Dspace-CRIS OAI-pmh Error
陳彥棠
I run Dspace-CRIS 5.5.0 OAI-pmh error ....
I see Dspace-CRIS Edit Collection Last Harvest Result=> Error occurred while processing an OAI record
So I checking dspace.log message
dspace.log message
INFO org.dspace.content.Item @ anonymous::update_item:item_id=4179
INFO org.dspace.content.WorkspaceItem @ anonymous::create_workspace_item:workspace_item_id=-1item_id=4179collection_id=1
ERROR org.dspace.harvest.OAIHarvester @ Harvesting error occurred while processing an OAI record: The 'item' schema has not been defined in this DSpace instance.
INFO org.dspace.content.Collection @ anonymous::update_collection:collection_id=1
INFO org.dspace.harvest.OAIHarvester @ Thread for collection 1 completes.
INFO org.dspace.harvest.OAIHarvester @ Done with iteration 5
INFO org.dspace.harvest.OAIHarvester @ Collections ready for immediate harvest: [1]
INFO org.dspace.harvest.OAIHarvester @ Thread queued up: Thread[Thread-228,5,main]
INFO org.dspace.harvest.OAIHarvester @ Thread started: Thread[Thread-229,5,main]
INFO org.dspace.harvest.OAIHarvester @ Thread for collection 1 starts.
INFO org.dspace.harvest.OAIHarvester @ HTTP Request: http://ntur.lib.ntu.edu.tw/ir-oai/request?verb=ListRecords&until=2016-11-22T02:45:42Z&set=hdl_246246_43199&metadataPrefix=oai_dc
INFO org.dspace.harvest.OAIHarvester @ Found 100 records to process
INFO org.dspace.content.Item @ anonymous::update_item:item_id=4180
INFO org.dspace.content.Item @ anonymous::create_item:item_id=4180
INFO org.dspace.content.Item @ anonymous::update_item:item_id=4180
INFO org.dspace.content.WorkspaceItem @ anonymous::create_workspace_item:workspace_item_id=-1item_id=4180collection_id=1
ERROR org.dspace.harvest.OAIHarvester @ Harvesting error occurred while processing an OAI record: The 'item' schema has not been defined in this DSpace instance.
INFO org.dspace.content.Collection @ anonymous::update_collection:collection_id=1
INFO org.dspace.harvest.OAIHarvester @ Thread for collection 1 completes.
WARN org.dspace.storage.rdbms.DatabaseManager @ Already closed.
java.sql.SQLException: Already closed.
at org.apache.commons.dbcp.PoolableConnection.close(PoolableConnection.java:114)
at org.apache.commons.dbcp.PoolingDataSource$PoolGuardConnectionWrapper.close(PoolingDataSource.java:191)
at org.dspace.storage.rdbms.DatabaseManager.freeConnection(DatabaseManager.java:676)
at org.dspace.core.Context.abort(Context.java:567)
at org.dspace.core.Context.finalize(Context.java:733)
at java.lang.System$2.invokeFinalize(Unknown Source)
at java.lang.ref.Finalizer.runFinalizer(Unknown Source)
at java.lang.ref.Finalizer.access$100(Unknown Source)
at java.lang.ref.Finalizer$FinalizerThread.run(Unknown Source)
It is my database schemas tables item => item_id=4179 (ps:item_id=4179)
but database have obviously data .....
I also tried using dspace 5.5 OAI-pmh on same condition
It is a successful execution(ps:dspace-5.5 jspui, dspace-5.5.log)
Why use dspace-cris oai in question?
I'm sorry that my English is not good ...
Description of the expression may not be clear.......
Regards
Sincerly yours, Yen-Tang Chen
Bollini Andrea
Hi
it looks as a bug in DSpace-CRIS. It should be enough to add this line
c.turnOffItemWrapper();
here
Unfortunately I have no time today to verify, can you run a fast test and report if it solves so to include the fix in the next release?
Andrea
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陳彥棠
Dear Bollini Andrea
I try to add this line 126 " c.turnOffItemWrapper(); " in the " C:\DSpace-dspace-cris-5.5.0\dspace-api\src\main\java\org\dspace\harvest\OAIHarvester.java "
but it is errors for the
mvn package , I can not find the method " turnOffItemWrapper()"... Would i need to add those parameters?
Regards
Sincerly yours, Yen-Tang Chen
陳彥棠
I try to add this line 126 " c.turnOffItemWrapper(); " in the " C:\DSpace-dspace-cris-5.5.0\dspace-api\src\main\java\org\dspace\harvest\OAIHarvester.java "
mvn package ..ok but it is failure on the windows 10..........
Error message => dspace-cris-oai_error.png
mvn package ..errorcetos 7 and windows 10 are same settings
Dspace-cris-5.6.1
tomcat 8.0.39
jdk 1.8.0
postgreSQL 9.5
I don't know error..... Fantastic results!!
Regards
Sincerly yours, Yen-Tang Chen
Bollini Andrea
the method turnOffItemWrapper() was introduced in April after the tag of the 5.5.0 version so it is only available on the maintenance branch and in the new versions (5.6.1).
