[e-link][explore][ldf] broken on freme 0.4 and later? #10

ArneBinder · 2016-04-11T16:23:23Z

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"

The text was updated successfully, but these errors were encountered:

ArneBinder · 2016-04-11T16:41:12Z

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

jnehring · 2016-04-12T13:57:10Z

**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 · 2016-04-12T14:04:49Z

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

m1ci · 2016-04-19T13:25:35Z

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 · 2016-04-19T14:12:08Z

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 · 2016-04-19T14:23:08Z

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 · 2016-04-20T07:51:06Z

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 · 2016-05-24T09:47:16Z

Maybe this will be fixed by updating Jena: freme-project/e-Link#69

ArneBinder · 2016-06-27T10:09:05Z

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

jnehring · 2016-07-14T14:20:19Z

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 · 2016-07-18T09:32:34Z

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 · 2016-07-18T10:47:30Z

@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.

ArneBinder added the bug label Apr 11, 2016

ArneBinder mentioned this issue Apr 11, 2016

Monitoring emails freme-project/Broker#160

Closed

ArneBinder changed the title ~~[e-link][explore][ldf] broken on freme 0.4 and following?~~ [e-link][explore][ldf] broken on freme 0.4 and later? Apr 11, 2016

jnehring assigned m1ci Apr 12, 2016

jnehring unassigned m1ci Apr 20, 2016

ArneBinder assigned jnehring Jun 30, 2016

jnehring removed their assignment Jul 14, 2016

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[e-link][explore][ldf] broken on freme 0.4 and later? #10

[e-link][explore][ldf] broken on freme 0.4 and later? #10

ArneBinder commented Apr 11, 2016

ArneBinder commented Apr 11, 2016

jnehring commented Apr 12, 2016

m1ci commented Apr 12, 2016

m1ci commented Apr 19, 2016

jnehring commented Apr 19, 2016

m1ci commented Apr 19, 2016

jnehring commented Apr 20, 2016

jnehring commented May 24, 2016

ArneBinder commented Jun 27, 2016 •

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jnehring commented Jul 14, 2016

ArneBinder commented Jul 18, 2016

jnehring commented Jul 18, 2016

[e-link][explore][ldf] broken on freme 0.4 and later? #10

[e-link][explore][ldf] broken on freme 0.4 and later? #10

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ArneBinder commented Apr 11, 2016

ArneBinder commented Apr 11, 2016

jnehring commented Apr 12, 2016

m1ci commented Apr 12, 2016

m1ci commented Apr 19, 2016

jnehring commented Apr 19, 2016

m1ci commented Apr 19, 2016

jnehring commented Apr 20, 2016

jnehring commented May 24, 2016

ArneBinder commented Jun 27, 2016 • edited Loading

jnehring commented Jul 14, 2016

ArneBinder commented Jul 18, 2016

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ArneBinder commented Jun 27, 2016 •

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