core issueshttps://git-r3lab.uni.lu/minerva/core/-/issues2024-03-14T09:48:20+01:00https://git-r3lab.uni.lu/minerva/core/-/issues/2012when caching data on project upload2024-03-14T09:48:20+01:00Piotr Gawronwhen caching data on project uploadlinks from annotation were not providedlinks from annotation were not providedv17.0.0~beta.6https://git-r3lab.uni.lu/minerva/core/-/issues/2009postgres restart breaks minerva service2024-02-29T12:39:37+01:00Piotr Gawronpostgres restart breaks minerva service17.0.0-beta.5https://git-r3lab.uni.lu/minerva/core/-/issues/2005orcid validation should not happen when orcidId is empty2024-03-05T12:55:17+01:00Piotr Gawronorcid validation should not happen when orcidId is empty17.0.0-beta.5https://git-r3lab.uni.lu/minerva/core/-/issues/1999after restart of application2024-03-05T12:57:27+01:00Piotr Gawronafter restart of applicationprobably issue with sessions (users are logged out)
```
2024-02-15 16:14:40,953 ERROR [http-nio-8080-exec-7] (BaseController.java:110) - org.apache.catalina.connector.ClientAbortException: java.io.IOException: Broken pipe
org.apache.cata...probably issue with sessions (users are logged out)
```
2024-02-15 16:14:40,953 ERROR [http-nio-8080-exec-7] (BaseController.java:110) - org.apache.catalina.connector.ClientAbortException: java.io.IOException: Broken pipe
org.apache.catalina.connector.ClientAbortException: java.io.IOException: Broken pipe
at org.apache.catalina.connector.OutputBuffer.realWriteBytes(OutputBuffer.java:348) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.connector.OutputBuffer.flushByteBuffer(OutputBuffer.java:777) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.connector.OutputBuffer.append(OutputBuffer.java:680) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.connector.OutputBuffer.writeBytes(OutputBuffer.java:383) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.connector.OutputBuffer.write(OutputBuffer.java:361) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.connector.CoyoteOutputStream.write(CoyoteOutputStream.java:97) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.springframework.security.web.util.OnCommittedResponseWrapper$SaveContextServletOutputStream.write(OnCommittedResponseWrapper.java:638) ~[spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.util.OnCommittedResponseWrapper$SaveContextServletOutputStream.write(OnCommittedResponseWrapper.java:638) ~[spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.util.StreamUtils$NonClosingOutputStream.write(StreamUtils.java:287) ~[spring-core-5.3.31.jar!/:5.3.31]
at com.fasterxml.jackson.core.json.UTF8JsonGenerator._flushBuffer(UTF8JsonGenerator.java:2171) ~[jackson-core-2.13.5.jar!/:2.13.5]
at com.fasterxml.jackson.core.json.UTF8JsonGenerator.flush(UTF8JsonGenerator.java:1184) ~[jackson-core-2.13.5.jar!/:2.13.5]
at com.fasterxml.jackson.databind.ObjectMapper.writeValue(ObjectMapper.java:3162) ~[jackson-databind-2.13.5.jar!/:2.13.5]
at com.fasterxml.jackson.core.base.GeneratorBase.writeObject(GeneratorBase.java:389) ~[jackson-core-2.13.5.jar!/:2.13.5]
at com.fasterxml.jackson.core.JsonGenerator.writeObjectField(JsonGenerator.java:2385) ~[jackson-core-2.13.5.jar!/:2.13.5]
at lcsb.mapviewer.api.configuration.MiriamTypeSerializer.serialize(MiriamTypeSerializer.java:22) ~[rest-api-17.0.0~beta.3.jar!/:?]
at lcsb.mapviewer.api.configuration.MiriamTypeSerializer.serialize(MiriamTypeSerializer.java:11) ~[rest-api-17.0.0~beta.3.jar!/:?]
