Error bean PubmedImportService - Version 6.3

[Leonardo Matos]

Hello friends,

I have a problem updating my dspace to version 6.3. The error occurs while starting tomcat. The error is below, Can anyone help me with this?

"Error creating bean with name 'importService' defined in URL [jar:file:/home/dspace/apache-tomcat-7.0.68/webapps/oai/WEB-INF/lib/dspace-api-6.3.jar!/spring/spring-dspace-addon-import-services.xml]: Unsatisfied dependency expressed through bean property 'importSources': : Error creating bean with name 'PubmedImportService': Injection of resource dependencies failed; nested exception is org.springframework.beans.factory.NoSuchBeanDefinitionException: No bean named 'maxRetry' is defined; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'PubmedImportService': Injection of resource dependencies failed; nested exception is org.springframework.beans.factory.NoSuchBeanDefinitionException: No bean named 'maxRetry' is defined"

"Error creating bean with name 'PubmedImportService': Injection of resource dependencies failed; nested exception is org.springframework.beans.factory.NoSuchBeanDefinitionException: No bean named 'maxRetry' is defined"

[Mark H. Wood]

On Tuesday, September 25, 2018 at 2:56:06 PM UTC-4, Leonardo Matos wrote:

I have a problem updating my dspace to version 6.3. The error occurs while starting tomcat. The error is below, Can anyone help me with this?

"Error creating bean with name 'PubmedImportService': Injection of resource dependencies failed; nested exception is org.springframework.beans.factory.NoSuchBeanDefinitionException: No bean named 'maxRetry' is defined"

maxRetry should be defined in '[DSpace]/config/spring/api/pubmed-integration.xml'.  It is required as a @Resource in org.dspace.importer.external.service.components.AbstractRemoteMetadataSource, and I expect that PubmedImportMetadataSource extends that.  I would first check pubmed-integration.xml for damage.

[Leonardo Matos]

Hi Mark,

Thanks for the feedback, I checked all the points you said and it's exactly as it should be. Look:

pubmed-integration.xml

AbstractRemoteMetadataSource.java

PubmedImportMetadataSourceServiceImpl.java

I'm using DSpace 6.3 without any changes. I looked at the spring-dspace-addon-import-services.xml file that references url http://eutils.ncbi.nlm.nih.gov/entrez/eutils/, can you tell me if the firewall or proxy of the company may be barring this connection?

[Leonardo Matos]

Hi Mark,

the images broke.
I will try again.

Thanks for the feedback, I checked all the points you said and it's exactly as it should be. Look:

pubmed-integration.xml

    <bean class="java.lang.Integer" id="maxRetry">
        <constructor-arg value="2"/>
    </bean>

AbstractRemoteMetadataSource.java

PubmedImportMetadataSourceServiceImpl.java implements interface

[Tim Donohue]

Hi Leonardo,

The original error is clearly pointing at DSpace not being able to "find" your setting for "maxRetry".  As Mark noted, the most important part of your error message is this note:

"Error creating bean with name 'PubmedImportService': Injection of resource dependencies failed; nested exception is org.springframework.beans.factory.NoSuchBeanDefinitionException: No bean named 'maxRetry' is defined" 

I would double check the "pubmed-integration.xml" file that is *installed* in the [dspace]/config/spring/api/ folder (note: this is not the "dspace-src" directory).  According to that error message, DSpace cannot find that "maxRetry" setting.  So, it's likely that either your "pubmed-integration.xml" file is missing that setting, or perhaps the file has an invalid character (which makes it not be valid XML), which could cause DSpace not to be able to parse that configuration file properly.

It's also possible that your upgrade to 6.3 did not properly replace all the Spring configuration in your [dspace]/config/spring/api/ folder (it should have done this during the "ant update" step of your upgrade).  If that's the case, assuming you haven't modified the Spring configuration manually, it is safe to *delete* the entire [dspace]/config/spring/api/ folder, and rerun "ant update" (which will replace it with the 6.3 version of the configurations).

In any case, this error definitely sounds like an issue in your configuration file. It would not be caused by a firewall or proxy problem.

Tim

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Tim Donohue
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[Leonardo Matos]

Hello Tim,

thanks for the feedback. I was able to fix the problem by following your guidelines, it really was not a proxy problem, but some corrupted file inside the / config directory.
What I did was update the directory again and it worked again.

Many thanks for your support.