[e-link][explore][ldf] broken on freme 0.4 and later?

[ArneBinder]

post /e-link/explore ldf seems to be broken. The following curl does not work:

`curl -X POST "http://api.freme-project.eu/0.4/e-link/explore?resource=http://dbpedia.org/resource/Berlin&endpoint=http://fragments.dbpedia.org/2014/en&endpoint-type=ldf"

result:

{
  "exception": "eu.freme.broker.exception.InternalServerErrorException",
  "path": "/e-link/explore",
  "message": "Unknown problem. Please contact us.",
  "error": "Internal Server Error",
  "status": 500,
  "timestamp": 1460391260772
}

explore sparql still works:

curl -X POST "http://api.freme-project.eu/0.4/e-link/explore?resource=http://dbpedia.org/resource/Berlin&endpoint=http://dbpedia.org/sparql&endpoint-type=sparql"

[ArneBinder]

I un-ignored the JUnit tests, they work (with the mockup endpoint).

[jnehring]

**I can reproduce the problem.

Explore sparql endpoint works:

curl -X POST "http://api.freme-project.eu/current/e-link/explore?resource=http%3A%2F%2Fdbpedia.org%2Fresource%2FBerlin&endpoint=http%3A%2F%2Fdbpedia.org%2Fsparql&endpoint-type=sparql"

I checked the logfiles. There is a NullPointerException and a stack trace:

2016-04-12 16:01:49 [INFO] eu.freme.bservices.filters.logging.LoggingFilter.logRequest(LoggingFilter.java:142) Request: request id=2; content type=text/plain;charset=UTF-8; uri=/e-link/explore?resource=http://dbpedia.org/resource/Berlin&endpoint=http://fragments.dbpedia.org&endpoint-type=ldf; payload=
2016-04-12 16:02:25 [WARN] org.apache.jena.riot.system.ErrorHandlerFactory$ErrorLogger.logWarning(ErrorHandlerFactory.java:77) Only triples or default graph data expected : named graph data ignored
2016-04-12 16:02:50 [ERROR] eu.freme.eservices.elink.api.DataEnricher.enrichViaLDFExplore(DataEnricher.java:216) java.lang.NullPointerException
    at java.nio.CharBuffer.wrap(CharBuffer.java:487)
    at com.github.fge.uritemplate.parse.URITemplateParser.parse(URITemplateParser.java:55)
    at com.github.fge.uritemplate.URITemplate.<init>(URITemplate.java:52)
    at org.linkeddatafragments.model.LinkedDataFragment.setTemplate(LinkedDataFragment.java:140)
    at org.linkeddatafragments.model.LinkedDataFragment.hydraParse(LinkedDataFragment.java:85)
    at org.linkeddatafragments.model.LinkedDataFragment.<init>(LinkedDataFragment.java:77)
    at org.linkeddatafragments.model.LinkedDataFragmentFactory.create(LinkedDataFragmentFactory.java:18)
    at org.linkeddatafragments.client.LinkedDataFragmentsClient.getBaseFragment(LinkedDataFragmentsClient.java:60)
    at org.linkeddatafragments.model.LinkedDataFragmentGraph.graphBaseSize(LinkedDataFragmentGraph.java:102)
    at com.hp.hpl.jena.graph.impl.GraphBase.size(GraphBase.java:344)
    at org.linkeddatafragments.solver.ReorderTransformationLDF.<init>(ReorderTransformationLDF.java:41)
    at org.linkeddatafragments.model.LinkedDataFragmentGraph.<init>(LinkedDataFragmentGraph.java:37)
    at eu.freme.eservices.elink.api.DataEnricher.enrichViaLDFExplore(DataEnricher.java:207)
    at eu.freme.eservices.elink.api.DataEnricher.exploreResource(DataEnricher.java:183)
    at eu.freme.eservices.elink.LinkingController.exploreResource(LinkingController.java:148)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:222)
    at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:137)
    at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:110)
    at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:775)
    at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:705)
    at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:85)
    at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:959)
    at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:893)
    at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:965)
    at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:867)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:648)
    at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:841)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at eu.freme.bservices.filters.cors.CORSFilter.doFilter(CORSFilter.java:33)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at eu.freme.bservices.filters.postprocessing.PostprocessingFilter.doFilter(PostprocessingFilter.java:58)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at eu.freme.bservices.filters.internationalizationfilter.InternationalizationFilter.doFilter(InternationalizationFilter.java:218)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at eu.freme.bservices.filters.logging.LoggingFilter.doFilterInternal(LoggingFilter.java:86)
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:113)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:103)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:113)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:154)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:45)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at eu.freme.common.security.ManagementEndpointAuthenticationFilter.doFilter(ManagementEndpointAuthenticationFilter.java:83)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at eu.freme.common.security.AuthenticationFilter.doFilter(AuthenticationFilter.java:92)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:110)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:57)
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:50)
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:192)
    at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.springframework.web.filter.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:77)
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:85)
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:212)
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106)
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:141)
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:521)
    at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1096)
    at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:674)
    at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1500)
    at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1456)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
    at java.lang.Thread.run(Thread.java:745)

