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Eureka! Clinical's web application development framework

Home Page: http://eurekaclinical.org

License: Apache License 2.0

Java 100.00%

framework

eurekaclinical-common's Introduction

Eureka! Clinical Common Web Application Framework

Georgia Clinical and Translational Science Alliance (Georgia CTSA), Emory University, Atlanta, GA

What does it do?

It implements a custom web application development framework that uses best of breed components:

Google Guice 3.0 (dependency injection)
Jersey 1.19.4 (REST)
Hibernate 5.0.12.Final (object-relational mapping)
Tomcat 7

It supports calling these components through the standard APIs specified in and provided by the Eureka! Clinical Web Application Standard APIs project.

It extends the functionality in the Eureka! Clinical Web Application Standard APIs project with the following features and implementations:

REST communication objects for users, roles, groups and authorization templates (org.eurekaclinical.common.comm)
Base classes for implementing REST clients (org.eurekaclinical.common.comm.clients)
Base classes for implementing Guice modules (org.eurekaclinical.common.config)
Servlet filters for user authorization (org.eurekaclinical.common.filter)
Servlets for login and logout; destroying a session; and proxying (org.eurekaclinical.common.servlet)

See Structure of Eureka! Clinical microservices for how to use the framework. The goal for the version 2.0 release is for all Eureka! Clinical web application components to use this framework.

Latest release:

Version 3.0

Removed RolesFromServiceFilter because Eureka! Clinical webapps no longer need role information.
Removed WebappServletModule, which was superceded by APIGatewayServletModule.
Removed AbstractAuthorizingServletModule and AbstractAuthorizingJerseyServletModule, which are unused.
Add POST and PUT calls for passing a string into an Eureka! Clinical API gateway proxy.
Require version 2.1 or greater of eurekaclinical-standard-apis.

Version 2.0

The goal of the 2.0 series is to have sufficient functionality for all Eureka! Clinical web applications to depend on eurekaclinical-common.

Version 1.0

Implemented partial functionality, and only some parts of Eureka! Clinical used it.

Build requirements

Runtime requirements

Building it

The project uses the maven build tool. Typically, you build it by invoking mvn clean install at the command line. For simple file changes, not additions or deletions, you can usually use mvn install. See https://github.com/eurekaclinical/dev-wiki/wiki/Building-Eureka!-Clinical-projects for more details.

Maven dependency

<dependency>
    <groupId>org.eurekaclinical</groupId>
    <artifactId>eurekaclinical-common</artifactId>
    <version>version</version>
</dependency>

Developer documentation

Getting help

Feel free to contact us at [email protected].

eurekaclinical-common's People

Contributors

Watchers

Forkers

candyam5522 akalsan hrathod dgunda1 nityanandareddy venkateshjavvaji ndeshpa

eurekaclinical-common's Issues

ProxyServlet doesn't pass HTTP headers

ProxyServlet assumes content and response are always JSON

This could create an issue for file transfers.

ClientSessionListener throws com.google.inject.OutOfScopeException

For example:

INFO: Destroying session for client org.eurekaclinical.user.client.EurekaClinicalUserClient for service /eureka-webapp
Aug 24, 2017 3:48:53 PM org.apache.catalina.session.StandardSession expire
SEVERE: Session event listener threw exception
com.google.inject.ProvisionException: Guice provision errors:

1) Error in custom provider, com.google.inject.OutOfScopeException: Cannot access scoped object. Either we are not currently inside an HTTP Servlet request, or you may have forgotten to apply com.google.inject.servlet.GuiceFilter as a servlet filter for this request.
  at edu.emory.cci.aiw.cvrg.eureka.webapp.config.AppModule.configure(AppModule.java:80)
  while locating org.eurekaclinical.user.client.EurekaClinicalUserClient

1 error
	at com.google.inject.internal.InjectorImpl$4.get(InjectorImpl.java:987)
	at com.google.inject.internal.InjectorImpl.getInstance(InjectorImpl.java:1013)
	at org.eurekaclinical.common.config.ClientSessionListener.sessionDestroyed(ClientSessionListener.java:83)
	at org.apache.catalina.session.StandardSession.expire(StandardSession.java:806)
	at org.apache.catalina.session.StandardSession.isValid(StandardSession.java:656)
	at org.apache.catalina.session.ManagerBase.processExpires(ManagerBase.java:532)
	at org.apache.catalina.session.ManagerBase.backgroundProcess(ManagerBase.java:517)
	at org.apache.catalina.core.ContainerBase.backgroundProcess(ContainerBase.java:1352)
	at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1530)
	at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1540)
	at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1540)
	at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1519)
	at java.lang.Thread.run(Thread.java:745)
Caused by: com.google.inject.OutOfScopeException: Cannot access scoped object. Either we are not currently inside an HTTP Servlet request, or you may have forgotten to apply com.google.inject.servlet.GuiceFilter as a servlet filter for this request.
	at com.google.inject.servlet.GuiceFilter.getContext(GuiceFilter.java:135)
	at com.google.inject.servlet.GuiceFilter.getRequest(GuiceFilter.java:121)
	at com.google.inject.servlet.ServletScopes$2$1.get(ServletScopes.java:114)
	at com.google.inject.internal.InternalFactoryToProviderAdapter.get(InternalFactoryToProviderAdapter.java:40)
	at com.google.inject.internal.InjectorImpl$4$1.call(InjectorImpl.java:978)
	at com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1024)
	at com.google.inject.internal.InjectorImpl$4.get(InjectorImpl.java:974)
	... 12 more

This appears to occur only when tomcat sweeps active sessions and cleans up any invalid ones. It appears to be a harmless error, but we should handle it (check isValid() ourselves?).

