Hi, Show I’m running Exomiser 13.0.0, hg38, data version 2109, on an AWS linux machine with Java 17 Corretto. java -Xms14g -Xmx14g -jar exomiser-cli-13.0.0.jar --analysis /data/analyses/EX76.analysis.ymlHere is the log that I’m getting: Welcome to: _____ _ _____ _ |_ _| |__ ___ | ____|_ _____ _ __ ___ (_)___ ___ _ __ | | | '_ \ / _ \ | _| \ \/ / _ \| '_ ` _ \| / __|/ _ \ '__| | | | | | | __/ | |___ > < (_) | | | | | | \__ \ __/ | |_| |_| |_|\___| |_____/_/\_\___/|_| |_| |_|_|___/\___|_| A Tool to Annotate and Prioritize Exome Variants v13.0.0 2021-10-13 13:33:59.201 INFO 7464 --- [ main] org.monarchinitiative.exomiser.cli.Main : Starting Main using Java 17 on ip-11-0-0-98.ec2.internal with PID 7464 (/home/ec2-user/exomiser-cli-13.0.0/exomiser-cli-13.0.0.jar started by ec2-user in /home/ec2-user/exomiser-cli-13.0.0) 2021-10-13 13:33:59.204 INFO 7464 --- [ main] org.monarchinitiative.exomiser.cli.Main : No active profile set, falling back to default profiles: default 2021-10-13 13:34:00.475 INFO 7464 --- [ main] o.m.exomiser.cli.config.MainConfig : Exomiser home: /home/ec2-user/exomiser-cli-13.0.0 2021-10-13 13:34:00.492 INFO 7464 --- [ main] o.m.exomiser.cli.config.MainConfig : Data source directory defined in properties as: /data 2021-10-13 13:34:00.493 INFO 7464 --- [ main] o.m.exomiser.cli.config.MainConfig : Root data source directory set to: /data 2021-10-13 13:34:00.499 INFO 7464 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialising Jannovar data from /data/2109_hg38/2109_hg38_transcripts_ensembl.ser 2021-10-13 13:34:02.316 INFO 7464 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialisation took 1.816 sec. 2021-10-13 13:34:04.122 INFO 7464 --- [ main] g.GenomeAnalysisServiceAutoConfiguration : Configured hg38 genome analysis service 2021-10-13 13:34:05.618 INFO 7464 --- [ main] o.m.exomiser.cli.config.MainConfig : Default results directory set to: /home/ec2-user/exomiser-cli-13.0.0/results 2021-10-13 13:34:05.672 WARN 7464 --- [ main] s.c.a.AnnotationConfigApplicationContext : Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'dataSource' defined in class path resource [org/springframework/boot/autoconfigure/jdbc/DataSourceConfiguration$Hikari.class]: Unsatisfied dependency expressed through method 'dataSource' parameter 0; nested exception is org.springframework.beans.factory.NoUniqueBeanDefinitionException: No qualifying bean of type 'org.springframework.boot.autoconfigure.jdbc.DataSourceProperties' available: expected single matching bean but found 3: spring.datasource-org.springframework.boot.autoconfigure.jdbc.DataSourceProperties,phenotypeDataSourceProperties,hg38genomeDataSourceProperties 2021-10-13 13:34:05.697 INFO 7464 --- [ main] ConditionEvaluationReportLoggingListener : Error starting ApplicationContext. To display the conditions report re-run your application with 'debug' enabled. 2021-10-13 13:34:05.715 ERROR 7464 --- [ main] o.s.b.d.LoggingFailureAnalysisReporter : *************************** APPLICATION FAILED TO START *************************** Description: Parameter 0 of method dataSource in org.springframework.boot.autoconfigure.jdbc.DataSourceConfiguration$Hikari required a single bean, but 3 were found: - spring.datasource-org.springframework.boot.autoconfigure.jdbc.DataSourceProperties: defined in null - phenotypeDataSourceProperties: defined by method 'phenotypeDataSourceProperties' in org.monarchinitiative.exomiser.autoconfigure.phenotype.PhenotypeProperties - hg38genomeDataSourceProperties: defined by method 'hg38genomeDataSourceProperties' in org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeProperties Action: Consider marking one of the beans as @Primary, updating the consumer to accept multiple beans, or using @Qualifier to identify the bean that should be consumedCould you please let me know if I’m doing something wrong or is this a bug? Thank you! Radu Questions : No ServletContext set2022-08-02T05:06:02+00:00 2022-08-02T05:06:02+00:00 213 Migrating from springboot 2.5.7 -> 2.6.1, anycodings_spring-boot class dependencies 2021.0.0 Was there a change that broke this? I have anycodings_spring-boot @EnableWebSecurity, and some anycodings_spring-boot @RestControllers, but not sure what could be anycodings_spring-boot causing it. Total Answers 4 28 Answers 1 : of No ServletContext setWell, we had the same behavior on our anycodings_spring-boot side when upgrading to 2.6.1. It appears anycodings_spring-boot that we used a ConversionService through anycodings_spring-boot constructor injection (for a MongoDB anycodings_spring-boot cache usage). We have changed the definition to a new anycodings_spring-boot instance of DefaultConversionService. Tell me if it helps 0 2022-08-02T05:06:02+00:00 2022-08-02T05:06:02+00:00Answer Link mRahman 5 Answers 2 : of No ServletContext setSame for us upgrading from 2.4.7 to anycodings_spring-boot 2.6.2. We also tried 2.5.8 but same anycodings_spring-boot result. This has no effect on runtime anycodings_spring-boot but the problems appears for our batch anycodings_spring-boot integration tests. 