at com.fasterxml.jackson.databind.ser.std.MapSerializer.serializeFieldsUsing(MapSerializer.java:905) ~[jackson-databind-2.13.5.jar!/:2.13.5]
at com.fasterxml.jackson.databind.ser.std.MapSerializer.serializeWithoutTypeInfo(MapSerializer.java:762) ~[jackson-databind-2.13.5.jar!/:2.13.5]
at com.fasterxml.jackson.databind.ser.std.MapSerializer.serialize(MapSerializer.java:720) ~[jackson-databind-2.13.5.jar!/:2.13.5]
at com.fasterxml.jackson.databind.ser.std.MapSerializer.serialize(MapSerializer.java:35) ~[jackson-databind-2.13.5.jar!/:2.13.5]
at com.fasterxml.jackson.databind.ser.BeanPropertyWriter.serializeAsField(BeanPropertyWriter.java:728) ~[jackson-databind-2.13.5.jar!/:2.13.5]
at com.fasterxml.jackson.databind.ser.std.BeanSerializerBase.serializeFields(BeanSerializerBase.java:774) ~[jackson-databind-2.13.5.jar!/:2.13.5]
at com.fasterxml.jackson.databind.ser.BeanSerializer.serialize(BeanSerializer.java:178) ~[jackson-databind-2.13.5.jar!/:2.13.5]
at com.fasterxml.jackson.databind.ser.DefaultSerializerProvider._serialize(DefaultSerializerProvider.java:480) ~[jackson-databind-2.13.5.jar!/:2.13.5]
at com.fasterxml.jackson.databind.ser.DefaultSerializerProvider.serializeValue(DefaultSerializerProvider.java:319) ~[jackson-databind-2.13.5.jar!/:2.13.5]
at com.fasterxml.jackson.databind.ObjectWriter$Prefetch.serialize(ObjectWriter.java:1518) ~[jackson-databind-2.13.5.jar!/:2.13.5]
at com.fasterxml.jackson.databind.ObjectWriter.writeValue(ObjectWriter.java:1007) ~[jackson-databind-2.13.5.jar!/:2.13.5]
at org.springframework.http.converter.json.AbstractJackson2HttpMessageConverter.writeInternal(AbstractJackson2HttpMessageConverter.java:456) ~[spring-web-5.3.31.jar!/:5.3.31]
at org.springframework.http.converter.AbstractGenericHttpMessageConverter.write(AbstractGenericHttpMessageConverter.java:104) ~[spring-web-5.3.31.jar!/:5.3.31]
at org.springframework.web.servlet.mvc.method.annotation.AbstractMessageConverterMethodProcessor.writeWithMessageConverters(AbstractMessageConverterMethodProcessor.java:290) ~[spring-webmvc-5.3.31.jar!/:5.3.31]
at org.springframework.web.servlet.mvc.method.annotation.RequestResponseBodyMethodProcessor.handleReturnValue(RequestResponseBodyMethodProcessor.java:183) ~[spring-webmvc-5.3.31.jar!/:5.3.31]
at org.springframework.web.method.support.HandlerMethodReturnValueHandlerComposite.handleReturnValue(HandlerMethodReturnValueHandlerComposite.java:78) ~[spring-web-5.3.31.jar!/:5.3.31]
at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:135) ~[spring-webmvc-5.3.31.jar!/:5.3.31]
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:895) ~[spring-webmvc-5.3.31.jar!/:5.3.31]
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:808) ~[spring-webmvc-5.3.31.jar!/:5.3.31]
at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87) ~[spring-webmvc-5.3.31.jar!/:5.3.31]
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1072) [spring-webmvc-5.3.31.jar!/:5.3.31]
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:965) [spring-webmvc-5.3.31.jar!/:5.3.31]
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1006) [spring-webmvc-5.3.31.jar!/:5.3.31]
at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:898) [spring-webmvc-5.3.31.jar!/:5.3.31]
at javax.servlet.http.HttpServlet.service(HttpServlet.java:529) [tomcat-embed-core-9.0.83.jar!/:?]
