Error running dspace database migrate

[Emilia Lobo]

I'm upgrading DSpace 7.6.1 to DSpace 7.6.2 on a development machine working with docker and git.
I made a backup of the DB.
Then I followed these steps:
git feth upstream (at https://github.com/DSpace/DSpace)
git merge dspace-7.6.2
docker exec -it dspace /dspace/bin/dspace database migrate
But I get the following errors:

sudo docker exec -it dspace /dspace/bin/dspace database migrate
Failure during kernel init: Error creating bean with name 'org.dspace.app.sherpa.SHERPAService': Unsatisfied dependency expressed through field 'configurationService'; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.dspace.importer.external.crossref.CrossRefAbstractProcessor] for bean with name 'crossrefAbstractMetadataProcessor' defined in file [/dspace/config/spring/api/crossref-integration.xml]; nested exception is java.lang.ClassNotFoundException: org.dspace.importer.external.crossref.CrossRefAbstractProcessor
org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'org.dspace.app.sherpa.SHERPAService': Unsatisfied dependency expressed through field 'configurationService'; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.dspace.importer.external.crossref.CrossRefAbstractProcessor] for bean with name 'crossrefAbstractMetadataProcessor' defined in file [/dspace/config/spring/api/crossref-integration.xml]; nested exception is java.lang.ClassNotFoundException: org.dspace.importer.external.crossref.CrossRefAbstractProcessor
at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.resolveFieldValue(AutowiredAnnotationBeanPostProcessor.java:660)
at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:640)
at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:119)
at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessProperties(AutowiredAnnotationBeanPostProcessor.java:399)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1431)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:619)
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.preInstantiateSingletons(DefaultListableBeanFactory.java:955)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:920)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:583)
at org.dspace.servicemanager.DSpaceServiceManager.startup(DSpaceServiceManager.java:280)
at org.dspace.servicemanager.DSpaceKernelImpl.start(DSpaceKernelImpl.java:153)
at org.dspace.servicemanager.DSpaceKernelImpl.start(DSpaceKernelImpl.java:128)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:71)
Caused by: org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.dspace.importer.external.crossref.CrossRefAbstractProcessor] for bean with name 'crossrefAbstractMetadataProcessor' defined in file [/dspace/config/spring/api/crossref-integration.xml]; nested exception is java.lang.ClassNotFoundException: org.dspace.importer.external.crossref.CrossRefAbstractProcessor
at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1556)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.determineTargetType(AbstractAutowireCapableBeanFactory.java:704)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.predictBeanType(AbstractAutowireCapableBeanFactory.java:674)
at org.springframework.beans.factory.support.AbstractBeanFactory.isFactoryBean(AbstractBeanFactory.java:1684)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.doGetBeanNamesForType(DefaultListableBeanFactory.java:570)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.getBeanNamesForType(DefaultListableBeanFactory.java:550)
at org.springframework.beans.factory.BeanFactoryUtils.beanNamesForTypeIncludingAncestors(BeanFactoryUtils.java:265)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.findAutowireCandidates(DefaultListableBeanFactory.java:1557)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1354)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1311)
at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.resolveFieldValue(AutowiredAnnotationBeanPostProcessor.java:657)
... 17 more
Caused by: java.lang.ClassNotFoundException: org.dspace.importer.external.crossref.CrossRefAbstractProcessor
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:581)
at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:527)
at java.base/java.lang.Class.forName0(Native Method)
at java.base/java.lang.Class.forName(Class.java:398)
at org.springframework.util.ClassUtils.forName(ClassUtils.java:284)
at org.springframework.beans.factory.support.AbstractBeanDefinition.resolveBeanClass(AbstractBeanDefinition.java:469)
at org.springframework.beans.factory.support.AbstractBeanFactory.doResolveBeanClass(AbstractBeanFactory.java:1621)
at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1548)
... 27 more
Exception in thread "main" java.lang.IllegalStateException: Failure during kernel init: Error creating bean with name 'org.dspace.app.sherpa.SHERPAService': Unsatisfied dependency expressed through field 'configurationService'; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.dspace.importer.external.crossref.CrossRefAbstractProcessor] for bean with name 'crossrefAbstractMetadataProcessor' defined in file [/dspace/config/spring/api/crossref-integration.xml]; nested exception is java.lang.ClassNotFoundException: org.dspace.importer.external.crossref.CrossRefAbstractProcessor
