Java21 (#4450)

* Initial commit including POM changes

* Converted ehcache to new format

* Modified .travis.yml

* Jakarta import corrections, EhCache config in app YML

* Fixed file upload and corrected some of the compile errors

* fixed final complilation errors

* Some correction for JSON, EhCache wip

* Expiry order changed

* Added Mail dep and commented out some cache resolver code

* Updated AuditInterceptor

* Fiexed merge with master

* Started java21 and fixed login

* Fixed the null inject and removed dep in travis

* Fixed travis java version

* Use proper protoc

* Relaced proto extensions for optional fields

* Removed some extensions from protos and updated usage

* Created a separate ehcache file for session cache and more proto corrections

* Fixed the cache conf file

* Remove StudyType and fixed study/initiative import

* Changed the proto to keep collected and protocol DTOs

* Fixed travis build and image upload

* Removed the remaining proto extends and updated search client files

* Changed magma version

* Fixed membership addition and DAR history page

* Fixed CacheResource and changed logback version

* Fixed charts, coverage for non-opal taxos and csv download

* Added legacy upgrade and chaged joda time version

* Replaced joda time with LocalDateTime

* Removed the legacy upgrade and removed required membership dto

* Fixed templates for using old fields

* Used 'double' for JSON's proto3 'int64' problem

* Removed DTO unkonwn fields

* Fixed the logs API

* Added a EhCache event logger; changed int64 -> double + ftl fix

* Use the getFileName

* Fixed Pop, DCE cache serialization and creating new contact

* Changed stats type in DTO

---------

Co-authored-by: Ramin Haeri Azad <rhaeri@maelstrom-reseach.org>

.travis.yml

@@ -1,9 +1,9 @@
 sudo: required
+dist: focal
 language: java
 jdk:
-  - openjdk8
+  - openjdk21
 before_install:
-  - sudo add-apt-repository -y ppa:chris-lea/node.js
   - sudo apt-get install -y nodejs devscripts
   - nvm install lts/gallium
   - node --version

