Dspace Orcid Integration authority-index script
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Mesut Güngör
Mar 5, 2018, 8:06:23 AM3/5/18
to DSpace Technical Support
I follow the tutorial in the below link to integrate orcid to dspace
When i run $HOME/bin/dspace index-authority i got the following error.
# /dspace/bin/dspace index-authority
Retrieving all data
Initialize org.dspace.authority.indexer.DSpaceAuthorityIndexer
[Fatal Error] :1:1: Content is not allowed in prolog.
Exception: null
java.lang.NullPointerException
at org.apache.xpath.XPathAPI.eval(XPathAPI.java:227)
at org.apache.xpath.XPathAPI.selectNodeList(XPathAPI.java:165)
at org.apache.xpath.XPathAPI.selectNodeList(XPathAPI.java:145)
at org.dspace.authority.util.XMLUtils.getNodeList(XMLUtils.java:80)
at org.dspace.authority.util.XMLUtils.getNodeListIterator(XMLUtils.java:88)
at org.dspace.authority.orcid.xml.XMLtoBio.convert(XMLtoBio.java:90)
at org.dspace.authority.orcid.Orcid.getBio(Orcid.java:54)
at org.dspace.authority.orcid.Orcid.queryAuthorityID(Orcid.java:83)
at org.dspace.authority.orcid.OrcidAuthorityValue.newInstance(OrcidAuthorityValue.java:246)
at org.dspace.authority.AuthorityValueGenerator.generateRaw(AuthorityValueGenerator.java:79)
at org.dspace.authority.AuthorityValueGenerator.generate(AuthorityValueGenerator.java:39)
at org.dspace.authority.indexer.DSpaceAuthorityIndexer.prepareNextValue(DSpaceAuthorityIndexer.java:201)
at org.dspace.authority.indexer.DSpaceAuthorityIndexer.hasMore(DSpaceAuthorityIndexer.java:132)
at org.dspace.authority.indexer.AuthorityIndexClient.main(AuthorityIndexClient.java:61)
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:226)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:78)
When i look at the with the tail for details i see the following related errors.
2018-03-05 14:54:09,673 INFO org.dspace.authority.indexer.AuthorityIndexClient @ Retrieving all data
2018-03-05 14:54:09,673 INFO org.dspace.authority.indexer.AuthorityIndexClient @ Initialize org.dspace.authority.indexer.DSpaceAuthorityIndexer
2018-03-05 14:54:09,730 INFO org.dspace.content.MetadataField @ Loading MetadataField elements into cache.
2018-03-05 14:54:09,750 INFO org.dspace.content.MetadataSchema @ Loading schema cache for fast finds
2018-03-05 14:54:09,776 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4747
2018-03-05 14:54:09,820 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4747
2018-03-05 14:54:09,830 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4748
2018-03-05 14:54:09,845 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4748
2018-03-05 14:54:09,853 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4745
2018-03-05 14:54:09,868 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4745
2018-03-05 14:54:09,876 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4745
2018-03-05 14:54:09,882 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4745
2018-03-05 14:54:09,888 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4745
2018-03-05 14:54:09,896 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4749
2018-03-05 14:54:09,908 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4749
2018-03-05 14:54:09,915 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4724
2018-03-05 14:54:09,923 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4751
2018-03-05 14:54:09,930 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4751
2018-03-05 14:54:09,932 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4732
2018-03-05 14:54:09,939 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4732
2018-03-05 14:54:09,942 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4730
2018-03-05 14:54:09,949 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4730
2018-03-05 14:54:09,954 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4731
2018-03-05 14:54:09,963 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4731
2018-03-05 14:54:09,966 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4733
2018-03-05 14:54:09,972 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4733
2018-03-05 14:54:09,975 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4734
2018-03-05 14:54:09,982 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4734
2018-03-05 14:54:09,988 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4791
2018-03-05 14:54:09,999 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4791
2018-03-05 14:54:10,008 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4727
2018-03-05 14:54:10,020 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4727
2018-03-05 14:54:10,028 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4728
2018-03-05 14:54:10,042 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4729
2018-03-05 14:54:10,054 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4729
2018-03-05 14:54:10,060 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4729
2018-03-05 14:54:10,072 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4757
2018-03-05 14:54:10,084 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4756
