This is an automated email from the ASF dual-hosted git repository. lahirujayathilake pushed a commit to branch cybershuttle-dev in repository https://gitbox.apache.org/repos/asf/airavata.git
commit 8b9ca6c94e65e0a3fd11627f5225b10fe3a11dcc Author: yasithdev <[email protected]> AuthorDate: Tue Mar 18 07:21:17 2025 +0000 migrate javax.mail to jakarta.mail to fix email-monitor bug. exclude conflicting angus-mail dependency. add missing @Deprecated tags. --- .../iam-admin-services-core/pom.xml | 6 ++++++ .../profile/user/cpi/UserProfileService.java | 1 + modules/agent-framework/agent-service/pom.xml | 5 ----- .../service/controllers/AgentController.java | 2 +- .../service/controllers/ExperimentController.java | 7 +++++- .../airavata/common/utils/ApplicationSettings.java | 3 +++ .../src/main/assembly/controller-bin-assembly.xml | 2 +- .../main/assembly/email-monitor-bin-assembly.xml | 4 ++-- .../src/main/assembly/parser-wm-bin-assembly.xml | 2 +- .../src/main/assembly/participant-bin-assembly.xml | 2 +- .../src/main/assembly/post-wm-bin-assembly.xml | 2 +- .../src/main/assembly/pre-wm-bin-assembly.xml | 2 +- modules/job-monitor/email-monitor/pom.xml | 9 +++----- .../airavata/monitor/email/EmailBasedMonitor.java | 25 +++++++++++++--------- .../email/parser/AiravataCustomMailParser.java | 4 ++-- .../airavata/monitor/email/parser/EmailParser.java | 4 ++-- .../monitor/email/parser/HTCondorEmailParser.java | 4 ++-- .../monitor/email/parser/LSFEmailParser.java | 4 ++-- .../monitor/email/parser/PBSEmailParser.java | 4 ++-- .../monitor/email/parser/SLURMEmailParser.java | 4 ++-- .../monitor/email/parser/UGEEmailParser.java | 4 ++-- modules/job-monitor/pom.xml | 11 +++------- pom.xml | 2 +- tools/load-client/pom.xml | 6 ++++++ 24 files changed, 66 insertions(+), 53 deletions(-) diff --git a/airavata-services/profile-service/iam-admin-services-core/pom.xml b/airavata-services/profile-service/iam-admin-services-core/pom.xml index 3c40866258..1d02d39acf 100644 --- a/airavata-services/profile-service/iam-admin-services-core/pom.xml +++ b/airavata-services/profile-service/iam-admin-services-core/pom.xml @@ -58,6 +58,12 @@ <groupId>org.keycloak</groupId> <artifactId>keycloak-admin-client</artifactId> <version>${keycloak.admin.client.version}</version> + <exclusions> + <exclusion> + <groupId>org.eclipse.angus</groupId> + <artifactId>angus-mail</artifactId> + </exclusion> + </exclusions> </dependency> <dependency> <groupId>org.apache.airavata</groupId> diff --git a/airavata-services/profile-service/profile-service-stubs/src/main/java/org/apache/airavata/service/profile/user/cpi/UserProfileService.java b/airavata-services/profile-service/profile-service-stubs/src/main/java/org/apache/airavata/service/profile/user/cpi/UserProfileService.java index 8bc718e7eb..f8f018f029 100644 --- a/airavata-services/profile-service/profile-service-stubs/src/main/java/org/apache/airavata/service/profile/user/cpi/UserProfileService.java +++ b/airavata-services/profile-service/profile-service-stubs/src/main/java/org/apache/airavata/service/profile/user/cpi/UserProfileService.java @@ -44,6 +44,7 @@ public class UserProfileService { * @param authzToken * @param userProfile */ + @Deprecated public java.lang.String addUserProfile(org.apache.airavata.model.security.AuthzToken authzToken, org.apache.airavata.model.user.UserProfile userProfile) throws org.apache.airavata.service.profile.user.cpi.exception.UserProfileServiceException, org.apache.airavata.model.error.AuthorizationException, org.apache.thrift.TException; public boolean updateUserProfile(org.apache.airavata.model.security.AuthzToken authzToken, org.apache.airavata.model.user.UserProfile userProfile) throws org.apache.airavata.service.profile.user.cpi.exception.UserProfileServiceException, org.apache.airavata.model.error.AuthorizationException, org.apache.thrift.TException; diff --git a/modules/agent-framework/agent-service/pom.xml b/modules/agent-framework/agent-service/pom.xml index b9dd019fe8..638ccb768a 100644 --- a/modules/agent-framework/agent-service/pom.xml +++ b/modules/agent-framework/agent-service/pom.xml @@ -100,11 +100,6 @@ <artifactId>grpc-server-spring-boot-starter</artifactId> <version>3.0.0.RELEASE</version> </dependency> - <dependency> - <groupId>javax.validation</groupId> - <artifactId>validation-api</artifactId> - <version>${javax.version}</version> - </dependency> <dependency> <groupId>javax.annotation</groupId> <artifactId>javax.annotation-api</artifactId> diff --git a/modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/controllers/AgentController.java b/modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/controllers/AgentController.java index c0380f7a2a..1c85c16148 100644 --- a/modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/controllers/AgentController.java +++ b/modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/controllers/AgentController.java @@ -7,7 +7,7 @@ import org.slf4j.LoggerFactory; import org.springframework.http.ResponseEntity; import org.springframework.web.bind.annotation.*; -import javax.validation.Valid; +import jakarta.validation.constraints.Valid; @RestController diff --git a/modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/controllers/ExperimentController.java b/modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/controllers/ExperimentController.java index 351f3caf2d..5b11bc2a28 100644 --- a/modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/controllers/ExperimentController.java +++ b/modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/controllers/ExperimentController.java @@ -8,9 +8,14 @@ import org.apache.airavata.model.experiment.ExperimentModel; import org.apache.airavata.model.process.ProcessModel; import org.springframework.http.MediaType; import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Component; import org.springframework.web.bind.annotation.*; -import javax.validation.Valid; +import jakarta.validation.constraints.Valid; + +class ExperimentController { + +}; @RestController @RequestMapping("/api/v1/exp") diff --git a/modules/commons/src/main/java/org/apache/airavata/common/utils/ApplicationSettings.java b/modules/commons/src/main/java/org/apache/airavata/common/utils/ApplicationSettings.java index 88c334dd97..5c0a218357 100644 --- a/modules/commons/src/main/java/org/apache/airavata/common/utils/ApplicationSettings.java +++ b/modules/commons/src/main/java/org/apache/airavata/common/utils/ApplicationSettings.java @@ -145,6 +145,7 @@ public class ApplicationSettings { * @throws ApplicationSettingsException If an error occurred while reading configurations. * @deprecated use #getSetting(String) instead */ + @Deprecated public String getAbsoluteSetting(String key) throws ApplicationSettingsException { String configurationValueWithVariables = ApplicationSettings.getSetting(key); @@ -290,6 +291,7 @@ public class ApplicationSettings { * @deprecated use {{@link #getSetting(String)}} * @return */ + @Deprecated public Properties getPropertiesImpl() { return properties; } @@ -501,6 +503,7 @@ public class ApplicationSettings { * @return * @throws ApplicationSettingsException */ + @Deprecated public static Properties getProperties() throws ApplicationSettingsException { return getInstance().properties; } diff --git a/modules/distribution/src/main/assembly/controller-bin-assembly.xml b/modules/distribution/src/main/assembly/controller-bin-assembly.xml index 29f17779cc..767d8360e4 100644 --- a/modules/distribution/src/main/assembly/controller-bin-assembly.xml +++ b/modules/distribution/src/main/assembly/controller-bin-assembly.xml @@ -133,7 +133,7 @@ <include>com.github.danielwegener:logback-kafka-appender:jar</include> <include>net.logstash.logback:logstash-logback-encoder:jar</include> <include>org.lz4:lz4-java:jar</include> - <include>javax.mail:mail:jar</include> + <include>jakarta.mail:jakarta.mail:jar</include> <include>io.dropwizard.metrics:metrics-core:jar</include> <include>org.jboss.netty:netty:jar</include> <include>org.apache.openjpa:openjpa:jar</include> diff --git a/modules/distribution/src/main/assembly/email-monitor-bin-assembly.xml b/modules/distribution/src/main/assembly/email-monitor-bin-assembly.xml index c0519fbb09..64400e89fb 100644 --- a/modules/distribution/src/main/assembly/email-monitor-bin-assembly.xml +++ b/modules/distribution/src/main/assembly/email-monitor-bin-assembly.xml @@ -92,8 +92,8 @@ <include>org.apache.airavata:airavata-data-models:jar</include> <include>org.apache.thrift:libthrift:jar</include> - <include>javax.mail:javax.mail-api:jar</include> - <include>com.sun.mail:javax.mail:jar</include> + <include>jakarta.mail:jakarta.mail-api:jar</include> + <include>jakarta.mail:jakarta.mail:jar</include> <include>javax.activation:activation:jar</include> <include>org.yaml:snakeyaml:jar</include> diff --git a/modules/distribution/src/main/assembly/parser-wm-bin-assembly.xml b/modules/distribution/src/main/assembly/parser-wm-bin-assembly.xml index fb69c836c4..3a30e919e5 100644 --- a/modules/distribution/src/main/assembly/parser-wm-bin-assembly.xml +++ b/modules/distribution/src/main/assembly/parser-wm-bin-assembly.xml @@ -138,7 +138,7 @@ <include>com.github.danielwegener:logback-kafka-appender:jar</include> <include>net.logstash.logback:logstash-logback-encoder:jar</include> <include>org.lz4:lz4-java:jar</include> - <include>javax.mail:mail:jar</include> + <include>jakarta.mail:jakarta.mail:jar</include> <include>io.dropwizard.metrics:metrics-core:jar</include> <include>org.jboss.netty:netty:jar</include> <include>org.apache.openjpa:openjpa:jar</include> diff --git a/modules/distribution/src/main/assembly/participant-bin-assembly.xml b/modules/distribution/src/main/assembly/participant-bin-assembly.xml index 1cc4499a97..5ea4d98327 100644 --- a/modules/distribution/src/main/assembly/participant-bin-assembly.xml +++ b/modules/distribution/src/main/assembly/participant-bin-assembly.xml @@ -139,7 +139,7 @@ <include>com.github.danielwegener:logback-kafka-appender:jar</include> <include>net.logstash.logback:logstash-logback-encoder:jar</include> <include>org.lz4:lz4-java:jar</include> - <include>javax.mail:mail:jar</include> + <include>jakarta.mail:jakarta.mail:jar</include> <include>io.dropwizard.metrics:metrics-core:jar</include> <include>org.jboss.netty:netty:jar</include> <include>org.apache.openjpa:openjpa:jar</include> diff --git a/modules/distribution/src/main/assembly/post-wm-bin-assembly.xml b/modules/distribution/src/main/assembly/post-wm-bin-assembly.xml index 2d5b00b9ad..6dab1016dd 100644 --- a/modules/distribution/src/main/assembly/post-wm-bin-assembly.xml +++ b/modules/distribution/src/main/assembly/post-wm-bin-assembly.xml @@ -138,8 +138,8 @@ <include>com.github.danielwegener:logback-kafka-appender:jar</include> <include>net.logstash.logback:logstash-logback-encoder:jar</include> <include>org.lz4:lz4-java:jar</include> - <include>javax.mail:mail:jar</include> <include>io.dropwizard.metrics:metrics-core:jar</include> + <include>jakarta.mail:jakarta.mail:jar</include> <include>org.jboss.netty:netty:jar</include> <include>org.apache.openjpa:openjpa:jar</include> <include>org.apache.airavata:platform-monitor:jar</include> diff --git a/modules/distribution/src/main/assembly/pre-wm-bin-assembly.xml b/modules/distribution/src/main/assembly/pre-wm-bin-assembly.xml index 75fa397967..d6b0e9ae5e 100644 --- a/modules/distribution/src/main/assembly/pre-wm-bin-assembly.xml +++ b/modules/distribution/src/main/assembly/pre-wm-bin-assembly.xml @@ -138,7 +138,7 @@ <include>com.github.danielwegener:logback-kafka-appender:jar</include> <include>net.logstash.logback:logstash-logback-encoder:jar</include> <include>org.lz4:lz4-java:jar</include> - <include>javax.mail:mail:jar</include> + <include>jakarta.mail:jakarta.mail:jar</include> <include>io.dropwizard.metrics:metrics-core:jar</include> <include>org.jboss.netty:netty:jar</include> <include>org.apache.openjpa:openjpa:jar</include> diff --git a/modules/job-monitor/email-monitor/pom.xml b/modules/job-monitor/email-monitor/pom.xml index 3a062933e8..ac66537f89 100644 --- a/modules/job-monitor/email-monitor/pom.xml +++ b/modules/job-monitor/email-monitor/pom.xml @@ -41,12 +41,9 @@ <artifactId>snakeyaml</artifactId> </dependency> <dependency> - <groupId>javax.mail</groupId> - <artifactId>javax.mail-api</artifactId> - </dependency> - <dependency> - <groupId>com.sun.mail</groupId> - <artifactId>javax.mail</artifactId> + <groupId>jakarta.mail</groupId> + <artifactId>jakarta.mail-api</artifactId> + <version>2.1.2</version> </dependency> </dependencies> </project> diff --git a/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/EmailBasedMonitor.java