Hello,
FYI, we are running DSpace 6.3 with Postgresql.
Here is an update:
I have not solved the configuration problem with xoai.xml, in trying for a
virtual set based on the presence of the string 'openAccess' in the
metadata field dc.rights. I fiddled and tried various things with the
file, but I always end up with this error breaking the oai page:
Type Exception Report
Message OAI 2.0 wasn't correctly initialized, please check the log for
previous errors
Description The server encountered an unexpected condition that prevented
it from fulfilling the request.
Exception
javax.servlet.ServletException: OAI 2.0 wasn't correctly initialized,
please check the log for previous errors
org.dspace.xoai.controller.DSpaceOAIDataProvider.contextAction(DSpaceOAIDataProvider.java:124)
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
java.lang.reflect.Method.invoke(Method.java:498)
org.springframework.web.method.support.InvocableHandlerMethod.invoke(InvocableHandlerMethod.java:215)
org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:132)
org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:104)
org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandleMethod(RequestMappingHandlerAdapter.java:743)
org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:672)
org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:82)
org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:933)
org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:867)
org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:951)
org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:842)
javax.servlet.http.HttpServlet.service(HttpServlet.java:635)
org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:827)
javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
Root Cause
org.dspace.xoai.services.api.config.XOAIManagerResolverException:
com.lyncode.xoai.dataprovider.exceptions.ConfigurationException: Metadata
FormatConfiguration referred as oaidc does not exist
org.dspace.xoai.services.impl.context.DSpaceXOAIManagerResolver.getManager(DSpaceXOAIManagerResolver.java:32)
org.dspace.xoai.controller.DSpaceOAIDataProvider.contextAction(DSpaceOAIDataProvider.java:86)
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
java.lang.reflect.Method.invoke(Method.java:498)
org.springframework.web.method.support.InvocableHandlerMethod.invoke(InvocableHandlerMethod.java:215)
org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:132)
org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:104)
org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandleMethod(RequestMappingHandlerAdapter.java:743)
org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:672)
org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:82)
org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:933)
org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:867)
org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:951)
org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:842)
javax.servlet.http.HttpServlet.service(HttpServlet.java:635)
org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:827)
javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
Root Cause
com.lyncode.xoai.dataprovider.exceptions.ConfigurationException: Metadata
FormatConfiguration referred as oaidc does not exist
com.lyncode.xoai.dataprovider.core.ContextManager.<init>(ContextManager.java:63)
com.lyncode.xoai.dataprovider.core.XOAIManager.<init>(XOAIManager.java:57)
org.dspace.xoai.services.impl.context.DSpaceXOAIManagerResolver.getManager(DSpaceXOAIManagerResolver.java:30)
org.dspace.xoai.controller.DSpaceOAIDataProvider.contextAction(DSpaceOAIDataProvider.java:86)
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
java.lang.reflect.Method.invoke(Method.java:498)
org.springframework.web.method.support.InvocableHandlerMethod.invoke(InvocableHandlerMethod.java:215)
org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:132)
org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:104)
org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandleMethod(RequestMappingHandlerAdapter.java:743)
org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:672)
org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:82)
org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:933)
org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:867)
org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:951)
org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:842)
javax.servlet.http.HttpServlet.service(HttpServlet.java:635)
org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:827)
javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
This error message is not helpful to me, and I do not see a way to debug
based on this. If someone can see it, please let me know! All I can do is
fiddle with the xml, and I have unfortunately come to the end of my ideas
about that. If I revert to the original xoai.xml, the error goes away. Of
course the oaidc format configuration is unchanged in both versions of
xoai.xml.
However, I had some success with the exception when updating the oai
index. When running
bin/dspace oai import -co
I had first gotten an out of memory error, which I mentioned above. I
raised the allotment for java in the dspace script, and that eliminated the
memory error. It allowed the process to go further however, to the point
at which it ran into a null pointer exception:
java.lang.NullPointerException
at org.dspace.xoai.app.XOAI.willChangeStatus(XOAI.java:441)
at org.dspace.xoai.app.XOAI.index(XOAI.java:368)
at org.dspace.xoai.app.XOAI.index(XOAI.java:280)
at org.dspace.xoai.app.XOAI.indexAll(XOAI.java:227) the
at org.dspace.xoai.app.XOAI.index(XOAI.java:134)
at org.dspace.xoai.app.XOAI.main(XOAI.java:560)
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.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
at
org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
I looked at willChangeStatus in XOAI.java, and found it was checking the
ResourcePolicy for the current item, and it was clear from the code that
the null pointer exception occurred when it ran policy.getGroup(). I
checked our resourcepolicy table in the database, and found 45 instances in
which an entry had a null for the epersongroup_id column. I do not know
why this error happened, but these were special cases instantiated by my
colleague (who is on vacation at the moment, so I cannot ask her. :-) ).
I added a check in the willChangeStatus method if policy.getGroup() were
null, to print out the item uuid. This confirmed that these items with the
nulls in the resourcepolicy table were the culprits. I filled these nulls
with the Administrator group id, and was able to run the full import
successfully.
But the unknown error(s) in xoai.xml are still causing the oai listSets
page to crash with the error listed above.
I know it is the time of year when people are on vacation, and do not have
time to check these pages. But I have spent enough time on this problem,
and I am ready to go back to my original idea, before I heard of virtual
sets: I will create a collection Open Access and copy in the items that are
open access. Then I can run the oai import, and presumably all these
items' metadata will appear in the oai page, and we will conform with the
DINI requirement. Uff.
Thanks for reading this to the end! ;-)
Best regards,
Paul
On Wednesday, August 18, 2021 at 11:38:16 AM UTC+2 [email protected] wrote:
> Thanks, Michael, for the tip! I ran a complete rebuild, and ran out of
> memory part way through. I increased the amount allotted to Java in the
> dspace script (-Xmx) and it ran fine the second time. It seemed to finish
> with the 103000 documents in our repository, then it started over, and at
> about 10000 hit a null pointer exception. I don't know why it started
> over, and would like to understand - but it seems not to have broken
> anything. I have a working oai system again. This refresh did find the
> file in my test open access collection and display the metadata in the oai
> interface.
>
> Anyway, more importantly, to answer your question, I would prefer to make
> the virtual set work (with all the open access documents in it) and avoid
> the maintenance of a separate oa collection holding duplicates of other
> collections. However, having tried Claudia Jürgen's seemingly clear
> instructions, I still do not have the virtual set appearing in my oai
> list. I have enclosed my xoai.xml - could someone take a look and tell me
> what I have done wrong?
>
> Thanks!!
>
> Best regards,
> Paul
>
> On Tuesday, August 17, 2021 at 5:39:09 PM UTC+2 Michael Plate wrote:
>
>> Hi Paul,
>>
>> Am 17.08.21 um 17:31 schrieb [email protected]:
>> > Hello,
>> >
>> > We are applying for dini certification, and we need an OAI-set for the
>> > open access documents. I have attempted two things:
>> >
>> > 1.
>> > I have created a collection named Open Access and put one of our open
>> > access documents in it as a test. This document belongs to another
>> > collection. After running discovery to update the solr index, the
>> > document now appears in both places.
>>
>> do you really want that ? Or do you want just to have any oa doc in a set
>> ?
>>
>> >
>> > But in the oai inteface, the collection appears, but the document does
>> not.
>> […]
>>
>> sounds like you missed updating the OAI cache:
>>
>> [bin]/dspace oai -h
>>
>>
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