I think that on windows you are using old code, probably the one from the 5.5.0 tag as your path suggest.
It was unclear to me if with such change on centos you have run successful the OAIHarvest or if right now you are just verified that the proposed patch compile. Can you please confirm?
Thanks,
Andrea
陳彥棠
Thank you so much Bollini Andrea :D
I try again to run OAIHarvest on windows 10 (dspace-cris-5.6.1).
I'll report to you later on .
Regards
Sincerly yours, Yen-Tang Chen
Bollini Andrea於 2016年11月24日星期四 UTC+8下午7時30分28秒寫道：
陳彥棠
1.
I run oai-pmh on the linux(centos7) (dspace-cris-oai_02.PNG)
My database format is like this (dspace-cris-oai_03.png)
ex: <dc:creator>吳密察</dc:creator>
<dc:date>1997-07-31</dc:date>
dspace-cris database format
<dc.contributor.author>
<dc.date.issued>
My oai-pmh don't obtain author and date, How to set the settings?(Do not change the data from the database)
ex: dspace 5.5 jspui => dspace.cfg webui.itemlist.columns = thumbnail, dc.date(date), dc.title, dc.creator
Which dspace.cfg parameter?
2.
I install dspace-cris-5.6.1 on the windows 10
add this line 126 " c.turnOffItemWrapper(); " in the " C:\DSpace-dspace-cris-5.6.1\dspace-api\src\main\java\org\dspace\harvest\OAIHarvester.java "
after mvn package is successful.
but step " Administrator Account: Create an initial administrator account" has been wrong!
dspace create-administrator error message => dspace-cris-5.6.1-create-administrator.png
"Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded"
Although dspace-cris-5.6.1 has started successfully , Administrator account is alway failure
I found that the use of dspace-cris-5.6.1([dspace]/bin) "dspace function" will fail....
I try to use dspace-cris-5.5.0 in the same environment that ([dspace]/bin) "dspace function" is successful (dspace-cris-5.5.0-create-administrator.png)
I don't know why this happened......
magical!
Installation environment
jdk1.8.0_101
postgresSQL 9.5
tomcat 8.0.37
dspace-cris-5.6.1
Regards
Sincerly yours, Yen-Tang Chen
Bollini Andrea
Hi Yen-Tang Chen,
1) this is the default behavior of DSpace, it is not a bug or something that you can configure nor in DSpace nor in DSpace-CRIS. It depends on the metadata format that you use: oai_dc in your case that in turn involve https://github.com/4Science/DSpace/blob/dspace-5_x_x-cris/dspace-api/src/main/java/org/dspace/content/crosswalk/OAIDCIngestionCrosswalk.java.
If you can try to use the qdc (Qualified Dublin Core) or the DIM as you are harvesting another DSpace instance. Here you can find some documentation about the Harvesting client
https://wiki.duraspace.org/display/DSDOC5x/OAI#OAI-HarvestingfromanotherDSpace
You can also configure the webui.itemlist.columns propert
https://github.com/4Science/DSpace/blob/dspace-5_x_x-cris/dspace/config/dspace.cfg#L2234
as you did in DSpace JSPUI 5.5 but I don't recommend that as you will keep in your database records with very poor metadata and you will need to fix the configuration in a lot of other places, as for instance define an authority on dc.creator
https://github.com/4Science/DSpace/blob/dspace-5_x_x-cris/dspace/config/dspace.cfg#L2321
change the browse, the cris-enhancers, the ORCID mapping and much more.
2) I guess that you have rebuild dspace-cris using an old build.properties that is missing of some key so in the generated configuration files you have something like
a-configuration-property = ${a-configuration-property}
that result in an infinite loop when the application (or a script) start so the out-of-memory
Try to take the current build.properties
https://github.com/4Science/DSpace/blob/dspace-5_x_x-cris/build.properties
and edit you configuration inside this file.
Hope this help,
Andrea
陳彥棠
1) I'll wait to try.
2) This is the build.properties that I use to mvn package and
ant fresh_install
What do I miss of some key ?Regards
Sincerly yours, Yen-Tang Chen
Bollini Andrea於 2016年11月29日星期二 UTC+8上午6時37分45秒寫道：
陳彥棠
Dear Bollini Andrea
2)
I use use the latest code dspace-cris_5_x_x on the windows 10
https://github.com/4Science/DSpace
But encountered the same problem....
mvn package and ant fresh_install are successful .
but step " Administrator Account: Create an initial administrator account" has been wrong!
dspace-cris-5_x_x-create-administrator_02.png
May be due to lack of java memory?
They are my setting java memory (java.png) and dspace.log.
Installation environment
jdk1.8.0_101
postgresSQL 9.5
tomcat 8.0.37
Bollini Andrea
I have found some time today to make a try.
A slightly modified fix has been committed to our maintenance repository
https://github.com/4Science/DSpace/commit/7d52138d90eb9d177ac09e45eba21e22c9a7a550
Harvesting via OAI-ORE from DSpace-CRIS of the Official Duraspace DSpace demo now succeed.
https://dspace-cris.4science.it/handle/123456789/59
Andrea