@m1ci any idea whats wrong?

[m1ci]

hard to say, no changes has been done in the recent period

[m1ci]

I tried to find the issue but without success. The issue seems to be between Jena/LDF dependencies in FREME. Probably something has changed during the migration to the new architecture.

[jnehring]

Probably something has changed during the migration to the new architecture.

The problem happens on FREME live which still runs the old architecture. Sorry milan this is an old bug :)

Does the bug occur on dbpedia only or is the endpoint LDF explore generally broken?

[m1ci]

The problem happens on FREME live which still runs the old architecture. Sorry milan this is an old bug :)

not really, see bellow :)

Does the bug occur on dbpedia only or is the endpoint LDF explore generally broken?

Very valid question, just checked and this particular LDF endpoint is broken. The LDF explore API is OK. For example, the ORCID endpoint (http://rv2622.1blu.de:5000/orcid) is working. Here is example:

curl -X POST --header "Content-Type: application/json" --header "Accept: text/turtle" "http://api.freme-project.eu/0.5/e-link/explore?resource=http%3A%2F%2Forcid.org%2F0000-0001-5000-0736&endpoint=http%3A%2F%2Frv2622.1blu.de%3A5000%2Forcid&endpoint-type=ldf" -v

[jnehring]

When it happens only at DBPedia then I guess the problem lies within DBPedia LDF endpoint and not within our codes. So we can do nothing about it. I leave the issue open so we can test it again in a few weeks. Maybe it solves itself by the next update in DBPedia.

[jnehring]

Maybe this will be fixed by updating Jena: https://github.com/freme-project/e-Link/issues/69

[ArneBinder]

I can not reproduce this anymore, is it fixed? Can we close this?

[jnehring]

The error still occurs. Now the CURL (see first comment) produces

{
  "exception": "eu.freme.common.exception.BadRequestException",
  "path": "/e-link/explore",
  "message": "Something went wrong when retrieving the content. Please contact the maintainers.",
  "error": "Bad Request",
  "status": 400,
  "timestamp": 1468505897979
}

I still think that the problem originates from within DBPedia.

[ArneBinder]

It is really strange that I get a result if endpointType is set to sparql (but using the ldf endpoint!):

curl -X POST "http://api-dev.freme-project.eu/current/e-link/explore?resource=http://dbpedia.org/resource/Berlin&endpoint=http://fragments.dbpedia.org/2014/en&endpoint-type=sparql"

Btw using endpointType=ldf gives this:

INFO    2016-07-18 11:25:08,093 [http-nio-8084-exec-2] eu.freme.bservices.filters.logging.LoggingFilter  - Request: request id=53; uri=/e-link/explore?resource=http://dbpedia.org/resource/Berlin&endpoint=http://fragments.dbpedia.org/2014/en&endpoint-type=ldf; payload=
WARN    2016-07-18 11:25:08,499 [http-nio-8084-exec-2] org.apache.jena.riot  - Only triples or default graph data expected : named graph data ignored
ERROR   2016-07-18 11:25:08,544 [http-nio-8084-exec-2] eu.freme.eservices.elink.api.DataEnricher  - java.lang.NullPointerException

especially: Only triples or default graph data expected : named graph data ignored Perhaps this can help in resolving this.

[jnehring]

@ArneBinder please do not invest more time on this. We think that this problem is dbpedia specific and the feature is not used by anyone anyways.