at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:883) [spring-webmvc-5.3.31.jar!/:5.3.31]
at javax.servlet.http.HttpServlet.service(HttpServlet.java:623) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:209) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51) [tomcat-embed-websocket-9.0.83.jar!/:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:178) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153) [tomcat-embed-core-9.0.83.jar!/:?]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:352) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.access.intercept.AuthorizationFilter.doFilter(AuthorizationFilter.java:100) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:126) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:120) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:131) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:85) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:100) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:164) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:63) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at lcsb.mapviewer.web.bean.utils.CORSFilter.doFilter(CORSFilter.java:48) [classes!/:?]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at lcsb.mapviewer.web.bean.utils.CacheFilter.doFilter(CacheFilter.java:56) [classes!/:?]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at lcsb.mapviewer.web.bean.utils.XFrameFilter.doFilter(XFrameFilter.java:42) [classes!/:?]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.session.ConcurrentSessionFilter.doFilter(ConcurrentSessionFilter.java:151) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.session.ConcurrentSessionFilter.doFilter(ConcurrentSessionFilter.java:129) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:227) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:221) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:227) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:221) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.oauth2.client.web.OAuth2AuthorizationRequestRedirectFilter.doFilterInternal(OAuth2AuthorizationRequestRedirectFilter.java:187) [spring-security-oauth2-client-5.8.9.jar!/:5.8.9]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117) [spring-web-5.3.31.jar!/:5.3.31]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:107) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:93) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.header.HeaderWriterFilter.doHeadersAfter(HeaderWriterFilter.java:90) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:75) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117) [spring-web-5.3.31.jar!/:5.3.31]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:117) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:62) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117) [spring-web-5.3.31.jar!/:5.3.31]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.session.DisableEncodeUrlFilter.doFilterInternal(DisableEncodeUrlFilter.java:42) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117) [spring-web-5.3.31.jar!/:5.3.31]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:225) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:190) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:354) [spring-web-5.3.31.jar!/:5.3.31]
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:267) [spring-web-5.3.31.jar!/:5.3.31]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:178) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153) [tomcat-embed-core-9.0.83.jar!/:?]
at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:201) [spring-web-5.3.31.jar!/:5.3.31]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117) [spring-web-5.3.31.jar!/:5.3.31]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:178) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:168) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:90) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:481) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:130) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:93) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:74) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:390) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:63) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:928) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1794) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:52) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1191) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat-embed-core-9.0.83.jar!/:?]
at java.base/java.lang.Thread.run(Thread.java:840) [?:?]
Suppressed: org.apache.catalina.connector.ClientAbortException: java.io.IOException: Broken pipe
at org.apache.catalina.connector.OutputBuffer.realWriteBytes(OutputBuffer.java:348) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.connector.OutputBuffer.flushByteBuffer(OutputBuffer.java:777) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.connector.OutputBuffer.append(OutputBuffer.java:680) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.connector.OutputBuffer.writeBytes(OutputBuffer.java:383) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.connector.OutputBuffer.write(OutputBuffer.java:361) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.connector.CoyoteOutputStream.write(CoyoteOutputStream.java:97) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.springframework.security.web.util.OnCommittedResponseWrapper$SaveContextServletOutputStream.write(OnCommittedResponseWrapper.java:638) ~[spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.util.OnCommittedResponseWrapper$SaveContextServletOutputStream.write(OnCommittedResponseWrapper.java:638) ~[spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.util.StreamUtils$NonClosingOutputStream.write(StreamUtils.java:287) ~[spring-core-5.3.31.jar!/:5.3.31]
at com.fasterxml.jackson.core.json.UTF8JsonGenerator._flushBuffer(UTF8JsonGenerator.java:2171) ~[jackson-core-2.13.5.jar!/:2.13.5]
at com.fasterxml.jackson.core.json.UTF8JsonGenerator.close(UTF8JsonGenerator.java:1214) ~[jackson-core-2.13.5.jar!/:2.13.5]
at org.springframework.http.converter.json.AbstractJackson2HttpMessageConverter.writeInternal(AbstractJackson2HttpMessageConverter.java:460) ~[spring-web-5.3.31.jar!/:5.3.31]
at org.springframework.http.converter.AbstractGenericHttpMessageConverter.write(AbstractGenericHttpMessageConverter.java:104) ~[spring-web-5.3.31.jar!/:5.3.31]
at org.springframework.web.servlet.mvc.method.annotation.AbstractMessageConverterMethodProcessor.writeWithMessageConverters(AbstractMessageConverterMethodProcessor.java:290) ~[spring-webmvc-5.3.31.jar!/:5.3.31]
at org.springframework.web.servlet.mvc.method.annotation.RequestResponseBodyMethodProcessor.handleReturnValue(RequestResponseBodyMethodProcessor.java:183) ~[spring-webmvc-5.3.31.jar!/:5.3.31]
at org.springframework.web.method.support.HandlerMethodReturnValueHandlerComposite.handleReturnValue(HandlerMethodReturnValueHandlerComposite.java:78) ~[spring-web-5.3.31.jar!/:5.3.31]
at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:135) ~[spring-webmvc-5.3.31.jar!/:5.3.31]
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:895) ~[spring-webmvc-5.3.31.jar!/:5.3.31]
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:808) ~[spring-webmvc-5.3.31.jar!/:5.3.31]
at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87) ~[spring-webmvc-5.3.31.jar!/:5.3.31]
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1072) [spring-webmvc-5.3.31.jar!/:5.3.31]
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:965) [spring-webmvc-5.3.31.jar!/:5.3.31]
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1006) [spring-webmvc-5.3.31.jar!/:5.3.31]
at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:898) [spring-webmvc-5.3.31.jar!/:5.3.31]
at javax.servlet.http.HttpServlet.service(HttpServlet.java:529) [tomcat-embed-core-9.0.83.jar!/:?]
