Unable to use Spring Boot Data on Websphere traditional 8.5 - spring

Question

I am trying to run a Spring Boot 1.5.9 application on Websphere 8.5.5.13 (class loading is parent last and I don't have shared library)
and when trying to call JpaRepository built in methods (I notice that the SQL query is being executed) but I am getting the following exception :
org.springframework.transaction.TransactionSystemException:
UOWManager transaction processing failed; nested exception is com.ibm.wsspi.uow.UOWException:
java.lang.LinkageError: com/ibm/websphere/uow/UOWSynchronizationRegistry.registerInterposedSynchronization
(Ljavax/transaction/Synchronization;)V (loaded from file:/D:/IBM/WebSphere/AppServer/plugins/com.ibm.ws.runtime.jar
by org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader#873a9f67)
called from class org.springframework.transaction.jta.WebSphereUowTransactionManager$UOWActionAdapter
(loaded from file:/D:/IBM/WebSphere/AppServer/profiles/AppSrv01/installedApps/D1SHLAPXXPWV1Node01Cell
/Spring.ear/SpringJSF.war/WEB-INF/lib/spring-tx-4.3.13.RELEASE.jar by
com.ibm.ws.classloader.CompoundClassLoader#7c146942[war:Spring/SpringJSF.war]
My pom file is as follows :
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<modelVersion>4.0.0</modelVersion>
<groupId>org.springframework</groupId>
<artifactId>SpringJSF</artifactId>
<version>1</version>
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>1.5.9.RELEASE</version>
</parent>
<properties>
<java.version>1.8</java.version>
</properties>
<packaging>war</packaging>
<dependencies>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<version>3.1.0</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-actuator</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-cache</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-mail</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-thymeleaf</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
<exclusions>
<exclusion>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-tomcat</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-data-jpa</artifactId>
<exclusions>
<exclusion>
<groupId>org.hibernate</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>4.2.15.Final</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-entitymanager</artifactId>
<version>4.2.15.Final</version>
</dependency>
<dependency>
<groupId>org.hibernate.javax.persistence</groupId>
<artifactId>hibernate-jpa-2.0-api</artifactId>
<version>1.0.0.Final</version>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-security</artifactId>
</dependency>
<dependency>
<groupId>javax</groupId>
<artifactId>javaee-api</artifactId>
<version>6.0</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>javax.el</groupId>
<artifactId>javax.el-api</artifactId>
<version>3.0.0</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.microsoft.sqlserver</groupId>
<artifactId>mssql-jdbc</artifactId>
<version>6.2.2.jre8</version>
</dependency>
<dependency>
<groupId>org.glassfish</groupId>
<artifactId>javax.faces</artifactId>
<version>2.2.9</version>
</dependency>
<dependency>
<groupId>javax.enterprise</groupId>
<artifactId>cdi-api</artifactId>
<version>1.2</version>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>jstl</artifactId>
</dependency>
<dependency>
<groupId>org.primefaces</groupId>
<artifactId>primefaces</artifactId>
<version>6.1</version>
</dependency>
<dependency>
<groupId>org.ocpsoft.rewrite</groupId>
<artifactId>rewrite-servlet</artifactId>
<version>3.4.1.Final</version>
</dependency>
<dependency>
<groupId>org.ocpsoft.rewrite</groupId>
<artifactId>rewrite-config-prettyfaces</artifactId>
<version>3.4.1.Final</version>
</dependency>
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
<version>1.10</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.5</version>