2018-03-05 14:54:10,091 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4759
2018-03-05 14:54:10,098 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4759
2018-03-05 14:54:10,101 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4758
2018-03-05 14:54:10,108 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4758
2018-03-05 14:54:10,114 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4784
2018-03-05 14:54:10,123 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4784
2018-03-05 14:54:10,129 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4739
2018-03-05 14:54:10,143 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4739
2018-03-05 14:54:10,150 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4739
2018-03-05 14:54:10,157 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4739
2018-03-05 14:54:10,165 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4742
2018-03-05 14:54:10,179 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4742
2018-03-05 14:54:10,190 INFO org.dspace.content.Item @ anonymous::update_item:item_id=4740
2018-03-05 14:54:11,601 ERROR org.dspace.authority.util.XMLUtils @ Error
org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)
at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source)
at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:121)
at org.dspace.authority.util.XMLUtils.convertStreamToXML(XMLUtils.java:141)
at org.dspace.authority.rest.RESTConnector.get(RESTConnector.java:54)
at org.dspace.authority.orcid.Orcid.getBio(Orcid.java:52)
at org.dspace.authority.orcid.Orcid.queryAuthorityID(Orcid.java:83)
at org.dspace.authority.orcid.OrcidAuthorityValue.newInstance(OrcidAuthorityValue.java:246)
at org.dspace.authority.AuthorityValueGenerator.generateRaw(AuthorityValueGenerator.java:79)
at org.dspace.authority.AuthorityValueGenerator.generate(AuthorityValueGenerator.java:39)
at org.dspace.authority.indexer.DSpaceAuthorityIndexer.prepareNextValue(DSpaceAuthorityIndexer.java:201)
at org.dspace.authority.indexer.DSpaceAuthorityIndexer.hasMore(DSpaceAuthorityIndexer.java:132)
at org.dspace.authority.indexer.AuthorityIndexClient.main(AuthorityIndexClient.java:61)
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:226)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:78)
What can cause the error.
On the other hand i see the lookup buttons in the xmlui web interface while submitting item. But there is no italic(that is from ORCID ) names in the search results
Alan Orth
Mar 12, 2018, 3:44:42 PM3/12/18
to Mesut Güngör, DSpace Technical Support
Hello,
First, the index-authority has never worked for me in DSpace 5.x. There are many issues in DSpace's Jira about null pointer exceptions with this script[0]. Some appear to be fixed, but nevertheless this script has never worked for us. I wrote a Python script to all our authority entries with ORCID identifiers from Solr's authority core to standard metadata[1]. We will move to using a controlled vocabulary lookup for our researcher ORCID identifiers.--
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Tim Donohue
Mar 21, 2018, 3:45:49 PM3/21/18
to Mesut Güngör, Alan Orth, DSpace Technical Support
Hello Mesut,
As noted by Alan Orth, ORCID integration with DSpace 5.x and 6.x is currently broken.
Tim
As noted by Alan Orth, ORCID integration with DSpace 5.x and 6.x is currently broken.
As of February 2018, the ORCID team removed all support for their old, version 1 API. Unfortunately, ORCID has provided no backwards compatibility in the version 2 API, which breaks all sites that still depend on the version 1 API (including DSpace 5.x and 6.x sites using ORCID).
We have a ticket that is tracking this issue in our JIRA system at:
https://jira.duraspace.org/browse/DS-3447
We have a ticket that is tracking this issue in our JIRA system at:
https://jira.duraspace.org/browse/DS-3447
The goal of that ticket is to quickly update DSpace 5.x and 6.x to the ORCID version 2 API, as that seems to be the only way to solve these ORCID issues.
Unfortunately, as of this moment, we don't have a fix to update the DSpace codebase to use the v2 API. Supposedly, there are several institutions working on fixes (see the ticket). But, as of yet, code fixes have not been provided back to the community. Since all DSpace development comes from our community (we don't have a centralized developer team), we are still waiting on a code fix to be submitted to our GitHub, so that we can release a fix to all users.
All in all, I'm hoping we'll have a fix soon. But, I'd encourage anyone interested in chipping in to join the discussion on the above ticket.
All in all, I'm hoping we'll have a fix soon. But, I'd encourage anyone interested in chipping in to join the discussion on the above ticket.
Tim
--
Tim Donohue
Technical Lead for DSpace & DSpaceDirect
DuraSpace.org | DSpace.org | DSpaceDirect.org
Technical Lead for DSpace & DSpaceDirect
DuraSpace.org | DSpace.org | DSpaceDirect.org
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