at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:883) [spring-webmvc-5.3.31.jar!/:5.3.31]
at javax.servlet.http.HttpServlet.service(HttpServlet.java:623) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:209) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51) [tomcat-embed-websocket-9.0.83.jar!/:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:178) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153) [tomcat-embed-core-9.0.83.jar!/:?]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:352) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.access.intercept.AuthorizationFilter.doFilter(AuthorizationFilter.java:100) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:126) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:120) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:131) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:85) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:100) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:164) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:63) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at lcsb.mapviewer.web.bean.utils.CORSFilter.doFilter(CORSFilter.java:48) [classes!/:?]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at lcsb.mapviewer.web.bean.utils.CacheFilter.doFilter(CacheFilter.java:56) [classes!/:?]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at lcsb.mapviewer.web.bean.utils.XFrameFilter.doFilter(XFrameFilter.java:42) [classes!/:?]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.session.ConcurrentSessionFilter.doFilter(ConcurrentSessionFilter.java:151) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.session.ConcurrentSessionFilter.doFilter(ConcurrentSessionFilter.java:129) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:227) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:221) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:227) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:221) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.oauth2.client.web.OAuth2AuthorizationRequestRedirectFilter.doFilterInternal(OAuth2AuthorizationRequestRedirectFilter.java:187) [spring-security-oauth2-client-5.8.9.jar!/:5.8.9]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117) [spring-web-5.3.31.jar!/:5.3.31]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:107) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:93) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.header.HeaderWriterFilter.doHeadersAfter(HeaderWriterFilter.java:90) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:75) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117) [spring-web-5.3.31.jar!/:5.3.31]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:117) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:62) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117) [spring-web-5.3.31.jar!/:5.3.31]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.session.DisableEncodeUrlFilter.doFilterInternal(DisableEncodeUrlFilter.java:42) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117) [spring-web-5.3.31.jar!/:5.3.31]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:361) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:225) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:190) [spring-security-web-5.8.9.jar!/:5.8.9]
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:354) [spring-web-5.3.31.jar!/:5.3.31]
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:267) [spring-web-5.3.31.jar!/:5.3.31]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:178) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153) [tomcat-embed-core-9.0.83.jar!/:?]
at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:201) [spring-web-5.3.31.jar!/:5.3.31]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117) [spring-web-5.3.31.jar!/:5.3.31]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:178) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:168) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:90) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:481) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:130) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:93) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:74) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:390) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:63) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:928) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1794) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:52) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1191) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659) [tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat-embed-core-9.0.83.jar!/:?]
at java.base/java.lang.Thread.run(Thread.java:840) [?:?]
Caused by: java.io.IOException: Broken pipe
at java.base/sun.nio.ch.FileDispatcherImpl.write0(Native Method) ~[?:?]
at java.base/sun.nio.ch.SocketDispatcher.write(SocketDispatcher.java:62) ~[?:?]
at java.base/sun.nio.ch.IOUtil.writeFromNativeBuffer(IOUtil.java:132) ~[?:?]
at java.base/sun.nio.ch.IOUtil.write(IOUtil.java:97) ~[?:?]
at java.base/sun.nio.ch.IOUtil.write(IOUtil.java:53) ~[?:?]
at java.base/sun.nio.ch.SocketChannelImpl.write(SocketChannelImpl.java:532) ~[?:?]
at org.apache.tomcat.util.net.NioChannel.write(NioChannel.java:136) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.tomcat.util.net.NioEndpoint$NioSocketWrapper.doWrite(NioEndpoint.java:1431) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.tomcat.util.net.SocketWrapperBase.doWrite(SocketWrapperBase.java:775) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.tomcat.util.net.SocketWrapperBase.writeBlocking(SocketWrapperBase.java:600) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.tomcat.util.net.SocketWrapperBase.write(SocketWrapperBase.java:544) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.coyote.http11.Http11OutputBuffer$SocketOutputBuffer.doWrite(Http11OutputBuffer.java:540) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.coyote.http11.filters.ChunkedOutputFilter.doWrite(ChunkedOutputFilter.java:110) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.coyote.http11.Http11OutputBuffer.doWrite(Http11OutputBuffer.java:193) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.coyote.Response.doWrite(Response.java:606) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.connector.OutputBuffer.realWriteBytes(OutputBuffer.java:335) ~[tomcat-embed-core-9.0.83.jar!/:?]