b/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/EmailBasedMonitor.java index 63f9e47ee5..9c35025f26 100644 --- a/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/EmailBasedMonitor.java +++ b/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/EmailBasedMonitor.java @@ -33,15 +33,15 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.yaml.snakeyaml.Yaml; -import javax.mail.Address; -import javax.mail.Flags; -import javax.mail.Folder; -import javax.mail.Message; -import javax.mail.MessagingException; -import javax.mail.Session; -import javax.mail.Store; -import javax.mail.search.FlagTerm; -import javax.mail.search.SearchTerm; +import jakarta.mail.Address; +import jakarta.mail.Flags; +import jakarta.mail.Folder; +import jakarta.mail.Message; +import jakarta.mail.MessagingException; +import jakarta.mail.Session; +import jakarta.mail.Store; +import jakarta.mail.search.FlagTerm; +import jakarta.mail.search.SearchTerm; import java.io.InputStream; import java.util.*; @@ -193,6 +193,9 @@ public class EmailBasedMonitor extends AbstractMonitor implements Runnable { emailFolder = store.getFolder(folderName); } log.info("[EJM]: Retrieving unseen emails"); + if (emailFolder == null) { + return; + } emailFolder.open(Folder.READ_WRITE); if (emailFolder.isOpen()) { // flush if any message left in flushUnseenMessage @@ -228,7 +231,9 @@ public class EmailBasedMonitor extends AbstractMonitor implements Runnable { log.error("[EJM]: Caught a throwable ", e); } finally { try { - emailFolder.close(false); + if (emailFolder != null) { + emailFolder.close(false); + } store.close(); } catch (MessagingException e) { log.error("[EJM]: Store close operation failed, couldn't close store", e); diff --git a/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/AiravataCustomMailParser.java b/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/AiravataCustomMailParser.java index ae0cecb900..20c561207e 100644 --- a/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/AiravataCustomMailParser.java +++ b/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/AiravataCustomMailParser.java @@ -26,8 +26,8 @@ import org.apache.airavata.registry.api.RegistryService; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import javax.mail.Message; -import javax.mail.MessagingException; +import jakarta.mail.Message; +import jakarta.mail.MessagingException; import java.util.regex.Matcher; import java.util.regex.Pattern; diff --git a/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/EmailParser.java b/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/EmailParser.java index d76f733c19..2996dd50cd 100644 --- a/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/EmailParser.java +++ b/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/EmailParser.java @@ -23,8 +23,8 @@ import org.apache.airavata.common.exception.AiravataException; import org.apache.airavata.monitor.JobStatusResult; import org.apache.airavata.registry.api.RegistryService; -import javax.mail.Message; -import javax.mail.MessagingException; +import jakarta.mail.Message; +import jakarta.mail.MessagingException; public interface EmailParser { static final String STATUS = "status"; diff --git a/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/HTCondorEmailParser.java b/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/HTCondorEmailParser.java index e91b0153ec..5e9d5d15ee 100644 --- a/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/HTCondorEmailParser.java +++ b/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/HTCondorEmailParser.java @@ -27,8 +27,8 @@ import org.apache.airavata.registry.api.RegistryService; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import javax.mail.Message; -import javax.mail.MessagingException; +import jakarta.mail.Message; +import jakarta.mail.MessagingException; import java.io.IOException; import java.util.List; import java.util.Optional; diff --git a/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/LSFEmailParser.java b/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/LSFEmailParser.java index 99660c2ae8..be61fad37e 100644 --- a/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/LSFEmailParser.java +++ b/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/LSFEmailParser.java @@ -26,8 +26,8 @@ import org.apache.airavata.registry.api.RegistryService; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import javax.mail.Message; -import javax.mail.MessagingException; +import jakarta.mail.Message; +import jakarta.mail.MessagingException; import java.io.IOException; import java.util.regex.Matcher; import java.util.regex.Pattern; diff --git a/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/PBSEmailParser.java b/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/PBSEmailParser.java index b0c22988e7..2da293d827 100644 --- a/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/PBSEmailParser.java +++ b/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/PBSEmailParser.java @@ -26,8 +26,8 @@ import org.apache.airavata.registry.api.RegistryService; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import javax.mail.Message; -import javax.mail.MessagingException; +import jakarta.mail.Message; +import jakarta.mail.MessagingException; import java.io.IOException; import java.util.regex.Matcher; import java.util.regex.Pattern; diff --git a/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/SLURMEmailParser.java b/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/SLURMEmailParser.java index eaae04071d..0e8b4b3386 100644 --- a/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/SLURMEmailParser.java +++ b/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/SLURMEmailParser.java @@ -26,8 +26,8 @@ import org.apache.airavata.registry.api.RegistryService; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import javax.mail.Message; -import javax.mail.MessagingException; +import jakarta.mail.Message; +import jakarta.mail.MessagingException; import java.util.regex.Matcher; import java.util.regex.Pattern; diff --git a/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/UGEEmailParser.java b/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/UGEEmailParser.java index ebaf84d90e..728182d128 100644 --- a/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/UGEEmailParser.java +++ b/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/UGEEmailParser.java @@ -26,8 +26,8 @@ import org.apache.airavata.registry.api.RegistryService; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import javax.mail.Message; -import javax.mail.MessagingException; +import jakarta.mail.Message; +import jakarta.mail.MessagingException; import java.io.IOException; import java.util.regex.Matcher; import java.util.regex.Pattern; diff --git a/modules/job-monitor/pom.xml b/modules/job-monitor/pom.xml index dc8657564d..8a62fcc7b2 100644 --- a/modules/job-monitor/pom.xml +++ b/modules/job-monitor/pom.xml @@ -44,14 +44,9 @@ <version>1.15</version> </dependency> <dependency> - <groupId>javax.mail</groupId> - <artifactId>javax.mail-api</artifactId> - <version>1.6.2</version> - </dependency> - <dependency> - <groupId>com.sun.mail</groupId> - <artifactId>javax.mail</artifactId> - <version>1.6.2</version> + <groupId>jakarta.mail</groupId> + <artifactId>jakarta.mail-api</artifactId> + <version>2.1.2</version> </dependency> <dependency> <groupId>org.apache.airavata</groupId> diff --git a/pom.xml b/pom.xml index db5cd8df9a..7c7c470ad1 100644 --- a/pom.xml +++ b/pom.xml @@ -154,7 +154,7 @@ <org.apache.commons.pool2.version>2.7.0</org.apache.commons.pool2.version> <helix.version>0.9.7</helix.version> <keycloak.admin.client.version>24.0.4</keycloak.admin.client.version> - <rest.easy.client.version>6.2.8.Final</rest.easy.client.version> + <rest.easy.client.version>6.2.12.Final</rest.easy.client.version> <httpclient.version>4.5.14</httpclient.version> <codehaus.jackson.version>1.9.13</codehaus.jackson.version> <spring.boot.version>3.2.4</spring.boot.version> diff --git a/tools/load-client/pom.xml b/tools/load-client/pom.xml index 499eb83329..3d880b001a 100644 --- a/tools/load-client/pom.xml +++ b/tools/load-client/pom.xml @@ -28,6 +28,12 @@ <groupId>org.keycloak</groupId> <artifactId>keycloak-admin-client</artifactId> <version>${keycloak.admin.client.version}</version> + <exclusions> + <exclusion> + <groupId>org.eclipse.angus</groupId> + <artifactId>angus-mail</artifactId> + </exclusion> + </exclusions> </dependency> <dependency> <groupId>org.apache.airavata</groupId>