mica-core/pom.xml

@@ -26,6 +26,15 @@
   </properties>
 
   <dependencies>
+    <dependency>
+      <groupId>jakarta.servlet</groupId>
+      <artifactId>jakarta.servlet-api</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>jakarta.ws.rs</groupId>
+      <artifactId>jakarta.ws.rs-api</artifactId>
+    </dependency>
+
     <dependency>
       <groupId>org.obiba.mica</groupId>
       <artifactId>mica-spi</artifactId>
@@ -39,32 +48,32 @@
       <artifactId>magma-datasource-excel</artifactId>
     </dependency>
     <dependency>
-      <groupId>com.codahale.metrics</groupId>
+      <groupId>io.dropwizard.metrics</groupId>
       <artifactId>metrics-core</artifactId>
     </dependency>
     <dependency>
-      <groupId>com.codahale.metrics</groupId>
+      <groupId>io.dropwizard.metrics</groupId>
       <artifactId>metrics-json</artifactId>
     </dependency>
     <dependency>
-      <groupId>com.codahale.metrics</groupId>
+      <groupId>io.dropwizard.metrics</groupId>
       <artifactId>metrics-ehcache</artifactId>
     </dependency>
     <dependency>
-      <groupId>com.codahale.metrics</groupId>
+      <groupId>io.dropwizard.metrics</groupId>
       <artifactId>metrics-graphite</artifactId>
     </dependency>
     <dependency>
-      <groupId>com.codahale.metrics</groupId>
+      <groupId>io.dropwizard.metrics</groupId>
       <artifactId>metrics-jvm</artifactId>
     </dependency>
     <dependency>
-      <groupId>com.codahale.metrics</groupId>
-      <artifactId>metrics-servlet</artifactId>
+      <groupId>io.dropwizard.metrics</groupId>
+      <artifactId>metrics-jakarta-servlet</artifactId>
     </dependency>
     <dependency>
-      <groupId>com.codahale.metrics</groupId>
-      <artifactId>metrics-servlets</artifactId>
+      <groupId>io.dropwizard.metrics</groupId>
+      <artifactId>metrics-jakarta-servlets</artifactId>
     </dependency>
     <dependency>
       <groupId>com.googlecode.protobuf-java-format</groupId>
@@ -131,10 +140,10 @@
       <groupId>com.fasterxml.jackson.core</groupId>
       <artifactId>jackson-databind</artifactId>
     </dependency>
-    <dependency>
-      <groupId>org.apache.geronimo.javamail</groupId>
-      <artifactId>geronimo-javamail_1.4_mail</artifactId>
-    </dependency>
+    <!--    <dependency>-->
+    <!--      <groupId>org.apache.geronimo.javamail</groupId>-->
+    <!--      <artifactId>geronimo-javamail_1.4_mail</artifactId>-->
+    <!--    </dependency>-->
     <dependency>
       <groupId>org.hibernate.validator</groupId>
       <artifactId>hibernate-validator</artifactId>
@@ -151,6 +160,19 @@
       <groupId>org.springframework.boot</groupId>
       <artifactId>spring-boot-loader-tools</artifactId>
     </dependency>
+    <dependency>
+      <groupId>org.springframework.boot</groupId>
+      <artifactId>spring-boot-starter-cache</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>org.ehcache</groupId>
+      <artifactId>ehcache</artifactId>
+      <classifier>jakarta</classifier>
+    </dependency>
+    <dependency>
+      <groupId>org.ehcache.integrations.shiro</groupId>
+      <artifactId>shiro-ehcache3</artifactId>
+    </dependency>
     <dependency>
       <groupId>org.springframework.boot</groupId>
       <artifactId>spring-boot-starter-logging</artifactId>
@@ -165,6 +187,12 @@
         </exclusion>
       </exclusions>
     </dependency>
+
+<!--    <dependency>-->
+<!--      <groupId>org.slf4j</groupId>-->
+<!--      <artifactId>jcl-over-slf4j</artifactId>-->
+<!--    </dependency>-->
+
     <dependency>
       <groupId>org.springframework.boot</groupId>
       <artifactId>spring-boot-starter-aop</artifactId>
@@ -242,10 +270,12 @@
     <dependency>
       <groupId>org.apache.shiro</groupId>
       <artifactId>shiro-core</artifactId>
+      <classifier>jakarta</classifier>
     </dependency>
     <dependency>
       <groupId>org.apache.shiro</groupId>
       <artifactId>shiro-spring</artifactId>
+      <classifier>jakarta</classifier>
     </dependency>
     <dependency>
       <groupId>org.apache.shiro</groupId>
@@ -255,6 +285,12 @@
       <groupId>eu.flatwhite.shiro</groupId>
       <artifactId>shiro-extras</artifactId>
     </dependency>
+    <dependency>
+      <groupId>org.apache.shiro</groupId>
+      <artifactId>shiro-web</artifactId>
+      <classifier>jakarta</classifier>
+    </dependency>
+
 
     <dependency>
       <groupId>org.obiba.commons</groupId>
@@ -274,6 +310,10 @@
       <groupId>com.itextpdf</groupId>
       <artifactId>itextpdf</artifactId>
     </dependency>
+      <dependency>
+          <groupId>org.obiba.commons</groupId>
+          <artifactId>obiba-password-hasher</artifactId>
+      </dependency>
 
   </dependencies>
 

mica-core/src/main/java/org/obiba/mica/access/service/DataAccessCollaboratorService.java

@@ -3,8 +3,8 @@
 
 import com.google.common.base.Strings;
 import com.google.common.eventbus.EventBus;
+import jakarta.ws.rs.ForbiddenException;
 import org.apache.shiro.SecurityUtils;
-import org.joda.time.DateTime;
 import org.json.JSONException;
 import org.json.JSONObject;
 import org.obiba.mica.access.DataAccessCollaboratorRepository;
@@ -28,7 +28,6 @@
 
 import javax.inject.Inject;
 import javax.validation.constraints.NotNull;
-import javax.ws.rs.ForbiddenException;
 import java.time.LocalDateTime;
 import java.util.List;
 import java.util.Map;
@@ -129,8 +128,8 @@ public void acceptCollaborator(@NotNull DataAccessRequest dar, String invitation
       if (!found) {
         throw new IllegalArgumentException("invitation-wrong-user");
       }
-      DateTime expired = DateTime.parse(jsonKey.getString(CREATED_KEY)).plusDays(dataAccessConfigService.getOrCreateConfig().getCollaboratorInvitationDays());
-      if (dar.hasAcceptedCollaboratorInvitation(invitation) || expired.isBefore(DateTime.now())) {
+      LocalDateTime expired = LocalDateTime.parse(jsonKey.getString(CREATED_KEY)).plusDays(dataAccessConfigService.getOrCreateConfig().getCollaboratorInvitationDays());
+      if (dar.hasAcceptedCollaboratorInvitation(invitation) || expired.isBefore(LocalDateTime.now())) {
         throw new IllegalArgumentException("invitation-expired");
       }
 