... 106 more
Caused by: java.io.IOException: Broken pipe
at java.base/sun.nio.ch.FileDispatcherImpl.write0(Native Method) ~[?:?]
at java.base/sun.nio.ch.SocketDispatcher.write(SocketDispatcher.java:62) ~[?:?]
at java.base/sun.nio.ch.IOUtil.writeFromNativeBuffer(IOUtil.java:132) ~[?:?]
at java.base/sun.nio.ch.IOUtil.write(IOUtil.java:97) ~[?:?]
at java.base/sun.nio.ch.IOUtil.write(IOUtil.java:53) ~[?:?]
at java.base/sun.nio.ch.SocketChannelImpl.write(SocketChannelImpl.java:532) ~[?:?]
at org.apache.tomcat.util.net.NioChannel.write(NioChannel.java:136) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.tomcat.util.net.NioEndpoint$NioSocketWrapper.doWrite(NioEndpoint.java:1431) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.tomcat.util.net.SocketWrapperBase.doWrite(SocketWrapperBase.java:775) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.tomcat.util.net.SocketWrapperBase.writeBlocking(SocketWrapperBase.java:600) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.tomcat.util.net.SocketWrapperBase.write(SocketWrapperBase.java:544) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.coyote.http11.Http11OutputBuffer$SocketOutputBuffer.doWrite(Http11OutputBuffer.java:540) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.coyote.http11.filters.ChunkedOutputFilter.doWrite(ChunkedOutputFilter.java:112) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.coyote.http11.Http11OutputBuffer.doWrite(Http11OutputBuffer.java:193) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.coyote.Response.doWrite(Response.java:606) ~[tomcat-embed-core-9.0.83.jar!/:?]
at org.apache.catalina.connector.OutputBuffer.realWriteBytes(OutputBuffer.java:335) ~[tomcat-embed-core-9.0.83.jar!/:?]
... 122 more
```17.0.0-beta.5https://git-r3lab.uni.lu/minerva/core/-/issues/1992Large map project upload stuck at "uninitialised"2024-02-22T20:46:45+01:00Marek OstaszewskiLarge map project upload stuck at "uninitialised"When uploaded the COVID-19 Disease Map:
https://covid19map.elixir-luxembourg.org > Info > Source file
with caching option **on**, the project is stuck in the "uninitialised" phase.
Upload/delete/archiving of other maps in parallel h...When uploaded the COVID-19 Disease Map:
https://covid19map.elixir-luxembourg.org > Info > Source file
with caching option **on**, the project is stuck in the "uninitialised" phase.
Upload/delete/archiving of other maps in parallel happened without problems.17.0.0-beta.4https://git-r3lab.uni.lu/minerva/core/-/issues/1990Incomplete logout2024-02-13T17:38:06+01:00Marek OstaszewskiIncomplete logoutAfter logging in and out, the "Add user overlay" is still available.
When trying to add an overlay, MINERVA throws a 403.After logging in and out, the "Add user overlay" is still available.
When trying to add an overlay, MINERVA throws a 403.17.0.0-beta.3https://git-r3lab.uni.lu/minerva/core/-/issues/1989refresh jobs are failing2024-02-13T13:04:30+01:00Piotr Gawronrefresh jobs are failing```
2024-02-13 11:10:24,942 ERROR [Thread-7] (MinervaJobService.java:199) - Problem with executing job: REFRESH_CACHE (job id: 179710)
lcsb.mapviewer.common.exception.InvalidArgumentException: Cache passed as argument cannot be null
...```
2024-02-13 11:10:24,942 ERROR [Thread-7] (MinervaJobService.java:199) - Problem with executing job: REFRESH_CACHE (job id: 179710)
lcsb.mapviewer.common.exception.InvalidArgumentException: Cache passed as argument cannot be null
at lcsb.mapviewer.annotation.cache.GeneralCacheWithExclusion.<init>(GeneralCacheWithExclusion.java:48) ~[annotation-17.0.0~beta.2.jar!/:?]