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:83)
Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'org.dspace.app.sherpa.SHERPAService': Unsatisfied dependency expressed through field 'configurationService'; nested exception is org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.dspace.importer.external.crossref.CrossRefAbstractProcessor] for bean with name 'crossrefAbstractMetadataProcessor' defined in file [/dspace/config/spring/api/crossref-integration.xml]; nested exception is java.lang.ClassNotFoundException: org.dspace.importer.external.crossref.CrossRefAbstractProcessor
at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.resolveFieldValue(AutowiredAnnotationBeanPostProcessor.java:660)
at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:640)
at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:119)
at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessProperties(AutowiredAnnotationBeanPostProcessor.java:399)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1431)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:619)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:542)
at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$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.preInstantiateSingletons(DefaultListableBeanFactory.java:955)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:920)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:583)
at org.dspace.servicemanager.DSpaceServiceManager.startup(DSpaceServiceManager.java:280)
at org.dspace.servicemanager.DSpaceKernelImpl.start(DSpaceKernelImpl.java:153)
at org.dspace.servicemanager.DSpaceKernelImpl.start(DSpaceKernelImpl.java:128)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:71)
Caused by: org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [org.dspace.importer.external.crossref.CrossRefAbstractProcessor] for bean with name 'crossrefAbstractMetadataProcessor' defined in file [/dspace/config/spring/api/crossref-integration.xml]; nested exception is java.lang.ClassNotFoundException: org.dspace.importer.external.crossref.CrossRefAbstractProcessor
at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1556)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.determineTargetType(AbstractAutowireCapableBeanFactory.java:704)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.predictBeanType(AbstractAutowireCapableBeanFactory.java:674)
at org.springframework.beans.factory.support.AbstractBeanFactory.isFactoryBean(AbstractBeanFactory.java:1684)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.doGetBeanNamesForType(DefaultListableBeanFactory.java:570)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.getBeanNamesForType(DefaultListableBeanFactory.java:550)
at org.springframework.beans.factory.BeanFactoryUtils.beanNamesForTypeIncludingAncestors(BeanFactoryUtils.java:265)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.findAutowireCandidates(DefaultListableBeanFactory.java:1557)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1354)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1311)
at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.resolveFieldValue(AutowiredAnnotationBeanPostProcessor.java:657)
... 17 more
Caused by: java.lang.ClassNotFoundException: org.dspace.importer.external.crossref.CrossRefAbstractProcessor
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:581)
at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:527)
at java.base/java.lang.Class.forName0(Native Method)
at java.base/java.lang.Class.forName(Class.java:398)
at org.springframework.util.ClassUtils.forName(ClassUtils.java:284)
at org.springframework.beans.factory.support.AbstractBeanDefinition.resolveBeanClass(AbstractBeanDefinition.java:469)
at org.springframework.beans.factory.support.AbstractBeanFactory.doResolveBeanClass(AbstractBeanFactory.java:1621)
at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1548)
... 27 more

[Emilia Lobo]

I found this other error:

sudo docker-compose -f docker-compose.yml up
[+] Building 0.0s (0/0)                                                                                                                                                           docker:default
[+] Running 3/0
 ✔ Container dspacedb    Created                                                                                                                                                            0.0s
 ✔ Container dspacesolr  Running                                                                                                                                                            0.0s
 ✔ Container dspace      Running                                                                                                                                                            0.0s
Attaching to dspace, dspacedb, dspacesolr
dspacedb    |
dspacedb    | PostgreSQL Database directory appears to contain a database; Skipping initialization
dspacedb    |
dspacedb    | 2024-12-06 18:54:44.128 UTC [1] FATAL:  database files are incompatible with server
dspacedb    | 2024-12-06 18:54:44.128 UTC [1] DETAIL:  The data directory was initialized by PostgreSQL version 13, which is not compatible with this version 15.10 (Debian 15.10-1.pgdg120+1).
dspacedb exited with code 1

Thanks, 

Emilia.-