DestroySessionServlet throws exception in RolesFromServiceFilter if session is dead

ProxyServlet does not handle 302 CAS redirects by the proxied call

302 from proxied call probably should return a 401 (not authorized) -- currently returns 200. Or, we need to make the proxied calls return 401.

JavaDoc

JavaDoc is not working with mvn install

NPE in ProxyServlet when no character encoding is sent in the HTTP headers

The problem is in extractContent, which in this case passes a null character encoding into new InputStreamReader.

Make application properties files support URLs with just a path so the hostname and port are inserted automatically

Uncaught exception in Eureka! Clinical client

A org.apache.http.client.CircularRedirectException occurs when the user is not fully authenticated, so we may want to catch this and respond with a 400 status code.

SEVERE: Servlet.service() for servlet [default] in context with path [/eureka-webapp] threw exception
com.sun.jersey.api.client.ClientHandlerException: org.apache.http.client.ClientProtocolException
        at com.sun.jersey.client.apache4.ApacheHttpClient4Handler.handle(ApacheHttpClient4Handler.java:187)
        at com.sun.jersey.api.client.filter.GZIPContentEncodingFilter.handle(GZIPContentEncodingFilter.java:123)
        at com.sun.jersey.api.client.Client.handle(Client.java:652)
        at com.sun.jersey.api.client.WebResource.handle(WebResource.java:682)
        at com.sun.jersey.api.client.WebResource.access$200(WebResource.java:74)
        at com.sun.jersey.api.client.WebResource$Builder.get(WebResource.java:509)
        at org.eurekaclinical.common.comm.clients.EurekaClinicalClient.doGetForProxy(EurekaClinicalClient.java:769)
        at org.eurekaclinical.common.comm.clients.ProxyingClient.proxyGet(ProxyingClient.java:70)
        at org.eurekaclinical.common.servlet.ProxyServlet.doGet(ProxyServlet.java:157)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:620)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
        at com.google.inject.servlet.ServletDefinition.doService(ServletDefinition.java:263)
        at com.google.inject.servlet.ServletDefinition.service(ServletDefinition.java:178)
        at com.google.inject.servlet.ManagedServletPipeline.service(ManagedServletPipeline.java:91)
        at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:62)
        at org.eurekaclinical.standardapis.filter.AbstractRolesFilter.doFilter(AbstractRolesFilter.java:85)
        at com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:163)
        at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:58)
        at com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:168)
        at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:58)
        at org.jasig.cas.client.util.AssertionThreadLocalFilter.doFilter(AssertionThreadLocalFilter.java:54)
        at com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:163)
        at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:58)
        at org.jasig.cas.client.util.HttpServletRequestWrapperFilter.doFilter(HttpServletRequestWrapperFilter.java:75)
        at com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:163)
        at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:58)
        at com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:168)
        at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:58)
        at com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:168)
        at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:58)
        at com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:168)
        at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:58)
        at com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:168)
        at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:58)
        at org.jasig.cas.client.session.SingleSignOutFilter.doFilter(SingleSignOutFilter.java:76)
        at com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:163)
        at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:58)
        at com.google.inject.servlet.ManagedFilterPipeline.dispatch(ManagedFilterPipeline.java:118)
        at com.google.inject.servlet.GuiceFilter.doFilter(GuiceFilter.java:113)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1040)
        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:313)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)
Caused by: org.apache.http.client.ClientProtocolException
        at org.apache.http.impl.client.AbstractHttpClient.execute(AbstractHttpClient.java:822)
        at org.apache.http.impl.client.AbstractHttpClient.execute(AbstractHttpClient.java:776)
        at com.sun.jersey.client.apache4.ApacheHttpClient4Handler.handle(ApacheHttpClient4Handler.java:173)
        ... 54 more
Caused by: org.apache.http.client.CircularRedirectException: Circular redirect to 'https://<hostname>/cas-server/login?service=https%3A%2F%2F<hostname>%2Feurekaclinical-user-service%2Fapi%2Fprotected%2Fusers%2Fme&gateway=true'
        at org.apache.http.impl.client.DefaultRedirectStrategy.getLocationURI(DefaultRedirectStrategy.java:168)
        at org.apache.http.impl.client.DefaultRedirectStrategy.getRedirect(DefaultRedirectStrategy.java:193)
        at org.apache.http.impl.client.DefaultRequestDirector.handleResponse(DefaultRequestDirector.java:1021)
        at org.apache.http.impl.client.DefaultRequestDirector.execute(DefaultRequestDirector.java:482)
        at org.apache.http.impl.client.AbstractHttpClient.execute(AbstractHttpClient.java:820)
        ... 56 more