at lcsb.mapviewer.annotation.cache.GeneralCache.execute(GeneralCache.java:499) ~[annotation-17.0.0~beta.2.jar!/:?]
at lcsb.mapviewer.annotation.cache.GeneralCache$$FastClassBySpringCGLIB$$a671643d.invoke(<generated>) ~[annotation-17.0.0~beta.2.jar!/:?]
at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218) ~[spring-core-5.3.31.jar!/:5.3.31]
at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:792) ~[spring-aop-5.3.31.jar!/:5.3.31]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.3.31.jar!/:5.3.31]
at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:762) ~[spring-aop-5.3.31.jar!/:5.3.31]
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:123) ~[spring-tx-5.3.31.jar!/:5.3.31]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:388) ~[spring-tx-5.3.31.jar!/:5.3.31]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:119) ~[spring-tx-5.3.31.jar!/:5.3.31]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.3.31.jar!/:5.3.31]
at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:762) ~[spring-aop-5.3.31.jar!/:5.3.31]
at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:707) ~[spring-aop-5.3.31.jar!/:5.3.31]
at lcsb.mapviewer.annotation.cache.GeneralCache$$EnhancerBySpringCGLIB$$1ad5fa24.execute(<generated>) ~[annotation-17.0.0~beta.2.jar!/:?]
at lcsb.mapviewer.services.impl.MinervaJobService$2.call(MinervaJobService.java:141) [service-17.0.0~beta.2.jar!/:?]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [?:1.8.0_392]
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180) [?:1.8.0_392]
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293) [?:1.8.0_392]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [?:1.8.0_392]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [?:1.8.0_392]
at java.lang.Thread.run(Thread.java:750) [?:1.8.0_392]
```17.0.0-beta.3https://git-r3lab.uni.lu/minerva/core/-/issues/1987don't try to get all expired cache entries at once2024-02-13T14:18:28+01:00Piotr Gawrondon't try to get all expired cache entries at once17.0.0~beta.2https://git-r3lab.uni.lu/minerva/core/-/issues/1986start of minerva service should not be blocked by the jobs in queue2024-02-15T15:16:27+01:00Piotr Gawronstart of minerva service should not be blocked by the jobs in queue17.0.0-beta.3https://git-r3lab.uni.lu/minerva/core/-/issues/1985minerva upgrade from 16.4 issue2024-02-13T13:31:27+01:00Piotr Gawronminerva upgrade from 16.4 issue```
dbconfig-common: flushing administrative password
mv: cannot stat '/var/lib/tomcat9/webapps/map_images/*': No such file or directory
dpkg: error processing package minerva (--configure):
installed minerva package post-installation s...```
dbconfig-common: flushing administrative password
mv: cannot stat '/var/lib/tomcat9/webapps/map_images/*': No such file or directory
dpkg: error processing package minerva (--configure):
installed minerva package post-installation script subprocess returned error exit status 1
Errors were encountered while processing:
minerva
needrestart is being skipped since dpkg has failed
E: Sub-process /usr/bin/dpkg returned an error code (1)
```17.0.0-beta.3https://git-r3lab.uni.lu/minerva/core/-/issues/1984cookie name should be MINERVA_xxx2024-02-15T17:56:22+01:00Piotr Gawroncookie name should be MINERVA_xxxcurrently it's default JSESSIONIDcurrently it's default JSESSIONID17.0.0-beta.3https://git-r3lab.uni.lu/minerva/core/-/issues/1983uploading project produces a lot of errors like: Problem with chcecking prope...2024-02-13T14:39:22+01:00Piotr Gawronuploading project produces a lot of errors like: Problem with chcecking property: private final byte java.lang.String.coderjava 17:
```
2024-02-09 12:12:36,559 ERROR [Thread-7] (ObjectValidator.java:257) - Problem with chcecking property: private boolean java.lang.String.hashIsZero
java.lang.reflect.InaccessibleObjectException: Unable to make field private ...java 17:
```
2024-02-09 12:12:36,559 ERROR [Thread-7] (ObjectValidator.java:257) - Problem with chcecking property: private boolean java.lang.String.hashIsZero
java.lang.reflect.InaccessibleObjectException: Unable to make field private boolean java.lang.String.hashIsZero accessible: module java.base does not "opens java.lang" to unnamed module @1c53fd30
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354) ~[?:?]
