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SCAI-BIO / sam

Terminology management service
https://sam.academia.scaiview.com
MIT License
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NPO when requesting custom terminology with ebi ols enabled #2

Open tiadams opened 9 months ago

tiadams commented 9 months ago

Reproduce: http://localhost:8053/api/v1/terminologies/gecco_plus/concepts/autocomplete?lang=en&page=0&q=a&size=10

With https://www.ebi.ac.uk/ols/api/ as additional ols endpoint, the request will crash with a NPE

{
  "timestamp": 1701697120960,
  "status": 500,
  "error": "Internal Server Error",
  "message": "No message available",
  "trace": "java.lang.NullPointerException\n\tat de.fraunhofer.scai.bio.sam.service.impl.ols.json.JSONSOLRConceptSearch.deserialize(JSONSOLRConceptSearch.java:55)\n\tat de.fraunhofer.scai.bio.sam.service.impl.ols.json.JSONSOLRConceptSearch.deserialize(JSONSOLRConceptSearch.java:16)\n\tat com.google.gson.internal.bind.TreeTypeAdapter.read(TreeTypeAdapter.java:69)\n\tat retrofit2.converter.gson.GsonResponseBodyConverter.convert(GsonResponseBodyConverter.java:39)\n\tat retrofit2.converter.gson.GsonResponseBodyConverter.convert(GsonResponseBodyConverter.java:27)\n\tat retrofit2.ServiceMethod.toResponse(ServiceMethod.java:122)\n\tat retrofit2.OkHttpCall.parseResponse(OkHttpCall.java:217)\n\tat retrofit2.OkHttpCall.execute(OkHttpCall.java:180)\n\tat de.fraunhofer.scai.bio.sam.service.impl.ols.OLSConceptServiceImpl.suggestConceptInTerminology(OLSConceptServiceImpl.java:557)\n\tat de.fraunhofer.scai.bio.sam.service.impl.delegator.ConceptServiceDelegator.lambda$suggestConceptInTerminology$18(ConceptServiceDelegator.java:316)\n\tat java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195)\n\tat java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:177)\n\tat java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1625)\n\tat java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)\n\tat java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)\n\tat java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:913)\n\tat java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)\n\tat java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:578)\n\tat de.fraunhofer.scai.bio.sam.service.impl.delegator.ConceptServiceDelegator.suggestConceptInTerminology(ConceptServiceDelegator.java:317)\n\tat de.fraunhofer.scai.bio.sam.controller.api.terminologies.ConceptSearchAndSuggestAPI.terminologyAutocompletion(ConceptSearchAndSuggestAPI.java:150)\n\tat java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\n\tat java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:564)\n\tat org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:190)\n\tat org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:138)\n\tat org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:105)\n\tat org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:879)\n\tat org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:793)\n\tat org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87)\n\tat org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1040)\n\tat org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:943)\n\tat org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1006)\n\tat org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:898)\n\tat javax.servlet.http.HttpServlet.service(HttpServlet.java:634)\n\tat org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:883)\n\tat javax.servlet.http.HttpServlet.service(HttpServlet.java:741)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)\n\tat org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)\n\tat org.springframework.boot.actuate.metrics.web.servlet.WebMvcMetricsFilter.doFilterInternal(WebMvcMetricsFilter.java:109)\n\tat org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)\n\tat org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:201)\n\tat org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)\n\tat org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:202)\n\tat org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)\n\tat org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:541)\n\tat org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:139)\n\tat org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92)\n\tat org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:74)\n\tat org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:343)\n\tat org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:373)\n\tat org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:65)\n\tat org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:868)\n\tat org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1594)\n\tat org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1130)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:630)\n\tat org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)\n\tat java.base/java.lang.Thread.run(Thread.java:832)\n",
  "path": "/api/v1/terminologies/gecco_plus/concepts/autocomplete"
}
tiadams commented 9 months ago

@JuergenKleinAtSCAI @MarcZimmermann passiert seit dem EBI OLS API update, ich vermute die Objektstruktur hat sich seitdem verändert und kann deshalb bei uns nicht mehr serialisiert werden, sollten wir uns bald mal anschauen. Sollte auch bei allen alten Instanzen die in irgendeiner Form EBI nutzen der Fall sein.

tiadams commented 9 months ago

TODO: Test with http://localhost:8053/api/v1/terminologies/snomed/concepts/autocomplete?lang=en&page=0&q=a&size=10