version '{}'",
p.getName(), p.getClass().getPackage().getImplementationVersion()));
listenerPlugins.forEach(p ->
logger.info("Loaded listener plugin '{}' version '{}'",
p.getName(), p.getClass().getPackage().getImplementationVersion()));
}

notification = GaswNotification.getInstance();
@PreDestroy
public void terminate() throws GaswException {
terminate(false);
}

} catch (IllegalArgumentException ex) {
throw new GaswException(ex);
public void terminate(boolean force) throws GaswException {
gaswNotification.terminate();
for (ExecutorPlugin executorPlugin : executorPlugins) {
executorPlugin.terminate(force);
}
}

public synchronized void setNotificationClient(Object client) {
notification.setClient(client);
for (ListenerPlugin listenerPlugin : listenerPlugins) {
listenerPlugin.terminate();
}
}

public synchronized String submit(GaswInput gaswInput) throws GaswException {

ExecutorPlugin executor = ExecutorFactory.getExecutor(gaswInput);
executor.load(gaswInput);
return executor.submit();
public void setNotificationClient(Object client) {
gaswNotification.setNotificationClient(client);
}

public synchronized List<GaswOutput> getFinishedJobs() {
return notification.getFinishedJobs();
public String submit(GaswInput gaswInput) throws GaswException {
return executorFactory.getExecutor().submit(gaswInput);
}

public synchronized void waitForNotification() {
notification.waitForNotification();
public List<GaswOutput> getFinishedJobs() {
return gaswNotification.getFinishedJobs();
}

public synchronized void terminate(boolean force) throws GaswException {
notification.terminate();
private void loadSEEntryPoints() throws GaswException {
try {
logger.info("Loading SEs entry points.");
ProcessBuilder builder = new ProcessBuilder("lcg-info", "--list-service",
"--vo", config.getVoName(), "--attrs", "ServiceEndpoint");

builder.redirectErrorStream(true);
Process process = builder.start();

BufferedReader r = new BufferedReader(new InputStreamReader(process.getInputStream()));
String s = null;
StringBuilder cout = new StringBuilder();

while ((s = r.readLine()) != null) {
cout.append(s);
if (s.startsWith("- Service: httpg://")) {
try {
URI service = new URI(s.split(" ")[2]);
seEntryPointsDAO.add(
new SEEntryPoint(new SEEntryPointID(
service.getHost(), service.getPort()),
service.getPath()));

} catch (URISyntaxException ex) {
logger.warn("Unable to read end point from: {}", s);
} catch (DAOException ex) {
if (!ex.getMessage().contains("duplicate key value")) {
logger.warn("Unable to save end point: {}", ex.getMessage());
}
}
}
}
r.close();
process.waitFor();

if (process.exitValue() != 0) {
logger.error(cout.toString());
throw new GaswException("Unable to load SEs entry points.");
}
} catch (InterruptedException ex) {
logger.error("Error:", ex);
throw new GaswException(ex);

if (GaswConfiguration.getInstance().isFailOverEnabled()) {
FailOver.getInstance().terminate();
} catch (IOException ex) {
logger.error("Error:", ex);
throw new GaswException(ex);
}

GaswConfiguration.getInstance().terminate(force);
}
}
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