@@ -232,7 +231,7 @@ private String makeInvitationKey(@NotNull DataAccessRequest dar, String email) {
       jsonKey.put(AUTHOR_KEY, SecurityUtils.getSubject().getPrincipal().toString());
       jsonKey.put(REQUEST_KEY, dar.getId());
       jsonKey.put(EMAIL_KEY, email);
-      jsonKey.put(CREATED_KEY, DateTime.now());
+      jsonKey.put(CREATED_KEY, LocalDateTime.now());
     } catch (JSONException e) {
       throw new IllegalArgumentException(e);
     }

mica-core/src/main/java/org/obiba/mica/access/service/DataAccessRequestUtilService.java

@@ -33,7 +33,7 @@
 import org.springframework.stereotype.Component;
 
 import javax.inject.Inject;
-import javax.ws.rs.BadRequestException;
+import jakarta.ws.rs.BadRequestException;
 import java.text.ParseException;
 import java.text.SimpleDateFormat;
 import java.util.Date;

mica-core/src/main/java/org/obiba/mica/cache/EhCacheEventLogger.java

@@ -0,0 +1,17 @@
+package org.obiba.mica.cache;
+
+import org.ehcache.event.CacheEvent;
+import org.ehcache.event.CacheEventListener;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class EhCacheEventLogger implements CacheEventListener<Object, Object> {
+
+  private static final Logger logger = LoggerFactory.getLogger(EhCacheEventLogger.class);
+
+  @Override
+  public void onEvent(CacheEvent cacheEvent) {
+    logger.info("Cache event = {}, Key = {},  Old value = {}, New value = {}", cacheEvent.getType(),
+      cacheEvent.getKey(), cacheEvent.getOldValue(), cacheEvent.getNewValue());
+  }
+}

mica-core/src/main/java/org/obiba/mica/cache/MicaEhCacheManagerFactory.java

@@ -0,0 +1,40 @@
+//package org.obiba.mica.cache;
+//
+//import org.apache.shiro.cache.CacheException;
+//import org.ehcache.CacheManager;
+//import org.ehcache.config.builders.CacheManagerBuilder;
+//import org.ehcache.xml.XmlConfiguration;
+//import org.slf4j.Logger;
+//import org.slf4j.LoggerFactory;
+//
+//import java.net.MalformedURLException;
+//import java.net.URL;
+//
+//public class MicaEhCacheManagerFactory {
+//  private static final Logger log = LoggerFactory.getLogger(MicaEhCacheManagerFactory.class);
+//
+//
+//  private static final String EHCACHE_CONFIG_FILE = "ehcache.xml";
+//
+//  // Implement a EhCache 3 CacheManager to be used in Spring boot 3 application
+//
+//  public CacheManager create() {
+//    // How to use Ehcache 3 in Spring boot 3
+//    // https://www.ehcache.org/documentation/3.8/getting-started.html
+//
+//    // https://www.ehcache.org/documentation/3.8/getting-started.html
+//
+//
+//
+//    log.info("Creating EhCache Manager");
+////    try {
+////      XmlConfiguration xmlConfiguration = new XmlConfiguration(new URL(EHCACHE_CONFIG_FILE));
+////      CacheManager cacheManager = CacheManagerBuilder.newCacheManager(xmlConfiguration);
+////      cacheManager.init();
+////
+////      return cacheManager;
+////    } catch (MalformedURLException e) {
+////      throw new CacheException(e);
+////    }
+//  }
+//}

mica-core/src/main/java/org/obiba/mica/config/CacheConfiguration.java

@@ -10,60 +10,12 @@
 
 package org.obiba.mica.config;
 