0 2022-08-02T05:06:02+00:00 2022-08-02T05:06:02+00:00Answer Link jidam 5 Answers 3 : of No ServletContext setI'm getting the same error when trying anycodings_spring-boot to upgrade my spring-boot-app from 2.5.9 anycodings_spring-boot to 2.6.3 It does start when i exclude my anycodings_spring-boot SecurityConfigurer. Any advice would be welcome. I'm getting a longer stacktrace, anycodings_spring-boot starting from the anycodings_spring-boot springSecurityFilterChain, but it does anycodings_spring-boot seem to be related. org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'springSecurityFilterChain' defined in org.springframework.security.config.annotation.web.configuration.WebSecurityConfiguration: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [javax.servlet.Filter]: Factory method 'springSecurityFilterChain' threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'mvcHandlerMappingIntrospector' defined in class path resource [org/springframework/boot/autoconfigure/web/servlet/WebMvcAutoConfiguration$EnableWebMvcConfiguration.class]: Invocation of init method failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'resourceHandlerMapping' defined in class path resource [org/springframework/boot/autoconfigure/web/servlet/WebMvcAutoConfiguration$EnableWebMvcConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.web.servlet.HandlerMapping]: Factory method 'resourceHandlerMapping' threw exception; nested exception is java.lang.IllegalStateException: No ServletContext set at org.springframework.beans.factory.support.ConstructorResolver.instantiate(ConstructorResolver.java:658) at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:486) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1352) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1195) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:582) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:542) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:322) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208) at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:953) at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918) at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:583) at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:145) at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:732) at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:414) at org.springframework.boot.SpringApplication.run(SpringApplication.java:302) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1303) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1292) at be.idewe.cobra.CobraBootApplication.main(CobraBootApplication.java:27) 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:498) at org.springframework.boot.devtools.restart.RestartLauncher.run(RestartLauncher.java:49) Caused by: org.springframework.beans.BeanInstantiationException: Failed to instantiate [javax.servlet.Filter]: Factory method 'springSecurityFilterChain' threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'mvcHandlerMappingIntrospector' defined in class path resource [org/springframework/boot/autoconfigure/web/servlet/WebMvcAutoConfiguration$EnableWebMvcConfiguration.class]: Invocation of init method failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'resourceHandlerMapping' defined in class path resource [org/springframework/boot/autoconfigure/web/servlet/WebMvcAutoConfiguration$EnableWebMvcConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.web.servlet.HandlerMapping]: Factory method 'resourceHandlerMapping' threw exception; nested exception is java.lang.IllegalStateException: No ServletContext set at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:185) at org.springframework.beans.factory.support.ConstructorResolver.instantiate(ConstructorResolver.java:653) ... 26 common frames omitted Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'mvcHandlerMappingIntrospector' defined in class path resource [org/springframework/boot/autoconfigure/web/servlet/WebMvcAutoConfiguration$EnableWebMvcConfiguration.class]: Invocation of init method failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'resourceHandlerMapping' defined in class path resource [org/springframework/boot/autoconfigure/web/servlet/WebMvcAutoConfiguration$EnableWebMvcConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.web.servlet.HandlerMapping]: Factory method 'resourceHandlerMapping' threw exception; nested exception is java.lang.IllegalStateException: No ServletContext set at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1804) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:620) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:542) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:213) at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1160) at org.springframework.security.config.annotation.web.configurers.CorsConfigurer$MvcCorsFilter.getMvcCorsFilter(CorsConfigurer.java:111) at