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297) ~[?:?]
at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:178) ~[?:?]
at java.base/java.lang.reflect.Field.setAccessible(Field.java:172) ~[?:?]
at lcsb.mapviewer.persist.ObjectValidator$3.doWith(ObjectValidator.java:212) [persist-17.1.0.jar!/:?]
at org.springframework.util.ReflectionUtils.doWithFields(ReflectionUtils.java:706) [spring-core-5.3.31.jar!/:5.3.31]
at org.springframework.util.ReflectionUtils.doWithFields(ReflectionUtils.java:685) [spring-core-5.3.31.jar!/:5.3.31]
at lcsb.mapviewer.persist.ObjectValidator.processValidationIssues(ObjectValidator.java:204) [persist-17.1.0.jar!/:?]
at lcsb.mapviewer.persist.ObjectValidator.fixValidationIssues(ObjectValidator.java:122) [persist-17.1.0.jar!/:?]
at lcsb.mapviewer.services.impl.ProjectService.fixProjectIssues(ProjectService.java:1154) [service-17.1.0.jar!/:?]
at lcsb.mapviewer.services.impl.ProjectService.updateProjectStatus(ProjectService.java:900) [service-17.1.0.jar!/:?]
at lcsb.mapviewer.services.impl.ProjectService.createModel(ProjectService.java:780) [service-17.1.0.jar!/:?]
at lcsb.mapviewer.services.impl.ProjectService$$FastClassBySpringCGLIB$$633ab1e2.invoke(<generated>) [service-17.1.0.jar!/:?]
at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218) [spring-core-5.3.31.jar!/:5.3.31]
at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:792) [spring-aop-5.3.31.jar!/:5.3.31]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) [spring-aop-5.3.31.jar!/:5.3.31]
at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:762) [spring-aop-5.3.31.jar!/:5.3.31]
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:123) [spring-tx-5.3.31.jar!/:5.3.31]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:388) [spring-tx-5.3.31.jar!/:5.3.31]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:119) [spring-tx-5.3.31.jar!/:5.3.31]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) [spring-aop-5.3.31.jar!/:5.3.31]
at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:762) [spring-aop-5.3.31.jar!/:5.3.31]
at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:707) [spring-aop-5.3.31.jar!/:5.3.31]
at lcsb.mapviewer.services.impl.ProjectService$$EnhancerBySpringCGLIB$$dc07d1c1.createModel(<generated>) [service-17.1.0.jar!/:?]
at lcsb.mapviewer.services.impl.ProjectService.createProject(ProjectService.java:425) [service-17.1.0.jar!/:?]
at lcsb.mapviewer.services.impl.ProjectService.execute(ProjectService.java:1261) [service-17.1.0.jar!/:?]
at lcsb.mapviewer.services.impl.ProjectService$$FastClassBySpringCGLIB$$633ab1e2.invoke(<generated>) [service-17.1.0.jar!/:?]
at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218) [spring-core-5.3.31.jar!/:5.3.31]
at org.springframework.aop.framework.CglibAopProxy.invokeMethod(CglibAopProxy.java:386) [spring-aop-5.3.31.jar!/:5.3.31]
at org.springframework.aop.framework.CglibAopProxy.access$000(CglibAopProxy.java:85) [spring-aop-5.3.31.jar!/:5.3.31]
at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:703) [spring-aop-5.3.31.jar!/:5.3.31]
at lcsb.mapviewer.services.impl.ProjectService$$EnhancerBySpringCGLIB$$dc07d1c1.execute(<generated>) [service-17.1.0.jar!/:?]
at lcsb.mapviewer.services.impl.MinervaJobService$2.call(MinervaJobService.java:141) [service-17.1.0.jar!/:?]
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) [?:?]
at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:304) [?:?]
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136) [?:?]
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) [?:?]
```17.0.0-beta.3https://git-r3lab.uni.lu/minerva/core/-/issues/1979UCSC connection stopped working2024-02-13T17:30:45+01:00Piotr GawronUCSC connection stopped working17.0.0~beta.1https://git-r3lab.uni.lu/minerva/core/-/issues/1976Project fails to initialise2024-02-13T14:11:57+01:00Marek OstaszewskiProject fails to initialiseAttached CellDesigner file, testing some new bugfixes, fails to initialise.
