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TIBHannover / ols4

The upcoming next version of the Ontology Lookup Service (OLS)
http://www.ebi.ac.uk/ols4/
Apache License 2.0
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Bugfix for null cases in some api endpoints #9

Open giraygi opened 2 months ago

giraygi commented 2 months ago

Describe the bug Some api endpoints do not handle null cases. Particularly solr searches and v1 ontologies list.

To Reproduce ./api/ontologies?page=0&size=1000 ./api/ontologies/getstatisticsbyschema

Expected behavior No exception error. And proper listing of ontologies in the respective endpoint.

Screenshots

Click to expand for ./api/ontologies?page=0&size=1000 13:04:12.907 [http-nio-8080-exec-5] ERROR o.a.c.c.C.[.[.[.[dispatcherServlet] - Servlet.service() for servlet [dispatcherServlet] in context with path [] threw exception [Request processing failed; nested exception is java.lang.UnsupportedOperationException: JsonNull] with root cause java.lang.UnsupportedOperationException: JsonNull at com.google.gson.JsonElement.getAsString(JsonElement.java:179) at uk.ac.ebi.spot.ols.repository.v1.JsonHelper.objectToString(JsonHelper.java:45) at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195) at java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1625) at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484) at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474) at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:913) at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:578) at uk.ac.ebi.spot.ols.repository.v1.JsonHelper.getStrings(JsonHelper.java:74) at uk.ac.ebi.spot.ols.repository.v1.mappers.V1OntologyMapper.mapOntology(V1OntologyMapper.java:46) at uk.ac.ebi.spot.ols.repository.v1.V1OntologyRepository.getAll(V1OntologyRepository.java:48) at uk.ac.ebi.spot.ols.repository.v1.V1OntologyRepository.getSchemaValues(V1OntologyRepository.java:311) at uk.ac.ebi.spot.ols.controller.api.v1.V1OntologyController.filterValues(V1OntologyController.java:137) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:564) at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:205) at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:150) at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:117) at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:895) at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:808) at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1071) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:964) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1006) at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:898) at javax.servlet.http.HttpServlet.service(HttpServlet.java:670) at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:883) at javax.servlet.http.HttpServlet.service(HttpServlet.java:779) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:227) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at uk.ac.ebi.spot.ols.config.CrossOriginResourceSharingFilter.doFilter(CrossOriginResourceSharingFilter.java:50) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:399) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at org.springframework.web.filter.RequestContextFilter.doFilterInternal(RequestContextFilter.java:100) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at org.springframework.web.filter.FormContentFilter.doFilterInternal(FormContentFilter.java:93) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:201) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:197) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:97) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:541) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:135) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:78) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:360) at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:399) at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:65) at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:893) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1789) at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49) at org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1191) at org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.base/java.lang.Thread.run(Thread.java:832)
Click to expand for solr error 13:16:14.545 [http-nio-8080-exec-2] DEBUG u.a.e.s.o.r.solr.OlsSolrClient - solr query had 0 result(s). 13:16:14.546 [http-nio-8080-exec-2] DEBUG u.a.e.s.o.r.solr.OlsSolrClient - Expected at least 1 result for solr getFirst for solr query = { "defType":"edismax", "fl":"_json", "q":"*:*", "fq":[ "str_type:(\"ontology\")", "str_ontologyId:(\"getstatisticsbyschema\")"]} 13:16:14.547 [http-nio-8080-exec-2] ERROR o.a.c.c.C.[.[.[.[dispatcherServlet] - Servlet.service() for servlet [dispatcherServlet] in context with path [] threw exception [Request processing failed; nested exception is java.lang.RuntimeException: Expected at least 1 result for solr getFirst] with root cause java.lang.RuntimeException: Expected at least 1 result for solr getFirst at uk.ac.ebi.spot.ols.repository.solr.OlsSolrClient.getFirst(OlsSolrClient.java:102) at uk.ac.ebi.spot.ols.repository.v1.V1OntologyRepository.get(V1OntologyRepository.java:37) at uk.ac.ebi.spot.ols.controller.api.v1.V1OntologyController.getOntology(V1OntologyController.java:82) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:564) at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:205) at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:150) at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:117) at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:895) at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:808) at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1071) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:964) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1006) at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:898) at javax.servlet.http.HttpServlet.service(HttpServlet.java:670) at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:883) at javax.servlet.http.HttpServlet.service(HttpServlet.java:779) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:227) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at uk.ac.ebi.spot.ols.config.CrossOriginResourceSharingFilter.doFilter(CrossOriginResourceSharingFilter.java:50) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:399) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at org.springframework.web.filter.RequestContextFilter.doFilterInternal(RequestContextFilter.java:100) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at org.springframework.web.filter.FormContentFilter.doFilterInternal(FormContentFilter.java:93) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:201) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:197) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:97) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:541) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:135) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:78) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:360) at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:399) at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:65) at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:893) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1789) at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49) at org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1191) at org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.base/java.lang.Thread.run(Thread.java:832)