org.springframework.security.config.annotation.web.configurers.CorsConfigurer$MvcCorsFilter.access$000(CorsConfigurer.java:94) at org.springframework.security.config.annotation.web.configurers.CorsConfigurer.getCorsFilter(CorsConfigurer.java:89) at org.springframework.security.config.annotation.web.configurers.CorsConfigurer.configure(CorsConfigurer.java:67) at org.springframework.security.config.annotation.web.configurers.CorsConfigurer.configure(CorsConfigurer.java:41) at org.springframework.security.config.annotation.AbstractConfiguredSecurityBuilder.configure(AbstractConfiguredSecurityBuilder.java:349) at org.springframework.security.config.annotation.AbstractConfiguredSecurityBuilder.doBuild(AbstractConfiguredSecurityBuilder.java:303) at org.springframework.security.config.annotation.AbstractSecurityBuilder.build(AbstractSecurityBuilder.java:38) at org.springframework.security.config.annotation.web.builders.WebSecurity.performBuild(WebSecurity.java:285) at org.springframework.security.config.annotation.web.builders.WebSecurity.performBuild(WebSecurity.java:83) at org.springframework.security.config.annotation.AbstractConfiguredSecurityBuilder.doBuild(AbstractConfiguredSecurityBuilder.java:305) at org.springframework.security.config.annotation.AbstractSecurityBuilder.build(AbstractSecurityBuilder.java:38) at org.springframework.security.config.annotation.web.configuration.WebSecurityConfiguration.springSecurityFilterChain(WebSecurityConfiguration.java:127) 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:498) at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:154) ... 27 common frames omitted Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'resourceHandlerMapping' defined in class path resource [org/springframework/boot/autoconfigure/web/servlet/WebMvcAutoConfiguration$EnableWebMvcConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.web.servlet.HandlerMapping]: Factory method 'resourceHandlerMapping' threw exception; nested exception is java.lang.IllegalStateException: No ServletContext set at org.springframework.beans.factory.support.ConstructorResolver.instantiate(ConstructorResolver.java:658) at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:638) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1352) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1195) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:582) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:542) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208) at org.springframework.beans.factory.support.DefaultListableBeanFactory.getBeansOfType(DefaultListableBeanFactory.java:671) at org.springframework.context.support.AbstractApplicationContext.getBeansOfType(AbstractApplicationContext.java:1308) at org.springframework.beans.factory.BeanFactoryUtils.beansOfTypeIncludingAncestors(BeanFactoryUtils.java:378) at org.springframework.web.servlet.handler.HandlerMappingIntrospector.initHandlerMappings(HandlerMappingIntrospector.java:226) at org.springframework.web.servlet.handler.HandlerMappingIntrospector.afterPropertiesSet(HandlerMappingIntrospector.java:115) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1863) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1800) ... 52 common frames omitted Caused by: org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.web.servlet.HandlerMapping]: Factory method 'resourceHandlerMapping' threw exception; nested exception is java.lang.IllegalStateException: No ServletContext set at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:185) at org.springframework.beans.factory.support.ConstructorResolver.instantiate(ConstructorResolver.java:653) ... 68 common frames omitted Caused by: java.lang.IllegalStateException: No ServletContext set at org.springframework.util.Assert.state(Assert.java:76) at org.springframework.web.servlet.config.annotation.WebMvcConfigurationSupport.resourceHandlerMapping(WebMvcConfigurationSupport.java:591) 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:498) at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:154) ... 69 common frames omitted0 2022-08-02T05:06:02+00:00 2022-08-02T05:06:02+00:00Answer Link jidam 5 Answers 4 : of No ServletContext setI've resolved this by removing all anycodings_spring-boot possible code that would create a anycodings_spring-boot minimum viable code example. In my case anycodings_spring-boot I was injecting a RestTemplate and the anycodings_spring-boot loader was getting confused. I moved it anycodings_spring-boot out into it's own class so it would anycodings_spring-boot avoid some circular dependencies. The anycodings_spring-boot newer spring version seems to be anycodings_spring-boot stricter and detect cycles. 0 2022-08-02T05:06:02+00:00 2022-08-02T05:06:02+00:00Answer Link raja |
Caused by: org/springframework beans Factory BeanCreationException at ConstructorResolver java 658
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