Upgrade jersey

[pbelmann]

The current implementation is based on jersey 1.19.x . We should upgrade to 2.x.

[pbelmann]

I created a branch https://github.com/BiBiServ/bibiserv/tree/feature/upgrade-jersey with my first attempt.

• Bibimainapp can be deployed
• Tools deployment does not work. It fails with the exception:

bibimain.log:

java.lang.IllegalStateException: The resource configuration is not modifiable in this context. [ToolRequestFilter.java:196]

server.log:

[2016-09-21T09:51:02.008+0200] [glassfish 4.1] [WARNING] [] [javax.enterprise.web] [tid: _ThreadID=38 _ThreadName=http-listener-2(3)] [timeMillis: 1474444262008] [levelValue: 900] [[
  StandardWrapperValve[REST]: Servlet.service() for servlet REST threw exception
java.lang.IllegalStateException: Cannot forward after response has been committed
        at org.apache.catalina.core.ApplicationDispatcher.doDispatch(ApplicationDispatcher.java:448)
        at org.apache.catalina.core.ApplicationDispatcher.dispatch(ApplicationDispatcher.java:428)
        at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:378)
        at de.unibi.cebitec.bibiserv.web.controller.ToolRequestFilter.doFilter(ToolRequestFilter.java:198)
        at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:237)
        at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
        at de.unibi.cebitec.bibiserv.web.controller.ResetPasswordFilter.doFilter(ResetPasswordFilter.java:90)
        at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:237)
        at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:369)
        at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:99)
        at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:83)
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
        at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:109)
        at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:83)
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
        at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:97)
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
        at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:100)
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
        at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:78)
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
        at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:54)
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
        at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:35)
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
        at org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilter(BasicAuthenticationFilter.java:177)
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
        at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:187)
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
        at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:105)
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
        at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:79)
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
        at org.springframework.security.web.access.channel.ChannelProcessingFilter.doFilter(ChannelProcessingFilter.java:109)
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
        at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:168)
        at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:237)
        at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:316)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:160)
        at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:734)

It seem to not accept the path /rest/manager.