</dependency>
<dependency>
<groupId>javax.mail</groupId>
<artifactId>mail</artifactId>
<version>1.4.7</version>
</dependency>
<dependency>
<groupId>commons-validator</groupId>
<artifactId>commons-validator</artifactId>
<version>1.6</version>
</dependency>
<dependency>
<groupId>commons-fileupload</groupId>
<artifactId>commons-fileupload</artifactId>
<version>1.3.3</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.5</version>
</dependency>
<dependency>
<groupId>joda-time</groupId>
<artifactId>joda-time</artifactId>
<version>2.9.9</version>
</dependency>
</dependencies>
<build>
<finalName>SpringJSF</finalName>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.20</version>
<configuration>
<argLine>-Dfile.encoding=UTF8</argLine>
</configuration>
</plugin>
</plugins>
</build>
<repositories>
<repository>
<id>spring-releases</id>
<name>Spring Releases</name>
<url>https://repo.spring.io/libs-release</url>
</repository>
<repository>
<id>org.jboss.repository.releases</id>
<name>JBoss Maven Release Repository</name>
<url>https://repository.jboss.org/nexus/content/repositories/releases</url>
</repository>
</repositories>
<pluginRepositories>
<pluginRepository>
<id>spring-releases</id>
<name>Spring Releases</name>
<url>https://repo.spring.io/libs-release</url>
</pluginRepository>
</pluginRepositories>
</project>
My repository interface :
public interface EmployeeRepository extends JpaRepository<Employee, Long> {
#Query("from Employee u where u.userName = :userName")
Employee findByUserName(#Param("userName") String username);
}
Maven dependency tree:
[INFO] org.springframework:SpringJSF:war:1
[INFO] +- javax.servlet:javax.servlet-api:jar:3.1.0:provided
[INFO] +- org.springframework.boot:spring-boot-starter-actuator:jar:1.5.9.RELEAS
E:compile
[INFO] | +- org.springframework.boot:spring-boot-starter:jar:1.5.9.RELEASE:comp
ile
[INFO] | | +- org.springframework.boot:spring-boot:jar:1.5.9.RELEASE:compile
[INFO] | | +- org.springframework.boot:spring-boot-autoconfigure:jar:1.5.9.REL
EASE:compile
[INFO] | | +- org.springframework.boot:spring-boot-starter-logging:jar:1.5.9.R
ELEASE:compile
[INFO] | | | +- ch.qos.logback:logback-classic:jar:1.1.11:compile
[INFO] | | | | \- ch.qos.logback:logback-core:jar:1.1.11:compile
[INFO] | | | +- org.slf4j:jul-to-slf4j:jar:1.7.25:compile
[INFO] | | | \- org.slf4j:log4j-over-slf4j:jar:1.7.25:compile
[INFO] | | \- org.yaml:snakeyaml:jar:1.17:runtime
[INFO] | \- org.springframework.boot:spring-boot-actuator:jar:1.5.9.RELEASE:com
pile
[INFO] +- org.springframework.boot:spring-boot-starter-cache:jar:1.5.9.RELEASE:c
ompile
[INFO] | +- org.springframework:spring-context:jar:4.3.13.RELEASE:compile
[INFO] | | +- org.springframework:spring-beans:jar:4.3.13.RELEASE:compile
[INFO] | | \- org.springframework:spring-expression:jar:4.3.13.RELEASE:compile
[INFO] | \- org.springframework:spring-context-support:jar:4.3.13.RELEASE:compi
le
[INFO] +- org.springframework.boot:spring-boot-starter-mail:jar:1.5.9.RELEASE:co
mpile
[INFO] | \- com.sun.mail:javax.mail:jar:1.5.6:compile
[INFO] +- org.springframework.boot:spring-boot-starter-thymeleaf:jar:1.5.9.RELEA
SE:compile
[INFO] | +- org.thymeleaf:thymeleaf-spring4:jar:2.1.6.RELEASE:compile
[INFO] | | +- org.thymeleaf:thymeleaf:jar:2.1.6.RELEASE:compile
[INFO] | | | +- ognl:ognl:jar:3.0.8:compile
[INFO] | | | \- org.unbescape:unbescape:jar:1.1.0.RELEASE:compile
[INFO] | | \- org.slf4j:slf4j-api:jar:1.7.25:compile
[INFO] | \- nz.net.ultraq.thymeleaf:thymeleaf-layout-dialect:jar:1.4.0:compile
[INFO] | \- org.codehaus.groovy:groovy:jar:2.4.13:compile
[INFO] +- org.springframework.boot:spring-boot-starter-test:jar:1.5.9.RELEASE:te
st
[INFO] | +- org.springframework.boot:spring-boot-test:jar:1.5.9.RELEASE:test