-import javax.annotation.PreDestroy;
-import javax.inject.Inject;
-
-import net.sf.ehcache.Cache;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.boot.autoconfigure.AutoConfigureAfter;
-import org.springframework.cache.CacheManager;
+import org.springframework.beans.factory.InitializingBean;
 import org.springframework.cache.annotation.EnableCaching;
-import org.springframework.cache.ehcache.EhCacheCacheManager;
-import org.springframework.cache.ehcache.EhCacheManagerFactoryBean;
-import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 
-import com.codahale.metrics.MetricRegistry;
-import com.codahale.metrics.ehcache.InstrumentedEhcache;
-
 @Configuration("cacheConfiguration")
 @EnableCaching
-@AutoConfigureAfter(value = { MetricsConfiguration.class })
 public class CacheConfiguration {
 
-  private static final Logger log = LoggerFactory.getLogger(CacheConfiguration.class);
-
-  @Inject
-  private MetricRegistry metricRegistry;
-
-  @PreDestroy
-  public void destroy() {
-    log.info("Remove Cache Manager metrics");
-    metricRegistry.getNames().forEach(metricRegistry::remove);
-  }
-
-  @Bean
-  public EhCacheManagerFactoryBean cacheManagerFactory() {
-    log.debug("Starting Ehcache");
-    EhCacheManagerFactoryBean factoryBean = new EhCacheManagerFactoryBean();
-    factoryBean.setCacheManagerName("mica");
-
-    return factoryBean;
-  }
-
-  @Bean
-  public CacheManager springCacheManager() {
-    log.debug("Starting Spring Cache");
-    net.sf.ehcache.CacheManager cacheManager = cacheManagerFactory().getObject();
-    EhCacheCacheManager ehCacheManager = new EhCacheCacheManager();
-    ehCacheManager.setCacheManager(cacheManager);
-    String[] cacheNames = cacheManager.getCacheNames();
-    for (String cacheName : cacheNames) {
-      Cache cache = cacheManager.getCache(cacheName);
-      cacheManager.replaceCacheWithDecoratedCache(cache, InstrumentedEhcache.instrument(metricRegistry, cache));
-    }
-    return ehCacheManager;
-  }
 }

mica-core/src/main/java/org/obiba/mica/config/MetricsConfiguration.java

@@ -14,11 +14,11 @@
 import java.net.InetSocketAddress;
 import java.util.concurrent.TimeUnit;
 
-import javax.annotation.PostConstruct;
 import javax.inject.Inject;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.InitializingBean;
 import org.springframework.boot.autoconfigure.condition.ConditionalOnClass;
 import org.springframework.context.EnvironmentAware;
 import org.springframework.context.annotation.Configuration;
@@ -85,7 +85,7 @@ public void configureReporters(MetricRegistry metricRegistry) {
 
   @Configuration
   @ConditionalOnClass(Graphite.class)
-  public static class GraphiteRegistry implements EnvironmentAware {
+  public static class GraphiteRegistry implements EnvironmentAware, InitializingBean {
 
     private final Logger log = LoggerFactory.getLogger(GraphiteRegistry.class);
 
@@ -99,8 +99,8 @@ public void setEnvironment(Environment environment) {
       this.environment = environment;
     }
 
-    @PostConstruct
-    private void init() {
+    @Override
+    public void afterPropertiesSet() throws Exception {
       Boolean graphiteEnabled = environment.getProperty(PROP_GRAPHITE_ENABLED, Boolean.class, false);
       if(graphiteEnabled) {
         log.info("Initializing Metrics Graphite reporting");

mica-core/src/main/java/org/obiba/mica/config/ValidationConfiguration.java

@@ -10,7 +10,7 @@
 
 package org.obiba.mica.config;
 
-import javax.validation.Validator;
+import jakarta.validation.Validator;
 
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;

mica-core/src/main/java/org/obiba/mica/core/domain/AbstractAttributeModelAware.java

@@ -10,11 +10,12 @@
 
 package org.obiba.mica.core.domain;
 
+import java.io.Serializable;
 import java.util.Map;
 
 import javax.annotation.Nullable;
 
-public abstract class AbstractAttributeModelAware implements AttributeAware, ModelAware {
+public abstract class AbstractAttributeModelAware implements AttributeAware, ModelAware, Serializable {
 
   private Attributes attributes;