DSpace7.x issue with harvesting metadata with references to bitstreams - link to original source not being generated

[Dimple Patel]

Hello All,

We have this issue with DSpace7.x including 7.4. While harvesting metadata from ORE-compliant repositories even though the option Metadata with references to bitstreams is selected, after harvesting the link to original sources are not being displayed in the brief layout of the metadata. Whereas, the DSpace6.3 version does this job. Can anyone throw light on this? We already have a production system of an OERs harvesting service for our university on DSpace6.3 and are planning to migrate to DSpace7.x.

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Regards,
Dimple,

CUHP,

Dharamshala, H.P.

India.

[Tim Donohue]

Hi Dimple,

Can you check your logs for any errors that DSpace 7 may have thrown during the harvesting process? 

It's very important to look for errors in your logs whenever you are reporting a possible issue.  Those errors in the logs are how we can help diagnose whether the problem is a possible configuration issue, or if there may be a bug in the system.

If you need help finding the errors in your logs, see our guide for Troubleshooting an Error: https://wiki.lyrasis.org/display/DSPACE/Troubleshoot+an+error#Troubleshootanerror-DSpace7.x(orabove)

Please share what you find to the list, that way others can see if they can either reproduce it, or find a clue to what may be going on.

Tim

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From: dspace-c...@googlegroups.com <dspace-c...@googlegroups.com> on behalf of Dimple Patel <dim...@drtc.isibang.ac.in>
Sent: Monday, October 17, 2022 3:46 AM
To: dspace-c...@googlegroups.com <dspace-c...@googlegroups.com>
Subject: [dspace-community] DSpace7.x issue with harvesting metadata with references to bitstreams - link to original source not being generated

 

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[Dimple Patel]

Hi Tim,

Thanks for your prompt response.

Operating system: Linux Mint 21 Cinnamon

DSpace: 7.4

Tomcat: 9

While harvesting metadata from ORE-compliant repositories even though the option Metadata with references to bitstreams is selected, after harvesting, the link to original sources are not being displayed in the brief layout of the metadata. Whereas, the DSpace6.3 version does this job. The error log is as follows:

 

