DSpace 7.2 Backend tomcat error

[Karol Sokalski]

Hi, 

when i try to run dspace 7.2 backend, after fresh installation i can't do this.

I see the following error in the tomcat logs:

[crit] The web application [server] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@6acfe330]) and a value of type [org.apache.logging.log4j.core.LoggerContext] (value [org.apache.logging.log4j.core.LoggerContext@785691c3]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.

Any sugessions? 

Thanks,

Karol

[Karol Sokalski]

I founded more errors:

[2022-03-15 09:39:35] [crit] A child container failed during start
[2022-03-15 09:39:35] [crit] java.util.concurrent.ExecutionException: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/server]]
[2022-03-15 09:39:35] [crit]     at java.base/java.util.concurrent.FutureTask.report(FutureTask.java:122)
[2022-03-15 09:39:35] [crit]     at java.base/java.util.concurrent.FutureTask.get(FutureTask.java:191)
[2022-03-15 09:39:35] [crit]     at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:916)
[2022-03-15 09:39:35] [crit]     at org.apache.catalina.core.StandardHost.startInternal(StandardHost.java:843)
[2022-03-15 09:39:35] [crit]     at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
[2022-03-15 09:39:35] [crit]     at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1384)
[2022-03-15 09:39:35] [crit]     at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1374)
[2022-03-15 09:39:35] [crit]     at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
[2022-03-15 09:39:35] [crit]     at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
[2022-03-15 09:39:35] [crit]     at java.base/java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:140)
[2022-03-15 09:39:35] [crit]     at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:909)
[2022-03-15 09:39:35] [crit]     at org.apache.catalina.core.StandardEngine.startInternal(StandardEngine.java:262)
[2022-03-15 09:39:35] [crit]     at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
[2022-03-15 09:39:35] [crit]     at org.apache.catalina.core.StandardService.startInternal(StandardService.java:434)
[2022-03-15 09:39:35] [crit]     at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
[2022-03-15 09:39:35] [crit]     at org.apache.catalina.core.StandardServer.startInternal(StandardServer.java:930)
[2022-03-15 09:39:35] [crit]     at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
[2022-03-15 09:39:35] [crit]     at org.apache.catalina.startup.Catalina.start(Catalina.java:772)
[2022-03-15 09:39:35] [crit]     at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[2022-03-15 09:39:35] [crit]     at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
[2022-03-15 09:39:35] [crit]     at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[2022-03-15 09:39:35] [crit]     at java.base/java.lang.reflect.Method.invoke(Method.java:566)
[2022-03-15 09:39:35] [crit]     at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:342)
[2022-03-15 09:39:35] [crit]     at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:477)
[2022-03-15 09:39:35] [crit] Caused by: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/server]]
[2022-03-15 09:39:35] [crit]     at org.apache.catalina.util.LifecycleBase.handleSubClassException(LifecycleBase.java:440)
[2022-03-15 09:39:35] [crit]     at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:198)
[2022-03-15 09:39:35] [crit]     at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1384)
[2022-03-15 09:39:35] [crit]     at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1374)
[2022-03-15 09:39:35] [crit]     at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
[2022-03-15 09:39:35] [crit]     at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
[2022-03-15 09:39:35] [crit]     at java.base/java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:140)
[2022-03-15 09:39:35] [crit]     at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:909)
[2022-03-15 09:39:35] [crit]     ... 21 more
[2022-03-15 09:39:35] [crit] Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'authenticationRestController': Unsatisfied dependency expressed through field 'converter'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'converterService': Unsatisfied dependency expressed through field 'webSecurityExpressionEvaluator'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'webSecurityExpressionEvaluator' defined in file [/dspace/webapps/server/WEB-INF/classes/org/dspace/app/rest/security/WebSecurityExpressionEvaluator.class]: Unsatisfied dependency expressed through constructor parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'springSecurityFilterChain' defined in class path resource [org/springframework/security/config/annotation/web/configuration/WebSecurityConfiguration.class]: 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 'restHandlerMapping' defined in class path resource [org/springframework/data/rest/webmvc/config/RepositoryRestMvcConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.data.rest.webmvc.support.DelegatingHandlerMapping]: Factory method 'restHandlerMapping' threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'jpaHelper' defined in class path resource [org/springframework/data/rest/webmvc/config/RepositoryRestMvcConfiguration.class]: Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory' defined in file [/dspace/config/spring/api/core-hibernate.xml]: Invocation of init method failed; nested exception is org.hibernate.tool.schema.spi.SchemaManagementException: Schema-validation: missing table [public.bitstream]

[Tim Donohue]

The key error in that long stack trace seems to be the very last line where it says...

"Schema-validation: missing table [public.bitstream]"

This error is saying that one of your DSpace tables (the "bitstream") table is missing from your database.

It sounds like you either forgot to initialize the database (by running "./dspace database migrate", see step 10 of the install instructions), *or* perhaps that database script threw an earlier error, which caused the tables to not be created.  https://wiki.lyrasis.org/display/DSDOC7x/Installing+DSpace#InstallingDSpace-BackendInstallation

You will need to rerun that "./dspace database migrate" command and check for any errors that may appear in your "dspace.log".  It sounds like it didn't work for some reason, so you need to fix those issues before DSpace will startup.  You can also use "./dspace database info" to check the status of the migrations...all of them should be listed as either "Success" or "Out of Order" (which means successful but ran in a different order).  If any are still listed as Pending or having failed, you'll need to look for errors in the dspace.log for why they are not running.

Good luck,

Tim