[resid_border_test.xml](/uploads/75c0e076a8ceca0bcb6d2fd0e2521b5b/resid_border_test.xml)Attached CellDesigner file, testing some new bugfixes, fails to initialise.
[resid_border_test.xml](/uploads/75c0e076a8ceca0bcb6d2fd0e2521b5b/resid_border_test.xml)17.0.0~beta.1https://git-r3lab.uni.lu/minerva/core/-/issues/1975Link to API docs is broken2024-02-15T18:09:50+01:00Marek OstaszewskiLink to API docs is brokenhttps://minerva-dev.lcsb.uni.lu/minerva/docs/
replies as in the screenshot
![Screenshot_2024-02-07_at_11.51.54](/uploads/ab57ce0ee88c755485d5de2329ea8c83/Screenshot_2024-02-07_at_11.51.54.png)https://minerva-dev.lcsb.uni.lu/minerva/docs/
replies as in the screenshot
![Screenshot_2024-02-07_at_11.51.54](/uploads/ab57ce0ee88c755485d5de2329ea8c83/Screenshot_2024-02-07_at_11.51.54.png)17.0.0~beta.1https://git-r3lab.uni.lu/minerva/core/-/issues/1974Manually-added user cannot agree to ToS2024-02-13T11:51:57+01:00Marek OstaszewskiManually-added user cannot agree to ToSI've added a user manually, tried to access a visible map.
I was prompted to accept the ToS, but my "OK" was rejected, see screenshot.
Javascript console says:
`{reason: "active can be updated by admin", error: "Access denied."}`
The u...I've added a user manually, tried to access a visible map.
I was prompted to accept the ToS, but my "OK" was rejected, see screenshot.
Javascript console says:
`{reason: "active can be updated by admin", error: "Access denied."}`
The user was set to be "Active" manually.
![Screenshot_2024-02-07_at_11.32.55](/uploads/91c09cdaa13cd93359903324ec3fce12/Screenshot_2024-02-07_at_11.32.55.png)17.0.0~beta.1https://git-r3lab.uni.lu/minerva/core/-/issues/1972Reviving project stuck on "Generating images"2024-02-09T10:54:16+01:00Marek OstaszewskiReviving project stuck on "Generating images"![Screenshot_2024-02-07_at_10.27.54](/uploads/0081998fec2c7eeb4480c155fd9b0ffb/Screenshot_2024-02-07_at_10.27.54.png)![Screenshot_2024-02-07_at_10.27.54](/uploads/0081998fec2c7eeb4480c155fd9b0ffb/Screenshot_2024-02-07_at_10.27.54.png)17.0.0~beta.1https://git-r3lab.uni.lu/minerva/core/-/issues/1969HGNC changed their links, reference by-symbol doesn't work2024-02-15T17:57:46+01:00Marek OstaszewskiHGNC changed their links, reference by-symbol doesn't workMINERVA links generated for HGNC Symbol annotation don't work:
https://www.genenames.org/cgi-bin/gene_symbol_report?match=MRPS16
Suggested solution is to use only HGNC id-based links, also for HGNC Symbol hyperlinks in the interface.MINERVA links generated for HGNC Symbol annotation don't work:
https://www.genenames.org/cgi-bin/gene_symbol_report?match=MRPS16
Suggested solution is to use only HGNC id-based links, also for HGNC Symbol hyperlinks in the interface.17.0.0-beta.3https://git-r3lab.uni.lu/minerva/core/-/issues/1967cache_type has invalid entry2024-02-09T10:39:07+01:00Piotr Gawroncache_type has invalid entryFor some reason there is lcsb.mapviewer.annotation.services.dapi.DapiConnectorImpl in cache_type_table
As a result refreshuing data from DAPI did not work properly
Reported by luizmaialadeira[at]gmail.comFor some reason there is lcsb.mapviewer.annotation.services.dapi.DapiConnectorImpl in cache_type_table
As a result refreshuing data from DAPI did not work properly
Reported by luizmaialadeira[at]gmail.com17.0.0~beta.1https://git-r3lab.uni.lu/minerva/core/-/issues/1964upload of invalid javascript plugin throws an exception2024-02-13T17:37:10+01:00Piotr Gawronupload of invalid javascript plugin throws an exceptionexample: https://raw.githubusercontent.com/mateusz-winiarczyk/xx/main/m-plugin-w.jsexample: https://raw.githubusercontent.com/mateusz-winiarczyk/xx/main/m-plugin-w.js17.0.0~beta.1