2022-10-18 19:44:44,407 ERROR unknown unknown org.dspace.harvest.OAIHarvester @ Harvesting error occurred while processing an OAI record: OAI server returned the following errors during getDescMD execution: [idDoesNotExist]
org.dspace.harvest.HarvestingException: OAI server returned the following errors during getDescMD execution: [idDoesNotExist]
at org.dspace.harvest.OAIHarvester.getMDrecord(OAIHarvester.java:883) ~[dspace-api-7.4.jar:7.4]
at org.dspace.harvest.OAIHarvester.processRecord(OAIHarvester.java:531) ~[dspace-api-7.4.jar:7.4]
at org.dspace.harvest.OAIHarvester.runHarvest(OAIHarvester.java:394) [dspace-api-7.4.jar:7.4]
at org.dspace.app.harvest.Harvest.runHarvest(Harvest.java:390) [dspace-api-7.4.jar:7.4]
at org.dspace.app.harvest.Harvest.internalRun(Harvest.java:208) [dspace-api-7.4.jar:7.4]
at org.dspace.scripts.DSpaceRunnable.run(DSpaceRunnable.java:104) [dspace-api-7.4.jar:7.4]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) [?:?]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) [?:?]
at java.lang.Thread.run(Thread.java:829) [?:?]
2022-10-18 19:44:46,547 WARN  unknown unknown org.dspace.harvest.OAIHarvester @ Unable to send email alert
com.sun.mail.util.MailConnectException: Couldn't connect to host, port: smtp.example.com, 25; timeout -1
at com.sun.mail.smtp.SMTPTransport.openServer(SMTPTransport.java:2209) ~[javax.mail-1.6.2.jar:1.6.2]
at com.sun.mail.smtp.SMTPTransport.protocolConnect(SMTPTransport.java:740) ~[javax.mail-1.6.2.jar:1.6.2]
at javax.mail.Service.connect(Service.java:366) ~[javax.mail-1.6.2.jar:1.6.2]
at javax.mail.Service.connect(Service.java:246) ~[javax.mail-1.6.2.jar:1.6.2]
at javax.mail.Service.connect(Service.java:195) ~[javax.mail-1.6.2.jar:1.6.2]
at javax.mail.Transport.send0(Transport.java:254) ~[javax.mail-1.6.2.jar:1.6.2]
at javax.mail.Transport.send(Transport.java:124) ~[javax.mail-1.6.2.jar:1.6.2]
at org.dspace.core.Email.send(Email.java:441) ~[dspace-api-7.4.jar:7.4]
at org.dspace.harvest.OAIHarvester.alertAdmin(OAIHarvester.java:849) [dspace-api-7.4.jar:7.4]
at org.dspace.harvest.OAIHarvester.runHarvest(OAIHarvester.java:430) [dspace-api-7.4.jar:7.4]
at org.dspace.app.harvest.Harvest.runHarvest(Harvest.java:390) [dspace-api-7.4.jar:7.4]
at org.dspace.app.harvest.Harvest.internalRun(Harvest.java:208) [dspace-api-7.4.jar:7.4]
at org.dspace.scripts.DSpaceRunnable.run(DSpaceRunnable.java:104) [dspace-api-7.4.jar:7.4]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) [?:?]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) [?:?]
at java.lang.Thread.run(Thread.java:829) [?:?]
Caused by: java.net.UnknownHostException: smtp.example.com
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:229) ~[?:?]
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) ~[?:?]
at java.net.Socket.connect(Socket.java:609) ~[?:?]
at java.net.Socket.connect(Socket.java:558) ~[?:?]
at com.sun.mail.util.SocketFetcher.createSocket(SocketFetcher.java:359) ~[javax.mail-1.6.2.jar:1.6.2]
at com.sun.mail.util.SocketFetcher.getSocket(SocketFetcher.java:238) ~[javax.mail-1.6.2.jar:1.6.2]
at com.sun.mail.smtp.SMTPTransport.openServer(SMTPTransport.java:2175) ~[javax.mail-1.6.2.jar:1.6.2]
... 15 more
2022-10-18 19:44:46,552 ERROR unknown unknown org.dspace.app.rest.scripts.handler.impl.RestDSpaceRunnableHandler @ Process id: 24, script name: harvest, message: null
org.hibernate.LazyInitializationException: failed to lazily initialize a collection of role: org.dspace.content.Collection.communities, could not initialize proxy - no Session
at org.hibernate.collection.internal.AbstractPersistentCollection.throwLazyInitializationException(AbstractPersistentCollection.java:612) ~[hibernate-core-5.6.5.Final.jar:5.6.5.Final]
at org.hibernate.collection.internal.AbstractPersistentCollection.withTemporarySessionIfNeeded(AbstractPersistentCollection.java:218) ~[hibernate-core-5.6.5.Final.jar:5.6.5.Final]
at org.hibernate.collection.internal.AbstractPersistentCollection.initialize(AbstractPersistentCollection.java:591) ~[hibernate-core-5.6.5.Final.jar:5.6.5.Final]
at org.hibernate.collection.internal.AbstractPersistentCollection.read(AbstractPersistentCollection.java:149) ~[hibernate-core-5.6.5.Final.jar:5.6.5.Final]
at org.hibernate.collection.internal.PersistentSet.toArray(PersistentSet.java:202) ~[hibernate-core-5.6.5.Final.jar:5.6.5.Final]
at org.dspace.content.Collection.getCommunities(Collection.java:263) ~[dspace-api-7.4.jar:7.4]
at org.dspace.content.CommunityServiceImpl.getAllParents(CommunityServiceImpl.java:336) ~[dspace-api-7.4.jar:7.4]
at org.dspace.content.CollectionServiceImpl.canEdit(CollectionServiceImpl.java:708) ~[dspace-api-7.4.jar:7.4]
at org.dspace.content.CollectionServiceImpl.update(CollectionServiceImpl.java:663) ~[dspace-api-7.4.jar:7.4]
at org.dspace.content.CollectionServiceImpl.update(CollectionServiceImpl.java:76) ~[dspace-api-7.4.jar:7.4]
at org.dspace.harvest.OAIHarvester.runHarvest(OAIHarvester.java:448) ~[dspace-api-7.4.jar:7.4]
at org.dspace.app.harvest.Harvest.runHarvest(Harvest.java:390) ~[dspace-api-7.4.jar:7.4]
at org.dspace.app.harvest.Harvest.internalRun(Harvest.java:208) ~[dspace-api-7.4.jar:7.4]
at org.dspace.scripts.DSpaceRunnable.run(DSpaceRunnable.java:104) [dspace-api-7.4.jar:7.4]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) [?:?]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) [?:?]
at java.lang.Thread.run(Thread.java:829) [?:?]
2022-10-18 21:01:53,608 WARN  33488686-beef-4af0-90cb-9bb9dd378a54 a5bd03c5-9c8c-41f0-9012-aadbb4ad20b7 org.dspace.app.rest.exception.DSpaceApiExceptionControllerAdvice @ An exception has occurred (status:404 exception: No such configuration property: google.analytics.key at: org.dspace.app.rest.repository.ConfigurationRestRepository.findOne(ConfigurationRestRepository.java:58))

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Regards,
Dimple

CUHP

Dharamshala, H.P.

India.

[Dimple Patel]

Hi All,

The example repository used for harvesting is OAI-ORE compliant (https://dspace.mit.edu//oai/request?verb=Identify). Moreover the same repository we are able to harvest with links to full-text in DSpace 6.3.

Also the same problem occurs when I tried it on https://demo7.dspace.org/home i.e. links to full text are not generated in the metadata. PFA screenshots from DSpace 7 and DSpace 6.3 for reference.

[Fatih Güneş]

Hi Dimple Patel,

I get the same error messages when testing OAI-ORE harvesting for Dspace 7.6.

Did you find any solution?