[INFO] | +- org.springframework.boot:spring-boot-test-autoconfigure:jar:1.5.9.R
ELEASE:test
[INFO] | +- com.jayway.jsonpath:json-path:jar:2.2.0:test
[INFO] | | \- net.minidev:json-smart:jar:2.2.1:test
[INFO] | | \- net.minidev:accessors-smart:jar:1.1:test
[INFO] | | \- org.ow2.asm:asm:jar:5.0.3:test
[INFO] | +- junit:junit:jar:4.12:test
[INFO] | +- org.assertj:assertj-core:jar:2.6.0:test
[INFO] | +- org.mockito:mockito-core:jar:1.10.19:test
[INFO] | | \- org.objenesis:objenesis:jar:2.1:test
[INFO] | +- org.hamcrest:hamcrest-core:jar:1.3:test
[INFO] | +- org.hamcrest:hamcrest-library:jar:1.3:test
[INFO] | +- org.skyscreamer:jsonassert:jar:1.4.0:test
[INFO] | | \- com.vaadin.external.google:android-json:jar:0.0.20131108.vaadin1
:test
[INFO] | +- org.springframework:spring-core:jar:4.3.13.RELEASE:compile
[INFO] | \- org.springframework:spring-test:jar:4.3.13.RELEASE:test
[INFO] +- org.springframework.boot:spring-boot-starter-web:jar:1.5.9.RELEASE:com
pile
[INFO] | +- org.hibernate:hibernate-validator:jar:5.3.6.Final:compile
[INFO] | | +- javax.validation:validation-api:jar:1.1.0.Final:compile
[INFO] | | \- com.fasterxml:classmate:jar:1.3.4:compile
[INFO] | +- com.fasterxml.jackson.core:jackson-databind:jar:2.8.10:compile
[INFO] | | +- com.fasterxml.jackson.core:jackson-annotations:jar:2.8.0:compile
[INFO] | | \- com.fasterxml.jackson.core:jackson-core:jar:2.8.10:compile
[INFO] | +- org.springframework:spring-web:jar:4.3.13.RELEASE:compile
[INFO] | \- org.springframework:spring-webmvc:jar:4.3.13.RELEASE:compile
[INFO] +- org.springframework.boot:spring-boot-starter-data-jpa:jar:1.5.9.RELEAS
E:compile
[INFO] | +- org.springframework.boot:spring-boot-starter-aop:jar:1.5.9.RELEASE:
compile
[INFO] | | \- org.aspectj:aspectjweaver:jar:1.8.13:compile
[INFO] | +- org.springframework.boot:spring-boot-starter-jdbc:jar:1.5.9.RELEASE
:compile
[INFO] | | +- org.apache.tomcat:tomcat-jdbc:jar:8.5.23:compile
[INFO] | | | \- org.apache.tomcat:tomcat-juli:jar:8.5.23:compile
[INFO] | | \- org.springframework:spring-jdbc:jar:4.3.13.RELEASE:compile
[INFO] | +- javax.transaction:javax.transaction-api:jar:1.2:compile
[INFO] | +- org.springframework.data:spring-data-jpa:jar:1.11.9.RELEASE:compile
[INFO] | | +- org.springframework.data:spring-data-commons:jar:1.13.9.RELEASE:
compile
[INFO] | | +- org.springframework:spring-orm:jar:4.3.13.RELEASE:compile
[INFO] | | +- org.springframework:spring-tx:jar:4.3.13.RELEASE:compile
[INFO] | | \- org.slf4j:jcl-over-slf4j:jar:1.7.25:compile
[INFO] | \- org.springframework:spring-aspects:jar:4.3.13.RELEASE:compile
[INFO] +- org.hibernate:hibernate-core:jar:4.2.15.Final:compile
[INFO] | +- antlr:antlr:jar:2.7.7:compile
[INFO] | +- org.jboss.logging:jboss-logging:jar:3.3.1.Final:compile
[INFO] | +- dom4j:dom4j:jar:1.6.1:compile
[INFO] | +- org.javassist:javassist:jar:3.21.0-GA:compile
[INFO] | +- org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:jar
:1.0.1.Final:compile
[INFO] | \- org.hibernate.common:hibernate-commons-annotations:jar:4.0.2.Final:
compile
[INFO] +- org.hibernate:hibernate-entitymanager:jar:4.2.15.Final:compile
[INFO] +- org.hibernate.javax.persistence:hibernate-jpa-2.0-api:jar:1.0.0.Final:
compile
[INFO] +- org.springframework.boot:spring-boot-starter-security:jar:1.5.9.RELEAS
E:compile
[INFO] | +- org.springframework:spring-aop:jar:4.3.13.RELEASE:compile
[INFO] | +- org.springframework.security:spring-security-config:jar:4.2.3.RELEA
SE:compile
[INFO] | | \- org.springframework.security:spring-security-core:jar:4.2.3.RELE
ASE:compile
[INFO] | \- org.springframework.security:spring-security-web:jar:4.2.3.RELEASE:
compile
[INFO] +- javax:javaee-api:jar:6.0:provided
[INFO] +- javax.el:javax.el-api:jar:3.0.0:provided
[INFO] +- com.microsoft.sqlserver:mssql-jdbc:jar:6.2.2.jre8:compile
[INFO] +- org.glassfish:javax.faces:jar:2.2.9:compile
[INFO] +- javax.enterprise:cdi-api:jar:1.2:compile
[INFO] | +- javax.interceptor:javax.interceptor-api:jar:1.2:compile
[INFO] | \- javax.inject:javax.inject:jar:1:compile
[INFO] +- javax.servlet:jstl:jar:1.2:compile
[INFO] +- org.primefaces:primefaces:jar:6.1:compile
[INFO] +- org.ocpsoft.rewrite:rewrite-servlet:jar:3.4.1.Final:compile
[INFO] +- org.ocpsoft.rewrite:rewrite-config-prettyfaces:jar:3.4.1.Final:compile
[INFO] | \- org.ocpsoft.rewrite:rewrite-integration-faces:jar:3.4.1.Final:compi
le
[INFO] +- commons-codec:commons-codec:jar:1.10:compile
[INFO] +- org.apache.commons:commons-lang3:jar:3.5:compile
[INFO] +- javax.mail:mail:jar:1.4.7:compile
[INFO] | \- javax.activation:activation:jar:1.1:compile
[INFO] +- commons-validator:commons-validator:jar:1.6:compile
[INFO] | +- commons-beanutils:commons-beanutils:jar:1.9.3:compile
[INFO] | +- commons-digester:commons-digester:jar:2.1:compile
[INFO] | +- commons-logging:commons-logging:jar:1.2:compile
[INFO] | \- commons-collections:commons-collections:jar:3.2.2:compile
[INFO] +- commons-fileupload:commons-fileupload:jar:1.3.3:compile
[INFO] +- commons-io:commons-io:jar:2.5:compile
[INFO] \- joda-time:joda-time:jar:2.9.9:compile
NOTE: any dao method annotated with #Query works fine with no issues, my current issue is with JpaRepository built in methods like findAll, it doesn't work and produces the above exception.
UPDATE 1 : I tried marking the class loading to be parent first, and move all the jars from my application lib folder and put them in an isolated shared library, but this solution make the application started without springboot being initialized and neither hibernate nor jsf, so it's not working.

Answer 1

The maven depdencency tree shows that you have 2 transaction API's as dependencies:
javax.transaction-api
jboss-transaction-api_1.1_spec
and both have scope compile.
When you look at the lib folder of your war you should find
javax.transaction-api-1.2.jar
jboss-transaction-api_1.1_spec-1.0.1.Final.jar
You must ensure that both are not in the lib folder, because the com.ibm.websphere.uow.UOWSynchronizationRegistry is loaded from another class loader and this class loader also contains a version of the transaction api.
Try to use the dependencyManagement to set the dependency scopes to provided. E.g.
<dependencyManagement>
<dependencies>
<dependency>
<groupId>javax.transaction</groupId>
<artifactId>javax.transaction-api</artifactId>
<version>1.2</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.jboss.spec.javax.transaction</groupId>
<artifactId>jboss-transaction-api_1.1_spec</artifactId>
<version>1.0.1.Final</version>
<scope>provided</scope>
</dependency>
</dependencies>
</dependencyManagement>

Answer 2

The problem is most likely caused by a copy of the JTA API packaged in the application loader. That would cause the Spring transaction class and the WAS transaction class to link against separate copies of the JTA class, and the duplicate visibility from the Spring class (directly from the application loader, indirectly through the WAS class) causes the LinkageError at runtime.
This specific issue could likely be resolved by removing the JTA API from the application. You may also want to reconsider the use of PARENT_LAST, unless you are certain it's required for your application - while it has its uses, it also greatly increases the likelihood of LinkageErrors and ClassCastExceptions, among other things, if the application's contents are not very tightly controlled. A safer alternative might be a shared library with an isolated class loader, containing ONLY the specific libraries for which you need to bring your own implementation rather than simply using the version included in the server.